Insights into Mechanisms Used by Staphylococcus aureus to Avoid Destruction by Human Neutrophils

This information is current as Jovanka M. Voyich, Kevin R. Braughton, Daniel E. of September 30, 2021. Sturdevant, Adeline R. Whitney, Battouli Saïd-Salim, Stephen F. Porcella, R. Daniel Long, David W. Dorward, Donald J. Gardner, Barry N. Kreiswirth, James M. Musser and Frank R. DeLeo

J Immunol 2005; 175:3907-3919; ; Downloaded from doi: 10.4049/jimmunol.175.6.3907 http://www.jimmunol.org/content/175/6/3907

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The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2005 by The American Association of Immunologists All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology

Insights into Mechanisms Used by Staphylococcus aureus to Avoid Destruction by Human Neutrophils1

Jovanka M. Voyich,* Kevin R. Braughton,* Daniel E. Sturdevant,* Adeline R. Whitney,* Battouli Saı¨d-Salim,§ Stephen F. Porcella,* R. Daniel Long,† David W. Dorward,‡ Donald J. Gardner,† Barry N. Kreiswirth,§ James M. Musser,¶ and Frank R. DeLeo2*

Polymorphonuclear leukocytes (PMNs, or neutrophils) are critical for human innate immunity and kill most invading bacteria. However, pathogens such as Staphylococcus aureus avoid destruction by PMNs to survive, thereby causing human infections. The molecular mechanisms used by pathogens to circumvent killing by the immune system remain largely undefined. To that end, we studied S. aureus pathogenesis and bacteria-PMN interactions using strains originally isolated from individuals with community- acquired (CA) and hospital-acquired infections. Compared with strains from hospital infections (COL and MRSA252), strain MW2 and a methicillin-susceptible relative, MnCop, were significantly more virulent in a mouse model of S. aureus infection, and Downloaded from caused the greatest level of pathology in major vital organs. Although phagocytosis of each strain triggered production of reactive oxygen species and granule-phagosome fusion, those from CA infections were significantly more resistant to killing by human PMNs and caused greater host cell lysis. Microarray analysis of the strains during neutrophil phagocytosis identified genes comprising a global S. aureus response to human innate host defense. Genes involved in capsule synthesis, gene regulation, oxidative stress, and virulence, were up-regulated following ingestion of the pathogen. Notably, phagocytosis of strains from CA http://www.jimmunol.org/ infections induced changes in gene expression not observed in the other strains, including up-regulation of genes encoding viru- lence factors and hypothetical proteins. Our studies reveal a gene transcription program in a prominent human pathogen that likely contributes to evasion of innate host defense. The Journal of Immunology, 2005, 175: 3907–3919.

olymorphonuclear leukocytes (PMNs,3 or neutrophils) are tizing pneumonia, endocarditis, and sepsis (1). Risk of S. aureus key effectors of the human innate immune system and pro- infection is increased during hospitalization, after surgery or dial- P vide critical defense against invading microorganisms. ysis, and in patients with indwelling percutaneous medical devices Phagocytosis of bacteria triggers production of reactive oxygen and/or catheters (1). Notably, there is an alarming increase in the

species (ROS) and release of microbicidal granule components incidence of community-acquired (CA) S. aureus infections in by guest on September 30, 2021 into forming phagosomes. Although PMN-derived antimicrobial seemingly healthy individuals, a problem which underscores the products are highly effective at killing most bacteria, some patho- need to better understand virulence mechanisms (2). A number of gens evade destruction by neutrophils to survive and cause human factors are known to contribute to pathogenesis (1–6); however, a infections. An enhanced understanding of the molecular mecha- comprehensive analysis of changes in S. aureus gene expression nisms used by pathogens to circumvent the immune system is es- that occur during interaction with the human innate immune sys- sential for developing new treatments for infectious diseases. tem has not been performed. Furthermore, our understanding of Staphylococcus aureus is a leading cause of human infections the molecular mechanisms used by pathogens to avoid destruction worldwide. The pathogen causes a variety of diseases including by innate host defense is limited. To that end, we studied S. aureus impetigo, cellulitis, food poisoning, toxic shock syndrome, necro- pathogenesis and global gene expression during phagocytic inter- action with human PMNs. *Laboratory of Human Bacterial Pathogenesis, †Rocky Mountain Veterinary Branch, and ‡Rocky Mountain Microscopy Branch, Rocky Mountain Laboratories, National Materials and Methods Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Bacterial strains and culture MT 59840; §Public Health Research Institute Tuberculosis Center, International Cen- ¶ ter for Public Health, Newark, NJ 07103; and Center for Human Bacterial Patho- Staphylococcus aureus strains MW2 (5, 7), MnCop (8), LAC (9–12), genesis Research, Department of Pathology, Baylor University College of Medicine, MRSA252 (13), and COL (14) were selected carefully for this study based Houston, TX 70030 on several criteria, including the type of human disease caused by each Received for publication February 25, 2005. Accepted for publication July 5, 2005. (e.g., MW2 as the prototype for CA methicillin-resistant S. aureus The costs of publication of this article were defrayed in part by the payment of page (MRSA), and MRSA252 for its high prevalence in hospitals in the United charges. This article must therefore be hereby marked advertisement in accordance States and United Kingdom), available genome sequence information with 18 U.S.C. Section 1734 solely to indicate this fact. (MW2, MRSA252, and COL), historical significance (COL), available ge- 1 This work was supported in part by the Intramural Research Program of the National notype information (e.g., MLST, spa type, agr type, and SCCmec type), Institutes of Health, National Institute of Allergy and Infectious Diseases. and methicillin susceptibility (MnCop). Specifically, MW2 (pulsed-field type USA400) was originally isolated from a healthy 16-mo-old girl in 2 Address correspondence and reprint requests to Dr. Frank R. DeLeo, Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of North Dakota who died of septicemia and septic arthritis in 1998 (7, 15). Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840. LAC (pulsed-field type USA300) has caused recent S. aureus outbreaks in E-mail address: [email protected] athletes, many of which are skin infections (10, 11, 16). Recent reports also describe USA300 as the causative agent of staphylococcal necrotizing fas- 3 Abbreviations used in this paper: PMN, polymorphonuclear leukocyte; ROS, reac- tive oxygen species; CA, community acquired; HA, hospital acquired; MRSA, me- ciitis (9) and severe community-onset pneumonia in healthy adults (12). thicillin-resistant S. aureus; MSSA, methicillin-susceptible S. aureus; DPBS, Dul- MnCop was originally isolated from an 8-mo-old infant who had S. aureus becco’s PBS; LDH, lactate dehydrogenase; TEM, transmission electron microscopy; toxic shock syndrome (8). Thus, each of the CA strains used in this study, GAS group A Streptococcus. i.e., MW2, MnCop, and LAC, has been linked to infections in individuals

Copyright © 2005 by The American Association of Immunologists, Inc. 0022-1767/05/$02.00 3908 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS with no known risk factors. In contrast, MRSA252 (pulsed-field type iden- bacteria:PMN. Plates were then centrifuged at 380 ϫ g for 8 min at 4°C to tical to EMRSA16), is the second leading cause of healthcare-associated S. synchronize phagocytosis (18). Samples were incubated at 37°C in a CO2 aureus infections in the United States (16). Descriptions of each strain are incubator for the indicated times (t ϭ 0 was processed immediately after summarized in Table I. centrifugation), medium was removed from the wells by aspiration, and S. aureus were grown in tryptic soy broth (BD Biosciences) containing cells were fixed on ice for 30 min with 4% paraformaldehyde. Fixative was 0.5% glucose. Bacterial cultures were inoculated from overnight cultures removed by aspiration, and uningested bacteria were counterstained with with a dilution of 1/200 for strains MW2, MnCop, and LAC, or 1/100 for AlexaFluor594 conjugated-Ab specific for AlexaFluor 488 for 15 min at strains COL and MRSA252, and incubated at 37°C with shaking (250 room temperature. Samples were visualized with a Zeiss Axioskop 2 Plus rpm). For in vitro microarray analyses, S. aureus strains were cultured to fluorescence microscope (Carl Zeiss) and imaged with a Zeiss Axiocam ϭ ϭ early exponential (EE, OD600 0.40), mid exponential (E1,OD600 0.75; digital camera. The total number of S. aureus bound and/or ingested ϭ ϭ E2,OD600 1.0) or early stationary (ES, OD600 2.0) phases of growth was evaluated in 50 neutrophils per assay from at least five separate and harvested immediately for RNA isolation. For all other assays, S. au- fields of view. Percent phagocytosis was calculated with the equation: reus were harvested at E1, washed in Dulbecco’s PBS (DPBS; Sigma- (number of ingested bacteria per cell/total number of PMN-associated Aldrich), and resuspended in RPMI 1640 medium (Invitrogen Life Tech- bacteria per cell, bound or ingested) ϫ 100. Statistics were performed nologies) buffered with 10 mM HEPES (RPMI/H, pH 7.2) to 108/ml. with a repeated-measures ANOVA and Tukey’s posttest for multiple comparisons (GraphPad Prism version 4.0 for Windows; GraphPad Mouse model of S. aureus disease Software). Images were adjusted for brightness and contrast with All animal studies conformed to National Institutes of Health guidelines Photoshop CS (Adobe Systems). and were approved by the Animal Use Committee at Rocky Mountain PMN ROS production Laboratories. Female CD1 Swiss mice were purchased from Charles River. Animals were between 10 and 12 wk of age, housed in microisolator cages, PMN ROS production was measured using a previously described method and received food and water ad libitum. S. aureus strains were grown to E1, (18) with minor modifications. PMNs were incubated with 25 ␮M2Ј,7Ј- Downloaded from washed twice with sterile DPBS, and resuspended to 108/100 ␮l in DPBS. dihydrodiclorofluorescein diacetate (DCF; Molecular Probes) for 20–30 Mice were inoculated with 108 S. aureus or with sterile DPBS via the tail min at room temperature in RPMI/H. DCF-containing PMNs (106) and vein. The experiment was performed once with 10 mice per S. aureus strain opsonized S. aureus were combined in wells of a 96-well microtiter plate and 5 mice for DPBS control. Criteria for determining morbidity/sickness at 4°C (ratio of 10 bacteria:PMN), centrifuged for 8 min at 380 ϫ g, and in mice included hunched posture, decreased activity, ruffled fur, and la- transferred to a microplate fluorometer (Spectramax Gemini; Molecular bored breathing. Animals were euthanized if unable to eat or drink, or if Devices). ROS production was measured continuously at 1-min intervals they became immobile. All mice were euthanized by 48 h. Survival sta- for up to 180 min at 37°C using excitation and emission wavelengths of tistics were performed with a log-rank test (GraphPad Prism version 4.0 for 485 and 538 nm, respectively. The rate of PMN ROS production over time http://www.jimmunol.org/ Windows; GraphPad Software). (second-order kinetics) were determined from the Vmax (max increase in To determine whether S. aureus had disseminated to large organs during fluorescence) within each 10-min time period. bacteremia, liver and lung tissues were harvested at time of animal death, homogenized, and aliquots of each homogenate were plated on tryptic soy PMN bactericidal activity agar. Colonies were enumerated the following day. Alternatively, parts of the liver, lung, kidney, heart, and brain were collected in parallel for his- Killing of S. aureus by human PMNs was determined as described (17) 6 ϳ 7 topathology. Tissues were fixed in 10% neutral-buffered formalin, pro- with some modification. Briefly, PMNs (10 ) were combined with 10 ϫ cessed for 12 h in an Excelsior Tissue Processor (ThermoShandon), and opsonized S. aureus in 24-well tissue culture plates, centrifuged at 380 dehydrated using a graded series of ethanol. Tissues were then cleared with g for 8 min and incubated at 37°C for up to 6 h. At indicated times, PMNs Histosolve (ThermoShandon) and infiltrated and embedded in paraffin. Par- were lysed with 0.1% saponin (20 min on ice) and S. aureus were plated affin blocks were sectioned at 5 microns and slides were stained with H&E. on tryptic soy agar. Colonies were enumerated the following day, and by guest on September 30, 2021 A trained veterinary pathologist (D. J. Gardner) examined all of the tissue percent S. aureus survival was calculated with the equation (CFUϩPMN at ϫ samples. Statistics for dissemination of S. aureus to the liver and lung were t/CFUϩPMN at t0) 100. The assay measures total number of viable in- performed with a Kruskal-Wallis analysis using Dunn’s posttest for mul- gested and uningested bacteria. Statistics were performed with a repeated- tiple comparisons. Images of organ sections were sharpened and adjusted measures ANOVA and Tukey’s posttest for multiple comparisons (Graph- equally for brightness and contrast with Photoshop CS (Adobe Systems). Pad Prism). Isolation of human PMNs S. aureus-induced PMN lysis PMNs were isolated from heparinized venous blood of healthy individuals Following phagocytosis of S. aureus, PMN lysis was determined with a in accordance with a protocol approved by the Institutional Review Board standard assay for release of lactate dehydrogenase (LDH) as described by for Human Subjects, National Institute of Allergy and Infectious Diseases. the manufacturer (Cytotoxicity Detection kit; Roche Applied Sciences). Briefly, blood was incubated for 20 min at room temperature at a 1:1 ratio Alternatively, PMN lysis was determined by counting intact cells on a with 0.9% sodium chloride (Irrigation USP; Baxter Healthcare) containing hemacytometer. Statistics were performed with a repeated-measures 3.0% Dextran T-500 (Amersham Biosciences) to sediment erythrocytes. ANOVA (LDH release) or one-way ANOVA (hemacytometer counts) and The leukocyte-containing supernatant was centrifuged at 670 ϫ g for 10 Tukey’s posttest for multiple comparisons (GraphPad Prism). min and resuspended in 35 ml of 0.9% sodium chloride. The cell suspen- sion was underlaid with 10 ml of Ficoll-PaquePLUS (1.077 g/L; Amersham Electron microscopy Biosciences) and centrifuged for 25 min to separate PMNs from PBMCs. For transmission electron microscopy (TEM), phagocytosis assays were PBMCs were removed by aspiration and erythrocytes were lysed with wa- performed as described above, but with the following modifications. PMNs ter (Irrigation USP; Baxter Healthcare) for 15–30 s followed by immediate (3 ϫ 105) were combined with 3 ϫ 106 serum-opsonized S. aureus in wells mixing with 1.7% sodium chloride. Purified PMNs were centrifuged at of a 24-well tissue culture plate containing serum-coated Thermanox cov- ϫ 380 g, resuspended in RPMI/H, and enumerated by microscopy. Purity erslips (Nalge Nunc International). Cells were incubated at 37°C with 5% of PMN preparations and cell viability were assessed by flow cytometry CO for up to 180 min. At the indicated times, cells were fixed in Kar- ϳ 2 (FACSCalibur; BD Biosciences). Cell preparations contained 99% novsky’s fixative containing 4% glutaraldehyde and 4% paraformaldehyde Ͻ PMNs and all reagents used contained 25.0 pg/ml endotoxin (Limulus in 0.1 M sodium phosphate buffer, pH 7.2 (Electron Microscopy Sciences). Amebocyte Lysate assay; Fisher Scientific). Samples were washed twice in 0.1 M phosphate, and postfixed in 1% Phagocytosis of S. aureus by human PMNs osmium/0.8% potassium ferrocyanide in 0.1 M phosphate. Following two additional washes in water, samples were stained in-block with 1% uranyl Phagocytosis of S. aureus by human PMNs was determined with fluores- acetate in water, washed again, and then dehydrated in ethanol, and em- cence microscopy as previously described (17). Bacteria were grown to E1, bedded in Spurr resin (Ted Pella), as described (19). Thin sections were opsonized with 50% normal human serum for 30 min at 37°C, and washed examined on a model H7500 TEM (Hitachi High Technologies) at 80 kV. in DPBS. After opsonization, bacteria were labeled with AlexaFluor 488 Images were captured with an Advantage HR digital camera system (Ad- (Molecular Probes) in DPBS for 20 min at 37°C, and unlabeled fluoro- vanced Microscopy Techniques) and adjusted for brightness and contrast chrome was removed by two washes with DPBS. PMNs (3 ϫ 105) were with Photoshop CS (Adobe Systems). For scanning electron microscopy, added to serum-coated glass coverslips in 24-well tissue culture plates and phagocytosis assays were performed as described above, but with the fol- allowed to adhere at room temperature for 15 min. Cells were chilled on ice lowing modifications. Cells were fixed in 0.15 M cacodylate buffer, pH 7.2, for 10 min and AlexaFluor 488-labeled bacteria were added at a ratio of 10 containing 2.5% glutaraldehyde and washed twice in cacodylate buffer. The Journal of Immunology 3909

Table I. S. aureus strains used in this studya

Strain MLST spa Type SCCmec Type agr Type PVLb

MW2: (pulsed-field type USA400) prototype ST1; 1-1-1-1-1-1-1 spa type 131; UJJFKBPE IV III ϩ CA-MRSA strain (5, 7, 36, 38, 41, 53) MnCop: CA-MSSA, nmTSS strain, otherwise ST1; 1-1-1-1-1-1-1 spa type 35; UKJFKBPE Ϫ III ϩ similar to MW2 (8) LAC: (pulsed-field type USA300) CA-MRSA, ST8; 3-3-1-1-4-4-3 spa type 1; YHGFMBQBLO IV I ϩ frequently isolated from skin infections (9, 10, 12, 16, 36) MRSA252: HA-MRSA, predominant in healthcare ST36; 2-2-2-2-3-3-2 spa type 16; WGKAKAOMQQQ II III Ϫ settings in U.S. and U.K. (13, 16) COL: HA-MRSA, isolate from Colindale, U.K. (14) ST250; 3-3-1-1-4-4-16 spa type 1; YHGFMBQBLO I I Ϫ

a CA, community acquired; HA, hospital acquired; MLST, multilocus sequence typing; PVL, Panton-Valentine Leukocidin; nmTSS, nonmenstrual, toxic-shock syndrome. b PVL was verified by DNA sequence analysis.

Samples were then postfixed with 1.0% osmium tetroxide in cacodylate buffer, washed twice with water, dehydrated with ethanol, and critical- point dried through carbon dioxide. After mounting on stubs, the samples Downloaded from were lightly coated with iridium using an ion beam sputterer (South Bay Technology), and examined with a Hitachi S4500 field emission scanning electron microscope (Hitachi High Technologies America). Digital images were collected with an Orion system (Focused Resolutions), and adjusted for brightness and contrast with Photoshop CS (Adobe Systems). Analysis of S. aureus gene expression http://www.jimmunol.org/ To compare transcript levels in vitro, S. aureus strains were cultured to the desired phase of growth and ϳ2.5 ϫ 109 cells were lysed with 700 ␮lof RLT buffer (Qiagen). Lysates were homogenized with an FP120 FastPrep system (QBiogene). Total RNA was isolated with RNeasy kits (Qiagen) and contaminating chromosomal DNA was removed by DNase treatment (Qiagen). Purified bacterial RNA was used to prepare fragmented and bi- otin-dUTP-labeled cDNA according to standard Affymetrix prokaryotic target preparation (͗www.affymetrix.com/support/downloads/manuals/ expression_s3_manual.pdf͘). Briefly, cDNA was synthesized from ϳ10 ␮g of total RNA in 1ϫ first-strand buffer containing 25 ng/␮l random primers

(Invitrogen Life Technologies), 10 mM DTT, 0.5 mM dNTPs (Amersham), by guest on September 30, 2021 0.5 U/␮l SUPERase In (Ambion), and 25 U/␮l SuperScript II (Invitrogen Life Technologies). Remaining RNA was removed by hydrolysis with 1 N NaOH and the reaction was neutralized with 1 N HCL. cDNA (ϳ3–6 ␮g/sample) was fragmented using ϳ0.6 U of DNase I (Amersham Phar- macia Biotech) per ␮g of cDNA in One-Phor-All Buffer (Amersham). The 3Ј termini of the fragmented cDNA was labeled using an Enzo BioArray Terminal Labeling kit with Biotin-dUTP (Enzo Diagnostics). The reaction was completed as suggested by Affymetrix using the Midi format. Biotin- ylated S. aureus cDNA was hybridized to custom Affymetrix GeneChips (RMLChips) containing 3961 probe sets from eight different S. aureus strains (COL, EMRSA16, MSSA476, RF122, TSS.8325, Mu50, and N315) and scanned according to standard GeneChip protocols (Affymetrix). Spe- cific details for Affymetrix hybridization and scanning protocols can be found at the internet address provided above. Each experiment was re- peated in triplicate. Data were analyzed with GeneChip Operating Software version 1.1 (Affymetrix) and GeneSpring version 6.0 (Silicon Genetics). Data was normalized using the mean signal from the S. aureus probe sets multiplied by a scale factor to obtain the target signal. Default detection thresholds of p ϭ 0.04 and p ϭ 0.06 were used to determine genes that were present and absent calls were assigned to values of p Ն 0.06. The Pearson correlation (GeneSpring) was used to evaluate the replicate cor- relation. Any nongrouping replicates were deleted from further evaluation. Quality filters based upon Present-Absent calls and signal intensities were used to create final gene lists (Microsoft Excel 2003). Microarray data are posted on the Gene Expression Omnibus (GEO, ͗www.ncbi.nlm.nih.gov/ geo/͘, accession number GSE2728). To measure S. aureus gene expression during S. aureus–PMN interac- FIGURE 1. S. aureus pathogenesis. A, Mouse survival. Mice were infected tion, bacteria were grown to E1, washed once in DPBS, and opsonized in with S. aureus strains by i.v. inoculation (tail vein), and health was monitored 50% normal human serum at 37°C for 30 min. PMNs (107) were combined for 48 h. Results are from 10 mice in each infection group and five mice in a with ϳ108 opsonized S. aureus in wells of a 12-well tissue culture plate on p ϭ 0.015, curves are different. B and C, Dissemination ,ء .PBS control group ice and centrifuged at 380 ϫ g for 10 min at 4°C to synchronize phago- cytosis (17, 18). Plates were transferred to a 37°C incubator with 5% CO of S. aureus. Homogenates from the liver and lung of animals infected as Ͻ ء 2 for the desired times and samples were lysed as described above. For the described in A were plated for CFUs. , p 0.05 vs PBS control mice. D–F, microarray data derived from S. aureus-PMN interaction, RNA was iso- Vital organ pathology in infected mice. Heart (D), kidney (E), and brain tissue lated from the combination of three populations of bacteria: 1) S. aureus (F) from several animals was examined for disease. Yellow arrows indicate bound to PMNs; 2) S. aureus ingested by PMNs; and 3) free (uningested) acute neutrophilic inflammation, bacterial colonies (solid purple matter), S. aureus. However, we determined in separate experiments using and/or regions of necrosis. Black squares, regions magnified ϫ20. 3910 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS

FIGURE 2. S. aureus-PMN inter- action. A, Phagocytosis of S. aureus. ,p Ͻ 0.05, strain COL vs MW2. B ,ء Representative micrographs of phagocytosis. White arrows indicate ingested S. aureus. C, Production of PMN ROS. D and E, S. aureus are exposed to microbicidal neutrophil granule contents after phagocytosis. Transmission electron micrographs of human PMNs 30 min after phago- cytosis of strain MW2. Yellow ar- rows indicate neutrophil granules that are fusing or have fused with phago- somes. The inset in D is a lower mag- nification of the same image, with the Downloaded from magnified area boxed in red. White letters “n” and “s” indicate neutrophil nucleus and S. aureus, respectively. F, Killing of S. aureus by PMNs. Percent S. aureus survival during in- teraction with neutrophils was deter- http://www.jimmunol.org/ mined with the equation (CFUϩPMN ϫ Ͻ at t/CFUϩPMN at t0)) 100. †, p 0.05, strain COL vs MW2, LAC, and p Ͻ ,ء ;MnCop at 30 and 90 min 0.01, strain MRSA252 vs LAC, p Ͻ ,ء ;MW2, and MnCop at 30 min 0.05, strain MRSA252 vs MW2 and p Ͻ ,ء ;MnCop at 90 and 180 min 0.001, strain MRSA252 vs MnCop at

360 min. Results are the mean Ϯ by guest on September 30, 2021 SEM of the indicated number of experiments.

fluorescence microscopy, and transmission and scanning electron TaqMan real-time RT-PCR analysis microscopy, that there were few, if any, free bacteria after 30 min of S. aureus-PMN interaction (see Fig. 2, and data not shown). Further, after 60 Phagocytosis experiments and RNA preparation for TaqMan analysis were min of S. aureus-PMN interaction, typically all neutrophil-associated bac- performed with procedures and conditions identical to those used for the teria were internalized (data not shown). At desired times, PMNs and bac- PMN-S. aureus microarray experiments. TaqMan real-time RT-PCR anal- teria in each well were lysed with 700 ␮l of RLT buffer (Qiagen). Isolation ysis of two separate phagocytosis experiments (each assayed in triplicate) of S. aureus RNA and microarray analyses were performed as described using PMNs from two human blood donors was performed with an ABI above, except that fold-changes for each gene were determined by com- 7500 thermocycler (Applied Biosystems). Relative quantification of S. aureus paring RMLChips hybridized with cDNA from S. aureus alone to those genes was determined by the change in expression of target transcripts relative with cDNA from S. aureus during PMN phagocytosis (time-matched). To to gyrB (housekeeping or calibration gene) according to the manufacturer’s be included in the final gene lists (e.g., see Figs. 5–9, and supplemental protocol (Applied Biosystems Relative Quantification Manual at ͗http:// 4 Table V ), genes must have met the quality filters described above, and docs.appliedbiosystems.com/genindex.taf͘, doc. index no. 4347824). changes in gene expression must have been at least 2-fold in one of the The primer-probe sequences used for confirmation of microarray data Ͼ Ͼ strains. For those genes ( 2-fold change in one strain), changes of 1.5- were as follows: gyrB forward primer, 5Ј-CAAATGATCACAGCATTT fold were also indicated for the other strains. PMN-S. aureus microarray GGTACAG-3Ј, gyrB probe 5Ј-AATCGGTGGCGACTTTGATCTAGCGAA experiments were performed three separate times with PMNs from three AG-3Ј, gyrB reverse primer 5Ј-CGGCATCAGTCATAATGACGAT3Ј; cap8C blood donors. Although the RMLChip was designed to avoid cross- forward primer, 5Ј-CGTGATTATTATGAAGATATGAACGGATT-3Ј, cap8C hybridization with human RNA or DNA, we determined empirically (using probe 5Ј-ATTAGTAATGCGAAGTTAGTTGTTGATG-3Ј, cap8C reverse neutrophils from three individuals) that PMN RNA failed to hybridize with Ј Ј Ј RMLChips. In our experiments, 3957 of 3961 probe sets had no significant primer 5 -CTTGTTGTGGCATTCGTTTAGG-3 ; mraY forward primer, 5 - Ј Ј cross-hybridization with PMN RNA. The four probe sets with noted TGGATTAGCAACTGGACTGTCAAT-3 , mraY probe, 5 -ATCGGATTTAC Ј Ј binding to neutrophil RNA were eliminated from the analysis. AATGTATGCCATCAT-3 , mraY reverse primer, 5 -GCCGTTTCTCCTAAC ACAAAGC-3Ј; vraR forward primer 5Ј-CGATGCAGTTCGTAAAA CTTCTAGAG-3Ј, vraR probe, 5Ј-AGAATCTGTTTTTGAACCGGAAGTT-3Ј, 4 The online version of this article contains supplemental material. vraR reverse primer, 5Ј-TTCATACGGTTACGCATTTTCACT-3Ј; agrA The Journal of Immunology 3911

