Community-Onset Fungemias: Epidemiology and Genomic Characterization

Background: Community-onset fungemia is a clinically significant syndrome frequently linked to recent healthcare exposure and significant morbidity and mortality. Methods: We performed a 21-year, single-center retrospective cohort of consecutive yeast bloodstream infections diagnosed at the Emergency Department (2004–2024). Clinical/epidemiological data, species identification (MALDI-TOF MS), antifungal susceptibility (CLSI M27; Sensititre YO10), and whole-genome sequencing (WGS) were analyzed. Results: Forty-eight episodes (51 isolates) were included; 56.3% were male, median age 74 years (IQR 63–82). Acquisition was healthcare-associated in 38/48 (79.2%). Sources were unknown (36.7%), abdominal (22.4%), urological (22.4%), catheter-related (14.3%) and 2.1% was attributed to a cardiovascular and a joint focus; 18.8% were polymicrobial. Crude mortality was 20.8% at 7 days (10/48) and 29.2% at 30 days (14/48). Species distribution: Candida albicans 41.2%, Nakaseomyces glabratus 27.5%, Candida parapsilosis 11.8%, Candida tropicalis 11.8%, Pichia kudriavzevii 3.9%, Clavispora lusitaniae 1.9%, and Candida orthopsilosis 1.9%. No isolate was resistant to anidulafungin, micafungin, or amphotericin B; one N. glabratus showed reduced susceptibility to caspofungin. Azole resistance occurred in one C. albicans and one N. glabratus isolate. WGS (44 isolates) confirmed MALDI-TOF identifications and characterized resistance markers. All 12 sequenced N. glabratus carried ERG2 I207V, PDR15/PDH1 E839D, and PDR1 V91I/L98S. Notable cases included one N. glabratus caspofungin-intermediate with FKS2 F659C, N. glabratus fluconazole-resistant with multiple PDR1 substitutions including a unique novel G857V, and C. albicans fluconazole-resistant harboring alterations in MRR1/MRR2, CDR1, and ERG11. Conclusions: In this 21-year cohort, community-onset fungemia was predominantly healthcare-associated, with C. albicans as the predominant species, followed by N. glabratus. Echinocandin resistance was not observed; azole resistance was uncommon. WGS provided precise speciation and actionable insight into resistance mechanisms, including a putatively novel PDR1 G857V in N. glabratus.