期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2022
卷号：119
期号：30
DOI：10.1073/pnas.2118262119
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance
Infections with methicillin-resistant
Staphylococcus aureus (MRSA) are associated with significant morbidity and mortality. Vancomycin is a last-line antibiotic used to treat MRSA infections; however, strains with decreased susceptibility to vancomycin (vancomycin-intermediate
S. aureus [VISA]) have been spreading, and VISA infections are associated with prolonged therapeutic treatment and treatment failure. To map out the evolutionary trajectory behind VISA development, we characterized the mutational, transcriptional, and phenotypic landscape of 10 lineages of
S. aureus USA300 strain JE2 that evolved in parallel to vancomycin. We demonstrate that MRSA strains adapt to vancomycin by divergent pathways leading to high or low oxacillin susceptibility characterized by mutational or transcriptional profiles. Our results point to diagnostic possibilities that may support personalized antibiotic treatment regimes.
Human infections with methicillin-resistant
Staphylococcus aureus (MRSA) are commonly treated with vancomycin, and strains with decreased susceptibility, designated as vancomycin-intermediate
S. aureus (VISA), are associated with treatment failure. Here, we profiled the phenotypic, mutational, and transcriptional landscape of 10 VISA strains adapted by laboratory evolution from one common MRSA ancestor, the USA300 strain JE2. Using functional and independent component analysis, we found that: 1) despite the common genetic background and environmental conditions, the mutational landscape diverged between evolved strains and included mutations previously associated with vancomycin resistance (in
vraT,
graS,
vraFG,
walKR, and
rpoBCD) as well as novel adaptive mutations (SAUSA300_RS04225,
ssaA,
pitAR, and
sagB); 2) the first wave of mutations affected transcriptional regulators and the second affected genes involved in membrane biosynthesis; 3) expression profiles were predominantly strain-specific except for
sceD and
lukG, which were the only two genes significantly differentially expressed in all clones; 4) three independent virulence systems (φSa3, SaeR, and T7SS) featured as the most transcriptionally perturbed gene sets across clones; 5) there was a striking variation in oxacillin susceptibility across the evolved lineages (from a 10-fold increase to a 63-fold decrease) that also arose in clinical MRSA isolates exposed to vancomycin and correlated with susceptibility to teichoic acid inhibitors; and 6) constitutive expression of the VraR regulon explained cross-susceptibility, while mutations in
walK were associated with cross-resistance. Our results show that adaptation to vancomycin involves a surprising breadth of mutational and transcriptional pathways that affect antibiotic susceptibility and possibly the clinical outcome of infections.
