Southeast Asia’s A. baumannii genomes reveal GC2 dominance and uneven surveillance

A large genomic survey of Acinetobacter baumannii across Southeast Asia has mapped the region’s population structure in unprecedented detail, analysing 853 publicly available genomes collected between 1996 and 2024. The study, published in MicrobiologyOpen, found that the Global Clone 2 (GC2) lineage, also known as International Clone 2, dominates the regional landscape, while revealing striking gaps in surveillance coverage: no genomes from Brunei, Laos, or the Philippines were identified in the public databases surveyed, and Indonesia was underrepresented geographically, with most available genomes originating from Sumatra and Java.

The researchers, drawing primarily on the PubMLST public database supplemented with Malaysian and Singaporean genomes from NCBI GenBank, applied strict quality filters, retaining only genomes with more than 90% completeness and less than 5% contamination. After removing 12 duplicate records, 932 unique genomes underwent quality assessment, of which 853 met the criteria. The dataset spans nearly three decades, with the earliest sequenced isolate originating from Singapore in 1996 and Thailand contributing the largest number of genomes in the region. A review of the genomic records showed that only a small number of isolates from 1996 to 2010 had been sequenced, followed by a marked increase beginning in 2011 that coincided with the rise of GC2 isolates, and a pronounced expansion in GC2 genomes in 2016, signifying what the authors describe as a major emergence of this high-risk clone across Southeast Asia.

Core-genome phylogenetic analysis confirmed the predominance of GC2 across the region and showed a distinct genetic separation between GC2 and other A. baumannii global clones. GC2 accounted for most genomes from Thailand, Vietnam, and Malaysia, but non-dominant global clones and non-GC isolates were also present throughout. When the 480 GC2 genomes were examined separately, several sub-clusters emerged, each composed predominantly of isolates from one country but including smaller numbers from neighbouring countries. A major clade designated 2.T, comprising 60 genomes, was centred on Thailand and included genomes from Cambodia, Myanmar, and Vietnam, all assigned to Pas-ST2 and all OCL1, with KL6 predominant. Another major clade, 2.V, comprising 75 genomes, was dominated by Vietnamese isolates of Pas-ST2, Pas-ST570, and Pas-ST571, together with smaller numbers from Cambodia, Thailand, and Singapore. The Malaysian-centric clade 2.M comprised 180 genomes, dominated by Pas-ST2 with several Oxford sequence types represented, particularly Oxf-ST195, Oxf-ST207, and Oxf-ST547, and was predominantly KL3 and KL2.

The authors caution that phylogenetic clustering alone cannot demonstrate direct transmission, but these mixed-country clusters are compatible with cross-border movement of successful GC2 sublineages. Using the Capybara classification tool, the majority of Southeast Asian GC2 isolates were assigned to the 2.5.6 clade, which has reportedly disseminated to over 45 countries since it emerged in East Asia before 2006. The Vietnam-centric 2.V clade belonged to 2.4.15, another primary clade found in East Asia, while the earliest genome in the dataset, the 1996 Singaporean GC2 isolate, was subcategorised as 2.3.2. The authors note that Oxf-ST195 appeared concentrated within the Malaysian-associated clade, though this sequence type is not unique to Malaysia and has also been reported in Hong Kong, Lebanon, and Germany.

Resistance profiling revealed widespread distribution of key antimicrobial resistance determinants across the dataset. The carbapenem resistance gene blaOXA-23 was detected in 611 genomes, or 71.6%, making it the most prevalent gene within its antimicrobial class, while tetB, a tetracycline resistance determinant, was found in 388 genomes, or 45.5%. Nearly all genomes harboured at least one copy of a blaADC gene, with 849 of 853 genomes, or 99.5%, positive; the exception was a small portion of GC11 genomes, just four of 85, in which the gene was not detected. The researchers investigated this anomaly carefully, noting that the four genome assemblies were not unusually fragmented, with N50 values of 175 to 199 kilobases and fewer than 100 contigs, and that independent screening with CARD and ResFinder likewise failed to detect blaADC. The most frequently detected blaADC allele was blaADC-73, found in 332 genomes, or 38.9%, though Vietnam stood out as a notable exception where blaADC-83 was the prevalent variant.

Country-level comparisons showed both regional convergence and local variation. The gyrA-S81L and parC-S84L mutations, both associated with fluoroquinolone resistance, were detected in genomes from all Southeast Asian countries examined, indicating widespread establishment of fluoroquinolone resistance traits in the regional population. Sulphonamide resistance gene profiles differed, with sul2 predominant in most countries but sul1 exceeding sul2 in Vietnam. Resistance island screening revealed clear lineage associations: AbaR-type islands were confined to GC1, with only two of the 25 Southeast Asian GC1 genomes harbouring AbaR7-type islands encoding aminoglycoside resistance genes together with sul1. In contrast, AbGRI1-type islands were strongly associated with GC2, identified in approximately 66.6% of GC2 genomes, with the dominant subtype AbGRI1-5 accounting for 53.4% of AbGRI1-positive GC2 genomes. These islands commonly carried aminoglycoside, tetracycline, macrolide, and sulphonamide resistance determinants, and AbGRI1-5 was found in the oldest sequenced isolate in the dataset, recovered from Singapore in 1996.

