joint isolates: Whole-genome sequencing demonstrates evidence of hospital transmission and common antimicrobial resistance.

Objective: We investigated genetic, epidemiologic, and environmental factors contributing to positive joint cultures.

Design: Retrospective cohort study with whole-genome sequencing (WGS).

Patients: We identified isolates from hip or knee cultures in patients with 1 or more prior corresponding intra-articular procedure at our hospital.

Methods: WGS and single-nucleotide polymorphism-based clonality analyses were performed, including species identification, in silico multilocus sequence typing (MLST), phylogenomic analysis, and genotypic assessment of the prevalence of specific antibiotic resistance and virulence genes. Epidemiologic review was performed to compare cluster and noncluster cases.

Results: In total, 60 phenotypically distinct isolates were identified. After removal of duplicates and impure samples, 48 isolates were used for the phylogenomic analysis, and 45 (93.7%) isolates were included in the clonality analysis. Notably, 5 strains (10.4%) showed phenotypic susceptibility to oxacillin yet harbored , and 3 (6.2%) strains showed phenotypic resistance despite not having . was found in all isolates, and positivity was not observed. We also identified 6 clonal clusters from the clonality analysis, which accounted for 14 (31.1%) of the 45 isolates. Our epidemiologic investigation revealed ties to common aspirations or operative procedures, although no specific common source was identified.

Conclusions: Most isolates from clinical joint samples are diverse in origin, but we identified an important subset of 31.1% that belonged to subclinical healthcare-associated clusters. Clusters appeared to resolve spontaneously over time, suggesting the benefit of routine hospital infection control and disinfection practices.