Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi. 2022

David R Greig, and Matthew T Bird, and Marie Anne Chattaway, and Gemma C Langridge, and Emma V Waters, and Paolo Ribeca, and Claire Jenkins, and Satheesh Nair
National Infection Service, UK Health Security Agency, London NW9 5EQ, UK.

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.

UI MeSH Term Description Entries
D010957 Plasmids Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS. Episomes,Episome,Plasmid
D001435 Bacteriophages Viruses whose hosts are bacterial cells. Phages,Bacteriophage,Phage
D001618 beta-Lactamases Enzymes found in many bacteria which catalyze the hydrolysis of the amide bond in the beta-lactam ring. Well known antibiotics destroyed by these enzymes are penicillins and cephalosporins. beta-Lactamase,beta Lactamase,beta Lactamases
D012485 Salmonella typhi A serotype of SALMONELLA ENTERICA which is the etiologic agent of TYPHOID FEVER. Salmonella enterica serovar Typhi,Salmonella typhosa
D017101 Bacteriophage P1 A species of temperate bacteriophage in the genus P1-like viruses, family MYOVIRIDAE, which infects E. coli. It is the largest of the COLIPHAGES and consists of double-stranded DNA, terminally redundant, and circularly permuted. Coliphage P1,Enterobacteria phage P1,P1 Phage,Phage P1,P1 Phages,Phage, P1,Phages, P1
D024901 Drug Resistance, Multiple, Bacterial The ability of bacteria to resist or to become tolerant to several structurally and functionally distinct drugs simultaneously. This resistance may be acquired through gene mutation or foreign DNA in transmissible plasmids (R FACTORS). Drug Resistance, Extensive, Bacterial,Drug Resistance, Extensively, Bacterial,Extensive Antibacterial Drug Resistance,Extensively Antibacterial Drug Resistance,Multidrug Resistance, Bacterial,Multiple Antibacterial Drug Resistance,Bacterial Multidrug Resistance,Bacterial Multidrug Resistances,Resistance, Bacterial Multidrug

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