DOCSLIB.ORG

Conserved SQ and QS Motifs in Bacterial Effectors Suggest

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Conserved SQ and QS Motifs in Bacterial Effectors Suggest BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Conserved SQ and QS motifs in bacterial effectors suggest pathogen interplay with the ATM kinase family during infection Davide Sampietro1,2, Hugo Sámano-Sánchez2,3, Norman E. Davey4, Malvika Sharan2, Bálint Mészáros2,5, Toby J. Gibson2, Manjeet Kumar2* 1. Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy. 2. Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, 69117, Germany 3. (Candidate for) Joint PhD degree from EMBL and Heidelberg University, Faculty of Biosciences. 4. UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland. 5. MTA-ELTE Momentum Bioinformatics Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest H-1117, Hungary. >sp|P55980|CAGA_HELPY Cytotoxicity-associated immunodominant antigen OS=Helicobacter pylori (strain ATCC 700392 / 26695) OX=85962 GN=cagA PE=1 SV=1 MTNETIDQTRTPDQTQSQTAFDPQQFINNLQVAFIKVDNVVASFDPDQKPIVDKNDRDNR QAFDGISQLREEYSNKAIKNPTKKNQYFSDFIDKSNDLINKDNLIDVESSTKSFQKFGDQ RYQIFTSWVSHQKDPSKINTRSIRNFMENIIQPPIPDDKEKAEFLKSAKQSFAGIIIGNQ IRTDQKFMGVFDESLKERQEAEKNGGPTGGDWLDIFLSFIFNKKQSSDVKEAINQEPVPH VQPDIATTTTDIQGLPPEARDLLDERGNFSKFTLGDMEMLDVEGVADIDPNYKFNQLLIH NNALSSVLMGSHNGIEPEKVSLLYAGNGGFGDKHDWNATVGYKDQQGNNVATLINVHMKN GSGLVIAGGEKGINNPSFYLYKEDQLTGSQRALSQEEIRNKVDFMEFLAQNNTKLDNLSE KEKEKFQNEIEDFQKDSKAYLDALGNDRIAFVSKKDTKHSALITEFNNGDLSYTLKDYGK KADKALDREKNVTLQGSLKHDGVMFVDYSNFKYTNASKNPNKGVGATNGVSHLEAGFNKV AVFNLPDLNNLAITSFVRRNLENKLTAKGLSLQEANKLIKDFLSSNKELAGKALNFNKAV AEAKSTGNYDEVKKAQKDLEKSLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEI FALINKEANRDARAIAYTQNLKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKA EETLKALKGSVKDLGINPEWISKVENLNAALNEFKNGKNKDFSKVTQAKSDLENSVKDVI INQKVTDKVDNLNQAVSVAKAMGDFSRVEQVLADLKNFSKEQLAQQAQKNEDFNTGKNSE LYQSVKNSVNKTLVGNGLSGIEATALAKNFSDIKKELNEKFKNFNNNNNGLKNSTEPIYA KVNKKKTGQVASPEEPIYTQVAKKVNAKIDRLNQIASGLGGVGQAAGFPLKRHDKVDDLS KVGLSASPEPIYATIDDLGGPFPLKRHDKVDDLSKVGRSRNQELAQKIDNLNQAVSEAKA GFFGNLEQTIDKLKDSTKKNVMNLYVESAKKVPASLSAKLDNYAINSHTRINSNIQNGAI NEKATGMLTQKNPEWLKLVNDKIVAHNVGSVSLSEYDKIGFNQKNMKDYSDSFKFSTKLN NAVKDIKSGFTHFLANAFSTGYYCLARENAEHGIKNVNTKGGFQKS Figure S1. Sequence of CagA (P55980). Many of the ST/Q and QS/T motifs highlighted in yellow are conserved across different Helicobacter strains. 1 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S2. Empirical cumulated distribution function (ecdf) for the residuals of the dipeptide in the disordered regions of the substrates of AADk. Each dot represents Yi , where i is the dipeptide (see Materials and Methods section). SQ, QS and QT dipeptides are marked with black arrows. While the y-axis denotes the cumulative probability, the x-axis denotes the range of values of Yi 2 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S3. Empirical cumulated distribution function (ecdf) for the residuals of the tripeptides in the disordered regions of the substrates of AADk. Each dot represents Yi, where i is the dipeptide (see Materials and Methods section). SQS, SQE, SQP and SSQ are shown. While the y-axis denotes the cumulative probability, the x-axis denotes the range of values of Yi 3 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S4 Top: fequency of each tetrapeptide in the disordered regions of the substrates of AADk. The diagonal is the 1:1 correlation line. The further the dot from the diagonal, the stronger the enrichment. Whatever is above the diagonal is enriched in the positive set. Bottom: Empirical cumulated distribution function (ecdf) for the residuals of the tetrapeptides in the disordered regions of the substrates of AADk. Each dot represents Yi , where i is the tetrapeptide (see Materials and Methods section). While the y-axis denotes the cumulative probability, the x-axis denotes the range of values of Yi 4 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S5 Alignment of Tir from E.coli (E.coli), Escherichia albertii (E.alb), Salmonella enterica (S.ent), Salmonella cholaraesius (S.cho). S/TQs are highlighted in black, QS/Ts in red. The motifs cluster together and often overlap. Blue highlights the percentage of identity for all the residues, except those highlighted in red and black. The Uniprot or UniRef accessions have been provided for all the sequences in the alignment. 