1
|
Bolden N, Mell JC, Logan JB, Planet PJ. Phylogenomics of nontuberculous mycobacteria respiratory infections in people with cystic fibrosis. Paediatr Respir Rev 2023; 46:63-70. [PMID: 36828670 PMCID: PMC10659050 DOI: 10.1016/j.prrv.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Nontuberculous mycobacteria (NTM) can cause severe pulmonary disease in people with cystic fibrosis (pwCF). These infections present unique challenges for diagnosis and treatment, prompting a recent interest in understanding NTM transmission and pathogenesis during chronic infection. Major gaps remain in our knowledge regarding basic pathogenesis, immune evasion strategies, population dynamics, recombination potential, and the evolutionary implications of host and antibiotic pressures of long-term NTM infections in pwCF. Phylogenomic techniques have emerged as an important tool for tracking global patterns of transmission and are beginning to be used to ask fundamental biological questions about adaptation to the host during pathogenesis. In this review, we discuss the burden of NTM lung disease (NTM-LD), highlight the use of phylogenomics in NTM research, and address the clinical implications associated with these studies.
Collapse
Affiliation(s)
- Nicholas Bolden
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Joshua Chang Mell
- Center for Genomic Sciences, Drexel University College of Medicine, Philadelphia, PA, United States; Department of Microbiology & Immunology, Drexel University, Philadelphia, PA, United States.
| | - Jennifer Bouso Logan
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pulmonary Medicine and Cystic Fibrosis Center, Lehigh Valley Reilly Children's Hospital, PA, United States.
| | - Paul J Planet
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Comparative Genomics, American Museum of Natural History, New York, NY, United States.
| |
Collapse
|
2
|
Allen JP, Snitkin E, Pincus NB, Hauser AR. Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning. Trends Microbiol 2021; 29:621-633. [PMID: 33455849 PMCID: PMC8187264 DOI: 10.1016/j.tim.2020.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022]
Abstract
The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity within many bacterial species. Awareness of this genetic heterogeneity has corresponded with a greater appreciation of intraspecies variation in virulence. A number of comparative genomic strategies have been developed to link these genotypic and pathogenic differences with the aim of discovering novel virulence factors. Here, we review recent advances in comparative genomic approaches to identify bacterial virulence determinants, with a focus on genome-wide association studies and machine learning.
Collapse
Affiliation(s)
- Jonathan P Allen
- Department of Microbiology and Immunology, Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA.
| | - Evan Snitkin
- Department of Microbiology and Immunology, Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nathan B Pincus
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA; Department of Medicine/Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
3
|
Sheka D, Alabi N, Gordon PMK. Oxford nanopore sequencing in clinical microbiology and infection diagnostics. Brief Bioinform 2021; 22:6109725. [PMID: 33483726 DOI: 10.1093/bib/bbaa403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/26/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Extended turnaround times and large economic costs hinder the usage of currently applied screening methods for bacterial pathogen identification (ID) and antimicrobial susceptibility testing. This review provides an overview of current detection methods and their usage in a clinical setting. Issues of timeliness and cost could soon be circumvented, however, with the emergence of detection methods involving single molecule sequencing technology. In the context of bringing diagnostics closer to the point of care, we examine the current state of Oxford Nanopore Technologies (ONT) products and their interaction with third-party software/databases to assess their capabilities for ID and antimicrobial resistance (AMR) prediction. We outline and discuss a potential diagnostic workflow, enumerating (1) rapid sample prep kits, (2) ONT hardware/software and (3) third-party software and databases to improve the cost, accuracy and turnaround times for ID and AMR. Multiple studies across a range of infection types support that the speed and accuracy of ONT sequencing is now such that established ID and AMR prediction tools can be used on its outputs, and so it can be harnessed for near real time, close to the point-of-care diagnostics in common clinical circumstances.
