Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens
Abstract
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-levelmore »
- Authors:
-
- Univ. of California San Francisco, San Francisco, CA (United States). Dept. of Medicine
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Div.
- Univ. of California, Berkeley, CA (United States)
- Victoria Univ. of Wellington, Wellington (New Zealand). School of BIological Sciences
- San Francisco General Hospital, San Francisco, CA (United States). Dept. of Medicine
- Univ. of California San Francisco, San Francisco, CA (United States). Clinical Microbiology Lab.
- Charité, Campus Benjamin Franklin, Berlin (Germany)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; National Institute of Health
- OSTI Identifier:
- 1212477
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PLoS ONE
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 2; Journal ID: ISSN 1932-6203
- Publisher:
- Public Library of Science
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; ribosomal RNA; sequence databases; sequence alignment; microbiology; bacterial pathogens; research laboratories; clinical microbiology; gram positive bacteria
Citation Formats
Srinivasan, Ramya, Karaoz, Ulas, Volegova, Marina, MacKichan, Joanna, Kato-Maeda, Midori, Miller, Steve, Nadarajan, Rohan, Brodie, Eoin L., Lynch, Susan V., and Heimesaat, Markus M. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. United States: N. p., 2015.
Web. doi:10.1371/journal.pone.0117617.
Srinivasan, Ramya, Karaoz, Ulas, Volegova, Marina, MacKichan, Joanna, Kato-Maeda, Midori, Miller, Steve, Nadarajan, Rohan, Brodie, Eoin L., Lynch, Susan V., & Heimesaat, Markus M. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. United States. https://doi.org/10.1371/journal.pone.0117617
Srinivasan, Ramya, Karaoz, Ulas, Volegova, Marina, MacKichan, Joanna, Kato-Maeda, Midori, Miller, Steve, Nadarajan, Rohan, Brodie, Eoin L., Lynch, Susan V., and Heimesaat, Markus M. Fri .
"Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens". United States. https://doi.org/10.1371/journal.pone.0117617. https://www.osti.gov/servlets/purl/1212477.
@article{osti_1212477,
title = {Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens},
author = {Srinivasan, Ramya and Karaoz, Ulas and Volegova, Marina and MacKichan, Joanna and Kato-Maeda, Midori and Miller, Steve and Nadarajan, Rohan and Brodie, Eoin L. and Lynch, Susan V. and Heimesaat, Markus M.},
abstractNote = {According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.},
doi = {10.1371/journal.pone.0117617},
journal = {PLoS ONE},
number = 2,
volume = 10,
place = {United States},
year = {Fri Feb 06 00:00:00 EST 2015},
month = {Fri Feb 06 00:00:00 EST 2015}
}
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Works referenced in this record:
Estimating Health Care-Associated Infections and Deaths in U.S. Hospitals, 2002
journal, March 2007
- Klevens, R. Monina; Edwards, Jonathan R.; Richards, Chesley L.
- Public Health Reports, Vol. 122, Issue 2
Bacterial Community Variation in Human Body Habitats Across Space and Time
journal, November 2009
- Costello, E. K.; Lauber, C. L.; Hamady, M.
- Science, Vol. 326, Issue 5960
Towards a Phylogeny and Definition of Species at the Molecular Level within the Genus Mycobacterium
journal, October 1990
- Rogall, T.; Wolters, J.; Flohr, T.
- International Journal of Systematic Bacteriology, Vol. 40, Issue 4
Clinical Importance of Delays in the Initiation of Appropriate Antibiotic Treatment for Ventilator-Associated Pneumonia
journal, July 2002
- Iregui, Manuel; Ward, Suzanne; Sherman, Glenda
- Chest, Vol. 122, Issue 1
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
Evaluation of three phenotypic identification systems for clinical isolates of Raoultella ornithinolytica
journal, January 2011
- Park, J. S.; Hong, K. H.; Lee, H. J.
- Journal of Medical Microbiology, Vol. 60, Issue 4
Molecular Typing of Bacteria Directly from Cerebrospinal Fluid
journal, September 2000
- Enright, M. C.; Knox, K.; Griffiths, D.
- European Journal of Clinical Microbiology & Infectious Diseases, Vol. 19, Issue 8
Species-Level Analysis of DNA Sequence Data from the NIH Human Microbiome Project
journal, October 2012
- Conlan, Sean; Kong, Heidi H.; Segre, Julia A.
- PLoS ONE, Vol. 7, Issue 10
16S rRNA sequencing in routine bacterial identification: A 30-month experiment
journal, December 2006
- Mignard, S.; Flandrois, J. P.