FIGURE 3. PMN lysis. Following phagocytosis, neutrophil lysis was measured by release of LDH (A)or with a hemacytometer (B). In A,†, p Ͻ 0.05, strain COL vs MW2, LAC, and MnCop at 6 h; †, p Ͻ 0.01 for Downloaded from p Ͻ 0.05, strain ,ء ;that at 9 h p Ͻ ,ء ;MRSA252 vs LAC at 6 h 0.05, MRSA252 vs MW2 at 9 h. In B, p Ͻ 0.01 vs PBS control; †, p Ͻ ,ء 0.01, strain COL vs all other strains. C, Progression of S. aureus-induced

PMN lysis visualized by scanning http://www.jimmunol.org/ electron microscopy. D, Ultrastruc- tural (TEM) analysis of S. aureus- PMN interaction. Yellow arrows in indicate representative MW2. In D, white letter “n” indicates neutrophil nucleus. by guest on September 30, 2021

forward primer 5Ј-CGTAAGCATGACCCAGTTGGT-3Ј, agrA probe, 5Ј- mice infected with MW2, MnCop, or LAC were moribund or notice- ATTATTTTCGTTACGAGTCACAGTGAAC-T-3Ј, agrA reverse primer 5Ј- ably sick (10 of 10 animals infected with each strain, see Materials Ј Ј CCATCGCTGCAACTTTGTAGAC-3 ; hlgA forward primer 5 -ACTTATTT and Methods for details). In contrast, those infected with COL or GCACAAGACCCAACTG-3Ј, hlgA probe 5Ј-CAGCAGCAAGAGACTA TTTCGTCCCAG-3Ј, hlgA reverse primer, 5Ј-CCACTTTGAATTAAAGGA MRSA252, a strain reported as highly virulent in humans (13), ap- GGTAATTGAT-3Ј; sarA forward primer, 5Ј-CAATGGTCACTTATGCT peared relatively healthy (0 of 10 animals infected with COL and 1 of GACAAATT-3Ј, sarA probe 5Ј-AGCTTTGAAGAATTCGCTGTATTGAC-3Ј, 10 of those infected with MRSA252 were sick). Correspondingly, sarA reverse primer 5Ј-TCTTTCTCTTTGTTTTCGCTGATG-3Ј; katA forward Ј Ј Ј mortality was significantly increased in those infected with MW2 or primer 5 -CCGTTTCTCTACTGTAGCAGGAGAAC-3 , katA probe, 5 -CT ϭ GCTGATGCGGAGCGTGACATTC-3Ј, katA reverse primer, 5Ј-TCAGTGTA MnCop ( p 0.015, log-rank test) (Fig. 1A). At the time of death, GAACTTTAACGCAAATCC-3Ј; lukD forward primer, 5Ј-TCAAATCAT major vital organs were evaluated for signs of infection (Fig. 1, B–E). CAGTTGTTACATCAAT-3Ј, lukD probe, 5Ј-CTGCTTTTGCTATCGAAT On average, more bacteria were recovered from the livers of animals ACAGTTGATGCAGC-3Ј, lukD reverse primer, 5Ј-TCTCGCTTACAGGTGT infected with MW2, MnCop, or LAC compared with the other strains Ј GATATGTTG-3 . (Fig. 1B). There were also a greater number of S. aureus recovered from lungs of mice infected with MW2 or MnCop compared with the Results other strains (Fig. 1C). These observations are consistent with the S. aureus virulence in a mouse infection model known capacity of MW2 and similar strains to cause necrotizing To gain new insight into S. aureus pathogenesis, we tested virulence pneumonia in healthy individuals (20). of strains originally isolated from individuals with CA (MW2, Mn- We next performed histopathology on selected organs to deter- Cop, and LAC) and hospital-acquired (HA; COL and MRSA252) mine the extent of disseminated disease caused by each strain (Fig. infections in a mouse model of bacteremia (Table I, and Fig. 1). All 1, D–F). Heart tissues from animals infected with MW2, MnCop, 3912 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS

providing further evidence for enhanced virulence in these strains (3 of 7 animals tested had diseased brain or spinal cord tissue) (Fig. 1, E and F). In contrast, organs from animals infected with COL or MRSA252 typically showed little or no overt signs of disease (Fig. 1, D and E, and data not shown). These results indicate that strains MW2, MnCop, or LAC are generally more virulent than either MRSA252 or COL. Inasmuch as PMNs are essential effectors of in- nate host defense against bacterial pathogens, the enhanced virulence of MW2, MnCop, and LAC in the mouse model may reflect increased resistance to neutrophil killing. This hypothesis is tested below.

Phagocytosis and killing of S. aureus by human PMNs To determine whether differences in virulence are due in part to varied capacity of the strains to interact with the innate immune system, we evaluated phagocytosis and killing of each by human neutrophils. Although there were differences in early uptake of the strains (e.g., ingestion of COL and MW2 at 5 min was 65.1 Ϯ 7.9% and 46.3 Ϯ 12.9%, respectively, p Ͻ 0.05, ANOVA with Tukey’s posttest), phagocytosis of each strain occurred rapidly and was essentially com- Downloaded from plete by 15 min (Fig. 2, A and B). Notably, uptake of each strain by PMNs was virtually identical by 60 min of S. aureus-PMN interaction and there were few or no free bacteria (Fig. 2, and data not shown). We next determined that ingested S. aureus were exposed to micro- FIGURE 4. Global gene expression in S. aureus strains of diverse ge- netic backgrounds. A–C, Comparative microarray analysis of S. aureus bicidal PMN ROS and granule contents (Fig. 2, C–E). Despite the http://www.jimmunol.org/ strains cultured in vitro was measured with custom Affymetrix microarrays exposure to neutrophil antibacterial components, there was significant containing 3961 open reading frames from eight S. aureus genomes. Genes S. aureus survival after phagocytosis (Fig. 2F), findings consistent were included in the analysis if they were called “present” at the phase of with studies by Gresham et al. (21). Further, survival was significantly growth indicated. A, Gene expression in MW2, COL, and MRSA252. B, better for strains isolated from patients with CA infections (e.g., survival Gene expression in MW2, MnCop, and LAC. C, Gene expression in LAC, at 30 min was 58.7 Ϯ 7.6% for MW2 vs 32.0 Ϯ 3.0% for MRSA252, COL, and MRSA252. Results are the average of three separate experiments p Ͻ 0.001, ANOVA with Tukey’s posttest) (Fig. 2F). These observations for each strain. Phases of growth are as follows: EE, early-exponential provide strong support to the notion that S. aureus infections are ϭ ϭ (OD600 0.4); E1, mid-exponential (OD600 0.75); E2, mid-exponential ϭ caused at least in part by evasion of neutrophil-mediated killing. (OD600 1.0); ES, early-stationary. The individual genes from which these comparisons were made are provided in supplemental Tables II–IV. by guest on September 30, 2021 Destruction of human PMNs by S. aureus Between 3 and 6 h after PMN phagocytosis, net growth of each S. or LAC had multifocal areas of necrosis and acute (neutrophilic) aureus strain increased significantly (Fig. 2F). Inasmuch as virtu- inflammation with bacterial colonies (Fig. 1D). Infection also ex- ally all pathogenic S. aureus produce leukocidins, such as ␥-he- tended to kidneys and brain in mice infected with MW2 or MnCop, molysins (22), we tested the hypothesis that late pathogen survival

FIGURE 5. Global changes in S. aureus gene expression during phagocytosis. S. aureus gene expres- sion was measured following PMN phagocytosis as described in Materi- als and Methods. The number of S. aureus genes up (red bars)- or down (blue bars)-regulated at 30, 60, or 180 min after phagocytosis is indicated for assigned functional categories for each strain. The percent genes changed is based on the total number of possible coding regions in each se- quenced strain (i.e., MW2, 2632 genes; MRSA252, 2673 genes; COL, 2721 genes). The Journal of Immunology 3913 Downloaded from http://www.jimmunol.org/ by guest on September 30, 2021

FIGURE 6. S. aureus genes differentially expressed during PMN phagocytosis. Results are presented as the mean fold-increase or -decrease of three separate experiments with PMNs from three different blood donors (comparison is with time-matched assays containing only opsonized S. aureus). White Gene expression data from ,ءء .asterisks indicate genes called “absent” before (for induced genes) or after (for repressed genes) interaction with neutrophils two probe sets was used to generate the information as displayed. An extended set of these data are published as supplemental Table V.

and growth after phagocytosis (i.e., after 3 h) is linked to the ability 25.0 Ϯ 4.0% for COL, p Ͻ 0.01, ANOVA with Tukey’s posttest) of each strain to lyse human PMNs (Fig. 3). Compared with COL (Fig. 3A). These results were verified by scanning and transmission and MRSA252, strains MW2, MnCop, and LAC caused signifi- electron microscopy (Fig. 3, C and D). The observation that heat- cantly more neutrophil destruction 6 h after phagocytosis (e.g., at killed MW2 failed to lyse neutrophils (Fig. 3A) is consistent with 6 h release of lactate dehydrogenase was 54.3 Ϯ 7.6% for MW2 vs the idea that S. aureus actively produces factors to evade killing by 3914 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS

PMNs. Importantly, ability of the strains to survive killing by neu- trophils and cause subsequent PMN lysis correlated generally with the mouse pathogenesis data. Gene expression in S. aureus strains from CA and HA infections As a first step toward understanding the molecular basis of differ- ences in virulence and interaction with neutrophils, we compared global gene expression in the strains grown in vitro with S. aureus microarrays (Table I, Fig. 4, and supplemental Tables II-IV). Col- lectively, expression of 210 genes differentiated MW2, MnCop, and LAC from MRSA252 and COL (supplemental Table II). Only 17 genes (not expressed in strains COL or MRSA252) were com- monly expressed in the three CA strains during growth in vitro (supplemental Table II). Nine of the 17 genes encoded hypothet- ical proteins, and 3 others were phage-encoded (supplemental Ta- ble II). The finding that MW2, MnCop, and LAC collectively ex- press a limited number of unique transcripts (not present in COL or MRSA252) is consistent with the genetic similarity between

LAC and COL based on MLST and spa typing, and gene expres- Downloaded from sion (Fig. 4C, and Table I). Although strain-specific gene expres- sion (Fig. 4) might underlie differences in pathogenesis, it is likely that many pathogen processes used to evade PMN killing are trig- gered by interaction with the innate immune system. PMN phagocytosis induces global changes in S. aureus gene http://www.jimmunol.org/ expression To further elucidate the molecular mechanisms used by the patho- gen to evade innate host defense, we measured global changes in S. aureus gene expression during phagocytic interaction with hu- man PMNs. We discovered that 21.8–39.1% of the genes in S. aureus were differentially regulated at any given time following phagocytic interaction (e.g., 593, 857, and 1029 genes in COL, MRSA252, and MW2, respectively, were up- or down-regulated at 180 min after phagocytosis) (Figs. 5–9, and supplemental Table by guest on September 30, 2021 V). Genes differentially expressed during PMN phagocytosis were divided into categories based on function or annotation. Genes encoding proteins with undefined function and those involved in metabolism comprised the two largest categories of S. aureus genes modulated by PMN phagocytosis (e.g., n ϭ 348 and 372 genes, respectively, for MW2 30 min after initial PMN interaction) (Figs. 5 and 8, and supplemental Table V). Notably, 26.8–38.8% of S. aureus genes were differentially regulated within 30 min after FIGURE 7. Genes encoding hypothetical proteins that are differentially PMN phagocytosis, depending on the strain analyzed (e.g., 26.8% expressed in CA S. aureus strains after PMN phagocytosis. Gene expres- of those in COL and 38.8% of those in MW2) (Fig. 5). sion was determined as described in the legend of Fig. 6. Genes encoding proteins that moderate oxidative stress, and those involved in metabolism and capsule synthesis are induced tant for survival once the pathogen is internalized. Alternatively, during phagocytosis induction of S. aureus capsule by PMN uptake might confer a Consistent with the finding that S. aureus was exposed to PMN- phagocytosis-resistant phenotype to bacteria that escape destruc- derived ROS (Fig. 2C), at least 25 stress response genes were tion from initial neutrophil interaction. up-regulated in the pathogen during phagocytosis (Fig. 6, and sup- There was striking up-regulation of genes involved in metabolism plemental Table V). For example, genes encoding catalase (katA), following pathogen uptake (Fig. 8, and supplemental Table V). thioredoxin (trxA), thioredoxin reductase (trxB), superoxide dis- Twelve genes encoding proteins of the tricarboxylic acid cycle, in- mutase (sodA, sodM), alkyl hydroperoxide reductase (ahpC, cluding aconitate hydratase (citB), isocitrate dehydrogenase (citC), ci- ahpF), and glutathione peroxidase (gpxA), were up-regulated in S. trate synthase (citZ), and fumarate hydratase (citG), were up-regulated aureus immediately following phagocytosis (at 30 and 60 min), a following phagocytosis by PMNs (Fig. 8, and supplemental Ta- period of time that corresponds with maximum generation of neu- ble V). These findings concur with recent studies that link tri- trophil ROS (Figs. 2C and 6). Genes encoding proteins involved in carboxylic acid cycle metabolism and pathogenesis (24). In capsular polysaccharide synthesis (capA-G, capI-P, and cap8I) contrast, genes encoding proteins involved in cell envelope syn- were up-regulated in all but one of the strains during initial S. thesis, cell division, and replication were generally down-reg- aureus-PMN interaction (Fig. 6, and supplemental Table V). Al- ulated immediately following phagocytosis (Figs. 6 and 9, and though there is evidence that capsule blocks phagocytosis (23), supplemental Table V). Thus, S. aureus gene-regulated pro- under our conditions each strain was readily ingested by neutro- cesses appear directed toward defense against neutrophil killing phils (Fig. 2A). Thus, the data suggest S. aureus capsule is impor- rather than for growth immediately after phagocytosis (within The Journal of Immunology 3915 Downloaded from

FIGURE 8. S. aureus genes in- volved in metabolism are differen- tially expressed following neutrophil http://www.jimmunol.org/ phagocytosis. Gene expression was determined as described in the legend of Fig. 6. by guest on September 30, 2021

30 or 60 min). This idea is supported by the lack of net S. tibiotic proteins (epiE, epiF), fibronectin-binding proteins ( fnb, aureus growth for up to 3 h after ingestion (Fig. 2F). fnbB), staphylocoagulase, and clumping factor (clfA) (Fig. 6). Genes encoding two-component ␥-hemolysins (hlgA, hlgB and Phagocytosis up-regulates S. aureus genes encoding proteins hlgC), which are known to destroy leukocytes, were induced in all that mediate virulence strains during PMN phagocytosis (Fig. 6) (22). In contrast, genes en- Within 30 min of S. aureus-PMN interaction, genes involved in coding several toxins, such as an exotoxin 2 homologue, set7, set11, virulence were up-regulated in each of the strains (Figs. 5 and 6, set14, lukD, lukE, and enterotoxin type C3 (sec3), as well as those and supplemental Table V). For example, at least 36 genes encod- encoding numerous hypothetical or hypothetical exported/surface-as- ing virulence factors and/or toxins were induced in MW2 30 min sociated proteins, were up-regulated only in strains causing CA in- after phagocytic interaction with neutrophils (Figs. 5 and 6, and fections (Figs. 6 and 7, and supplemental Table V). Further studies are supplemental Table V). These genes encode toxins, secreted exo- needed to determine whether these genes underlie the noted variances proteins, and cell-wall associated adhesions, such as extracellular in strain pathogenesis (Fig. 1) and enhanced ability of MW2, MnCop, matrix and plasma binding protein (ssp), epidermin immunity/lan- and LAC to circumvent killing by neutrophils (Fig. 3). 3916 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS Downloaded from http://www.jimmunol.org/

FIGURE 9. Phagocytosis triggers differen- tial regulation of S. aureus genes involved in cell division, replication, and biosynthetic ac- tivity. Gene expression was determined as de- scribed in the legend of Fig. 6. by guest on September 30, 2021

S. aureus genes involved in transcriptional regulation are characteristic is due partially to several gene-regulatory systems modulated by neutrophil phagocytosis that tightly regulate expression of S. aureus virulence genes (25). Transcripts encoding S. aureus gene-regulatory systems VraSR, S. aureus adapts to varied host environments and thus inhabits SaeSR, and SarA were up-regulated significantly by PMN phagocy- skin, mucous membranes, blood, and deeper tissues (1–6). This tosis (Fig. 6). The VraSR two-component gene regulatory system is The Journal of Immunology 3917 induced by cell-wall synthesis inhibitors and/or cell envelope damage script levels were measured at 60 and 180 min after PMN phago- (26), observations most compatible with our results. SarA is known to cytosis in strains MRSA252 and MW2. There was a strong cor- control expression of S. aureus virulence factors and is thus important relation between TaqMan and microarray results (83.3%), for pathogen survival during host-pathogen interaction (21, 27) (Fig. consistent with previous comparisons (17, 19, 31–35). 6). Our observation that sarA is induced, and alternative ␴ factor B (sigB) and accessory gene regulator (agr) operons are repressed dur- Discussion ing PMN phagocytosis, corresponded with concomitant regulation of S. aureus is one of the most prominent human pathogens and is a number of putative and proven virulence factors, such as the gene responsible for diverse infections worldwide (1). Risk of S. aureus encoding ␥-hemolysin (hld) and the anti-holin encoding operon lgrAB infection is increased during or after hospitalization, and there is a (Fig. 6, and supplemental Table V) (28–30). Taken together, these serious problem with antibiotic resistance in the pathogen in findings suggest that evasion of human innate immunity by S. aureus is regulated at the level of gene transcription. healthcare settings (1, 2). In contrast, there has been a dramatic increase in the number of S. aureus infections occurring in healthy Confirmation of microarray data by TaqMan real-time RT-PCR individuals with no apparent risk factors for disease (2, 7, 9, 10, 12, (TaqMan analysis) 15, 36–43). The molecular basis for these infections is largely unknown, although it is likely that a combination of pathogen vir- We used TaqMan real-time RT-PCR to confirm changes in gene ulence mechanisms and host susceptibility factors contribute to expression identified by microarray analysis (Fig. 10). Eight S. disease. aureus genes identified by microarrays as differentially transcribed Neutrophils are a critical component of innate immunity and are during PMN phagocytosis were evaluated by TaqMan analysis. essential for controlling bacterial infections (44–50). Defects that Downloaded from Genes were selected from several functional categories and tran- alter normal PMN function, such as chronic granulomatous disease and leukocyte adhesion deficiency, predispose individuals to seri- ous S. aureus infections (reviewed in Ref. 44). Further, it has long been known that individuals with neutropenia are more susceptible to bacterial infections, including those caused by S. aureus (45–

48). Recent studies in animal models of S. aureus disease support http://www.jimmunol.org/ these observations unambiguously (49, 50). Inasmuch as evasion of innate immunity plays a critical role in bacterial pathogenesis (17, 19, 51), a significant part of our study investigated the inter- action of human PMNs with S. aureus.OftheS. aureus strains used in our study, those originally isolated from individuals with CA infections (no established risk factors) evaded killing by hu- man neutrophils better than those isolated from hospital infections (Table I and Fig. 2F). Differences in pathogen survival were not due to altered neutrophil function, because phagocytosis, ROS pro- by guest on September 30, 2021 duction and degranulation were ultimately comparable for each of the strains tested (Fig. 2). Rather, the data indicate that strains MW2, MnCop, and LAC are more resistant to destruction per se and/or produce factors that cause more rapid host cell lysis by comparison (Fig. 3). Notably, there was no net growth by any of the strains during phagocytic interaction with human neutrophils until sometime after3hofculture (Fig. 2F). The increased sur- vival/growth by MW2, MnCop, and LAC at 6 h was reflected generally by the degree of PMN lysis caused by the strains (com- pare Fig. 2F with Fig. 3, A and B). Thus, our data indicate that some S. aureus survived intraphagosomally without multiplying, but produced factors that cause PMN lysis. Results from the neutrophil-S. aureus experiments were paral- leled by the mouse pathogenesis data, which indicate MW2, Mn- Cop, and LAC (those from community infections) are more viru- lent than COL or MRSA252 (Fig. 1), consistent with recent studies indicating strain-to-strain variability in S. aureus virulence (52). Strains LAC (pulsed-field type USA300) and MW2 (pulsed-field type USA400) are MRSA strains closely associated with commu- nity outbreaks of S. aureus disease in the United States (5, 7, 9, 10, 12, 36, 38, 41, 53). For example, recent reports indicate USA300 is a causative agent of staphylococcal necrotizing fasciitis (9) and severe community-onset pneumonia in healthy adults (12). In con- trast, MRSA252 is a leading cause of hospital infections in the FIGURE 10. TaqMan real-time RT-PCR confirmation of microarray re- United States and United Kingdom (16), but to our knowledge is sults. Genes (n ϭ 8) identified as differentially transcribed by S. aureus microarrays (A, MRSA252; B, MW2) were selected from several catego- not a typical source of disease in individuals without associated ries for confirmation by TaqMan real-time RT-PCR. Transcript levels were risk factors. We note also that methicillin resistance has little to do measured at 60 min (black bars) and 180 min (red bars) after phagocytosis with virulence per se, because MnCop, an MSSA strain closely as indicated. There was a strong positive correlation between TaqMan and related to MW2, was similar to MW2 in the mouse model of in- microarray results (83.3%), consistent with previous comparisons (11, 13). fection and in each of our host-pathogen assay systems (Figs. 1–3, 3918 S. aureus EVADE KILLING BY HUMAN NEUTROPHILS

6, and 7). Taken together, our findings provide strong support to An enhanced understanding of the molecular mechanisms used the idea that enhanced strain virulence is linked to (or results from) by S. aureus to circumvent the human innate immune system will evasion of killing by neutrophils, which likely underlies the ability facilitate development of new treatments for bacterial infections. of MW2, MnCop, and LAC to cause disease in individuals without Our previous work with the prominent human pathogen GAS in- known risk factors. dicated that ϳ16% of its genes are differentially regulated during Several observations support the idea that the global pathogen phagocytic interaction with neutrophils (19). By comparison, we response described herein is used by S. aureus to circumvent in- determined that up to ϳ39% of the genes in S. aureus changed nate immunity and thereby promote disease in humans. Notably, following phagocytosis (Fig. 5, see MW2 at 180 min). Differences global changes in S. aureus gene expression were triggered by in the sensitivity of the methods used (spotted vs oligonucleotide PMN phagocytosis, and neutrophils are the predominant host cells microarrays) may account for some of the differences. However, used in defense against bacterial infections. Immediate (within 30 the two pathogens are quite distinct with regard to genome size, min) up-regulation of genes involved in virulence, metabolism, their interaction with human neutrophils, and in the types of dis- capsule synthesis, and gene regulation after ingestion by neutro- ease caused by each. For example, GAS produces numerous mol- phils correlated with S. aureus survival, which was Ն30% for all ecules that inhibit PMN phagocytosis (reviewed in Ref. 56), strains within the first 90 min after phagocytosis (Ն44% for MW2, whereas S. aureus is readily ingested. Nonetheless, each pathogen MnCop, and LAC) (Figs. 2F and 6). Given the noted increases in uses strategies to prolong intraphagosomal survival and cause expression of ahpC, ahpF, katA, gpxA, sodA, sodM, trxA, and trxB eventual host cell lysis (Figs. 2 and 3) (19, 51, 56). Thus, there after phagocytosis, the strains used in this study are probably not likely exist some common molecular mechanisms for immune eva- susceptible to destruction by primary neutrophil-derived reactive sion between the two pathogens. Downloaded from oxygen species, i.e., superoxide and hydrogen peroxide. Prelimi- We used microarrays to generate a global view of the genes and nary studies by our laboratory have shown that there is Ն60% gene regulatory networks involved in bacterial pathogenesis and survival for each of the S. aureus strains after culture with up to 50 therefore generated a vast repository of information from which mM hydrogen peroxide (K. Braughton and F. DeLeo, unpublished many new studies of S. aureus pathogenesis will emerge. The observations). global pathogen response revealed by our studies identified dozens One of the highlights of our study is that several S. aureus gene of potential vaccine Ags and targets for therapeutics designed to http://www.jimmunol.org/ control S. aureus infections. regulatory systems were induced after interaction with PMNs. We previously identified a pathogen survival response in group A Streptococcus (GAS, Streptococcus pyogenes) triggered by Acknowledgments neutrophils through ihk-irr, a two component gene regulatory We are grateful to Michael Otto and Scott Kobayashi for critical review of system required for virulence (19, 51). The ihk-irr survival re- the manuscript and Layre Parkins for technical assistance. sponse is activated by exposure to neutrophil ␣-granule compo- nents and reactive oxygen species (51). Because there is significant Disclosures

S. aureus survival after interaction with neutrophils, a similar as The authors have no financial conflict of interest. by guest on September 30, 2021 yet undefined mechanism must exist in this pathogen. As such, many of the genes reported herein likely comprise a S. aureus References pathogen survival response controlled directly or indirectly by one 1. Lowy, F. D. 1998. Staphylococcus aureus infections. N. Engl. J. Med. 339: or more of the gene regulatory systems induced by phagocytosis. 520–532. 2. Said-Salim, B., B. Mathema, and B. N. Kreiswirth. 2003. Community-acquired Consistent with this notion, Gresham et al. (21) reported that methicillin-resistant Staphylococcus aureus: an emerging pathogen. Infect. Con- survival of S. aureus within PMNs was linked to a global gene trol Hosp. Epidemiol. 24: 451–455. regulator called sar, and sarA was up-regulated in all S. aureus 3. Dinges, M. M., P. M. Orwin, and P. M. Schlievert. 2000. Exotoxins of Staphy- lococcus aureus. Clin. Microbiol. Rev. 13: 16–34. strains following PMN phagocytosis in our present work (Fig. 6). 4. Bae, T., A. K. Banger, A. Wallace, E. M. Glass, F. Aslund, O. Schneewind, and Taken together, these findings are consistent with the idea that D. M. Missiakas. 2004. Staphylococcus aureus virulence genes identified by sarA is important for evasion of killing by neutrophils. A system- bursa aurealis mutagenesis and nematode killing. Proc. Natl. Acad. Sci. USA 101: 12312–12317. atic investigation of each of the gene regulators identified in our 5. Baba, T., F. Takeuchi, M. Kuroda, H. Yuzawa, K. Aoki, A. Oguchi, Y. Nagai, study by targeted gene mutagenesis and/or knockout studies will N. Iwama, K. Asano, T. Naimi, et al. 2002. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359: 1819–1827. be necessary to elucidate the role of each in pathogenesis. 6. Fitzgerald, J. R., D. E. Sturdevant, S. M. Mackie, S. R. Gill, and J. M. Musser. Significant emphasis has been placed on determining principal 2001. Evolutionary genomics of Staphylococcus aureus: insights into the origin virulence factors responsible for the spread of CA S. aureus in- of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc. Natl. Acad. Sci. USA 98: 8821–8826. fections. The Panton-Valentine leukocidin (encoded by lukF-PV 7. From the Centers for Disease Control and Prevention. 1999. Four pediatric deaths and lukS-PV, or simply pvl) has been linked to CA infections re- from community-acquired methicillin-resistant Staphylococcus aureus–Minne- sulting from methicillin-resistant S. aureus (20, 36, 38, 39, 54). sota and North Dakota, 1997–1999. J. Am. Med. Assoc. 282: 1123–1125. 8. Rizkallah, M. F., A. Tolaymat, J. S. Martinez, P. M. Schlievert, and E. M. Ayoub. Although our studies failed to address pvl expression in S. aureus 1989. Toxic shock syndrome caused by a strain of Staphylococcus aureus that during PMN phagocytosis, a recent study by Said-Salim et al. (55) produces enterotoxin C but not toxic shock syndrome toxin-1. Am. J. Dis. Child. 143: 848–849. demonstrated that there is no correlation between neutrophil lysis 9. Miller, L. G., F. Perdreau-Remington, G. Rieg, S. Mehdi, J. Perlroth, A. S. Bayer, and presence of pvl. Importantly, our work identified many other A. W. Tang, T. O. Phung, and B. Spellberg. 2005. Necrotizing fasciitis caused by genes potentially responsible for the differences in PMN lysis and community-associated methicillin-resistant Staphylococcus aureus in Los Ange- les. N. Engl. J. Med. 352: 1445–1453. strain virulence, and thus, a possible explanation for the increased 10. Kazakova, S. V., J. C. Hageman, M. Matava, A. Srinivasan, L. Phelan, virulence of CA strains such as MW2 (Figs. 1, 6, and 7, and sup- B. Garfinkel, T. Boo, S. McAllister, J. Anderson, B. Jensen, et al. 2005. A clone plemental Table V). For example, several putative membrane or of methicillin-resistant Staphylococcus aureus among professional football play- ers. N. Engl. J. Med. 352: 468–475. exported proteins of uncharacterized or unknown function were 11. Begier, E. M., K. Frenette, N. L. Barrett, P. Mshar, S. Petit, D. J. Boxrud, up-regulated only in strains that cause CA infections (Figs. 6 and K. Watkins-Colwell, S. Wheeler, E. A. Cebelinski, A. Glennen, et al. 2004. A high-morbidity outbreak of methicillin-resistant Staphylococcus aureus among 7, and supplemental Table V). These genes clearly merit further players on a college football team, facilitated by cosmetic body shaving and turf investigation. burns. Clin. Infect. Dis. 39: 1446–1453. The Journal of Immunology 3919

