Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi

Abstract

Antimicrobial-resistance (AMR) genes can be transferred between microbial cells via horizontal gene transfer (HGT), which involves mobile and integrative elements such as plasmids, bacteriophages, transposons, integrons and pathogenicity islands. Bacteriophages are found in abundance in the microbial world, but their role in virulence and AMR has not fully been elucidated in the Enterobacterales. With short-read sequencing paving the way to systematic high-throughput AMR gene detection, long-read sequencing technologies now enable us to establish how such genes are structurally connected into meaningful genomic units, raising questions about how they might cooperate to achieve their biological function. Here, we describe a novel ~98 kbp circular P1-bacteriophage-like plasmid termed ph681355 isolated from a clinical Salmonella enterica serovar Typhi isolate. It carries bla _CTX-M-15, an IncY plasmid replicon (repY gene) and the ISEcP1 mobile element and is, to our knowledge, the first reported P1-bacteriophage-like plasmid (phage-plasmid) in S. enterica Typhi. We compared ph681355 to two previously described phage-plasmids, pSJ46 from S. enterica serovar Indiana and pMCR-1-P3 from Escherichia coli, and found high nucleotide similarity across the backbone. However, we saw low ph681355 backbone similarity to plasmid p60006 associated with the extensively drug-resistant S. enterica Typhi outbreak isolate in Pakistan, providing evidence of an alternative route for bla _CTX-M-15 transmission. Our discovery highlights the importance of utilizing long-read sequencing in interrogating bacterial genomic architecture to fully understand AMR mechanisms and their clinical relevance. It also raises questions regarding how widespread bacteriophage-mediated HGT might be, suggesting that the resulting genomic plasticity might be higher than previously thought.

Keywords: Illumina; Nanopore; Salmonella enterica serovar Typhi; bacteriophage; phage-plasmid; plasmid.

Fig. 1.

brig plot of ph681355 as the reference versus PMCR-1-P3 phage-plasmid shown as the blue ring (GenBank accession no. KX880944) – E coli plasmid; bacteriophage P1 as the red ring (accession no. AF234172); plasmid p60006 as the green ring (accession no. LT906492) – S . enterica Typhi; and finally SJ46 phage-plasmid (accession no. NC_031129) shown as the yellow ring. Also shown are CDSs (genes) on the outer ring, with green showing AMR cassette, blue showing plasmid maintenance genes, black showing bacteriophage-associated genes and red showing hypothetical proteins.

Fig. 2.

Integrative Genomics Viewer (igv) visualization of the alignment of reads for the region of ph681355 where the bla _CTX-M-15 is located (top). Also showing the same alignment with only reads spanning across the bla _CTX-M-15 mobile genetic element (middle). Finally, showing the alignment of reads with the bla _CTX-M-15 mobile genetic element removed in silico (bottom). The red line above each part of the figure (top, middle, bottom) indicates the tnpA-Hypo-bla-Hypo element.