A dissection of the genomic antimicrobial resistance epidemiology of Salmonella Typhimurium
Kaur, S.; Payne, M.; Partridge, S. R.; Sintchenko, V.; Lan, R.
Show abstract
Salmonella Typhimurium (STm) is a globally prevalent pathogen. We compiled a dataset comprising [~]65,000 publicly available STm isolates and analysed the predicted-resistance to 15 key antibiotics. Additionally, we typed all isolates using a standardized typing method, multilevel genome typing (MGT), and characterised the resistance profiles by MGT sequence types (ST). We identified 407 MGT STs wherein at least 80% of the isolates were non-susceptible to at least one antibiotic. For the key antibiotics prescribed for severe salmonellosis, we identified three ciprofloxacin non-susceptible MGT STs, and eight cefotaxime non-susceptible MGT STs in the last two years of the dataset (2021-2022). While the ciprofloxacin non-susceptible MGT STs comprised isolates predominantly from the UK; only one cefotaxime non-susceptible MGT ST comprised isolates predominantly from UK and associated with swine, with others from USA, and associated with cattle and poultry. Integration of AMR predictions with MGT strain typing provides sharable, standardised, and specific identification and tracking of resistant isolates. This integrated analysis presents a unique approach for the global surveillance of antimicrobial resistance and resistant strains.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Consideration of within-patient diversity highlights transmission pathways and antimicrobial resistance gene variability in vancomycin resistant Enterococcus faecium 95%
- Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study 95%
- Emergence of a cephalosporin reduced susceptible Neisseria gonorrhoeae clone between 2014-2019 in Amsterdam, the Netherlands, revealed by a genomic population analysis 95%
Similar papers in this journal
- Piperacillin/tazobactam resistant, cephalosporin susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types 96%
- Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study 95%
- The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom 95%
Similar papers in this journal
- A Panel of Diverse Pseudomonas aeruginosa Clinical Isolates for Research and Development 93%
- Predominance of multidrug-resistant (MDR) bacteria causing urinary tract infections (UTIs) among symptomatic patients in East Africa: a call for action 93%
- Tracking Antimicrobial Resistant Organisms Timely (TAROT): A Workflow Validation Study for Successive Core-genome SNP-based Nosocomial Transmission Analysis 93%
Similar papers in this journal
- Genomic surveillance of antimicrobial resistance shows cattle are a moderate source of multi-drug resistant non-typhoidal Salmonella in Mexico 95%
- Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content 95%
- Missing pstS locus associated with an insertion in tetM in vancomycin resistant Enterococcus faecium 95%
Similar papers in this journal
- Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit 94%
- GPT-4 based AI agents - the new expert system for detection of antimicrobial resistance mechanisms? 93%
- The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates 93%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.