- Journal of Microbiological Methods, Vol. 67, Issue 3
Prospects for the Future Using Genomics and Proteomics in Clinical Microbiology
journal, October 2011
- Fournier, Pierre-Edouard; Raoult, Didier
- Annual Review of Microbiology, Vol. 65, Issue 1
Identification of pathogenic Leptospira species by conventional or real-time PCR and sequencing of the DNA gyrase subunit B encoding gene
journal, October 2006
- Slack, Andrew T.; Symonds, Meegan L.; Dohnt, Michael F.
- BMC Microbiology, Vol. 6, Issue 1, p. 95
Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges.
journal, November 1997
- Håvarstein, L. S.; Hakenbeck, R.; Gaustad, P.
- Journal of Bacteriology, Vol. 179, Issue 21
The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier
journal, January 2012
- Newton, Irene LG; Roeselers, Guus
- BMC Microbiology, Vol. 12, Issue 1
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007
- Wang, Q.; Garrity, G. M.; Tiedje, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 16
The growing burden of antimicrobial resistance
journal, September 2008
- Hawkey, P. M.
- Journal of Antimicrobial Chemotherapy, Vol. 62, Issue Supplement 1
Automated Identification of Medically Important Bacteria by 16S rRNA Gene Sequencing Using a Novel Comprehensive Database, 16SpathDB
journal, March 2011
- Woo, P. C. Y.; Teng, J. L. L.; Yeung, J. M. Y.
- Journal of Clinical Microbiology, Vol. 49, Issue 5
A Rapid PCR Based Method to Distinguish between Lactococcus and Enterococcus
journal, December 2000
- Deasy, B. M.; Rea, M. C.; Fitzgerald, G. F.
- Systematic and Applied Microbiology, Vol. 23, Issue 4
The rpoB gene as a tool for clinical microbiologists
journal, January 2009
- Adékambi, Toïdi; Drancourt, Michel; Raoult, Didier
- Trends in Microbiology, Vol. 17, Issue 1
Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases
journal, October 2004
- Clarridge, J. E.
- Clinical Microbiology Reviews, Vol. 17, Issue 4
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
journal, November 2008
- Huse, Susan M.; Dethlefsen, Les; Huber, Julie A.
- PLoS Genetics, Vol. 4, Issue 11
Update on the Burkholderia cepacia complex
journal, January 2005
- LiPuma, John J.
- Current Opinion in Pulmonary Medicine, Vol. 11, Issue 6
Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing
journal, September 2003
- Woo, P. C. Y.
- Journal of Clinical Pathology, Vol. 56, Issue 9
Neisseria meningitidis PorA variable regions: rapid detection of P1·7 and P1·19 variants by PCR : Rapid detection of
journal, July 2007
- De Filippis, I.; De Andrade, C. F.; De Almeida, A. E. C. C.
- Letters in Applied Microbiology, Vol. 45, Issue 4
Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies
journal, August 2012
- Klindworth, Anna; Pruesse, Elmar; Schweer, Timmy
- Nucleic Acids Research, Vol. 41, Issue 1
Laboratory Maintenance of Bordetella pertussis
journal, November 2009
- Hulbert, Robin R.; Cotter, Peggy A.
- Current Protocols in Microbiology, Vol. 15, Issue 1
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
journal, January 2009
- Cole, J. R.; Wang, Q.; Cardenas, E.
- Nucleic Acids Research, Vol. 37, Issue Database
Inappropriate antibiotic therapy in Gram-negative sepsis increases hospital length of stay*
journal, January 2011
- Shorr, Andrew F.; Micek, Scott T.; Welch, Emily C.
- Critical Care Medicine, Vol. 39, Issue 1
SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
journal, November 2007
- Pruesse, E.; Quast, C.; Knittel, K.
- Nucleic Acids Research, Vol. 35, Issue 21
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
journal, June 2012
- ,
- PLoS ONE, Vol. 7, Issue 6
RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
journal, January 2002
- Harmsen, D.
- Nucleic Acids Research, Vol. 30, Issue 1
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
A multiplex real-time PCR assay for rapid detection and differentiation of 25 bacterial and fungal pathogens from whole blood samples
journal, November 2007
- Lehmann, Lutz Eric; Hunfeld, Klaus-Peter; Emrich, Thomas
- Medical Microbiology and Immunology, Vol. 197, Issue 3
Rapid diagnosis of Clostridium difficile infection by multiplex real-time PCR
journal, April 2011
- Barbut, F.; Monot, M.; Rousseau, A.
- European Journal of Clinical Microbiology & Infectious Diseases, Vol. 30, Issue 10
Confirmation of Nontypeable Streptococcus pneumoniae-Like Organisms Isolated from Outbreaks of Epidemic Conjunctivitis as Streptococcus pneumoniae
journal, September 2003
- Carvalho, M. G. S.; Steigerwalt, A. G.; Thompson, T.
