Campylobacter sequence typing databases: applications and future prospects

Colles, Frances M.; Maiden, Martin C. J.

doi:10.1099/mic.0.062000-0

Cited by 61 publications

(62 citation statements)

References 155 publications

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“…Although the epidemiology of human Campylobacter infections has been investigated for more than 35 years (26), a better understanding of the transmission of infections to humans is needed (27). Most infections are apparently sporadic and occur in patients of all ages and socioeconomic backgrounds, and detection of the sources of sporadic infections remains unclear.…”

Section: Discussionmentioning

confidence: 99%

Multilocus Sequence Typing (MLST) and Whole-Genome MLST of Campylobacter jejuni Isolates from Human Infections in Three Districts during a Seasonal Peak in Finland

et al. 2014

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Section: Discussionmentioning

confidence: 99%

Multilocus Sequence Typing (MLST) and Whole-Genome MLST of Campylobacter jejuni Isolates from Human Infections in Three Districts during a Seasonal Peak in Finland

et al. 2014

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“…However, as correctly determined sequence data are absolute, the insights obtained from MLST-based analyses remain relevant and MLST data are "forward compatible" with NGS data . For example, a major early finding was that related STs are grouped into "clonal complexes" that can be pragmatically defined as groups of isolates with STs that share identical alleles at four or more MLST loci with a definable "central genotype" (Dingle et al 2008;Colles and Maiden 2012). The use of the clonal complex as a primary unit of analysis has been of great value in a wide range of studies of Campylobacter, and whole genome sequence (WGS) analyses have confirmed that the members of clonal complexes correspond to bacterial lineages, the members of which share a common ancestor and, therefore, frequently also share phenotypic properties.…”

Section: The Impact Of Sequence-based Molecular Typingmentioning

confidence: 99%

The Evolution ofCampylobacter jejuniandCampylobacter coli

Sheppard

Maiden

2015

Cold Spring Harb Perspect Biol

136

127

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The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure.

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“…At the international level, in 2010 a collaborative network involving 15 human and veterinary laboratories in 10 countries unequivocally demonstrated the European-wide dissemination of closely-related strains of multidrug-resistant monophasic S. Typhimurium in food animals and humans (Hopkins et al, 2010). For Campylobacter, an international database of MLST types has been established (Colles and Maiden, 2012) and is widely used for outbreak investigations and source attribution studies (see 4.6.3 below).…”

Section: Past and Current Experiences Employing Molecular Typing Methodsmentioning

confidence: 99%

“…By contrast, C. jejuni comprises a large number of genetic types, with widespread evidence for recombination throughout the species. Notwithstanding recombination, the extensive diversity of these organisms is structured into a large number of distinct lineages identified as 'clonal complexes' by multilocus sequence typing (MLST), which is also a reliable approach for the speciation and the identification of C. coli lineages (Colles and Maiden, 2012).…”

Section: Campylobacter Sppmentioning

confidence: 99%

See 1 more Smart Citation

Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)

2013

EFS2

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An evaluation of molecular typing methods that can be applied to the food‐borne pathogens Salmonella, Campylobacter, Shiga toxin‐producing Escherichia coli and Listeria monocytogenes is presented. This evaluation is divided in two parts. Firstly, commonly used molecular typing methods are assessed against a set of predefined criteria relating to discriminatory capacity, reproducibility, repeatability and current or potential suitability for international harmonisation. Secondly, the methods are evaluated for their appropriateness for use in different public health‐related applications. These applications include outbreak detection and investigation, attribution modelling, the potential for early identification of food‐borne strains with epidemic potential and the integration of the resulting data in risk assessment. The results of these evaluations provide updated insights into the use and potential for use of molecular characterisation methods, including whole genome sequencing technologies, in microbial food safety. Recommendations are also made in order to encourage a holistic and structured approach to the use of molecular characterisation methods for food‐borne pathogens; in particular, on the importance of structured co‐ordination at international level to help overcome current limitations in harmonisation of data analysis and interpretation.

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Campylobacter sequence typing databases: applications and future prospects

Cited by 61 publications

References 155 publications

Multilocus Sequence Typing (MLST) and Whole-Genome MLST of Campylobacter jejuni Isolates from Human Infections in Three Districts during a Seasonal Peak in Finland

Multilocus Sequence Typing (MLST) and Whole-Genome MLST of Campylobacter jejuni Isolates from Human Infections in Three Districts during a Seasonal Peak in Finland

The Evolution ofCampylobacter jejuniandCampylobacter coli

Scientific Opinion on the evaluation of molecular typing methods for major food‐borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 1 (evaluation of methods and applications)

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