DOCSLIB.ORG

An Update on Antimicrobial Susceptibility Testing

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Update on Antimicrobial Susceptibility Testing Bacterial Identification by Mass Spectrometry 0.00 x104 * *with with marc\0_A10\1\1SLin, marc\0_A8\1\1SLin, "Baseline subt." 3.0 Intens. [a.u.] Intens. [a.u.] 2.52.0 1.52.0 1.5 1.0 1.0 0.5 0.0 20004 4000 6000 8000 10000 12000 14000 16000 .] m/z Mark Fisher, Ph.D., D(ABMM) Assistant Professor of Pathology, University of Utah School of Medicine, Medical Director, ARUP Bacteriology and Antimicrobials Disclosures Subtitle Here • Unrelated grant from Meridian Diagnostics • I’m a microbiologist (not a mass spectrometrist) Objectives Subtitle Here Discuss relevant principles of mass spectrometry Review advantages and disadvantages of available platforms Discuss use of mass spectrometry in the clinical microbiology laboratory Fermentation Subtitle Here • Beer, wine and bread existed among the earliest civilizations. – Beer = civilized • Robert Koch – growth on solid media 1880s – Different substrates + indicator (pH) = fermentation-based identification system Manual ID systems Subtitle Here CDC/Dr. Gilda Jones • An abnormal/weak/misread well can change ID Automated ID systems Subtitle Here • State of the art fermentation Mass spectrometry Subtitle Here • Highly accurate method for measuring masses of ionized atoms/molecules – “smallest scales in the world” • Developed around 1900 – Often destructive ionization methods • “soft” ionization methods biological samples – Electrospray, 1968 – MALDI, 1981 • Matrix Assisted Laser Desorption-Ionization • Bacterial analysis and identification, 1975/1994 Electrospray ionization Subtitle Here Ion source Ion separation in mass analyzer Ion detector Sample Data analysis Ion detector Charged steel capillary +5 + + + +2 + + + + +6 + + + + +3 + + + ++4 + + - MALDI-TOF Ion separation in mass analyzer Ion source (flight tube) Ion detector Data Sample analysis Matrix + Laser pulse (ns) Ion detector analyte triggers clock α-cyano-hydroxy + cinnamic acid - Intensity Intensity (abundance) m/z (time) MALDI-TOF Ion separation in mass analyzer Ion source (flight tube) Ion detector Data Sample analysis Matrix + Laser pulse (ns) Ion detector analyte triggers clock α-cyano-hydroxy + cinnamic acid - Intensity Intensity (abundance) m/z (time) MALDI-TOF Ion separation in mass analyzer Ion source (flight tube) Ion detector Data Sample analysis Matrix + Laser pulse (ns) Ion detector analyte triggers clock Field free + + + + α-cyano-hydroxy + cinnamic acid - Intensity Intensity (abundance) m/z (time) Electrospray Subtitle Here • Advantages • Disadvantages – mass range up to ~70 kDa – salts and complex mixtures reduce – femtomole to low picomole sensitivity sensitivity – multiple charges confusing in – softest ionization complex samples – compatible with chromatography – requires high sample purity – multiple charges = high masses – potential run-to-run carryover on low m/z instrument – no matrix interference good for smaller molecules M+3H M+4H M+2H MALDI Subtitle Here • Advantages • Disadvantages – mass range of up to ~300 kDa; – matrix signal problematic for low ~2-20 kDa for bacterial ID MW compounds (≤~700 Da) – allows complex mixtures – laser may degrade photosensitive – sensitivity of femtomole to molecules picomole; generally not a problem – organic acid matrix may degrade with bacterial ID some compounds – soft ionization = little fragmentation – tolerates salts (mM range) 0.00 x104 * *with with marc\0_A10\1\1SLin, marc\0_A8\1\1SLin, "Baseline subt." 3.0 Escherichia coli Intens. [a.u.] Intens. [a.u.] 2.52.0 1.52.0 1.5 1.0 1.0 0.5 0.0 20004 4000 6000 8000 10000 12000 14000 16000 .] m/z MS for Microbiology Subtitle Here • Assay formats: • DNA – PCR/ESI – Ibis/Abbott – PCR/transcription/fragmentation/MALDI – Sequenom – Tagged PCR/APCI - Agilent • Protein – Direct smear (whole cell)/extraction – Bruker, Shimadzu/Saramis (bioMerieux), Andromas DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition www.noaa.gov DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition www.noaa.gov DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition A23G18C20T22 + A22G20C18T23 = org A/B www.noaa.gov DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition A23G18C20T22 + A22G20C18T23 = org A/B www.noaa.gov DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition A23G18C20T22 + A22G20C18T23 = org A/B A18G21C19T24 + A24G19C21T18 = org A www.noaa.gov DNA – Ibis T5000/Abbott Plex-ID Multiplex PCR cleanup ESI-MS broad-range/specific desalt, strand separation base composition A23G18C20T22 + A22G20C18T23 = org A/B A18G21C19T24 + A24G19C21T18 = org A www.noaa.gov • Multiple broad-range PCRs allow ID by mass “triangulation” • Direct from specimen • Several hours DNA – Sequenom iSeq PCR transcription cleavage MALDI <800bp both orientations 4-30 base fragments base composition 5’ promoter tag 3’ promoter tag Transcription (w/ dUTPs) www.noaa.gov DNA – Sequenom iSeq PCR transcription cleavage MALDI <800bp both orientations 4-30 base fragments base composition 5’ promoter tag C or U cleavages 3’ promoter tag “G or A” cleavages Transcription (w/ dUTPs) www.noaa.gov DNA – Sequenom iSeq PCR transcription cleavage MALDI <800bp both orientations 4-30 base fragments base composition 5’ promoter tag C or U cleavages 3’ promoter tag “G or A” cleavages Transcription (w/ dUTPs) • Fragment mass/size analysis for all reactions to deduce www.noaa.gov sequence • ~99% concordance with Sanger sequencing • ~1 day process DNA - MassTag PCR Briese, EID ‘05 11:310 • Can be highly multiplexed (64 different tags) • Direct from specimen • Limited by the primers in each assay (ability to multiplex, range of organisms, sensitivity) Protein – Bruker (or Shimadzu) Subtitle Here Culture extract/smear MALDI actively growing cytoplasmic proteins pattern matching Ethanol wash 70% formic acid + acetonitrile • Analyze 2-20 kDa proteins • Compare spectrum 0.0 x104 * with marc\0_A8\1\1SLin, "Baseline subt." 3.0 Intens. [a.u.] 2.5 with database of 2.0 1.5 >4600 organisms 1.0 0.5 0.0 2000 4000 6000 8000 10000 12000 14000 16000 m/z • 1.5h / 96 isolates Protein – Bruker (or Shimadzu) Subtitle Here Culture extract/smear MALDI actively growing cytoplasmic proteins pattern matching Ethanol wash 70% formic acid + acetonitrile • Analyze 2-20 kDa proteins • Compare spectrum 0.0 x104 * with marc\0_A8\1\1SLin, "Baseline subt." 3.0 Intens. [a.u.] 2.5 with database of 2.0 1.5 >4600 organisms 1.0 0.5 0.0 2000 4000 6000 8000 10000 12000 14000 16000 m/z • 1.5h / 96 isolates Protein – Bruker (or Shimadzu) Subtitle Here Culture extract/smear MALDI actively growing cytoplasmic proteins pattern matching Ethanol wash 70% formic acid + acetonitrile • Analyze 2-20 kDa proteins • Compare spectrum 0.0 x104 * with marc\0_A8\1\1SLin, "Baseline subt." 3.0 Intens. [a.u.] 2.5 with database of 2.0 1.5 >4600 organisms 1.0 0.5 0.0 2000 4000 6000 8000 10000 12000 14000 16000 m/z • 1.5h / 96 isolates MALDI-TOF spectra Subtitle4 Here * 12-15-09 test samples\0_C1\1\1SLin, "Baseline subt." x10 Staphylococcus aureus 5 Intens. [a.u.] 4 3 2 1 000 4 * with marc\0_A8\1\1SLin, "Baseline subt." x104 * with marc\0_A10\1\1SLin, "Baseline subt." 3.0 Streptococcus pneumoniae Intens. [a.u.] Intens. [a.u.] 2.52.0 2.0 1.5 1.5 1.0 1.0 0.5 0.0000 x104 * *with with marc\0_A10\1\1SLin, marc\0_A8\1\1SLin, "Baseline subt." 3.0 Escherichia coli Intens. [a.u.] Intens. [a.u.] 2.52.0 1.52.0 1.5 1.0 1.0 0.5 0.0 20004 4000 6000 8000 10000 12000 14000 16000 .] m/z MALDI-TOF