- Journal of Clinical Microbiology, Vol. 41, Issue 9
Genetic Relationships between Clinical Isolates of Streptococcus pneumoniae, Streptococcus oralis, and Streptococcus mitis: Characterization of "Atypical" Pneumococci and Organisms Allied to S. mitis Harboring S. pneumoniae Virulence Factor-Encoding Genes
journal, March 2000
- Whatmore, A. M.; Efstratiou, A.; Pickerill, A. P.
- Infection and Immunity, Vol. 68, Issue 3
Impact of Rapid Methicillin-Resistant Staphylococcus aureus Polymerase Chain Reaction Testing on Mortality and Cost Effectiveness in Hospitalized Patients with Bacteraemia: A Decision Model
journal, July 2010
- Brown, Jack; Paladino, Joseph A.
- PharmacoEconomics, Vol. 28, Issue 7
The rate and cost of hospital-acquired infections occurring in patients admitted to selected specialties of a district general hospital in England and the national burden imposed
journal, March 2001
- Plowman, R.; Graves, N.; Griffin, M. A. S.
- Journal of Hospital Infection, Vol. 47, Issue 3
Serratia marcescens
journal, November 1997
- Hejazi, A.; Falkiner, F. R.
- Journal of Medical Microbiology, Vol. 46, Issue 11
Endocarditis Due to Rare and Fastidious Bacteria
journal, January 2001
- Brouqui, P.; Raoult, D.
- Clinical Microbiology Reviews, Vol. 14, Issue 1
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes
journal, February 2014
- Teng, Jade L. L.; Ho, Tom C. C.; Yeung, Ronald S. Y.
- Diagnostic Microbiology and Infectious Disease, Vol. 78, Issue 2
Usefulness of the MicroSeq 500 16S Ribosomal DNA-Based Bacterial Identification System for Identification of Clinically Significant Bacterial Isolates with Ambiguous Biochemical Profiles
journal, May 2003
- Woo, P. C. Y.; Ng, K. H. L.; Lau, S. K. P.
- Journal of Clinical Microbiology, Vol. 41, Issue 5
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys
journal, June 2011
- Werner, Jeffrey J.; Koren, Omry; Hugenholtz, Philip
- The ISME Journal, Vol. 6, Issue 1
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
journal, July 2010
- Schloss, Patrick D.
- PLoS Computational Biology, Vol. 6, Issue 7
Community Factors in the Development of Antibiotic Resistance
journal, April 2007
- Larson, Elaine
- Annual Review of Public Health, Vol. 28, Issue 1
Species-level classification of the vaginal microbiome
journal, December 2012
- Fettweis, Jennifer M.; Serrano, Myrna G.; Sheth, Nihar U.
- BMC Genomics, Vol. 13, Issue S8
Comparison of Three Commercial Rapid Identification Systems for the Unusual Gram-Positive Cocci Dolosigranulum pigrum, Ignavigranum ruoffiae, andFacklamia Species
journal, January 2000
- LaClaire, Leslye L.; Facklam, Richard R.
- Journal of Clinical Microbiology, Vol. 38, Issue 6
Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy
journal, April 2020
- Blum, Faith C.; Hardy, Britney L.; Bishop-Lilly, Kimberly A.
- Scientific Reports, Vol. 10, Issue 1
Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
journal, August 2010
- Pei, Anna Y.; Oberdorf, William E.; Nossa, Carlos W.
- Applied and Environmental Microbiology, Vol. 76, Issue 15
Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of Acinetobacter baumannii
journal, June 2007
- Bartual, Sergio G.; Seifert, Harald; Hippler, Corinna
- Journal of Clinical Microbiology, Vol. 45, Issue 6
Inappropriate Antibiotic Therapy In Gram-Negative Sepsis Increases Hospital Length Of Stay
conference, May 2010
- Shorr, Andrew; Micek, Scott; Welch, Emily
- American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans, A24. SEPSIS: MECHANISMS AND TREATMENT
Влияние мутаций по внеклеточной нуклеазе на свойства пигментообразующего и беспигментного штаммов Serratia marcescens
journal, January 2016
- Низамутдинова, Э. Х.; Ширшикова, Т. В.; Марданова, А. М.
- Микробиология, Vol. 85, Issue 1
The epidemiology of sepsis in the United States from 1979 through 2000*
journal, August 2003
- Martin, G. S.; Mannino, D. M.; Eaton, S.
- Obstetrics & Gynecology, Vol. 102, Issue 2, p. 411
Serratia marcescens
journal, October 1987
- Yannelli, Barbara; Schoch, Paul E.; Cunha, Burke A.