5 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S6. Alignment of lpg2577 from Legionella pneumophila (L.pne), Legionella feeleii (L.fee), Legionella quateriensis (L.qua), Tatlockia micdadei(T.mic), Legionella lansingensis (L.lan), Legionella pasculli (L.pas), Legionella wadsworthii (L.wad), Legionella moravica (L.mor), Legionella israelensis (L.isr), Legionella jamestowniensis (L.jam), Legionella fallonii (L.faa). S/TQs are highlighted in black, QS/Ts in red. The motifs cluster together and often overlap. In grey a docking site (DOC_PIKK_1) for AADks kinases involved in DNA-damage response is shown. Blue highlights the percentage of identity for all the residues, except those highlighted in red and black. The Uniprot or UniRef accessions have been provided for all the sequences in the alignment. 6 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S7. Alignment of sidG from Legionella pneumophila (L.pne), Legionella moravica (L.mor), Legionella sainthelensi (L.sai), Legionella santicrucis (L.san). S/TQs are highlighted in red, QS/Ts in black. Blue highlights the percentage of identity for all the residues, except those highlighted in red and black. The Uniprot or UniRef accessions have been provided for all the sequences in the alignment. 7 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S8. Distribution of the SQ - QS distances in the disordered region of the AADk substrates. The theoretical distribution of the minimal distances (black), the minimal distances between the experimentally validated pSQ - QS (yellow) and the minimal distances between all the SQs, (experimentally and not experimentally validated) (green) are compared. Top: 2 - 150 amino acid SQ - QS distances. Bin size = 10 SQ-QS distances, overlapping. Binned distribution was preferred to the real one due to the lack of data. Bottom: Bin size = 3 SQ-QS distances. Due to the fact that we are analysing only the amino acid sequence of the protein, large distances (larger than 150-200) are not considered as we cannot foresee their vicinity in the 3D structure of the protein by just looking at its sequence. By looking at the binned distribution, we noticed that there seems to be a difference between the two distributions between 7 and 26 SQ-QS distances. Due to this, we did a Chi-square test to compare the theoretical distribution vs the real ones, which is given in the text. 8 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Figure S9. Box plot for the IUPred score of the experimentally validated phosphorylation sites in the substrates of the AADks. 9 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Table S1. List of effectors possibly multi-phosphorylated by AADks. Uniprot ID Gene name SQ TQ QS QT Organism P55980 CagA 5 5 4 4 Helicobacter pylori B7UM99 Tir 2 2 2 3 Escherichia coli O127:H6 C8TWM3 map 1 5 3 4 Escherichia coli O103:H2 Q5ZSE2 lpg2577 0 1 1 0 Legionella pneumophila Q5ZRN6 lpg2844 12 1 12 3 Legionella pneumophila Q5ZVT5 sidG 5 2 2 2 Legionella pneumophila B7UKZ9 yhhA 3 4 1 3 Escherichia coli O127:H6 Q87GF9 VPA1357 12 26 6 35 Vibrio parahaemolyticus serotype O3:K6 Q9RBS0 PopA 4 1 8 0 Ralstonia solanacearum Q9RBS1 PopB 3 1 1 3 Ralstonia solanacearum 10 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Table S2. Data for the p-value distribution of the probability of relative local conservation. Due to the extreme difference in the size of the positive and negative control, for each dipeptide, we sampled from the bigger database (negative control) a number of unit equal to the one in the smaller one (positive control). We iterated this process 5000 times. Each time, we calculated the p-values using the Wilcoxon-Mann-Whitney-Test. Dipeptide Mean Median Standard deviation SQ 3.2089E-06 1.3642E-08 3.208E-05 TQ 0.06741190 0.031 0.089 QS 0.0223 0.005 0.043 QT 0.080678 0.0415 0.098 11 BioRxiv: SQ-QS, Effectors and ATM Supplementary materials Table S3. Comparison between human and four different bacterial proteomes. P-value suggests the absence of significant difference in the composition of the disordered regions. Comparison p-value (Wilcoxon signed) P-value (Wilcoxon signed) Homo - Chlamydia 0.81 Homo - Coxiella 0.64 Homo - Legionella 0.78 Homo - Pseudomonas 0.67 12 .
