Identification of Klebsiella capsule synthesis loci from whole genome data

Kelly L. Wyres, Ryan R. Wick, Claire Gorrie, Adam Jenney, Rainer Follador, Nicholas R. Thomson, Kathryn E. Holt

Research output: Contribution to journalArticleResearchpeer-review

Abstract

Klebsiella pneumoniae is a growing cause of healthcare-associated infections for which multi-drug resistance is a concern. Its polysaccharide capsule is a major virulence determinant and epidemiological marker. However, little is known about capsule epidemiology since serological typing is not widely accessible and many isolates are serologically non-typeable. Molecular typing techniques provide useful insights, but existing methods fail to take full advantage of the information in whole genome sequences. We investigated the diversity of the capsule synthesis loci (K-loci) among 2503 K. pneumoniae genomes. We incorporated analyses of full-length K-locus nucleotide sequences and also clustered protein-encoding sequences to identify, annotate and compare K-locus structures. We propose a standardized nomenclature for K-loci and present a curated reference database. A total of 134 distinct K-loci were identified, including 31 novel types. Comparative analyses indicated 508 unique protein-encoding gene clusters that appear to reassort via homologous recombination. Extensive intra- and inter-locus nucleotide diversity was detected among the wzi and wzc genes, indicating that current molecular typing schemes based on these genes are inadequate. As a solution, we introduce Kaptive, a novel software tool that automates the process of identifying K-loci based on full locus information extracted from whole genome sequences (https://github.com/katholt/Kaptive). This work highlights the extensive diversity of Klebsiella K-loci and the proteins that they encode. The nomenclature, reference database and novel typing method presented here will become essential resources for genomic surveillance and epidemiological investigations of this pathogen.

Original languageEnglish
Article numbere000102
Number of pages15
JournalMicrobial genomics
Volume2
Issue number12
DOIs
Publication statusPublished - 1 Dec 2016
Externally publishedYes

Keywords

  • Klebsiella capsule K-locus genomic surveillance

Cite this

Wyres, Kelly L. ; Wick, Ryan R. ; Gorrie, Claire ; Jenney, Adam ; Follador, Rainer ; Thomson, Nicholas R. ; Holt, Kathryn E. / Identification of Klebsiella capsule synthesis loci from whole genome data. In: Microbial genomics. 2016 ; Vol. 2, No. 12.
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Identification of Klebsiella capsule synthesis loci from whole genome data. / Wyres, Kelly L.; Wick, Ryan R.; Gorrie, Claire; Jenney, Adam; Follador, Rainer; Thomson, Nicholas R.; Holt, Kathryn E.

In: Microbial genomics, Vol. 2, No. 12, e000102, 01.12.2016.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - Identification of Klebsiella capsule synthesis loci from whole genome data

AU - Wyres, Kelly L.

AU - Wick, Ryan R.

AU - Gorrie, Claire

AU - Jenney, Adam

AU - Follador, Rainer

AU - Thomson, Nicholas R.

AU - Holt, Kathryn E.

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