Collapse
Affiliation(s)
- Dropen Sheka
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nikolay Alabi
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Paul M K Gordon
- Cumming School of Medicine Centre for Health Genomics and Informatics, University of Calgary
| |
Collapse
|
4
|
Brown AC. Whole-Genome Sequencing of Mycobacterium tuberculosis Directly from Sputum Samples. Methods Mol Biol 2021; 2314:459-480. [PMID: 34235666 DOI: 10.1007/978-1-0716-1460-0_20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing pathogens, such as Mycobacterium tuberculosis. However, clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variations found within M. tuberculosis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of M. tuberculosis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
Collapse
Affiliation(s)
- Amanda Claire Brown
- Oxford Gene Technology, Oxford, UK. .,Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL), College Station, TX, USA. .,Department of Animal Science, Texas A&M University, Kleberg Center, College Station, TX, USA.
| |
Collapse
|
5
|
Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
Collapse
|
6
|
Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
Collapse
Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
| |
Collapse
|
7
|
Weldatsadik R, Datta N, Kolmeder C, Vuopio J, Kere J, Wilkman S, Flatt J, Vuento R, Haapasalo K, Keskitalo S, Varjosalo M, Jokiranta T. Pool-seq driven proteogenomic database for Group G Streptococcus. J Proteomics 2019; 201:84-92. [DOI: 10.1016/j.jprot.2019.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/29/2019] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
|
8
|
Nadon C, Van Walle I, Gerner-Smidt P, Campos J, Chinen I, Concepcion-Acevedo J, Gilpin B, Smith AM, Man Kam K, Perez E, Trees E, Kubota K, Takkinen J, Nielsen EM, Carleton H. PulseNet International: Vision for the implementation of whole genome sequencing (WGS) for global food-borne disease surveillance. ACTA ACUST UNITED AC 2017; 22:30544. [PMID: 28662764 PMCID: PMC5479977 DOI: 10.2807/1560-7917.es.2017.22.23.30544] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/11/2017] [Indexed: 11/21/2022]
Abstract
PulseNet International is a global network dedicated to laboratory-based surveillance for food-borne diseases. The network comprises the national and regional laboratory networks of Africa, Asia Pacific, Canada, Europe, Latin America and the Caribbean, the Middle East, and the United States. The PulseNet International vision is the standardised use of whole genome sequencing (WGS) to identify and subtype food-borne bacterial pathogens worldwide, replacing traditional methods to strengthen preparedness and response, reduce global social and economic disease burden, and save lives. To meet the needs of real-time surveillance, the PulseNet International network will standardise subtyping via WGS using whole genome multilocus sequence typing (wgMLST), which delivers sufficiently high resolution and epidemiological concordance, plus unambiguous nomenclature for the purposes of surveillance. Standardised protocols, validation studies, quality control programmes, database and nomenclature development, and training should support the implementation and decentralisation of WGS. Ideally, WGS data collected for surveillance purposes should be publicly available, in real time where possible, respecting data protection policies. WGS data are suitable for surveillance and outbreak purposes and for answering scientific questions pertaining to source attribution, antimicrobial resistance, transmission patterns, and virulence, which will further enable the protection and improvement of public health with respect to food-borne disease.
Collapse
Affiliation(s)
- Celine Nadon
- Public Health Agency of Canada, National Microbiology Laboratory, Canada.,These authors contributed equally to this work
| | - Ivo Van Walle
- These authors contributed equally to this work.,European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Josefina Campos
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | - Isabel Chinen
- National Institute of Infectious Diseases "Dr Carlos G. Malbran", Argentina
| | | | - Brent Gilpin
- Institute of Environmental Science and Research Limited; Christchurch, New Zealand
| | | | - Kai Man Kam
- Chinese University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Enrique Perez
- Pan American Health Organization/World Health Organization, Washington, DC, United States
| | - Eija Trees
- Centers for Disease Control and Prevention, United States
| | - Kristy Kubota
- Association of Public Health Laboratories, United States
| | - Johanna Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | -
- The members of the FWD-NEXT Expert Panel are listed at the end of the article
| |
Collapse
|
9
|
Motro Y, Moran-Gilad J. Next-generation sequencing applications in clinical bacteriology. BIOMOLECULAR DETECTION AND QUANTIFICATION 2017; 14:1-6. [PMID: 29255684 PMCID: PMC5727008 DOI: 10.1016/j.bdq.2017.10.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 10/01/2017] [Accepted: 10/12/2017] [Indexed: 12/15/2022]
Abstract
With the rapid advances in next generation sequencing (NGS) technologies, clinical and public health microbiology laboratories are increasingly adopting NGS technology in their workflows into their existing diagnostic cycles. In this bacteriology focused review, we review aspects and considerations for applying NGS in the clinical microbiology settings, and highlight the impact of such implementation on the analytical and post-analytical stages of diagnosis
Collapse
Affiliation(s)
- Yair Motro
- Department of Health System Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Jacob Moran-Gilad
- Department of Health System Management, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- Public Health Services, Ministry of Health, Jerusalem, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
- Corresponding author at: Dept. of Health Systems Management, Faculty of Health Sciences, Ben-Gurion University of the Negev POB 653, Beer-Sheva, 8410501, Israel.