Load more

Recommended publications
  • Legionella Shows a Diverse Secondary Metabolism Dependent on a Broad Spectrum Sfp-Type Phosphopantetheinyl Transferase
    Legionella shows a diverse secondary metabolism dependent on a broad spectrum Sfp-type phosphopantetheinyl transferase Nicholas J. Tobias1, Tilman Ahrendt1, Ursula Schell2, Melissa Miltenberger1, Hubert Hilbi2,3 and Helge B. Bode1,4 1 Fachbereich Biowissenschaften, Merck Stiftungsprofessur fu¨r Molekulare Biotechnologie, Goethe Universita¨t, Frankfurt am Main, Germany 2 Max von Pettenkofer Institute, Ludwig-Maximilians-Universita¨tMu¨nchen, Munich, Germany 3 Institute of Medical Microbiology, University of Zu¨rich, Zu¨rich, Switzerland 4 Buchmann Institute for Molecular Life Sciences, Goethe Universita¨t, Frankfurt am Main, Germany ABSTRACT Several members of the genus Legionella cause Legionnaires’ disease, a potentially debilitating form of pneumonia. Studies frequently focus on the abundant number of virulence factors present in this genus. However, what is often overlooked is the role of secondary metabolites from Legionella. Following whole genome sequencing, we assembled and annotated the Legionella parisiensis DSM 19216 genome. Together with 14 other members of the Legionella, we performed comparative genomics and analysed the secondary metabolite potential of each strain. We found that Legionella contains a huge variety of biosynthetic gene clusters (BGCs) that are potentially making a significant number of novel natural products with undefined function. Surprisingly, only a single Sfp-like phosphopantetheinyl transferase is found in all Legionella strains analyzed that might be responsible for the activation of all carrier proteins in primary (fatty acid biosynthesis) and secondary metabolism (polyketide and non-ribosomal peptide synthesis). Using conserved active site motifs, we predict Submitted 29 June 2016 some novel compounds that are probably involved in cell-cell communication, Accepted 25 October 2016 Published 24 November 2016 differing to known communication systems.
    [Show full text]
  • The Risk to Human Health from Free-Living Amoebae Interaction with Legionella in Drinking and Recycled Water Systems
    THE RISK TO HUMAN HEALTH FROM FREE-LIVING AMOEBAE INTERACTION WITH LEGIONELLA IN DRINKING AND RECYCLED WATER SYSTEMS Dissertation submitted by JACQUELINE MARIE THOMAS BACHELOR OF SCIENCE (HONOURS) AND BACHELOR OF ARTS, UNSW In partial fulfillment of the requirements for the award of DOCTOR OF PHILOSOPHY in ENVIRONMENTAL ENGINEERING SCHOOL OF CIVIL AND ENVIRONMENTAL ENGINEERING FACULTY OF ENGINEERING MAY 2012 SUPERVISORS Professor Nicholas Ashbolt Office of Research and Development United States Environmental Protection Agency Cincinnati, Ohio USA and School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Professor Richard Stuetz School of Civil and Environmental Engineering Faculty of Engineering The University of New South Wales Sydney, Australia Doctor Torsten Thomas School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia ORIGINALITY STATEMENT '1 hereby declare that this submission is my own work and to the best of my knowledge it contains no materials previously published or written by another person, or substantial proportions of material which have been accepted for the award of any other degree or diploma at UNSW or any other educational institution, except where due acknowledgement is made in the thesis. Any contribution made to the research by others, with whom 1 have worked at UNSW or elsewhere, is explicitly acknowledged in the thesis. I also declare that the intellectual content of this thesis is the product of my own work, except to the extent that assistance from others in the project's design and conception or in style, presentation and linguistic expression is acknowledged.' Signed ~ ............................
