Short tandem repeat genotyping of Pichia kudriavzevii isolates reveals long-standing clinical clade with high transmission potential

Pichia kudriavzevii (previously known as Candida krusei) is among the top five causative agents of candidemia, mainly affecting neonates. The yeast is intrinsically resistant to fluconazole and nosocomial transmission has been reported. Recently, whole genome sequencing (WGS) analysis on 24 out of 165 clinical P. kudriavzevii isolates from Delhi, India showed two clusters, indicating nosocomial transmission. To further increase our insight on the transmission of this fungus in healthcare settings, we performed short tandem repeat (STR) genotyping of 106 isolates from Delhi, India and compared outcomes to STR genotypes and WGS data of isolates originating from various countries. A total of 52 unique genotypes were identified, in addition to five clusters comprising two to 22 isolates. Four of these clusters were restricted to a single hospital, while the largest cluster included six hospitals. Interestingly, when compared to a global collection, Iranian clinical isolates were identical to the multicenter cluster and also related to isolates from the Netherlands and Sri Lanka, the latter isolate being collected in 1935. WGS analysis on a selection of isolates confirmed the clusters identified by STR analysis, underscoring the high discriminatory power of the STR genotyping scheme. In short, we report several events of single-center nosocomial transmission of P. kudriavzevii in India. One multicenter cluster was found which was closely related to isolates originating from diverse countries, suggesting a fitness advantage or elevated transmission potential for this lineage.