| |
Collapse
|
10
|
Carkaci D, Højholt K, Nielsen XC, Dargis R, Rasmussen S, Skovgaard O, Fuursted K, Andersen PS, Stegger M, Christensen JJ. Genomic characterization, phylogenetic analysis, and identification of virulence factors in Aerococcus sanguinicola and Aerococcus urinae strains isolated from infection episodes. Microb Pathog 2017; 112:327-340. [PMID: 28943151 DOI: 10.1016/j.micpath.2017.09.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 11/18/2022]
Abstract
Aerococcus sanguinicola and Aerococcus urinae are emerging pathogens in clinical settings mostly being causative agents of urinary tract infections (UTIs), urogenic sepsis and more seldomly complicated infective endocarditis (IE). Limited knowledge exists concerning the pathogenicity of these two species. Eight clinical A. sanguinicola (isolated from 2009 to 2015) and 40 clinical A. urinae (isolated from 1984 to 2015) strains from episodes of UTIs, bacteremia, and IE were whole-genome sequenced (WGS) to analyze genomic diversity and characterization of virulence genes involved in the bacterial pathogenicity. A. sanguinicola genome sizes were 2.06-2.12 Mb with 47.4-47.6% GC-contents, and 1783-1905 genes were predicted whereof 1170 were core-genes. In case of A. urinae strains, the genome sizes were 1.93-2.44 Mb with 41.6-42.6% GC-contents, and 1708-2256 genes of which 907 were core-genes. Marked differences were observed within A. urinae strains with respect to the average genome sizes, number and sequence identity of core-genes, proteome conservations, phylogenetic analysis, and putative capsular polysaccharide (CPS) loci sequences. Strains of A. sanguinicola showed high degree of homology. Phylogenetic analyses showed the 40 A. urinae strains formed two clusters according to two time periods: 1984-2004 strains and 2010-2015 strains. Genes that were homologs to virulence genes associated with bacterial adhesion and antiphagocytosis were identified by aligning A. sanguinicola and A. urinae pan- and core-genes against Virulence Factors of Bacterial Pathogens (VFDB). Bacterial adherence associated gene homologs were present in genomes of A. sanguinicola (htpB, fbpA, lmb, and ilpA) and A. urinae (htpB, lap, lmb, fbp54, and ilpA). Fifteen and 11-16 CPS gene homologs were identified in genomes of A. sanguinicola and A. urinae strains, respectively. Analysis of these genes identified one type of putative CPS locus within all A. sanguinicola strains. In A. urinae genomes, five different CPS loci types were identified with variations in CPS locus sizes, genetic content, and structural organization. In conclusion, this is the first study dealing with WGS and comparative genomics of clinical A. sanguinicola and A. urinae strains from episodes of UTIs, bacteremia, and IE. Gene homologs associated with antiphagocytosis and bacterial adherence were identified and genetic variability was observed within A. urinae genomes. These findings contribute with important knowledge and basis for future molecular and experimental pathogenicity study of UTIs, bacteremia, and IE causing A. sanguinicola and A. urinae strains.
Collapse
Affiliation(s)
- Derya Carkaci
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark; Department of Science and Environment, Roskilde University, Roskilde, Denmark; Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark.
| | - Katrine Højholt
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark; Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | | | - Rimtas Dargis
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark.
| | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.
| | - Kurt Fuursted
- Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark.
| | - Paal Skytt Andersen
- Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark; Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Marc Stegger
- Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark.
| | - Jens Jørgen Christensen
- Department of Clinical Microbiology, Slagelse Hospital, Slagelse, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
11
|
Brown AC, Christiansen MT. Whole-Genome Enrichment Using RNA Probes and Sequencing of Chlamydia trachomatis Directly from Clinical Samples. Methods Mol Biol 2017; 1616:1-22. [PMID: 28600759 DOI: 10.1007/978-1-4939-7037-7_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow-growing, or obligate intracellular pathogens, such as Chlamydia trachomatis. However clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a non-mutagenic approach, we can capture all known variations found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
Collapse
Affiliation(s)
- Amanda Claire Brown
- Oxford Gene Technology, Oxford, OX5 1PF, UK.
