Biology subjects

Chowdhary, A.

Publications and source records attributed to Chowdhary, A..

11 recordsLinked to original sources

bioRxiv2026

Candida auris can acquire antifungal resistance without selection pressure

The human fungal pathogen Candidozyma auris (formerly Candida auris) can cause prolonged infection outbreaks with high mortality rates in healthcare settings. Treatment failures of patients arise not only from antifungal drug resistance, but also from intra-species variability in pathogenicity as well as induced hypermutation events in response to clinical therapy. Whole genome sequencing was used to identify genetic mutations using the CDC mycoSNPs pipeline. Antifungal susceptibility testing was performed based on Clinical and Laboratory Standards Institute (CLSI) methods. We report here that the interlaboratory exchange of C. auris clinical isolates dried on sterile filter paper, resulted in the emergence of at least three distinct morphotypes following reconstitution. These distinct morphotypes exhibited differences in drug resistance and morphogenesis, linked to the accumulation of mutations in genes associated with azole and echinocandin resistance. Using whole genome sequencing, we identified several variants in TAC1B, MRR1 and FKS2 that correlate with altered drug susceptibilities. Experiments recapitulating filter paper shipment conditions revealed genetic and epigenetic changes, explaining the morphogenetic switching and altered azole resistance. Our findings demonstrate that C. auris can acquire mutations affecting drug resistance traits even in the absence of antifungal exposure, raising concerns about shipment preparation procedures across mycology laboratories. The results are of broad relevance for the medical mycology community, as they call for standardized protocols for exchanging clinical strains, but also experiments to verify phenotypic traits between laboratories. ImportancePathogenesis and antifungal drug resistance traits of Candida auris vary widely across clinical strains and are often attributed to elevated mutation rates. In fungal pathogen research, clinical strains are commonly exchanged between laboratories by transfer on filter paper, a convenient and widely used practice. However, in the case of a C. auris clinical strain received from a collaborating laboratory, we identified multiple acquired mutations. These genetic alterations caused marked changes in morphogenesis and antifungal susceptibility, demonstrating that resistance in C. auris can arise without antifungal selection pressure. Our findings highlight the potential for genetic and phenotypic diversification during routine strain handling and underscore the need for standardized protocols for exchanging clinical C. auris strains across mycology laboratories.

microbiology↗

bioRxiv2025

Antifungal susceptibility profile of clinically relevant species of the genus Sporothrix: establishment of Epidemiological Cutoff Values (ECVs) according to CLSI broth microdilution methodology

Sporotrichosis is a globally distributed subcutaneous mycosis caused mainly by Sporothrix brasiliensis, S. schenckii, and S. globosa. Cat-transmitted sporotrichosis, primarily caused by S. brasiliensis in South America and to a lesser extent by S. schenckii in Southeast Asia, is emerging as a significant public health concern, due its outbreak potential. Itraconazole is the first-choice drug for treatment of human and cats, but reduced susceptibility has been reported based on previously proposed epidemiological cut-off values (ECVs). To support resistance surveillance, we aimed to establish CLSI-endorsed ECVs for these clinically relevant Sporothrix species. A total of 3,588 minimum inhibitory concentration (MIC) values for seven antifungal agents (amphotericin B, itraconazole, posaconazole, voriconazole, isavuconazole, olorofim, and terbinafine) were obtained from 19 international laboratories. Four of seven antifungals met the CLSI M57 guidelines criteria to determine the ECV. Established ECVs for amphotericin B were found to be high with 8 {micro}g/mL for S. brasiliensis and S. globosa, and 4 {micro}g/mL for S. schenckii. Itraconazole ECVs were 4 {micro}g/mL for S. brasiliensis and S. schenckii. Posaconazole ECVs were 4 {micro}g/mL for all three species (tentative for S. globosa), while the terbinafine ECV for S. brasiliensis was 0.12 {micro}g/mL. Olorofim demonstrated good in vitro activity, particularly against S. brasiliensis. Overall, this study establishes validated ECVs for key antifungals against Sporothrix species and identifies a low prevalence of non-wild type (NWT) isolates, supporting ongoing antifungal resistance monitoring.

