Genomic characterization and transcriptomic profile of Candida krusei in a neonatal intensive care unit in Delhi, India

ABSTRACT: In the last decade, Candida krusei has caused multiple outbreaks of candidemia in Neonatal Intensive Care Units (NICUs) in low-and middle-income countries such as Brazil, India, and South Africa. In India, C. krusei ranks as the sixth cause of candidemia in adult ICUs. Additionally, sporadic outbreaks of nosocomial candidemia in the NICUs are widely reported from India. However, the genetic population of C. krusei causing outbreaks remain largely unknown. In the present study, we used whole genome sequencing to examine the genetic structure of C. krusei population causing candidemia spanning a period of five years (2015-20) in a single NICU in Delhi, India. Further, to evaluate the mechanisms of azole antifungal resistance in C. krusei, we compare the transcriptomic profiles of fluconazole susceptible (FLU-S) and resistant (FLU-R) isolates. Transcriptomic assay was performed in logarithmically growing C. krusei clinical isolates 123/P/19 and 1390/P/18 strains. STAR aligner v.2.5.2b was used to sequence the trimmed reads with the specified reference genome of P. kudriavzevii to determine the unique gene hit counts. A total of 178 genes were differentially expressed by at least 1.5-fold in 1390/P/18 as compared to 123/P/19 isolate. Principal component analysis (PCA) of normalized read counts also depicted almost similar transcriptomic profile between the two C. krusei strains with 53 % variance at principal component 1. Out of 178 differentially expressed genes, 72 were up-regulated and 106 were down-regulated in 1390/P/18 strain compared to 123/P/19 strain. Functionally, genes associated with transport (n=10), mitogen activated protein kinase signaling (MAPK; n=8), transcription factors (TF; n=6) and ergosterol biosynthesis (n=3) were expressed differentially.

ORGANISM(S): Pichia kudriavzevii

PROVIDER: GSE262836 | GEO | 2025/09/18

REPOSITORIES: GEO