1887

Abstract

Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a gene conferring extended-spectrum beta-lactamase (ESBL) resistance in serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in , in this study we carried out a follow-up retrospective analysis of UK isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene , identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to . Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in , our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.

Funding
This study was supported by the:
  • National Institute for Health Research Health Protection Research Unit (Award Gastrointestinal Infections)
    • Principle Award Recipient: PaoloRibeca
  • National Institute for Health Research Health Protection Research Unit (Award Gastrointestinal Infections)
    • Principle Award Recipient: XavierDidelot
  • National Institute for Health Research Health Protection Research Unit (Award Gastrointestinal Infections)
    • Principle Award Recipient: DavidR Greig
  • National Institute for Health Research Health Protection Research Unit (Award Healthcare Associated Infections and Antimicrobial Resistance)
    • Principle Award Recipient: MatthewBird
  • National Institute for Health Research Health Protection Research Unit (Award Genomics and Enabling Data)
    • Principle Award Recipient: PaoloRibeca
  • National Institute for Health Research Health Protection Research Unit (Award Genomics and Enabling Data)
    • Principle Award Recipient: XavierDidelot
  • National Institute for Health Research Health Protection Research Unit (Award Genomics and Enabling Data)
    • Principle Award Recipient: MarieChattaway
  • National Institute for Health Research Health Protection Research Unit (Award Genomics and Enabling Data)
    • Principle Award Recipient: CaitlinCollins
  • National Institute for Health Research Health Protection Research Unit (Award Genomics and Enabling Data)
    • Principle Award Recipient: ClareR Barker
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-05-08
2024-05-26
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