Genetic variation and mutational determinants of azole resistance in Candida albicans strains of oropharyngeal colonization in HIV patients and bloodstream infections

Objectives We aimed to analyze the genomic variations associated with high azole resistance in the C. albicans isolates of intensive care unit (ICU) patients with Candida bloodstream infections (BSIs) and those from oropharyngeal colonization in HIV patients. Methods The genomic DNA of azole-resistant C. albicans isolates was analyzed using the Oxford Nanopore platform. Subsequent analyses included ERG11 alignment to determine the extent and distribution of missense substitutions, Ka/Ks calculations to test for positive selection on ERG11 , and detailed CDR1 and CDR2 mutational analysis across the coding sequence. Efflux function was assessed by measuring the fold reduction in the minimum inhibitory concentration (MIC) of azole drugs in the presence of milbemycin. Results A total of 27 azole-resistant C. albicans isolates from ICU patients with Candida BSIs and HIV patients’ oropharyngeal colonization were identified and analyzed. The C. albicans isolates of HIV patients had significantly higher azole resistance when compared with those of the ICU patients, which indicated additional mechanisms. The central role of ERG11 mutations was supported by the presence of ERG11 missense mutations in all azole-resistant C. albicans isolates. The ERG11 coding regions analyses showed no evidence of positive selection (Ka/Ks < 1.0) and no specific mutation unique to the C. albicans isolates of the HIV patients, but unique missense mutations only in CDR1 / CDR2 were noted. Milbemycin significantly decreased the azole MICs in all C. albicans isolates and confirmed the efflux pump involvement. The effects of milbemycin were significantly lower in C. albicans of the HIV patients than those from the ICU patients. Furthermore, unique ERG11 promoter variants, including changes at the Hap43p/Hap5p sites, were noted in the C. albicans isolates of the HIV patients. Conclusions While ERG11 structural mutations are foundational, the elevated azole resistance in the C. albicans isolates of HIV patients indicated specific CDR1 / CDR2 mutations and distinct ERG11 promoter variants.