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Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England
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Halachev, Mihail R., Chan, Jacqueline, Constantinidou, Chrystala, Cumley, Nicola, Bradley, Craig, Smith-Banks, Matthew, Oppenheim, Beryl and Pallen, Mark J. (2014) Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England. Genome Medicine, Volume 6 (Number 11). pp. 1-13. Article number 70. doi:10.1186/s13073-014-0070-x ISSN 1756-994X.
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Official URL: http://dx.doi.org/10.1186/s13073-014-0070-x
Abstract
Background:
Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform infection control. Here, we describe a protracted hospital outbreak of multidrug-resistant A. baumannii, in which whole-genome sequencing (WGS) was used to obtain a high-resolution view of the relationships between isolates.
Methods:
To delineate and investigate the outbreak, we attempted to genome-sequence 114 isolates that had been assigned to the A. baumannii complex by the Vitek2 system and obtained informative draft genome sequences from 102 of them. Genomes were mapped against an outbreak reference sequence to identify single nucleotide variants (SNVs).
Results:
We found that the pulsotype 27 outbreak strain was distinct from all other genome-sequenced strains. Seventy-four isolates from 49 patients could be assigned to the pulsotype 27 outbreak on the basis of genomic similarity, while WGS allowed 18 isolates to be ruled out of the outbreak. Among the pulsotype 27 outbreak isolates, we identified 31 SNVs and seven major genotypic clusters. In two patients, we documented within-host diversity, including mixtures of unrelated strains and within-strain clouds of SNV diversity. By combining WGS and epidemiological data, we reconstructed potential transmission events that linked all but 10 of the patients and confirmed links between clinical and environmental isolates. Identification of a contaminated bed and a burns theatre as sources of transmission led to enhanced environmental decontamination procedures.
Conclusions:
WGS is now poised to make an impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant timeframe and allowing infection control teams to track, and even prevent, the spread of drug-resistant hospital pathogens.
Item Type: | Journal Article | ||||||||
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Subjects: | Q Science > QR Microbiology | ||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School |
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Library of Congress Subject Headings (LCSH): | Acinetobacter infections, Multidrug resistance, Infection -- Prevention, Drug resistance in microorganisms -- Genetic aspects | ||||||||
Journal or Publication Title: | Genome Medicine | ||||||||
Publisher: | BioMed Central Ltd. | ||||||||
ISSN: | 1756-994X | ||||||||
Official Date: | 20 November 2014 | ||||||||
Dates: |
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Volume: | Volume 6 | ||||||||
Number: | Number 11 | ||||||||
Page Range: | pp. 1-13 | ||||||||
Article Number: | Article number 70 | ||||||||
DOI: | 10.1186/s13073-014-0070-x | ||||||||
Status: | Peer Reviewed | ||||||||
Publication Status: | Published | ||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||
Date of first compliant deposit: | 28 July 2016 | ||||||||
Date of first compliant Open Access: | 28 July 2016 | ||||||||
Funder: | Medical Research Council (Great Britain) (MRC), National Institute for Health Research (Great Britain) (NIHR) | ||||||||
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