title: Population structures in the SARA and SARB reference collections of Salmonella enterica according to MLST, MLEE and microarray hybridization.
abstract: In the 1980's and 1990's, population genetic analyses based on Multilocus Enzyme Electrophoresis (MLEE) provided an initial overview of the genetic diversity of multiple bacterial species, including Salmonella enterica. The genetic diversity within S. enterica subspecies enterica according to MLEE is represented by the SARA and SARB reference collections, each consisting of 72 isolates, which have been extensively used for comparative analyses. MLEE has subsequently been replaced by Multilocus Sequence Typing (MLST). Our initial MLST results indicated that some strains within the SARB collection differed from their published descriptions. We therefore performed MLST on four versions of the SARB collection from different sources and one collection of SARA, and found that multiple isolates in SARB and SARA differ in serovar from their original description, and other SARB isolates differed between different sources. Comparisons with a global MLST database allowed a plausible reconstruction of the serovars of the original collection. MLEE, MLST and microarrays were largely concordant at recognizing closely related strains. MLST was particularly effective at recognizing discrete population genetic groupings while the two other methods provided hints of higher order relationships. However, quantitative pair-wise phylogenetic distances differed considerably between all three methods. Our results provide a translation dictionary from MLEE to MLST for the extant SARA and SARB collections which can facilitate genomic comparisons based on archival insights from MLEE.
authors.affiliation: Department of Microbiology and Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland. achtmanmark@gmail.com
authors.forename: Mark
authors.initials: M
authors.lastname: Achtman
authors.forename: James
authors.initials: J
authors.lastname: Hale
authors.forename: Ronan A
authors.initials: RA
authors.lastname: Murphy
authors.forename: E Fidelma
authors.initials: EF
authors.lastname: Boyd
authors.forename: Steffen
authors.initials: S
authors.lastname: Porwollik
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics; D030541:Databases, Genetic; D014644:Genetic Variation; D006801:Humans; D006824:Hybridization, Genetic; D016014:Linear Models; D058885:Multilocus Sequence Typing / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D010802:Phylogeny; D012015:Reference Standards; D012480:Salmonella Infections / Q000382:microbiology; D012481:Salmonella Infections, Animal / Q000382:microbiology; D019779:Salmonella enterica / Q000145:classification* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial