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

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

Paul G Higgins  1   2 , Karola Prior  3 , Dag Harmsen  3 , Harald Seifert  1   2
Affiliations

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

Paul G Higgins et al. PLoS One. .

Abstract

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.

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Conflict of interest statement

Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests. DH is co-developer of the Ridom SeqSphere+ software mentioned in the paper, a development of Ridom GmbH (Münster, Germany), which is partially owned by him. The other authors declare no conflicts of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. Minimum spanning tree based on cgMLST allelic profiles of 53 A. baumannii isolates.
Each circle represents an allelic profile based on sequence analysis of 2,390 cgMLST target genes. The numbers on the connecting lines illustrate the numbers of target genes with different alleles. Colours of the circles represent the different isolation sources. Closely related genotypes (≤10 alleles difference) are shaded and clusters are numbered consecutively (I to XIII). Isolates belonging to the same IC lineage are surrounded by dotted circles.
See this image and copyright information in PMC

References

    1. Peleg AY, Seifert H, Paterson DL (2008) Acinetobacter baumannii: Emergence of a successful pathogen. Clin Microbiol Rev 21: 538–582. 10.1128/CMR.00058-07 - DOI - PMC - PubMed
    1. Dijkshoorn L, Nemec A, Seifert H (2007) An increasing threat in hospitals: multidrug-resistant Acinetobacter baumannii. Nature Rev Microbiol 5: 939–951. - PubMed
    1. Wagenvoort JHT, De Brauwer EIGB, Toenbreker HMJ, van der Linden CJ (2002) Epidemic Acinetobacter baumannii strain with MRSA-like behaviour carried by healthcare staff. Eur J Clin Microbiol Infect Dis 21: 326–327. 10.1007/s10096-002-0716-2 - DOI - PubMed
    1. Husni RN, Goldstein LS, Arroliga AC, Hall GS, Fatica C, Stoller JK, et al. (1999) Risk factors for an outbreak of multi-drug-resistant Acinetobacter nosocomial pneumonia among intubated patients. Chest 115: 1378–1382. - PubMed
    1. Chmielarczyk A, Higgins PG, Wojkowska-Mach J, Synowiec E, Zander E, Romaniszyn D, et al. (2012) Control of an outbreak of Acinetobacter baumannii infections using vaporized hydrogen peroxide. J Hosp Infect 81: 239–245. 10.1016/j.jhin.2012.05.010 - DOI - PubMed

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