microbiology↗

bioRxiv2024

Genomic epidemiology of emerging terbinafine-resistant Trichophyton indotineae

Dermatophyte skin infections affect around a quarter of the worlds population and are a growing public health concern due to increasing incidence of novel species causing severe infections that are resistant to antifungal treatments. Trichophyton species cause the greatest burden of dermatophytosis worldwide, with the T. mentagrophytes species complex being particularly associated with the emergence of new aggressive infections. One emerging species, T. indotineae (originally T. mentagrophytes genotype VIII) is notable for the extensive nature of the often inflammatory infection, its clinical resistance to terbinafine antifungal treatment, and its rapid global spread. To better understand the epidemiology of this disease, we sourced isolates from severe cases of dermatophytosis in the United Kingdom, Ireland, France, Canada and India for the period 2018-2023, including the type strain from Japan. We used whole-genome sequencing to confirm 90 isolates were T. indotineae, and antifungal susceptibility testing indicated that over half of these (62%) were resistant to terbinafine (MIC [≥]1 mg/L). Pairwise genetic distances showed very high identity with only 147 (1-414) SNPs separating isolates that were nested within a monophyletic phylogeny, supporting a single evolutionary origin of T. indotineae. That no clear geographic clustering of isolates was observed confirms the rapid transcontinental spread of T. indotineae from its likely centre of diversity in Asia. Genome-wide analyses identified multiple non-synonymous SNPs in SQLE (ERG1), the squalene epoxidase target of terbinafine, that were associated with terbinafine in vitro resistance [≥]1 mg/L. However, five isolates exhibited high MIC values without SQLE mutations, suggesting the presence of alternative resistance mechanisms. Our findings highlight the importance of better genomic surveillance to understand and manage this severe and rapidly emerging terbinafine-resistant dermatophyte.

genomics↗

bioRxiv2024

Carbon Dioxide Controls Fungal Fitness and Skin Tropism of Candida auris

The pronounced skin tropism and pan-antifungal resistance traits of the fungal pathogen Candida auris stand out as a serious health threat. Here, we show that a carbonic sensing pathway (CSP) promotes development of resistance to amphotericin B through a reactive oxygen species (ROS) response, as well as ectopic cell wall and membrane lipid homeostasis. Mechanistically, the transcription factor Rca1 acts in cooperation with Efg1 to control the expression and activity of the carbonic anhydrase Nce103 as a key effector component. The conversion of carbon dioxide to bicarbonate provides a direct link to energy metabolism, facilitating colonization and growth on skin tissues. Native mouse and human skin models unequivocally show that the CSP is essential for maintaining skin tropism as well as fungal fitness. Curiously, upon ablation of Rca1 and Efg1, C. auris debilitates efficient growth on native skin. Collectively, our findings highlight critical roles of the CSP in C. auris skin tropism and antifungal drug resistance. The work suggests therapeutic options for disrupting skin colonization and thus preventing infections. Highlights{checkmark} Proteo-transcriptomics links a carbonic sensing pathway (CSP) to C. auris multidrug resistance {checkmark}The Nce103 carbonic anhydrase controls drug resistance as a key component of the CSP {checkmark}The transcription factors Rca1 and Efg1 control Nce103 and link CSP with C. auris skin tropism {checkmark}CSP acts through ectopic ROS response, cell wall architecture and membrane lipid function {checkmark}CSP is required for C. auris fitness and efficient growth and colonization of skin tissues Result contents{checkmark} Integrated omics reveals multidrug-resistant mechanisms in C. auris {checkmark}CO2-sensing controls amphotericin B resistance (AMBR) traits through Rca1 and Efg1 {checkmark}The carbonic anhydrase Nce103 governs susceptibility to amphotericin B {checkmark}The CSP influences AMBR by maintaining reactive oxygen species homeostasis {checkmark}The CSP controls AMBR via cell membrane and cell wall remodelling {checkmark}The CSP regulates fungal fitness through controlling energy metabolism {checkmark}C. auris requires the CSP for skin colonization

microbiology↗

bioRxiv2024

The Candida auris Hog1 MAP kinase is essential for the colonization of murine skin and intradermal persistence

