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 but with no amino acid substitution in ERG2, ERG3, ERG5, and ERG6 as compared to the reference strain B8441 in any of our strains. In addition, 55% of C. auris isolates likely 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 is an emerging global public health threat and is resistant to most antifungal agents. Though fungi are significant pathogens for animals, the role of C. auris in animal health remains unexplored. Here, we analysed the microbial cultures of skin and ear swabs of 87 dogs in Delhi and performed fungal meta-barcode sequencing of ear and skin samples of 7 dogs with confirmed otitis externa (OE). Overall, 4.5% of dogs (4/87) with chronic skin infections contained evidence of C. auris in their ear canal (n = 3) and on their skin surface (n = 1). Of the three OE dogs with C. auris infection/colonisation, a diversity of fungi was observed, and their meta-barcode ITS sequence reads for C. auris ranged from 0.06% to 0.67%. Whole-genome sequencing of six C. auris strains obtained in culture from two dogs showed relatedness with Clade I clinical strains. The report highlights the isolation of C. auris from an animal source; however, the routes of transmission of this yeast to dogs and the clinical significance of transmission between dogs and humans remain to be investigated.

Candida auris is a recently emerged human fungal pathogen that has posed a significant threat to public health. Since its first identification in 2009, this fungus has caused nosocomial infections in over 47 countries across all inhabited continents. As of May 2023, the whole-genome sequences of over 4000 strains have been reported and a diversity of mutations, including in genes known to be associated with drug resistance in other human fungal pathogens, have been described. Among them, 387 strains contained antifungal-susceptibility information for which different methods might be used depending on the drugs and/or investigators. In most reports on C. auris so far, the number of strains analyzed was very small, from one to a few dozen, and the statistical significance of the relationships between these genetic variants and their antifungal susceptibilities could not be assessed. In this study, we conducted genome-wide association studies on individual clades based on previously published C. auris isolates to investigate the statistical association between genomic variants and susceptibility differences to nine antifungal drugs belonging to four major drug categories: 5-fluorocytosine, amphotericin B, fluconazole, voriconazole, itraconazole, posaconazole, anidulafungin, caspofungin, and micafungin. Due to the small sample sizes for Clades II, V, and VI, this study only assessed Clades I, III, and IV. Our analyses revealed 15 single nucleotide polymorphisms (SNPs) in Clade I (10 in coding and 5 in noncoding regions), 24 SNPs in Clade III (11 in coding and 13 in noncoding regions), and 13 SNPs in clade IV (10 in coding and 3 in noncoding regions) as statistically significantly associated with susceptibility differences to one or more of the nine antifungal drugs. While four SNPs in genes encoding lanosterol 14-α-demethylase (ERG11) and the catalytic subunit of 1,3-beta-D-glucan synthase (FKS1) were shared between clades, including the experimentally confirmed Ser639Phe/Pro missense substitutions in FKS1 for echinocandin resistance, most of the identified SNPs were clade specific, consistent with their recent independent origins. Interestingly, the majority of the antifungal resistance-associated SNPs were novel, and in genes and intergenic regions that have never been reported before as associated with antifungal resistance. While targeted study is needed to confirm the role of each novel SNP, the diverse mechanisms of drug resistance in C. auris revealed here indicate both challenges for infection control and opportunities for the development of novel antifungal drugs against this and other human fungal pathogens.

Aspergillus fumigatus is a ubiquitous fungus and the main agent of aspergillosis, a common fungal infection in the immunocompromised population. Triazoles such as itraconazole and voriconazole are the common first-line drugs for treating aspergillosis. However, triazole resistance in A. fumigatus has been reported in an increasing number of countries. While most studies of triazole resistance have focused on mutations in the triazole target gene cyp51A, >70% of triazole-resistant strains in certain populations showed no mutations in cyp51A. To identify potential non-cyp51A mutations associated with triazole resistance in A. fumigatus, we analyzed the whole genome sequences and triazole susceptibilities of 195 strains from 12 countries. These strains belonged to three distinct clades. Our genome-wide association study (GWAS) identified a total of six missense mutations significantly associated with itraconazole resistance and 18 missense mutations with voriconazole resistance. In addition, to investigate itraconazole and pan-azole resistance, Fisher’s exact tests revealed 26 additional missense variants tightly linked to the top 20 SNPs obtained by GWAS, of which two were consistently associated with triazole resistance. The large number of novel mutations related to triazole resistance should help further investigations into their molecular mechanisms, their clinical importance, and the development of a comprehensive molecular diagnosis toolbox for triazole resistance in A. fumigatus.

Amphotericin B (AMB) is a major fungicidal polyene agent that has a broad spectrum of action against invasive fungal infections. AMB is typically used as the last-line drug against serious and life-threatening infections when other drugs have failed to eliminate the fungal pathogens. Recently, AMB resistance in Aspergillus fumigatus has become more evident. For example, a high rate of AMB resistance (96%) was noted in the A. fumigatus population in Hamilton, Ontario, Canada. AMB-resistant strains have also been found in other countries. However, the mechanism of AMB resistance remains largely unknown. Here, we investigated the potential genes and mutations associated with AMB resistance using whole-genome sequences and examined AMB resistance distribution among genetic populations. A total of 196 whole-genome sequences representing strains from 11 countries were examined. Analyses of single nucleotide polymorphisms (SNPs) at the whole-genome level revealed that these strains belonged to three divergent genetic clusters, with the majority (90%) of AMB resistant strains located in one of the three clusters, Cluster 2. Our analyses identified over 60 SNPs significantly associated with AMB resistance. Together, these SNPs represent promising candidates from which to investigate the putative molecular mechanisms of AMB resistance and for their potential use in developing rapid diagnostic markers for clinical screening of AMB resistance in A. fumigatus.

Background: To investigate the prevalence of concomitant bacterial infection across common viral infections. Methods: This population-based cohort study included patients infected with influenza A and B (FLUA, FLUB) and respiratory syncytial virus (RSV) in Ontario between 2017 and 2019 and patients with SARS-CoV-2 between 2020 and 2021. Specific bacteria present in concomitant infections were identified. Concomitant infections were further classified into different categories (eg, coinfection −2 to +2 days from viral infection and secondary infection >2 days after viral infection). We used logistic regression models to estimate the odds of bacterial infections for FLUA, FLUB, and RSV relative to SARS-CoV-2 while adjusting for confounders. Results: A total of 4230 (0.5%, 885 004) viral cases had concomitant bacterial infections, encompassing 422 of FLUB (4.7%, 8891), 861 of FLUA (3.9%, 22 313), 428 of RSV (3.4%, 12 774), and 2519 of COVID-19 (0.3%, 841 026). The most prevalent species causing concomitant bacterial infection were Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa. When compared with SARS-CoV-2, the adjusted odds ratio for bacterial infection was 1.69 (95% CI, 1.48–1.93) for FLUA, 2.30 (95% CI, 1.97–2.69) for FLUB, and 1.56 (95% CI, 1.33–1.82) for RSV. The adjusted odds of coinfection in patients with SARS-CoV-2 were lower but higher for secondary infection as compared with the other viruses. Conclusions: A higher prevalence and risk of concomitant bacterial infection were found in FLUA, FLUB, and RSV as compared with SARS-CoV-2, although this is largely driven by coinfections. Ongoing surveillance efforts are needed to compare the risk of concomitant infections during periods when these viruses are cocirculating.