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

by McCarthy, Noel D. , Earle, Sarah G. , Bray, James E. , Maiden, Martin C. J. , van Rensburg, Melissa J. Jansen , Ford, Suzanne A. , Jolley, Keith A.

in 631/114/129/2043 / 631/114/2402 / 631/114/739 / 631/326/325 / Alleles / Bacteria / Bacteria - classification / Bacteria - genetics / Bacterial genetics / Bacterial Typing Techniques - methods / Base Sequence / Data processing / Databases, Genetic / DNA sequencing / Enzymes / Evolution, Molecular / Genes / Genetic Variation / Genome, Bacterial / Genomes / Genomics / Genomics - methods / Infectious Diseases / Life Sciences / Medical Microbiology / Methods / Microbiology / Multilocus Sequence Typing - methods / Mutation / Nucleotide sequencing / opinion-2 / Parasitology / Pathogens / RNA, Bacterial - analysis / RNA, Bacterial - genetics / RNA, Ribosomal, 16S - analysis / RNA, Ribosomal, 16S - genetics / Taxonomy / Virology

2013

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

by McCarthy, Noel D. , Earle, Sarah G. , Bray, James E. , Maiden, Martin C. J. , van Rensburg, Melissa J. Jansen , Ford, Suzanne A. , Jolley, Keith A.

2013

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

by McCarthy, Noel D. , Earle, Sarah G. , Bray, James E. , Maiden, Martin C. J. , van Rensburg, Melissa J. Jansen , Ford, Suzanne A. , Jolley, Keith A.

2013

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Journal Article

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

McCarthy, Noel D.,

Earle, Sarah G.,

Bray, James E.,

Maiden, Martin C. J.,

van Rensburg, Melissa J. Jansen,

Ford, Suzanne A.,

Jolley, Keith A.

2013

Overview

Assessing the genetic variation of bacteria has become ever more complex as more sequencing data has become available. Here, Maiden and colleagues propose a gene-by-gene approach of analysing whole-genome data; this approach is based on their experience with multilocus sequence typing (MLST) and reflects the functional and evolutionary relationships among bacteria. 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.

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Publisher

Nature Publishing Group UK,Nature Publishing Group

Subject

/ Alleles

/ Bacteria - classification