Candida auris, a multidrug-resistant human fungal pathogen, was first identified in 2009 in Japan. Since then, systemic C. auris infections have now been reported in more than 50 countries, with mortality rates of 30-60%. A major contributing factor to its high inter- and intrahospital clonal transmission is that C. auris, unlike most Candida species, displays unique skin tropism and can stay on human skin for a prolonged period. However, the molecular mechanisms responsible for C. auris skin colonization, intradermal persistence, and systemic virulence are poorly understood. Here, we report that C. auris Hog1 mitogen-activated protein kinase (MAPK) is essential for efficient skin colonization, intradermal persistence, as well as systemic virulence. RNA-seq analysis of wildtype parental and hog1{Delta} mutant strains revealed marked down-regulation of genes involved in processes such as cell adhesion, cell-wall rearrangement, and pathogenesis in hog1{Delta} mutant compared to the wildtype parent. Consistent with these data, we found a prominent role for Hog1 in maintaining cell-wall architecture, as the hog1{Delta} mutant demonstrated a significant increase in cell-surface {beta}-glucan exposure and a concomitant reduction in chitin content. Additionally, we observed that Hog1 was required for biofilm formation in vitro and fungal survival when challenged with primary murine macrophages and neutrophils ex vivo. Collectively, these findings have important implications for understanding the C. auris skin adherence mechanisms and penetration of skin epithelial layers preceding bloodstream infections. ImportanceCandida auris is a World Health Organization (WHO) fungal priority pathogen and an urgent public health threat recognized by the Centers for Disease Control and Prevention (CDC). C. auris has a unique ability to colonize human skin. It also persists on abiotic surfaces in healthcare environments for an extended period of time. These attributes facilitate the inter- and intrahospital clonal transmission of C. auris. Therefore, understanding C. auris skin colonization mechanisms are critical for infection control, especially in hospitals and nursing homes. However, despite its profound clinical relevance, the molecular and genetic basis of C. auris skin colonization mechanisms are poorly understood. Herein, we present data on the identification of the Hog1 MAP kinase as a key regulator of C. auris skin colonization. These findings lay foundation for further characterization of unique mechanisms that promote fungal persistence on human skin.

microbiology↗

bioRxiv2023

Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci

Splicing quantitative trait loci (QTLs) have been implicated as a common mechanism underlying complex trait associations. However, utilising splicing QTLs in target discovery and prioritisation has been challenging due to extensive data normalisation which often renders the direction of the genetic effect as well as its magnitude difficult to interpret. This is further complicated by the fact that strong expression QTLs often manifest as weak splicing QTLs and vice versa, making it difficult to uniquely identify the underlying molecular mechanism at each locus. We find that these ambiguities can be mitigated by visualising the association between the genotype and average RNA sequencing read coverage in the region. Here, we generate these QTL coverage plots for 1.7 million molecular QTL associations in the eQTL Catalogue identified with five quantification methods. We illustrate the utility of these QTL coverage plots by performing colocalisation between vitamin D levels in the UK Biobank and all molecular QTLs in the eQTL Catalogue. We find that while visually confirmed splicing QTLs explain just 6/53 of the colocalising signals, they are significantly less pleiotropic than eQTLs and identify a prioritised causal gene in 4/6 cases. All our association summary statistics and QTL coverage plots are freely available at https://www.ebi.ac.uk/eqtl/.

genomics↗

bioRxiv2021

Rare modification in the ergosterol biosynthesis pathway leads to amphotericin B resistance in Candida auris clinical isolates