    [Show full text]
  • Genetic and Functional Studies of the Mip Protein of Legionella
    t1.ì. Genetic and Functional Studies of the Mip Protein of Legionella Rodney Mark Ratcliff, BSc (Hons)' MASM Infectious Diseases Laboratories Institute of Medical and Veterinary Science and Department of Microbiology and Immunology UniversitY of Adelaide. Adelaide, South Australia A thesis submitted to the University of Adelaide for the degree of I)octor of Philosophy 15'h March 2000 amended 14th June 2000 Colonies of several Legionella strains on charcoal yeast extract agar (CYE) after 4 days incubation at 37"C in air. Various magnifications show typical ground-glass opalescent appearance. Some pure strains exhibit pleomorphic growth or colour. The top two photographs demonstrate typical red (LH) and blue-white (RH) fluorescence exhibited by some species when illuminated by a Woods (IJV) Lamp. * t Table of Contents .1 Chapter One: Introduction .1 Background .............'. .2 Morphology and TaxonomY J Legionellosis ............. 5 Mode of transmission "..'....'. 7 Environmental habitat 8 Interactions between Legionella and phagocytic hosts 9 Attachment 11 Engulfment and internalisation.'.. 13 Intracellular processing 13 Intracellular replication of legionellae .. " "' " "' 15 Host cell death and bacterial release 18 Virulence (the Genetic factors involved with intracellular multiplication and host cell killing .20 icm/dot system) Legiolysin .25 Msp (Znn* metaloprotease) ...'..... .25 .28 Lipopolysaccharide .29 The association of flagella with disease.. .30 Type IV fimbriae.... .31 Major outer membrane proteins....'.......'. JJ Heat shock proteins'.'. .34 Macrophage infectivity potentiator (Mip) protein Virulenceiraits of Legionella species other than L. pneumophila..........' .39 phylogeny .41 Chapter One (continued): Introduction to bacterial classification and .41 Identificati on of Legionella...'.,..'.. .46 Phylogeny .52 Methods of phylogenetic analysis' .53 Parsimony methods.'.. .55 Distance methods UPGMA cluster analYsis.'.'...
    [Show full text]
  • Electronic Laboratory Reporting Use Case January 2011
    ILLINOIS HEALTH INFORMATION EXCHANGE Electronic Laboratory Reporting Use Case Electronic Laboratory Reporting and Health Information Exchange Illinois Health Information Exchange Public Health Work Group January 2011 Electronic Laboratory Reporting Use Case January 2011 Table of Contents 1.0 Executive Summary……………………………………………………………………….3 2.0 Introduction…………………………………………………………………...……………..5 3.0 Scope……………………………………..………………………………………………………5 4.0 Use Case Stakeholders…………………………………………………………….….....6 5.0 Issues and Obstacles……………………………………………………………………...8 6.0 Use Case Pre-Conditions .………………….…………………………………………...8 7.0 Use Case Post-Conditions.……………………………………………………………...9 8.0 Detailed Scenarios/Technical Specifications.………………………………10 9.0 Validation and Certification………………………………………………………...12 Appendix ………………………………………………………………………………………….....13 Page 2 Electronic Laboratory Reporting Use Case January 2011 1.0 Executive Summary This Use Case is a product of the Public Health Work Group (PHWG) of the Illinois Health Information Exchange (HIE) Advisory Committee. The Illinois HIE Advisory Committee was constituted as the diverse public healthcare stakeholder body providing input and recommendations on the creation of the Illinois Health Information Exchange Authority (“the Authority”) as the Illinois vehicle for designing and implementing electronic health information exchange in Illinois. The establishment of the Authority marks the formal transition of the work of the HIE Advisory Committee and the Work Groups into alignment with the provisions of Illinois
    [Show full text]
  • WO 2016/188962 Al 1 December 2016 (01.12.2016) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/188962 Al 1 December 2016 (01.12.2016) P O P C T (51) International Patent Classification: (74) Agents: GOODFELLOW, Hugh Robin et al; Carpmaels C12Q 1/68 (2006.01) & Ransford LLP, One Southampton Row, London WC1B 5HA (GB). (21) International Application Number: PCT/EP2016/061599 (81) Designated States (unless otherwise indicated, for every kind of national protection available): AE, AG, AL, AM, (22) Date: International Filing AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, 23 May 20 16 (23.05.2016) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (25) Filing Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (26) Publication Language: English KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, (30) Priority Data: MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, 1508860.2 22 May 2015 (22.05.2015) GB PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, (71) Applicant: NATIONAL UNIVERSITY OF IRELAND, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. GALWAY [IE/IE]; University Road, Galway (IE). (84) Designated States (unless otherwise indicated, for every (72) Inventors: REDDINGTON, Kate Mary; Deerpack East, kind of regional protection available): ARIPO (BW, GH, Newport Road, Westport, Co.
