Jepson, R. | bioRxiv Science

bioRxiv2026

New paradigm of CRISPR spacerome for classification of global Escherichia coli lineages

Our research team has recently identified a proof-of-concept for a previously unrecognized spacerome signature in a subset of globally distributed E. coli. Motivated by our initial observation, we pursued a more in-depth CRISPR spacerome analysis, which revealed a novel insight in discrimination of global E. coli sequence type (ST) lineages. We systematically retrieved publicly available E. coli complete genomes, analyzed and compared CRISPR spacerome of globally distributed strains. We found that global strains harbored spacerome that has remained conserved spaceromes for decades across multiple continents. Strains with the conserved spacerome belong to specific ST lineages of clinical importance. In addition, most protospacers were assigned to Gammaproteobacteria and Caudoviricetes. Our findings reveal unexpected long-term conservation of CRISPR spaceromes and their potential as high-resolution markers for E. coli epidemiological tracking.

microbiology↗

bioRxiv2025

A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre

IntroductionThere are currently no standardised guidelines for genomic surveillance of One Health (OH) antimicrobial resistance (AMR). This project aimed to utilise metagenomics to identify AMR genes present in a companion animal hospital and compare these with phenotypic results from bacterial isolates from clinical specimens from the same veterinary hospital. MethodsSamples were collected from sites around a primary companion animal veterinary hospital in North London. Metagenomic DNA was sequenced using Oxford Nanopore Technologies (ONT) MinION. The sequencing data were analysed for AMR genes, plasmids and clinically relevant pathogen species. These data were compared to phenotypic speciation and antibiotic susceptibility tests (ASTs) of bacteria isolates from patients. ResultsThe most common resistance genes identified were aph (n=101 times genes were isolated across 48 metagenomic samples), sul (84), blaCARB (63), tet (58) and blaTEM (46). In clinical isolates, a high proportion of phenotypic resistance to the {beta}-lactams was identified. Rooms with the greatest mean number of resistance genes identified per swab site were the medical preparation room, dog ward and surgical preparation room. Twenty-four Gram-positive and four enterobacterial plasmids were identified. Sequencing reads matched with 14/22 (64%) of the phenotypically isolated bacterial species. DiscussionMetagenomics identified AMR genes, plasmids and species of relevance to human and animal medicine. Communal animal-handling areas harboured more AMR genes than areas animals did not frequent. When considering infection prevention and control (IPC) measures, adherence to, and frequency of, cleaning schedules, alongside potentially more comprehensive disinfection of animal-handling areas may reduce the number of potentially harmful bacteria present. PubMed "veterinary" or "companion" AND "AMR" or "resistan*" NOT (Review[Publication Type]) (2018-2023) "veterinary" or "companion" AND "AMR" or "resist*" AND "sequencing" or "metagenomic*" "veterinary" or "companion" AND "AMR" or "resistan*" NOT (Review[Publication Type]) (2018-2023) https://www.iscaid.org/clinical-practice

genomics↗