- Clinical Microbiology Newsletter, Vol. 9, Issue 20
Serratia marcescens
journal, August 1979
- ,
- New England Journal of Medicine, Vol. 301, Issue 7, p. 388-388
Evaluation of the ability of a commercial system to identifyAcinetobacter genomic species
journal, April 1996
- Bernards, A. T.; Toorn, J.; Boven, C. P. A.
- European Journal of Clinical Microbiology & Infectious Diseases, Vol. 15, Issue 4
Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods
journal, September 2020
- Omori, Michi; Kato-Kogoe, Nahoko; Sakaguchi, Shoichi
- Clinical Oral Investigations, Vol. 25, Issue 5
Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes
journal, February 2014
- Teng, Jade L. L.; Ho, Tom C. C.; Yeung, Ronald S. Y.
- Diagnostic Microbiology and Infectious Disease, Vol. 78, Issue 2
Investigating a common approach to DNA profile interpretation using probabilistic software
journal, May 2015
- Cooper, Stuart; McGovern, Catherine; Bright, Jo-Anne
- Forensic Science International: Genetics, Vol. 16
The rpoB gene as a tool for clinical microbiologists
journal, January 2009
- Adékambi, Toïdi; Drancourt, Michel; Raoult, Didier
- Trends in Microbiology, Vol. 17, Issue 1
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Evaluation of a biochemical test scheme for identifying clinical isolates of Enterococcus faecalis and Enterococcus faecium
journal, November 2001
- Day, A. M.; Sandoe, J. A. T.; Cove, J. H.
- Letters in Applied Microbiology, Vol. 33, Issue 5
The Epidemiology of Sepsis in the United States from 1979 through 2000
journal, April 2003
- Martin, Greg S.; Mannino, David M.; Eaton, Stephanie
- New England Journal of Medicine, Vol. 348, Issue 16
RIDOM: Ribosomal Differentiation of Medical Micro-organisms Database
journal, January 2002
- Harmsen, D.
- Nucleic Acids Research, Vol. 30, Issue 1
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
journal, January 2009
- Cole, J. R.; Wang, Q.; Cardenas, E.
- Nucleic Acids Research, Vol. 37, Issue Database
Update on the Burkholderia cepacia complex
journal, January 2005
- LiPuma, John J.
- Current Opinion in Pulmonary Medicine, Vol. 11, Issue 6
Measuring the effect of inappropriate initial antibiotic therapy on outcomes of patients with Gram-negative sepsis: An imprecise science*
journal, January 2011
- Sexton, Daniel J.; Miller, Becky A.; Anderson, Deverick J.
- Critical Care Medicine, Vol. 39, Issue 1
Towards a Phylogeny and Definition of Species at the Molecular Level within the Genus Mycobacterium
journal, October 1990
- Rogall, T.; Wolters, J.; Flohr, T.
- International Journal of Systematic Bacteriology, Vol. 40, Issue 4
Serratia marcescens
journal, November 1997
- Hejazi, A.; Falkiner, F. R.
- Journal of Medical Microbiology, Vol. 46, Issue 11
Evaluation of three phenotypic identification systems for clinical isolates of Raoultella ornithinolytica
journal, January 2011
- Park, J. S.; Hong, K. H.; Lee, H. J.
- Journal of Medical Microbiology, Vol. 60, Issue 4
Effect of a very low-energy diet on moderate and severe obstructive sleep apnoea: case reports
journal, February 2011
- Johansson, K.
- Clinical Obesity, Vol. 1, Issue 1
Molecular Epidemiology of Tuberculosis: Current Insights
journal, October 2006
- Mathema, B.; Kurepina, N. E.; Bifani, P. J.
- Clinical Microbiology Reviews, Vol. 19, Issue 4
What Happened to the Streptococci: Overview of Taxonomic and Nomenclature Changes
journal, October 2002
- Facklam, R.
- Clinical Microbiology Reviews, Vol. 15, Issue 4
Natural competence in the genus Streptococcus: evidence that streptococci can change pherotype by interspecies recombinational exchanges.
journal, November 1997
- Håvarstein, L. S.; Hakenbeck, R.; Gaustad, P.
- Journal of Bacteriology, Vol. 179, Issue 21
Using Multilocus Sequence Data To Define the Pneumococcus
journal, August 2005
- Hanage, W. P.; Kaijalainen, T.; Herva, E.
- Journal of Bacteriology, Vol. 187, Issue 17
Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical Laboratory
journal, October 2006
- Simmon, K. E.; Croft, A. C.; Petti, C. A.