    [Show full text]
  • EVALUATION of the P45 MOBILE INTEGRATIVE ELEMENT and ITS ROLE IN
    EVALUATION OF THE p45 MOBILE INTEGRATIVE ELEMENT AND ITS ROLE IN Legionella pneumophila VIRULENCE A Dissertation by LANETTE M. CHRISTENSEN Submitted to the Office of Graduate and Professional Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Chair of Committee, Jeffrey D. Cirillo Committee Members, James Samuel Jon Skare Farida Sohrabji Head of Program, Warren Zimmer May 2018 Major Subject: Medical Sciences Copyright 2018 Lanette Christensen ABSTRACT Legionella pneumophila are aqueous environmental bacilli that live within protozoal species and cause a potentially fatal form of pneumonia called Legionnaires’ disease. Not all L. pneumophila strains have the same capacity to cause disease in humans. The majority of strains that cause clinically relevant Legionnaires’ disease harbor the p45 mobile integrative genomic element. Contribution of the p45 element to L. pneumophila virulence and ability to withstand environmental stress were addressed in this study. The L. pneumophila Philadelphia-1 (Phil-1) mobile integrative element, p45, was transferred into the attenuated strain Lp01 via conjugation, designating p45 an integrative conjugative element (ICE). The resulting trans-conjugate, Lp01+p45, was compared with strains Phil-1 and Lp01 to assess p45 in virulence using a guinea pig model infected via aerosol. The p45 element partially recovered the loss of virulence in Lp01 compared to that of Phil-1 evident in morbidity, mortality, and bacterial burden in the lungs at the time of death. This phenotype was accompanied by enhanced expression of type II interferon in the lungs and spleens 48 hours after infection, independent of bacterial burden.
    [Show full text]
  • Susceptibility and Resistance Data
    toku-e logo For a complete list of references, please visit antibiotics.toku-e.com Levofloxacin Microorganism Genus, Species, and Strain (if shown) Concentration Range (μg/ml)Susceptibility and Aeromonas spp. 0.0625 Minimum Inhibitory Alcaligenes faecalis 0.39 － 25 Bacillus circulans Concentration0.25 － 8 (MIC) Data Bacillus subtilis (ATCC 6051) 6.25 Issue date 01/06/2020 Bacteroides capillosus ≤0.06 － >8 Bacteroides distasonis 0.5 － 128 Bacteroides eggerthii 4 Bacteroides fragilis 0.5 － 128 Bacteroides merdae 0.25 － >32 Bacteroides ovatus 0.25 － 256 Bacteroides thetaiotaomicron 1 － 256 Bacteroides uniformis 4 － 128 Bacteroides ureolyticus ≤0.06 － >8 Bacteroides vulgatus 1 － 256 Bifidobacterium adolescentis 0.25 － >32 Bifidobacterium bifidum 8 Bifidobacterium breve 0.25 － 8 Bifidobacterium longum 0.25 － 8 Bifidobacterium pseudolongum 8 Bifidobacterium sp. 0.25 － >32 Bilophila wadsworthia 0.25 － 16 Brevibacterium spp. 0.12 － 8 Brucella melitensis 0.5 Burkholderia cepacia 0.25 － 512 Campylobacter coli 0.015 － 128 Campylobacter concisus ≤0.06 － >8 Campylobacter gracilis ≤0.06 － >8 Campylobacter jejuni 0.015 － 128 Campylobacter mucosalis ≤0.06 － >8 Campylobacter rectus ≤0.06 － >8 Campylobacter showae ≤0.06 － >8 Campylobacter spp. 0.25 Campylobacter sputorum ≤0.06 － >8 Capnocytophaga ochracea ≤0.06 － >8 Capnocytophaga spp. 0.006 － 2 Chlamydia pneumonia 0.125 － 1 Chlamydia psittaci 0.5 Chlamydia trachomatis 0.12 － 1 Chlamydophila pneumonia 0.5 Citrobacter diversus 0.015 － 0.125 Citrobacter freundii ≤0.00625 － >64 Citrobacter koseri 0.015 －
    [Show full text]
  • Aquascreen® Legionella Species Qpcr Detection Kit
