Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response

Aarestrup, Frank Møller; Brown, Eric W.; Detter, Chris; Gerner‐Smidt, Peter; Gilmour, Matthew W.; Harmsen, Dag; Hendriksen, René S.; Hewson, Roger; Heymann, David L.; Johansson, Karin; Ijaz, Kashef; Keim, Paul; Koopmans, Marion; Kroneman, Annelies; Wong, Danilo Lo Fo; Lund, Ole; Palm, Daniel; Sawanpanyalert, Pathom; Sobel, Jeremy; Schlundt, Jørgen

doi:10.3201/eid1811.120453

Cited by 69 publications

(33 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Thus, allele-based methods largely reduce the conflicting signals of recombination in determining genetic relatedness of bacteria (41)(42)(43)(44)(45). 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).…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

View full text Add to dashboard Cite

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...

show abstract

Section: Discussionmentioning

confidence: 99%

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

et al. 2016

View full text Add to dashboard Cite

show abstract

“…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%

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

“…Consequently, the molecular methods used for diagnosis do not have to be characterized by the same high sensitivity that is required for the methods used for asymptomatic individual screening [9]. PCR, reverse transcription PCR (RT-PCR), real-time RT-PCR and nucleic acid amplification tests (ΝΑΤ) are some of the molecular methods used for identification of viruses, depending on the requirements.…”

Section: Molecular Epidemiology Infectious Diseasesmentioning

confidence: 99%

“…The findings from genetic fingerprinting help classify a case as endemic or imported which is valuable information not only for the purposes of surveillance but for case management as well. When virus genotype of laboratory-confirmed cases is known, the case can be classified as endemic or imported depending on whether the genotype detected belongs to the endemic genotypes or not [8,9].…”

Section: Molecular Epidemiology Infectious Diseasesmentioning

confidence: 99%

Role of Molecular Epidemiology in Infectious Disease Surveillance

Gupte

Ravikant

Kaur³

2016

JHVRV

View full text Add to dashboard Cite

Molecular epidemiology is progressively a vast area of research and now molecular biology techniques have become increasingly integrated into the practice of infectious disease epidemiology. By definition molecular epidemiology is molecular strain-typing or we can say fingerprinting techniques regardless any epidemiologic application. Molecular is basically the use of the techniques of molecular biology and the epidemiology is the study of the distribution and determinants of disease occurrence in human populations. The benefits and challenges of applying these techniques to disease and their affected host is the core which gets served by molecular epidemiologist.

show abstract

Integrating Genome-based Informatics to Modernize Global Disease Monitoring, Information Sharing, and Response

Cited by 69 publications

References 43 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

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

Role of Molecular Epidemiology in Infectious Disease Surveillance

Contact Info

Product

Resources

About