- Journal of Clinical Microbiology, Vol. 44, Issue 12
16S Ribosomal DNA Sequence Analysis of a Large Collection of Environmental and Clinical Unidentifiable Bacterial Isolates
journal, January 2000
- Drancourt, Michel; Bollet, Claude; Carlioz, Antoine
- Journal of Clinical Microbiology, Vol. 38, Issue 10
Evaluation of the VITEK 2 System for the Identification and Susceptibility Testing of Three Species of Nonfermenting Gram-Negative Rods Frequently Isolated from Clinical Samples
journal, September 2001
- Joyanes, P.; del Carmen Conejo, M.; Martinez-Martinez, L.
- Journal of Clinical Microbiology, Vol. 39, Issue 9
Comparative Assessment of Genotyping Methods for Epidemiologic Study of Burkholderia cepacia Genomovar III
journal, September 2002
- Coenye, T.; Spilker, T.; Martin, A.
- Journal of Clinical Microbiology, Vol. 40, Issue 9
Evaluation of the MicroSeq System for Identification of Mycobacteria by 16S Ribosomal DNA Sequencing and Its Integration into a Routine Clinical Mycobacteriology Laboratory
journal, April 2003
- Hall, L.; Doerr, K. A.; Wohlfiel, S. L.
- Journal of Clinical Microbiology, Vol. 41, Issue 4
Clinical Impact of a PCR Assay for Identification of Staphylococcus aureus and Determination of Methicillin Resistance Directly from Blood Cultures
journal, August 2003
- Hallin, M.; Maes, N.; Byl, B.
- Journal of Clinical Microbiology, Vol. 41, Issue 8
Ribosomal DNA Sequencing for Identification of Aerobic Gram-Positive Rods in the Clinical Laboratory (an 18-Month Evaluation)
journal, September 2003
- Bosshard, P. P.; Abels, S.; Zbinden, R.
- Journal of Clinical Microbiology, Vol. 41, Issue 9
PCR-Based Assay for Differentiation of Pseudomonas aeruginosa from Other Pseudomonas Species Recovered from Cystic Fibrosis Patients
journal, May 2004
- Spilker, T.; Coenye, T.; Vandamme, P.
- Journal of Clinical Microbiology, Vol. 42, Issue 5
Use of the MicroSeq 500 16S rRNA Gene-Based Sequencing for Identification of Bacterial Isolates That Commercial Automated Systems Failed To Identify Correctly
journal, February 2005
- Fontana, C.; Favaro, M.; Pelliccioni, M.
- Journal of Clinical Microbiology, Vol. 43, Issue 2
Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of Acinetobacter baumannii
journal, September 2005
- Bartual, S. G.; Seifert, H.; Hippler, C.
- Journal of Clinical Microbiology, Vol. 43, Issue 9
Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing
journal, September 2003
- Woo, P. C. Y.
- Journal of Clinical Pathology, Vol. 56, Issue 9
Estimating Health Care-Associated Infections and Deaths in U.S. Hospitals, 2002
journal, March 2007
- Klevens, R. Monina; Edwards, Jonathan R.; Richards, Chesley L.
- Public Health Reports, Vol. 122, Issue 2
The effect of training set on the classification of honey bee gut microbiota using the Naïve Bayesian Classifier
journal, January 2012
- Newton, Irene LG; Roeselers, Guus
- BMC Microbiology, Vol. 12, Issue 1
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
journal, July 2010
- Schloss, Patrick D.
- PLoS Computational Biology, Vol. 6, Issue 7
Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing
journal, November 2008
- Huse, Susan M.; Dethlefsen, Les; Huber, Julie A.
- PLoS Genetics, Vol. 4, Issue 11
Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research
journal, June 2012
- ,
- PLoS ONE, Vol. 7, Issue 6
Clinical Importance of Delays in the Initiation of Appropriate Antibiotic Treatment for Ventilator-Associated Pneumonia
journal, July 2002
- Iregui, Manuel; Ward, Suzanne; Sherman, Glenda
- Chest, Vol. 122, Issue 1
Works referencing / citing this record:
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journal, January 2019
- Kai, Shinichi; Matsuo, Yoshiyuki; Nakagawa, So
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journal, December 2018
- Megat Mohd Azlan, Putri‐Intan‐Hafizah; Chin, Siok‐Fong; Low, Teck Yew
- PROTEOMICS, Vol. 19, Issue 10
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journal, March 2018
- Ghavami, Mohammad Bagher; Mirzadeh, Habibeh; Mohammadi, Jamshid
- Parasitology Research, Vol. 117, Issue 5
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journal, December 2019
- Ding, Yijun; Wang, Qing; Li, Dongfang
- European Journal of Clinical Microbiology & Infectious Diseases, Vol. 39, Issue 3
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journal, November 2018
- Chaprão, Marco José; da Silva, Rita de Cássia F. Soares; Rufino, Raquel D.
