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Peer-reviewedCC BYMicrobiologyOpen

Charting the Voyages of Acinetobacter baumannii in Southeast Asia: Mapping the Regional Genomic Landscape.

  • Soo Sum Lean1,2
  • Prasit Palittapongarnpim3
  • Stuart C Clarke1,4,5,6,7
  • Chew Chieng Yeo7
7 affiliations
  1. 1Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.
  2. 2Centre for Infectious Diseases and Microbiology - Public Health, Faculty of Medicine and Health, University of Sydney, Westmead, New South Wales, Australia.
  3. 3Center for Microbial Genomics (CENMIG), Faculty of Science, Mahidol University, Bangkok, Thailand.
  4. 4NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.
  5. 5Insititute of Research, Development and Innovation (IRDI), IMU University, Kuala Lumpur, Malaysia.
  6. 6Depatment of Biological Sciences, Faculty of Science, Universiti Tunku Abdil Rahman, Kampar, Malaysia.
  7. 7Centre for Research in Infectious Diseases & Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Kuala Terengganu, Malaysia.
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Abstract

Acinetobacter baumannii is a critical-priority nosocomial pathogen, yet its genomic epidemiology in Southeast Asia remains fragmented. We analysed publicly available genomes to define the regional A. baumannii population structure, resistome, mobile genetic elements, and phage defence repertoire. Following quality filtering, 853 genomes from Southeast Asia which were retrieved from PubMLST and NCBI, were subjected to multilocus sequence typing, pangenome-based phylogenetic analysis, antimicrobial resistance gene screening, plasmid and resistance island characterisation, and defence-system profiling. The dataset spanned 1996-2024 and included genomes from seven Southeast Asian countries, with Thailand contributing the largest number. The Global Clone 2 (GC2) lineage dominated the regional A. baumannii population and formed major country-associated clades, although non-dominant GCs and non-GC isolates persisted throughout the sampling period. blaOXA-23, blaADC-73, and tetB were the most prevalent acquired resistance determinants, while the gyrA-S81L and parC-S84L mutations, which are associated with fluoroquinolone resistance, were widespread across the Southeast Asian isolates. AbaR-type resistance islands were confined to GC1, whereas AbGRI-type islands predominated in GC2, especially AbGRI1-5. R3-type plasmids were the most widely distributed plasmid family overall, although RP-type plasmids predominated in Indonesia. Phage defence systems were lineage-associated, with GC2 enriched for SspBCDE and Gao-type systems and other lineages showing distinct defence combinations. Southeast Asian A. baumannii is therefore characterised by dominant GC2 circulation, broad dissemination of key resistance determinants, diverse mobile genetic elements, and heterogeneous phage defence repertoires. These findings provide a regional genomic baseline for surveillance and highlight the need for broader, geographically representative sampling across Southeast Asia.

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Cite

BibTeXRIS
BibTeX
@article{lean2026charting,
  title = {{Charting the Voyages of Acinetobacter baumannii in Southeast Asia: Mapping the Regional Genomic Landscape.}},
  author = {Soo Sum Lean and Prasit Palittapongarnpim and Stuart C Clarke and Chew Chieng Yeo},
  journal = {MicrobiologyOpen},
  year = {2026},
  month = oct,
  doi = {10.1002/mbo3.70446},
  url = {https://europepmc.org/article/MED/42961112},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - Charting the Voyages of Acinetobacter baumannii in Southeast Asia: Mapping the Regional Genomic Landscape.
AU  - Soo Sum Lean
AU  - Prasit Palittapongarnpim
AU  - Stuart C Clarke
AU  - Chew Chieng Yeo
PY  - 2026
DA  - 2026/10/30
JO  - MicrobiologyOpen
DO  - 10.1002/mbo3.70446
UR  - https://europepmc.org/article/MED/42961112
AB  - Acinetobacter baumannii is a critical-priority nosocomial pathogen, yet its genomic epidemiology in Southeast Asia remains fragmented. We analysed publicly available genomes to define the regional A. baumannii population structure, resistome, mobile genetic elements, and phage defence repertoire. Following quality filtering, 853 genomes from Southeast Asia which were retrieved from PubMLST and NCBI, were subjected to multilocus sequence typing, pangenome-based phylogenetic analysis, antimicrobial resistance gene screening, plasmid and resistance island characterisation, and defence-system profiling. The dataset spanned 1996-2024 and included genomes from seven Southeast Asian countries, with Thailand contributing the largest number. The Global Clone 2 (GC2) lineage dominated the regional A. baumannii population and formed major country-associated clades, although non-dominant GCs and non-GC isolates persisted throughout the sampling period. blaOXA-23, blaADC-73, and tetB were the most prevalent acquired resistance determinants, while the gyrA-S81L and parC-S84L mutations, which are associated with fluoroquinolone resistance, were widespread across the Southeast Asian isolates. AbaR-type resistance islands were confined to GC1, whereas AbGRI-type islands predominated in GC2, especially AbGRI1-5. R3-type plasmids were the most widely distributed plasmid family overall, although RP-type plasmids predominated in Indonesia. Phage defence systems were lineage-associated, with GC2 enriched for SspBCDE and Gao-type systems and other lineages showing distinct defence combinations. Southeast Asian A. baumannii is therefore characterised by dominant GC2 circulation, broad dissemination of key resistance determinants, diverse mobile genetic elements, and heterogeneous phage defence repertoires. These findings provide a regional genomic baseline for surveillance and highlight the need for broader, geographically representative sampling across Southeast Asia.
SN  - 2045-8827
ER  -