a pilot study on fungal diversity from axillary and groin swabs

The skin mycobiome is a largely unexplored component of the human microbiome, especially in critically ill patients. Fungal colonisation in the Intensive Care Unit (ICU) may be influenced by underlying comorbidities and hospital-related risk factors, potentially impacting patient outcomes. This pilot study aimed to characterize the diversity and abundance of skin fungi in ICU patients during their first week of hospitalization. A total of 35 ICU patients were recruited and divided into two groups: Group 1 (patients with 1–2 comorbidities and ICU risk factors) and Group 2 (patients with more than 2 comorbidities and ICU risk factors). Bilateral axillary-groin swabs were collected on admission day (D1) and after one week of ICU stay (D8) for fungal identification. Culture-based methods and MALDI-TOF MS were initially used, followed by Internal Transcribed Spacer 2 (ITS2) sequencing via the Illumina MiSeq platform for in-depth analysis of fungal communities. Fungal diversity and relative abundance were assessed using standard alpha and beta diversity metrics. Culture and MALDI-TOF MS identified only Candida spp., suggesting limited diversity. ITS2 sequencing revealed that Candida (69.3%) was the most prevalent genus, followed by Penicillium (10.3%) and Cladosporium (4.0%), with Malassezia being rare (0.7%). Diversity analysis indicated a relatively stable fungal community throughout the first week (ANOSIM, p = 0.499), with no significant changes in species richness or community structure. By Day 8, Candida spp. represented 79.9% and 78.9% of the mycobiome in Groups 1 and 2, respectively. Preliminary data suggest that the ICU skin mycobiome is dominated by Candida spp. and exhibits low fungal diversity. These findings provide foundational insight into the skin mycobiome of critically ill patients and underscore the need for further research to elucidate its clinical significance and potential role in patient management.