Genomic epidemiology of the
            <i>Escherichia coli</i>
            O104:H4 outbreaks in Europe, 2011

Grad, Yonatan H.; Lipsitch, Marc; Feldgarden, Michael; Arachchi, Harindra; Cerqueira, Gustavo C.; FitzGerald, Michael G.; Godfrey, Paul A.; Haas, Brian J.; Murphy, Cheryl I.; Russ, Carsten; Sykes, Sean M.; Walker, Bruce J.; Wortman, Jennifer; Young, Sarah; Zeng, Qiandong; Abouelleil, Amr; Bochicchio, James; Chauvin, Sara; DeSmet, Timothy; Gujja, Sharvari; McCowan, Caryn; Montmayeur, Anna; Steelman, Scott; Frimodt-Møller, Jakob; Petersen, Andreas Munk; Struve, Carsten; Krogfelt, Karen A.; Bingen, Édouard; Weill, François‐Xavier; Lander, Eric S.; Nusbaum, Chad; Birren, Bruce W.; Hung, Deborah T.; Hanage, William P.

doi:10.1073/pnas.1121491109

Cited by 258 publications

(241 citation statements)

References 22 publications

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“…To construct the complete nucleotide sequence of a genome, multiple short sequence reads must be assembled based on overlapping regions (de novo assembly), or comparisons with previously sequenced 'reference' genomes (resequencing). WGS is becoming a powerful and highly attractive tool for epidemiological investigations [85][86][87][88] and it is highly likely that in the near future WGS technology for routine clinical use will permit accurate identification and characterisation of bacterial isolates. However, the key challenge will not be to produce the sequence data, but to rapidly compute and interpret the relevant information from large data sets.…”

Section: Whole Genome Sequencingmentioning

confidence: 99%

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

et al. 2013

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Typing methods for discriminating different bacterial isolates of the same species are essential epidemiological tools in infection prevention and control. Traditional typing systems based on phenotypes, such as serotype, biotype, phage-type, or antibiogram, have been used for many years. However, more recent methods that examine the relatedness of isolates at a molecular level have revolutionised our ability to differentiate among bacterial types and subtypes. Importantly, the development of molecular methods has provided new tools for enhanced surveillance and outbreak detection. This has resulted in better implementation of rational infection control programmes and efficient allocation of resources across Europe. The emergence of benchtop sequencers using next generation sequencing technology makes bacterial whole genome sequencing (WGS) feasible even in small research and clinical laboratories. WGS has already been used for the characterisation of bacterial isolates in several large outbreaks in Europe and, in the near future, is likely to replace currently used typing methodologies due to its ultimate resolution. However, WGS is still too laborious and time-consuming to obtain useful data in routine surveillance. Also, a largely unresolved question is how genome sequences must be examined for epidemiological characterisation. In the coming years, the lessons learnt from currently used molecular methods will allow us to condense the WGS data into epidemiologically useful information. On this basis, we have reviewed current and new molecular typing methods for outbreak detection and epidemiological surveillance of bacterial pathogens in clinical practice, aiming to give an overview of their specific advantages and disadvantages.

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Section: Whole Genome Sequencingmentioning

confidence: 99%

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

et al. 2013

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“…Rapid responses in sequencing efforts during the EAEC O104:H4 outbreak suggest that genomic epidemiology will become a standard molecular strategy to elucidate infectious disease outbreaks. 72 animal models investigating infantile and childhood eaeC induced diarrhea. A global analysis of child mortality in 2008 estimated that infectious diseases cause the majority (68%) of deaths in children younger than 5 y of age worldwide.…”

mentioning

confidence: 99%

Animal models of enteroaggregativeEscherichia coliinfection

2013

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“…A popular method has been to construct phylogenies on the basis of SNPs (single-nucleotide differences among samples) that have been identified either by the mapping of short-read sequence data to a reference genome, or by aligning de novo-assembled sequences to a reference genome 37,40 . This approach has been used successfully to investigate the epidemiology and evolution of a number of single-clone pathogens or members of the same lineage [41][42][43][44][45][46][47][48][49][50][51][52] , but it is limited by its requirement for a reference sequence or whole-genome alignment 40 . The analysis of diverse or highly recombining organisms in this way will prove challenging because the number of total polymorphisms increases as the number of polymorphisms conforming to a clonal model of descent decreases (BOX 1).…”

Section: Post-wgs Cataloguing Of Diversitymentioning

confidence: 99%

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

et al. 2013

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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...

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Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011

Cited by 258 publications

References 22 publications

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

Overview of molecular typing methods for outbreak detection and epidemiological surveillance

Animal models of enteroaggregativeEscherichia coliinfection

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

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