Plasmid analysis added another layer of genomic plasticity. R3-type plasmids were the most widely distributed family across Southeast Asia, except in Indonesia where Rp-type plasmids predominated, though the authors caution this is based on a small number of Indonesian genomes from which only 20 plasmids were identified. At the subtype level, R3T1 was the most prevalent plasmid subtype overall, detected in isolates from Cambodia, Myanmar, Malaysia, Singapore, and Thailand, while Rp-T1 predominated in Indonesia and Vietnam. A total of 136 genomes, or 15.9%, had no detectable plasmid replicon. Plasmid-associated resistance determinants linked mainly to R3-type plasmids included tet39-tetR modules mediating tetracycline resistance, the beta-lactam resistance genes blaTEM-1 and blaOXA-72, and aminoglycoside resistance determinants. The authors note that not all Acinetobacter plasmids are typeable, citing their recent report of a large non-typeable multidrug-resistant plasmid harbouring carbapenemase genes among non-GC clones in Malaysia.

Beyond antimicrobial resistance, the survey examined phage defence systems, revealing considerable lineage-level heterogeneity. GC2 was mainly associated with SspBCDE and Gao-type systems, whereas GC1 isolates more commonly carried Gabija and restriction-modification systems. Among other global clones, restriction-modification systems predominated in GC7, GC8, GC10, and GC11, though each lineage showed a different secondary defence system: GC11 isolates harboured Septu, GC7 was more commonly associated with CRISPR-Cas subtype I-F, and GC5 was notable for carrying only the Paris defence system. Non-GC isolates differed from the dominant GC2 population, with restriction-modification systems again the most frequent, followed by PD-type and CRISPR-Cas-type systems. The authors suggest these patterns support the view that phage defence systems in A. baumannii are shaped by clonal background and may influence susceptibility to different phages, a consideration increasingly relevant as phage therapy gains renewed attention for multidrug-resistant A. baumannii, since different clones may require different phages or tailored phage cocktails.

The study’s authors emphasise that the current Southeast Asian genomic picture is limited by strong clinical and human-sampling bias, and that the dataset should be regarded as a regional baseline rather than a comprehensive picture of A. baumannii diversity. Because public genomes from several countries were derived from a limited number of hospitals or research projects, the study cannot fully distinguish between country-wide patterns and institution-specific local expansions, an issue illustrated for Malaysia where many publicly available genomes originated from a single hospital. The authors also highlight the persistence of non-dominant and non-GC lineages, noting that some carried substantial repertoires of resistance determinants, implying that clinically important resistance potential is not confined to the dominant GC2 background. They point to recent studies of community-derived A. baumannii in Malaysia, where community isolates were generally more genetically diverse than hospital collections and mostly non-GC, yet still carried intrinsic beta-lactamase genes, virulence-associated determinants, and plasmids, suggesting community-associated isolates may act as a reservoir of genomic diversity that partly overlaps with clinical populations.

Looking forward, the authors argue that the next step for Southeast Asian countries is not simply to accumulate more genomes, but to broaden sampling in a geographically, epidemiologically, and ecologically representative manner, including under-sampled countries, community carriage, non-GC lineages, and non-human reservoirs such as livestock, wastewater, and aquatic environments. They also note that addressing disparities in regional capacity will be equally important, since generating timely genomic surveillance data requires not only access to sequencing technologies but also adequate computational infrastructure, bioinformatics expertise, and sustained workforce capacity. A practical next step, they propose, would be the development of a coordinated Southeast Asian pathogen genomics surveillance consortium applying shared minimum sampling and metadata standards, supporting sequencing and computational infrastructure in under-represented settings, incorporating community and One Health reservoirs, and promoting timely deposition of genomic and epidemiological data in public repositories. The study serves, in the authors’ words, as an early map of the voyages of A. baumannii in Southeast Asia, one that already reveals the regional dominance of GC2 and the resistance- and defence-associated elements shaping its evolution, even as the map remains far from complete.

Subject of Research: Genomic population structure, antimicrobial resistome, plasmids, resistance islands and phage defence systems of Acinetobacter baumannii in Southeast Asia

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

Article References: Lean, S. S., Palittapongarnpim, P., Clarke, S. C., & Yeo, C. C. (2026). Charting the Voyages of Acinetobacter baumannii in Southeast Asia: Mapping the Regional Genomic Landscape. MicrobiologyOpen, 15(6), Article e70446. https://doi.org/10.1002/mbo3.70446

Image Credits: AI Generated

DOI: 10.1002/mbo3.70446

Keywords: Acinetobacter baumannii, genomic surveillance, Global Clone 2, antimicrobial resistance, Southeast Asia, resistance islands, plasmids, phage defence systems, blaOXA-23, PubMLST, hospital-associated pathogens, One Health