Respiratory fungal colonization in hospitalized patients in western Iran: species distribution and antifungal susceptibility patterns

Respiratory fungal colonization is frequently observed among hospitalized patients with underlying pulmonary disorders; however, its clinical significance, species distribution, and local antifungal susceptibility patterns remain incompletely characterized, particularly in low- and middle-income countries. This study aimed to determine the frequency of culture-confirmed fungal detection in respiratory specimens, describe the distribution of fungal species, assess antifungal susceptibility profiles of predominant isolates, and examine associations between culture positivity and selected demographic and clinical characteristics in western Iran. This prospective cross-sectional observational study was conducted over a 12-month period (July 2020–July 2021) at two tertiary-care hospitals in western Iran. A total of 127 consecutive respiratory specimens, including sputum (with quality assessment using Bartlett criteria), bronchoalveolar lavage, and tracheal aspirates, were examined by direct microscopy and fungal culture. Fungal isolates were identified using a combination of conventional phenotypic and molecular methods. CHROMagar, germ tube testing, and carbohydrate assimilation profiling were applied exclusively to yeast isolates, while filamentous fungi were identified using phenotypic methods and confirmed by ITS rDNA sequencing for representative isolates. Antifungal susceptibility testing of predominant isolates was conducted using CLSI broth microdilution methods (M27 A4 for yeasts, M38 A2 for filamentous fungi). MICs were interpreted using CLSI species-specific breakpoints or epidemiological cutoff values where available; for Candida glabrata , fluconazole MICs were categorized as Susceptible Dose-Dependent (SDD), and for Aspergillus species, isolates were categorized as wild-type (WT) or non-wild-type (NWT) based on ECVs. Demographic and clinical data were extracted from medical records. Fungal growth was detected in 62 of 127 respiratory specimens (48.8%). Yeasts constituted the majority of isolates (71.0%). Candida albicans was the most frequently identified species (37.1%), followed by C. glabrata (17.7%), C. tropicalis (9.7%), and C. parapsilosis (6.5%). Among filamentous fungi, Aspergillus flavus was the most commonly isolated mold (9.7%), followed by Rhizopus spp. (6.5%), A. fumigatus (4.8%), A. niger (4.8%), and Penicillium spp. (3.2%). Culture positivity was highest in sputum specimens (51.9%), followed by bronchoalveolar lavage (44.4%) and tracheal aspirates (33.3%); however, these differences were not statistically significant ( p = 0.19). No significant associations were found between culture positivity and demographic or clinical variables, including age, sex, COPD, pneumonia, malignancy, diabetes mellitus, or COVID-19 status; however, these findings should be interpreted with caution due to the limited sample size. C. albicans isolates exhibited high susceptibility to the tested antifungal agents (with MIC₅₀ and MIC₉₀ values of 0.5 and 2 µg/mL for fluconazole), whereas elevated fluconazole MICs (with 36.4% of isolates categorized as SDD) were observed among C. glabrata isolates. All A. flavus isolates tested were categorized as wild-type for amphotericin B and voriconazole based on CLSI ECVs. Culture-confirmed fungal detection was common in respiratory specimens from hospitalized patients with suspected lower respiratory tract disorders. Yeasts, particularly Candida species, predominated, while A. flavus was the leading mold isolate, reflecting regional epidemiological patterns. The high proportion of Candida isolates should be interpreted with caution, as recovery of Candida from respiratory secretions almost always represents colonization rather than infection and should not routinely prompt antifungal therapy in non-neutropenic patients. No significant associations were observed between culture positivity and the evaluated clinical variables, although this may be attributable to the limited sample size and incomplete data on clinically relevant risk factors such as ICU admission, mechanical ventilation, and corticosteroid exposure. These findings emphasize the need for cautious interpretation of respiratory fungal culture results, species-level identification, and antifungal susceptibility testing as components of antifungal stewardship. Larger multicenter studies with comprehensive risk factor assessment, fungal biomarkers, and longitudinal follow-up are needed to clarify the clinical significance of respiratory fungal colonization and its potential progression to invasive disease.