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA.
| | | |
Collapse
|
12
|
Shelburne SA, Ajami NJ, Chibucos MC, Beird HC, Tarrand J, Galloway-Peña J, Albert N, Chemaly RF, Ghantoji SS, Marsh L, Pemmaraju N, Andreeff M, Shpall EJ, Wargo JA, Rezvani K, Alousi A, Bruno VM, Futreal PA, Petrosino JF, Kontoyiannis DP. Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis. PLoS One 2015; 10:e0139851. [PMID: 26556047 PMCID: PMC4640583 DOI: 10.1371/journal.pone.0139851] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/17/2015] [Indexed: 12/19/2022] Open
Abstract
Disease can be conceptualized as the result of interactions between infecting microbe and holobiont, the combination of a host and its microbial communities. It is likely that genomic variation in the host, infecting microbe, and commensal microbiota are key determinants of infectious disease clinical outcomes. However, until recently, simultaneous, multiomic investigation of infecting microbe and holobiont components has rarely been explored. Herein, we characterized the infecting microbe, host, micro- and mycobiomes leading up to infection onset in a leukemia patient that developed invasive mucormycosis. We discovered that the patient was infected with a strain of the recently described Mucor velutinosus species which we determined was hypervirulent in a Drosophila challenge model and has a predisposition for skin dissemination. After completing the infecting M. velutinosus genome and genomes from four other Mucor species, comparative pathogenomics was performed and assisted in identifying 66 M. velutinosus-specific putatively secreted proteins, including multiple novel secreted aspartyl proteinases which may contribute to the unique clinical presentation of skin dissemination. Whole exome sequencing of the patient revealed multiple non-synonymous polymorphisms in genes critical to control of fungal proliferation, such as TLR6 and PTX3. Moreover, the patient had a non-synonymous polymorphism in the NOD2 gene and a missense mutation in FUT2, which have been linked to microbial dysbiosis and microbiome diversity maintenance during physiologic stress, respectively. In concert with host genetic polymorphism data, the micro- and mycobiome analyses revealed that the infection developed amid a dysbiotic microbiome with low α-diversity, dominated by staphylococci. Additionally, longitudinal mycobiome data showed that M. velutinosus DNA was detectable in oral samples preceding disease onset. Our genome-level study of the host-infecting microbe-commensal triad extends the concept of personalized genomic medicine to the holobiont-infecting microbe interface thereby offering novel opportunities for using synergistic genetic methods to increase understanding of infectious diseases pathogenesis and clinical outcomes.
Collapse
Affiliation(s)
- Samuel A. Shelburne
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nadim J. Ajami
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Marcus C. Chibucos
- Department of Microbiology & Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hannah C. Beird
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeffrey Tarrand
- Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jessica Galloway-Peña
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Nathan Albert
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Roy F. Chemaly
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Shashank S. Ghantoji
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lisa Marsh
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Naveen Pemmaraju
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Michael Andreeff
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jennifer A. Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Amin Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Vincent M. Bruno
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Phillip A. Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- The Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dimitrios P. Kontoyiannis
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
13
|
Hugon P, Dufour JC, Colson P, Fournier PE, Sallah K, Raoult D. A comprehensive repertoire of prokaryotic species identified in human beings. THE LANCET. INFECTIOUS DISEASES 2015; 15:1211-1219. [PMID: 26311042 DOI: 10.1016/s1473-3099(15)00293-5] [Citation(s) in RCA: 197] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 02/17/2015] [Accepted: 02/27/2015] [Indexed: 02/07/2023]
Abstract
The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.
