Collateral Resistance and Sensitivity Modulate Evolution of High-Level Resistance to Drug Combination Treatment in Staphylococcus aureus

Abstract

As drug-resistant pathogens continue to emerge, combination therapy will increasingly be relied upon to treat infections and to help combat further development of multidrug resistance. At present a dichotomy exists between clinical practice, which favors therapeutically synergistic combinations, and the scientific model emerging from in vitro experimental work, which maintains that this interaction provides greater selective pressure toward resistance development than other interaction types. We sought to extend the current paradigm, based on work below or near minimum inhibitory concentration levels, to reflect drug concentrations more likely to be encountered during treatment. We performed a series of adaptive evolution experiments using Staphylococcus aureus. Interestingly, no relationship between drug interaction type and resistance evolution was found as resistance increased significantly beyond wild-type levels. All drug combinations, irrespective of interaction types, effectively limited resistance evolution compared with monotreatment. Cross-resistance and collateral sensitivity were found to be important factors in the extent of resistance evolution toward a combination. Comparative genomic analyses revealed that resistance to drug combinations was mediated largely by mutations in the same genes as single-drug-evolved lineages highlighting the importance of the component drugs in determining the rate of resistance evolution. Results of this work suggest that the mechanisms of resistance to constituent drugs should be the focus of future resistance evolution work.

Antimicrobial interactions: mechanisms and implications for drug discovery and resistance evolution

“…Several studies investigated the effects of antibiotic combinations with different drug interactions on spontaneous resistance evolution and revealed a general trend that antagonistic drug combinations lead to slower resistance evolution than synergistic ones [11,12]. However, recent work on S. aureus suggested that this trend may not hold generally when bacteria evolve higher levels of resistance as the drug interactions themselves might change due to resistance mutations [75].…”

History of Antibiotic Adaptation Influences Microbial Evolutionary Dynamics During Subsequent Treatment

“…For consistency, stocks were revived from Days 0 (Ancestor), 5,10,15,19,20,25,30,35 During analysis of the mutations, we deduced that there were some cross-contaminations between replicates in a few lineages. Namely, we saw sets of mutations that were identical in 2 replicates.…”

“…Collateral sensitivities between drugs have been used to design drug cycling strategies and to explain the decreased rate of adaptation to certain antibiotics [12,14,[18][19][20][21][22][23]. Drug deployment strategies that exploit such collateral sensitivities between pairs of antibiotics to minimize resistance evolution have been tested in vitro.…”

Comprehensive antibiotic-linked mutation assessment by resistance mutation sequencing (RM-seq)

“…The demonstration that several specific rifampicin resistance mutations can prevent bacterial clearance by daptomycin in vitro can have potential clinical implication regarding the usage rifampicin and daptomycin in combination therapy. A deeper understanding of how evolution of microbial resistance towards a given antibiotic influences susceptibility or resistance to other drugs would have profound impact as it could be exploited to fight resistance rise through combination therapy or by the temporal cycling of different antibiotics [18, 64, 65]. …”

“…Because of their implications in central cell processes, such as DNA replication, translation, transcription and cell-wall metabolism regulation, mutations arising in these genes have been associated with a broad range of pleiotropic effects in addition to the antibiotic resistance that they cause [17]. An increasing body of literature shows that antibiotic resistance mutations can lead to broader negative therapeutic consequences through cross-resistance to other antimicrobials [18–20], increased biofilm formation [21], increased virulence [22–25] and enhanced immune evasion [25–28]. However, there is currently no efficient method to identify pleiotropic mutations.…”