- Ecotoxicology, Vol. 27, Issue 10
Diversity of β-lactam resistance genes in gram-negative rods isolated from a municipal wastewater treatment plant
journal, February 2019
- Piotrowska, Marta; Kowalska, Sylwia; Popowska, Magdalena
- Annals of Microbiology, Vol. 69, Issue 6
Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
journal, January 2019
- Yeh, Hwey-Chin; Lu, Jang-Jih; Chang, Shih-Cheng
- Scientific Reports, Vol. 9, Issue 1
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journal, December 2017
- Gato, Worlanyo Eric; Posick, Chad; Williams, Ashley
- Deviant Behavior, Vol. 39, Issue 9
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posted_content, January 2019
- Kai, Shinichi; Matsuo, Yoshiyuki; Nakagawa, So
- FEBS Open Bio
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posted_content, August 2019
- Neuenschwander, Stefan Moritz; Miani, Miguel Angel Terrazos; Amlang, Heiko
- Journal of Clinical Microbiology
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
posted_content, March 2020
- Escapa, Isabel F.; Huang, Yanmei; Chen, Tsute
- bioRxiv
Microbiome patterns reveal the transmission of pathogenic bacteria in hilsa fish ( Tenualosa ilisha ) marketed for human consumption in Bangladesh
journal, January 2019
- Foysal, M. J.; Momtaz, F.; Robiul Kawser, A. Q. M.
- Journal of Applied Microbiology, Vol. 126, Issue 6
Detection and characterization of multidrug‐resistant Salmonella enterica serovar Infantis as an emerging threat in poultry farms of Faisalabad, Pakistan
journal, March 2019
- Wajid, M.; Saleemi, M. K.; Sarwar, Y.
- Journal of Applied Microbiology, Vol. 127, Issue 1
The Gut Microbiome and Mental Health: What Should We Tell Our Patients?: Le microbiote Intestinal et la Santé Mentale : que Devrions-Nous dire à nos Patients?
journal, September 2019
- Butler, Mary I.; Mörkl, Sabrina; Sandhu, Kiran V.
- The Canadian Journal of Psychiatry, Vol. 64, Issue 11
The occurrence of ESBL-producing Escherichia coli carrying aminoglycoside resistance genes in urinary tract infections in Saudi Arabia
journal, January 2017
- Alyamani, Essam J.; Khiyami, Anamil M.; Booq, Rayan Y.
- Annals of Clinical Microbiology and Antimicrobials, Vol. 16, Issue 1
The gut microbiome of horses: current research on equine enteral microbiota and future perspectives
journal, November 2019
- Kauter, Anne; Epping, Lennard; Semmler, Torsten
- Animal Microbiome, Vol. 1, Issue 1
Expression of DnaK and HtrA genes under high temperatures and their impact on thermotolerance of a Salmonella serotype isolated from tahini product
journal, October 2019
- Gaafar, Reda M.; Hamouda, Marwa M.; El-Dougdoug, Khalid A.
- Journal of Genetic Engineering and Biotechnology, Vol. 17, Issue 1
Antimicrobial resistance surveillance among gram-negative bacterial isolates from patients in hospitals in Khartoum State, Sudan
journal, January 2019
- Elbadawi, Hana Salaheldin; Elhag, Kamal Mustafa; Mahgoub, Elsheikh
- F1000Research, Vol. 8
Rapid detection of periprosthetic joint infection using a combination of 16s rDNA polymerase chain reaction and lateral flow immunoassay: A Pilot Study
journal, January 2018
- Janz, V.; Schoon, J.; Morgenstern, C.
- Bone & Joint Research, Vol. 7, Issue 1
Species identification and molecular typing of human Brucella isolates from Kuwait
journal, August 2017
- Mustafa, Abu S.; Habibi, Nazima; Osman, Amr
- PLOS ONE, Vol. 12, Issue 8
Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification
journal, July 2019
- Rocca, María Florencia; Barrios, Rubén; Zintgraff, Jonathan
- PLOS ONE, Vol. 14, Issue 7
Rapid metagenomics analysis of EMS vehicles for monitoring pathogen load using nanopore DNA sequencing
journal, July 2019
- Sheahan, Taylor; Hakstol, Rhys; Kailasam, Senthilkumar
- PLOS ONE, Vol. 14, Issue 7
Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!
journal, June 2016
- Simões, Alexandra S.; Couto, Isabel; Toscano, Cristina
- Frontiers in Microbiology, Vol. 7
Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients
journal, July 2018
- Kitsios, Georgios D.; Fitch, Adam; Manatakis, Dimitris V.
