![]() Clade I originated in South Asia, clade II in East Asia, clade III in Africa, clade IV in South America, and clade V in the Middle East (Iran) ( 13). auris is classified into several genetically distinct clades. parapsilosis has been a major pathogen causing late-onset sepsis among hospitalized neonates in low- and middle-income countries because of its ability to colonize the skin of hospitalized patients and healthcare workers, persist on hospital surfaces, and adhere to indwelling medical devices, characteristics that are also applicable to C. ![]() auris has caused outbreaks involving neonates and has subsequently become endemic in many hospitals in South Africa ( 7– 10). auris are occasionally documented, although early outbreaks in South Africa occurred mainly among critically ill adults ( 7). auris a global public health concern the World Health Organization has designated it a critical-priority fungal pathogen ( 5, 6). The rapid emergence and international spread during 2014–2023, high crude mortality rates (30%–60%), and antifungal resistance make C. auris bloodstream infection in 2009 at a Johannesburg academic hospital ( 4). Those cases prompted a retrospective review of surveillance isolates that identified a case of C. auris was initially described in 2009 in Japan, the earliest cases of infection in South Africa were reported in 2014 ( 3). The outbreak may have originated through transmission from infected or colonized patients, colonized healthcare workers, or contaminated equipment/environment.Ĭandida auris is a multidrug-resistant yeast that causes invasive infections with high associated mortality in acute and long-term healthcare facilities worldwide ( 1, 2). Dominated by clade III, the neonatal unit outbreak accounted for 32% (91/287) of all cases during the study period. All 181/188 isolates that had a fluconazole MIC >32 µg/mL had ERG11 mutations clade III isolates had VF125AL substitutions, and clade IV isolates had K177R/N335S/E343D substitutions. auris infection identified through laboratory surveillance, 207 (72%) had viable isolates and 188 (66%) were processed for whole-genome sequencing. auris in the same hospital during 2016–2020 the neonatal unit had a persistent outbreak beginning in June 2019. We used whole-genome sequencing to describe the molecular epidemiology of C. The plugin is fully compatible with the Microbial Genomics Pro Suite, CLC Genomics Workbench*, and Biomedical Genomics Workbench* * The plugin requires an up to date version of the CLC Microbial Genomics Module to be installed.Candida auris was first detected at a university-affiliated hospital in Johannesburg, South Africa, in 2009. Bacteria, virus, parasite, fungi and antibiotic resistance databases.Antibiotic resistance and virulence factors.Visualization including heat maps and principal component analysis (PCA).Bioinformatics, statistical, and comparative analyses.Explore your metagenomic data through a tried and trusted interface and tap into the deep NGS toolbox included in QIAGEN’s bioinformatics solution for microbial genomics. Ease of useĬosmosID installs into CLC Genomics Workbench. GenBook® is derived from private and public databases of assembled genomes and constitutes hundreds of millions of marker sequences representing both coding and non-coding sequences that are shared or uniquely identified across taxonomic or phylogenetic levels. It is able to discriminate pathogens and commensals from their ‘near neighbors’ using statistical and computational methods, with no prior assumptions as to what is present in the sample.ĬosmosID uses raw, unassembled reads as input and matches the sequence against GenBook®, our expertly curated reference database. Deeper insight through expert curated reference dataĬosmosID identifies bacteria, viruses, fungi, and protists, as well as, antibiotic resistance and virulence factors in a whole genome shotgun metagenomic sample. With the use of our curated genome databases and unrivalled sensitivity and specificity (>95%, and >99% respectively) we are unmatched in our ability to detect microorganisms in metagenomic samples. CosmosID gives you fast, accurate and comprehensive analyses of unassembled next generation sequencing reads. CosmosID Plugin for Qiagen CLC Detect microbes in metagenomic samples with confidenceĮxplore your metagenomic samples with CosmosID and QIAGEN Bioinformatics.
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