Mutational signature analysis predicts bacterial hypermutation and multidrug resistance

Kalen M. Hall, Leonard G. Williams, Richard D. Smith, Erin A. Kuang, Robert K. Ernst, Christine M. Bojanowski, William C. Wimley, Lisa A. Morici () and Zachary F. Pursell ()
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Kalen M. Hall: School of Medicine, Tulane University
Leonard G. Williams: School of Medicine, Tulane University
Richard D. Smith: School of Dentistry, University of Maryland
Erin A. Kuang: School of Medicine, Tulane University
Robert K. Ernst: School of Dentistry, University of Maryland
Christine M. Bojanowski: School of Medicine, Tulane University
William C. Wimley: School of Medicine, Tulane University
Lisa A. Morici: School of Medicine, Tulane University
Zachary F. Pursell: School of Medicine, Tulane University

Nature Communications, 2025, vol. 16, issue 1, 1-16

Abstract: Abstract Bacteria of clinical importance, such as Pseudomonas aeruginosa, can become hypermutators upon loss of DNA mismatch repair (MMR) and are clinically correlated with high rates of multidrug resistance (MDR). Here, we demonstrate that hypermutated MMR-deficient P. aeruginosa has a unique mutational signature and rapidly acquires MDR upon repeated exposure to first-line or last-resort antibiotics. MDR acquisition was irrespective of drug class and instead arose through common resistance mechanisms shared between the initial and secondary drugs. Rational combinations of drugs having distinct resistance mechanisms prevented MDR acquisition in hypermutated MMR-deficient P. aeruginosa. Mutational signature analysis of P. aeruginosa across different human disease contexts identified appreciable quantities of MMR-deficient clinical isolates that were already MDR or prone to future MDR acquisition. Mutational signature analysis of patient samples is a promising diagnostic tool that may predict MDR and guide precision-based medical care.

Date: 2025
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DOI: 10.1038/s41467-024-55206-w

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