Limit of detection of genomic DNA by conventional PCR for estimating the load of Staphylococcus aureus and Escherichia coli associated with bovine mastitis

Development and validation of a long-read metabarcoding platform for the detection of filarial worm pathogens of animals and humans

BACKGROUND

Filarial worms are important vector-borne pathogens of a large range of animal hosts, including humans, and are responsible for numerous debilitating neglected tropical diseases such as, lymphatic filariasis caused by Wuchereria bancrofti and Brugia spp., as well as loiasis caused by Loa loa. Moreover, some emerging or difficult-to-eliminate filarioid pathogens are zoonotic using animals like canines as reservoir hosts, for example Dirofilaria sp. 'hongkongensis'. Diagnosis of filariasis through commonly available methods, like microscopy, can be challenging as microfilaremia may wane below the limit of detection. In contrast, conventional PCR methods are more sensitive and specific but may show limited ability to detect coinfections as well as emerging and/or novel pathogens. Use of deep-sequencing technologies obviate these challenges, providing sensitive detection of entire parasite communities, whilst also being better suited for the characterisation of rare or novel pathogens. Therefore, we developed a novel long-read metabarcoding assay for deep-sequencing the filarial nematode cytochrome c oxidase subunit I gene on Oxford Nanopore Technologies' (ONT) MinION™ sequencer. We assessed the overall performance of our assay using kappa statistics to compare it to commonly used diagnostic methods for filarial worm detection, such as conventional PCR (cPCR) with Sanger sequencing and the microscopy-based modified Knott's test (MKT).

RESULTS

We confirmed our metabarcoding assay can characterise filarial parasites from a diverse range of genera, including, Breinlia, Brugia, Cercopithifilaria, Dipetalonema, Dirofilaria, Onchocerca, Setaria, Stephanofilaria and Wuchereria. We demonstrated proof-of-concept for this assay by using blood samples from Sri Lankan dogs, whereby we identified infections with the filarioids Acanthocheilonema reconditum, Brugia sp. Sri Lanka genotype and zoonotic Dirofilaria sp. 'hongkongensis'. When compared to traditionally used diagnostics, such as the MKT and cPCR with Sanger sequencing, we identified an additional filarioid species and over 15% more mono- and coinfections.

CONCLUSIONS

Our developed metabarcoding assay may show broad applicability for the metabarcoding and diagnosis of the full spectrum of filarioids from a wide range of animal hosts, including mammals and vectors, whilst the utilisation of ONT' small and portable MinION™ means that such methods could be deployed for field use.

Addressing Current Challenges in Poultry Meat Safety: Development of a Cultivation and Colony Hybridization Approach to Recover Enterotoxigenic Clostridium perfringens from Broiler Chicken Carcasses

Enterotoxigenic Clostridium perfringens is one of the main causes of foodborne illness in Canada. The use of a conventional bacterial culture approach to isolate enterotoxigenic C. perfringens from poultry meat is common. This approach is based on the phenotype attributable to a double hemolysis phenomenon, whereas few enterotoxigenic strains of C. perfringens produce it, which further complicates the study of the reservoirs of this important pathogen. The objectives of the current study were to validate the ability of a digoxigenin-labeled probe to detect the C. perfringens cpe gene and to validate the use of either a filtration or a direct plating approach, combined with colony hybridization to detect enterotoxigenic C. perfringens. Pure DNA and pure colonies of enterotoxigenic C. perfringens and broiler chicken carcass rinsate samples were subjected to colony hybridization. The results showed that the synthesized DNA probe can detect the cpe gene from both DNA and pure colonies of enterotoxigenic C. perfringens, and from colonies grown from carcass rinsates artificially contaminated with enterotoxigenic C. perfringens. Our study suggests that this isolation method is a promising tool for a better understanding of the epidemiology of this zoonotic pathogen.

Estimation of the performance of two real-time polymerase chain reaction assays for detection of Staphylococcus aureus, Streptococcus agalactiae, and Streptococcus dysgalactiae in pooled milk samples in a field study

