Open AccessDevelopment and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii
Author(s) -
Paul G. Higgins,
Karola Prior,
Dag Harmsen,
Harald Seifert
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0179228
Subject(s) - multilocus sequence typing , acinetobacter baumannii , genome , biology , typing , genetics , whole genome sequencing , pulsed field gel electrophoresis , gene , genotype , pseudomonas aeruginosa , bacteria
We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii . To define a core genome we downloaded a total of 1,573 putative A . baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A . baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A . baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities. We defined a core genome of 2,390 genes of which an average 98.4% were called successfully from 1,339 A . baumannii genomes, while Acinetobacter nosocomialis , Acinetobacter pittii , and Acinetobacter calcoaceticus resulted in 71.2%, 33.3%, and 23.2% good targets, respectively. When tested against the previously identified outbreak strains, we found good correlation between PFGE and cgMLST clustering, with 0–8 allelic differences within a pulsotype, and 40–2,166 differences between pulsotypes. The highest number of allelic differences was between the isolates representing the international clones. This typing scheme was highly discriminatory and identified separate A . baumannii outbreaks. Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.