Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology

Mkit: A mobile nucleic acid assay based on a chitosan-modified minimalistic microfluidic chip (CM3-chip) and smartphone

Mobile sensing enabled by MS² technology, which integrates microfluidic and smartphone components, has seen many applications in recent years. In this direction, we developed an MS² platform (an integrated kit) for nucleic acid assay, which included a chitosan-modified minimalistic microfluidic chip (CM³-chip), a smartphone-based fluorescence detector (SF-detector), an APP for imaging and analysis, reagents, and accessories. Once the lysed sample was loaded into the CM³-chip modified by 1% concentration and 200-260 kDa molecular weight of chitosan, the following assay can be completed in approximately 1 h. The Mkit can detect 3 × 10° copies μL^-1 of plasmid DNA and its polymerase chain reaction (PCR) efficiency was 96.8%. The CM³-chip equipped for the Mkit can enrich nucleic acid from the pH = 5 of lysis buffer, instead of using conventional adsorption mediums such as the magnetic beads and silica gel membranes, which could result in unexpected impurity residuals and tedious cleaning operations. In addition, the performance of the Mkit equipped with the pristine chip was demonstrated to perform poorer than that coupled with the CM³-chip in which the enriched nucleic acid can be all used for "in-situ PCR". The universality, selectivity, and user-friendliness of the Mkit were also validated. We finally demonstrated the feasibility of the Mkit for testing artificially prepared infected samples. H5N6 and IAV-infected saliva samples provided the limits of detection of 5 × 10² copies mL^-1 and 3.24 × 10² copies mL^-1 per chamber, respectively. The streamlined assay and compact device should enable the great potential of the Mkit in research and potential diagnostic uses.

Roles for Pathogen Interference in Influenza Vaccination, with Implications to Vaccine Effectiveness (VE) and Attribution of Influenza Deaths

Pathogen interference is the ability of one pathogen to alter the course and clinical outcomes of infection by another. With up to 3000 species of human pathogens the potential combinations are vast. These combinations operate within further immune complexity induced by infection with multiple persistent pathogens, and by the role which the human microbiome plays in maintaining health, immune function, and resistance to infection. All the above are further complicated by malnutrition in children and the elderly. Influenza vaccination offers a measure of protection for elderly individuals subsequently infected with influenza. However, all vaccines induce both specific and non-specific effects. The specific effects involve stimulation of humoral and cellular immunity, while the nonspecific effects are far more nuanced including changes in gene expression patterns and production of small RNAs which contribute to pathogen interference. Little is known about the outcomes of vaccinated elderly not subsequently infected with influenza but infected with multiple other non-influenza winter pathogens. In this review we propose that in certain years the specific antigen mix in the seasonal influenza vaccine inadvertently increases the risk of infection from other non-influenza pathogens. The possibility that vaccination could upset the pathogen balance, and that the timing of vaccination relative to the pathogen balance was critical to success, was proposed in 2010 but was seemingly ignored. Persons vaccinated early in the winter are more likely to experience higher pathogen interference. Implications to the estimation of vaccine effectiveness and influenza deaths are discussed.

Application of MRT-qPCR for pathogen detection of lower respiratory tract infection

OBJECTIVE

To analyze and clarify the application value of multiplex quantitative real-time PCR (MRT-PCR) assay in detecting pathogens involved in lower respiratory tract infection (LRTI), so as to realize accurate and rapid detection of respiratory pathogens.

METHODS

Bronchial alveolar lavage fluid (BALF) specimens from 186 patients with LRTI collected in the Cangzhou Central Hospital from June 2020 to September 2021 were analyzed retrospectively. Pathogen detection was performed by both MRT-PCR and direct immunofluorescence assay (DFA), and the results of different inspection methods were compared.

RESULTS

Among the seven pathogens detected by MRT-PCR, 140 positive specimens were identified out of the 186 patients, with the top three pathogens with the highest positive rates being influenza A virus (Flu A; 36 [19.35%]), respiratory syncytial virus (RSV; 30 [16.13%]) and human adenovirus (HAdV; 23 [12.37%]), and the pathogen with the lowest positive rate being parainfluenza virus type 3 (PIV3; 9 [4.84%]). DFA showed 110 pathogen-positive specimens, and the top three pathogens with the highest positive rates were Flu A (30 [16.13%]), HAdV (21 [11.29%]) and RSV (19 [10.22%]). The total sensitivity and accuracy of MRT-PCR assay were 93.01% and 98.69% respectively, which were statistically higher than those of 48.45% and 91.24% of DFA (P<0.05). The two inspection methods showed no significant difference in specificity (99.4% for MRT-PCR assay and 97.28% for DFA) (P>0.05).

CONCLUSIONS

MRT-PCR is rapid, accurate and specific in detecting pathogens of LRTI, which significantly improves the detection rate, with reliable performance and it has high clinical application value.