Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

Kohl, Thomas A.; Diel, Roland; Harmsen, Dag; Rothgänger, Jörg; Walter, Karen Meywald; Merker, Matthias; Weniger, Thomas; Niemann, Stefan

doi:10.1128/jcm.00567-14

Cited by 175 publications

(213 citation statements)

References 21 publications

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“…wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. After the introduction of WGS as a typing tool with high potential, gene-by-gene comparison of WGS data has been applied successfully for several species in outbreak settings (22)(23)(24)(25)(26)(27). To our knowledge, this large multicenter study is the first to apply wgMLST for typing of Enterobacteriaceae in nonoutbreak settings and to include a comprehensive evaluation of its performance in a large collection of isolates without a clear epidemiological link.…”

Section: Discussionmentioning

confidence: 99%

“…Another major advantage of this gene-by-gene allelic profiling method is the immediate and automated assignment of novel allele variants, which enables a standardized and universal nomenclature and is a prerequisite for successful interlaboratory exchange of data (46). Most studies on wgMLST have used the absolute number of allele differences to compare isolates, which is highly dependent on the number of targets that are compared (22,23,26,27). In the present study, differences in the numbers of targets compared were taken into account by defining genetic distance as the proportion of allele differences.…”

Section: Discussionmentioning

confidence: 99%

“…Whole-genome multilocus sequence typing (wgMLST) is a WGS-based typing method that extends MLST to the genome level (20). Today, such gene-bygene comparison of WGS data has been applied successfully for several species in outbreak settings, but data for Enterobacteriaceae and nonoutbreak settings are still limited (22)(23)(24)(25)(26)(27). The aim of this study was to develop representative wgMLST schemes for the Citation Kluytmans-van den Bergh MFQ, Rossen JWA, Bruijning-Verhagen PCJ, Bonten MJM, Friedrich AW, Vandenbroucke-Grauls CMJE, Willems RJL, Kluytmans JAJW, on behalf of the SoM Study Group.…”

mentioning

confidence: 99%

“…However, sequence conservation in housekeeping genes limits its discriminatory power and thus its use in outbreak investigations (16)(17)(18). Whole-genome sequencing (WGS) has emerged as an ultimate typing tool that fits any bacterial species, study type, and laboratory (19)(20)(21)(22)(23)(24)(25)(26)(27). Knowledge of the sequence of the entire genome, rather than of only a few loci, has greatly increased the precision of molecular epidemiologic data and allows its use in infection control, where questions of similarity of isolates focus on recently diverged isolates.…”

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confidence: 99%

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Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

et al. 2016

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e Molecular typing has become indispensable in the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings, but current methods are labor-intensive, are difficult to standardize, or have limited resolution. Whole-genome multilocus sequence typing (wgMLST) has emerged as a whole-genome sequencing (WGS)-based gene-by-gene typing method that may overcome these limitations and has been applied successfully for several species in outbreak settings. In this study, genus-, genetic-complex-, and species-specific wgMLST schemes were developed for Citrobacter spp., the Enterobacter cloacae complex, Escherichia coli, Klebsiella oxytoca, and Klebsiella pneumoniae and used to type a national collection of 1,798 extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) isolates obtained from patients in Dutch hospitals. Genus-, genetic-complex-, and species-specific thresholds for genetic distance that accurately distinguish between epidemiologically related and unrelated isolates were defined for Citrobacter spp., the E. cloacae complex, E. coli, and K. pneumoniae. wgMLST was shown to have higher discriminatory power and typeability than in silico MLST. In conclusion, the wgMLST schemes developed in this study facilitate high-resolution WGS-based typing of the most prevalent ESBL-producing species in clinical practice and may contribute to further elucidation of the complex epidemiology of antimicrobial-resistant Enterobacteriaceae. wgMLST opens up possibilities for the creation of a Web-accessible database for the global surveillance of ESBL-producing bacterial clones. The continuing global spread of extended-spectrum-beta-lactamase-producing Enterobacteriaceae (ESBL-E) constitutes a major public health threat in both health care and community settings (1-4). Extended-spectrum beta-lactamases (ESBL) confer resistance to the majority of beta-lactam antibiotics, including third-generation cephalosporins, which limits the options for antimicrobial therapy and results in increased morbidity and mortality and health care costs (5, 6). Infection control guidelines recommend prevention of the spread of ESBL-E in health care settings (7,8). Molecular typing has become an important tool in infection control, as it enables the detection of nosocomial transmission of bacterial pathogens and the identification of sources and routes of transmission in outbreak settings. Different molecular typing methods have been used, ranging from fingerprintbased methods, like pulsed-field gel electrophoresis (PFGE) and amplified fragment length polymorphism (AFLP), to sequencebased methods, like multilocus sequence typing (MLST) (9-11). Although widely adopted, PFGE is labor-intensive and difficult to standardize and has limited interlaboratory reproducibility (12)(13)(14). AFLP is less time-consuming than PFGE but may have lower discriminatory power for typing of Enterobacteriaceae (13, 15). MLST targets 7 or 8 housekeeping genes, depending on the Ent...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

