Biology subjects

Silva, K. P. T.

Publications and source records attributed to Silva, K. P. T..

2 recordsLinked to original sources

bioRxiv2025

Genetic determinants of gene amplifications alter frequency and evolutionary trajectory of antibiotic resistance in Staphylococcus aureus

Gene amplifications are thought to be common in bacterial populations, providing a rapid reversible mode of adaptation to diverse stresses, including the acquisition of antibiotic resistance. We previously showed that the opportunistic pathogen Staphylococcus aureus evolves resistance to the dual-targeting fluoroquinolone delafloxacin (DLX) that inhibits both the DNA gyrase and DNA topoisomerase IV via gene amplifications of an efflux pump encoding gene sdrM. However, the pathways that control the formation or selection of gene amplifications, and consequently adaptive trajectories, remain understudied, especially in gram-positive bacteria like S. aureus. Here, we show that specific DNA repair and chromosomal separation pathways alter the frequency of formation and selection of gene amplifications in S. aureus. Through a screen of 36 mutants deficient in various DNA processes, we found that while sdrM amplification was still the almost universal path to DLX resistance, other mutations that increased sdrM expression reduced the selection frequency of sdrM amplifications, demonstrating the critical role of sdrM in DLX resistance. We found that similar to other bacteria, the formation and loss of sdrM amplifications required a functional RecA recombinase, but multiple other mutants in pathways required for amplifications in other species still exhibited frequent sdrM amplifications, suggesting that S. aureus may have alternate routes of amplification formation. Finally, mutants in the tyrosine recombinase XerC that is involved in chromosomal separation were deficient for sdrM amplifications, indicating that XerC is a novel modulator of amplification formation, maintenance, or selection. Thus, our work sheds light on genetic factors that alter gene amplification-mediated evolutionary trajectories to antibiotic resistance in S. aureus and can potentially unlock mechanisms by which such evolution of resistance can be inhibited.

microbiology↗

bioRxiv2022

Efflux pump gene amplifications bypass necessity of multiple target mutations for resistance against dual-targeting antibiotic

The rise of antimicrobial resistance has motivated the development of antibiotics that have multiple cellular targets, to theoretically reduce the frequency of resistance evolution, but adaptive trajectories and genetic determinants of resistance against such antibiotics are understudied. Here we investigate these in methicillin resistant Staphylococcus aureus (MRSA) using experimental evolution of ten independent populations in the presence of delafloxacin (DLX), a novel fluoroquinolone that targets both DNA gyrase and topoisomerase IV. We show that coding sequence mutations and genomic amplifications of the gene encoding a poorly characterized efflux pump, SdrM, lead to the evolution of high DLX resistance, circumventing the requirement for mutations in the target enzymes. Almost all of our evolved populations had one of two SdrM coding sequence mutations, which led to moderate DLX resistance. Additionally, these populations had 13 distinct genomic amplifications, each containing sdrM and two adjacent genes encoding efflux pumps, which resulted in up to 100-fold higher DLX resistance. While increased sdrM expression provided the selective advantage of the amplification in the DLX evolution, the adjacent efflux pumps hitchhiking in the genomic amplification contributed to cross-resistance against the aminoglycoside streptomycin. Finally, lack of sdrM necessitated mutations in both DNA gyrase and topoisomerase IV to evolve DLX resistance, and the presence of sdrM thus increased the frequency of resistance evolution. Our study highlights that instead of reduced rates of resistance, evolution of resistance to antibiotics with multiple cellular targets can involve alternate high-frequency evolutionary paths such as genomic amplifications of efflux pumps, that may cause unexpected alterations of the fitness landscape, including antibiotic cross-resistance.

microbiology↗