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

Broad-spectrum analysis for pathogens in patients with respiratory tract infections is becoming more relevant as the number of potential infectious agents is still increasing. Here we describe the new multiparameter RespiFinder assay, which is based on the multiplex ligation-dependent probe amplification (MLPA) technology. This assay detects 15 respiratory viruses in one reaction. The MLPA reaction is preceded by a preamplification step which ensures the detection of both RNA and DNA viruses with the same specificity and sensitivity as individual monoplex real-time reverse transcription-PCRs. The RespiFinder assay was validated with 144 clinical samples, and the results of the assay were compared to those of cell culture and a respiratory syncytial virus (RSV)-specific immunochromatography assay (ICA). Compared to the cell culture results, the RespiFinder assay showed specificities and sensitivities of 98.2% and 100%, respectively, for adenovirus; 96.4% and 100%, respectively, for human metapneumovirus; 98.2% and 100%, respectively, for influenza A virus (InfA); 99.1% and 100%, respectively, for parainfluenza virus type 1 (PIV-1); 99.1% and 80%, respectively, for PIV-3; 90.1% and 100%, respectively, for rhinovirus; and 94.6% and 100%, respectively, for RSV. Compared to the results of the RSV-specific ICA, the RespiFinder assay gave a specificity and a sensitivity of 82.4% and 80%, respectively. PIV-2, PIV-4, influenza B virus, InfA H5N1, and coronavirus 229E were not detected in the clinical specimens tested. The use of the RespiFinder assay resulted in an increase in the diagnostic yield compared to that obtained by cell culture (diagnostic yields, 60% and 35.5%, respectively). In conclusion, the RespiFinder assay provides a user-friendly and high-throughput tool for the simultaneous detection of 15 respiratory viruses with excellent overall performance statistics.

The AsperGenius assay had a good diagnostic performance on BAL and differentiated WT from Aspergillus fumigatus with RAMs, including in culture-negative BAL samples. Most importantly, detection of RAMs was associated with azole treatment failure.

Quantitative real-time PCR (qPCR) is increasingly used to detect Pneumocystis jirovecii for the diagnosis of Pneumocystis pneumonia (PCP), but there are differences in the nucleic acids targeted, DNA only versus whole nucleic acid (WNA), and also the target genes for amplification. Through the Fungal PCR Initiative, a working group of the International Society for Human and Animal Mycology, a multicenter and monocenter evaluation of PCP qPCR assays was performed. For the multicenter study, 16 reference laboratories from eight different countries, performing 20 assays analyzed a panel consisting of two negative and three PCP positive samples. Aliquots were prepared by pooling residual material from 20 negative or positive- P. jirovecii bronchoalveolar lavage fluids (BALFs). The positive pool was diluted to obtain three concentrations (pure 1:1; 1:100; and 1:1000 to mimic high, medium, and low fungal loads, respectively). The monocenter study compared five in-house and five commercial qPCR assays testing 19 individual BALFs on the same amplification platform. Across both evaluations and for all fungal loads, targeting WNA and the mitochondrial small sub-unit (mtSSU) provided the earliest Cq values, compared to only targeting DNA and the mitochondrial large subunit, the major surface glycoprotein or the beta-tubulin genes. Thus, reverse transcriptase-qPCR targeting the mtSSU gene could serve as a basis for standardizing the P. jirovecii load, which is essential if qPCR is to be incorporated into clinical care pathways as the reference method, accepting that additional parameters such as amplification platforms still need evaluation.

Background Treatment‐resistant dermatophytosis caused by Trichophyton mentagrophytes/interdigitale complex has emerged as a global public health threat, particularly in endemic countries like India and has spread to many other countries. This veritable spread is alarming due to increase in resistance to terbinafine, which targets the ergosterol biosynthetic pathway by inhibiting the enzyme squalene epoxidase (SQLE). About two third of studies worldwide have reported amino acid substitutions Phe397Leu and Leu393Phe in the SQLE protein to be responsible for high terbinafine MICs. Objectives We evaluated the efficacy of the newly developed DermaGenius® Resistance real‐time PCR assay to rapidly identify Trichophyton isolates harbouring most common SQLE mutant (Phe397Leu and Leu393Phe) conferring high terbinafine resistance from wild‐type susceptible isolates. Methods A total of 97 Trichophyton isolates confirmed by ITS sequencing as T. mentagrophytes/interdigitale (recently named T. indotineae n = 90), T. rubrum/T. soudanense (n = 3), T mentagrophytes (n = 2) and T tonsurans (n = 2) were analysed to evaluate DermaGenius® Resistance real‐time PCR assay. All 40 T. indotineae isolates exhibiting amino acid substitutions Phe397Leu or Leu393Phe identified by SQLE gene sequencing were evaluated for detection of non‐wild‐type strains by real‐time PCR. Antifungal susceptibility testing for terbinafine was done by CLSI microbroth dilution method. Results All terbinafine‐resistant isolates harbouring amino acid substitutions Phe397Leu or Leu393Phe in SQLE gene were correctly recorded as SQLE mutants by the DermaGenius® Resistance real‐time PCR assay. Conclusions The DermaGenius® Resistance real‐time PCR assay effectively identified Trichophyton species and distinguished wild‐type from SQLE mutant genotype that harbour Phe397Leu and Leu393Phe amino acid substitutions.

The AsperGenius assay detects several Aspergillus species and the A. fumigatus Cyp51A mutations TR/L98H/T289A/Y121F that are associated with azole resistance. We evaluated its contribution in identifying A. lentulus and A. felis, 2 rare but intrinsically azole-resistant sibling species within the Aspergillus section Fumigati. Identification of these species with conventional culture techniques is difficult and time-consuming. The assay was tested on (i) 2 A. lentulus and A. felis strains obtained from biopsy proven invasive aspergillosis and (ii) control A. fumigatus (n=3), A. lentulus (n=6) and A. felis species complex (n=12) strains. The AsperGenius resistance PCR did not detect the TR target in A. lentulus and A. felis in contrast to A. fumigatus. Melting peaks for L98H and Y121F markers differed and those of the Y121F marker were particularly suitable to discriminate the 3 species. In conclusion, the assay can be used to rapidly discriminate A. fumigatus, A. lentulus and A. felis.

No abstract

No abstract