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. 2012 Apr 12;3(2):261-77.
doi: 10.3390/genes3020261.

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter

Samuel K Sheppard  1 , Keith A Jolley  2 , Martin C J Maiden  3
Affiliations

A Gene-By-Gene Approach to Bacterial Population Genomics: Whole Genome MLST of Campylobacter

Samuel K Sheppard et al. Genes (Basel). .

Abstract

Campylobacteriosis remains a major human public health problem world-wide. Genetic analyses of Campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of Campylobacter genotypes isolated from human infection, farm animals, and retail food. These studies have demonstrated that Campylobacter populations are highly structured, with distinct genotypes associated with particular wild or domestic animal sources, and that chicken meat is the most likely source of most human infection in countries such as the UK. The availability of multiple whole genome sequences from Campylobacter isolates presents the prospect of identifying those genes or allelic variants responsible for host-association and increased human disease risk, but the diversity of Campylobacter genomes present challenges for such analyses. We present a gene-by-gene approach for investigating the genetic basis of phenotypes in diverse bacteria such as Campylobacter, implemented with the BIGSdb software on the pubMLST.org/campylobacter website.

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Figures

Figure 1
Figure 1
Gene-by-gene analysis of Campylobacter genomes. (A) Defined loci are entered into the database, from the finished NCTC 11168 genome; (B) Whole genome sequence data, such as contigs generated from parallel sequencing technologies or complete assembled genomes, are entered with isolate provenance and phenotype information; (C) Sequences are compared to defined loci using BLAST and allelic variants are tagged. The result is an allelic profile that catalogues variation across the genome.
Figure 2
Figure 2
Schematic diagram of the gene-by-gene analysis pipeline.
See this image and copyright information in PMC

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