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bioRxiv · 10.1101/2025.06.20.660601

Loss of DNA mismatch repair genes leads to acquisition of antibiotic resistance independent of secondary mutations

Bautista, D. E.·Whitehead, C. R.·Mitchell, A. M.
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Abstract

Antibiotic resistant bacteria have been a rising clinical concern for decades. Beyond acquisition of alleles conferring resistance, bacteria under stress (e.g., from changing environmental conditions or mutations) can have higher intrinsic resistance to antibiotics than unstressed cells. This concern is expanded for gram-negative bacteria which have a protective outer membrane serving as an additional barrier against harmful molecules such as antibiotics. Here, we report a pathway which increases antibiotic resistance (i.e., minimum inhibitory concentration) in response to inactivation of the DNA Mismatch Repair pathway (MMR). This pathway led to increased intrinsic resistance and was independent of secondary mutations. Specifically, deletion of the DNA mismatch repair genes mutL or mutS caused resistance to various antibiotics spanning different classes, molecular sizes, and mechanisms of action in several different E. coli K-12 MG1655 strains, and in Salmonella enterica serovar Typhimurium LT2. This pathway was independent of the SOS response (severe DNA damage response). However, the patterns of resistance correlated with previously reported increases in MMR mutants in rates of homoeologous recombination, homologous recombination between non-identical DNA strands. Mutations expected to lower rates of recombination in MMR mutants also decreased the resistance to most antibiotics. Finally, we found lysis occurs in MMR mutants and may contribute to resistance to other antibiotics. Our results have demonstrated a novel mechanism that increases antibiotic resistance in direct response to loss of MMR genes, and we propose this resistance involves increased rates of homoeologous recombination and cell lysis. The increased antibiotic resistance of MMR mutants provides a path for these cells to survive in antibiotics long enough to develop more specific resistance mutations and so may contribute to the development of new clinical resistance alleles. Author SummaryAntibiotic resistance has become a worldwide clinical threat and understanding resistance mechanisms is essential for continued treatment of bacterial infections. Here, we investigate a novel mechanism acting in E. coli and Salmonella when DNA mismatch repair (MMR) is lost that increases the concentration of many antibiotics needed to kill cells and does not require secondary mutations. Our data suggest increased rates of homoeologous recombination (between non-identical DNA strands) and the lysis of some cells within a population are involved in this resistance. This pathway provides a mechanism through which cells with an increased mutation rate due to loss of MMR could survive long enough in the presence of antibiotics to develop new resistance mutations, leading to the spread of antibiotic resistance.

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Bautista, D. E., Whitehead, C. R., Mitchell, A. M.. 2025-06-25. Loss of DNA mismatch repair genes leads to acquisition of antibiotic resistance independent of secondary mutations. https://doi.org/10.1101/2025.06.20.660601

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