Collapse
Affiliation(s)
- Perrine Hugon
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Jean-Charles Dufour
- Assistance Publique des Hôpitaux de Marseille, BioSTIC, Pôle de Santé Publique, Marseille, France; Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Philippe Colson
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Pierre-Edouard Fournier
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Kankoe Sallah
- Aix-Marseille Université, UMR912 SESSTIM (AMU-INSERM-IRD), Marseille, France
| | - Didier Raoult
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
| |
Collapse
|
14
|
The Resistant-Population Cutoff (RCOFF): a New Concept for Improved Characterization of Antimicrobial Susceptibility Patterns of Non-Wild-Type Bacterial Populations. J Clin Microbiol 2015; 53:1806-11. [PMID: 25762769 DOI: 10.1128/jcm.03505-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 01/11/2015] [Indexed: 11/20/2022] Open
Abstract
This study aimed to determine resistant-population cutoffs (RCOFFs) to allow for improved characterization of antimicrobial susceptibility patterns in bacterial populations. RCOFFs can complement epidemiological cutoff (ECOFF)-based settings of clinical breakpoints (CBPs) by systematically describing the correlation between non-wild-type and wild-type populations. We illustrate this concept by describing three paradigmatic examples of wild-type and non-wild-type Escherichia coli populations from our clinical strain database of disk diffusion diameters. The statistical determination of RCOFFs and ECOFFs and their standardized applications in antimicrobial susceptibility testing (AST) facilitates the assignment of isolates to wild-type or non-wild-type populations. This should improve the correlation of in vitro AST data and distinct antibiotic resistance mechanisms with clinical outcome facilitating the setting and validation of CBPs.
Collapse
|
15
|
Christiansen MT, Brown AC, Kundu S, Tutill HJ, Williams R, Brown JR, Holdstock J, Holland MJ, Stevenson S, Dave J, Tong CYW, Einer-Jensen K, Depledge DP, Breuer J. Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples. BMC Infect Dis 2014; 14:591. [PMID: 25388670 PMCID: PMC4233057 DOI: 10.1186/s12879-014-0591-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/27/2014] [Indexed: 12/30/2022] Open
Abstract
Background Chlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases of sexually transmitted infections annually. Whole-genome sequencing is a powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The objective of this study was to perform whole-genome enrichment and sequencing of C. trachomatis directly from clinical samples. Methods C. trachomatis positive samples comprising seven vaginal swabs and three urine samples were sequenced without prior in vitro culture in addition to nine cultured C. trachomatis samples, representing different serovars. A custom capture RNA bait set, that captures all known diversity amongst C. trachomatis genomes, was used in a whole-genome enrichment step during library preparation to enrich for C. trachomatis DNA. All samples were sequenced on the MiSeq platform. Results Full length C. trachomatis genomes (>95-100% coverage of a reference genome) were successfully generated for eight of ten clinical samples and for all cultured samples. The proportion of reads mapping to C. trachomatis and the mean read depth across each genome were strongly linked to the number of bacterial copies within the original sample. Phylogenetic analysis confirmed the known population structure and the data showed potential for identification of minority variants and mutations associated with antimicrobial resistance. The sensitivity of the method was >10-fold higher than other reported methodologies. Conclusions The combination of whole-genome enrichment and deep sequencing has proven to be a non-mutagenic approach, capturing all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature. Electronic supplementary material The online version of this article (doi:10.1186/s12879-014-0591-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mette T Christiansen
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Amanda C Brown
- Oxford Gene Technology, Begbroke, Oxfordshire, OX5 1PF, UK. .,Present address: Department of Microbiology and Immunology, Cornell University, Ithaca, NY, 14853, USA.
| | - Samit Kundu
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK. .,School of Human and Life Sciences, Canterbury Christchurch University, Canterbury, Kent, CT1 1QU, UK.
| | - Helena J Tutill
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Rachel Williams
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | | | | | - Martin J Holland
- London School of Hygiene and Tropical Medicine (LSHTM), London, WC1E 7HT, UK.
| | - Simon Stevenson
- University College London Hospital (UCLH), London, WC1E 6DE, UK.
| | | | | | | | - Daniel P Depledge
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| | - Judith Breuer
- Division of Infection and Immunity University College London (UCL), London, WC1E 6BT, UK.
