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

## TL;DR

Bacteria with broken DNA repair systems become more resistant to antibiotics without needing new mutations, possibly due to increased DNA mixing and cell death.

## Contribution

A novel antibiotic resistance mechanism is revealed that arises from loss of DNA mismatch repair genes, independent of secondary mutations.

## Key findings

- Deletion of MMR genes mutL or mutS increases antibiotic resistance in E. coli and Salmonella.
- Increased resistance correlates with higher homoeologous recombination rates and cell lysis in MMR mutants.
- This resistance pathway allows bacteria to survive antibiotics long enough to develop specific resistance mutations.

## Abstract

Antibiotic resistant bacteria have been a major 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 that serves 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 did not change outer membrane permeability or efflux rates. However, the patterns of resistance in MMR mutants correlated with previously reported increases 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 some antibiotics. Finally, we found lysis occurs in MMR mutants and may contribute to resistance. 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.

Antibiotic 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 when DNA mismatch repair (MMR) is lost that increases the concentration of many antibiotics needed to kill cells and that does not require secondary mutations. We observed this increase in resistance in both E. coli and Salmonella. 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 for 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.