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.

Candida auris: Epidemiology, Diagnosis, Pathogenesis, Antifungal Susceptibility, and Infection Control Measures to Combat the Spread of Infections in Healthcare Facilities

“…More importantly, gene replacement studies confirmed the role of the most common (A640V) TAC1B mutation as this mutation increased fluconazole MIC 8-fold when introduced into a fluconazolesusceptible strain while the reverse experiment caused 16-fold decrease in fluconazole MIC [138]. Furthermore, a nonsynonymous (G145D) mutation has also been found in YMC1, encoding several transmembrane transporter activities essential in mitochondrial transport in some fluconazole-resistant C. auris isolates lacking the K143R mutation in ERG11 [79]. Thus, mutations in TAC1B and YMC1 also contribute to clinical fluconazole resistance in C. auris.…”

“…Definitive identification is usually achieved by the PCR amplification of the internal transcribed spacer (ITS) region of rDNA and/or by PCR sequencing of the ITS region or the D1/D2 domains of rDNA [29][30][31][32]41,93,106]. Although whole genome sequencing has been performed to determine phylogenetic relationships among C. auris isolates during outbreak investigations, a highly discriminatory, 12-loci-based short tandem repeat typing scheme has also recently been described for the routine fingerprinting of C. auris isolates, which yields nearly comparable results [56,58,79,109].…”

“…auris strains from around the world exhibit a clade-specific resistance to fluconazole but varying susceptibility to other triazoles, amphotericin B, and echinocandins [62,72,73,89,155]. For instance, nearly 90%, 30%, and~5% of C. auris isolates from the USA have been reported to be resistant to fluconazole, amphotericin B, and echinocandins, while the corresponding values for C. auris isolates from India have been reported as 90-95%, 7-37%, and <2%, respectively [71,73,79]. Although the resistance rates to fluconazole are usually very high, only a few Clade II isolates are resistant to fluconazole and susceptibility to other triazoles varies widely even among isolates belonging to the same clade [39,58,62,73,95,157].…”

“…Three nonsynonymous (F126L, Y132F, and K143R) mutations have been detected in ERG11 in fluconazole-resistant C. auris isolates belonging to different genetic clades with Y132F and K143R being more common [71,73,89]. Although ERG11 gene mutations are strongly associated with resistance to fluconazole in clinical C. auris isolates, their presence alone does not completely explain the entirety of resistance observed clinically, clearly implying the role(s) of other genetic and molecular mechanisms in fluconazole resistance [41,58,71,79,158]. Indeed, recent studies have shown that the molecular basis of resistance to triazoles is much more complex than previously thought.…”

“…Indeed, recent studies have shown that the molecular basis of resistance to triazoles is much more complex than previously thought. C. auris genome encodes several members of the ATP-binding cassette (ABC) transporters (CDR1) and major facilitator superfamily (MFS) members (MDR1) that coincides with the exceptional multidrug resistance characteristic of this organism and some C. auris isolates with K143R mutation in ERG11 gene were found to contain two copies of the MDR1 gene encoding for a major facilitator transporter [79,89,[136][137][138].…”