Harry A Thorpe

Abstract Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmision Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host.

Abstract Bacterial polysaccharide capsules contribute to antigenic diversity and immune evasion. Escherichia coli infections, including those caused by extraintestinal pathogenic E. coli (ExPEC), cause substantial antimicrobial resistance-associated morbidity and mortality. However, much-needed genotypic methods for E. coli capsule typing to aid epidemiological analysis and therapeutic design are lacking.

Introduction Klebsiella pneumoniae is a WHO priority pathogen that can cause serious disease in humans and animals.1 Health-care associated K pneumoniae strains, such as ST307 and ST11, can harbour plasmids encoding resistance to carbapenems, or multiple antimicrobials.2 These lineages are largely distinct from those responsible for severe disease in the community (hypervirulent K pneumoniae), which carry plasmids harbouring multiple virulence loci, such as those encoding siderophores (eg,...