Global genomic dissection of antimicrobial resistance inSalmonellaTyphimurium

Abstract

AbstractBackgroundSalmonellaTyphimurium (STm) is a globally prevalent pathogen causing disease in both humans and animals. Antibiotics are required for the treatment of invasive salmonellosis and increasing resistance poses a treatment challenge. Comprehensive whole-genome sequencing based surveillance efforts, especially of USA and UK, and open access databases presented an opportunity to comprehensively analyse the genomic antimicrobial resistance (AMR) to key clinically-relevant antibiotics within this dataset.MethodsIn this study, we identified and analysed resistance to fourteen key antibiotics using AbritAMR, and integrated the identified resistance with multilevel genome typing (MGT). AMR carriage and trends were assessed by genomic types at different MGT levels.FindingsIn the complete dataset, 47% of the isolates were resistant to at least one drug – however resistance varied considerably by genomic types, geography, and time. When comparing data from 2019-2022, we observed USA had higher resistance to cefotaxime (AmpC) and gentamicin, whereas UK had higher resistance to multiple drugs including azithromycin and cefotaxime (ESBL). Within the 2015-2022 isolates, we identified 166 sequence types (STs) at different MGT levels with >80% resistance to at least one drug. We grouped these STs over time to reveal 20 predominant temporal patterns. We also identified STs that were expanding regionally, and those were source specific.InterpretationThe availability of global datasets enabled delineation of AMR trends within STm. Furthermore, integration of AMR with MGT genome typing provided sharable, standardised, and specific identification and tracking of resistant genomic types. This integrated analysis presents a unique approach for global surveillance of AMR and AMR strains.