spectra Subtitle4 Here * 12-15-09 test samples\0_C1\1\1SLin, "Baseline subt." x10 Staphylococcus aureus 5 Intens. [a.u.] 4 3 2 1 000 4 * with marc\0_A8\1\1SLin, "Baseline subt." x104 * with marc\0_A10\1\1SLin, "Baseline subt." 3.0 Streptococcus pneumoniae Intens. [a.u.] Intens. [a.u.] 2.52.0 2.0 1.5 1.5 1.0 1.0 0.5 0.0000 x104 * *with with marc\0_A10\1\1SLin, marc\0_A8\1\1SLin, "Baseline subt." 3.0 Escherichia coli Intens. [a.u.] Intens. [a.u.] 2.52.0 1.52.0 1.5 1.0 1.0 0.5 0.0 20004 4000 6000 8000 10000 12000 14000 16000 .] m/z Spectrum matching Subtitle Here Test spectrum Reference spectrum Spectrum matching Subtitle Here Test spectrum Reference spectrum Results table Subtitle Here • Generated via automated analysis runs Score Description 1.900 ... 3.000 species identification 1.700 ... 1.899 genus identification 0.000 ... 1.699 not reliable identification Detailed results Subtitle Here Detailed results Subtitle Here Early evaluation: HACEK organisms Subtitle Here • Haemophilus parainfluenzae, Aggregatibacter aphrophilus, A. actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, Kingella kingae – Fastidious GNRs – Cause endocarditis, head and neck infections, abscesses, septic arthritis – Most are difficult to definitively ID • 16S rRNA gene sequencing in our laboratory • 103 HACEK and 20 H. influenzae isolates analyzed by 16S vs. MALDI HACEK identification Subtitle Here Couturier et al JCM’11 49:1104 Customization of database Subtitle Here • Many isolates of Cardiobacterium hominis and Aggregatibacter aphrophilus had low scores • 50% C. hominis = no ID, 17% = species level • 58% A. aphrophilus = genus level, 37% = species level – Added one clinical isolate of each species to the database for each species • Not part of the study set • 3 replicate cultures, multiple spots, combine spectra
Load more

Recommended publications
  • Phylogenomic Networks Reveal Limited Phylogenetic Range of Lateral Gene Transfer by Transduction
    The ISME Journal (2017) 11, 543–554 OPEN © 2017 International Society for Microbial Ecology All rights reserved 1751-7362/17 www.nature.com/ismej ORIGINAL ARTICLE Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction Ovidiu Popa1, Giddy Landan and Tal Dagan Institute of General Microbiology, Christian-Albrechts University of Kiel, Kiel, Germany Bacteriophages are recognized DNA vectors and transduction is considered as a common mechanism of lateral gene transfer (LGT) during microbial evolution. Anecdotal events of phage- mediated gene transfer were studied extensively, however, a coherent evolutionary viewpoint of LGT by transduction, its extent and characteristics, is still lacking. Here we report a large-scale evolutionary reconstruction of transduction events in 3982 genomes. We inferred 17 158 recent transduction events linking donors, phages and recipients into a phylogenomic transduction network view. We find that LGT by transduction is mostly restricted to closely related donors and recipients. Furthermore, a substantial number of the transduction events (9%) are best described as gene duplications that are mediated by mobile DNA vectors. We propose to distinguish this type of paralogy by the term autology. A comparison of donor and recipient genomes revealed that genome similarity is a superior predictor of species connectivity in the network in comparison to common habitat. This indicates that genetic similarity, rather than ecological opportunity, is a driver of successful transduction during microbial evolution. A striking difference in the connectivity pattern of donors and recipients shows that while lysogenic interactions are highly species-specific, the host range for lytic phage infections can be much wider, serving to connect dense clusters of closely related species.
