Satheesh Nair​, Clare R. Barker​, Matthew Bird​, David R. Greig​, Caitlin Collins, Anaïs Painset​Marie Chattaway​, Derek Pickard​, Lesley Larkin​, Saheer Gharbia,​ Xavier Didelot​ and Paolo Ribeca

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 blaCTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, 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. Microbial Genomics. May 2024

Rapid expansion and international spread of M1UK in the post-pandemic UK upsurge of Streptococcus pyogenes

The UK observed a marked increase in scarlet fever and invasive group A streptococcal infection in 2022 with severe outcomes in children and similar trends worldwide. Here we report lineage M1_UK to be the dominant source of invasive infections in this upsurge. Compared with ancestral M1_global strains, invasive M1_UK strains exhibit reduced genomic diversity and fewer mutations in two-component regulator genes covRS. The emergence of M1_UK is dated to 2008. Following a bottleneck coinciding with the COVID-19 pandemic, three emergent M1_UK clades underwent rapid nationwide expansion, despite lack of detection in previous years. All M1_UK isolates thus-far sequenced globally have a phylogenetic origin in the UK, with dispersal of the new clades in Europe. While waning immunity may promote streptococcal epidemics, the genetic features of M1_UK point to a fitness advantage in pathogenicity, and a striking ability to persist through population bottlenecks. Nature Communications. May 2024