We determined amphotericin B (AmB) susceptibility and sequenced key genes of the ergosterol biosynthesis pathway implicated in AmB resistance (ERG2, ERG3, ERG6, ERG11) of 321 clinical isolates of Candida auris. In antifungal susceptibility testing, 19 (5.9%) isolates were categorized as AmB-resistant (MIC [≥]2 mg/l). Only one AmB-resistant isolate presented a unique non-wild-type ERG6 genotype that was confirmed to confer amphotericin B resistance (MIC >32 mg/l) when introduced into a susceptible strain (MIC = 0.5 mg/l).

microbiology↗

bioRxiv2020

Confirmation of interpersonal expectations is intrinsically rewarding

People want to interact successfully with other individuals, and they invest significant efforts in attempting to do so. Decades of research have demonstrated that to simplify the dauntingly complex task of interpersonal communication, perceivers use stereotypes and other sources of prior knowledge to predict the responses of individuals in their environment. Here, we show that these top-down expectations can also shape the subjective value of expectation-consistent and expectation-violating targets. Specifically, in two neuroimaging experiments (n = 58), we observed increased activation in brain regions associated with reward processing--including the nucleus accumbens--when perceivers observed information consistent with their social expectations. In two additional behavioral experiments (n = 704), we observed that perceivers were willing to forgo money to encounter an expectation-consistent target and avoid an expectation-violating target. Together, these findings suggest that perceivers value having their social expectations confirmed, much like food or monetary rewards.

neuroscience↗

bioRxiv2019

Development of Candida auris microsatellite typing and its application on a global collection of isolates

Candida auris is a pathogenic yeast that causes invasive infections with high mortality. Infections most often occur in intensive care units of healthcare facilities. It is crucial to trace the source and prevent further spread of C. auris during an outbreak setting, therefore, genotyping of C. auris is required. To enable fast and cost-effective genotyping, we developed a microsatellite typing assay for C. auris.\n\nShort tandem repeats (STRs) in C. auris were identified, and a novel STR typing assay for C. auris was developed using 4 panels of three multiplex PCRs. Having shown that the microsatellite typing assay was highly reproducible and specific, a robust set of 444 C. auris isolates was investigated to identify genotypic diversity. In concordance with whole-genome sequencing (WGS) analysis we identified five major different C. auris clusters, namely, South-America, South-Asia, Africa, East-Asia and Iran. Overall, a total of 40 distinct genotypes were identified, with the largest variety in the East Asian clade. Comparison with WGS demonstrated that isolates with <20 SNPs are mostly not differentiated by STR analysis, while isolates with 30 or more SNPs usually have differences in one or more STR markers.\n\nAltogether, a highly reproducible and specific microsatellite typing assay for C. auris was developed, which distinguishes the five different C. auris clades in identical fashion to WGS, while most isolates differing >20 SNPs, as determined via WGS, are also separated. This new C. auris specific genotyping technique is a rapid, reliable, cost-effective alternative to WGS analysis to speedily investigate outbreaks.\n\nImportanceCandida auris is an emerging fungal pathogen now recognized as a threat to public health. The pathogen has spread worldwide and mainly causes hospital associated outbreaks. To track and trace outbreaks and to relate them to new introductions from elsewhere, whole genome sequencing and amplified fragment length polymorphism (AFLP) have been used for molecular typing. While the former is costly and only available in few centers, AFLP is a complicated technique and standardization is not possible. We describe a novel simple microsatellite genotyping technique based on small tandem repeats in the C. auris genome. Further we show that this microsatellite based genotyping technique has been proven comparable to WGS. Overall, this work provides a novel, rapid, reliable and cost-effective method of molecular outbreaks investigations of C. auris.

microbiology↗

bioRxiv2018

Correlation of in vitro susceptibility based on MICs and SQLE mutations with clinical response to terbinafine in patients with tinea corporis/cruris

