August 4, 2025

Isolation genomic characterisation of a Multidrug-Resistant Acinetobacter baumannii ST149 from India: An emerging threat beyond the known international clones

Key Points

A multidrug-resistant Acinetobacter baumannii strain ST149 was isolated from discarded culture plates.
The strain lacks association with known international clones but carries multiple antimicrobial resistance genes.
Whole genome sequencing revealed complex profiles of mobile genetic elements enhancing virulence potential.
This research underscores the emerging threat posed by rare sequence types like ST149 in clinical settings.

Abstract

Abstract Background Multidrug-resistant (MDR) Acinetobacter baumannii is a Gram-negative, non-motile, non-fermenting, and strictly aerobic bacillus. It causes high mortality and morbidity rates among hospitalized patients with a compromised immune system. Whole genome sequencing, Multilocus sequence typing (MLST) and clonal complex (CC) analysis enable us to get more information about the clonal diversity, molecular epidemiology of the bacteria, their AMR phenotype and virulence potential. This study was aimed to explore the genomic attributes of an A. baumannii strain isolated from the discarded culture plates infection to determine its virulence and antimicrobial resistance traits. Methods Here, we isolated a clinical isolate of carbapenem-resistant A. baumannii. Then we performed Transmission Electron Microscopy (TEM) and whole genome sequencing (WGS) through Illumina sequencing, followed by bioinformatics analyses. The genome was analysed for the phylogeny, antimicrobial resistance (AMR) genes, prophage regions and virulence-related genes, as well as the mobile genetic elements(MGEs) using various bioinformatics tools. Findings: Multilocus sequence typing (MLST) suggests the isolate as Acinetobacter baumannii ST149, a sequence type that is rarely reported in clinical settings. Phylogenetic analysis revealed that this strain does not cluster with the known International Clones (ICs), yet it harbors a broad repertoire of antimicrobial resistance (AMR) genes. Despite its low prevalence, this isolate (ST149) may pose a significant clinical threat due to its multidrug-resistant (MDR) phenotype and potentially hypervirulent nature. Whole-genome sequencing analysis further uncovered a complex resistome profile associated with various mobile genetic elements (MGEs), including integrons, gene cassettes, and prophage elements, all contributing to its adaptability and pathogenicity. Additionally, the genome encodes numerous hypothetical proteins, many of which remain functionally uncharacterized. Notably, structural prediction using AlphaFold2 identified one such hypothetical protein as a putative member of the Major Facilitator Superfamily (MFS) of transporters, suggesting a potential role in antimicrobial resistance.

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