Universität zu Köln

Higgins, Paul G. ORCID: 0000-0001-8677-9454, Prior, Karola, Harmsen, Dag and Seifert, Harald (2017). Development and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii. PLoS One, 12 (6). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

We have employed whole genome sequencing to define and evaluate a core genome multi-locus 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 pulso-types. 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.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Higgins, Paul G. UNSPECIFIED orcid.org/0000-0001-8677-9454 UNSPECIFIED Prior, Karola UNSPECIFIED UNSPECIFIED UNSPECIFIED Harmsen, Dag UNSPECIFIED UNSPECIFIED UNSPECIFIED Seifert, Harald UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-227914
DOI:	10.1371/journal.pone.0179228
Journal or Publication Title:	PLoS One
Volume:	12
Number:	6
Date:	2017
Publisher:	PUBLIC LIBRARY SCIENCE
Place of Publication:	SAN FRANCISCO
ISSN:	1932-6203
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language GEL-ELECTROPHORESIS PROTOCOLS; MOLECULAR EPIDEMIOLOGY; INTERLABORATORY REPRODUCIBILITY; REP-PCR; OUTBREAK; STRAIN; MLST; STANDARDIZATION; IDENTIFICATION; POPULATIONS Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/22791