Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii

PLoS One. 2017 Jun 8;12(6):e0179228. doi: 10.1371/journal.pone.0179228. eCollection 2017.


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.

MeSH terms

  • Acinetobacter baumannii / genetics*
  • Acinetobacter baumannii / isolation & purification
  • Alleles
  • Calibration
  • Cluster Analysis
  • Genome, Bacterial*
  • Multilocus Sequence Typing / methods*
  • Phylogeny
  • Sequence Analysis, DNA / methods*

Grant support

PGH was supported by grant FOR-2251 from the German Research Council (DFG) ( The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.