Real-time PCR and multiplex approaches

Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology

Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.

Multiplexed Continuous Biosensing by Single-Molecule Encoded Nanoswitches

Single-molecule techniques have become impactful in bioanalytical sciences, though the advantages for continuous biosensing are yet to be discovered. Here we present a multiplexed, continuous biosensing method, enabled by an analyte-sensitive, single-molecular nanoswitch with a particle as a reporter. The nanoswitch opens and closes under the influence of single target molecules. This reversible switching yields binary transitions between two highly reproducible states, enabling reliable quantification of the single-molecule kinetics. The multiplexing functionality is encoded per particle via the dissociation characteristics of the nanoswitch, while the target concentration is revealed by the association characteristics. We demonstrate by experiments and simulations the multiplexed, continuous monitoring of oligonucleotide targets, at picomolar concentrations in buffer and in filtered human blood plasma.

Exploiting the Advantages of Molecular Tools for the Monitoring of Fungal Indoor Air Contamination: First Detection of Exophiala jeanselmei in Indoor Air of Air-Conditioned Offices

Today, indoor air pollution is considered a public health issue. Among the impacting pollutants, indoor airborne fungi are increasingly highlighted. Most of the monitoring protocols are culture-based, but these are unable to detect the uncultivable and/or dead fraction or species suppressed by fast-growing fungi, even though this fraction could impact health. Among the contaminants suspected to be part of this fraction, Exophiala jeanselmei is an interesting case study. Known to be pathogenic, this black yeast grows in humid environments such as air-conditioning systems, where it has been previously detected using classical culture-based methods. However, until now, this fungus was never detected in indoor air in contact with these air-conditioning systems. This study shows the first detection of E. jeanselmei in indoor air collected from offices in contact with contaminated air-conditioning reservoirs. While its presence in indoor air could not be demonstrated with culture-based methods, it was found by real-time PCR and massive parallel sequencing. The latter also allowed obtaining a broader view on the fungal diversity in the tested samples. Similar approaches were applied on water samples collected from the conditioning reservoirs to trace the source of contamination. The comparison of results obtained with both methods confirmed that the molecular tools could improve indoor air monitoring, especially of dead and/or uncultivable contaminants or when competition between species could occur.

Development and performance assessment of a luminex xMAP® direct hybridization assay for the detection and identification of indoor air fungal contamination

Considered as a public health problem, indoor fungal contamination is generally monitored using classical protocols based on culturing. However, this culture dependency could influence the representativeness of the fungal population detected in an analyzed sample as this includes the dead and uncultivable fraction. Moreover, culture-based protocols are often time-consuming. In this context, molecular tools are a powerful alternative, especially those allowing multiplexing. In this study a Luminex xMAP® assay was developed for the simultaneous detection of 10 fungal species which are most frequently in indoor air and that may cause health problems. This xMAP® assay was found to be sensitive, i.e. its limit of detection is ranging between 0.05 and 0.01 ng of gDNA. The assay was subsequently tested with environmental air samples which were also analyzed with a classical protocol. All the species identified with the classical method were also detected with the xMAP® assay, however in a shorter time frame. These results demonstrate that the Luminex xMAP® fungal assay developed in this study could contribute to the improvement of public health and specifically to the indoor fungal contamination treatment.

Multiplex qPCR assay for identification and differentiation of Amblyomma americanum, Amblyomma cajennense, and Amblyomma maculatum (Ixodida: Ixodidae) tick species in the eastern United States

Many ticks of the genus Amblyomma are vectors of human pathogens, and the correct species identification is medically and epidemiologically important. Morphological identification is time-consuming and requires a high level of expertise. Identification of engorged, immature, or damaged ticks and the differentiation of closely related species remain problematic. Here, we report the development of a real-time TaqMan assay for the genomic identification and differentiation of Amblyomma americanum (L.), Amblyomma cajennense (F.), and Amblyomma maculatum (Koch), which are human-biting species found in the eastern United States. New species-specific sets of oligonucleotides for the multiplex reaction that detect and differentiate the ITS2 genomic regions of three target species were designed using Visual OMP; the previously published A. americanum oligonucleotide set was also incorporated into our assay. Specificity and sensitivity tests for two multiplex master mixes using different A. americanum sets were performed using individual and pooled samples of adult, nymphal, and larval ticks, and optimization procedures were applied. The multiplex assay successfully differentiates between genomes of three target species and does not cross-react with DNAs of ticks from other genera. Rare cases of nonspecific amplification occurred with DNAs of A. imitator and Amblyomma triste Koch misidentified as A. americanum and A. maculatum, respectively. However, this cross-reaction does not diminish the usefulness of the developed assay east of the 95th meridian, where neither A. imitator nor A. triste are found. Two master mixes incorporating the previously published or newly developed A. americanum sets are being recommended for identification of individual ticks or pooled samples, respectively.