Heterogeneous collateral effects in daptomycin-resistant E. faecalis

Abstract

Daptomycin, a cyclic lipopeptide antibiotic that targets the cell membrane, is an important therapeutic option for treating multi-drug-resistant infections, including vancomycin-resistant enterococci (VRE). Recent work has uncovered an array of daptomycin resistance mechanisms in enterococci, but relatively little is known about how these molecular defenses contribute to collateral effects-that is, to increased resistance or sensitivity to other drugs. In this work, we investigate collateral effects that arise during daptomycin adaptation of E. faecalis in four independent laboratory-evolved populations. Using a combination of growth assays and both single isolate and population sequencing, we identified DAP-resistant lineages with mutations in one or more genes previously associated with DAP resistance, and these isolates are characterized by divergent phenotypic properties-including different levels of DAP resistance and different growth rates (i.e. fitness costs) in drug-free media. Interestingly, we also observed strongly divergent collateral responses to different antibiotics, particularly CRO, with collateral resistance arising in mutants harboring DAP-resistance mutations in cardiolipin synthetase (cls) or in genes linked to the two-component signaling system YxdJK (bceR or a regulated transporter ycvR). By contrast, mutations in liaX, a component of a LiaFSR two-component signaling system, arose in two of the four populations, with point mutations associated with CRO-sensitivity and a large structural integration of plasmid pTEF3 associated with extreme CRO-sensitivity and a dramatically reduced growth rate. Our results reveal considerable phenotypic differences in mutations targeting the LiaSFR system and highlight trade-offs between resistance to daptomycin, collateral profiles (most notably to CRO), and drug-free growth rates in evolving lineages. As a whole, these results underscore how rich-and remarkably diverse-evolutionary dynamics can emerge even in parallel populations adapting to simple daptomycin escalation protocols.