Multidrug Intrinsic Resistance Factors in Staphylococcus aureus Identified by Profiling Fitness within High-Diversity Transposon Libraries

Abstract

Staphylococcus aureus is a leading cause of life-threatening infections worldwide. The MIC of an antibiotic against S. aureus, as well as other microbes, is determined by the affinity of the antibiotic for its target in addition to a complex interplay of many other cellular factors. Identifying nontarget factors impacting resistance to multiple antibiotics could inform the design of new compounds and lead to more-effective antimicrobial strategies. We examined large collections of transposon insertion mutants in S. aureus using transposon sequencing (Tn-Seq) to detect transposon mutants with reduced fitness in the presence of six clinically important antibiotics—ciprofloxacin, daptomycin, gentamicin, linezolid, oxacillin, and vancomycin. This approach allowed us to assess the relative fitness of many mutants simultaneously within these libraries. We identified pathways/genes previously known to be involved in resistance to individual antibiotics, including graRS and vraFG (graRS/vraFG), mprF, and fmtA, validating the approach, and found several to be important across multiple classes of antibiotics. We also identified two new, previously uncharacterized genes, SAOUHSC_01025 and SAOUHSC_01050, encoding polytopic membrane proteins, as important in limiting the effectiveness of multiple antibiotics. Machine learning identified similarities in the fitness profiles of graXRS/vraFG, SAOUHSC_01025, and SAOUHSC_01050 mutants upon antibiotic treatment, connecting these genes of unknown function to modulation of crucial cell envelope properties. Therapeutic strategies that combine a known antibiotic with a compound that targets these or other intrinsic resistance factors may be of value for enhancing the activity of existing antibiotics for treating otherwise-resistant S. aureus strains.

Chemical Genetic Interaction Profiling Reveals Determinants of Intrinsic Antibiotic Resistance in Mycobacterium tuberculosis

“…This might have been due to increased cell envelope permeability and antibiotic uptake resulting from a compromised cell envelope; alternatively, the loss of function of genes involved in cell envelope processes might sensitize M. tuberculosis to normally sublethal levels of antibiotic-induced cell envelope damage. Similarly, a TnSeq screen for intrinsic resistance factors in Staphylococcus aureus identified multicomponent sensing systems that regulate the expression of cell wall biosynthetic genes and modulators of cell surface charge (42).…”

Prevalence, antimicrobial susceptibility, and molecular characterization of Staphylococcus aureus isolated from dairy herds in northern China

“…aureus to survive specific antimicrobial stress (Baym et al, 2016). It possesses numerous intrinsic factors that limit the effectiveness of specific antimicrobial agents (Rajagopal et al, 2016) and can develop acquired resistance to many other antimicrobial agents by carrying various Prevalence, antimicrobial susceptibility, and molecular characterization of Staphylococcus aureus isolated from dairy herds in northern China Huimin Liu,* † 1 Songli Li,* † 1 Lu Meng,* † 1 Lei Dong,* † Shengguo Zhao,* † Xinyi Lan,* † Jiaqi Wang,* † and Nan Zheng* † 2 8797 resistance traits on plasmids or transposons (Chajecka-Wierzchowska et al, 2015). Acquired antimicrobial resistance has a transmission potential to humans (Ruegg et al, 2015).…”

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

“…changes in pH, antibiotics) trigger complex ‘multi-level’ responses that remain hard to predict (Tomasz, 1979; Vakulenko and Mobashery, 2003; Floss and Yu, 2005; Drlica et al , 2008; van Opijnen and Camilli, 2012; Rajagopal et al , 2016; van Opijnen et al , 2016). Such responses can be separated into at least two organizational levels.…”