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Leukocyte Biol. 73: 315–322. and expression of Panton-Valentine leukocidin among community-acquired 33. Kobayashi, S. D., J. M. Voyich, K. R. Braughton, and F. R. DeLeo. 2003. Down- methicillin resistant Staphylococcus aureus strains. J. Clin. Microbiol. 43: regulation of proinflammatory capacity during apoptosis in human polymorpho- 3373–3379. nuclear leukocytes. J. Immunol. 170: 3357–3368. 56. Voyich, J. M., J. M. Musser, and F. R. DeLeo. 2004. Streptococcus pyogenes and 34. Kobayashi, S. D., J. M. Voyich, K. R. Braughton, A. R. Whitney, W. M. Nauseef, human neutrophils: a paradigm for evasion of innate host defense by bacterial H. L. Malech, and F. R. DeLeo. 2004. Gene expression profiling provides insight pathogens. Microbes. Infect. 6: 1117–1123. ID Probe set Original annotation E-value GI # "BLAST" results

MW2, MnCop, and LAC (17 genes) 5766 SauMSSA476_575g-427_x_at Unique predicted open reading frames 2.0E-95 49485181 conserved hypothetical protein (S. aureus, MSSA476) 5798 SauMSSA476_575g-589_x_at Unique predicted open reading frames 4.0E-69 49485228 conserved hypothetical protein (S. aureus, MSSA476) 6130 SauMu50ChORFSAV0302_s_at conserved hypothetical protein 6.0E-93 15923292 conserved hypothetical protein (S. aureus, Mu50) 7183 SauMu50ChORFSAV1543_s_at hypothetical protein 3.0E-96 27315693 DNA transport machinery protein comGB (S. epidermidis, ATCC 12228) 8350 Sau8325ChORF247_s_at Unique predicted open reading frames 1.0E-116 6176434 exotoxin 1 (S. aureus) 7528 SauMu50ChORFSAV1946_s_at holin homolog 9.0E-42 49484188 holin (S. aureus, MRSA252) 5705 SauMSSA476_400g-319_at Unique predicted open reading frames 2.0E-74 49244245 hypothetical phage protein (S. aureus, MSSA476) 8174 SauN315ChORF1782_x_at hypothetical protein 2.0E-32 15927548 hypothetical protein (Bacteriophage phiN315) (S. aureus N315) 5849 SauMSSA476_J8624-69_x_at Unique predicted open reading frames 3.0E-84 21282930 hypothetical protein (S. aureus, MW2) 5009 SauCOLChORF02984_at hypothetical protein - - no hits 7532 SauMu50ChORFSAV1951_s_at hypothetical protein 7.0E-37 9635186 orf 22 (S. aureus, bacteriophage PVL) 8175 SauN315ChORF1783_at hypothetical protein 3.0E-36 9635218 orf 54 (S. aureus, bacteriophage PVL) 5713 SauMSSA476_400g-69_s_at Unique predicted open reading frames 4.0E-79 49244278 phage regulatory protein (S. aureus, MSSA476) 8145 SauN315_pN315ORF006_s_at CadX 4.0E-49 49398107 putative cadmium efflux system regulatory protein (S. aureus, MSSA476) 6048 SauMu50ChORFSAV0201_s_at hypothetical protein 0.0E+00 49485077 putative membrane protein (S. aureus, MSSA476) 7561 SauMu50ChORFSAV1982_s_at hypothetical protein 1.0E-151 49486795 putative phage regulatory protein (S. aureus, MSSA476) 8302 Sau8325ChORF1946_s_at Unique predicted open reading frames 0.0E+00 49486784 putative terminase-large subunit (S. aureus, MSSA476)

MRSA252 and COL (193 genes) 4494 SauCOLChORF00489_s_at ORF00489 isopropylmalate synthase-related protein 1.0E-36 47556842 2-isopropylmalate synthase (Bacillus cereus G9241) 7541 SauMu50ChORFSAV1961_s_at hypothetical protein 7.0E-47 41189553 77orf 042 (Bacteriophage 77) 6616 SauMu50ChORFSAV0877_x_at hypothetical protein 1.0E-19 40557269 77orf 069 (Bacteriophage 77) 6618 SauMu50ChORFSAV0879_s_at hypothetical protein 9.0E-32 41189571 77orf 072 (Bacteriophage 77) 4911 SauCOLChORF02801_s_at ORF02801 hypothetical protein 2.0E-27 41189575 77orf 085 (Bacteriophage 77) 5210 SauEMRSA16ChORF1681_at Unique predicted open reading frames 1.0E-132 49242757 ABC transporter ATP-binding protein (S. aureus, MRSA252) 5575 SauEMRSA16ChORF468_at Unique predicted open reading frames 0.0E+00 15923652 ABC transporter permease (S. aureus, Mu50) 5154 SauEMRSA16ChORF1466_at Unique predicted open reading frames 0.0E+00 49243024 ABC transporter permease protein (S. aureus, MRSA252) 5131 SauEMRSA16ChORF1404_at Unique predicted open reading frames 3.0E-11 27316592 acyltransferase (S. epidermidis, ATCC 12228) 7739 SauMu50ChORFSAV2207_s_at alpha-acetolactate synthase 0.0E+00 15925197 alpha-acetolactate synthase (S. aureus, Mu50) 4916 SauCOLChORF02806_at ORF02806 prophage L54a, antirepressor, putative 1.0E-146 18920494 anti-repressor (S. aureus, phage phi 11) 7853 SauMu50ChORFSAV2334_s_at hypothetical protein 1.0E-175 49487116 arginase family protein (S. aureus, MSSA476) 5449 SauEMRSA16ChORF2703_at Unique predicted open reading frames 5.0E-51 49241033 arsenical pump membrane protein 1 (S. aureus, MRSA252) 5074 SauEMRSA16ChORF1184_s_at Unique predicted open reading frames 0.0E+00 49245276 autoinducer sensor protein (S. aureus, MSSA476) 5047 SauEMRSA16ChORF1100_at Unique predicted open reading frames 3.0E-38 49242153 CAAX amino terminal protease family protein (S. aureus, MRSA252) 5526 SauEMRSA16ChORF2915_s_at Unique predicted open reading frames 2.0E-42 49240524 capsular polysaccharide synthesis enzyme (S. aureus, MRSA252) 6008 SauMu50ChORFSAV0157_s_at capsular polysaccharide synthesis enzyme Cap5I 0.0E+00 15923147 capsular polysaccharide synthesis enzyme Cap5I (S. aureus, Mu50) 4835 SauCOLChORF02490_at ORF02490 cassette chromosome recombinase A1 (ccrA1) 0.0E+00 6332766 cassette chromosome recombinase A1 (S. aureus,) 4898 SauCOLChORF02766_x_at ORF02766 conserved hypothetical protein 2.0E-73 49485176 conserved hypothetical cytosolic protein (S. aureus, MSSA476) 4594 SauCOLChORF01152_at ORF01152 conserved hypothetical protein 3.0E-55 49241614 conserved hypothetical protein (S. aureus, MRSA252) 5095 SauEMRSA16ChORF1288_x_at Unique predicted open reading frames 6.0E-21 49242994 conserved hypothetical protein (S. aureus, MRSA252) 5289 SauEMRSA16ChORF195_x_at Unique predicted open reading frames 2.0E-97 49240663 conserved hypothetical protein (S. aureus, MRSA252) 5170 SauEMRSA16ChORF1512_s_at Unique predicted open reading frames 1.0E-133 49242980 conserved hypothetical protein (S. aureus, MRSA252) 5236 SauEMRSA16ChORF1750_at Unique predicted open reading frames 2.0E-69 49242653 conserved hypothetical protein (S. aureus, MRSA252) 5215 SauEMRSA16ChORF1690_at Unique predicted open reading frames 1.0E-130 49242746 conserved hypothetical protein (S. aureus, MRSA252) 4832 SauCOLChORF02486_x_at ORF02486 hypothetical protein 3.0E-09 27466972 conserved hypothetical protein (S. epidermidis ATCC 12228) 5036 SauEMRSA16ChORF1061_at Unique predicted open reading frames 0.0E+00 15924686 D-serine/D-alanine/glycine transporter (S. aureus, Mu50) 4945 SauCOLChORF02839_s_at ORF02839 prophage L54a, deoxyuridine 5'-triphospha 2.0E-97 18920563 dUTPase (S. aureus, phage phi 12) 7233 SauMu50ChORFSAV1601_s_at enterotoxin homolog 1.0E-30 15924591 enterotoxin homolog (S. aureus, Mu50) 5470 SauEMRSA16ChORF275_at Unique predicted open reading frames 1.0E-121 49240791 exotoxin (S. aureus, MRSA252) 5123 SauEMRSA16ChORF1375_x_at Unique predicted open reading frames 1.0E-42 49242833 fibronectin-binding protein precursor (S. aureus, MRSA252) 5591 SauEMRSA16ChORF515_s_at Unique predicted open reading frames 6.0E-50 49241080 fluoroquinolone resistance protein (S. aureus, MRSA252) 5267 SauEMRSA16ChORF1857_s_at Unique predicted open reading frames 1.0E-56 15925150 FmtB protein (S. aureus, Mu50) 7852 SauMu50ChORFSAV2333_s_at fosfomycin resistance protein fofB 1.0E-70 15925323 fosfomycin resistance protein fofB (S. aureus, Mu50) 5125 SauEMRSA16ChORF1383_at Unique predicted open reading frames 0.0E+00 21284164 fructose-bisphosphatase (S. aureus, MW2) 4726 SauCOLChORF02043_s_at ORF02043 conserved hypothetical protein 4.0E-54 27316428 general stress protein 26 (S. epidermidis, ATCC 12228) 5909 SauMu50ChORFSAV0039_s_at glycerophosphoryl diester phosphodiesterase homolog 1.0E-139 29165616 glycerophosphoryldiester phosphodiesterase homologue (S. aureus, N315) 7737 SauMu50ChORFSAV2204_s_at conserved hypothetical protein 8.0E-35 52005442 HAD-superfamily hydrolase, subfamily IIB (Bacillus licheniformis ATCC 14580) 4920 SauCOLChORF02811_at ORF02811 conserved hypothetical protein 4.0E-68 49241858 hypothetical phage protein (S. aureus, MRSA252) 7542 SauMu50ChORFSAV1962_s_at hypothetical protein 1.0E-47 49484205 hypothetical phage protein (S. aureus, MRSA252) 7549 SauMu50ChORFSAV1969_s_at hypothetical protein 2.0E-77 49484213 hypothetical phage protein (S. aureus, MRSA252) 4919 SauCOLChORF02810_at ORF02810 conserved hypothetical protein 1.0E-30 49241859 hypothetical phage protein (S. aureus, MRSA252) 8341 Sau8325ChORF2354_at Unique predicted open reading frames 7.0E-42 49241852 hypothetical phage protein (S. aureus, MRSA252) 5709 SauMSSA476_400g-57_s_at Unique predicted open reading frames 5.0E-53 49244254 hypothetical phage protein (S. aureus, MSSA476) 4993 SauEMRSA16ChORF2805_s_at Unique predicted open reading frames 7.0E-11 19745456 hypothetical phage protein (Streptococcus pyogenes MGAS8232) 4876 SauCOLChORF02651_s_at ORF02651 hypothetical protein 4.0E-12 37812000 hypothetical protein (Aeromonas hydrophila) 5920 SauMu50ChORFSAV0050_s_at hypothetical protein 1.0E-126 11278755 hypothetical protein (imported) 5901 SauMu50ChORFSAV0026_s_at hypothetical protein 9.0E-37 11356428 hypothetical protein (imported) - S. aureus,(fragment) 5392 SauEMRSA16ChORF250_s_at Unique predicted open reading frames 1.0E-56 15927589 hypothetical protein (Pathogenicity island SaPIn1) (S. aureus, N315) 4624 SauCOLChORF01438_s_at ORF01438 hypothetical protein 1.0E-99 49242173 hypothetical protein (S. aureus, MRSA252) 4819 SauCOLChORF02432_s_at ORF02432 hypothetical protein 5.0E-90 49243026 hypothetical protein (S. aureus, MRSA252) 5053 SauEMRSA16ChORF1114_s_at Unique predicted open reading frames 2.0E-38 49242183 hypothetical protein (S. aureus, MRSA252) 5383 SauEMRSA16ChORF247_s_at Unique predicted open reading frames 2.0E-60 49240740 hypothetical protein (S. aureus, MRSA252) 4593 SauCOLChORF01151_at ORF01151 hypothetical protein 2.0E-52 49241613 hypothetical protein (S. aureus, MRSA252) 5270 SauEMRSA16ChORF188_s_at Unique predicted open reading frames 3.0E-36 49240655 hypothetical protein (S. aureus, MRSA252) 5288 SauEMRSA16ChORF1948_at Unique predicted open reading frames 2.0E-58 49242381 hypothetical protein (S. aureus, MRSA252) 4757 SauCOLChORF02170_s_at ORF02170 conserved hypothetical protein 6.0E-71 49243421 hypothetical protein (S. aureus, MSSA476) 5059 SauEMRSA16ChORF1137_x_at Unique predicted open reading frames 5.0E-11 49244440 hypothetical protein (S. aureus, MSSA476) 5411 SauEMRSA16ChORF2562_x_at Unique predicted open reading frames 5.0E-09 49243488 hypothetical protein (S. aureus, MSSA476) 6549 SauMu50ChORFSAV0793_s_at hypothetical protein 3.0E-50 15923783 hypothetical protein (S. aureus, Mu50) 7973 SauMu50ChORFSAV2483_s_at hypothetical protein 3.0E-58 15925473 hypothetical protein (S. aureus, Mu50) 6223 SauMu50ChORFSAV0416_s_at hypothetical protein 2.0E-99 15923406 hypothetical protein (S. aureus, Mu50) 6553 SauMu50ChORFSAV0806_s_at hypothetical protein 1.0E-32 15923796 hypothetical protein (S. aureus, Mu50) 7837 SauMu50ChORFSAV2314_s_at hypothetical protein 7.0E-58 15925304 hypothetical protein (S. aureus, Mu50) 5403 SauEMRSA16ChORF2533_at Unique predicted open reading frames 2.0E-45 15924146 hypothetical protein (S. aureus, Mu50) 6550 SauMu50ChORFSAV0799_s_at hypothetical protein 3.0E-67 15923789 hypothetical protein (S. aureus, Mu50) 7557 SauMu50ChORFSAV1977_s_at hypothetical protein 8.0E-65 15924967 hypothetical protein (S. aureus, Mu50) 7577 SauMu50ChORFSAV1999_at hypothetical protein 1.0E-146 15924989 hypothetical protein (S. aureus, Mu50) 4838 SauCOLChORF02493_at ORF02493 hypothetical protein 0.0E+00 7592618 hypothetical protein (S. aureus) 5947 SauMu50ChORFSAV0080_s_at hypothetical protein 1.0E-107 49482321 hypothetical protein SAR0078 (S. aureus, MRSA252)

1 5840 SauMSSA476_J8624-248_x_at Unique predicted open reading frames 1.0E-58 49486621 hypothetical protein SAS1722 (S. aureus, MSSA476) 4702 SauCOLChORF01851_x_at ORF01851 hypothetical protein 4.0E-04 49486996 hypothetical protein SAS2107 (S. aureus, MSSA476) 5091 SauEMRSA16ChORF1252_s_at Unique predicted open reading frames 3.0E-20 21282592 hypothetical protein, similar to cell surface protein Map-w (S. aureus, MW2) 4701 SauCOLChORF01848_s_at ORF01848 surface protein, putative 1.0E-57 24636608 hypothetical protein, similar to MHC class II analog (S. aureus) 5409 SauEMRSA16ChORF2546_at Unique predicted open reading frames 3.0E-58 49241399 inositol monophosphatase family protein (S. aureus, MRSA252) 8119 SauMu50ChORFSAV2667_s_at intercellular adhesion protein D 1.0E-40 49487446 intercellular adhesion protein D (S. aureus, MSSA476) 5634 SauEMRSA16ChORF752_x_at Unique predicted open reading frames 5.0E-29 49241421 iron-regulated heme-iron binding protein (S. aureus, MRSA252) 5506 SauEMRSA16ChORF2845_at Unique predicted open reading frames 2.0E-06 28211180 lipase (Clostridium tetani E88) 8363 Sau8325ChORF2919_at Unique predicted open reading frames 5.0E-21 49482275 metallo-beta-lactamase superfamily protein (S. aureus, MRSA252) 5912 SauMu50ChORFSAV0042_s_at methicillin resistance protein 0.0E+00 49482292 methicillin resistance protein MecR1 (S. aureus, MRSA252) 7589 SauMu50ChORFSAV2017_s_at hypothetical protein 5.0E-05 8489481 M-like protein Szp3 precursor (Streptococcus equi subsp. zooepidemicus) 5230 SauEMRSA16ChORF1721_at Unique predicted open reading frames 7.0E-46 52140939 multidrug resistance protein A (Bacillus cereus ZK) 5563 SauEMRSA16ChORF435_at Unique predicted open reading frames 1.0E-49 27314859 Na+/H+ antiporter (S. epidermidis, ATCC 12228) 6107 SauMu50ChORFSAV0272_x_at NADH dehydrogenase subunit 7.0E-23 15923262 NADH dehydrogenase subunit (S. aureus, Mu50) 4573 SauCOLChORF01088_at ORF01088 hypothetical protein ORF01088 - - no hits 4732 SauCOLChORF02072_at ORF02072 hypothetical protein - - no hits 4746 SauCOLChORF02139_x_at ORF02139 hypothetical protein - - no hits 4797 SauCOLChORF02325_at ORF02325 hypothetical protein - - no hits 4922 SauCOLChORF02813_at ORF02813 conserved hypothetical protein - - no hits 4493 SauCOLChORF00479_at ORF00479 hypothetical protein - - no hits 4905 SauCOLChORF02775_x_at ORF02775 hypothetical protein - - no hits 5175 SauEMRSA16ChORF1532_x_at Unique predicted open reading frames - - no hits 5418 SauEMRSA16ChORF2575_s_at Unique predicted open reading frames - - no hits 5427 SauEMRSA16ChORF2641_s_at Unique predicted open reading frames - - no hits 4520 SauCOLChORF00679_at ORF00679 hypothetical protein - - no hits 4682 SauCOLChORF01693_at hypothetical protein - - no hits 5716 SauMSSA476_400g-86_at Unique predicted open reading frames 0.0E+00 12719447 orf 488 (S. aureus temperate phage phiSLT) 5390 SauEMRSA16ChORF249_s_at Unique predicted open reading frames 3.0E-98 11094381 orf 7 (S. aureus) 5911 SauMu50ChORFSAV0041_s_at penicillin binding protein 2 prime 0.0E+00 49482291 penicillin-binding protein 2 prime (S. aureus, MRSA252) 4700 SauCOLChORF01846_s_at ORF01846 M23/M37 peptidase domain protein 1.0E-162 49242552 peptidase family M23/M37 protein (S. aureus, MRSA252) 5325 SauEMRSA16ChORF2092_at Unique predicted open reading frames 3.0E-35 52004756 peptidase S9, serine active site (Bacillus licheniformis ATCC 14580) 4975 SauCOLChORF02873_at ORF02873 prophage L54a, amidase, putative 0.0E+00 18920590 peptidoglycan hydrolase (S. aureus, phage phi 12) 5560 SauEMRSA16ChORF432_at Unique predicted open reading frames 1.0E-101 49240979 phage integrase family protein (S. aureus, MRSA252) 4950 SauCOLChORF02846_x_at ORF02846 hypothetical protein 2.0E-76 49241828 phage regulatory protein (S. aureus, MRSA252) 5022 SauEMRSA16ChORF1004_x_at Unique predicted open reading frames 3.0E-39 49241828 phage regulatory protein (S. aureus, MRSA252) 4924 SauCOLChORF02815_x_at ORF02815 conserved hypothetical protein 1.0E-22 12719405 phi PVL ORF 38 homologue (S. aureus, temperate phage phiSLT) 8195 SauN315ChORFS063_x_at hypothetical protein (Bacteriophage phiN315) 5.0E-16 9635690 phi PVL ORF 38 homologue (S. aureus,prophage phiPV83) 4939 SauCOLChORF02832_s_at ORF02832 conserved hypothetical protein 1.0E-51 18920508 phi PVL orf 50-like protein (S. aureus, phage phi 11) 8176 SauN315ChORF1785_x_at hypothetical protein (BacteriophagephiN315) 6.0E-38 18920510 phi PVL orf 52-like protein (S. aureus, phage phi 11) 5629 SauEMRSA16ChORF712_at Unique predicted open reading frames 0.0E+00 21282682 phosphoribosylpyrophosphate amidotransferase PurF (S. aureus, MW2) 5903 SauMu50ChORFSAV0031_s_at plasmid recombination enzyme 0.0E+00 49482282 plasmid recombination enzyme (S. aureus, MRSA252) 8189 SauN315ChORF1806_s_at probable ATP-dependent helicase (Bacteriophage phi 1.0E-175 29028621 Pol III-like ATP dependent helicase (S. aureus, phage phi 12) 4844 SauCOLChORF02499_at ORF02499 conserved hypothetical protein 0.0E+00 27316862 poly (glycerol-phosphate) alpha-glucosyltransferase (S. epidermidis, ATCC 12228) 8165 SauN315ChORF0069_s_at potassium-transporting ATPase A-chain homologue 2.0E-59 11356435 potassium-transporting ATPase(A chain) (imported) 5246 SauEMRSA16ChORF1813_at Unique predicted open reading frames 1.0E-108 50590563 predicted transcriptional regulator (Streptococcus suis, 89/1591) 4827 SauCOLChORF02476_s_at ORF02476 HMG-CoA synthase, truncation 5.0E-25 15923028 probable HMG-CoA synthase (S. aureus, Mu50) 4498 SauCOLChORF00508_s_at ORF00508 oligopeptide ABC transporter, permease pr 1.0E-153 15923984 probable oligopeptide transport system permease protein (S. aureus, Mu50) 6235 SauMu50ChORFSAV0432_s_at probable restriction modification system specifici 0.0E+00 15923422 probable restriction modification system specificity subunit (S. aureus, Mu50) 8157 SauN315_pN315ORF022_s_at hypothetical protein, similar to ABC transporter, ATP-bi 1.0E-92 49398099 putative ABC transporter ATP binding protein (S. aureus, MSSA476) 5092 SauEMRSA16ChORF1253_at Unique predicted open reading frames 2.0E-63 49486995 putative acetolactate synthase (S. aureus, MSSA476) 5182 SauEMRSA16ChORF1584_at Unique predicted open reading frames 1.0E-116 49242885 putative acetyltransferase (S. aureus, MRSA252) 5128 SauEMRSA16ChORF1397_at Unique predicted open reading frames 0.0E+00 49242878 putative ATP-dependent protease ATP-binding subunit ClpL (S. aureus, MRSA252) 5584 SauEMRSA16ChORF499_s_at Unique predicted open reading frames 0.0E+00 49241053 putative cation exporting ATPase protein (S. aureus, MRSA252) 7544 SauMu50ChORFSAV1964_s_at hypothetical protein 1.0E-126 49484207 putative Clp protease (S. aureus, MRSA252) 5479 SauEMRSA16ChORF2784_at Unique predicted open reading frames 2.0E-25 49485324 putative Cys/Met metabolism PLP-dependent enzyme (S. aureus, MSSA476) 5579 SauEMRSA16ChORF48_s_at Unique predicted open reading frames 1.0E-99 49240466 putative DNA-binding protein (S. aureus, MRSA252) 4584 SauCOLChORF01141_at ORF01141 hypothetical protein 4.0E-99 49241604 putative exported protein (S. aureus, MRSA252) 4585 SauCOLChORF01142_at ORF01142 traG protein, putative 0.0E+00 49241605 putative exported protein (S. aureus, MRSA252) 5647 SauEMRSA16ChORF902_at Unique predicted open reading frames 1.0E-50 49241605 putative exported protein (S. aureus, MRSA252) 7969 SauMu50ChORFSAV2476_x_at hypothetical protein 9.0E-61 49242820 putative exported protein (S. aureus, MRSA252) 5186 SauEMRSA16ChORF1609_s_at Unique predicted open reading frames 1.0E-177 49242845 putative fatty acid desaturase (S. aureus, MRSA252) 5544 SauEMRSA16ChORF307_at Unique predicted open reading frames 0.0E+00 49240828 putative glycosyl hydrolase (S. aureus, MRSA252) 6174 SauMu50ChORFSAV0363_s_at hypothetical protein 0.0E+00 49482593 putative GTP-binding protein (S. aureus, MRSA252) 5452 SauEMRSA16ChORF2719_s_at Unique predicted open reading frames 2.0E-16 49485437 putative haloacid dehalogenase-like hydrolase (S. aureus, MSSA476) 5422 SauEMRSA16ChORF2596_s_at Unique predicted open reading frames 1.0E-132 49482745 putative insertion element protein (S. aureus, MRSA252) 5521 SauEMRSA16ChORF2904_at Unique predicted open reading frames 1.0E-103 49240558 putative isochorismatase (S. aureus, MRSA252) 4663 SauCOLChORF01617_at ORF01617 hypothetical protein 4.0E-10 49486814 putative leukocidin F subunit (S. aureus, MSSA476) 5119 SauEMRSA16ChORF1370_at Unique predicted open reading frames 1.0E-71 49242826 putative lipoprotein (S. aureus, MRSA252) 5601 SauEMRSA16ChORF56_x_at Unique predicted open reading frames 1.0E-125 49240475 putative lipoprotein (S. aureus, MRSA252) 5391 SauEMRSA16ChORF2491_at Unique predicted open reading frames 6.0E-63 49241603 putative lipoprotein (S. aureus, MRSA252) 5492 SauEMRSA16ChORF281_x_at Unique predicted open reading frames 1.0E-114 49240795 putative lipoprotein (S. aureus, MRSA252) 7135 SauMu50ChORFSAV1490_s_at hypothetical protein 1.0E-137 49486328 putative lipoprotein (S. aureus, MSSA476) 5355 SauEMRSA16ChORF2335_x_at Unique predicted open reading frames 3.0E-79 49486325 putative lipoprotein (S. aureus, MSSA476) 5145 SauEMRSA16ChORF1447_at Unique predicted open reading frames 1.0E-100 49245878 putative lipoprotein (S. aureus, MSSA476) 4586 SauCOLChORF01143_at ORF01143 conserved hypothetical protein 0.0E+00 49241606 putative membrane protein (S. aureus, MRSA252) 4590 SauCOLChORF01147_at ORF01147 conserved hypothetical protein 2.0E-33 49241610 putative membrane protein (S. aureus, MRSA252) 4591 SauCOLChORF01149_s_at ORF01149 conserved hypothetical protein 1.0E-163 49241611 putative membrane protein (S. aureus, MRSA252) 5648 SauEMRSA16ChORF903_at Unique predicted open reading frames 6.0E-34 49241610 putative membrane protein (S. aureus, MRSA252) 6127 SauMu50ChORFSAV0297_s_at hypothetical protein 4.0E-32 49240661 putative membrane protein (S. aureus, MRSA252) 5015 SauCOLChORF03303_s_at ORF03303 conserved hypothetical protein 9.0E-19 49240417 putative membrane protein (S. aureus, MRSA252) 5232 SauEMRSA16ChORF1732_at Unique predicted open reading frames 9.0E-61 49242678 putative membrane protein (S. aureus, MRSA252) 5388 SauEMRSA16ChORF2485_x_at Unique predicted open reading frames 2.0E-47 49241609 putative membrane protein (S. aureus, MRSA252) 5121 SauEMRSA16ChORF1373_x_at Unique predicted open reading frames 4.0E-39 49242831 putative membrane protein (S. aureus, MRSA252) 4842 SauCOLChORF02497_at ORF02497 conserved domain protein 2.0E-42 49484959 putative membrane protein (S. aureus, MSSA476) 4814 SauEMRSA16ChORF1463_at Unique predicted open reading frames 1.0E-162 49243020 putative nickel transport protein (S. aureus, MRSA252) 5235 SauEMRSA16ChORF175_s_at Unique predicted open reading frames 0.0E+00 49240629 putative nitric oxide reductase (S. aureus, MRSA252) 5213 SauEMRSA16ChORF1688_at Unique predicted open reading frames 1.0E-134 49242748 putative nitrite transporter (S. aureus, MRSA252) 5618 SauEMRSA16ChORF656_at Unique predicted open reading frames 1.0E-175 49241279 putative oligopeptide transport ATP-binding protein (S. aureus, MRSA252) 5295 SauEMRSA16ChORF1961_s_at Unique predicted open reading frames 7.0E-15 49486795 putative phage regulatory protein (S. aureus, MSSA476) 5443 SauEMRSA16ChORF2696_s_at Unique predicted open reading frames 6.0E-86 49241052 putative resolvase (S. aureus, MRSA252) 5485 SauEMRSA16ChORF2797_at Unique predicted open reading frames 7.0E-37 49240790 putative restriction and modification system specificity protein (S. aureus, MRSA252) 5503 SauEMRSA16ChORF2835_s_at Unique predicted open reading frames 1.0E-118 49240705 putative Sec-independent protein translocase protein (S. aureus, MRSA252) 4982 SauCOLChORF02901_s_at ORF02901 MttB family protein 1.0E-109 49485226 putative Sec-independent protein translocase protein (S. aureus, MSSA476)