    [Show full text]
  • Bacterial Diversity Within the Human Subgingival Crevice
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln U.S. Department of Veterans Affairs Staff Publications U.S. Department of Veterans Affairs 12-7-1999 Bacterial diversity within the human subgingival crevice Ian Kroes Stanford University School of Medicine Paul W. Lepp Stanford University School of Medicine, [email protected] David A. Relman Stanford University School of Medicine, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/veterans Kroes, Ian; Lepp, Paul W.; and Relman, David A., "Bacterial diversity within the human subgingival crevice" (1999). U.S. Department of Veterans Affairs Staff Publications. 18. https://digitalcommons.unl.edu/veterans/18 This Article is brought to you for free and open access by the U.S. Department of Veterans Affairs at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in U.S. Department of Veterans Affairs Staff Publications by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Bacterialdiversity within the human subgingivalcrevice Ian Kroes, Paul W. Lepp, and David A. Relman* Departmentsof Microbiologyand Immunology,and Medicine,Stanford University School of Medicine,Stanford, CA 94305, and VeteransAffairs Palo Alto HealthCare System, Palo Alto,CA 94304 Editedby Stanley Falkow, Stanford University, Stanford, CA, and approvedOctober 15, 1999(received for review August 2, 1999) Molecular, sequence-based environmental surveys of microorgan- associated with disease (9-11). However, a directcomparison isms have revealed a large degree of previously uncharacterized between cultivation-dependentand -independentmethods has diversity. However, nearly all studies of the human endogenous not been described. In this study,we characterizedbacterial bacterial flora have relied on cultivation and biochemical charac- diversitywithin a specimenfrom the humansubgingival crevice terization of the resident organisms.
    [Show full text]
  • Bacterial Diversity and Functional Analysis of Severe Early Childhood
    www.nature.com/scientificreports OPEN Bacterial diversity and functional analysis of severe early childhood caries and recurrence in India Balakrishnan Kalpana1,3, Puniethaa Prabhu3, Ashaq Hussain Bhat3, Arunsaikiran Senthilkumar3, Raj Pranap Arun1, Sharath Asokan4, Sachin S. Gunthe2 & Rama S. Verma1,5* Dental caries is the most prevalent oral disease afecting nearly 70% of children in India and elsewhere. Micro-ecological niche based acidifcation due to dysbiosis in oral microbiome are crucial for caries onset and progression. Here we report the tooth bacteriome diversity compared in Indian children with caries free (CF), severe early childhood caries (SC) and recurrent caries (RC). High quality V3–V4 amplicon sequencing revealed that SC exhibited high bacterial diversity with unique combination and interrelationship. Gracillibacteria_GN02 and TM7 were unique in CF and SC respectively, while Bacteroidetes, Fusobacteria were signifcantly high in RC. Interestingly, we found Streptococcus oralis subsp. tigurinus clade 071 in all groups with signifcant abundance in SC and RC. Positive correlation between low and high abundant bacteria as well as with TCS, PTS and ABC transporters were seen from co-occurrence network analysis. This could lead to persistence of SC niche resulting in RC. Comparative in vitro assessment of bioflm formation showed that the standard culture of S. oralis and its phylogenetically similar clinical isolates showed profound bioflm formation and augmented the growth and enhanced bioflm formation in S. mutans in both dual and multispecies cultures. Interaction among more than 700 species of microbiota under diferent micro-ecological niches of the human oral cavity1,2 acts as a primary defense against various pathogens. Tis has been observed to play a signifcant role in child’s oral and general health.
