Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

Köser, Claudio U.; Ellington, Matthew J.; Cartwright, Edward; Gillespie, Stephen H.; Brown, Nicholas M.; Farrington, M.; Holden, Matthew T. G.; Dougan, Gordon; Bentley, Stephen D.; Parkhill, Julian; Peacock, Sharon J.

doi:10.1371/journal.ppat.1002824

Cited by 475 publications

(408 citation statements)

References 114 publications

Supporting

Mentioning

395

Contrasting

Unclassified

Order By: Relevance

Section: Discussionmentioning

confidence: 99%

“…WGS studies of bacteria are currently in a golden age, with many resources and much interest being dedicated to the area as a whole and especially to WGS applications for clinical problems [36][37][38]63 . However, when this initial excitement has passed, it will be Europe PMC Funders Author Manuscripts necessary to move into a more prosaic exploitation phase, which will require the construction of sustainable infrastructures -sustainable both intellectually (that is, the concept of relating WGS data to typing and taxonomy) and physically (that is, the use of inter-operable data sets that are archived in accessible databases).…”

Section: Discussionmentioning

confidence: 99%

“…This, in turn, depends on the particular question being addressed, as some questions require more discrimination among specimens than others. To use the clinical setting as an example: very high resolution is necessary for the detection of outbreaks and the investigation of within-patient variation 43 ; lower resolution is required to determine the membership of a particular clonal complex or lineage 61 ; and even lower resolution is sufficient for determining the species causing an infection 37,62,63 . The gene-bygene approach is inherently hierarchical and scalable, as fewer genes can be used for lowerresolution typing, whereas higher levels of resolution can be attained by increasing the number of genes included in the analysis.…”

Section: Post-wgs Cataloguing Of Diversitymentioning

confidence: 99%

“…The need for effective data repositories is well recognized, as is evident from the interest generated by initiatives such as the Global Microbial Identifier [63][64][65] , and the power of such infrastructure is illustrated by the success of the 16S rRNA sequence and MLST databases 20,62 . For example, there are many MLST databases available on a number of websites (see PubMLST, the MLST homepage, the MLST databases at the ERI, UCC (Environmental Research Institute, University College Cork, Ireland) and the Institut Pasteur MLST databases), and these databases enable data generated in different laboratories to be efficiently compared.…”

Section: Gene-by-gene Typing Infrastructurementioning

confidence: 99%

See 3 more Smart Citations

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

View full text Add to dashboard Cite

Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.Advances in nucleotide-sequencing technology have provided unparalleled access to the enormous genetic diversity that has accumulated in the bacterial domain during 3.5-4 billion years of evolution 1 . Numerous sets of whole-genome sequencing (WGS) data for bacterial isolates (BOX 1) are available 2 , and metagenomic studies using these technologies continue to reveal further, seemingly boundless, diversity in bacterial communities 3 . Faced with this plethora of information, microbiologists must develop structured means of describing this diversity and of linking phenotype and genotype, thereby facilitating an improved understanding of the microbiological world. Given that we have precise information on the function of only a very small proportion of bacterial genes, and no knowledge at all about most, this is a formidable, if extremely exciting, challenge.Here, we focus primarily on pathogenic bacteria, although the concepts discussed are applicable more widely to all bacteria and archaea. Bacterial pathogens played a crucial part in the development of experimental microbiology and remain the most intensively studied prokaryotes more than 100 years later 4 . Pathogens have emerged across the diversity of the bacterial -but, interestingly, not the archaeal -domain on many occasions and are both polyphyletic and highly diverse. Thus, although pathogens represent only a tiny subset of the bacterial world, the challenges faced by the clinical microbiology laboratory are representative of those faced by microbiology as a whole.Taxonomic and functional analyses are based on the observations that diversity among bacteria is not continuous and that distinct, stable types with particular properties exist 5 . These founding principles of microbiology 6 have been upheld by much subsequent research, but the study of such clusters remains largely descriptive, and the evolutionary mechanisms that led to cluster emergence and persistence remain incompletely understood 7,8 . Structuring is also evident within bacterial genomes, as diversity is unevenly distributed among genes Pre-WGS cataloguing of diversityA major advance in defining bacterial diversity was the proposal, by the late Carl Woese and colleagues, of a universal and 'natural' -that is, genealogical -classification system based on small-su...

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Post-wgs Cataloguing Of Diversitymentioning

confidence: 99%

Section: Gene-by-gene Typing Infrastructurementioning

confidence: 99%

See 2 more Smart Citations

MLST revisited: the gene-by-gene approach to bacterial genomics

et al. 2013

View full text Add to dashboard Cite

show abstract

“…All other molecular-based techniques, either DNA fragment based such as pulsed-field gel electrophoresis (PFGE) (Schwartz et al, 1983), amplified fragment length polymorphism (AFLP) (Vos et al, 1995), restric-204 Werner Ruppitsch tion fragment length polymorphism (RFLP), and random amplified polymorphic DNA (RAPD) or sequence based such as multi-locus sequence typing (MLST) (Maiden et al, 1998) , multi-virulence-locus sequence typing (MV-LST) (Zhang et al, 2004), and WGS (Köser et al, 2012) are more time consuming and more cost-intensive approaches (van Belkum et al, 2007;Köser et al, 2012). A disadvantage of the PCR-based method is the fact that for each target, you need a specific pair of primers.…”

Section: Pcr-based Typing Methodsmentioning

confidence: 99%

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

Ruppitsch

2016

Die Bodenkultur: Journal of Land Management, Food and Environment

View full text Add to dashboard Cite

SummaryConstant confrontations with microbial threats pose major challenges to human and animal health, agricultural and food production, and public safety. Identifying pathogenic bacteria (species) and tracking strains (by series of well-characterized isolates) to their sources are especially important in outbreak investigations. Compared to the identification of the species, the identification of the source and spread of microbial infections represents a major-and many times futile-challenge. This is due to the multitude of ways microorganisms can occur and spread within healthcare facilities and in the community; how, when, and where they can contaminate the complex nutrition chain, leading to natural and man-made outbreaks. Typing is the characterization of isolates or strains below species or subspecies level. Typing of bacterial isolates is an essential procedure to identify the microbe causing the illness or to track down an outbreak to the suspected source. In the genomic era, the introduction of molecular methods has largely replaced phenotypic methods and "molecular epidemiology" has emerged as a new discipline. The current molecular typing methods can be classified into three categories: (a) PCR-based methods, (b) DNA fragment analysis-based methods, and (c) DNA sequence-based methods, including the new exciting era of high-throughput genome sequencing. Keywords

show abstract

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

Ellington²,

et al. 2013

Self Cite

View full text Add to dashboard Cite

IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these. CONCLUSIONS AND RELEVANCE The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.

show abstract

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

Cited by 475 publications

References 114 publications

MLST revisited: the gene-by-gene approach to bacterial genomics

MLST revisited: the gene-by-gene approach to bacterial genomics

Molecular typing of bacteria for epidemiological surveillance and outbreak investigation / Molekulare Typisierung von Bakterien für die epidemiologische Überwachung und Ausbruchsabklärung

Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

Contact Info

Product

Resources

About