Prevalence, Antifungal Susceptibility and Molecular Characterization of Isolated Candida Species from Bloodstream of Critical Care Unit Patients in Nairobi Hospital, Kenya

Abstract

Upsurge of candidemia in the past years has been a burden on public health and the number of deaths caused by candidemia particularly in critical care unit patients has been increased. Candida species account for 30-60% mortality rate and compared to healthy individuals or those with less serious illnesses, the incidence is increased to 60 to 80% in those who are chronically ill. Grounded on a recent report from Nairobi Hospital showing the emergence of previously unobserved species; Candida auris, this study aimed to determine the prevalence, antifungal susceptibility profile and genotypic characterization of candidemia in critical care unit patients of the hospital. A total of 378 Critical Care Unit patients were enrolled for the study. Positive archived isolates were sub-cultured using Saboraud Dextrose Agar. Candida species were identified utilizing API20C AUX and Vitek-2. Antifungal susceptibility testing was conducted using the Liofilchem MIC Test strip. Genomic DNA was extracted using QUICK DNA miniprep extraction kit, amplified using PCR and outsourced to macrogen for purification and sequencing. Out of 378 patients, thirty-one presented a positive culture for Candida species. The prevalence of Candidemia was 8.2% with 9 (29.03%) Candida auris, 8 (25.81%) Candida albicans, 6 (19.35%) Candida parapsilosis, 3 (9.68%) Candida famata, 3 (9.68%) Candida tropicalis, 1 (3.23%) Candida duobushaemolumonii, and 1 (3.23%) Candida lusitaniae. A resistance pattern to Fluconazole was observed among Candida auris, and Candida parapsilosis, and resistance to Flucytosine was observed in Candida tropicalis, whereas susceptible MIC values were obtained for the other drugs. Sequencing of resistant isolates’ ERG 11 and FUR1 gene obtained 6 SNPs (Erg11C374T, Erg11C376T, Erg11A395T, Erg11T729C, Erg11T1126A, FUR1C297T) and 4 amino acid substitutions (A125V, L126F, Y132F, L376V). There is an increase in candidemia among critical care unit patients in Nairobi Hospital and onset of new species; Candida auris. The uniform resistance of Candida auris, Candida parapsilosis, and Candida tropicalis towards Fluconazole and Flucytosine and the mutation analysis obtained three previously undocumented amino acid substitutions and one substitution which has been documented in two continents other than Africa of which the latter is elucidated in causing resistance to fluconazole and one of the previously undocumented substitutions might also have a role in the resistance patterns of fluconazole. Based on the results obtained in this study there is a necessity of constant drug monitoring for empirical treatment regime. Therefore, the high potency of Echinocandins demonstrate them as the drug of choice.