    [Show full text]
  • Accurate Identification of Fastidious Gram-Negative Rods: Integration Ofboth Conventional Phenotypic Methods and 16S Rrna Gene Analysis
    Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2013 Accurate identification of fastidious Gram-negative rods: integration ofboth conventional phenotypic methods and 16S rRNA gene analysis de Melo Oliveira, Maria G ; Abels, Susanne ; Zbinden, Reinhard ; Bloemberg, Guido V ; Zbinden, Andrea Abstract: BACKGROUND: Accurate identification of fastidious Gram-negative rods (GNR) by conven- tional phenotypic characteristics is a challenge for diagnostic microbiology. The aim of this study was to evaluate the use of molecular methods, e.g., 16S rRNA gene sequence analysis for identification of fastid- ious GNR in the clinical microbiology laboratory. RESULTS: A total of 158 clinical isolates covering 20 genera and 50 species isolated from 1993 to 2010 were analyzed by comparing biochemical and 16S rRNA gene sequence analysis based identification. 16S rRNA gene homology analysis identified 148/158 (94%) of the isolates to species level, 9/158 (5%) to genus and 1/158 (1%) to family level. Compared to 16S rRNA gene sequencing as reference method, phenotypic identification correctly identified 64/158 (40%) isolates to species level, mainly Aggregatibacter aphrophilus, Cardiobacterium hominis, Eikenella corro- dens, Pasteurella multocida, and 21/158 (13%) isolates correctly to genus level, notably Capnocytophaga sp.; 73/158 (47%) of the isolates were not identified or misidentified. CONCLUSIONS: We herein propose an efficient strategy for accurate identification of fastidious GNR in the clinical microbiology laboratory by integrating both conventional phenotypic methods and 16S rRNA gene sequence analysis. We con- clude that 16S rRNA gene sequencing is an effective means for identification of fastidious GNR, which are not readily identified by conventional phenotypic methods.
    [Show full text]
  • Multiple Myeloma Complicated with Pseudomonas Endocartiditis Mieloma Múltiplo Complicado Com Endocardite Infecciosa Por Pseudomonas
    CASE REPORT Multiple myeloma complicated with pseudomonas endocartiditis Mieloma múltiplo complicado com endocardite infecciosa por pseudomonas Juliana Todaro1, Patrícia Weinschenker Bollmann1, Amit Nussbacher1, Luis Fernando Aranha Camargo1, Bento Fortunato Cardoso dos Santos1, Daniel Alvarenga1, Laercio Alberto Rosemberg1, David Costa de Souza Le Bihan1, Cláudio Henrique Fischer1, Auro del Giglio1 ABSTRACT associated to this disease(1). The immunosuppression Patients diagnosed with multiple myeloma are more susceptible to seen in those patients occurs by reductions in functional infections which are the major causes of morbidity and mortality antibodies as well as in granulocytes activity and associated to this disease. The main infectious agents involved are complement release(2). Infections are higher within first Gram-positive bacteria. However, after chemotherapy an increase in months after diagnosis and among patients with renal the incidence of Gram-negative strains is observed. These bacteria insufficiency(2,3). Gram-positive microorganisms are the are also responsible for most cases of urinary tract infections. Here is major causative agents, however, after chemotherapy reported a rare case in a 73-year-old man with multiple myeloma who developed endocarditis due to pseudomonas. an increase in the frequency of Gram-negative bacteria is observed being these agents responsible for cases of (2,3) Keywords: Multiple myeloma; Endocarditis; Pseudomonas; Case reports pneumonias and urinary tract infections . Despite the high incidence of infections, endocarditis is rare and often caused by Gram-positive bacteria(4). RESUMO This paper reports a case of infective endocarditis (IE) Pacientes diagnosticados com mieloma múltiplo são mais suscetíveis in mitral valve caused by Pseudomonas aeruginosa in a a infecções, que é a principal causa de morbidade e mortalidade patient with MM, and who were receiving chemotherapy.
