ABSTRACT
Oral fungal infections are a worldwide healthcare problem. Although Candida albicans is still the most common yeast involved in the infections of oral cavity, non-Candida albicans Candida species (NCACs) have been highly related to these infections, particularly in older, immunosuppressed or patients with long exposure to antimicrobial drugs. The goal of this work was to perform a quick epidemiological and mycological study on the oral samples collected from a laboratory of a hospital in Slovakia, for 60 days. The samples' identification was performed by Germ-tube formation test, CHROMID® Candida, Auxacolor 2, ID 32C automated method, and the antifungal susceptibility testing determined by E-test®. Results confirm that comparing with bacteria, yeasts still occur in the lower number, but there is a high rate of antifungal resistance (81.6%)-to, at least one drug-among the collected samples, particularly to azoles and 5'-FC, which is clinically noteworthy.
Subject(s)
Antifungal Agents , Candida , Aged , Antifungal Agents/pharmacology , Antifungal Agents/therapeutic use , Fluconazole , Hospitals , Humans , Microbial Sensitivity Tests , Prevalence , Slovakia/epidemiologyABSTRACT
The emergence of a novel SARS-CoV-2 B.1.1.7 variant sparked global alarm due to increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus accelerating efforts to detect and track the variant. Current approaches to detect B.1.1.7 include sequencing and RT-qPCR tests containing a target assay that fails or results in reduced sensitivity towards the B.1.1.7 variant. Since many countries lack genomic surveillance programs and failed assays detect unrelated variants containing similar mutations as B.1.1.7, we used allele-specific PCR, and judicious placement of LNA-modified nucleotides to develop an RT-qPCR test that accurately and rapidly differentiates B.1.1.7 from other SARS-CoV-2 variants. We validated the test on 106 clinical samples with lineage status confirmed by sequencing and conducted a country-wide surveillance study of B.1.1.7 prevalence in Slovakia. Our multiplexed RT-qPCR test showed 97% clinical sensitivity and retesting 6,886 SARS-CoV-2 positive samples obtained during three campaigns performed within one month, revealed pervasive spread of B.1.1.7 with an average prevalence of 82%. Labs can easily implement this test to rapidly scale B.1.1.7 surveillance efforts and it is particularly useful in countries with high prevalence of variants possessing only the ΔH69/ΔV70 deletion because current strategies using target failure assays incorrectly identify these as putative B.1.1.7 variants.