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

Candida auris 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 C. auris 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% (n = 12/32) patients developed colonisation by C. auris 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 C. auris in rooms about 8.5 days after C. auris 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 C. auris isolates were resistant to amphotericin B and a novel amino acid substitution, G145D in ERG2 gene, was detected in all amphotericin B resistant isolates. In addition, 55% of C. auris isolates had two copies of the MDR1 gene. Our results suggest significant genetic and ecological diversities of C. auris in healthcare setting. The WGS and microsatellite genotyping methods provided complementary results in genotype identification.

Keywords: Candida auris; ERG11; ERG2; India; TAC1B; amphotericin B resistance in C. auris; colonisation; microsatellite typing; whole genome sequencing.

Figure 1

Maximum likelihood phylogenetic tree constructed based on 1000 bootstrap constructed by RAxML. Relationships among our nine strains and South Asian strains including 18 previously published Indian C. auris strains (B11200, B11201, B11205-B11207, B11209, B11210, B11212-B11218, VPCI_510/P/14, VPCI_692/P/12, VPCI_550/P/14, VPCI_479/P/13), and one reference Clade I strain B8441 from Pakistan.

Figure 2

Maximum clade credibility phylogenetic tree of 9 Candida auris strains (clinical, n = 4; environmental, n = 5) isolated in the present study, and 18 previously published Indian C. auris strains, (B11200, B11201, B11205-B11207, B11209, B11210, B11212-B11218, VPCI_510/P/14, VPCI_692/P/12, VPCI_550/P/14, VPCI_479/P/13) along with Clade1 isolate (B8441) using BEAST strict clock model and coalescent model. Values indicate the posterior probability of the nodes in the maximum clade credibility tree. Purple bars indicate 95% highest posterior density.