- Frontiers in Microbiology, Vol. 9
Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation
journal, November 2018
- Dai, Dongjuan; Rhoads, William J.; Edwards, Marc A.
- Frontiers in Microbiology, Vol. 9
Sepsis: Precision-Based Medicine for Pregnancy and the Puerperium
journal, October 2019
- Greer, Orene; Shah, Nishel Mohan; Sriskandan, Shiranee
- International Journal of Molecular Sciences, Vol. 20, Issue 21
Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
journal, December 2019
- Winand, Raf; Bogaerts, Bert; Hoffman, Stefan
- International Journal of Molecular Sciences, Vol. 21, Issue 1
Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins
journal, April 2017
- Zhu, Yan; Hassan, Yousef; Lepp, Dion
- Toxins, Vol. 9, Issue 4
Phylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity
journal, November 2019
- Seribelli, Amanda Ap.; Gonzales, Júlia C.; de Almeida, Fernanda
- Brazilian Journal of Microbiology, Vol. 51, Issue 1
Isolation and characterization of Bacillus sp. strain BC01 from soil displaying potent antagonistic activity against plant and fish pathogenic fungi and bacteria
journal, December 2018
- Foysal, Md Javed; Lisa, Asura Khanam
- Journal of Genetic Engineering and Biotechnology, Vol. 16, Issue 2
Identification and Analysis of Informative Single Nucleotide Polymorphisms in 16S rRNA Gene Sequences of the Bacillus cereus Group
journal, August 2016
- Hakovirta, Janetta R.; Prezioso, Samantha; Hodge, David
- Journal of Clinical Microbiology, Vol. 54, Issue 11
A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing.
text, January 2020
- Neuenschwander, Stefan Moritz; Terrazos Miani, Miguel Angel; Amlang, Heiko
- American Society for Microbiology
Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets
journal, May 2020
- F. Escapa, Isabel; Huang, Yanmei; Chen, Tsute
- Microbiome, Vol. 8, Issue 1
The gut microbiome of horses: current research on equine enteral microbiota and future perspectives
text, January 2019
- Kauter, Anne; Epping, Lennard; Semmler, Torsten
- Robert Koch-Institut
A Sample-to-Report Solution for Taxonomic Identification of Cultured Bacteria in the Clinical Setting Based on Nanopore Sequencing
journal, May 2020
- Neuenschwander, Stefan Moritz; Terrazos Miani, Miguel Angel; Amlang, Heiko
- Journal of Clinical Microbiology, Vol. 58, Issue 6
Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION™ nanopore sequencer
journal, January 2019
- Kai, Shinichi; Matsuo, Yoshiyuki; Nakagawa, So
- FEBS Open Bio, Vol. 9, Issue 3
Neisseria meningitidis and cytomegalovirus simultaneous detection in the filmarray meningitis/encephalitis panel and its clinical relevance
journal, January 2019
- Sorek, Nadav; Ashkenazi, Shai; Livni, Gilat
- IDCases, Vol. 17
RE: ‘Streptococcus pluranimalium : A novel human pathogen?’
journal, January 2017
- Pongratz, Peter; Ebbers, Meinolf; Geerdes-Fenge, Hilte
- International Journal of Surgery Case Reports, Vol. 41
Fecal microbial characterization of hospitalized patients with suspected infectious diarrhea shows significant dysbiosis
journal, April 2017
- Braun, Tzipi; Di Segni, Ayelet; BenShoshan, Marina
- Scientific Reports, Vol. 7, Issue 1
Detection of 16S rRNA and KPC Genes from Complex Matrix Utilizing a Molecular Inversion Probe Assay for Next-Generation Sequencing
journal, February 2018
- Stefan, Christopher P.; Hall, Adrienne T.; Minogue, Timothy D.
- Scientific Reports, Vol. 8, Issue 1
Identification of microbiota in peri-implantitis pockets by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry
journal, January 2019
- Yeh, Hwey-Chin; Lu, Jang-Jih; Chang, Shih-Cheng
- Scientific Reports, Vol. 9, Issue 1
Restriction Profiling of 23S Microheterogenic Ribosomal Repeats for Detection and Characterizing ofE. coliand Their Clonal, Pathogenic, and Phylogroups
journal, January 2015
- Jayasree Rajagopalan Nair, Parvathi; Singh, Sunita
- Journal of Pathogens, Vol. 2015
Facile aerobic construction of iron based ferromagnetic nanostructures by a novel microbial nanofactory isolated from tropical freshwater wetlands
journal, October 2017
- Jacob, Patricia Jayshree; Masarudin, Mas Jaffri; Hussein, Mohd Zobir
- Microbial Cell Factories, Vol. 16, Issue 1
The occurrence of ESBL-producing Escherichia coli carrying aminoglycoside resistance genes in urinary tract infections in Saudi Arabia
journal, January 2017
- Alyamani, Essam J.; Khiyami, Anamil M.; Booq, Rayan Y.
