Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

Dingle, K. E.; Freeman, J.; Didelot, X.; Eyre, D. W.; Swann, J.; Spittal, W.; Clark, E. V.; Jolley, K. A.; Walker, A. S.; Wilcox, M. H.; Crook, D. W.

doi:10.1101/2022.05.23.493179

bioRxiv · 10.1101/2022.05.23.493179

Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

Dingle, K. E.·Freeman, J.·Didelot, X.·Eyre, D. W.·Swann, J.·Spittal, W.·Clark, E. V.·Jolley, K. A.·Walker, A. S.·Wilcox, M. H.·Crook, D. W.

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Abstract

Clostridioides difficile remains a key cause of healthcare-associated infection, with multi-drug-resistant (MDR) lineages causing high mortality ([≥]20%) outbreaks. Cephalosporin treatment is a long-established risk factor, and antimicrobial stewardship a key control. A mechanism underlying raised cephalosporin MICs has not been identified in C. difficile, but among other species resistance is often acquired via amino acid substitutions in cell wall transpeptidases (penicillin binding proteins, PBPs). Here, we investigated five C. difficile transpeptidases (PBP1-5) for recent substitutions. Previously published genome assemblies (n=7096) were obtained, representing sixteen geographically widespread lineages, including healthcare-associated MDR ST1(027), ST3(001) and ST17(018). Recent amino acid substitutions were found within PBP1 (n=50) and PBP3 (n=48), ranging from 1-10 substitutions per genome. {beta}-lactam MICs were measured for closely related pairs of wild-type and PBP substituted isolates separated by 20-273 SNPs. Recombination-corrected, dated phylogenies were constructed to date substitution acquisition. Key substitutions such as PBP3 V497L and PBP1 T674I/N/V emerged independently across multiple lineages. They were associated with extremely high cephalosporin MICs; 1-4 doubling dilutions >wild-type up to [≤]1506g/ml. Substitution patterns varied by lineage and clade, showed geographic structure, and notably occurred post-1990, coincident with the acquisition of gyrA/B substitutions conferring fluoroquinolone resistance. In conclusion, recent PBP1 and PBP3 substitutions are associated with raised cephalosporin MICs in C. difficile. The co-occurrence of resistance to cephalosporins and fluoroquinolones hinders attempts to understand their relative importance in the dissemination of epidemic lineages. Further controlled studies of cephalosporin and fluoroquinolone stewardship are needed to determine their relative effectiveness in outbreak control. IMPORTANCEFluoroquinolone and cephalosporin prescribing in healthcare settings have triggered outbreaks of high-mortality, multi-drug resistant C. difficile infection. Here, we identify a mechanism of acquired cephalosporin resistance in C. difficile, comprising amino acid substitutions in two cell-wall transpeptidase enzymes (penicillin binding proteins). The higher the number of substitutions, the greater the impact on phenotype. Dated phylogenies revealed that resistance to both cephalosporins and fluoroquinolones was co-acquired immediately before clinically important, outbreak strains emerged. PBP substitutions were geographically structured within genetic lineages, suggesting adaptation to local antimicrobial prescribing. Antimicrobial stewardship of cephalosporins and fluoroquinolones is an effective means of C. difficile outbreak control. Genetic changes conferring resistance likely impart a fitness-cost after antibiotic withdrawal. Our study identifies a mechanism that may explain the contribution of cephalosporin stewardship to resolving outbreak conditions. However, due to the co-occurrence of cephalosporin and fluoroquinolone resistance, further work is needed to determine the relative importance of each.

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Dingle, K. E., Freeman, J., Didelot, X., Eyre, D. W., Swann, J., Spittal, W., Clark, E. V., Jolley, K. A., Walker, A. S., Wilcox, M. H., Crook, D. W.. 2022-05-25. Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile. https://doi.org/10.1101/2022.05.23.493179

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