    AquaScreen® Legionella species qPCR Detection Kit INSTRUCTIONS FOR USE FOR USE IN RESEARCH AND QUALITY CONTROL Symbols Lot No. Cat. No. Expiry date Storage temperature Number of reactions Manufacturer INDICATION The AquaScreen® Legionella species qPCR Detection kit is specifically designed for the quantitative detection of several Legionella species in water samples prepared with the AquaScreen® FastExt- ract kit. Its design complies with the requirements of AFNOR T90-471 and ISO/TS 12869:2012. Legionella are ubiquitous bacteria in surface water and moist soil, where they parasitize protozoa. The optimal growth temperature lies between +15 and +45 °C, whereas these gram-negative bacteria are dormant below 20 °C and do not survive above 60 °C. Importantly, Legionella are well-known as opportunistic intracellular human pathogens causing Legionnaires’ disease and Pontiac fever. The transmission occurs through inhalation of contami- nated aerosols generated by an infected source (e.g. human-made water systems like shower- heads, sink faucets, heaters, cooling towers, and many more). In order to efficiently prevent Legionella outbreaks, water safety control measures need syste- matic application but also reliable validation by fast Legionella testing. TEST PRINCIPLE The AquaScreen® Legionella species Kit uses qPCR for quantitative detection of legionella in wa- ter samples. In contrast to more time-consuming culture-based methods, AquaScreen® assays need less than six hours including sample preparation and qPCR to reliably detect Legionella. Moreover, the AquaScreen® qPCR assay has proven excellent performance in terms of specificity and sensitivity: other bacterial genera remain undetected whereas linear quantification is obtai- ned up to 1 x 106 particles per sample, therefore requiring no material dilution.
    [Show full text]
  • Immunoproteomic Identification of Biomarkers for Diagnosis of Legionellosis
    Immunoproteomic identification of biomarkers for diagnosis of legionellosis Submitted in total fulfilment of the requirements for the degree of Doctor of philosophy by Kaylass Poorun Department of Chemistry and Biotechnology Faculty of Science, Engineering and Technology Swinburne University of Technology Australia 2014 Abstract Abstract Legionellosis, a disease with significant mortality and morbidity rates, is considered to be the second most frequent cause of severe community-acquired pneumonia. It is difficult to distinguish from other types of pneumonia due to similar clinical manifestations. Several studies have demonstrated the inadequacies of current diagnostic tests for confirming Legionella infections. This study was aimed at identifying biomarkers that can be used in an improved test. A comparative proteomic analysis, using DIGE, was carried out between L. pneumophila ATCC33152 and L. longbeachae NSW150 and D4968 isolates. While many homologous proteins were found to be commonly expressed, numerous others were identified to be differentially expressed under similar in vitro conditions suggesting that the two species have different lifestyles and infection strategies. The bacterial immunoglobulin domain containing protein, found to share sequence homology to Type V secretion proteins intimin and invasin, is not known to be present in Legionella. Human sera containing antibodies against Legionella from a set of blind samples were identified by ELISA. Downstream analyses revealed that diverse immunogens may be responsible for eliciting immune response in different Legionella species which in turn show little to no congeneric cross-reactivity. To the best of our knowledge, this is a unique finding not previously reported. Several serological diagnostic tests currently in use do not include many Legionella species in their testing panel, which may be a reason for many Legionella species being under-reported.