| |
Collapse
|
16
|
Long SW, Olsen RJ, Mehta SC, Palzkill T, Cernoch PL, Perez KK, Musick WL, Rosato AE, Musser JM. PBP2a mutations causing high-level Ceftaroline resistance in clinical methicillin-resistant Staphylococcus aureus isolates. Antimicrob Agents Chemother 2014; 58:6668-74. [PMID: 25155594 PMCID: PMC4249384 DOI: 10.1128/aac.03622-14] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/16/2014] [Indexed: 12/25/2022] Open
Abstract
Ceftaroline is the first member of a novel class of cephalosporins approved for use in the United States. Although prior studies have identified eight ceftaroline-resistant methicillin-resistant Staphylococcus aureus (MRSA) isolates in Europe and Asia with MICs ranging from 4 to 8 mg/liter, high-level resistance to ceftaroline (>32 mg/liter) has not been described in MRSA strains isolated in the United States. We isolated a ceftaroline-resistant (MIC > 32 mg/liter) MRSA strain from the blood of a cystic fibrosis patient and five MRSA strains from the respiratory tract of this patient. Whole-genome sequencing identified two amino acid-altering mutations uniquely present in the ceftaroline-binding pocket of the transpeptidase region of penicillin-binding protein 2a (PBP2a) in ceftaroline-resistant isolates. Biochemical analyses and the study of isogenic mutant strains confirmed that these changes caused ceftaroline resistance. Thus, we identified the molecular mechanism of ceftaroline resistance in the first MRSA strain with high-level ceftaroline resistance isolated in the United States.
Collapse
Affiliation(s)
- S Wesley Long
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Randall J Olsen
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Shrenik C Mehta
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology, Baylor College of Medicine, Houston, Texas, USA
| | - Patricia L Cernoch
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - Katherine K Perez
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - William L Musick
- Department of Pharmacy, Houston Methodist Hospital, Houston, Texas, USA
| | - Adriana E Rosato
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| | - James M Musser
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Hospital and Houston Methodist Research Institute, Houston, Texas, USA
| |
Collapse
|
17
|
Steiner A, Stucki D, Coscolla M, Borrell S, Gagneux S. KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes. BMC Genomics 2014; 15:881. [PMID: 25297886 PMCID: PMC4197298 DOI: 10.1186/1471-2164-15-881] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 10/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-throughput DNA sequencing produces vast amounts of data, with millions of short reads that usually have to be mapped to a reference genome or newly assembled. Both reference-based mapping and de novo assembly are computationally intensive, generating large intermediary data files, and thus require bioinformatics skills that are often lacking in the laboratories producing the data. Moreover, many research and practical applications in microbiology require only a small fraction of the whole genome data. RESULTS We developed KvarQ, a new tool that directly scans fastq files of bacterial genome sequences for known variants, such as single nucleotide polymorphisms (SNP), bypassing the need of mapping all sequencing reads to a reference genome and de novo assembly. Instead, KvarQ loads "testsuites" that define specific SNPs or short regions of interest in a reference genome, and directly synthesizes the relevant results based on the occurrence of these markers in the fastq files. KvarQ has a versatile command line interface and a graphical user interface. KvarQ currently ships with two "testsuites" for Mycobacterium tuberculosis, but new "testsuites" for other organisms can easily be created and distributed. In this article, we demonstrate how KvarQ can be used to successfully detect all main drug resistance mutations and phylogenetic markers in 880 bacterial whole genome sequences. The average scanning time per genome sequence was two minutes. The variant calls of a subset of these genomes were validated with a standard bioinformatics pipeline and revealed >99% congruency. CONCLUSION KvarQ is a user-friendly tool that directly extracts relevant information from fastq files. This enables researchers and laboratory technicians with limited bioinformatics expertise to scan and analyze raw sequencing data in a matter of minutes. KvarQ is open-source, and pre-compiled packages with a graphical user interface are available at http://www.swisstph.ch/kvarq.
Collapse
Affiliation(s)
| | | | | | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, Basel 4051, Switzerland.
| |
Collapse
|
18
|
Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study. J Clin Microbiol 2014; 52:4210-6. [PMID: 25253790 DOI: 10.1128/jcm.02164-14] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Large hospital-based clinical laboratories must be prepared to rapidly investigate potential infectious disease outbreaks. To challenge the ability of our molecular diagnostics laboratory to use whole-genome sequencing in a potential outbreak scenario and identify impediments to these efforts, we studied 84 invasive serotype emm59 group A streptococcus (GAS) strains collected in the United States. We performed a rapid-response exercise to the mock outbreak scenario using whole-genome sequencing, genome-wide transcript analysis, and mouse virulence studies. The protocol changes installed in response to the lessons learned were tested in a second iteration. The initial investigation was completed in 9 days. Whole-genome sequencing showed that the invasive infections were caused by multiple subclones of epidemic emm59 GAS strains likely spread to the United States from Canada. The phylogenetic tree showed a strong temporal-spatial structure with diversity in mobile genetic element content, features that are useful for identifying closely related strains and possible transmission events. The genome data informed the epidemiology, identifying multiple patients who likely acquired the organisms through direct person-to-person transmission. Transcriptome analysis unexpectedly revealed significantly altered expression of genes encoding a two-component regulator and the hyaluronic acid capsule virulence factor. Mouse infection studies confirmed a high-virulence capacity of these emm59 organisms. Whole-genome sequencing, coupled with transcriptome analysis and animal virulence studies, can be rapidly performed in a clinical environment to effectively contribute to patient care decisions and public health maneuvers.
