Spontaneous mutations in braRS and braAB and the IS1181-related deletion of vraDE genes increase the susceptibility of Staphylococcus aureus clinical isolates to epidermin

Suzuki, Y.; Odawara, A.; Kawada-Matsuo, M.; Hisatsune, J.; Arai, C.; Nishihama, S.; Shiba, H.; Sugai, M.; Yanamoto, S.; Sakaguchi, T.; Komatsuzawa, H.

doi:10.1101/2025.09.27.678946

bioRxiv · 10.1101/2025.09.27.678946

Spontaneous mutations in braRS and braAB and the IS1181-related deletion of vraDE genes increase the susceptibility of Staphylococcus aureus clinical isolates to epidermin

Suzuki, Y.·Odawara, A.·Kawada-Matsuo, M.·Hisatsune, J.·Arai, C.·Nishihama, S.·Shiba, H.·Sugai, M.·Yanamoto, S.·Sakaguchi, T.·Komatsuzawa, H.

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Abstract

Bacteriocins, which are antimicrobial factors produced by bacteria, are expected to be candidates for a novel class of antimicrobial agents against antimicrobial-resistant bacteria, including methicillin-resistant Staphylococcus aureus. To evaluate its effectiveness, the examination of susceptibility using multiple clinical isolates is necessary. In this study, we focused on epidermin, a class I bacteriocin produced by Staphylococcus epidermidis. Among the 146 S. aureus clinical isolates, 77% did not show susceptibility to epidermin, but the susceptibility of some of the strains was significantly higher. Knowing that the two-component regulatory system BraRS affects the susceptibility to epidermin, we analyzed the inducibility of the effector gene vraD in susceptible strains and found that its ability is lost in highly susceptible strains. Some of these strains harbor frameshift or nonsense mutations in BraR, BraA and BraB. Interestingly, the vraDE genes with 35,005 bp neighboring genomic regions, including the icaRADBC and histidine biosynthesis operons, were lost in some highly susceptible strains. In addition, all the vraDE-deficient strains were CC121, and IS1181 sequences located immediately upstream and downstream of the deleted region were found in some vraDE-positive CC121 strains. The deleted region was replaced by one copy of the IS1181 sequence in vraDE-deficient strains. Subculturing of the vraDE-positive CC121 strain generated a vraDE-deficient mutant with increased susceptibility to epidermin at a rate of approximately 1%, suggesting that recombination between IS1181 sequences results in the deletion of the genomic region, including vraDE, in some CC121 strains.

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Suzuki, Y., Odawara, A., Kawada-Matsuo, M., Hisatsune, J., Arai, C., Nishihama, S., Shiba, H., Sugai, M., Yanamoto, S., Sakaguchi, T., Komatsuzawa, H.. 2025-09-27. Spontaneous mutations in braRS and braAB and the IS1181-related deletion of vraDE genes increase the susceptibility of Staphylococcus aureus clinical isolates to epidermin. https://doi.org/10.1101/2025.09.27.678946

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