Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains

Author:

Artuso Irene1ORCID,Lucidi Massimiliano1ORCID,Visaggio Daniela21ORCID,Capecchi Giulia1ORCID,Lugli Gabriele Andrea3ORCID,Ventura Marco3ORCID,Visca Paolo21ORCID

Affiliation:

1. Department of Science, Roma Tre University, Viale G. Marconi 446, 00146 Rome, Italy

2. Santa Lucia Fundation IRCCS, Via Ardeatina 306-354, 00179 Rome, Italy

3. Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parco Area delle Scienze 11a, 43124 Parma, Italy

Abstract

Acinetobacter baumannii has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. A. baumannii ATCC 19606T is the species type strain, and a reference organism in many laboratories due to its low virulence, amenability to genetic manipulation and extensive antibiotic susceptibility. We wondered if frequent propagation of A. baumannii ATCC 19606T in different laboratories may have driven micro- and macro-evolutionary events that could determine inter-laboratory differences of genome-based data. By combining Illumina MiSeq, MinION and Sanger technologies, we generated a high-quality whole-genome sequence of A. baumannii ATCC 19606T, then performed a comparative genome analysis between A. baumannii ATCC 19606T strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606T genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus Vieuvirus. Two plasmids, pMAC and p1ATCC19606, were invariably detected in all tested strains. The presence of a putative replicase, a replication origin containing four 22-mer direct repeats, and a toxin-antitoxin system implicated in plasmid stability were predicted by in silico analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the A. baumannii ATCC 19606T genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.

Funder

Ministero dell’Istruzione, dell’Università e della Ricerca

Regione Lazio

Publisher

Microbiology Society

Subject

General Medicine

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