Finding a Needle in a Haystack – In Silico Search for Environmental Traces of &lt;i&gt;Candida auris &lt;/i&gt;

Irinyi, László; Roper, Michael; Malík, Richard; Meyer, Wieland

doi:10.7883/yoken.jjid.2022.068

Cited by 13 publications

(24 citation statements)

References 42 publications

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“…Recently, searches of the Sequence Read Archive of the NCBI database detected C . auris sequences from historic environmental samples [ 92 ] and identified 7 C . auris metabarcoding datasets, some of which were obtained from environmental samples collected from different parts of the world.…”

Section: Candida Auris Persistence and Cycling In The Enviro...mentioning

confidence: 99%

“…The C. auris genome also provides evidence for the environmental selection of antifungal resistance genes in C. auris [91]. Recently, searches of the Sequence Read Archive of the NCBI database detected C. auris sequences from historic environmental samples [92] and identified 7 C. auris metabarcoding datasets, some of which were obtained from environmental samples collected from different parts of the world. Taken together, the available evidence strongly supports the hypothesis that C. auris emerged from reservoirs in the natural environment under various environmental stress including selection pressure from antifungals.…”

Section: Candida Auris Persistence and Cycling In The Environmentmentioning

confidence: 99%

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Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris

2023

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Candia auris is an emerging human pathogenic yeast; yet, despite phenotypic attributes and genomic evidence suggesting that it probably emerged from a natural reservoir, we know nothing about the environmental phase of its life cycle and the transmission pathways associated with it. The thermotolerant characteristics of C. auris have been hypothesised to be an environmental adaptation to increasing temperatures due to global warming (which may have facilitated its ability to tolerate the mammalian thermal barrier that is considered a protective strategy for humans against colonisation by environmental fungi with pathogenic potential). Thus, C. auris may be the first human pathogenic fungus to have emerged as a result of climate change. In addition, the release of antifungal chemicals, such as azoles, into the environment (from both pharmaceutical and agricultural sources) is likely to be responsible for the environmental enrichment of resistant strains of C. auris; however, the survival and dissemination of C. auris in the natural environment is poorly understood. In this paper, we critically review the possible pathways through which C. auris can be introduced into the environment and evaluate the environmental characteristics that can influence its persistence and transmission in natural environments. Identifying potential environmental niches and reservoirs of C. auris and understanding its emergence against a backdrop of climate change and environmental pollution will be crucial for the development of effective epidemiological and environmental management responses.

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Section: Candida Auris Persistence and Cycling In The Enviro...mentioning

confidence: 99%

Section: Candida Auris Persistence and Cycling In The Environmentmentioning

confidence: 99%

Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris

2023

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“…16 A recent in silico species-specific sequence search in the world's largest sequence repository, the Sequence Read Archive (SRA) at NCBI identified potential environmental sources of C. auris such as airborne dust, activated sludge, peanut fields, and faeces. 17 These results suggest a possible ecological niche of C. auris in wetlands where it can be associated with amphibians, from where it can spread via water, aerosols or bird species to human or animal habitats. The same study concluded that C. auris could infect other animals such as dogs and amphibians beside humans.…”

Section: Environmental Sourcesmentioning

confidence: 75%

“…The same study concluded that C. auris could infect other animals such as dogs and amphibians beside humans. 17 In addition, it has been shown that the life cycle could be completed by excretion of C. auris from infected humans/ animals via faeces, which then contaminate wastewater, in which it is able to survive despite wastewater treatment (sludge) prior to returning to wetlands. 17…”

Section: Environmental Sourcesmentioning

confidence: 99%

Candida auris: the most talked about multidrug-resistant emerging fungal pathogen

Irinyi

Malík²,

Meyer³

2022

Microbiol. Aust.

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Currently Candida auris is the most talked about multidrug-resistant emerging fungal pathogen. It can cause difficult-to-control nosocomial outbreaks worldwide, being highly contagious, and poses serious challenges to public health authorities. A wide spectrum of infections, ranging from superficial mucosal infections, candidemia to disseminated deep-seated disease, having been reported from more than 40 countries, including Australia. Outbreaks are associated with high mortality rates due to rapid transmission and challenges in prevention, control, and treatment. It is shows a high multidrug-resistance (with 90% of isolates resistant to fluconazole), and is extremely tolerant to conditions which usually limit fungal transmission, including commonly used disinfectants. Whole genome analysis has revealed five different closely related clades (named after the geographical areas they have been first encoundered) with distinct clonal lineages. Its environmental niche remained a mystery until recently when it was found in India in association with costal aquatic environments.

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“…However, it is also equally likely that C. auris might have been spread into aquatic environment from contaminated wastewater after being excreted from the gastrointestinal tract or washed off the skin of a colonized people (34). These findings point to its most likely mode of spread (any aquatic stream or aqueous medium) between the human populations and environment and vice versa (35).…”

Section: Discussionmentioning

confidence: 92%

FindingCandida aurisin public metagenomic repositories

Mario-Vasquez,

Bagal,

Lowe

et al. 2023

Preprint

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Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing.

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Finding a Needle in a Haystack – In Silico Search for Environmental Traces of <i>Candida auris </i>

Cited by 13 publications

References 42 publications

Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris

Environmental reservoirs of the drug-resistant pathogenic yeast Candida auris

Candida auris: the most talked about multidrug-resistant emerging fungal pathogen

FindingCandida aurisin public metagenomic repositories

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