The early detection of major mastitis pathogens is crucial for the udder health management of dairy herds. Testing of pooled milk samples, either individual test-day cow samples (TDCS) or aseptically collected pre-milk quarter samples (PMQS) may provide an easy to use and cost-effective group level screening tool. Therefore, the aim of this study was (1) to evaluate the sensitivity (Se) and specificity (Sp) of 2 commercial multiplex real-time PCR test kits applied to pooled milk samples using a Bayesian latent class analysis and (2) to estimate the probability of detection in relation to the pool size and the number of cows positively tested by bacteriological culture (BC) within a pool. Pools of 10, 20 and 50 cows were assembled from 1,912 test-day samples and 7,336 PMQS collected from a total of 2,045 cows from 2 commercial dairy farms. Two commercial quantitative real-time PCR kits were applied to detect Staphylococcus aureus, Streptococcus agalactiae, and Streptococcus dysgalactiae in the pooled samples, and a BC was applied to PMQS yielding a cumulative pool result. A pool was considered BC-positive if it contained at least one BC-positive PMQS. Pathogens were more frequently detected in the PMQS pools than in the TDCS pools. Pools of 10 cows showed the highest probability of detection irrespective of sample type or type of PCR kit compared with larger pool sizes. Estimation with a Bayesian latent class analysis resulted in a median Se in PMQS pools of 10 cows for Staph. aureus of 63.3% for PCR kit I, 78.1% for PCR kit II, and 95.5% for BC; the Sp values were 97.0%, 97.6%, and 89.1%, respectively. The estimated median Se for Strep. species for PCR kits ranged between 77.5 and 85.6% and for BC between 73.7% and 79.2%; the median Sp values ranged between 93.6 and 99.2% for PCR kits, and between 96.9% and 97.4% for BC. In addition, the probability of detection increased with an increasing number of BC-positive cows per pool. To achieve a probability of detection of 90%, the estimated number of positive cows in PMQS pools of 10 cows for kit I was 4.1 for Staph. aureus, 1.5 for Strep. agalactiae, and 1.3 for Strep. dysgalactiae; for the equivalent TDCS pools and pathogens, 6.9, 1.9, and 2.0 positive cows were required, respectively. For Kit II and PMQS pools, the number of positive cows required was 2.8 for Staph. aureus, 1.4 for Strep. agalactiae, and 1.2 for Strep. dysgalactiae; for the equivalent TDCS pools and pathogens, 5.3, 1.8, and 2.0 positive cows were required, respectively. In conclusion, the type of samples used for pooling, the pool size and the number of infected cows per pool determine the probability of detecting an infection with major mastitis pathogens within a pool by PCR testing.

Development of an on-site lateral flow immune assay based on mango leaf derived colloidal silver nanoparticles for rapid detection of Staphylococcus aureus in milk

In order to ensure food safety, screening food samples for the presence of pathogens has been categorised as a legal testing item throughout the globe. One of the most prevalent zoonotic bacteria transmitted through dairy milk is Staphylococcus aureus. Given the limitations of the conventional detection methods, in the current study we desigined a competitive lateral flow immune assay (LFIA) using colloidal silver nanoparticles derived from mango leaves for the detection of Staphylococcus aureus in cow milk. SpA, a recombinant protein of Staphylococcus aureus, was used to raised hyperimmune sera used for developing the assay followed by conjugation with the synthesized nanoparticles. To increase the specificity of the assay, the milk samples were prenriched with selective agar exclusively require for Staphyloccocus aureus. The assay was found to be completed within 7-8 h by observing test and control lines in LFIA strips. The developed assay was found to specifically detect the bacteria as low as 1000 cfu/ml of milk samples. With a total 230 number of raw and clinical mastitis milk samples, the assay was validated and achieved relative accuracy, specificity, and sensitivity values of 97.39, 98.03, and 96.1%, respectively. The developed LFIA, which uses economically feasible and stable silver nanoparticles derived from mango leaves, has the potential for routine screening of milk samples for the presence of Staphylococcus aureus, especially in low-resource settings, allowing for early diagnosis, which facilitates effective treatment for the dairy animals and prevents the transmission of the disease in consumers.

Recent innovations in cost-effective polymer and paper hybrid microfluidic devices

Hybrid microfluidic systems that are composed of multiple different types of substrates have been recognized as a versatile and superior platform, which can draw benefits from different substrates while avoiding their limitations. This review article introduces the recent innovations of different types of low-cost hybrid microfluidic devices, particularly focusing on cost-effective polymer- and paper-based hybrid microfluidic devices. In this article, the fabrication of these hybrid microfluidic devices is briefly described and summarized. We then highlight various hybrid microfluidic systems, including polydimethylsiloxane (PDMS)-based, thermoplastic-based, paper/polymer hybrid systems, as well as other emerging hybrid systems (such as thread-based). The special benefits of using these hybrid systems have been summarized accordingly. A broad range of biological and biomedical applications using these hybrid microfluidic devices are discussed in detail, including nucleic acid analysis, protein analysis, cellular analysis, 3D cell culture, organ-on-a-chip, and tissue engineering. The perspective trends of hybrid microfluidic systems involving the improvement of fabrication techniques and broader applications are also discussed at the end of the review.

Antibody Immobilization in Zinc Oxide Thin Films as an Easy-Handle Strategy for Escherichia coli Detection

The antibody immobilization compatible with low-cost materials and label-free strategies is a challenge for biosensor device fabrication. In this study, ZnO thin film deposition was carried out on corning glass substrates by ultrasonic spray pyrolysis at 200 °C. The thin films were analyzed as platforms for enteropathogenic Escherichia coli (E. coli EPEC) antibody immobilization. The modification of thin films from the functionalization and antibody immobilization steps was visualized using Fourier transform infrared spectroscopy (FTIR) spectroscopy, and surface changes were observed by atomic force microscopy. The obtained FTIR spectra after functionalization showed a contribution of the amino group (NH₂) derived from silane (3-aminopropyltrimethoxysilane). The antibody immobilization showed an amide I conserved signal corresponding to the C=O stretching vibrations and the amide II signal related to the N-H scissor vibration mode. In this way, the signals observed are correlated with the presence of antibody immobilized on the film. The ZnO film morphology changes after every stage of the process and allows observing the antibody distribution on the immobilized surface. In order to validate the antibody recognition capability as well as the E. coli EPEC detection in situ, polymerase chain reaction was used.