Using Genetic Distance from Archived Samples for the Prediction of Antibiotic Resistance in Escherichia coli.

Antimicrobial Agents and Chemotherapy
Derek R MacFaddenWilliam P Hanage

Abstract

The rising rates of antibiotic resistance increasingly compromise empirical treatment. Knowing the antibiotic susceptibility of a pathogen's close genetic relative(s) may improve empirical antibiotic selection. Using genomic and phenotypic data for Escherichia coli isolates from three separate clinically derived databases, we evaluated multiple genomic methods and statistical models for predicting antibiotic susceptibility, focusing on potentially rapidly available information, such as lineage or genetic distance from archived isolates. We applied these methods to derive and validate the prediction of antibiotic susceptibility to common antibiotics. We evaluated 968 separate episodes of suspected and confirmed infection with Escherichia coli from three geographically and temporally separated databases in Ontario, Canada, from 2010 to 2018. Across all approaches, model performance (area under the curve [AUC]) ranges for predicting antibiotic susceptibility were the greatest for ciprofloxacin (AUC, 0.76 to 0.97) and the lowest for trimethoprim-sulfamethoxazole (AUC, 0.51 to 0.80). When a model predicted that an isolate was susceptible, the resulting (posttest) probabilities of susceptibility were sufficient to warrant empirical t...Continue Reading

References

Apr 25, 2002·Emerging Infectious Diseases·Marc Lipsitch, Matthew H Samore
Sep 19, 2007·Pediatrics·Dimitrios DoganisKonstantinos Sinaniotis
Mar 12, 2011·The Journal of Antimicrobial Chemotherapy·Humera NazirDiarmaid Hughes
Jun 27, 2014·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Derek R MacFaddenNick Daneman
Nov 3, 2016·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·Tristan T TimbrookKerry L LaPlante
Mar 20, 2019·Nature Reviews. Genetics·Manish BoolchandaniGautam Dantas
Feb 12, 2020·Nature Microbiology·Karel BřindaWilliam P Hanage

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Citations

Jul 14, 2020·Bioinformatics·Camille MarchetRayan Chikhi

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Software Mentioned

NextSeq
Mash
Nextera

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