et al. 2016

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“…The cgMLST methods address this problem by comparing only genes common to a set of bacterial isolates (2). These methods are now mature and have been applied successfully to the analysis of a number of bacterial outbreaks (8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21).Given the developments in WGS-based strain typing described above, there is much excitement about applying these methods to real-time hospital epidemiology, but the actual cost-benefit equation, the feasibility of achieving results on an actionable time scale, and the technical requirements for implementation in a "real world" clinical microbiology laboratory are difficult to study. In work published in this issue of the Journal of Clinical Microbiology, …”

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confidence: 99%

Commentary: Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

Dekker

Frank

2016

J Clin Microbiol

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M ultilocus sequencing typing (MLST), introduced by Maiden and colleagues in 1998, has come to represent one of the most widely used and successful molecular methods for strainlevel classification of bacterial isolates (1). MLST schemes work by indexing sequence variation in a small set of housekeeping genes to a numerical classification system. Each novel sequence occurring at any of the selected loci is named as a unique numbered allele, and the profile of a given isolate is specified by the numbers representing the allelic composition. Each combination of alleles is assigned a unique sequence type (ST), and STs, in turn, can be grouped into higher levels of classification (2, 3). The ability of MLST to resolve closely related strains is limited in principle by the absolute sequence diversity present in the loci covered by the scheme and by the manner in which this sequence diversity distributes across the population to be classified. As MLST schemes require conserved PCR primer binding sites, the targets must also be sufficiently conserved so that the method works robustly, and this puts limits on the resolution of classical MLST (3). MLST schemes have now been developed for Ͼ100 genera and species, and continuously updated databases are maintained by the University of Oxford, United Kingdom (pubmlst.org), Imperial College London, London, United Kingdom (http://www.mlst.net/), and others.Classical MLST analysis, developed to be compatible with Sanger sequencing methods, is based on 400-to-500-nucleotide segments of (usually) seven genes, encompassing Ͻ0.2% of the bacterial genome in many cases (3). Advances in whole-genome sequencing (WGS) and the availability of a large number of assembled bacterial genomes have made possible new approaches to strain-and clone-level epidemiologic tracking of isolates, including the ability to apply MLST schemes on a genome-wide scale. Inference of clonal relationships from the comparison of wholegenome sequences for the purpose of epidemiologic investigations can involve a bit more subtlety than classical MLST analysis, however, and there are abundant opportunities for drawing incorrect conclusions. Perhaps the simplest of the many available approaches is that of direct-alignment-based (single nucleotide polymorphism [SNP]-based) phylogenetic analysis, often built on the underlying statistical assumptions of independent individual substitution events. Direct-alignment-based phylogenetic analyses have been used to study the population structures of bacterial outbreaks and to construct transmission maps in a variety of epidemiologic investigations (4-6). However, single recombination events, mobile genetic element insertions, or other horizontal genetic transfer events can result in multiple SNPs or more-complex rearrangements over a contiguously exchanged or interrupted region. Consequently, genome-wide direct-alignment methods, in addition to being computationally expensive, may result in the generation of incorrect tree topologies due to such rearrangements (7). Alternative...

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Evolution and Molecular Characteristics of Mycobacterium tuberculosis and Mycobacterium bovis

et al. 2023

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Whole-Genome-Based Mycobacterium tuberculosis Surveillance: a Standardized, Portable, and Expandable Approach

Cited by 175 publications

References 21 publications

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

Whole-Genome Multilocus Sequence Typing of Extended-Spectrum-Beta-Lactamase-Producing Enterobacteriaceae

Commentary: Next-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy

Evolution and Molecular Characteristics of Mycobacterium tuberculosis and Mycobacterium bovis

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