    [Show full text]
  • A Pediatric Case of Cardiobacterium Hominis Endocarditis After Right
    D ious isea ct se fe s & In f T Journal of Infectious Diseases and o h l e a r a n r p Gribaa et al., J Infect Dis Ther 2015, 3:2 u y o J Therapy DOI: 10.4172/2332-0877.1000210 ISSN: 2332-0877 Case Report Open Access A Pediatric Case of Cardiobacterium Hominis Endocarditis after Right Ventricular Outflow Tract Reconstruction Mehdi Slim⃰, Rym Gribaa, Elies Neffati, Sana Ouali, Fehmi Remadi and Essia Boughzela Department of Cardiology, Sahloul Hospital, Sousse, Tunisia ⃰ Corresponding author: Mehdi Slim, Hôpital Sahloul, Route de la ceinture, Hammam Sousse 4054, Sousse, Tunisia, Tel : +216 98696847; Fax : +216 73 367 451; E- mail: [email protected] Received date: January 30, 2015, Accepted date: April 11, 2015, Published date: April 18, 2015 Copyright: © 2015 Slim M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Cardiobacterium hominis, a member of the HACEK group of organisms, is a rare cause of endocarditis and is even rarer in pediatric population. In this report, we present a case of infective endocarditis caused by C. hominis in a 16-year-old Tunisian girl who had undergone right ventricular outflow tract reconstruction using a Hancock® heterograft for double outlet right ventricle with pulmonary stenosis. Two weeks before admission, the patient suffered from worsened shortness of breath and fever. Tranthoracic echocardiography revealed right ventricular outflow tract stenosis and vegetation attached to the leaflet conduit.
    [Show full text]
  • Aquatic Microbial Ecology 80:15
    The following supplement accompanies the article Isolates as models to study bacterial ecophysiology and biogeochemistry Åke Hagström*, Farooq Azam, Carlo Berg, Ulla Li Zweifel *Corresponding author: [email protected] Aquatic Microbial Ecology 80: 15–27 (2017) Supplementary Materials & Methods The bacteria characterized in this study were collected from sites at three different sea areas; the Northern Baltic Sea (63°30’N, 19°48’E), Northwest Mediterranean Sea (43°41'N, 7°19'E) and Southern California Bight (32°53'N, 117°15'W). Seawater was spread onto Zobell agar plates or marine agar plates (DIFCO) and incubated at in situ temperature. Colonies were picked and plate- purified before being frozen in liquid medium with 20% glycerol. The collection represents aerobic heterotrophic bacteria from pelagic waters. Bacteria were grown in media according to their physiological needs of salinity. Isolates from the Baltic Sea were grown on Zobell media (ZoBELL, 1941) (800 ml filtered seawater from the Baltic, 200 ml Milli-Q water, 5g Bacto-peptone, 1g Bacto-yeast extract). Isolates from the Mediterranean Sea and the Southern California Bight were grown on marine agar or marine broth (DIFCO laboratories). The optimal temperature for growth was determined by growing each isolate in 4ml of appropriate media at 5, 10, 15, 20, 25, 30, 35, 40, 45 and 50o C with gentle shaking. Growth was measured by an increase in absorbance at 550nm. Statistical analyses The influence of temperature, geographical origin and taxonomic affiliation on growth rates was assessed by a two-way analysis of variance (ANOVA) in R (http://www.r-project.org/) and the “car” package.
    [Show full text]
  • Rapid Identification of Cardiobacterium Hominis by MALDI-TOF Mass Spectrometry During Infective Endocarditis
    Jpn. J. Infect. Dis., 64, 327-329, 2011 Short Communication Rapid Identification of Cardiobacterium hominis by MALDI-TOF Mass Spectrometry during Infective Endocarditis Fráedáeric Wallet1,2*, Caroline Loäƒez1,2, Christophe Decoene1,2, and Renáe Courcol1,2 1University of Lille Nord de France, Lille; and 2CHU Lille, Lille, France (Received April 8, 2011. Accepted May 11, 2011) SUMMARY:WereportanewcaseofCardiobacterium hominis endocarditis identified during an acute coronary syndrome. The positivity of the blood cultures was confirmed rapidly (50 h) as a result of im- provements to the automated detection system, whereby it is no longer necessary to incubate the vials for long periods of time when Aggregatibacter-Cardiobacterium-Eikenella-Kingella infections is sus- pected. The phenotype-based VITEK 2 NH identification system is not able to distinguish between the two species of Cardiobacterium, as it does not contain C. valvarum in its library. The method for 16S rRNA gene sequence analysis is able to separate the two species but is not available in all laboratories. We used MALDI-TOF mass spectrometry, as an alternative, to rapidly distinguish between C. hominis and C. valvarum, because both species are contained in the system library. A 60-year-old man, without coronary history, was this Gram-negative rod was pleiomorphic, and pairs, hospitalized in the cardiologic ward for an atypical chest short chains, and filaments could be seen. Some of these constrictive pain. Initial examination showed that his organisms retained a variable amount of Gram-positive pulse was regular at 80/min and that his blood pressure stain in the end or in central portions.
