Rising daptomycin resistance in Enterococcus faecium across a hospital system occurred via rampant recurrent evolution and occasional transmission between patients.

The rise of antibiotic resistance in a population involves two distinct processes: the origin of resistance and its spread. Here we study the contribution of both processes to the increase in daptomycin resistance in Enterococcus faecium in a hospital system. This case-control genomic study includes whole-genome sequencing of 82 isolates obtained from 24 case patients with clinically determined daptomycin-resistance and 24 controls. Among the case patients, the first isolate was resistant in 15 patients (R patients) while in the remaining nine the first isolate was susceptible but was followed by one or more resistant isolates (SR patients). Mutations in a set of candidate daptomycin resistance genes were compared within and between all patients. Additionally, among closely related isolates, mutations were identified across the entire assembled genome. Daptomycin resistance evolved separately multiple times and there was no phylogenetic clustering of the R or the SR groups. Six of the nine SR pairs gained mutations in previously identified candidate loci for daptomycin resistance, with the major cardiolipin synthase (clsA) being mutated most frequently. The hospital-wide increases in daptomycin resistance in E. faecium was the result of recurrent evolution taking multiple evolutionary pathways and occasional transmission of resistant isolates between patients. ImportanceAntimicrobial resistance in healthcare settings presents an important challenge, because infections with resistant organisms are associated with higher cost, longer hospital stays and worse outcomes for patients. However, it can be difficult to identify the factors driving the increase in resistance, specifically the relative contribution of resistance arising anew through mutation versus the transmission of resistant organisms from patient to patient. We study a hospital where resistance to daptomycin was increasing among Enterococcus faecium, an important hospital pathogen. We find the increase in resistance was the results of resistance arising many times independently. We also identify occasional transmission of daptomycin resistant organisms. Thus, control of daptomycin resistance in E. faecium may require interventions that both slow the emergence of resistance within patients and slow its spread. This work sheds light on the complex population dynamics leading to antibiotic resistance in hospitals.