    [Show full text]
  • APUTS) Reporting Terminology and Codes Microbiology (V1.0
    AUSTRALIAN PATHOLOGY UNITS AND TERMINOLOGY (APUTS) Reporting Terminology and Codes Microbiology (v1.0) 1 12/02/2013 APUTS Report Information Model - Urine Microbiology Page 1 of 1 Specimen Type Specimen Macro Time Glucose Bilirubin Ketones Specific Gravity pH Chemistry Protein Urobilinogen Nitrites Haemoglobin Leucocyte Esterases White blood cell count Red blood cells Cells Epithelial cells Bacteria Microscopy Parasites Microorganisms Yeasts Casts Crystals Other elements Antibacterial Activity No growth Mixed growth Urine MCS No significant growth Klebsiella sp. Bacteria ESBL Klebsiella pneumoniae Identification Virus Fungi Growth of >10^8 org/L 10^7 to 10^8 organism/L of mixed Range or number Colony Count growth of 3 organisms 19090-0 Culture Organism 1 630-4 LOINC >10^8 organisms/L LOINC Significant growth e.g. Ampicillin 18864-9 LOINC Antibiotics Susceptibility Method Released/suppressed None Organism 2 Organism 3 Organism 4 None Consistent with UTI Probable contamination Growth unlikely to be significant Comment Please submit a repeat specimen for testing if clinically indicated Catheter comments Sterile pyuria Notification to infection control and public health departments PUTS Urine Microbiology Information Model v1.mmap - 12/02/2013 - Mindjet 12/02/2013 APUTS Report Terminology and Codes - Microbiology - Urine Page 1 of 3 RCPA Pathology Units and Terminology Standardisation Project - Terminology for Reporting Pathology: Microbiology : Urine Microbiology Report v1 LOINC LOINC LOINC LOINC LOINC LOINC LOINC Urine Microbiology Report
    [Show full text]
  • WO 2012/055408 Al
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date . 3 May 2012 (03.05.2012) WO 2012/055408 Al (51) International Patent Classification: DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, CI2Q 1/68 (2006.01) HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, (21) International Application Number: ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, PCT/DK20 11/000120 NO, NZ, OM, PE, PG, PH, PL, PT, QA, RO, RS, RU, (22) International Filing Date: RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, 27 October 201 1 (27.10.201 1) TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ, 61/407,122 27 October 2010 (27.10.2010) US UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, PA 2010 70455 27 October 2010 (27.10.2010) DK RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, (71) Applicant (for all designated States except US): QUAN- LT, LU, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, TIBACT A/S [DK/DK]; Kettegards Alle 30, DK-2650 SE, SI, SK, SM, TR), OAPI (BF, BJ, CF, CG, CI, CM, Hvidovre (DK).
    [Show full text]
  • Testing Different Membrane Filters for 16S Rrna Gene-Based Metabarcoding in Karstic Springs
    Testing different membrane filters for 16S rRNA gene-based metabarcoding in karstic springs Oana Teodora Moldovan 1*, Andreea Baricz 2,3,4*, Edina Szekeres 2,3,4, Marius Kenesz 1, Marial Alexandra Hoaghia 5, Erika Andrea Levei 5, Ionuț Cornel Mirea 6, Ruxandra Năstase-Bucur 1, Traian Brad 1, Iulia Chiciudean 2,3, Horia Leonard Banciu 2,3 Figure S1. Piper diagram of the chemical elements for the studied springs Table S1. The relative abundance of the Bacteria phyla in the analyzed membranes, with the dominant Proteobacteria (see also Figure 3). BANPOTOC BAITA RAPOLTEL Phylum/Percentage AE20 AE21 AE22 AE23 AE24 AE25 AE26 AE4 AE27 BE11 BE12 BE18 BE16 BE15 BE13 BE19 BE17 BE14 CE29 CE31 CE32 CE30 CE34 CE33 CE2 CE28 CE35 CE3 non-identified 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Acidobacteria 0,01 0,00 0,00 0,01 0,00 0,01 0,01 0,15 0,00 0,96 0,86 0,85 1,08 0,83 2,32 1,95 0,39 0,21 0,00 0,00 0,21 0,14 0,00 0,20 0,10 0,07 0,08 0,00 Actinobacteria 4,05 4,68 6,59 7,00 6,96 8,37 8,08 3,20 11,37 3,75 4,55 6,78 6,58 5,72 7,74 8,28 2,97 1,40 2,28 3,65 1,04 0,52 2,16 2,24 3,59 11,54 2,98 1,14 Aquificae 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Armatimonadetes 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,01 0,01 0,00 0,00 0,00 0,01 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 0,00 Bacteroidetes 0,17 0,06 0,10 0,09 0,13 0,17 0,10 2,28 0,06 32,55
    [Show full text]