Convergent evolution of Enterobacteriaceae in epidemiological networks with high antimicrobial use
An overlooked research focus concerning antimicrobial resistance (AMR) is the evolutionary prerequisites that precede AMR emergence. Previous studies investigating AMR in Shigella epidemics co-circulating among men who have sex with men (MSM) in the UK showed that horizontal transfer of plasmids carrying AMR facilitated and enhanced disease transmission, indicating high antimicrobial selection pressure in this demographic. Here, we used these isolates to identify non-AMR changes in Shigella sp. that act as preliminary steps, or 'stepping stones', to AMR evolution. Through genomic and phylogenetic analyses of 3,745 S. sonnei isolates obtained through routine UK surveillance, we identified an association of MSM-status with a phage-plasmid (P-P) borne extra copy of metG, encoding methionine-tRNA synthetase. This gene has been shown previously to be related to antibiotic tolerance, a precursor phenotype for the development of resistance. Post-hoc analyses revealed that the metG-bearing P-P, pWPMR2, was significantly associated with patient MSM-status and increased metG copy number. Extensive sequence variation in the extra metG copies across the dataset suggested that there was unconstrained evolution in the P-P-encoded gene. To explore cognate phenotypic changes, we conducted Bulk Phenotyping of Epidemiological Replicates (BPER) (De Silva et al., 2023) on a phylogenetic subsample of 189 isolates, revealing a longer lag period for the strains carrying the divergent P-P metG copy. This BPER screen is also being complemented by functional microbiology experiments in E. coli to determine the effect of the variant metG on persistence and tolerance to clinically relevant antibiotics. This work shows population-level evidence for antibiotic tolerance accelerating AMR in a real world epidemiological scenario, highlighting the utility of public health genomic surveillance data to accelerate discovery in fundamental pathogen biology.
An overlooked research focus concerning antimicrobial resistance (AMR) is the evolutionary prerequisites that precede AMR emergence. Previous studies investigating AMR in Shigella epidemics co-circulating among men who have sex with men (MSM) in the UK showed that horizontal transfer of plasmids carrying AMR facilitated and enhanced disease transmission, indicating high antimicrobial selection pressure in this demographic. Here, we used these isolates to identify non-AMR changes in Shigella sp. that act as preliminary steps, or 'stepping stones', to AMR evolution. Through genomic and phylogenetic analyses of 3,745 S. sonnei isolates obtained through routine UK surveillance, we identified an association of MSM-status with a phage-plasmid (P-P) borne extra copy of metG, encoding methionine-tRNA synthetase. This gene has been shown previously to be related to antibiotic tolerance, a precursor phenotype for the development of resistance. Post-hoc analyses revealed that the metG-bearing P-P, pWPMR2, was significantly associated with patient MSM-status and increased metG copy number. Extensive sequence variation in the extra metG copies across the dataset suggested that there was unconstrained evolution in the P-P-encoded gene. To explore cognate phenotypic changes, we conducted Bulk Phenotyping of Epidemiological Replicates (BPER) (De Silva et al., 2023) on a phylogenetic subsample of 189 isolates, revealing a longer lag period for the strains carrying the divergent P-P metG copy. This BPER screen is also being complemented by functional microbiology experiments in E. coli to determine the effect of the variant metG on persistence and tolerance to clinically relevant antibiotics. This work shows population-level evidence for antibiotic tolerance accelerating AMR in a real world epidemiological scenario, highlighting the utility of public health genomic surveillance data to accelerate discovery in fundamental pathogen biology.
University of Cambridge