Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals, while also clearing essential staff to continue work. At the current time a number of qRT-PCR assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains it is prudent to monitor circulating viruses for variants that might compromise these assays. Here we report the identification of a C-to-U transition at position 26,340 of the SARS-CoV-2 genome which is associated with failure of the cobas® SARS-CoV-2 E-gene qRT-PCR in eight patients. As the cobas® SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called as SARS-CoV-2 positive. Whole genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of SNPs which might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.

A spergillus fumigatus is the most frequent cause of invasive mold infections in immunocompromised patients. The mortality rate from these infections varies substantially and depends on patient characteristics and the extent of disease. Mortality in intensive care unit (ICU) patients with invasive aspergillosis (IA) can be as high as 90% (1). In hematology patients, a relatively low mortality is observed when the diagnosis is made early and treatment with voriconazole, the current standard of care (2), is initiated promptly (3). In 2002, the landmark study by Herbrecht et al. (4) showed that the treatment of IA with voriconazole resulted in improved survival. However, a series of recent publications described the appearance of azole resistance in A. fumigatus (5-10). This resistance is caused by a mutation in the CYP51A gene of A. fumigatus at position 98 (L98H), together with a 34-bp tandem repeat (TR) in the promoter region (TR34). CYP51A encodes cytochrome p450 sterol 14␣-demethylase, the target of azoles. The majority of these mutated strains were cultured from patients who were never exposed to azoles. It is assumed that resistance development is caused by environmental azole exposure (11). More recently, van der Linden et al. (12) described a second mutation, a 46-bp TR combined with the point mutations Y121F and T289A (12). In this study, 47 of 921 patients (5.1%) were diagnosed with TR34-L98H and 13 (1.4%) with the TR46-Y121F-T289A mutations. Other mutations have also been described (13-16). Infections with azole-resistant strains are associated with a very high mortality rate (17).Currently, the absence of a non-culture-based, fast, and readily available azole susceptibility testing method compromises the identification of azole resistance. This is a major limitation, as the mortality of IA increases substantially when the initiation of adequate therapy is delayed (18). Furthermore, most Aspergillus infections are diagnosed indirectly using galactomannan (or ␤-1,3-D-glucan) testing, because cultures remain negative in most patients. Therefore, even if culture-based azole resistance testing became broadly available, this would be helpful in only a subset of patients.This study describes the laboratory and first clinical validation of the AsperGenius, a new Aspergillus real-time PCR assay that detects Aspergillus species directly from bronchoalveolar lavage

Dermatophytes are amongst the most common fungal agents causing superficial skin infections. The epidemiology of dermatophytosis has changed during the last century under the influence of socioeconomic factors, modern life, intensification of travel, migration of populations from the southern to the northern hemisphere. As result, Trichophyton rubrum has become the most frequent species worldwide, causing mainly tinea pedis and tinea unguium, while Microsporum canis is still the main agent in tinea corporis and capitis in Mediterranean countries. However, the prevalence of anthropophilic dermatophytes causing tinea capitis in young children is increasing overall in the big cities of Europe and America, causing epidemics and becoming a public health concern. This review summarizes the current status of dermatophyte infection in Europe, Africa, Asia and America and gives an overview of the most recent molecular methods currently available for the laboratory diagnosis of dermatophytosis.

Moonmilk speleothems of limestone caves host a rich microbiome, among which Actinobacteria represent one of the most abundant phyla. Ancient medical texts reported that moonmilk had therapeutical properties, thereby suggesting that its filamentous endemic actinobacterial population might be a source of natural products useful in human treatment. In this work, a screening approach was undertaken in order to isolate cultivable Actinobacteria from moonmilk of the Grotte des Collemboles in Belgium, to evaluate their taxonomic profile, and to assess their potential in biosynthesis of antimicrobials. Phylogenetic analysis revealed that all 78 isolates were exclusively affiliated to the genus Streptomyces and clustered into 31 distinct phylotypes displaying various pigmentation patterns and morphological features. Phylotype representatives were tested for antibacterial and antifungal activities and their genomes were mined for secondary metabolite biosynthetic genes coding for non-ribosomal peptide synthetases (NRPSs), and polyketide synthases (PKS). The moonmilk Streptomyces collection was found to display strong inhibitory activities against a wide range of reference organisms, as 94, 71, and 94% of the isolates inhibited or impaired the growth of Gram-positive, Gram-negative bacteria, and fungi, respectively. Interestingly, 90% of the cave strains induced strong growth suppression against the multi-drug resistant Rasamsonia argillacea, a causative agent of invasive mycosis in cystic fibrosis and chronic granulomatous diseases. No correlation was observed between the global antimicrobial activity of an individual strain and the number of NRPS and PKS genes predicted in its genome, suggesting that approaches for awakening cryptic metabolites biosynthesis should be applied to isolates with no antimicrobial phenotype. Overall, our work supports the common belief that moonmilk might effectively treat various infectious diseases thanks to the presence of a highly diverse population of prolific antimicrobial producing Streptomyces, and thus may indeed constitute a promising reservoir of potentially novel active natural compounds.