title: Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data.
abstract: BACKGROUND
  Multi-locus sequence typing (MLST) is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited by a paucity of variation within selected loci. For Bartonella henselae (B. henselae), although the MLST scheme currently used has been proven useful in defining the overall population structure of the species, its reliability for the accurate delineation of closely-related sequence types, between which allelic variation is usually limited to, at most, one or two nucleotide polymorphisms. Exploitation of high-throughput sequencing data allows a more informed selection of MLST loci and thus, potentially, a means of enhancing the sensitivity of the schemes they comprise.
  
  
  METHODS
  We carried out SOLiD resequencing on 12 representative B. henselae isolates and explored these data using single nucleotide polymorphism (SNP) analysis. We determined the number and distribution of SNPs in the genes targeted by the established MLST scheme and modified the position of loci within these genes to capture as much genetic variation as possible.
  
  
  RESULTS
  Using genome-wide SNP data, we found the distribution of SNPs within each open reading frame (ORF) of MLST loci, which were not represented by the established B. henselae MLST scheme. We then modified the position of loci in the MLST scheme to better reflect the polymorphism in the ORF as a whole. The use of amended loci in this scheme allowed previously indistinguishable ST1 strains to be differentiated. However, the diversity of B. henselae was still rare in China.
  
  
  CONCLUSIONS
  Our study demonstrates the use of SNP analysis to facilitate the selection of MLST loci to augment the currently-described scheme for B. henselae. And the diversity among B. henselae strains in China is markedly less than that observed in B. henselae populations elsewhere in the world.
authors.affiliation: State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Zhao
authors.forename: Gemma
authors.initials: G
authors.lastname: Chaloner
authors.forename: Alistair
authors.initials: A
authors.lastname: Darby
authors.forename: Xiu-Ping
authors.initials: XP
authors.lastname: Song
authors.forename: Dong-Mei
authors.initials: DM
authors.lastname: Li
authors.forename: Richard
authors.initials: R
authors.lastname: Birtles
authors.forename: Qi-Yong
authors.initials: QY
authors.lastname: Liu
mesh_terms: D018416:Bartonella henselae / Q000235:genetics*; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing / Q000379:methods*; D016366:Open Reading Frames / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*