1887

Abstract

has emerged as an important opportunistic pathogen worldwide, being responsible for large outbreaks for nosocomial infections, primarily in intensive care units. ATCC 19606 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 ATCC 19606 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 ATCC 19606, then performed a comparative genome analysis between ATCC 19606 strains from several research laboratories and a reference collection. Differences between publicly available ATCC 19606 genome sequences were observed, including SNPs, macro- and micro-deletions, and the uneven presence of a 52 kb prophage belonging to genus . 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 analysis of p1ATCC19606, and experimentally confirmed. This work refines the sequence, structure and functional annotation of the ATCC 19606 genome, and highlights some remarkable differences between domesticated strains, likely resulting from genetic drift.

Funding
This study was supported by the:
  • Regione Lazio (Award no. A0375-2020-36558 GAVAP)
    • Principle Award Recipient: PaoloVisca
  • Regione Lazio (Award no. 85-2017-13763 ANTIMET)
    • Principle Award Recipient: PaoloVisca
  • Ministero dell’Istruzione, dell’Università e della Ricerca (Award PRIN 2017 (Prot. 20177J5Y3P))
    • Principle Award Recipient: PaoloVisca
  • Ministero dell’Istruzione, dell’Università e della Ricerca (Award Excellence Departments grant (art. 1, commi 314–337 Legge 232/2016) to the Department of Science, Roma Tre University)
    • Principle Award Recipient: NotApplicable
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2022-05-18
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