    [Show full text]
  • Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes
    Structural and Functional Insights from the Metagenome of an Acidic Hot Spring Microbial Planktonic Community in the Colombian Andes Diego Javier Jime´nez1,5*, Fernando Dini Andreote3, Diego Chaves1, Jose´ Salvador Montan˜ a1,2, Cesar Osorio-Forero1,4, Howard Junca1,4, Marı´a Mercedes Zambrano1,4, Sandra Baena1,2 1 Colombian Center for Genomic and Bioinformatics from Extreme Environments (GeBiX), Bogota´, Colombia, 2 Departamento de Biologı´a, Unidad de Saneamiento y Biotecnologı´a Ambiental, Pontificia Universidad Javeriana, Bogota´, Colombia, 3 Department of Soil Science, ‘‘Luiz de Queiroz’’ College of Agriculture, University of Sao Paulo, Piracicaba, Brazil, 4 Molecular Genetics and Microbial Ecology Research Groups, Corporacio´n CorpoGen, Bogota´, Colombia, 5 Department of Microbial Ecology, Center for Ecological and Evolutionary Studies (CEES), University of Groningen, Groningen, The Netherlands Abstract A taxonomic and annotated functional description of microbial life was deduced from 53 Mb of metagenomic sequence retrieved from a planktonic fraction of the Neotropical high Andean (3,973 meters above sea level) acidic hot spring El Coquito (EC). A classification of unassembled metagenomic reads using different databases showed a high proportion of Gammaproteobacteria and Alphaproteobacteria (in total read affiliation), and through taxonomic affiliation of 16S rRNA gene fragments we observed the presence of Proteobacteria, micro-algae chloroplast and Firmicutes. Reads mapped against the genomes Acidiphilium cryptum JF-5, Legionella pneumophila str. Corby and Acidithiobacillus caldus revealed the presence of transposase-like sequences, potentially involved in horizontal gene transfer. Functional annotation and hierarchical comparison with different datasets obtained by pyrosequencing in different ecosystems showed that the microbial community also contained extensive DNA repair systems, possibly to cope with ultraviolet radiation at such high altitudes.
    [Show full text]
  • Serratia Marcescens Tricuspid Valve Vegetation and Successful Use of the Angiovac® System
    Open Access Case Report DOI: 10.7759/cureus.10010 Serratia marcescens Tricuspid Valve Vegetation and Successful Use of the AngioVac® System Sean M. Winkle 1 , Salem Gaballa 1 , Areeka Memon 2 , Jeremy B. Miller 1 , Ryan Curfiss 1 1. Internal Medicine, LewisGale Medical Center, Salem, USA 2. Osteopathic Medicine, Edward Via College of Osteopathic Medicine, Blacksburg, USA Corresponding author: Sean M. Winkle, [email protected] Abstract Serratia marcescens bacteremia is common in patient populations with a history of intravenous drug use (IVDU), but it rarely causes infective endocarditis. We are reporting a 27-year-old female with a medical history significant for IVDU and hepatitis C virus infection who presented to the emergency department complaining of fever and shortness of breath. Computed tomography of the chest with intravenous (IV) contrast revealed extensive bilateral pulmonary infiltrates with multiple cavitary lesions. The patient was treated with IV vancomycin and piperacillin/tazobactam. Blood culture grows methicillin-sensitive Staphylococcus aureus (MSSA) and S. marcescens, both sensitive to cefepime/meropenem. Transesophageal echocardiogram revealed 3.4 x 2 cm tricuspid valve vegetation. Cardiothoracic surgery was consulted, who recommended transcatheter aspiration with the AngioVac® system (AngioDynamics Inc., Latham, NY). Post- procedure transesophageal echocardiogram revealed a significant reduction of vegetation size. Vegetation tissue culture grew MSSA and S. marcescens. The repeated blood culture revealed no
    [Show full text]
  • December 2018 Thomas Herchline, Editor