2 5199 SauEMRSA16ChORF1634_s_at Unique predicted open reading frames 1.0E-141 49484686 putative short chain dehydrogenase (S. aureus, MRSA252) 5529 SauEMRSA16ChORF2932_at Unique predicted open reading frames 1.0E-161 49240485 putative siderophore transport system permease (S. aureus, MRSA252) 5105 SauEMRSA16ChORF1335_x_at Unique predicted open reading frames 1.0E-64 49242733 putative small heat shock protein (S. aureus, MRSA252) 5438 SauEMRSA16ChORF2684_at Unique predicted open reading frames 1.0E-10 49485562 putative sodium:sulfate symporter protein (S. aureus, MSSA476) 4869 SauEMRSA16ChORF79_at Unique predicted open reading frames 1.0E-127 49240501 putative sugar transferase (S. aureus, MRSA252) 5395 SauEMRSA16ChORF251_x_at Unique predicted open reading frames 1.0E-104 49240744 putative terminase small subunit (S. aureus, MRSA252) 5908 SauMu50ChORFSAV0037_s_at transposase for IS-like element 1.0E-76 49482280 putative transposase (S. aureus, MRSA252) 5872 SauMu50ChORFSAV0027_s_at transposase for IS-like element 1.0E-123 49482280 putative transposase (S. aureus, MRSA252) 8280 Sau8325ChORF1200_x_at Unique predicted open reading frames 9.0E-80 49484382 putative transposase (S. aureus, MRSA252) 5257 SauEMRSA16ChORF1843_at Unique predicted open reading frames 0.0E+00 49242520 putative UTP--glucose-1-phosphate uridylyltransferase (S. aureus, MRSA252) 5604 SauEMRSA16ChORF582_at Unique predicted open reading frames 0.0E+00 46395522 ribonuclease R (S. aureus, Mu50) 5611 SauEMRSA16ChORF592_at Unique predicted open reading frames 3.0E-23 14132772 secreted von Willebrand factor-binding protein (S. aureus,) 4636 SauCOLChORF01455_s_at ORF01455 serine protease SplE, putative 1.0E-127 9739160 serine protease SplE (S. aureus) 5311 SauEMRSA16ChORF2071_at Unique predicted open reading frames 4.0E-42 9739160 serine protease SplE (S. aureus) 5184 SauEMRSA16ChORF1586_at Unique predicted open reading frames 1.0E-155 16077610 similar to antibiotic transport-associated protein (Bacillus subtilis) 5512 SauEMRSA16ChORF2860_s_at hypothetical protein 2.0E-15 46395560 similar to DNA segregation ATPase and related proteins (S. aureus, Mu50) 4588 SauCOLChORF01145_at ORF01145 conserved hypothetical protein 0.0E+00 16077561 similar to transposon protein (Bacillus subtilis) 4953 SauCOLChORF02849_s_at ORF02849 terminase large subunit, putative 0.0E+00 49244281 terminase large subunit (S. aureus, MSSA476) 4776 SauCOLChORF02233_s_at ORF02233 pyruvate oxidase 0.0E+00 49242869 thiamine pyrophosphate enzyme (S. aureus, MRSA252) 4678 SauCOLChORF01664_s_at ORF01664 threonine dehydratase (ilvA) 0.0E+00 49486855 threonine dehydratase biosynthetic (S. aureus, MSSA476) 4592 SauCOLChORF01150_at ORF01150 conserved hypothetical protein 6.0E-42 22537094 Tn916, transcriptional regulator, putative (Streptococcus agalactiae, 2603V/R) 4582 SauCOLChORF01138_at ORF01138 integrase/recombinase, core domain family 1.0E+00 9635740 transposase (S. aureus,prophage phiPV83) 6885 SauMu50ChORFSAV1195_x_at truncated transposase 7.0E-32 15924185 truncated transposase (S. aureus, Mu50) 7049 SauMu50ChORFSAV1390_x_at truncated transposase 8.0E-49 15924380 truncated transposase (S. aureus, Mu50) 7391 SauMu50ChORFSAV1787_x_at truncated transposase 1.0E-150 15924777 truncated transposase (S. aureus, Mu50) 5548 SauEMRSA16ChORF381_at Unique predicted open reading frames 1.0E-137 27314778 UDP-glucose 4-epimerase related protein (S. epidermidis, ATCC 12228) 4480 SauCOLChORF00404_s_at ORF00404 pathogenicity island protein 1.0E-119 15625515 unknown (S. aureus) 6595 SauMu50ChORFSAV0856_s_at hypothetical protein 1.0E-36 29028571 unknown protein (S. aureus, phage phi 11) 5675 SauEMRSA16ChORF981_s_at Unique predicted open reading frames 5.0E-53 49241754 very large surface anchored protein (S. aureus, MRSA252) 5375 SauEMRSA16ChORF2417_s_at Unique predicted open reading frames 0.0E+00 49241754 very large surface anchored protein (S. aureus, MRSA252)

3 ID Probe set Growth Phase E-value GI # "BLAST" result

MW2 (121 genes) 8336 Sau8325Chorf 2045_at ES 1.0E-21 21359773 4 phiPVL orf 17-like protein (S. aureus bacteriophage phi 53) 8174 SauN315Chorf 1782_x_at EE E1 E2 ES 6.0E-28 40557269 77orf 069 (Bacteriophage 77)* 6045 SauMu50Chorf SAV0198_s_at EE E2 ES 1.0E-124 49243517 ABC transporter, ATP-binding protein (S. aureus, MSSA476) 5772 SauMSSA476_575g-484_at EE E1 E2 ES 5.0E-25 50591584 abortive infection bacteriophage resistance protein (Streptococcus suis 89/1591) 7896 SauMu50Chorf SAV2382_s_at EE E1 E2 ES 1.0E-20 16077489 alternate gene name: yzzA~similar to general stress protein (Bacillus subtilis) 8292 Sau8325Chorf 1929_s_at E2 ES 3.0E-60 9635199 anti-repressor (S. aureus bacteriophage PVL) 5760 SauMSSA476_575g-359_s_at E2 ES 1.0E-132 49485079 ATP-binding transport protein (S. aureus, MSSA476) 8145 SauN315_pN315orf 006_s_at EE E1 E2 ES 0.0E+00 CadX 6539 SauMu50Chorf SAV0779_s_at EE E1 E2 ES 0.0E+00 carboxyesterase precursor 5850 SauMSSA476_J8624-70_at EE E1 E2 ES 0.0E+00 27315460 cardiolipin synthetase-like protein (S. epidermidis ATCC 12228)* 5776 SauMSSA476_575g-488_at E2 ES 2.0E-12 47019089 conserved hypothetical protein (Listeria monocytogenes str. 4b H7858) 5792 SauMSSA476_575g-562_at E1 E2 ES 2.0E-12 47019089 conserved hypothetical protein (Listeria monocytogenes str. 4b H7858) 5764 SauMSSA476_575g-425_x_at EE E1 E2 ES 3.0E-96 49485179 conserved hypothetical protein (S. aureus, MSSA476) 5765 SauMSSA476_575g-426_x_at E2 ES 4.0E-95 49485180 conserved hypothetical protein (S. aureus, MSSA476) 5766 SauMSSA476_575g-427_x_at EE E2 ES 2.0E-95 49485181 conserved hypothetical protein (S. aureus, MSSA476) 5777 SauMSSA476_575g-489_at EE E1 E2 ES 1.0E-47 49485282 conserved hypothetical protein (S. aureus, MSSA476) 5779 SauMSSA476_575g-491_at EE E1 E2 ES 1.0E-129 49243727 conserved hypothetical protein (S. aureus, MSSA476) 6130 SauMu50Chorf SAV0302_s_at E2 5.0E-93 15923292 conserved hypothetical protein (S. aureus, Mu50) 6706 SauMu50Chorf SAV0978_s_at E2 1.0E-119 15923968 conserved hypothetical protein (S. aureus, Mu50) 7183 SauMu50Chorf SAV1543_s_at E2 ES 3.0E-96 27315693 DNA transport machinery protein comGB (S. epidermidis, ATCC 12228) 5753 SauMSSA476_575g-259_at E2 ES 1.0E-127 49484957 enterotoxin H (S. aureus, MSSA476) 7582 SauMu50Chorf SAV2008_s_at E1 E2 ES 0.0E+00 enterotoxin L, sel 5754 SauMSSA476_575g-260_at E2 ES 6.0E-25 37681483 enterotoxin SEN variant (S. aureus) 7583 SauMu50Chorf SAV2009_s_at EE E1 E2 ES 0.0E+00 enterotoxin type C3, sec3 5780 SauMSSA476_575g-492_x_at EE E1 E2 ES 1.0E-124 49485288 exotoxin (S. aureus, MSSA476)* 5782 SauMSSA476_575g-504_at EE E2 ES 1.0E-119 49485301 exotoxin (S. aureus, MSSA476)* 8350 Sau8325Chorf 247_s_at EE E2 ES 1.0E-116 6176434 exotoxin 1 (S. aureus)* 7987 SauMu50Chorf SAV2503_s_at EE E1 E2 ES 0.0E+00 fibronectin-binding protein homolog, fnb* 5736 SauMSSA476_575g-127_x_at E2 1.0E-41 21205592 fibronectin-binding protein homolog, fnbB (S. aureus, MW2)* 5821 SauMSSA476_575g-871_at EE E1 E2 ES 0.0E+00 49245722 fibronectin-binding protein precursor (S. aureus, MSSA476)* 5830 SauMSSA476_575g-983_at EE E1 E2 ES 1.0E-177 38604897 formimidoylglutamase, arginase family protein (S. aureus, MSSA476) 5828 SauMSSA476_575g-906_at EE E1 E2 ES 0.0E+00 21284101 glycine betaine/carnitine/choline ABC transporter (S. aureus, Mu50)* 7528 SauMu50Chorf SAV1946_s_at E1 0.0E+00 holin homolog* 5802 SauMSSA476_575g-7_at E2 ES 0.0E+00 49486992 hyaluronate lyase precursor 2 (S. aureus, MSSA476)* 5705 SauMSSA476_400g-319_at EE E1 E2 ES 2.0E-74 49244245 hypothetical phage protein (S. aureus, MSSA476) 7533 SauMu50Chorf SAV1952_s_at EE E1 E2 ES 5.0E-21 49486768 hypothetical phage protein (S. aureus, MSSA476) 8194 SauN315Chorf S060_at E2 5.0E-27 15927525 hypothetical protein (Bacteriophage phiN315) 8164 SauN315_pN315orf 030_at E1 E2 ES 2.0E-06 32470380 hypothetical protein (S. aureus) 5650 SauEMRSA16Chorf 907_at ES 4.0E-52 49241624 hypothetical protein (S. aureus, MRSA252) 5697 SauMSSA476_324f-21_x_at E1 E2 ES 1.0E-55 49168431 hypothetical protein (S. aureus, MSSA476) 5699 SauMSSA476_324f-9_at EE E1 E2 ES 1.0E-168 49168439 hypothetical protein (S. aureus, MSSA476) 5757 SauMSSA476_575g-279_at EE E1 E2 ES 0.0E+00 49243421 hypothetical protein (S. aureus, MSSA476) 5791 SauMSSA476_575g-561_at E2 ES 7.0E-99 49243723 hypothetical protein (S. aureus, MSSA476) 5848 SauMSSA476_J8624-68_at ES 1.0E-61 49244597 hypothetical protein (S. aureus, MSSA476) 6224 SauMu50Chorf SAV0419_x_at E1 3.0E-21 15923409 hypothetical protein (S. aureus, Mu50) 6544 SauMu50Chorf SAV0786_at ES 9.0E-36 15923776 hypothetical protein (S. aureus, Mu50) 7401 SauMu50Chorf SAV1803_s_at E2 ES 1.0E-106 15924793 hypothetical protein (S. aureus, Mu50) 5849 SauMSSA476_J8624-69_x_at E2 ES 3.0E-84 21282930 hypothetical protein (S. aureus, MW2) 8160 SauN315_pN315orf 026_s_at E1 E2 ES 4.0E-34 16119226 hypothetical protein (S. aureus, N315) 8275 Sau8325Chorf 1118_s_at E2 3.0E-39 49486774 hypothetical protein 13 - S. aureus phage phi PVL 8266 Sau8325Chorf 1080_s_at ES 2.0E-25 9635220 hypothetical protein 56 - S. aureus phage phi PVL 8163 SauN315_pN315orf 029_x_at EE E1 E2 ES 2.0E-08 49398104 hypothetical protein pSAS07 (S. aureus, MSSA476) 5775 SauMSSA476_575g-487_at EE E1 E2 ES 0.0E+00 49485278 hypothetical protein SAS0375 (S. aureus, MSSA476) 4625 SauMSSA476_J8624-292_at E2 6.0E-83 49486623 hypothetical protein SAS1724 (S. aureus, MSSA476) 5729 SauMSSA476_484h-358_x_at E2 ES 1.0E-04 20878455 hypothetical protein XP_157338 (Mus musculus) 5731 SauMSSA476_575g-106_at EE E1 E2 ES 0.0E+00 15925431 hypothetical protein, similar to beta-lactamase 4672 SauCOLChorf 01628_at ES integrase/recombinase-related protein* 5771 SauMSSA476_575g-464_at E2 ES 3.0E-32 47014950 iron permease FTR1 family family (Listeria monocytogenes str. 1/2a F6854) 5009 SauCOLChorf 02984_at E2 ES - - no hits 8308 Sau8325Chorf 1952_s_at EE E1 E2 ES 2.0E-60 9635174 orf 10 (S. aureus bacteriophage PVL) 8313 Sau8325Chorf 1957_s_at EE E1 E2 ES 0.0E+00 9635179 orf 15 (S. aureus bacteriophage PVL) 8303 Sau8325Chorf 1947_s_at E1 E2 3.0E-36 9635168 orf 3 (S. aureus bacteriophage PVL) 8301 Sau8325Chorf 1945_s_at EE E1 E2 ES 8.0E-75 9635166 orf 4 (S. aureus bacteriophage PVL) 8304 Sau8325Chorf 1948_s_at EE E1 E2 ES 1.0E-129 9635717 orf 40~phi PVL orf 4 (S. aureus prophage phiPV83) 8305 Sau8325Chorf 1949_s_at EE E1 E2 ES 1.0E-107 9635718 orf 41~phi PVL orf 5 and 6 (S. aureus prophage phiPV83) 8307 Sau8325Chorf 1951_s_at E1 E2 ES 3.0E-57 9635721 orf 44a~phi PVL orf 9 (S. aureus prophage phiPV83) 7561 SauMu50Chorf SAV1982_s_at E1 E2 ES 1.0E-154 9635211 orf 46 (S. aureus bacteriophage PVL) 8175 SauN315Chorf 1783_at E1 E2 ES 3.0E-36 9635218 orf 54 (S. aureus bacteriophage PVL) 5688 SauMSSA476_207h-91_at EE E2 ES 1.0E-120 9635223 orf 59 (S. aureus bacteriophage PVL) 8298 Sau8325Chorf 1942_s_at EE E2 ES 5.0E-63 9635711 orf 61 (S. aureus bacteriophage PVL) 5798 SauMSSA476_575g-589_x_at EE E1 E2 ES 1.0E-31 50590085 phage envelope protein (Streptococcus suis 89/1591) 5713 SauMSSA476_400g-69_s_at E2 4.0E-79 49244278 phage regulatory protein (S. aureus, MSSA476) 6626 SauRF122_1030-33_s_at E2 0.0E+00 18920518 phi Mu50B-like protein (S. aureus phage phi 11)* 8309 Sau8325Chorf 1953_s_at EE E1 E2 ES 1.0E-64 9635723 phi PVL orf 11 homologue (S. aureus prophage phiPV83) 8310 Sau8325Chorf 1954_s_at EE E1 E2 ES 1.0E-69 18920629 phi PVL orf 12-like protein (S. aureus phage phi 13) 8311 Sau8325Chorf 1955_s_at EE E1 E2 ES 1.0E-155 29028706 phi PVL orf 13-like protein (S. aureus phage phi 13)* 8302 Sau8325Chorf 1946_s_at EE E1 E2 ES 0.0E+00 9635715 phi PVL orf 2 homologue (S. aureus prophage phiPV83) 7532 SauMu50Chorf SAV1951_s_at EE E1 E2 ES 1.0E-32 41189555 phi PVL orf 22-like protein (S. aureus phage phi 13) 7574 SauMu50Chorf SAV1996_at EE E1 E2 ES 2.0E-41 18920596 phi PVL orf 32-like protein (S. aureus phage phi 13) 7573 SauMu50Chorf SAV1995_s_at EE E1 E2 ES 1.0E-100 18920597 phi PVL orf 33-like protein (S. aureus phage phi 13) 6614 SauMu50Chorf SAV0875_x_at E2 ES 4.0E-37 9635705 phi PVL orf 52 homologue (S. aureus prophage phiPV83)* 8299 Sau8325Chorf 1943_s_at E2 ES 7.0E-71 18920617 phi PVL orf 62-like protein (S. aureus phage phi 13) 8300 Sau8325Chorf 1944_s_at EE E1 E2 ES 1.0E-67 9635713 phi PVL orf 63 homologue (S. aureus prophage phiPV83) 5694 SauMSSA476_324f-11_at EE E1 E2 ES 3.0E-98 21205820 potential DNA invertase (S. aureus) 7580 SauMu50Chorf SAV2006_s_at EE E1 E2 ES 0.0E+00 38604903 probable succinyl-diaminopimelate desuccinylase (SDAP)* 5815 SauMSSA476_575g-714_x_at EE E1 E2 ES 4.0E-41 49243378 putative 5'-nucleotidase (S. aureus, MSSA476)* 5732 SauMSSA476_575g-1062_at EE E1 E2 ES 0.0E+00 49486995 putative acetolactate synthase (S. aureus, MSSA476) 5721 SauMSSA476_484h-257_x_at E2 5.0E-52 49485659 putative exported protein (S. aureus, MSSA476) 5773 SauMSSA476_575g-485_at E1 E2 ES 4.0E-57 49485275 putative exported protein (S. aureus, MSSA476) 5787 SauMSSA476_575g-553_x_at E2 ES 1.0E-45 49485302 putative exported protein (S. aureus, MSSA476) 5796 SauMSSA476_575g-566_at EE E1 E2 ES 5.0E-74 49485275 putative exported protein (S. aureus, MSSA476) 5824 SauMSSA476_575g-880_at EE E2 ES 1.0E-139 49487265 putative exported protein (S. aureus, MSSA476) 5825 SauMSSA476_575g-882_x_at EE E1 E2 ES 2.0E-66 49487261 putative exported protein (S. aureus, MSSA476)

4 5744 SauMSSA476_575g-207_at EE E1 E2 ES 1.0E-180 49245878 putative lipoprotein (S. aureus, MSSA476) 5784 SauMSSA476_575g-506_at E2 ES 1.0E-155 49485304 putative lipoprotein (S. aureus, MSSA476) 5302 SauEMRSA16Chorf 1981_s_at E2 ES 4.0E-63 49484192 putative membrane protein (S. aureus, MRSA252) 5774 SauMSSA476_575g-486_at EE E2 ES 1.0E-24 49485277 putative membrane protein (S. aureus, MSSA476) 5800 SauMSSA476_575g-653_at E1 E2 ES 1.0E-20 49485076 putative membrane protein (S. aureus, MSSA476) 5827 SauMSSA476_575g-885_x_at EE E1 E2 ES 6.0E-67 49487258 putative membrane protein (S. aureus, MSSA476) 5831 SauMSSA476_J8624-112_s_at E1 E2 ES 7.0E-92 49486219 putative membrane protein (S. aureus, MSSA476) 5838 SauMSSA476_J8624-246_at EE E1 E2 ES 1.0E-143 49486619 putative membrane protein (S. aureus, MSSA476) 5843 SauMSSA476_J8624-293_at E1 E2 ES 6.0E-62 49486619 putative membrane protein (S. aureus, MSSA476) 6043 SauMu50Chorf SAV0196_s_at E2 ES 4.0E-70 49485072 putative membrane protein (S. aureus, MSSA476) 6047 SauMu50Chorf SAV0200_s_at EE E1 E2 ES 1.0E-20 49485076 putative membrane protein (S. aureus, MSSA476) 6048 SauMu50Chorf SAV0201_s_at E2 ES 0.0E+00 49485077 putative membrane protein (S. aureus, MSSA476) 6049 SauMu50Chorf SAV0202_s_at E2 ES 4.0E-59 49485078 putative membrane protein (S. aureus, MSSA476) 6167 SauMu50Chorf SAV0350_s_at EE E1 E2 ES 2.0E-83 49485230 putative membrane protein (S. aureus, MSSA476) 5799 SauMSSA476_575g-590_at EE E1 E2 ES 1.0E-122 49485226 putative Sec-independent protein translocase protein (S. aureus, MSSA476) 8276 Sau8325Chorf 1119_s_at EE E2 ES 1.0E-48 49486784 putative terminase-large subunit (S. aureus, MSSA476) phage phi PVL* 5719 SauMSSA476_484h-210_s_at EE E1 E2 ES 2.0E-19 14132772 secreted von Willebrand factor-binding protein (S. aureus)* 6541 SauMu50Chorf SAV0783_at E2 1.0E-30 47019611 site-specific recombinase, phage integrase family, putative (Listeria monocytogenes str. 4b H7858)* 5761 SauMSSA476_575g-377_at EE E1 E2 ES 0.0E+00 49243550 staphylocoagulase precursor (S. aureus, MSSA476)* 8346 Sau8325Chorf 2369_at E1 E2 ES 0.0E+00 21283130 terminase large subunit (S. aureus, MW2)* 5740 SauMSSA476_575g-157_at EE E1 E2 ES 8.0E-81 49487332 TetR family regulatory protein (S. aureus, MSSA476) 7625 SauMu50Chorf SAV2061_s_at E1 E2 ES 0.0E+00 threonine dehydratase, ilvA 5820 SauMSSA476_575g-845_at EE E1 E2 ES 0.0E+00 49487318 thiamine pyrophosphate enzyme (S. aureus, MSSA476) 5696 SauMSSA476_324f-2_x_at EE E2 ES 1.0E-51 21205825 truncated Pre protein (S. aureus) 5695 SauMSSA476_324f-17_s_at EE E1 E2 ES 1.0E-125 21205815 truncated probable transposase (S. aureus)* 5698 SauMSSA476_324f-6_x_at E2 ES 1.0E-41 21205807 truncated putative replication initiation protein Rep (S. aureus)* 5803 SauMSSA476_575g-700_at E2 ES 1.0E-116 21281778 truncated transposase (S. aureus, MW2)* 5833 SauMSSA476_J8624-138_at E1 ES 7.0E-57 49241754 very large surface anchored protein (S. aureus, MRSA252)

