Background Acinetobacter baumannii is classified as a World Health Organization (WHO) priority pathogen and represents a major public health threat, particularly in low-resource settings. Despite its clinical importance, regional genomic data from East Africa remain scarce, limiting the understanding of its population structure and antimicrobial resistance (AMR) landscape. To address this gap, we sought to characterize the pangenomic structure of A. baumannii isolates from East Africa and place them within a broader global genomic context. Methods We conducted a comparative genomic analysis of 104 A. baumannii isolates using publicly available whole-genome sequencing datasets, including 46 isolates originating from Tanzania, Kenya, and Uganda. The analysis integrated multilocus sequence typing (MLST), capsular (K locus) and lipooligosaccharide (O locus) typing, pangenome reconstruction, single-nucleotide polymorphism (SNP)-based phylogenomics, resistome and mobilome profiling, and plasmid replicon characterization to assess population structure, genetic diversity, and resistance determinants. Results The genomic analyses revealed a predominance of high-risk international clones among East African isolates, notably IC1/ST1 and IC2/ST2, alongside the identification of four novel sequence types. Extensive surface polysaccharide diversity was observed, consistent with ongoing recombination and horizontal gene transfer. Pangenome analysis demonstrated an open pangenome with high adaptive potential, comprising 21,831 gene families, of which 76% were classified as cloud genes. Core genome SNP-based phylogeny suggested multiple introductions of global clones into East Africa, with clustering patterns consistent with localized clonal expansion. The resistome analysis revealed widespread intrinsic and acquired AMR determinants, particularly efflux pump systems and clinically significant carbapenemases, including OXA-69, OXA-23, and NDM-1. Additionally, a high abundance of mobile genetic elements associated with resistance was detected, including rare R3-type plasmids carrying multiple AMR genes and linked to high-risk clones. Conclusion The available East African A. baumannii genomes demonstrate genomic signatures consistent with repeated introductions of global high-risk clones and extensive mobilome-driven resistance diversification. These findings underscore the urgent need for expanded, region-specific genomic surveillance and the implementation of more targeted intervention strategies to mitigate the spread and impact of A. baumannii in both clinical and environmental settings across East Africa.

Pangenomic insights into multidrug-resistant Acinetobacter baumannii isolates from East Africa

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2026年4月13日

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Samweli Y. Bahati,
Reuben S. Maghembe

摘要

Background

Acinetobacter baumannii is classified as a World Health Organization (WHO) priority pathogen and represents a major public health threat, particularly in low-resource settings. Despite its clinical importance, regional genomic data from East Africa remain scarce, limiting the understanding of its population structure and antimicrobial resistance (AMR) landscape. To address this gap, we sought to characterize the pangenomic structure of A. baumannii isolates from East Africa and place them within a broader global genomic context.

Methods

We conducted a comparative genomic analysis of 104 A. baumannii isolates using publicly available whole-genome sequencing datasets, including 46 isolates originating from Tanzania, Kenya, and Uganda. The analysis integrated multilocus sequence typing (MLST), capsular (K locus) and lipooligosaccharide (O locus) typing, pangenome reconstruction, single-nucleotide polymorphism (SNP)-based phylogenomics, resistome and mobilome profiling, and plasmid replicon characterization to assess population structure, genetic diversity, and resistance determinants.

Results

The genomic analyses revealed a predominance of high-risk international clones among East African isolates, notably IC1/ST1 and IC2/ST2, alongside the identification of four novel sequence types. Extensive surface polysaccharide diversity was observed, consistent with ongoing recombination and horizontal gene transfer. Pangenome analysis demonstrated an open pangenome with high adaptive potential, comprising 21,831 gene families, of which 76% were classified as cloud genes. Core genome SNP-based phylogeny suggested multiple introductions of global clones into East Africa, with clustering patterns consistent with localized clonal expansion. The resistome analysis revealed widespread intrinsic and acquired AMR determinants, particularly efflux pump systems and clinically significant carbapenemases, including OXA-69, OXA-23, and NDM-1. Additionally, a high abundance of mobile genetic elements associated with resistance was detected, including rare R3-type plasmids carrying multiple AMR genes and linked to high-risk clones.

Conclusion

The available East African A. baumannii genomes demonstrate genomic signatures consistent with repeated introductions of global high-risk clones and extensive mobilome-driven resistance diversification. These findings underscore the urgent need for expanded, region-specific genomic surveillance and the implementation of more targeted intervention strategies to mitigate the spread and impact of A. baumannii in both clinical and environmental settings across East Africa.