Collapse
|
19
|
Deriving group A Streptococcus typing information from short-read whole-genome sequencing data. J Clin Microbiol 2014; 52:1871-6. [PMID: 24648555 DOI: 10.1128/jcm.00029-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Typing of group A Streptococcus (GAS) is crucial for infection control and epidemiology. While whole-genome sequencing (WGS) is revolutionizing the way that bacterial organisms are typed, it is necessary to provide backward compatibility with currently used typing schemas to facilitate comparisons and understanding of epidemiological trends. Here, we sequenced the genomes of 191 GAS isolates representing 42 different emm types and used bioinformatics tools to derive commonly used GAS typing information directly from the short-read WGS data. We show that emm typing and multilocus sequence typing can be achieved rapidly and efficiently using this approach, which also permits the determination of the presence or absence of genes associated with GAS tissue tropism. We also report on how the WGS data analysis was instrumental in identifying ambiguities present in the commonly used emm type database hosted by the U.S. Centers for Disease Control and Prevention.
Collapse
|
20
|
Abstract
Medical microbiology involves the identification of microorganisms for the diagnosis of infectious diseases and the assessment of likely response to specific therapeutic interventions. Major categories of organisms include bacteria, mycobacteria, fungi, viruses, and parasites. Microbiological methods combined with clinical symptoms, additional laboratory tests, and imaging techniques are used in combination to distinguish a true disease-associated infection from colonization with normal flora or other conditions, such as malignancies, inflammatory disorders, or autoimmune disorders, all of which have unique therapies and prognoses for the patient. Laboratories combine the use of traditional microscopy and culture methods, with a rapidly evolving set of molecular and proteomic techniques. Given the increase in immunocompromised patients due to an increase in transplantations, the human immunodeficiency virus epidemic, and the use of immunosuppressive agents to treat autoimmune disorders, diagnosis of microbial infections continues to be essential for many patients.
Collapse
|
21
|
Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic. Emerg Microbes Infect 2013; 2:e13. [PMID: 26038455 PMCID: PMC3630956 DOI: 10.1038/emi.2013.13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 01/15/2013] [Accepted: 02/07/2013] [Indexed: 01/06/2023]
Abstract
Analysis of microbial epidemics has been revolutionized by whole-genome sequencing. We recently sequenced the genomes of 601 type emm59 Group A Streptococcus (GAS) organisms responsible for an ongoing epidemic of invasive infections in Canada and some of the United States. The epidemic has been caused by the emergence of a genetically distinct, hypervirulent clone that has genetically diversified. The ease of obtaining genomic data contrasts with the relatively difficult task of translating them into insightful epidemiological information. Here, we sequenced the genomes of 90 additional invasive Canadian emm59 GAS organisms, including 80 isolated recently in 2010–2011. We used an improved bioinformatics pipeline designed to rapidly process and analyze whole-genome data and integrate strain metadata. We discovered that emm59 GAS organisms are undergoing continued multiclonal evolutionary expansion. Previously identified geographic patterns of strain dissemination are being diluted as mixing of subclones over time and space occurs. Our integrated data analysis strategy permits prompt and accurate mapping of the dissemination of bacterial organisms in an epidemic wave, permitting rapid generation of hypotheses that inform public health and virulence studies.
Collapse
|
22
|
A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol 2013; 51:1272-7. [PMID: 23345298 DOI: 10.1128/jcm.03237-12] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Next-generation sequencing technology is available to many clinical laboratories; however, it is not yet widely used in routine microbiology practice. To demonstrate the feasibility of using whole-genome sequencing in a routine clinical microbiology workflow, we sequenced the genome of every organism isolated in our laboratory for 1 day.
Collapse
|
23
|
Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012; 8:e1002824. [PMID: 22876174 PMCID: PMC3410874 DOI: 10.1371/journal.ppat.1002824] [Citation(s) in RCA: 396] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|