New isolates from the 1970s to early 2000s provide insights into the evolution of Acinetobacter baumannii international clone 2 and its resistome

Neil, Matthew, Grenier, Frédéric, Allard, Nancy, Langridge, Gemma C., Castillo-Ramirez, Santiago, Haraoui, Louis-Patrick and Evans, Benjamin A. ORCID: https://orcid.org/0000-0001-6849-9758 (2026) New isolates from the 1970s to early 2000s provide insights into the evolution of Acinetobacter baumannii international clone 2 and its resistome. Microbial Genomics. ISSN 2057-5858 (In Press)

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Abstract

Acinetobacter baumannii remains a pervasive nosocomial pathogen, with international clone 2 (IC2) being the most successful lineage. IC2 is often discussed as a singular entity, and the genomic factors behind its success over other lineages are poorly characterised. This study aimed to track genomic changes occurring around the expansion of IC2 and further determine the within-clone population structure. A set of historical A. baumannii isolates from the 1970s to early 2000s were long-read sequenced and assembled into high-quality chromosomes. These were then used to supplement publicly available A. baumannii genomes, producing a dataset of 1,281 chromosomes derived from isolates collected across six continents. A recombination-free phylogeny was produced and combined with antimicrobial resistance gene (ARG) presence/absence data. Analysis showed that IC2 became the dominant lineage around 2005, which coincides with the acquisition of oxa23 and AbGRI3. Further, IC2 can be split into at least four distinct groups. Groups 1, 2, and 3 represent incremental evolution of the A. baumannii chromosome over time, while group 4 represents a separate evolutionary path distinct from the main IC2 lineage, which has recently been isolated at higher frequency.

Item Type:	Article
Additional Information:	Data summary: Sequencing data and assembled genomes for all isolates sequenced in this study is available on the sequence read archive (SRA) and GenBank respectively under BioProject PRJNA1404816. BioSample accessions for individual isolates can be found in Table S1.
Uncontrolled Keywords:	antimicrobial resistance,pathogen evolution,bacterial genomics,mobile genetic element
Faculty \ School:	Faculty of Science Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Groups > Pathogen Biology Group Faculty of Medicine and Health Sciences > Research Groups > Gastroenterology and Gut Biology Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Depositing User:	LivePure Connector
Date Deposited:	16 Jun 2026 09:20
Last Modified:	18 Jun 2026 21:01
URI:	https://ueaeprints.uea.ac.uk/id/eprint/103407
DOI:

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