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

Nurul Saidah Din; Farahiyah Mohd Rani; Ahmed Ghazi Alattraqchi; Salwani Ismail; Nor Iza A Rahman; David W Cleary; Stuart C Clarke; Chew Chieng Yeo

doi:10.1099/mgen.0.001345

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

Nurul Saidah Din, Farahiyah Mohd Rani, Ahmed Ghazi Alattraqchi, Salwani Ismail, Nor Iza A Rahman, David W Cleary, Stuart C Clarke, Chew Chieng Yeo

Microbes, Infection and Microbiomes

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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 ST2_Pasteur of the Global Clone 2 lineage identified as the dominant ST ( n=76/126; 60.3%). The ST2_Pasteurisolates could be subdivided into six Oxford STs with the majority being ST195_Oxford ( n=35) and ST208_Oxford ( 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 ST2_Pasteur 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 ST2_Pasteur lineage, indicating the entrenchment of this clone in the hospital.

Original language	English
Article number	001345
Number of pages	19
Journal	Microbial Genomics
Volume	11
Issue number	2
DOIs	https://doi.org/10.1099/mgen.0.001345
Publication status	Published - 5 Feb 2025

Keywords

Acinetobacter baumannii/genetics
Malaysia/epidemiology
Tertiary Care Centers
Humans
Whole Genome Sequencing
Drug Resistance, Multiple, Bacterial/genetics
Acinetobacter Infections/microbiology
Multilocus Sequence Typing
Anti-Bacterial Agents/pharmacology
Microbial Sensitivity Tests
Genome, Bacterial
Male
beta-Lactamases/genetics
Adult
Female
Middle Aged
Aged
Bacterial Proteins/genetics
Young Adult
Phylogeny
Adolescent
Aged, 80 and over
Child

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1099/mgen.0.001345Licence: Creative Commons: Attribution (CC BY)

DinNS2025Whole-genomeFinal published version, 7.87 MBLicence: Creative Commons: Attribution (CC BY)

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Din, N. S., Mohd Rani, F., Alattraqchi, A. G., Ismail, S., A Rahman, N. I., Cleary, D. W., Clarke, S. C., & Yeo, C. C. (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), Article 001345. https://doi.org/10.1099/mgen.0.001345

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title = "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",

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. ",

keywords = "Acinetobacter baumannii/genetics, Malaysia/epidemiology, Tertiary Care Centers, Humans, Whole Genome Sequencing, Drug Resistance, Multiple, Bacterial/genetics, Acinetobacter Infections/microbiology, Multilocus Sequence Typing, Anti-Bacterial Agents/pharmacology, Microbial Sensitivity Tests, Genome, Bacterial, Male, beta-Lactamases/genetics, Adult, Female, Middle Aged, Aged, Bacterial Proteins/genetics, Young Adult, Phylogeny, Adolescent, Aged, 80 and over, Child",

author = "Din, \{Nurul Saidah\} and \{Mohd Rani\}, Farahiyah and Alattraqchi, \{Ahmed Ghazi\} and Salwani Ismail and \{A Rahman\}, \{Nor Iza\} and Cleary, \{David W\} and Clarke, \{Stuart C\} and Yeo, \{Chew Chieng\}",

year = "2025",

month = feb,

day = "5",

doi = "10.1099/mgen.0.001345",

language = "English",

volume = "11",

journal = "Microbial Genomics",

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number = "2",

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Din, NS, Mohd Rani, F, Alattraqchi, AG, Ismail, S, A Rahman, NI, Cleary, DW, Clarke, SC & Yeo, CC 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, vol. 11, no. 2, 001345. https://doi.org/10.1099/mgen.0.001345

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. / Din, Nurul Saidah; Mohd Rani, Farahiyah; Alattraqchi, Ahmed Ghazi et al.
In: Microbial Genomics, Vol. 11, No. 2, 001345, 05.02.2025.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - 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

AU - Din, Nurul Saidah

AU - Mohd Rani, Farahiyah

AU - Alattraqchi, Ahmed Ghazi

AU - Ismail, Salwani

AU - A Rahman, Nor Iza

AU - Cleary, David W

AU - Clarke, Stuart C

AU - Yeo, Chew Chieng

PY - 2025/2/5

Y1 - 2025/2/5

N2 - 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.

AB - 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.

KW - Acinetobacter baumannii/genetics

KW - Malaysia/epidemiology

KW - Tertiary Care Centers

KW - Humans

KW - Whole Genome Sequencing

KW - Drug Resistance, Multiple, Bacterial/genetics

KW - Acinetobacter Infections/microbiology

KW - Multilocus Sequence Typing

KW - Anti-Bacterial Agents/pharmacology

KW - Microbial Sensitivity Tests

KW - Genome, Bacterial

KW - Male

KW - beta-Lactamases/genetics

KW - Adult

KW - Female

KW - Middle Aged

KW - Aged

KW - Bacterial Proteins/genetics

KW - Young Adult

KW - Phylogeny

KW - Adolescent

KW - Aged, 80 and over

KW - Child

U2 - 10.1099/mgen.0.001345

DO - 10.1099/mgen.0.001345

M3 - Article

C2 - 39908088

SN - 2057-5858

VL - 11

JO - Microbial Genomics

JF - Microbial Genomics

IS - 2

M1 - 001345

ER -

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

Abstract

Keywords

UN SDGs

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