In silico and in vitro comparative analysis of 79 Acinetobacter baumannii clinical isolates

Scarrone, Martina; Turner, Dann; Dion, Moïra; Tremblay, Denise; Moineau, Sylvain

Abstract

Acinetobacter baumannii is a significant nosocomial bacterial pathogen that poses a substantial infection risk due to its high resistance to antibiotics and ability to survive in hospital environments. In this study, we performed comprehensive in silico and in vitro analyses on 79 A. baumannii clinical isolates from different geographical locations to uncover their genomic and epidemiological characteristics as well as their antibiotic and phage susceptibilities. Our findings revealed considerable genomic diversity among the isolates, as shown by average nucleotide identity (ANI) heat maps, multilocus sequence typing (MLST), and core genome MLST (cgMLST). We identified several international clones known for their high antibiotic resistance and global prevalence. Surprisingly, we also observed that the number of antimicrobial resistance genes (ARGs) was higher in isolates containing CRISPR-Cas systems. Plaque assays with 13 phages indicated that Acinetobacter phages have a narrow host range, with capsule loci (KL) serving as a good indicator of phage-bacteria interactions. The presence of CRISPR-Cas systems and other antiviral defense mechanisms in A. baumannii genomes also appears to play a key role in providing phage resistance, regardless of the phage receptors. We also found that spacers associated with subtypes I-F1 and I-F2 CRISPR-Cas systems predominantly target prophages, suggesting a role in maintaining genomic stability and contributing to phage-bacteria co-evolution. Overall, this study provides a set of highly characterized A. baumannii clinical isolates for future studies on antibiotic-phage-bacteria interactions.

• Journal Article Type: Article
• Acceptance Date: Apr 8, 2025
• Online Publication Date: May 16, 2025
• Publication Date: Jul 11, 2025
• Deposit Date: Jun 26, 2025
• Publicly Available Date: Jul 25, 2025
• Journal: Microbiology Spectrum
• Electronic ISSN: 2165-0497
• Publisher: American Society for Microbiology
• Peer Reviewed: Peer Reviewed
• Volume: 13
• Issue: 7
• Article Number: e02849-24
• DOI: https://doi.org/10.1128/spectrum.02849-24
• Public URL: https://uwe-repository.worktribe.com/output/14449386
• Publisher URL: https://journals.asm.org/
• Additional Information: Received: 2024-11-12; Accepted: 2025-04-08; Published: 2025-05-16