- Annals of Clinical Microbiology and Antimicrobials, Vol. 16, Issue 1
Expression of DnaK and HtrA genes under high temperatures and their impact on thermotolerance of a Salmonella serotype isolated from tahini product
journal, October 2019
- Gaafar, Reda M.; Hamouda, Marwa M.; El-Dougdoug, Khalid A.
- Journal of Genetic Engineering and Biotechnology, Vol. 17, Issue 1
Species identification and molecular typing of human Brucella isolates from Kuwait
journal, August 2017
- Mustafa, Abu S.; Habibi, Nazima; Osman, Amr
- PLOS ONE, Vol. 12, Issue 8
Utility of platforms Viteks MS and Microflex LT for the identification of complex clinical isolates that require molecular methods for their taxonomic classification
journal, July 2019
- Rocca, María Florencia; Barrios, Rubén; Zintgraff, Jonathan
- PLOS ONE, Vol. 14, Issue 7
Dangerous passengers: Multidrug-resistant bacteria on hands and mobile phones.
text, January 2019
- Martina, Pablo F.; Martinez, Mónica; Centeno, Celia K.
- Journal of Preventive Medicine and Hygiene
Dirty Money on Holy Ground: Isolation of Potentially Pathogen-ic Bacteria and Fungi on Money Collected from Church Offer-ings
journal, November 2019
- Abia, Akebe Luther King; Ubomba-Jaswa, Eunice
- Iranian Journal of Public Health
The fallopian tube microbiome: implications for reproductive health
journal, April 2018
- Pelzer, Elise S.; Willner, Dana; Buttini, Melissa
- Oncotarget, Vol. 9, Issue 30
Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!
journal, June 2016
- Simões, Alexandra S.; Couto, Isabel; Toscano, Cristina
- Frontiers in Microbiology, Vol. 7
Identification of Variable Traits among the Methicillin Resistant and Sensitive Coagulase Negative Staphylococci in Milk Samples from Mastitic Cows in India
journal, July 2017
- Mahato, Sudipta; Mistry, Hiral U.; Chakraborty, Shalini
- Frontiers in Microbiology, Vol. 8
Respiratory Microbiome Profiling for Etiologic Diagnosis of Pneumonia in Mechanically Ventilated Patients
journal, July 2018
- Kitsios, Georgios D.; Fitch, Adam; Manatakis, Dimitris V.
- Frontiers in Microbiology, Vol. 9
Shotgun Metagenomics Reveals Taxonomic and Functional Shifts in Hot Water Microbiome Due to Temperature Setting and Stagnation
journal, November 2018
- Dai, Dongjuan; Rhoads, William J.; Edwards, Marc A.
- Frontiers in Microbiology, Vol. 9
A Comparison of Three Different Bioinformatics Analyses of the 16S–23S rRNA Encoding Region for Bacterial Identification
journal, April 2019
- Peker, Nilay; Garcia-Croes, Sharron; Dijkhuizen, Brigitte
- Frontiers in Microbiology, Vol. 10
The Human Microbiota and Obesity: A Literature Systematic Review of In Vivo Models and Technical Approaches
journal, November 2018
- Carrera-Quintanar, Lucrecia; Ortuño-Sahagún, Daniel; Franco-Arroyo, Noel
- International Journal of Molecular Sciences, Vol. 19, Issue 12
Sepsis: Precision-Based Medicine for Pregnancy and the Puerperium
journal, October 2019
- Greer, Orene; Shah, Nishel Mohan; Sriskandan, Shiranee
- International Journal of Molecular Sciences, Vol. 20, Issue 21
Targeting the 16S rRNA Gene for Bacterial Identification in Complex Mixed Samples: Comparative Evaluation of Second (Illumina) and Third (Oxford Nanopore Technologies) Generation Sequencing Technologies
journal, December 2019
- Winand, Raf; Bogaerts, Bert; Hoffman, Stefan
- International Journal of Molecular Sciences, Vol. 21, Issue 1
Strategies and Methodologies for Developing Microbial Detoxification Systems to Mitigate Mycotoxins
journal, April 2017
- Zhu, Yan; Hassan, Yousef; Lepp, Dion
- Toxins, Vol. 9, Issue 4
First-tier detection of intragenomic 16S rRNA gene variation in culturable endophytic bacteria from cacao seeds
journal, November 2019
- da Silva, Cleiziane Bispo; dos Santos, Hellen Ribeiro Martins; Marbach, Phellippe Arthur Santos
- PeerJ, Vol. 7