4750 SauCOLChorf 02155_s_at EE E1 E2 ES 0.0E+00 3-oxoacyl-(acyl carrier protein) reductase 4942 SauCOLChorf 02835_s_at E2 ES 5.0E-63 41189543 77orf 030 (Bacteriophage 77) 4944 SauCOLChorf 02837_s_at E1 E2 ES 1.0E-45 40557251 77orf 039 (Bacteriophage 77) 6610 SauMu50Chorf SAV0871_x_at E2 ES 1.0E-34 41189564 77orf 059 (Bacteriophage 77) 4946 SauCOLChorf 02840_at E1 E2 ES 6.0E-20 40557269 77orf 069 (Bacteriophage 77)* 4947 SauCOLChorf 02841_s_at E2 ES 4.0E-29 40557273 77orf 074 (Bacteriophage 77) 4675 SauCOLChorf 01636_s_at EE E1 E2 ES 0.0E+00 accessory gene regulator protein B (agrB) 4677 SauCOLChorf 01639_s_at EE E1 E2 ES 0.0E+00 accessory gene regulator protein C (argC) 4676 SauCOLChorf 01637_x_at EE E1 E2 ES 0.0E+00 accessory gene regulator protein D (agrD) 4618 SauCOLChorf 01410_s_at EE E1 E2 ES 0.0E+00 arsenate reductase (arsC)** 4910 SauCOLChorf 02800_at EE E1 E2 ES 1.0E-123 40557233 Bacteriophage 77 4943 SauCOLChorf 02836_s_at ES 3.0E-60 41189548 Bacteriophage 77 4914 SauCOLChorf 02804_s_at E2 ES 3.0E-41 40557258 Bacteriophage 77 6009 SauMu50Chorf SAV0158_s_at EE E1 E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme Cap5J 6010 SauMu50Chorf SAV0159_s_at EE E1 E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme Cap5K 6007 SauMu50Chorf SAV0156_s_at EE E1 E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme O-acetyl transferase Cap5H 4452 SauCOLChorf 00347_s_at EE E1 E2 ES 0.0E+00 carboxylesterase 4834 SauCOLChorf 02489_at EE E1 E2 ES 0.0E+00 cassette chromosome recombinase B 6853 SauMu50Chorf SAV1156_s_at E2 ES 1.0E-03 49242314 chemotaxis-inhibiting protein CHIPS (S. aureus, MRSA252)** 4571 SauCOLChorf 01067_s_at EE E1 E2 ES 0.0E+00 chorismate synthase (aroC)** 4705 SauCOLChorf 01854_s_at EE E1 E2 ES 0.0E+00 ClpA-related protein 4896 SauCOLChorf 02763_x_at E2 ES 1.0E-49 49485181 conserved hypothetical protein (S. aureus, MSSA476) 4555 SauCOLChorf 00919_x_at EE 1.0E-05 15924328 conserved hypothetical protein (S. aureus, Mu50) 4902 SauCOLChorf 02771_x_at E1 E2 ES 1.0E-73 15923289 conserved hypothetical protein (S. aureus, Mu50) 4904 SauCOLChorf 02774_x_at EE E2 ES 1.0E-70 15923284 conserved hypothetical protein (S. aureus, Mu50) 4751 SauCOLChorf 02158_s_at EE E1 E2 ES 1.0E-44 27314612 conserved hypothetical protein (S. epidermidis, ATCC 12228) 4767 SauCOLChorf 02201_s_at E1 E2 ES 0.0E+00 drug transporter, putative 8349 Sau8325Chorf 246_at E2 1.0E-71 49485293 exotoxin (S. aureus, MSSA476)* 4996 SauCOLChorf 02957_s_at E1 E2 ES 0.0E+00 exotoxin 3, putative* 4997 SauCOLChorf 02963_s_at ES 0.0E+00 exotoxin, putative* 4763 SauCOLChorf 02184_s_at EE E1 E2 ES 0.0E+00 fibronectin binding protein B (fnbB)* 4764 SauCOLChorf 02186_s_at E1 E2 ES 0.0E+00 fibronectin-binding protein A (fnbA)* 4845 SauCOLChorf 02500_at EE E1 E2 ES 0.0E+00 glycosyl transferase, group 1 family prot 4806 SauCOLChorf 02405_s_at EE E1 E2 ES 0.0E+00 histidinol dehydrogenase (hisD) 4938 SauCOLChorf 02831_at E2 ES 5.0E-40 18920507 HTH DNA binding protein (S. aureus phage phi 11) 4699 SauCOLChorf 01845_s_at EE E1 E2 ES 0.0E+00 hyaluronate lyase (hysA)* 4941 SauCOLChorf 02834_at E2 ES 3.0E-32 49485819 hypothetical phage protein (S. aureus, MSSA476) 4707 SauCOLChorf 01857_at EE E1 E2 ES 1.0E-42 23103504 hypothetical protein (Azotobacter vinelandii) 4626 SauMSSA476_J8624-292_s_at E2 6.0E-83 49486623 hypothetical protein (S. aureus) 5949 SauMu50Chorf SAV0082_s_at EE E1 E2 ES 0.0E+00 6332753 hypothetical protein (S. aureus) 4833 SauCOLChorf 02487_x_at E2 1.0E-63 7592623 hypothetical protein (S. aureus) 4836 SauCOLChorf 02491_at EE E2 ES 1.0E-113 13928276 hypothetical protein (S. aureus) 4891 SauCOLChorf 02745_s_at E1 E2 ES 1.0E-53 6967300 hypothetical protein (S. aureus) 4897 SauCOLChorf 02764_x_at EE E1 E2 ES 2.0E-56 6967304 hypothetical protein (S. aureus) 4595 SauCOLChorf 01153_x_at E2 3.0E-48 49241615 hypothetical protein (S. aureus, MRSA252 4992 SauCOLChorf 02938_at EE E1 E2 ES 3.0E-37 49240758 hypothetical protein (S. aureus, MRSA252) 5078 SauEMRSA16Chorf 1212_s_at E2 1.0E-48 49242448 hypothetical protein (S. aureus, MRSA252) 8360 Sau8325Chorf 2773_at ES 4.0E-27 49243723 hypothetical protein (S. aureus, MSSA476) 4994 SauCOLChorf 02953_x_at EE E1 E2 ES 3.0E-12 49243724 hypothetical protein (S. aureus, MSSA476) 5010 SauCOLChorf 02985_at EE E1 E2 3.0E-14 49243757 hypothetical protein (S. aureus, MSSA476) 4451 SauCOLChorf 00338_x_at E1 1.0E-07 15925247 hypothetical protein (S. aureus, Mu50) 4456 SauCOLChorf 00351_s_at EE E1 E2 ES 8.0E-46 15923797 hypothetical protein (S. aureus, Mu50) 6545 SauMu50Chorf SAV0788_s_at E2 2.0E-33 15923778 hypothetical protein (S. aureus, Mu50) 6548 SauMu50Chorf SAV0792_s_at EE E1 E2 ES 3.0E-83 15923782 hypothetical protein (S. aureus, Mu50) 6602 SauMu50Chorf SAV0863_s_at E1 E2 4.0E-15 15923853 hypothetical protein (S. aureus, Mu50) 6990 SauMu50Chorf SAV1314_s_at E2 5.0E-29 15924304 hypothetical protein (S. aureus, Mu50) 7588 SauMu50Chorf SAV2016_s_at EE E1 E2 ES 3.0E-22 15923787 hypothetical protein (S. aureus, Mu50) 7594 SauMu50Chorf SAV2024_s_at E2 ES 6.0E-33 15925014 hypothetical protein (S. aureus, Mu50) 7972 SauMu50Chorf SAV2482_s_at EE E1 E2 ES 4.0E-48 15925472 hypothetical protein (S. aureus, Mu50) 4703 SauCOLChorf 01852_s_at EE E1 E2 ES 3.0E-07 24372479 hypothetical protein (Shewanella oneidensis MR-1) 4706 SauCOLChorf 01855_s_at EE E1 E2 ES 1.0E-66 15485433 hypothetical protein (Streptococcus thermophilus) 4831 SauCOLChorf 02485_x_at E1 E2 1.0E-49 49482304 hypothetical protein SAR0057 (S. aureus, MRSA252) 4880 SauCOLChorf 02676_s_at ES 2.0E-31 49485104 hypothetical protein SAS0203 (S. aureus, MSSA476) 4623 SauCOLChorf 01437_s_at EE E1 E2 ES 8.0E-56 49486621 hypothetical protein SAS1722 (S. aureus, MSSA476) 6587 SauMu50Chorf SAV0847_at E2 0.0E+00 integrase* 4818 SauCOLChorf 02431_s_at EE E1 E2 ES 0.0E+00 integrase/recombinase, core domain family*

5 4662 SauCOLChorf 01613_s_at E1 E2 ES 0.0E+00 map protein, authentic frameshift (map) 4843 SauCOLChorf 02498_at EE E1 E2 ES 0.0E+00 methicillin-resistant surface protein (pls) 7982 SauMu50Chorf SAV2496_s_at EE E1 E2 ES 1.0E-160 12644358 methicillin-resistant surface protein precursor 7983 SauMu50Chorf SAV2497_s_at EE E1 E2 ES 3.0E-61 12644358 methicillin-resistant surface protein precursor 4846 SauCOLChorf 02502_at EE E1 E2 ES 0.0E+00 Mur ligase family protein, authentic frameshift 8316 Sau8325Chorf 2010_s_at E2 ES - - no hits 4440 SauCOLChorf 00231_s_at E2 - - no hits 4457 SauCOLChorf 00352_at EE E1 E2 ES - - no hits 4489 SauCOLChorf 00428_s_at EE E1 E2 ES - - no hits 4652 SauCOLChorf 01494_at EE E1 E2 ES - - no hits 4658 SauCOLChorf 01585_at EE E1 E2 ES - - no hits 4684 SauCOLChorf 01705_at EE E1 E2 ES - - no hits 4714 SauCOLChorf 01917_x_at E2 ES - - no hits 4722 SauCOLChorf 01998_at EE E1 E2 ES - - no hits 4741 SauCOLChorf 02118_s_at E2 - - no hits 4777 SauCOLChorf 02240_x_at EE E1 E2 ES - - no hits 4778 SauCOLChorf 02241_s_at EE E1 E2 ES - - no hits 4847 SauCOLChorf 02503_at E2 - - no hits 4848 SauCOLChorf 02504_x_at E1 E2 - - no hits 4849 SauCOLChorf 02505_x_at E2 - - no hits 4851 SauCOLChorf 02508_at EE E1 E2 ES - - no hits 4906 SauCOLChorf 02783_s_at E2 - - no hits 4915 SauCOLChorf 02805_at EE E1 E2 ES - - no hits 4925 SauCOLChorf 02816_x_at E1 E2 ES - - no hits 4933 SauCOLChorf 02825_at EE E1 E2 ES - - no hits 4927 SauCOLChorf 02819_at E1 E2 ES 1.0E-19 13095694 orf 14 (bacteriophage bIL285) 4934 SauCOLChorf 02827_x_at EE E1 E2 ES 7.0E-36 17426252 orf 24~unknown (bacteriophage phi ETA) 4476 SauCOLChorf 00400_at E1 E2 0.0E+00 pathogenicity island protein 4475 SauCOLChorf 00399_x_at E2 0.0E+00 pathogenicity island protein 4466 SauCOLChorf 00389_at EE E1 E2 ES 0.0E+00 pathogenicity island protein, integrase O 4469 SauCOLChorf 00392_at EE E1 E2 ES 0.0E+00 pathogenicity island, lipoprotein, putative 4665 SauCOLChorf 01619_s_at EE E1 E2 ES 0.0E+00 peptidase, M20/M25/M40 family, authentic 4936 SauCOLChorf 02829_s_at E1 E2 ES 2.0E-68 18920609 phi ETA orf 25-like protein (S. aureus phage phi 13) 4930 SauCOLChorf 02822_s_at E1 E2 ES 1.0E-132 18920502 phi PV83 orf 20-like protein (S. aureus phage phi 11) 4926 SauCOLChorf 02817_x_at E1 E2 ES 1.0E-39 18920498 phi PVL orf 39-like protein (S. aureus phage phi 11) 4940 SauCOLChorf 02833_x_at E1 E2 ES 1.0E-37 9635703 phi PVL orf 51 homologue (S. aureus prophage phiPV83)** 5017 SauCOLChorf A00001_at EE E1 E2 ES 0.0E+00 plasmid recombination enzyme (pre) 4913 SauCOLChorf 02803_at EE E1 E2 ES 0.0E+00 prophage L54a, Cro-related protein 4974 SauCOLChorf 02872_s_at E1 E2 ES 0.0E+00 prophage L54a, holin* 4932 SauCOLChorf 02824_s_at EE E1 E2 ES 0.0E+00 prophage L54a, replicative DNA helicase 4928 SauCOLChorf 02820_at EE E1 E2 ES 0.0E+00 prophage L54a, single-stranded DNA binding 4935 SauCOLChorf 02828_at EE E1 E2 ES 1.0E-12 23505488 putative DNA methyltransferase (Salmonella typhimurium phage ST64B) 4486 SauCOLChorf 00415_s_at E2 2.0E-20 49483489 putative DNA-binding protein (S. aureus, MRSA252) 4627 SauCOLChorf 01440_x_at E2 2.0E-13 49242177 putative exported protein (S. aureus, MRSA252) 5520 SauEMRSA16Chorf 2898_at E1 E2 8.0E-03 49485086 putative gamma-glutamyltranspeptidase (S. aureus, MSSA476) 5410 SauEMRSA16Chorf 2554_s_at E1 E2 2.0E-38 49483255 putative lipoprotein (S. aureus, MRSA252) 4583 SauCOLChorf 01140_x_at E1 E2 ES 5.0E-26 49241603 putative lipoprotein (S. aureus, MRSA252) 4863 SauCOLChorf 02534_s_at EE E1 E2 ES 1.0E-111 49240475 putative lipoprotein (S. aureus, MRSA252) 5005 SauCOLChorf 02977_s_at EE E1 E2 ES 1.0E-114 49240798 putative lipoprotein (S. aureus, MRSA252) 5006 SauCOLChorf 02978_s_at EE E1 E2 ES 1.0E-118 49240794 putative lipoprotein (S. aureus, MRSA252) 6245 SauMu50Chorf SAV0444_s_at EE E1 E2 ES 1.0E-107 49240798 putative lipoprotein (S. aureus, MRSA252) 4577 SauCOLChorf 01095_s_at EE E1 E2 ES 1.0E-154 49486325 putative lipoprotein (S. aureus, MSSA476) 4576 SauCOLChorf 01093_s_at E1 E2 1.0E-149 49486325 putative lipoprotein (S. aureus, MSSA476) 5004 SauCOLChorf 02974_at EE E1 E2 ES 1.0E-109 49485307 putative lipoprotein (S. aureus, MSSA476) 4589 SauCOLChorf 01146_x_at E2 ES 5.0E-47 49241609 putative membrane protein (S. aureus, MRSA252) 4890 SauCOLChorf 02744_s_at E1 E2 ES 4.0E-58 49240657 putative membrane protein (S. aureus, MRSA252) 6361 SauMu50Chorf SAV0574_s_at ES 3.0E-31 49240932 putative membrane protein (S. aureus, MRSA252) 8289 Sau8325Chorf 181_s_at EE E1 E2 ES 4.0E-99 49485174 putative membrane protein (S. aureus, MSSA476) 4817 SauCOLChorf 02430_s_at EE E1 E2 ES 2.0E-25 49487481 putative membrane protein (S. aureus, MSSA476) 4821 SauCOLChorf 02434_s_at EE E1 E2 ES 4.0E-25 49487481 putative membrane protein (S. aureus, MSSA476) 4899 SauCOLChorf 02767_x_at EE E1 E2 ES 4.0E-95 49485174 putative membrane protein (S. aureus, MSSA476) 4870 SauEMRSA16Chorf 79_s_at ES 1.0E-127 49240501 putative sugar transferase (S. aureus, MRSA252) 4840 SauCOLChorf 02495_at EE E1 E2 ES 1.0E-54 29339746 pyridine nucleotide-disulphide oxidoreductase (Bacteroides thetaiotaomicron VPI-5482)** 5019 SauCOLChorf A00003_at EE E1 E2 ES 0.0E+00 replication initiation protein (repC)* 4689 SauCOLChorf 01772_s_at EE E1 E2 ES 0.0E+00 SAP domain protein 7407 SauMu50Chorf SAV1810_s_at E2 ES 0.0E+00 serine protease 4688 SauCOLChorf 01771_at EE E1 E2 ES 0.0E+00 site-specific recombinase family protein* 4881 SauCOLChorf 02680_s_at EE E1 E2 ES 0.0E+00 staphylocoagulase precursor* 6071 SauMu50Chorf SAV0230_s_at ES 0.0E+00 staphylocoagulase precursor* 4761 SauCOLChorf 02181_s_at E2 0.0E+00 staphylococcal accessory regulator T (sarT) 4482 SauCOLChorf 00411_at EE E1 E2 ES 0.0E+00 staphylococcal enterotoxin B (seb) 8278 Sau8325Chorf 1126_s_at EE E1 E2 ES 0.0E+00 38604903 succinyl-diaminopimelate desuccinylase (S. epidermidis ATCC 12228)* 5001 SauCOLChorf 02970_s_at E1 E2 ES 0.0E+00 surface protein, putative 4481 SauCOLChorf 00410_s_at EE E1 E2 ES 0.0E+00 terminase, small subunit 4671 SauCOLChorf 01626_s_at E2 0.0E+00 terminase, small subunit, putative 5018 SauCOLChorf A00002_at EE E1 E2 ES 0.0E+00 tetracycline resistance protein (tet) 5966 SauMu50Chorf SAV0108_s_at E1 E2 3.0E-74 42737689 transcriptional regulator, GntR family (Bacillus cereus, ATCC 10987)** 4768 SauCOLChorf 02202_s_at E2 0.0E+00 transcriptional regulator, MarR family 4472 SauCOLChorf 00395_at E1 E2 ES 0.0E+00 transcriptional regulator, putative 5965 SauMu50Chorf SAV0107_s_at ES 2.0E-56 49185497 transporter, EamA family (Bacillus anthracis str. Sterne) 7985 SauMu50Chorf SAV2501_s_at EE E1 E2 ES 0.0E+00 transposase* 4621 SauCOLChorf 01426_s_at ES 0.0E+00 transposase, IS200 family* 4559 SauCOLChorf 00974_x_at EE E2 ES 0.0E+00 transposase, putative* 5691 SauMSSA476_306h-5_at ES 9.0E-50 21283815 truncated FmtB protein (S. aureus, MW2) 8340 Sau8325Chorf 226_s_at E2 1.0E-02 44522944 unknown (environmental sequence) 4478 SauCOLChorf 00401_at E2 ES 1.0E-57 563258 virulence-associated protein E

5190 SauEMRSA16Chorf 162_at EE E1 E2 ES 1.0E-128 38258228 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (MEP cytidylyltransferase) (MCT) 5372 SauEMRSA16Chorf 2392_at EE E1 E2 ES 0.0E+00 49241782 3-phosphoshikimate 1-carboxyvinyltransferase (S. aureus, MRSA252) 5265 SauEMRSA16Chorf 1851_at EE E1 E2 ES 1.0E-170 49242515 arginase (S. aureus, MRSA252) 7546 SauMu50Chorf SAV1966_s_at E2 ES 0.0E+00 40557219 77orf 003 (Bacteriophage 77) 7543 SauMu50Chorf SAV1963_s_at EE E1 E2 ES 0.0E+00 40557222 77orf 006 (Bacteriophage 77) 7545 SauMu50Chorf SAV1965_s_at EE E2 ES 0.0E+00 41189523 77orf 008 (Bacteriophage 77) 5299 SauMu50Chorf SAV1957_s_at EE E2 ES 1.0E-119 40557236 77orf 020 (Bacteriophage 77) 7538 SauMu50Chorf SAV1958_s_at EE E2 ES 6.0E-56 41189540 77orf 027 (Bacteriophage 77)

6 7539 SauMu50Chorf SAV1959_s_at EE E2 ES 9.0E-58 40557243 77orf 029 (Bacteriophage 77) 7540 SauMu50Chorf SAV1960_s_at EE E2 ES 7.0E-66 41189545 77orf 033 (Bacteriophage 77) 7547 SauMu50Chorf SAV1967_s_at E2 ES 8.0E-59 41189549 77orf 037 (Bacteriophage 77) 7548 SauMu50Chorf SAV1968_s_at E2 ES 1.0E-42 41189551 77orf 040 (Bacteriophage 77) 5176 SauEMRSA16Chorf 1539_at EE E1 E2 ES 1.0E-115 27316659 ABC transporter (ATP-binding protein) (S. epidermidis, ATCC 12228) 5102 SauEMRSA16Chorf 1319_s_at EE E1 E2 ES 1.0E-133 49242710 ABC transporter ATP_binding protein (S. aureus, MRSA252) 5228 SauEMRSA16Chorf 1714_at E2 4.0E-69 49242710 ABC transporter ATP_binding protein (S. aureus, MRSA252) 5203 SauEMRSA16Chorf 1648_at EE E1 E2 ES 1.0E-114 49242800 ABC transporter ATP-binding protein (S. aureus, MRSA252) 5598 SauEMRSA16Chorf 546_at EE E1 E2 ES 1.0E-139 49241121 ABC transporter ATP-binding protein (S. aureus, MRSA252) 5379 SauEMRSA16Chorf 2444_x_at E1 E2 3.0E-53 49486233 ABC transporter ATP-binding protein (S. aureus, MSSA476) 5103 SauEMRSA16Chorf 1320_s_at EE E1 E2 ES 4.0E-80 22536443 ABC transporter efflux protein, DrrB family, putative (Streptococcus agalactiae 2603V/R) 5342 SauEMRSA16Chorf 2151_at EE E1 E2 ES 0.0E+00 49242081 acetate kinase (S. aureus, MRSA252) 5214 SauEMRSA16Chorf 1689_at EE E1 E2 ES 1.0E-101 49242747 acetyltransferase (GNAT) family protein (S. aureus, MRSA252) 5240 SauEMRSA16Chorf 1766_at EE E1 E2 ES 1.0E-148 49242625 acetyltransferase (GNAT) family protein (S. aureus, MRSA252) 5415 SauEMRSA16Chorf 2570_at EE E1 E2 ES 5.0E-69 49241347 acetyltransferase (GNAT) family protein (S. aureus, MRSA252) 5401 SauEMRSA16Chorf 2531_at E1 E2 ES 1.0E-120 15924153 alpha-hemolysin precursor (S. aureus, Mu50) 5677 SauEMRSA16Chorf 985_at E2 2.0E-31 49483627 amino acid permease (S. aureus, MRSA252) 5339 SauEMRSA16Chorf 2146_at EE E1 E2 ES 0.0E+00 49242086 aminotransferase class-V protein (S. aureus, MRSA252) 5284 SauEMRSA16Chorf 1940_at EE E1 E2 0.0E+00 49242398 ammonium transporter family protein (S. aureus, MRSA252) 5663 SauEMRSA16Chorf 947_at EE E1 E2 ES 9.0E-57 23097980 anthranilate phosphoribosyltransferase 5660 SauEMRSA16Chorf 945_at EE E1 E2 0.0E+00 49241690 anthranilate synthase component I (S. aureus, MRSA252) 5662 SauEMRSA16Chorf 946_at E2 1.0E-108 49241691 anthranilate synthase component II (S. aureus, MRSA252) 8185 SauN315Chorf 1801_at EE E2 ES 0.0E+00 antirepressor 6540 SauMu50Chorf SAV0781_s_at EE E2 0.0E+00 Arabidopsis thaliana genomic DNA 5577 SauEMRSA16Chorf 472_at EE E1 E2 ES 0.0E+00 49485539 AraC family regulatory protein (S. aureus, MSSA476) 5522 SauEMRSA16Chorf 2908_at EE E1 E2 ES 0.0E+00 21281886 arginine biosynthesis bifunctional protein homologue (S. aureus, Mu50) 8154 SauN315_pN315orf 018_at EE E1 E2 ES 0.0E+00 arsenate reductase** 5043 SauEMRSA16Chorf 1096_at E2 1.0E-175 231565 arsenical pump membrane protein 8152 SauN315_pN315orf 016_at EE E1 E2 ES 0.0E+00 arsenical resistance operon repressor 8153 SauN315_pN315orf 017_at EE E1 E2 ES 0.0E+00 arsenic efflux pump protein 5217 SauEMRSA16Chorf 1692_s_at EE E1 E2 ES 8.0E-49 49242744 assimilatory nitrite reductase small subunit (S. aureus, MRSA252) 5626 SauEMRSA16Chorf 704_at EE E1 E2 ES 0.0E+00 49241350 autolysis and methicillin resistant-related protein (S. aureus, MRSA252) 5360 SauEMRSA16Chorf 2340_at EE E1 E2 ES 6.0E-75 40557239 Bacteriophage 77 5066 SauEMRSA16Chorf 1175_at EE E1 E2 ES 1.0E-158 97786 beta-hemolysin (S. aureus) 5331 SauEMRSA16Chorf 2117_at EE E1 E2 ES 0.0E+00 49242121 beta-lactamase regulatory protein (S. aureus, MRSA252) 5906 SauMu50Chorf SAV0034_s_at EE E1 E2 ES 0.0E+00 bleomycin resistance protein 5052 SauEMRSA16Chorf 1113_at EE E1 E2 ES 1.5E-02 538636 botulinum neurotoxin type C1 precursor-Clostridium botulinum phage (type C, strain c-st) 5070 SauEMRSA16Chorf 1179_at EE E1 E2 ES 2.0E-25 47777797 CAAX amino terminal protease family protein (Bacillus anthracis str. Ames 0581) 5046 SauEMRSA16Chorf 1099_at EE E1 E2 ES 1.0E-85 49242153 CAAX amino terminal protease family protein (S. aureus, MRSA252) 5588 SauEMRSA16Chorf 501_at E2 ES 3.0E-61 14020985 cadmium resistance protein B (S. aureus) 5668 SauEMRSA16Chorf 96_at EE E2 ES 1.0E-124 49240522 capsular polysaccharide synthesis enzyme (S. aureus, MRSA252) 5272 SauEMRSA16Chorf 1891_at EE E1 E2 ES 1.0E-132 15923154 capsular polysaccharide synthesis enzyme Cap5P (S. aureus, Mu50) 5672 SauEMRSA16Chorf 978_at E2 6.0E-51 27315590 cell wall enzyme EbsB (S. epidermidis ATCC 12228) 8170 SauN315Chorf 1755_s_at EE E1 E2 ES 4.0E-80 49242314 chemotaxis-inhibiting protein CHIPS (S. aureus, MRSA252)** 5371 SauEMRSA16Chorf 2390_at EE E1 E2 ES 0.0E+00 49241784 chorismate synthase (S. aureus, MRSA252)** 5607 SauEMRSA16Chorf 588_at EE E1 E2 ES 0.0E+00 49241173 clumping factor (S. aureus, MRSA252) 5117 SauEMRSA16Chorf 1367_at EE E1 E2 ES 9.0E-34 49242814 conserved hypothetical protein (S. aureus, MRSA252) 5147 SauEMRSA16Chorf 1449_at EE E1 E2 ES 1.0E-50 49242982 conserved hypothetical protein (S. aureus, MRSA252) 5169 SauEMRSA16Chorf 1512_at EE E1 E2 ES 1.0E-133 49242980 conserved hypothetical protein (S. aureus, MRSA252) 5294 SauEMRSA16Chorf 196_at EE E1 E2 ES 8.0E-54 49243625 conserved hypothetical protein (S. aureus, MSSA476) 5298 SauEMRSA16Chorf 197_x_at E2 1.0E-42 49243625 conserved hypothetical protein (S. aureus, MSSA476) 5350 SauEMRSA16Chorf 226_x_at EE E2 ES 1.0E-13 15923331 conserved hypothetical protein (S. aureus, Mu50) 5100 SauEMRSA16Chorf 1304_at EE E1 E2 ES 1.0E-111 27316374 conserved hypothetical protein (S. epidermidis, ATCC 12228) 5104 SauEMRSA16Chorf 1332_x_at EE E2 ES 1.0E-21 27316429 conserved hypothetical protein (S. epidermidis, ATCC 12228) 5194 SauEMRSA16Chorf 1625_x_at EE E1 E2 ES 2.0E-30 27314646 conserved hypothetical protein (S. epidermidis, ATCC 12228) 5278 SauEMRSA16Chorf 1916_at EE E1 E2 ES 1.0E-114 27316142 conserved hypothetical protein (S. epidermidis, ATCC 12228) 5547 SauEMRSA16Chorf 344_at EE E1 E2 ES 1.0E-148 49240870 dihydropteroate synthase (S. aureus, MRSA252) 5585 SauEMRSA16Chorf 5_at EE E1 E2 ES 0.0E+00 49240388 DNA gyrase subunit A (S. aureus, MRSA252) 5060 SauEMRSA16Chorf 1144_at E2 2.0E-68 49242274 DNA ligase (S. aureus, MRSA252) 5344 SauEMRSA16Chorf 2156_at EE E1 E2 ES 0.0E+00 49242073 DNA polymerase III alpha subunit (S. aureus, MRSA252) 5620 SauEMRSA16Chorf 679_at EE E1 E2 ES 1.0E-07 49328373 DNA-3-methyladenine glycosylase II (Bacillus cereus, G9241) 5497 SauEMRSA16Chorf 2822_at EE E1 E2 ES 2.0E-95 49240729 DNA-binding protein (S. aureus, MRSA252) 5333 SauEMRSA16Chorf 2119_at EE E1 E2 ES 3.0E-89 421394 DNA-invertase (S. aureus, transposon Tn552) 5162 SauEMRSA16Chorf 1488_at EE E2 ES 0.0E+00 7522176 Drp35 protein (S. aureus) 5231 SauEMRSA16Chorf 1722_at EE E1 E2 ES 1.0E-146 49187459 drug resistance transporter, EmrB/QacA family (Bacillus anthracis str. Sterne) 7420 SauMu50Chorf SAV1825_s_at EE 0.0E+00 enterotoxin 7422 SauMu50Chorf SAV1827_s_at EE E2 0.0E+00 enterotoxin 7421 SauMu50Chorf SAV1826_s_at EE 0.0E+00 enterotoxin 5307 SauEMRSA16Chorf 2064_at EE E2 1.0E-137 49242199 enterotoxin (S. aureus, MRSA252) (enterotoxin type M variant) 5306 SauEMRSA16Chorf 2063_at EE E2 1.0E-139 49242200 enterotoxin (S. aureus, MRSA252) (SEO homolog) 5308 SauEMRSA16Chorf 2065_s_at EE E1 E2 ES 1.0E-140 49242198 enterotoxin SEI variant (S. aureus) 5396 SauEMRSA16Chorf 2527_at E2 1.0E-133 49241459 exotoxin (S. aureus, MRSA252)* 5397 SauEMRSA16Chorf 2528_at EE E1 E2 ES 1.0E-130 49241458 exotoxin (S. aureus, MRSA252)* 5398 SauEMRSA16Chorf 2529_at EE E2 ES 1.0E-127 49241457 exotoxin (S. aureus, MRSA252)* 5431 SauEMRSA16Chorf 266_at ES 1.0E-130 49240780 exotoxin (S. aureus, MRSA252)* 5436 SauEMRSA16Chorf 267_at EE E1 E2 ES 1.0E-179 49240781 exotoxin (S. aureus, MRSA252)* 5437 SauEMRSA16Chorf 268_at EE E2 1.0E-120 49240782 exotoxin (S. aureus, MRSA252)* 5487 SauEMRSA16Chorf 2799_at E2 ES 3.0E-13 49240782 exotoxin (S. aureus, MRSA252)* 5447 SauEMRSA16Chorf 270_at EE E2 1.0E-108 3806106 exotoxin 1 (S. aureus)* 5486 SauEMRSA16Chorf 2798_at EE E2 ES 1.0E-49 3806104 exotoxin 2 (S. aureus)* 5439 SauEMRSA16Chorf 269_at EE E2 1.0E-123 49240784 exotoxin 3 (S. aureus, MRSA252)* 5453 SauEMRSA16Chorf 272_at EE E2 ES 1.0E-115 49240787 exotoxin 4 (S. aureus, MRSA252)* 7419 SauMu50Chorf SAV1824_s_at EE 0.0E+00 extracellular enterotoxin type G precursor 5254 SauEMRSA16Chorf 1839_at EE E1 E2 ES 1.0E-175 49242525 FecCD transport family protein (S. aureus, MRSA252) 5599 SauEMRSA16Chorf 547_at EE E1 E2 ES 1.0E-140 27314979 ferrichrome ABC transporter (S. epidermidis, ATCC 12228) 5402 SauEMRSA16Chorf 2532_at E1 E2 6.0E-59 49241448 fibrinogen-binding protein precursor (S. aureus, MRSA252)* 5638 SauEMRSA16Chorf 775_at EE E1 E2 ES 4.0E-75 49241448 fibrinogen-binding protein precursor (S. aureus, MRSA252)* 5122 SauEMRSA16Chorf 1374_x_at E2 ES 3.0E-25 49242833 fibronectin-binding protein precursor (S. aureus, MRSA252)* 5192 SauEMRSA16Chorf 1620_at EE E1 E2 ES 0.0E+00 49242833 fibronectin-binding protein precursor (S. aureus, MRSA252)* 5516 SauEMRSA16Chorf 2878_at EE E1 E2 ES 0.0E+00 49240603 flavohemoprotein (S. aureus, MRSA252) 5592 SauEMRSA16Chorf 516_at EE E1 E2 ES 1.0E-180 49241080 fluoroquinolone resistance protein, norA (S. aureus, MRSA252) 5111 SauEMRSA16Chorf 1344_at EE E1 E2 ES 0.0E+00 21205505 fmhA protein (S. aureus, MW2) 5084 SauEMRSA16Chorf 1235_at E1 E2 ES 1.0E-20 7415524 FmtB (S. aureus)** 5268 SauEMRSA16Chorf 1858_at EE E1 E2 ES 0.0E+00 15925150 FmtB protein (S. aureus, Mu50)** 5625 SauEMRSA16Chorf 702_at E2 6.0E-57 49244331 glutamyl endopeptidase precursor (S. aureus, MRSA252) 5249 SauEMRSA16Chorf 1832_at EE E1 E2 ES 0.0E+00 15927765 glycine betaine transporter opuD homolog (S. aureus, Mu50)*