Recalcitrant dermatophytoses are on the rise and recent publications have documented high minimum inhibitory concentrations (MICs) to TRB and squalene epoxidase (SQLE) mutations. However, literature correlating the laboratory the data with clinical response is lacking.\n\nThis study was conducted to study the clinico-mycological profile of tinea corporis and cruris, including antifungal susceptibility testing (AFST) and SQLE mutation analysis and correlate these with clinical response to TRB. Skin scrapings of patients with tinea corporis with/without tinea cruris were subjected to species identification, AFST and SQLE gene analysis (on 15 isolates). KOH confirmed cases were started on TRB 250mg once a day (OD). If >50% clinical clearance was achieved by 3 weeks; the same dose was continued.(Group 1). If clinical clearance at 3 weeks was <50%, the dose was increased to 250mg twice a day (BD) (Group 2). If the response still remained below 50% after 3 weeks of BD, the patients were treated with itraconazole (ITR)(Group 3). Trichophyton interdigitale was confirmed on all 64 isolates obtained on culture. Forty four (68.7%) isolates had high ([≥]1 g/ml) MICs to TRB. Six isolates were found to have aminoacid substitution Leu393Phe in SQLE protein, while one had the substitution Phe397Leu. The difference in modal MICs to TRB between the 3 clinical response groups (1.5157g/ml, 5.0396 g/ml and 20.1587g/ml respectively for group 1,2 and 3) was highly significant. Clinical response was achieved in 68% of those resistant by MIC data, and 42.8% of SQLE mutation harboring isolates, by increasing drug (TRB) exposure.\n\nWe infer that TRB resistance in dermatophytes has reached alarming proportions in our patients. Though improved outcomes were achieved with higher drug exposure, with the high failure rate seen in the study, the case for shifting to another class of antifungals as first line agent against dermatophytoses is strong.

microbiology↗

bioRxiv2017

Population Genomics Of Cryptococcus neoformans var. grubii Reveals New Biogeographic Relationships And Finely Maps Hybridization

Cryptococcus neoformans var. grubii is the causative agent of cryptococcal meningitis, a significant source of mortality in immunocompromised individuals, typically HIV/AIDS patients from developing countries. Despite the worldwide emergence of this ubiquitous infection, little is known about the global molecular epidemiology of this fungal pathogen. Here we sequence the genomes of 188 diverse isolates and characterized the major subdivisions, their relative diversity and the level of genetic exchange between them. While most isolates of C. neoformans var. grubii belong to one of three major lineages (VNI, VNII, and VNB), some haploid isolates show hybrid ancestry including some that appear to have recently interbred, based on the detection of large blocks of each ancestry across each chromosome. Many isolates display evidence of aneuploidy, which was detected for all chromosomes. In diploid isolates of C. neoformans var. grubii (serotype A/A) and of hybrids with C. neoformans var. neoformans (serotype A/D) such aneuploidies have resulted in loss of heterozygosity, where a chromosomal region is represented by the genotype of only one parental isolate. Phylogenetic and population genomic analyses of isolates from Brazil revealed that the previously African VNB lineage occurs naturally in the South American environment. This suggests migration of the VNB lineage between Africa and South America prior to its diversification, supported by finding ancestral recombination events between isolates from different lineages and regions. The results provide evidence of substantial population structure, with all lineages showing multi-continental distributions demonstrating the highly dispersive nature of this pathogen.\n\nAuthor SummaryCryptococcus neoformans var. grubii is a human fungal pathogen of immunocompromised individuals that has global clinical impact, causing half a million deaths per year. Substantial genetic substructure exists for this pathogen, with two lineages found globally (VNI, VNII) whereas a third has appeared confined to sub-Saharan Africa (VNB). Here, we utilized genome sequencing of a large set of global isolates to examine the genetic diversity, hybridization, and biogeography of these lineages. We found that while the three major lineages are well separated, recombination between the lineages has occurred, notably resulting in hybrid isolates with segmented ancestry across the genome. In addition, we showed that isolates from South America are placed within the VNB lineage, formerly thought to be confined to Africa, and that there is phylogenetic separation between these geographies that substantially expands the diversity of these lineages. Our findings provide a new framework for further studies of the dynamics of natural populations of C. neoformans var. grubii.

genomics↗