Whole genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020) revealed the predominance of the Global Clone 2 lineage
Whole genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020) revealed the predominance of the Global Clone 2 lineage
Carbapenem-resistant Acinetobacter baumannii is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 A. baumannii isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011–2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (n=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu A. baumannii clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2Pasteur of the Global Clone 2 lineage identified as the dominant ST (n=76/126; 60.3%). The ST2Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195Oxford (n=35) and ST208Oxford (n=17). Various antimicrobial resistance genes were identified with the bla OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (n=90/126; 71.4%). Plasmid-encoded rep genes were identified in nearly all (n=122/126; 96.8%) of the isolates with the majority being Rep_3 family (n=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2Pasteur isolates harbouring them. This study provided a genomic snapshot of the A. baumannii isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2Pasteur lineage, indicating the entrenchment of this clone in the hospital.
Acinetobacter baumannii, GC2 lineage, Malaysia, genome sequencing, multidrug resistant
Din, Nurul Saidah
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Mohd Rani, Farahiyah
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Alattraqchi, Ahmed Ghazi
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Ismail, Salwani
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Rahman, Nor Iza A.
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Cleary, David W.
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Clarke, Stuart C.
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Yeo, Chew Chieng
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5 February 2025
Din, Nurul Saidah
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Mohd Rani, Farahiyah
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Alattraqchi, Ahmed Ghazi
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Ismail, Salwani
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Rahman, Nor Iza A.
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Cleary, David W.
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Clarke, Stuart C.
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Yeo, Chew Chieng
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Din, Nurul Saidah, Mohd Rani, Farahiyah, Alattraqchi, Ahmed Ghazi, Ismail, Salwani, Rahman, Nor Iza A., Cleary, David W., Clarke, Stuart C. and Yeo, Chew Chieng
(2025)
Whole genome sequencing of Acinetobacter baumannii clinical isolates from a tertiary hospital in Terengganu, Malaysia (2011-2020) revealed the predominance of the Global Clone 2 lineage.
Microbial Genomics, 11 (2), [001345].
(doi:10.1099/mgen.0.001345).
Abstract
Carbapenem-resistant Acinetobacter baumannii is recognized by the World Health Organization (WHO) as one of the top priority pathogens. Despite its public health importance, genomic data of clinical isolates from Malaysia remain scarce. In this study, whole-genome sequencing was performed on 126 A. baumannii isolates collected from the main tertiary hospital in the state of Terengganu, Malaysia, over a 10-year period (2011–2020). Antimicrobial susceptibilities determined for 20 antibiotics belonging to 8 classes showed that 77.0% (n=97/126) of the isolates were categorized as multidrug resistant (MDR), with all MDR isolates being carbapenem resistant. Multilocus sequence typing analysis categorized the Terengganu A. baumannii clinical isolates into 34 Pasteur and 44 Oxford sequence types (STs), with ST2Pasteur of the Global Clone 2 lineage identified as the dominant ST (n=76/126; 60.3%). The ST2Pasteur isolates could be subdivided into six Oxford STs with the majority being ST195Oxford (n=35) and ST208Oxford (n=17). Various antimicrobial resistance genes were identified with the bla OXA-23-encoded carbapenemase being the predominant acquired carbapenemase gene (n=90/126; 71.4%). Plasmid-encoded rep genes were identified in nearly all (n=122/126; 96.8%) of the isolates with the majority being Rep_3 family (n=121). Various virulence factors were identified, highlighting the pathogenic nature of this bacterium. Only 14/126 (11.1%) of the isolates were positive for the carriage of CRISPR-Cas arrays with none of the prevalent ST2Pasteur isolates harbouring them. This study provided a genomic snapshot of the A. baumannii isolates obtained from a single tertiary healthcare centre in Malaysia over a 10-year period and showed the predominance of a single closely related ST2Pasteur lineage, indicating the entrenchment of this clone in the hospital.
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Din et al. (Revised with track changes_v12-12-2024)_V2
- Accepted Manuscript
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mgen001345
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Accepted/In Press date: 13 December 2024
Published date: 5 February 2025
Keywords:
Acinetobacter baumannii, GC2 lineage, Malaysia, genome sequencing, multidrug resistant
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Local EPrints ID: 498152
URI: http://eprints.soton.ac.uk/id/eprint/498152
ISSN: 2057-5858
PURE UUID: 07f6e392-64ca-46f2-bca1-2024f4efdc55
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Date deposited: 11 Feb 2025 17:47
Last modified: 22 Aug 2025 01:56
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Contributors
Author:
Nurul Saidah Din
Author:
Farahiyah Mohd Rani
Author:
Ahmed Ghazi Alattraqchi
Author:
Salwani Ismail
Author:
Nor Iza A. Rahman
Author:
David W. Cleary
Author:
Chew Chieng Yeo
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