7 5338 SauEMRSA16Chorf 2138_at EE E2 ES 0.0E+00 49244998 haptoglobin-binding surface anchored protein (S. aureus, MSSA476) 5865 SauMu50_VRSAporf 016_at E2 5.0E-04 23484103 histone deacetylase family, putative (Plasmodium yoelii yoelii) 5051 SauEMRSA16Chorf 1112_at EE E2 ES 0.0E+00 49242179 hyaluronate lyase precursor (Streptococcus constellatus)* 5090 SauEMRSA16Chorf 1251_at E2 0.0E+00 49242551 hyaluronate lyase precursor (Streptococcus constellatus)* 8021 SauMu50Chorf SAV2545_s_at EE E1 E2 ES 0.0E+00 hydroxymethylglutaryl-CoA reductase 8372 Sau8325Chorf 946_s_at EE E1 E2 ES 6.0E-53 49242373 hypothetical phage protein (S. aureus, MRSA252) 5024 SauEMRSA16Chorf 1006_s_at ES 1.0E-18 49241831 hypothetical phage protein (S. aureus, MRSA252) 5026 SauEMRSA16Chorf 1012_at EE E1 E2 ES 4.0E-73 49241864 hypothetical phage protein (S. aureus, MRSA252) 5297 SauEMRSA16Chorf 1966_s_at EE E1 E2 ES 6.0E-67 49484216 hypothetical phage protein (S. aureus, MRSA252) 5364 SauEMRSA16Chorf 2354_at EE E1 E2 2.0E-51 49241827 hypothetical phage protein (S. aureus, MRSA252) 7537 SauMu50Chorf SAV1956_s_at EE E2 4.0E-60 49484199 hypothetical phage protein (S. aureus, MRSA252) 8186 SauN315Chorf 1802_s_at EE E2 ES 2.0E-53 49242368 hypothetical phage protein (S. aureus, MRSA252) 8187 SauN315Chorf 1803_at EE E1 E2 ES 7.0E-26 49242369 hypothetical phage protein (S. aureus, MRSA252) 5023 SauEMRSA16Chorf 1005_s_at E2 3.0E-34 49485833 hypothetical phage protein (S. aureus, MSSA476) 8177 SauN315Chorf 1787_at E2 9.0E-42 49244260 hypothetical phage protein (S. aureus, MSSA476) 5056 SauEMRSA16Chorf 1117_at EE E1 E2 ES 1.0E-71 19746692 hypothetical phage protein (Streptococcus pyogenes MGAS8232) 5905 SauMu50Chorf SAV0033_s_at EE E2 7.0E-28 11356424 hypothetical protein (imported) (S. aureus-fragment) 5918 SauMu50Chorf SAV0048_s_at EE E2 ES 1.0E-40 28465867 hypothetical protein (S. aureus) 5045 SauEMRSA16Chorf 1098_at E1 E2 ES 3.0E-80 49242151 hypothetical protein (S. aureus, MRSA252) 5132 SauEMRSA16Chorf 1407_at EE E1 E2 ES 1.0E-92 49242900 hypothetical protein (S. aureus, MRSA252) 5223 SauEMRSA16Chorf 1698_at EE E1 E2 ES 1.0E-81 49242738 hypothetical protein (S. aureus, MRSA252) 5271 SauEMRSA16Chorf 189_s_at EE E1 E2 ES 0.0E+00 49240656 hypothetical protein (S. aureus, MRSA252) 5275 SauEMRSA16Chorf 191_at EE E1 E2 ES 6.0E-80 49240658 hypothetical protein (S. aureus, MRSA252) 5281 SauEMRSA16Chorf 192_at EE E1 E2 ES 1.0E-78 49240659 hypothetical protein (S. aureus, MRSA252) 5314 SauEMRSA16Chorf 2077_at E2 0.0E+00 49242184 hypothetical protein (S. aureus, MRSA252) 5322 SauEMRSA16Chorf 2085_at EE E1 E2 ES 1.0E-103 49242175 hypothetical protein (S. aureus, MRSA252) 5323 SauEMRSA16Chorf 2086_at E2 0.0E+00 49242174 hypothetical protein (S. aureus, MRSA252) 5373 SauEMRSA16Chorf 241_at E2 7.0E-68 49240734 hypothetical protein (S. aureus, MRSA252) 5376 SauEMRSA16Chorf 242_x_at E2 7.0E-60 49240735 hypothetical protein (S. aureus, MRSA252) 5377 SauEMRSA16Chorf 243_at E2 1.0E-160 49240736 hypothetical protein (S. aureus, MRSA252) 5381 SauEMRSA16Chorf 246_at EE E2 ES 1.0E-120 49240739 hypothetical protein (S. aureus, MRSA252) 5386 SauEMRSA16Chorf 248_at EE E1 E2 ES 1.0E-105 49240741 hypothetical protein (S. aureus, MRSA252) 5399 SauEMRSA16Chorf 253_at EE E1 E2 ES 2.0E-70 49240746 hypothetical protein (S. aureus, MRSA252) 5446 SauEMRSA16Chorf 2699_s_at E1 E2 3.0E-55 49241048 hypothetical protein (S. aureus, MRSA252) 5456 SauEMRSA16Chorf 2722_at E2 ES 6.0E-33 49240977 hypothetical protein (S. aureus, MRSA252) 5496 SauEMRSA16Chorf 2820_s_at EE E1 E2 ES 1.0E-163 49240748 hypothetical protein (S. aureus, MRSA252) 5499 SauEMRSA16Chorf 2824_at EE E1 E2 ES 1.0E-133 49240727 hypothetical protein (S. aureus, MRSA252) 5511 SauEMRSA16Chorf 2859_at E1 E2 1.0E-60 49240656 hypothetical protein (S. aureus, MRSA252) 5555 SauEMRSA16Chorf 40_at EE E1 E2 ES 0.0E+00 49240452 hypothetical protein (S. aureus, MRSA252) 5558 SauEMRSA16Chorf 43_s_at EE E1 E2 ES 6.0E-85 49240455 hypothetical protein (S. aureus, MRSA252) 5567 SauEMRSA16Chorf 44_at EE E1 E2 9.0E-55 49240457 hypothetical protein (S. aureus, MRSA252) 5590 SauEMRSA16Chorf 51_at EE E1 E2 ES 1.0E-50 49240470 hypothetical protein (S. aureus, MRSA252) 5619 SauEMRSA16Chorf 678_at EE E1 E2 ES 1.0E-129 49241306 hypothetical protein (S. aureus, MRSA252) 5656 SauEMRSA16Chorf 92_at E1 E2 ES 1.0E-143 49240518 hypothetical protein (S. aureus, MRSA252) 5657 SauEMRSA16Chorf 92_s_at E2 ES 1.0E-143 49240518 hypothetical protein (S. aureus, MRSA252) 8252 SauTSS339-60_at EE E1 E2 ES 4.0E-41 49240654 hypothetical protein (S. aureus, MRSA252) 5356 SauEMRSA16Chorf 2336_at EE E1 E2 ES 2.0E-79 49244770 hypothetical protein (S. aureus, MSSA476) 5029 SauEMRSA16Chorf 1016_at E2 2.0E-06 15924479 hypothetical protein (S. aureus, Mu50) 5106 SauEMRSA16Chorf 1337_at E2 ES 3.0E-08 15925451 hypothetical protein (S. aureus, Mu50) 5921 SauMu50Chorf SAV0051_s_at E1 E2 5.0E-26 15923041 hypothetical protein (S. aureus, Mu50) 5928 SauMu50Chorf SAV0058_s_at EE E2 ES 4.0E-80 15923048 hypothetical protein (S. aureus, Mu50) 5945 SauMu50Chorf SAV0078_s_at E2 2.0E-78 15923068 hypothetical protein (S. aureus, Mu50) 6219 SauMu50Chorf SAV0412_at ES 3.0E-54 15923402 hypothetical protein (S. aureus, Mu50) 6239 SauMu50Chorf SAV0437_s_at EE E2 ES 1.0E-141 15923427 hypothetical protein (S. aureus, Mu50) 6551 SauMu50Chorf SAV0801_at EE E1 E2 ES 1.0E-179 15923791 hypothetical protein (S. aureus, Mu50) 7400 SauMu50Chorf SAV1802_s_at EE E2 ES 1.0E-58 15924792 hypothetical protein (S. aureus, Mu50) 5357 SauEMRSA16Chorf 2337_at EE E1 E2 ES 1.0E-94 21283172 hypothetical protein (S. aureus, MW2) 8142 SauN315_pN315orf 002_at EE E1 E2 ES 4.0E-53 16119202 hypothetical protein (S. aureus, N315) 5143 SauEMRSA16Chorf 1445_at EE E1 E2 ES 2.0E-02 27316718 hypothetical protein (S. epidermidis, ATCC 12228) 5932 SauMu50Chorf SAV0064_s_at E2 1.0E-53 49482309 hypothetical protein SAR0062 (S. aureus, MRSA252) 5933 SauMu50Chorf SAV0065_s_at EE E1 E2 ES 0.0E+00 49482310 hypothetical protein SAR0063 (S. aureus, MRSA252) 5942 SauMu50Chorf SAV0075_s_at EE E1 E2 ES 1.0E-158 49482316 hypothetical protein SAR0074 (S. aureus, MRSA252) 5944 SauMu50Chorf SAV0077_s_at EE E1 E2 ES 1.0E-16 49482318 hypothetical protein SAR0075a (S. aureus, MRSA252) 5630 SauEMRSA16Chorf 720_at EE E1 E2 ES 9.0E-89 49485920 hypothetical protein SAS1017 (S. aureus, MSSA476) 7154 SauMu50Chorf SAV1510_s_at EE E2 ES 0.0E+00 15924500 hypothetical protein, similar to export protein SpcT protein (S. aureus, N315) 5258 SauEMRSA16Chorf 1844_at EE E1 E2 ES 1.0E-112 15927750 hypothetical protein, similar to hemolysin III (S. aureus, N315) 5260 SauEMRSA16Chorf 1845_at EE E1 E2 ES 1.0E-176 21283824 hypothetical protein, similar to multidrug transporter (S. aureus, MW2) 5221 SauEMRSA16Chorf 1696_at EE E1 E2 ES 1.0E-107 21284046 hypothetical protein, similar to nitrate reductase delta chain (S. aureus, MW2) 5676 SauEMRSA16Chorf 982_at E2 9.0E-53 21283053 hypothetical protein, similar to streptococcal adhesin emb (S. aureus, MW2) 5238 SauEMRSA16Chorf 1761_at E2 ES 1.0E-127 21283934 hypothetical protein, similar to urea transporter (S. aureus, MW2) 5292 SauN315Chorf 1804_s_at E2 ES 2.0E-42 30043984 hypothetical transcriptional regulator (S. phage phiN315) 5172 SauEMRSA16Chorf 1524_at EE E1 E2 ES 6.0E-86 49242964 immunodominant antigen B (S. aureus, MRSA252) 5632 SauEMRSA16Chorf 739_at EE E1 E2 ES 1.0E-156 49241399 inositol monophosphatase family protein (S. aureus, MRSA252) 5639 SauEMRSA16Chorf 776_at EE E1 E2 ES 2.0E-22 29028716 involved in expression of fibrinogen binding protein (S. aureus phage phi 13) 5404 SauEMRSA16Chorf 2537_at EE E1 E2 ES 1.0E-152 49241421 iron-regulated heme-iron binding protein (S. aureus, MRSA252) 5406 SauEMRSA16Chorf 2538_at EE E1 E2 0.0E+00 49241420 iron-regulated heme-iron binding protein (S. aureus, MRSA252) 5939 SauMu50Chorf SAV0072_at E2 0.0E+00 K+-transporting ATPase chain A 5907 SauMu50Chorf SAV0035_s_at EE E1 E2 ES 0.0E+00 kanamycin nucleotidyltransferase 5208 SauEMRSA16Chorf 1675_at E2 5.0E-29 477911 leucocidin R, component F (S. aureus) 5114 SauEMRSA16Chorf 1348_at EE E1 E2 ES 1.0E-169 477911 leukocidin R, component F (S. aureus) 5346 SauEMRSA16Chorf 2176_at EE E1 E2 ES 0.0E+00 49242053 lysine-specific permease (S. aureus, MRSA252) 5445 SauEMRSA16Chorf 2698_at EE E1 E2 ES 1.0E-145 49241050 LysR family regulatory protein (S. aureus, MRSA252) 5602 SauEMRSA16Chorf 571_at EE E1 E2 ES 0.0E+00 28270739 malolactic enzyme (Lactobacillus plantarum, WCFS1) 5082 SauEMRSA16Chorf 1234_at EE E1 E2 ES 0.0E+00 49242510 mannitol-1-phosphate 5-dehydrogenase (Vibrio cholerae) 5369 SauEMRSA16Chorf 238_at EE E1 E2 2.0E-35 47531063 mechanosensitive ion channel family protein (Bacillus anthracis str. Ames 0581) 5370 SauEMRSA16Chorf 238_s_at EE E1 E2 2.0E-35 49481188 mechanosensitive ion channel family protein (Bacillus thuringiensis serovar konkukian str. 97-27) 5915 SauMu50Chorf SAV0045_s_at E2 1.0E-48 49484962 metallo-beta-lactamase superfamily protein (S. aureus, MSSA476) 5916 SauMu50Chorf SAV0046_s_at E2 1.0E-145 49484962 metallo-beta-lactamase superfamily protein (S. aureus, MSSA476) 5913 SauMu50Chorf SAV0043_s_at EE E1 E2 ES 0.0E+00 methicillin resistance regulatory protein 5303 SauEMRSA16Chorf 1988_at EE E1 E2 ES 0.0E+00 49242309 MHC class II analog (S. aureus, MRSA252) 5442 SauEMRSA16Chorf 2695_at E2 ES 2.0E-94 49241054 multicopper oxidase protein (S. aureus, MRSA252) 5587 SauEMRSA16Chorf 500_s_at EE E1 E2 ES 0.0E+00 49241054 multicopper oxidase protein (S. aureus, MRSA252) 5263 SauEMRSA16Chorf 1848_at EE E1 E2 ES 1.0E-145 27316223 multidrug resistance protein (S. epidermidis ATCC 12228) 5564 SauEMRSA16Chorf 436_at EE E1 E2 ES 4.0E-38 27314860 Na+/H+ antiporter (S. epidermidis, ATCC 12228) 5109 SauEMRSA16Chorf 1341_at EE E1 E2 ES 1.0E-68 49242742 nitrate reductase alpha chain (S. aureus, MRSA252) 5219 SauEMRSA16Chorf 1694_at EE E1 E2 ES 0.0E+00 49242742 nitrate reductase alpha chain (S. aureus, MRSA252)