    INFECTIOUS DISEASES NEWSLETTER December 2018 Thomas Herchline, Editor LOCAL NEWS Montgomery County Mosquito Surveillance and Control October brought an end to Public Health’s mosquito surveillance and control activities for 2018. This year, with the assistance of two Wright State University Environmental Health interns, Public Health collected 9,466 mosquitoes from 125 different trap locations in Montgomery County. This resulted in 410 mosquito pools being tested, with 71 testing positive for West Nile Virus. A mosquito pool consists of a collection of up to 50 mosquitoes that are submitted to the Ohio Department of Health laboratory for testing. State-wide there were 16,902 mosquito pools tested. In Montgomery County 17% of the mosquito pools tested positive for WNV, which was similar to the state-wide percentage (19%). There were three confirmed human cases of WNV reported in Montgomery County with a total of 57 cases occurring in 25 other counties. In response to WNV positive mosquito pools, Public Health conducted truck-mounted applications of mosquito adulticides on 8 separate occasions. There were no locally-acquired human cases of Zika Virus reported in Ohio. The mosquito species capable of spreading the Zika Virus was found in 4% of the mosquitoes collected in Montgomery County (compared to 1% statewide). Montgomery County Hepatitis A Hepatitis A outbreaks have been occurring in multiple states across the U.S., including several bordering Ohio. The Ohio Department of Health declared a statewide community outbreak for Hepatitis A on June 22. As of October 29, Ohio had 761 confirmed cases and Montgomery County had a total of 148 cases.
    [Show full text]
  • A Conserved Inner Membrane Protein of Aggregatibacter Actinomycetemcomitans Is Integral for Membrane Function Kenneth Smith University of Vermont
    University of Vermont ScholarWorks @ UVM Graduate College Dissertations and Theses Dissertations and Theses 2015 A conserved Inner Membrane Protein of Aggregatibacter actinomycetemcomitans is integral for membrane function Kenneth Smith University of Vermont Follow this and additional works at: https://scholarworks.uvm.edu/graddis Part of the Microbiology Commons Recommended Citation Smith, Kenneth, "A conserved Inner Membrane Protein of Aggregatibacter actinomycetemcomitans is integral for membrane function" (2015). Graduate College Dissertations and Theses. 417. https://scholarworks.uvm.edu/graddis/417 This Dissertation is brought to you for free and open access by the Dissertations and Theses at ScholarWorks @ UVM. It has been accepted for inclusion in Graduate College Dissertations and Theses by an authorized administrator of ScholarWorks @ UVM. For more information, please contact [email protected]. A CONSERVED INNER MEMBRANE PROTEIN OF AGGREGATIBACTER ACTINOMYCETEMCOMITANS IS INTEGRAL FOR MEMBRANE FUNCTION A Dissertation Presented by Kenneth P. Smith to The Faculty of the Graduate College of The University of Vermont In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Specializing in Microbiology and Molecular Genetics October, 2015 Defense Date: June 15, 2015 Dissertation Examination Committee: Keith P. Mintz, Ph.D., Advisor Teresa Ruiz, Ph.D., Chairperson John M. Burke, Ph.D. Aimee Shen, Ph.D. Matthew J. Wargo, Ph.D. Cynthia J. Forehand, Ph.D., Dean of the Graduate College ABSTRACT The cell envelope of Aggregatibacter actinomycetemcomitans, a Gram-negative pathogenic bacterium implicated in human oral and systemic disease, plays a critical role in maintenance of cellular homeostasis, resistance to external stress, and host–pathogen interactions. Our laboratory has identified a novel gene product, morphogenesis protein C (MorC), deletion of which leads to multiple pleotropic effects pertaining to membrane structure and function.
    [Show full text]