Colonisation and Transmission Dynamics of Candida auris among Chronic Respiratory Diseases Patients Hospitalised in a Chest Hospital, Delhi, India: A Comparative Analysis of Whole Genome Sequencing and Microsatellite Typing

Abstract

<i>Candida auris</i> is a nosocomial pathogen responsible for an expanding global public health threat. This ascomycete yeast has been frequently isolated from hospital environments, representing a significant reservoir for transmission in healthcare settings. Here, we investigated the relationships among <i>C. auris</i> isolates from patients with chronic respiratory diseases admitted in a chest hospital and from their fomites, using whole-genome sequencing (WGS) and multilocus microsatellite genotyping. Overall, 37.5% (<i>n</i> = 12/32) patients developed colonisation by <i>C. auris</i> including 9.3% of the screened patients that were colonised at the time of admission and 75% remained colonised till discharge. Furthermore, 10% of fomite samples contained <i>C. auris</i> in rooms about 8.5 days after <i>C. auris</i> colonised patients were admitted. WGS and microsatellite typing revealed that multiple strains contaminated the fomites and colonised different body sites of patients. Notably, 37% of <i>C. auris</i> isolates were resistant to amphotericin B and a novel amino acid substitution, G145D in <i>ERG2</i> gene, was detected in all amphotericin B resistant isolates. In addition, 55% of <i>C. auris</i> isolates had two copies of the <i>MDR1</i> gene. Our results suggest significant genetic and ecological diversities of <i>C. auris</i> in healthcare setting. The WGS and microsatellite genotyping methods provided complementary results in genotype identification.