8 5108 SauEMRSA16Chorf 1340_at E1 E2 ES 1.0E-57 49487179 nitrate reductase alpha chain (S. aureus, MSSA476) 5220 SauEMRSA16Chorf 1695_at EE E1 E2 ES 0.0E+00 49242741 nitrate reductase beta chain (S. aureus, MRSA252) 7901 SauMu50Chorf SAV2388_s_at EE E1 E2 ES 0.0E+00 nitrite extrusion protein 5216 SauEMRSA16Chorf 1691_at EE E1 E2 ES 0.0E+00 49242745 nitrite reductase large subunit (S. aureus, MRSA252) 5110 SauEMRSA16Chorf 1342_at EE E1 E2 ES 9.0E-29 49487182 nitrite reductase large subunit (S. aureus, MSSA476) 5201 SauEMRSA16Chorf 1642_at EE E2 1.0E-143 49242807 oligopeptide transporter putative ATPase domain (S. aureus, MRSA252) 5923 SauMu50Chorf SAV0053_s_at EE E1 E2 ES 0.0E+00 O-nucleotidylltransferase 7560 SauMu50Chorf SAV1981_x_at EE E2 ES 6.0E-38 9635212 orf 47 (S. aureus bacteriophage PVL) 7591 SauMu50Chorf SAV2021_s_at EE E2 ES 1.0E-150 11094388 orf 14 (S. aureus) 5389 SauEMRSA16Chorf 249_at EE E1 E2 ES 2.0E-98 11094381 orf 7 (S. aureus) 5659 SauEMRSA16Chorf 941_at EE E1 E2 ES 0.0E+00 15924350 oxacillin resistance-related FmtC protein (S. aureus, MW2) 5354 SauEMRSA16Chorf 2321_s_at EE E2 1.0E-146 49241889 PfkB family carbohydrate kinase (S. aureus, MRSA252) 5142 SauEMRSA16Chorf 1442_at EE E1 E2 1.0E-46 27316697 phage infection protein (S. epidermidis ATCC 12228) 8243 SauTSS336-11_at ES 1.0E-150 29028706 phi PVL orf 13-like protein (S. aureus phage phi 13)* 5063 SauEMRSA16Chorf 1164_s_at E2 2.0E-92 9635727 phi PVL orf 15 and 16 homologue (S. aureus prophage phiPV83) 5300 SauEMRSA16Chorf 1978_s_at E2 ES 0.0E+00 15924945 phi PVL orf 15 and 16 homologue (S. aureus prophage phiPV83) 5064 SauEMRSA16Chorf 1165_at E2 3.0E-58 15924945 phi PVL orf 15 and 16 homologue (S. aureus, Mu50) 6613 SauMu50Chorf SAV0874_x_at EE 9.0E-42 9635703 phi PVL orf 51 homologue (S. aureus prophage phiPV83)** 5296 SauEMRSA16Chorf 1964_at EE E2 ES 4.0E-37 9635705 phi PVL orf 52 homologue (S. aureus prophage phiPV83)* 5637 SauEMRSA16Chorf 772_at EE E1 E2 ES 3.0E-20 47093492 phosphoesterase family protein (Listeria monocytogenes str. 4b H7858) 5940 SauMu50Chorf SAV0073_s_at EE E2 ES 0.0E+00 potassium-transporting ATPase B chain homologue 5941 SauMu50Chorf SAV0074_s_at EE E1 E2 ES 0.0E+00 potassium-transporting ATPase C chain homologue 5441 SauEMRSA16Chorf 2693_s_at EE E1 E2 ES 0.0E+00 49241056 probable cadmium-transporting ATPase (S. aureus, MRSA252) 5040 SauEMRSA16Chorf 1089_at EE E1 E2 ES 1.0E-160 46395533 probable NAD(FAD)-utilizing dehydrogenases (S. aureus, Mu50) 7418 SauMu50Chorf SAV1823_s_at E1 E2 2.0E-25 42518378 prophage protein (Lactobacillus johnsonii, NCC 533) 5098 SauEMRSA16Chorf 1298_at E2 1.0E-53 49487106 PTS system, arbutin-like IIBC component (S. aureus, MSSA476) 5089 SauEMRSA16Chorf 1247_at E2 ES 1.0E-63 24379884 PTS system, lactose-specific enzyme IIBC EIIBC-LAC) (Streptococcus mutans, UA159) 5081 SauEMRSA16Chorf 1231_at EE E2 ES 0.0E+00 49486947 PTS system, mannitol-specific IIBC component (S. aureus, MSSA476) 5269 SauEMRSA16Chorf 1859_at E2 4.0E-65 49486947 PTS system, mannitol-specific IIBC component (S. aureus, MSSA476) 5593 SauEMRSA16Chorf 521_at EE E1 E2 0.0E+00 49241085 PTS transport system, fructose-specific IIABC component (S. aureus, MRSA252) 5540 SauEMRSA16Chorf 2988_x_at E1 E2 ES 5.0E-45 49240405 putative 5'-nucleotidase (S. aureus, MRSA252)* 5574 SauEMRSA16Chorf 467_at EE E1 E2 ES 1.0E-137 49241018 putative ABC transporter protein (S. aureus, MRSA252) 5549 SauEMRSA16Chorf 382_at EE E1 E2 ES 0.0E+00 49240913 putative aminotransferase (S. aureus, MRSA252) 5185 SauEMRSA16Chorf 1588_at EE E1 E2 ES 1.0E-47 49242878 putative ATP-dependent protease ATP-binding subunit ClpL (S. aureus, MRSA252) 5234 SauEMRSA16Chorf 1749_at EE E1 E2 ES 0.0E+00 49242654 putative bifunctional protein (S. aureus, MRSA252) 5440 SauEMRSA16Chorf 2692_s_at EE E1 E2 ES 9.0E-63 49241057 putative cadmium efflux system accessory protein (S. aureus, MRSA252) 5603 SauEMRSA16Chorf 581_at EE E1 E2 ES 1.0E-141 49241166 putative carboxylesterase (S. aureus, MRSA252) 5652 SauEMRSA16Chorf 911_at EE E1 E2 ES 0.0E+00 49241639 putative cardiolipin synthase (S. aureus, MRSA252)* 5152 SauEMRSA16Chorf 1462_at EE E1 E2 ES 1.0E-106 49243019 putative DNA-binding protein (S. aureus, MRSA252) 5044 SauEMRSA16Chorf 1097_at E2 ES 4.0E-64 15924767 putative DNA-binding protein (S. aureus, MSSA476) 5345 SauEMRSA16Chorf 2162_at E1 E2 3.0E-55 49486522 putative D-serine/D-alanine/glycine transporter (S. aureus, MSSA476) 5050 SauEMRSA16Chorf 1111_at E2 3.0E-35 49242181 putative exported protein (S. aureus, MRSA252) 5141 SauEMRSA16Chorf 1437_s_at EE E1 E2 ES 2.0E-28 49242965 putative exported protein (S. aureus, MRSA252) 5160 SauEMRSA16Chorf 1480_at EE E1 E2 ES 1.0E-115 49243027 putative exported protein (S. aureus, MRSA252) 5282 SauEMRSA16Chorf 1928_at EE 2.0E-58 49242416 putative exported protein (S. aureus, MRSA252) 5316 SauEMRSA16Chorf 2079_x_at EE E1 E2 ES 5.0E-76 49242181 putative exported protein (S. aureus, MRSA252) 5317 SauEMRSA16Chorf 2080_at EE E1 E2 ES 3.0E-45 49242180 putative exported protein (S. aureus, MRSA252) 5318 SauEMRSA16Chorf 2081_x_at EE E2 3.0E-57 49242181 putative exported protein (S. aureus, MRSA252) 5320 SauEMRSA16Chorf 2083_at E2 ES 2.0E-74 49242177 putative exported protein (S. aureus, MRSA252) 5321 SauEMRSA16Chorf 2084_at EE 2.0E-68 49242176 putative exported protein (S. aureus, MRSA252) 5413 SauEMRSA16Chorf 2568_at EE E1 E2 ES 0.0E+00 49241349 putative exported protein (S. aureus, MRSA252) 5458 SauEMRSA16Chorf 2725_at E2 4.0E-28 49240972 putative exported protein (S. aureus, MRSA252) 5472 SauEMRSA16Chorf 276_at EE E2 ES 0.0E+00 49240792 putative exported protein (S. aureus, MRSA252) 5610 SauEMRSA16Chorf 591_at E2 0.0E+00 49241174 putative exported protein (S. aureus, MRSA252) 5197 SauEMRSA16Chorf 1631_x_at EE E1 E2 ES 1.0E-53 49245703 putative exported protein (S. aureus, MSSA476) 5168 SauEMRSA16Chorf 151_at EE E1 E2 ES 1.0E-129 49240598 putative glutamine amidotransferase class-I (S. aureus, MRSA252) 5518 SauEMRSA16Chorf 2883_at E2 3.0E-62 49240598 putative glutamine amidotransferase class-I (S. aureus, MRSA252) 5144 SauEMRSA16Chorf 1446_at EE E1 E2 ES 3.0E-05 33565730 putative hemolysin (Bordetella bronchiseptica) 5020 SauEMRSA16Chorf 10_at EE E1 E2 ES 1.0E-159 27314471 putative homoserine-o-acetyltransferase (S. epidermidis, ATCC 12228) 5537 SauEMRSA16Chorf 2947_s_at EE E1 E2 ES 0.0E+00 49240463 putative hydratase (S. aureus, MRSA252) 5093 SauEMRSA16Chorf 1254_s_at EE E1 E2 ES 1.0E-142 49483539 putative insertion element protein (S. aureus, MRSA252) 5498 SauEMRSA16Chorf 2823_at EE E1 E2 ES 0.0E+00 49240728 putative integrase (S. aureus, MRSA252)* 5291 SauEMRSA16Chorf 1952_at EE E1 E2 ES 0.0E+00 49242377 putative leukocidin F subunit (S. aureus, MRSA252) 5290 SauEMRSA16Chorf 1951_at EE E1 E2 ES 0.0E+00 49242378 putative leukocidin S subunit (S. aureus, MRSA252) 5049 SauEMRSA16Chorf 1108_x_at EE E1 E2 ES 4.0E-97 49242171 putative lipoprotein (S. aureus, MRSA252) 5193 SauEMRSA16Chorf 1624_x_at EE E1 E2 ES 1.0E-149 49242826 putative lipoprotein (S. aureus, MRSA252) 5226 SauEMRSA16Chorf 1711_at EE E1 E2 ES 4.0E-72 49242715 putative lipoprotein (S. aureus, MRSA252) 5477 SauEMRSA16Chorf 278_s_at E2 ES 1.0E-146 49240795 putative lipoprotein (S. aureus, MRSA252) 5482 SauEMRSA16Chorf 2793_at E2 3.0E-51 49240797 putative lipoprotein (S. aureus, MRSA252) 5501 SauEMRSA16Chorf 283_x_at EE E2 ES 1.0E-122 49240798 putative lipoprotein (S. aureus, MRSA252) 5505 SauEMRSA16Chorf 284_at EE E1 E2 ES 1.0E-155 49240799 putative lipoprotein (S. aureus, MRSA252) 7578 SauMu50Chorf SAV2001_s_at EE E1 E2 ES 2.0E-28 49484246 putative lipoprotein (S. aureus, MRSA252) 5480 SauEMRSA16Chorf 279_x_at E2 ES 3.0E-49 49485304 putative lipoprotein (S. aureus, MSSA476) 5488 SauEMRSA16Chorf 280_at EE E2 ES 2.0E-58 49485304 putative lipoprotein (S. aureus, MSSA476) 5187 SauEMRSA16Chorf 1610_s_at E1 E2 ES 4.0E-87 49242844 putative LysE type translocator (S. aureus, MRSA252) 5188 SauEMRSA16Chorf 1613_at EE E1 E2 ES 0.0E+00 49242841 putative membrane protein (S. aureus, MRSA252) 5204 SauEMRSA16Chorf 1649_at EE E1 E2 ES 1.0E-138 49242799 putative membrane protein (S. aureus, MRSA252) 5229 SauEMRSA16Chorf 1715_at EE E2 ES 1.0E-102 49242709 putative membrane protein (S. aureus, MRSA252) 5233 SauEMRSA16Chorf 1738_at EE E1 E2 ES 4.0E-69 49242671 putative membrane protein (S. aureus, MRSA252) 5255 SauEMRSA16Chorf 1841_at EE E1 E2 ES 0.0E+00 49242523 putative membrane protein (S. aureus, MRSA252) 5261 SauEMRSA16Chorf 1846_at EE E1 E2 ES 5.0E-69 49242517 putative membrane protein (S. aureus, MRSA252) 5274 SauEMRSA16Chorf 190_at EE E1 E2 ES 1.0E-106 49240657 putative membrane protein (S. aureus, MRSA252) 5283 SauEMRSA16Chorf 193_at EE E2 5.0E-67 49240660 putative membrane protein (S. aureus, MRSA252) 5327 SauEMRSA16Chorf 2097_at EE E1 E2 ES 2.0E-76 49242152 putative membrane protein (S. aureus, MRSA252) 5348 SauEMRSA16Chorf 2239_at EE E1 E2 ES 0.0E+00 49241978 putative membrane protein (S. aureus, MRSA252) 5351 SauEMRSA16Chorf 230_at EE E2 ES 0.0E+00 49240704 putative membrane protein (S. aureus, MRSA252) 5352 SauEMRSA16Chorf 231_at EE E1 E2 ES 3.0E-74 49240709 putative membrane protein (S. aureus, MRSA252) 5408 SauEMRSA16Chorf 254_at EE E1 E2 ES 3.0E-64 49240747 putative membrane protein (S. aureus, MRSA252) 5444 SauEMRSA16Chorf 2697_at E1 E2 ES 3.0E-75 49241051 putative membrane protein (S. aureus, MRSA252) 5454 SauEMRSA16Chorf 2720_at E2 0.0E+00 49240987 putative membrane protein (S. aureus, MRSA252) 5455 SauEMRSA16Chorf 2721_at EE E1 E2 ES 1.0E-23 49240985 putative membrane protein (S. aureus, MRSA252) 5457 SauEMRSA16Chorf 2723_at EE E2 ES 1.0E-123 49240976 putative membrane protein (S. aureus, MRSA252) 5461 SauEMRSA16Chorf 2730_at E2 ES 2.0E-87 49240955 putative membrane protein (S. aureus, MRSA252) 5462 SauEMRSA16Chorf 2735_at EE E1 E2 ES 3.0E-65 49482814 putative membrane protein (S. aureus, MRSA252) 5536 SauEMRSA16Chorf 2946_s_at EE E1 E2 ES 7.0E-53 49240464 putative membrane protein (S. aureus, MRSA252) 5583 SauEMRSA16Chorf 498_at E2 ES 1.0E-163 49241051 putative membrane protein (S. aureus, MRSA252)

9 5605 SauEMRSA16Chorf 584_at E2 8.0E-87 49241169 putative membrane protein (S. aureus, MRSA252) 5943 SauMu50Chorf SAV0076_s_at EE E1 E2 ES 5.0E-99 49240437 putative membrane protein (S. aureus, MRSA252) 5946 SauMu50Chorf SAV0079_s_at EE E1 E2 ES 9.0E-47 49240449 putative membrane protein (S. aureus, MRSA252) 6380 SauMu50Chorf SAV0599_s_at EE E2 ES 1.0E-103 49240958 putative membrane protein (S. aureus, MRSA252) 5088 SauEMRSA16Chorf 1241_at E2 1.0E-72 49486963 putative membrane protein (S. aureus, MSSA476) 5919 SauMu50Chorf SAV0049_s_at EE E2 ES 2.0E-37 49484959 putative membrane protein (S. aureus, MSSA476) 5936 SauMu50Chorf SAV0069_s_at EE E1 E2 ES 5.0E-91 49486009 putative membrane protein (S. aureus, MSSA476) 7968 SauMu50Chorf SAV2475_x_at EE E2 ES 5.0E-59 49487258 putative membrane protein (S. aureus, MSSA476) 5129 SauEMRSA16Chorf 1399_at E2 1.0E-21 21218965 putative membrane transport protein (Streptomyces coelicolor, A3(2)) 5242 SauEMRSA16Chorf 1771_at EE E1 E2 ES 6.0E-89 49242619 putative molybdenum cofactor biosynthesis protein B (S. aureus, MRSA252) 5153 SauEMRSA16Chorf 1464_at EE E1 E2 ES 1.0E-154 49243021 putative N-acetyltransferase (S. aureus, MRSA252) 5576 SauEMRSA16Chorf 47_s_at EE E1 E2 ES 1.0E-21 49487477 putative N-acetyltransferase (S. aureus, MSSA476) 5561 SauEMRSA16Chorf 433_s_at EE E1 E2 ES 2.0E-43 49240980 putative NADH-Ubiquinone/plastoquinone (complex I) oxidoreductase protein (S. aureus, MRSA252) 5562 SauEMRSA16Chorf 434_at EE E1 E2 ES 0.0E+00 49240980 putative NADH-Ubiquinone/plastoquinone (complex I) oxidoreductase protein (S. aureus, MRSA252) 5565 SauEMRSA16Chorf 437_at EE E1 E2 ES 0.0E+00 49240983 putative NADH-Ubiquinone/plastoquinone (complex I) oxidoreductase protein (S. aureus, MRSA252) 5468 SauEMRSA16Chorf 2748_at EE E1 E2 ES 0.0E+00 49240908 putative peptidase (S. aureus, MRSA252) 5627 SauEMRSA16Chorf 708_at EE E1 E2 ES 1.0E-129 49241359 putative phosphoribosylaminoimidazole-succinocarboxamide synthase (S. aureus, MRSA252) 5330 SauEMRSA16Chorf 2110_at EE E1 E2 ES 0.0E+00 49242130 putative polysaccharide biosynthesis protein (S. aureus, MRSA252) 5553 SauEMRSA16Chorf 396_at EE E1 E2 ES 0.0E+00 49240931 putative proline/betaine transporter (S. aureus, MRSA252) 5948 SauMu50Chorf SAV0081_s_at EE E1 E2 ES 0.0E+00 49482322 putative protein kinase (S. aureus, MRSA252) 5025 SauEMRSA16Chorf 1011_at EE E1 E2 ES 2.0E-66 49241863 putative regulatory protein (S. aureus, MRSA252) 5582 SauEMRSA16Chorf 497_s_at EE E1 E2 ES 2.0E-84 16119201 putative replication initiation protein Rep (S. aureus, N315)* 5568 SauEMRSA16Chorf 45_at EE E1 E2 ES 0.0E+00 49240458 putative restriction enzyme (S. aureus, MRSA252) 5570 SauEMRSA16Chorf 46_at EE E2 ES 0.0E+00 49240459 putative restriction enzyme modulator protein (S. aureus, MRSA252) 5573 SauEMRSA16Chorf 466_at EE E1 E2 ES 1.0E-178 49241017 putative sensor histidine kinase protein (S. aureus, MRSA252) 5621 SauEMRSA16Chorf 69_at E2 ES 0.0E+00 49240490 putative siderophore biosynthesis protein (S. aureus, MRSA252) 5528 SauEMRSA16Chorf 2931_at EE E1 E2 ES 1.0E-128 49240486 putative siderophore transport system permease (S. aureus, MRSA252) 5616 SauEMRSA16Chorf 65_at EE E1 E2 ES 1.0E-26 49240486 putative siderophore transport system permease (S. aureus, MRSA252) 5158 SauEMRSA16Chorf 1479_at EE E1 E2 ES 1.0E-152 49243028 putative subtilase family protease (S. aureus, MRSA252) 5329 SauEMRSA16Chorf 2109_at EE E1 E2 ES 0.0E+00 49242132 putative surface anchored protein (S. aureus, MRSA252) 5513 SauEMRSA16Chorf 2866_at EE E1 E2 0.0E+00 49240640 putative transport protein (S. aureus, MRSA252) 5262 SauEMRSA16Chorf 1847_at EE E1 E2 ES 1.0E+00 49486956 putative transport protein (S. aureus, MSSA476) 5252 SauEMRSA16Chorf 1838_at EE E1 E2 ES 0.0E+00 49242526 putative transport system binding lipoprotein (S. aureus, MRSA252) 5535 SauEMRSA16Chorf 2945_s_at EE E1 E2 ES 0.0E+00 49240465 putative transporter protein (S. aureus, MRSA252) 5589 SauEMRSA16Chorf 502_s_at EE E2 ES 1.0E-130 49482930 putative transposase (S. aureus, MRSA252)* 5935 SauMu50Chorf SAV0068_s_at E2 3.0E-55 49482311 putative transposase (S. aureus, MRSA252)* 5645 SauEMRSA16Chorf 897_at EE E1 E2 ES 1.0E-176 49241595 putative tRNA delta 2-isopentenylpyrophosphate transferase (S. aureus, MRSA252) 5644 SauEMRSA16Chorf 867_at EE E1 E2 ES 1.0E-173 49241563 putative tRNA pseudouridine synthase B (S. aureus, MRSA252) 5421 SauEMRSA16Chorf 2594_at EE E1 E2 ES 1.0E-177 49241288 putative tryptophanyl-tRNA synthetase (S. aureus, MRSA252) 5313 SauEMRSA16Chorf 2076_at EE E1 E2 ES 0.0E+00 49242185 putative type I restriction modification DNA specificity protein (S. aureus, MRSA252) 5363 SauEMRSA16Chorf 2348_at EE E1 E2 ES 9.0E-12 18920559 PVL orf 52-like protein (S. aureus phage phi 12) 5917 SauMu50Chorf SAV0047_s_at E2 1.0E-61 34396345 pyridine nucleotide-disulphide oxidoreductase family protein (Porphyromonas gingivalis, W83)** 5149 SauEMRSA16Chorf 1458_at EE E1 E2 ES 1.0E-120 49243014 pyrrolidone-carboxylate peptidase (S. aureus, MRSA252) 8151 SauN315_pN315orf 015_at ES 0.0E+00 recombinase Sin 8188 SauN315Chorf 1805_s_at EE E1 E2 ES 0.0E+00 repressor homolog (BacteriophagephiN315) 5655 SauEMRSA16Chorf 915_at EE E2 ES 5.0E-90 49241643 response regulator (S. aureus, MRSA252) 5937 SauMu50Chorf SAV0070_s_at EE E1 E2 ES 1.0E-113 49482312 response regulator protein (S. aureus, MRSA252) 5922 SauMu50Chorf SAV0052_s_at EE E1 E2 ES 0.0E+00 rRNA methylase 5609 SauEMRSA16Chorf 590_at EE E1 E2 ES 1.0E-164 14132772 secreted von Willebrand factor-binding protein (S. aureus)* 5654 SauEMRSA16Chorf 914_at EE E1 E2 ES 0.0E+00 49241642 sensor kinase protein (S. aureus, MRSA252) 5938 SauMu50Chorf SAV0071_s_at EE E1 E2 ES 0.0E+00 49240442 sensor kinase protein (S. aureus, MRSA252) 5551 SauEMRSA16Chorf 388_at EE E1 E2 ES 0.0E+00 21282245 Ser-Asp rich fibrinogen-binding, bone sialoprotein-binding protein (S. aureus, Mu50) 5309 SauEMRSA16Chorf 2069_at E1 E2 ES 1.0E-113 49242189 serine protease (S. aureus, MRSA252) 5310 SauEMRSA16Chorf 2070_at E2 ES 1.0E-131 49242188 serine protease (S. aureus, MRSA252) 5312 SauEMRSA16Chorf 2072_at EE E1 E2 ES 1.0E-50 49242188 serine protease (S. aureus, MRSA252) 5058 SauEMRSA16Chorf 1121_at EE E1 E2 ES 7.0E-95 21436690 signal transduction protein TRAP (S. aureus) 5464 SauEMRSA16Chorf 2741_x_at E2 ES 2.0E-03 27662282 similar to Apolipoprotein L3 (ApoL-III) (Rattus norvegicus) 5465 SauEMRSA16Chorf 2742_x_at E1 E2 2.0E-03 27662282 similar to Apolipoprotein L3 (ApoL-III) (Rattus norvegicus) 5097 SauEMRSA16Chorf 1291_at E1 E2 ES 1.0E-39 16078281 similar to formate dehydrogenase (Bacillus subtilis) 5507 SauEMRSA16Chorf 2850_at EE E2 ES 0.0E+00 49240675 sodium:solute symporter family protein (S. aureus, MRSA252) 5180 SauEMRSA16Chorf 1580_at EE E1 E2 ES 0.0E+00 49242891 squalene synthase (S. aureus, MRSA252) 5159 SauEMRSA16Chorf 148_at EE E1 E2 0.0E+00 13620256 staphylocoagulase precursor (S. aureus, MRSA252)* 5171 SauEMRSA16Chorf 1513_at EE E1 E2 ES 1.0E-143 27316716 streptococcal hemagglutinin protein (S. epidermidis ATCC 12228) 8220 SauRF122_1030-27_at E2 1.0E-100 18920526 structural phi Mu50B (S. aureus phage phi 11)* 5068 SauEMRSA16Chorf 1176_at EE E1 E2 ES 1.0E-145 27314676 succinyl-diaminopimelate desuccinylase (S. epidermidis ATCC 12228)* 5543 SauEMRSA16Chorf 306_at EE E1 E2 ES 0.0E+00 49240827 sugar-specific PTS transport system, IIBC component (S. aureus, MRSA252) 5534 SauEMRSA16Chorf 2943_at E2 2.0E-14 27887376 superfamily I DNA helicase (Fusobacterium nucleatum subsp. vincentii, ATCC 49256) 5594 SauEMRSA16Chorf 53_at EE E1 E2 ES 4.0E-93 27887376 superfamily I DNA helicase (Fusobacterium nucleatum subsp. vincentii, ATCC 49256) 5334 SauEMRSA16Chorf 2120_s_at EE E1 E2 ES 0.0E+00 27316936 Tn552 transposase (S. epidermidis, ATCC 12228)* 5999 SauMu50Chorf SAV0147_s_at EE E2 ES 6.0E-76 47017695 transcription regulator (Listeria monocytogenes, str. 4b H7858) 5124 SauEMRSA16Chorf 1380_at EE E1 E2 1.0E-97 15612995 transcriptional regulator (GntR family) (Bacillus halodurans)** 4822 SauEMRSA16Chorf 1478_at EE E2 ES 5.0E-23 22537855 transcriptional regulator, Cro/CI family (Streptococcus agalactiae, 2603V/R) 5623 SauEMRSA16Chorf 696_at EE E2 ES 1.0E-165 49241332 transport system extracellular binding lipoprotein (S. aureus, MRSA252) 5209 SauEMRSA16Chorf 1680_at EE E1 E2 ES 1.0E-127 49242758 transport system membrane protein (S. aureus, MRSA252) 5433 SauEMRSA16Chorf 2662_at EE E1 E2 ES 1.0E-36 27888096 transporter, drug/ metabolite exporter family (Fusobacterium nucleatum subsp. vincentii, ATCC 49256) 5934 SauMu50Chorf SAV0067_s_at EE E2 0.0E+00 transposase* 5387 SauEMRSA16Chorf 973_s_at EE E1 E2 ES 5.0E-58 9635740 transposase (S. aureus prophage phiPV83)* 5556 SauEMRSA16Chorf 41_x_at EE E1 E2 ES 1.0E-50 49240453 transposase (S. aureus, MRSA252)* 5926 SauMu50Chorf SAV0056_s_at EE E1 E2 ES 0.0E+00 transposase A 5156 SauEMRSA16Chorf 1467_x_at EE E1 E2 ES 1.0E-60 48826639 transposase and inactivated derivatives, IS30 family (Enterococcus faecium) 5925 SauMu50Chorf SAV0055_s_at EE E1 E2 ES 0.0E+00 transposase B 5546 SauEMRSA16Chorf 33_s_at EE E1 E2 ES 5.0E-23 49482301 transposase B 1 (S. aureus, MRSA252) 5924 SauMu50Chorf SAV0054_s_at EE E1 E2 ES 0.0E+00 transposase C 5927 SauMu50Chorf SAV0057_s_at ES 0.0E+00 truncated hypothetical protein 5902 SauMu50Chorf SAV0029_s_at EE E1 E2 ES 0.0E+00 truncated replication protein for pUB110 plasmid 7390 SauMu50Chorf SAV1786_x_at EE E1 E2 ES 0.0E+00 truncated transposase* 7402 SauMu50Chorf SAV1804_at EE E1 E2 0.0E+00 truncated transposase* 5572 SauEMRSA16Chorf 465_at EE E1 E2 ES 1.0E-114 27314888 two-component response regulator (S. epidermidis, ATCC 12228) 5218 SauEMRSA16Chorf 1693_s_at EE E1 E2 ES 1.0E-179 15925388 uroporphyrin-III C-methyl transferase (S. aureus, Mu50) 5140 SauEMRSA16Chorf 1436_at E2 ES 1.0E-61 49242963 zinc metalloproteinase aureolysin precursor (S. aureus neutral proteinase) 5173 SauEMRSA16Chorf 1525_at EE E1 E2 ES 0.0E+00 49242963 zinc metalloproteinase aureolysin precursor (S. aureus, MRSA252) 5077 SauEMRSA16Chorf 1197_at E2 ES 0.0E+00 49242415

10

11 ID Probe set Growth Phase E-value GI # "BLAST" results

MW2 (21 genes) 6618 SauMu50ChORFSAV0879_s_at E2 9.0E-32 41189571 77orf 072 (Bacteriophage 77) 4835 SauCOLChORF02490_at E1 0.0E+00 cassette chromosome recombinase A1 (ccrA1) 5200 SauEMRSA16ChORF1635_at E2 1.0E-146 49242814 conserved hypothetical protein (S. aureus, MRSA252) 5596 SauEMRSA16ChORF544_at E2 1.0E-135 49241119 FecCD transport family protein (S. aureus, MRSA252) 5650 SauEMRSA16ChORF907_at ES 4.0E-52 49241624 hypothetical protein (S. aureus, MRSA252) 5791 SauMSSA476_575g-561_at E2 ES 7.0E-99 49243723 hypothetical protein (S. aureus, MSSA476) 4525 SauCOLChORF00704_x_at E2 9.0E-05 15925660 hypothetical protein (S. aureus, Mu50) 4929 SauCOLChORF02821_s_at ES 1.0E-127 15923856 hypothetical protein (S. aureus, Mu50) 6544 SauMu50ChORFSAV0786_at ES 1.0E-35 15923776 hypothetical protein (S. aureus, Mu50) 7732 SauMu50ChORFSAV2198_s_at E1 5.0E-24 15925188 hypothetical protein (S. aureus, Mu50) 7745 SauMu50ChORFSAV2213_s_at ES 3.0E-22 15925203 hypothetical protein (S. aureus, Mu50) 7590 SauMu50ChORFSAV2020_s_at E2 1.0E-56 49482609 hypothetical protein SAR0376 (S. aureus, MRSA252) 4498 SauCOLChORF00508_s_at E2 0.0E+00 oligopeptide ABC transporter, permease 4480 SauCOLChORF00404_s_at E2 0.0E+00 pathogenicity island protein 6626 SauRF122_1030-33_s_at E2 0.0E+00 18920518 phi Mu50B-like protein (S. aureus phage phi 11) 6614 SauMu50ChORFSAV0875_x_at E2 ES 4.0E-37 9635705 phi PVL orf 52 homologue (S. aureus prophage phiPV83) 8336 Sau8325ChORF2045_at ES 1.0E-38 18920535 phi SLT orf 99-like protein (S. aureus, phage phi 11) 4909 SauCOLChORF02799_at E2 ES 0.0E+00 prophage L54a, integrase (int)* 5524 SauEMRSA16ChORF2909_at E2 1.0E-144 49240553 putative amino acid kinase (S. aureus, MRSA252) 5121 SauEMRSA16ChORF1373_x_at E1 4.0E-39 49242831 putative membrane protein (S. aureus, MRSA252) 5538 SauEMRSA16ChORF2964_at E1 E2 0.0E+00 49240436 site-specific recombinase (S. aureus, MRSA252)

