Exploring the extent of uncatalogued genetic variation in antimicrobial resistance gene families inEscherichia coli
Authors: Lipworth Samuel , Crook Derrick , Walker A. Sarah , Peto Tim , Stoesser Nicole 
Published: March 2023

Background

Antimicrobial resistance (AMR) inE. coliis a global problem associated with substantial morbidity and mortality. AMR-associated genes are typically annotated based on similarity to a variants in a curated reference database with an implicit assumption that uncatalogued genetic variation within these is phenotypically unimportant. In this study we evaluated the potential for discovering new AMR-associated gene families and characterising variation within existing ones to improve genotype-to-susceptibility-phenotype prediction inE. coli.

Methods

We assembled a global dataset of 9001E. colisequences of which 8586 had linked antibiotic susceptibility data. Raw reads were assembled using Shovill and AMR genes extracted using the NCBI AMRFinder tool. Mash was used to calculate the similarity between extracted genes using Jaccard distances. We empirically reclustered extracted gene sequences into AMR-associated gene families (70% match) and alleles (ARGs, 100% match).

Results

The performance of the AMRFinder database for genotype-to-phenotype predictions using strict 100% identity and coverage thresholds did not meet FDA thresholds for any of the eight antibiotics evaluated. Relaxing filters to default settings improved sensitivity with a specificity cost. For all antibiotics, a small number of genes explained most resistance although a proportion could not be explained by known ARGs; this ranged from 75.1% for co-amoxiclav to 3.4% for ciprofloxacin. Only 17,177/36,637 (47%) of ARGs detected had a 100% identity and coverage match in the AMRFinder database. After empirically reclassifying genes at 100% nucleotide sequence identity, we identified 1292 unique ARGs of which 158 (12%) were present ≥10 times, 374 (29%) were present 2-9 times and 760 (59%) only once. Simulated accumulation curves revealed that discovery of new (100%-match) ARGs present more than once in the dataset plateaued relatively quickly whereas new singleton ARGs were discovered even after many thousands of isolates had been included. We identified a strong correlation (Spearman coefficient 0.76 (95% CI 0.72-0.79, p<0.001)) between the number of times an ARG was observed in Oxfordshire and the number of times it was seen internationally, with ARGs that were observed 7 times in Oxfordshire always being found elsewhere. Finally, using the example ofblaTEM-1, we demonstrated that uncatalogued variation, including synonymous variation, is associated with potentially important phenotypic differences (e.g. two common, uncataloguedblaTEM-1alleles with only synonymous mutations compared to the known reference were associated with reduced resistance to co-amoxiclav [aOR 0.57, 95%CI 0.34-0.93, p=0.03] and piperacillin-tazobactam [aOR 0.54, 95%CI 0.32-0.87, p=0.01]).

Conclusions

Overall we highlight substantial uncatalogued genetic variation with respect to known ARGs, although a relatively small proportion of these alleles are repeatedly observed in a large international dataset suggesting strong selection pressures. The current approach of using fuzzy matching for ARG detection, ignoring the unknown effects of uncatalogued variation, is unlikely to be acceptable for future clinical deployment. The association of synonymous mutations with potentially important phenotypic differences suggests that relying solely on amino acid-based gene detection to predict resistance is unlikely to be sufficient. Finally, the inability to explain all resistance using existing knowledge highlights the importance of new target gene discovery.