MnCop (32 genes) 5215 SauEMRSA16Chorf1690_at E2 1.0E-130 49242746 conserved hypothetical protein (S. aureus, MRSA252) 5768 SauMSSA476_575g-429_s_at EE E2 2.0E-93 49243626 conserved hypothetical protein (S. aureus, MSSA476) 5788 SauMSSA476_575g-555_at E2 ES 3.0E-57 49485293 exotoxin (S. aureus, MSSA476)** 5789 SauMSSA476_575g-556_at ES 6.0E-09 49485292 exotoxin 3 (S. aureus, MSSA476)** 8347 Sau8325Chorf2386_s_at E2 2.0E-50 49485859 holin (S. aureus, MSSA476)** 5132 SauEMRSA16Chorf1407_at E2 1.0E-92 49242900 hypothetical protein (S. aureus, MRSA252) 5795 SauMSSA476_575g-565_x_at E2 ES 8.0E-20 49243723 hypothetical protein (S. aureus, MSSA476) 5964 SauMu50ChorfSAV0105_at E2 2.0E-26 15923095 hypothetical protein (S. aureus, Mu50) 6638 SauMu50ChorfSAV0900_s_at ES 3.0E-42 15923890 hypothetical protein (S. aureus, Mu50) 7702 SauMu50ChorfSAV2150_s_at E1 E2 9.0E-27 15925140 hypothetical protein (S. aureus, Mu50) 5793 SauMSSA476_575g-563_at E2 3.0E-76 49485279 hypothetical protein SAS0376 (S. aureus, MSSA476) 8323 Sau8325Chorf2023_at ES 1.0E-75 477925 int gene activator RinA - phage phi-11 6587 SauMu50ChorfSAV0847_at E2 0.0E+00 integrase* 4635 SauCOLChorf01453_at ES - - no hits 4755 SauCOLChorf02165_s_at E2 - - no hits 4906 SauCOLChorf02783_s_at E2 - - no hits 8312 Sau8325Chorf1956_s_at E2 1.0E-65 9635178 orf 14 (S. aureus, bacteriophage PVL) 8318 Sau8325Chorf2012_at E1 3.0E-94 12719408 orf 178 (S. aureus, temperate phage phiSLT) 4930 SauCOLChorf02822_s_at ES 1.0E-132 18920502 phi PV83 orf 20-like protein (S. aureus, phage phi 11) 5063 SauEMRSA16Chorf1164_s_at ES 2.0E-92 9635727 phi PVL orf 15 and 16 homologue (S. aureus, prophage phiPV83)** 8195 SauN315ChorfS063_x_at E1 ES 5.0E-16 9635690 phi PVL orf 38 homologue (S. aureus, prophage phiPV83)** 6174 SauMu50ChorfSAV0363_s_at E2 0.0E+00 49482593 putative GTP-binding protein (S. aureus, MRSA252) 5410 SauEMRSA16Chorf2554_s_at E1 E2 ES 2.0E-38 49483255 putative lipoprotein (S. aureus, MRSA252) 5103 SauEMRSA16Chorf1320_s_at ES 0.0E+00 49242711 putative membrane protein (S. aureus, MRSA252) 5197 SauEMRSA16Chorf1631_x_at E2 2.0E-66 49242819 putative membrane protein (S. aureus, MRSA252) 5570 SauEMRSA16Chorf46_at ES 0.0E+00 49240459 putative restriction enzyme modulator protein (S. aureus, MRSA252) 5105 SauEMRSA16Chorf1335_x_at E2 1.0E-64 49242733 putative small heat shock protein (S. aureus, MRSA252) 5813 SauMSSA476_575g-711_at E2 0.0E+00 49243381 putative type I restriction enzyme specificity protein (S. aureus, MSSA476) 6071 SauMu50ChorfSAV0230_s_at ES 0.0E+00 staphylocoagulase precursor** 7984 SauMu50ChorfSAV2499_s_at E2 0.0E+00 staphylococcal accessory regulator A homolog 4482 SauCOLChorf00411_at E2 0.0E+00 staphylococcal enterotoxin B (seb) 5675 SauEMRSA16Chorf981_s_at E1 E2 5.0E-53 49241754 very large surface anchored protein (S. aureus, MRSA252)

LAC (194 genes) 4750 SauCOLChorf02155_s_at EE E1 E2 ES 0.0E+00 3-oxoacyl-(acyl carrier protein) reductas 7546 SauMu50ChorfSAV1966_s_at EE E1 E2 ES 0.0E+00 40557219 77orf 003 (Bacteriophage 77) 7545 SauMu50ChorfSAV1965_s_at EE E1 E2 ES 0.0E+00 41189523 77orf 008 (Bacteriophage 77) 4910 SauCOLChorf02800_at EE E1 E2 ES 1.0E-123 40557233 77orf 017 (Bacteriophage 77) 5299 SauMu50ChorfSAV1957_s_at EE E1 E2 ES 1.0E-119 40557236 77orf 020 (Bacteriophage 77) 7549 SauMu50ChorfSAV1969_s_at EE E1 E2 ES 1.0E-76 40557240 77orf 026 (Bacteriophage 77) 7540 SauMu50ChorfSAV1960_s_at EE E1 E2 ES 7.0E-66 41189545 77orf 033 (Bacteriophage 77) 7537 SauMu50ChorfSAV1956_s_at EE E1 E2 ES 4.0E-60 41189546 77orf 034 (Bacteriophage 77) 7547 SauMu50ChorfSAV1967_s_at E1 E2 ES 8.0E-59 41189549 77orf 037 (Bacteriophage 77) 7548 SauMu50ChorfSAV1968_s_at EE E1 E2 ES 1.0E-42 41189551 77orf 040 (Bacteriophage 77) 4675 SauCOLChorf01636_s_at EE E1 E2 ES 0.0E+00 accessory gene regulator protein B (agrB) 4677 SauCOLChorf01639_s_at EE E1 E2 ES 0.0E+00 accessory gene regulator protein C (argC) 5038 SauEMRSA16Chorf1080_s_at ES 6.0E-46 49486558 acetyl-coenzyme A synthetase (S. aureus, MSSA476) 7739 SauMu50ChorfSAV2207_s_at EE E1 E2 ES 0.0E+00 alpha-acetolactate synthase 6650 SauMu50ChorfSAV0913_at ES 0.0E+00 amidase 4618 SauCOLChorf01410_s_at EE E1 E2 ES 0.0E+00 arsenate reductase (arsC) 6008 SauMu50ChorfSAV0157_s_at E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme Cap5I 6009 SauMu50ChorfSAV0158_s_at EE E1 E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme Cap5J 6010 SauMu50ChorfSAV0159_s_at EE E1 E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme Cap5K 6007 SauMu50ChorfSAV0156_s_at EE E2 ES 0.0E+00 capsular polysaccharide synthesis enzyme O-acetyl transferase Cap5H 4452 SauCOLChorf00347_s_at EE E1 E2 ES 0.0E+00 carboxylesterase (est) 8170 SauN315Chorf1755_s_at EE E1 E2 ES 4.0E-80 49242314 chemotaxis-inhibiting protein CHIPS (S. aureus, MRSA252) 4705 SauCOLChorf01854_s_at EE E1 E2 ES 0.0E+00 ClpA-related protein 4898 SauCOLChorf02766_x_at EE E1 E2 ES 2.0E-73 49485176 conserved hypothetical cytosolic protein (S. aureus, MSSA476) 4588 SauCOLChorf01145_at E2 ES 0.0E+00 49241608 conserved hypothetical protein (S. aureus, MRSA252) 4592 SauCOLChorf01150_at EE E1 E2 ES 0.0E+00 49241612 conserved hypothetical protein (S. aureus, MRSA252) 4594 SauCOLChorf01152_at EE E2 ES 3.0E-55 49241614 conserved hypothetical protein (S. aureus, MRSA252) 4904 SauCOLChorf02774_x_at EE E2 ES 4.0E-78 49243626 conserved hypothetical protein (S. aureus, MSSA476) 4555 SauCOLChorf00919_x_at E2 1.0E-05 15924328 conserved hypothetical protein (S. aureus, Mu50) 4896 SauCOLChorf02763_x_at E2 ES 4.0E-55 15923284 conserved hypothetical protein (S. aureus, Mu50) 4902 SauCOLChorf02771_x_at E2 ES 2.0E-73 15923289 conserved hypothetical protein (S. aureus, Mu50) 4903 SauCOLChorf02773_s_at E2 3.0E-78 15923291 conserved hypothetical protein (S. aureus, Mu50)

12 5965 SauMu50ChorfSAV0107_s_at ES 1.0E-132 15923097 conserved hypothetical protein (S. aureus, Mu50) 8147 SauN315_pN315orf008_s_at EE E1 E2 ES 1.0E-174 16119208 conserved hypothetical protein (S. aureus, N315) 4832 SauCOLChorf02486_x_at E2 ES 3.0E-09 27466972 conserved hypothetical protein (S. epidermidis, ATCC 12228) 5584 SauEMRSA16Chorf499_s_at E2 0.0E+00 27314586 copper-transporting ATPase copA (S. epidermidis, ATCC 12228) 4767 SauCOLChorf02201_s_at EE E1 E2 ES 0.0E+00 drug transporter, putative 7553 SauMu50ChorfSAV1974_at EE E1 E2 ES 0.0E+00 dUTP pyrophosphatase 8349 Sau8325Chorf246_at E2 ES 1.0E-71 49485293 exotoxin (S. aureus, MSSA476)** 8359 Sau8325Chorf2768_at ES 5.0E-21 49485293 exotoxin (S. aureus, MSSA476)** 4996 SauCOLChorf02957_s_at E1 E2 ES 0.0E+00 exotoxin 3, putative** 5453 SauEMRSA16Chorf272_at ES 1.0E-115 49240787 exotoxin 4 (S. aureus, MRSA252) 4997 SauCOLChorf02963_s_at ES 0.0E+00 exotoxin, putative* 4763 SauCOLChorf02184_s_at EE E1 E2 ES 0.0E+00 fibronectin binding protein B (fnbB) 4764 SauCOLChorf02186_s_at EE E1 E2 ES 0.0E+00 fibronectin-binding protein A (fnbA) 5125 SauEMRSA16Chorf1383_at E1 0.0E+00 15925506 fructose-bisphosphatase (S. aureus, Mu50) 4806 SauCOLChorf02405_s_at EE E1 E2 ES 0.0E+00 histidinol dehydrogenase (hisD) 8372 Sau8325Chorf946_s_at EE E1 E2 ES 7.0E-53 49242373 hypothetical phage protein (S. aureus, MRSA252) 4911 SauCOLChorf02801_s_at EE E1 E2 ES 2.0E-30 49242374 hypothetical phage protein (S. aureus, MRSA252) 5297 SauEMRSA16Chorf1966_s_at EE E1 E2 ES 6.0E-67 49242345 hypothetical phage protein (S. aureus, MRSA252) 7538 SauMu50ChorfSAV1958_s_at EE E1 E2 ES 7.0E-56 49484202 hypothetical phage protein (S. aureus, MRSA252) 7541 SauMu50ChorfSAV1961_s_at EE E1 E2 ES 7.0E-47 49484204 hypothetical phage protein (S. aureus, MRSA252) 7542 SauMu50ChorfSAV1962_s_at EE E1 E2 ES 1.0E-47 49484205 hypothetical phage protein (S. aureus, MRSA252) 7543 SauMu50ChorfSAV1963_s_at EE E1 E2 ES 0.0E+00 49484206 hypothetical phage protein (S. aureus, MRSA252) 7559 SauMu50ChorfSAV1980_at EE E1 E2 ES 3.0E-53 49486793 hypothetical phage protein (S. aureus, MSSA476) 8182 SauN315Chorf1798_s_at ES 9.0E-50 15927564 hypothetical protein (Bacteriophage phiN315) (S. aureus, N315) 8186 SauN315Chorf1802_s_at EE E1 E2 ES 4.0E-55 15927570 hypothetical protein (Bacteriophage phiN315) (S. aureus, N315) 8187 SauN315Chorf1803_at EE E1 E2 ES 1.0E-26 15927571 hypothetical protein (Bacteriophage phiN315) (S. aureus, N315) 4707 SauCOLChorf01857_at EE E1 E2 ES 7.0E-54 15645293 hypothetical protein (Helicobacter pylori 26695) 4836 SauCOLChorf02491_at EE 0.0E+00 6332765 hypothetical protein (S. aureus) 4624 SauCOLChorf01438_s_at EE E1 E2 ES 1.0E-99 49242173 hypothetical protein (S. aureus, MRSA252) 4819 SauCOLChorf02432_s_at EE E1 E2 ES 5.0E-90 49243026 hypothetical protein (S. aureus, MRSA252) 5373 SauEMRSA16Chorf241_at EE E1 E2 ES 8.0E-68 49240734 hypothetical protein (S. aureus, MRSA252) 8360 Sau8325Chorf2773_at ES 4.0E-27 49243723 hypothetical protein (S. aureus, MSSA476) 4757 SauCOLChorf02170_s_at EE E1 E2 ES 6.0E-71 49243421 hypothetical protein (S. aureus, MSSA476) 5010 SauCOLChorf02985_at EE E1 E2 ES 3.0E-14 49243757 hypothetical protein (S. aureus, MSSA476) 8289 Sau8325Chorf181_s_at EE E1 E2 ES 2.0E-99 15923285 hypothetical protein (S. aureus, Mu50) 4456 SauCOLChorf00351_s_at EE E1 E2 ES 8.0E-46 15923797 hypothetical protein (S. aureus, Mu50) 4863 SauCOLChorf02534_s_at EE E1 E2 ES 1.0E-135 15923090 hypothetical protein (S. aureus, Mu50) 4899 SauCOLChorf02767_x_at EE E2 ES 3.0E-95 15923285 hypothetical protein (S. aureus, Mu50) 5006 SauCOLChorf02978_s_at EE E1 E2 ES 1.0E-118 15923427 hypothetical protein (S. aureus, Mu50) 4993 SauEMRSA16Chorf2805_s_at ES 3.0E-56 15923407 hypothetical protein (S. aureus, Mu50) 5548 SauEMRSA16Chorf381_at ES 1.0E-173 15923543 hypothetical protein (S. aureus, Mu50) 5928 SauMu50ChorfSAV0058_s_at E2 4.0E-80 15923048 hypothetical protein (S. aureus, Mu50) 6219 SauMu50ChorfSAV0412_at ES 4.0E-54 15923402 hypothetical protein (S. aureus, Mu50) 6551 SauMu50ChorfSAV0801_at EE E1 E2 ES 1.0E-179 15923791 hypothetical protein (S. aureus, Mu50) 6590 SauMu50ChorfSAV0850_s_at EE E1 E2 ES 8.0E-75 15923840 hypothetical protein (S. aureus, Mu50) 6648 SauMu50ChorfSAV0911_s_at E2 8.0E-70 15923901 hypothetical protein (S. aureus, Mu50) 6853 SauMu50ChorfSAV1156_s_at E2 ES 2.0E-70 15924146 hypothetical protein (S. aureus, Mu50) 6990 SauMu50ChorfSAV1314_s_at EE E2 5.0E-29 15924304 hypothetical protein (S. aureus, Mu50) 7539 SauMu50ChorfSAV1959_s_at ES 9.0E-71 15924949 hypothetical protein (S. aureus, Mu50) 7554 SauMu50ChorfSAV1975_at EE E1 E2 ES 6.0E-39 15924965 hypothetical protein (S. aureus, Mu50) 7555 SauMu50ChorfSAV1976_at EE E1 E2 ES 4.0E-27 15924966 hypothetical protein (S. aureus, Mu50) 7556 SauMu50ChorfSAV1977_at EE E1 E2 ES 8.0E-65 15924967 hypothetical protein (S. aureus, Mu50) 7853 SauMu50ChorfSAV2334_s_at EE E1 E2 ES 1.0E-177 15925324 hypothetical protein (S. aureus, Mu50) 7972 SauMu50ChorfSAV2482_s_at EE E1 E2 ES 4.0E-48 15925472 hypothetical protein (S. aureus, Mu50) 8142 SauN315_pN315orf002_at EE E1 E2 ES 4.0E-53 16119202 hypothetical protein (S. aureus, N315) 8143 SauN315_pN315orf003_at EE E1 E2 ES 1.0E-121 16119203 hypothetical protein (S. aureus, N315) 4897 SauCOLChorf02764_x_at EE E1 E2 ES 2.0E-56 6967304 hypothetical protein (S. aureus) 5949 SauMu50ChorfSAV0082_s_at EE E1 E2 ES 0.0E+00 6332753 hypothetical protein (S. aureus) 4703 SauCOLChorf01852_s_at EE E1 E2 ES 3.0E-07 24372479 hypothetical protein (Shewanella oneidensis MR-1) 4706 SauCOLChorf01855_s_at EE E1 E2 ES 2.0E-66 15485433 hypothetical protein (Streptococcus thermophilus) 4623 SauCOLChorf01437_s_at EE E1 E2 ES 9.0E-56 49486621 hypothetical protein SAS1722 (S. aureus, MSSA476) 4626 SauMSSA476_J8624-292_s_at E2 6.0E-83 49486623 hypothetical protein SAS1724 (S. aureus, MSSA476) 8356 Sau8325Chorf2707_at ES 9.0E-13 49486888 hypothetical protein SAS1998b (S. aureus, MSSA476) 8148 SauN315_pN315orf009_s_at E2 ES 1.0E-74 16119209 hypothetical protein, similar to MarR family (S. aureus, N315) 5292 SauN315Chorf1804_s_at EE E1 E2 ES 2.0E-42 30043984 hypothetical transcriptional regulator (Staphylococcus phage phiN315) 4582 SauCOLChorf01138_at EE E1 E2 ES 0.0E+00 integrase/recombinase, core domain family 4818 SauCOLChorf02431_s_at EE E1 E2 ES 0.0E+00 integrase/recombinase, core domain family 8119 SauMu50ChorfSAV2667_s_at E2 0.0E+00 intercellular adhesion protein D 4829 SauCOLChorf02483_at E2 0.0E+00 IS1272, transposase 4700 SauCOLChorf01846_s_at EE E1 E2 ES 0.0E+00 M23/M37 peptidase domain protein 4662 SauCOLChorf01613_s_at EE E1 E2 ES 0.0E+00 map protein, authentic frameshift (map) 4982 SauCOLChorf02901_s_at EE E1 E2 ES 0.0E+00 MttB family protein 8316 Sau8325Chorf2010_s_at ES - - no hits 4440 SauCOLChorf00231_s_at E2 - - no hits 4457 SauCOLChorf00352_at EE E1 E2 ES - - no hits 4489 SauCOLChorf00428_s_at EE E1 E2 ES - - no hits 4652 SauCOLChorf01494_at EE E2 ES - - no hits 4658 SauCOLChorf01585_at EE E1 E2 ES - - no hits 4682 SauCOLChorf01693_at ES - - no hits 4697 SauCOLChorf01838_x_at E2 ES - - no hits 4722 SauCOLChorf01998_at EE E2 ES - - no hits 4727 SauCOLChorf02044_at ES - - no hits 4741 SauCOLChorf02118_s_at E2 - - no hits 4742 SauCOLChorf02125_x_at ES - - no hits 4777 SauCOLChorf02240_x_at EE E1 E2 ES - - no hits 4778 SauCOLChorf02241_s_at EE E1 E2 ES - - no hits 4789 SauCOLChorf02288_x_at ES - - no hits 4849 SauCOLChorf02505_x_at EE E2 - - no hits 4851 SauCOLChorf02508_at EE E1 E2 ES - - no hits 4905 SauCOLChorf02775_x_at EE E1 E2 ES - - no hits 7560 SauMu50ChorfSAV1981_x_at EE E1 E2 ES 6.0E-38 9635212 orf 47 (S. aureus, bacteriophage PVL) 6599 SauMu50ChorfSAV0860_s_at ES 4.0E-50 12719406 orf 100a (S. aureus, temperate phage phiSLT) 5390 SauEMRSA16Chorf249_s_at E2 3.0E-98 11094381 orf 7 (S. aureus,)

13 4466 SauCOLChorf00389_at EE E1 E2 ES 0.0E+00 pathogenicity island protein, integrase O 4665 SauCOLChorf01619_s_at EE E1 E2 ES 0.0E+00 peptidase, M20/M25/M40 family, authentic 7536 SauMu50ChorfSAV1955_at ES 0.0E+00 phi PVL orf 15 and 16 homologue** 4924 SauCOLChorf02815_x_at ES 3.0E-22 29028676 phi PVL orf 38-like protein (S. aureus, phage phi 13)** 8317 Sau8325Chorf2011_x_at ES 2.0E-44 18920498 phi PVL orf 39-like protein (S. aureus, phage phi 11) 8267 Sau8325Chorf1081_at E1 7.0E-32 12719418 phi PVL orf 51 homologue (S. aureus temperate phage phiSLT) 8189 SauN315Chorf1806_s_at EE E1 E2 ES 0.0E+00 probable ATP-dependent helicase (Bacteriophage phi) 6235 SauMu50ChorfSAV0432_s_at EE E1 E2 ES 0.0E+00 probable restriction modification system specificity subunit 8278 Sau8325Chorf1126_s_at EE E1 E2 ES 0.0E+00 38604903 probable succinyl-diaminopimelate desuccinylase (SDAP) 4975 SauCOLChorf02873_at ES 0.0E+00 prophage L54a, amidase, putative 4974 SauCOLChorf02872_s_at ES 0.0E+00 prophage L54a, holin** 5098 SauEMRSA16Chorf1298_at ES 1.0E-53 49487106 PTS system, arbutin-like IIBC component (S. aureus, MSSA476) 4584 SauCOLChorf01141_at E2 ES 4.0E-99 49241604 putative exported protein (S. aureus, MRSA252) 4627 SauCOLChorf01440_x_at E2 2.0E-13 49242177 putative exported protein (S. aureus, MRSA252) 5001 SauCOLChorf02970_s_at EE E1 E2 ES 0.0E+00 49240792 putative exported protein (S. aureus, MRSA252) 5091 SauEMRSA16Chorf1252_s_at E2 ES 2.0E-60 49242554 putative exported protein (S. aureus, MRSA252) 5647 SauEMRSA16Chorf902_at ES 1.0E-50 49241605 putative exported protein (S. aureus, MRSA252) 5520 SauEMRSA16Chorf2898_at E1 E2 8.0E-03 49485086 putative gamma-glutamyltranspeptidase (S. aureus, MSSA476) 4583 SauCOLChorf01140_x_at E2 5.0E-26 49241603 putative lipoprotein (S. aureus, MRSA252) 5005 SauCOLChorf02977_s_at EE E1 E2 ES 1.0E-114 49240798 putative lipoprotein (S. aureus, MRSA252) 5391 SauEMRSA16Chorf2491_at E2 ES 6.0E-63 49241603 putative lipoprotein (S. aureus, MRSA252) 5477 SauEMRSA16Chorf278_s_at EE E2 ES 1.0E-146 49240795 putative lipoprotein (S. aureus, MRSA252) 6242 SauMu50ChorfSAV0440_s_at E2 1.0E-109 49240795 putative lipoprotein (S. aureus, MRSA252) 6243 SauMu50ChorfSAV0441_s_at EE ES 2.0E-96 49240799 putative lipoprotein (S. aureus, MRSA252) 6245 SauMu50ChorfSAV0444_s_at EE E1 E2 ES 1.0E-107 49240798 putative lipoprotein (S. aureus, MRSA252) 4577 SauCOLChorf01095_s_at EE E1 E2 ES 1.0E-154 49486325 putative lipoprotein (S. aureus, MSSA476) 5004 SauCOLChorf02974_at EE E1 E2 ES 1.0E-109 49485307 putative lipoprotein (S. aureus, MSSA476) 6246 SauMu50ChorfSAV0445_s_at ES 1.0E-140 49243751 putative lipoprotein (S. aureus, MSSA476) 7135 SauMu50ChorfSAV1490_s_at EE E1 E2 ES 1.0E-137 49486328 putative lipoprotein (S. aureus, MSSA476) 4586 SauCOLChorf01143_at EE E1 E2 ES 0.0E+00 49241606 putative membrane protein (S. aureus, MRSA252) 4589 SauCOLChorf01146_x_at E2 ES 6.0E-47 49241609 putative membrane protein (S. aureus, MRSA252) 4590 SauCOLChorf01147_at EE ES 2.0E-33 49241610 putative membrane protein (S. aureus, MRSA252) 4591 SauCOLChorf01149_s_at E2 ES 1.0E-163 49241611 putative membrane protein (S. aureus, MRSA252) 4817 SauCOLChorf02430_s_at EE E1 E2 ES 4.0E-26 49243025 putative membrane protein (S. aureus, MRSA252) 4821 SauCOLChorf02434_s_at EE E1 E2 ES 9.0E-26 49243025 putative membrane protein (S. aureus, MRSA252) 4890 SauCOLChorf02744_s_at E1 E2 ES 4.0E-58 49240657 putative membrane protein (S. aureus, MRSA252) 4891 SauCOLChorf02745_s_at E1 E2 ES 3.0E-66 49240660 putative membrane protein (S. aureus, MRSA252) 5648 SauEMRSA16Chorf903_at E1 E2 ES 5.0E-34 49241610 putative membrane protein (S. aureus, MRSA252) 4751 SauCOLChorf02158_s_at EE E1 E2 ES 1.0E-62 49487259 putative membrane protein (S. aureus, MSSA476) 5512 SauEMRSA16Chorf2860_s_at ES 5.0E-21 49485166 putative membrane protein (S. aureus, MSSA476) 6591 SauMu50ChorfSAV0851_s_at EE E1 E2 ES 1.0E-52 49485803 putative phage regulatory protein (S. aureus, MSSA476) 6592 SauMu50ChorfSAV0852_at E2 5.0E-29 49244247 putative phage regulatory protein (S. aureus, MSSA476) 5582 SauEMRSA16Chorf497_s_at EE E1 E2 ES 2.0E-84 16119201 putative replication initiation protein Rep (S. aureus, N315) 8188 SauN315Chorf1805_s_at EE E1 E2 ES 1.0E-132 49484242 putative repressor (S. aureus, MRSA252) 5604 SauEMRSA16Chorf582_at EE 0.0E+00 49241167 putative ribonuclease R (S. aureus, MRSA252) 5503 SauEMRSA16Chorf2835_s_at EE E1 E2 ES 1.0E-118 49240705 putative Sec-independent protein translocase protein (S. aureus, MRSA252) 7982 SauMu50ChorfSAV2496_s_at EE E1 E2 ES 0.0E+00 48428191 putative surface protein SA2285 precursor 7983 SauMu50ChorfSAV2497_s_at EE E1 E2 ES 0.0E+00 48428262 putative surface protein SAV2496/SAV2497 precursor 7558 SauMu50ChorfSAV1978_x_at EE ES 8.0E-41 18920558 PVL orf 51-like protein (S. aureus, phage phi 12) 4776 SauCOLChorf02233_s_at EE E1 E2 ES 0.0E+00 pyruvate oxidase 4689 SauCOLChorf01772_s_at EE E1 E2 ES 0.0E+00 SAP domain protein 5311 SauEMRSA16Chorf2071_at E2 4.0E-42 9739160 serine protease SplE (S. aureus,) 4688 SauCOLChorf01771_at EE E1 E2 ES 0.0E+00 site-specific recombinase family protein, 5507 SauEMRSA16Chorf2850_at ES 0.0E+00 49240675 sodium:solute symporter family protein (S. aureus, MRSA252) 4881 SauCOLChorf02680_s_at EE E1 E2 ES 0.0E+00 staphylocoagulase precursor** 4761 SauCOLChorf02181_s_at EE E2 0.0E+00 staphylococcal accessory regulator T (sarT) 4701 SauCOLChorf01848_s_at E1 E2 ES 0.0E+00 surface protein, putative 4953 SauCOLChorf02849_s_at ES 0.0E+00 terminase large subunit, putative 5018 SauCOLChorfA00002_at ES 0.0E+00 tetracycline resistance protein (tet) 4678 SauCOLChorf01664_s_at E1 E2 ES 0.0E+00 threonine dehydratase (ilvA) 4585 SauCOLChorf01142_at E1 E2 ES 0.0E+00 traG protein, putative 5966 SauMu50ChorfSAV0108_s_at EE E1 E2 3.0E-74 42737689 transcriptional regulator, GntR family (Bacillus cereus, ATCC 10987) 4768 SauCOLChorf02202_s_at EE E2 0.0E+00 transcriptional regulator, MarR family 4472 SauCOLChorf00395_at EE E1 E2 ES 0.0E+00 transcriptional regulator, putative 7985 SauMu50ChorfSAV2501_s_at EE E1 E2 ES 0.0E+00 transposase 4621 SauCOLChorf01426_s_at ES 0.0E+00 transposase, IS200 family 8340 Sau8325Chorf226_s_at E2 1.1E-02 44522944 unknown (environmental sequence) 8291 Sau8325Chorf1927_s_at EE E1 E2 ES 1.0E-112 29028669 unknown (S. aureus, phage phi 13) 8219 SauRF122_1030-26b_at E1 3.0E-53 18920527 unknown phi protein (S. aureus, phage phi 11)

14