The development and deployment of a field-based loop mediated isothermal amplification assay for virulent Dichelobacter nodosus detection on Australian sheep

Development of molecular detection methods of Bovicola ovis from sheep fleece

The sheep body louse (Bovicola ovis) commonly referred to as sheep lice are small chewing ectoparasites of sheep. Infection results in significant economic costs to the Australian sheep industry due to reduced wool quality caused by chronic itching from sheep rubbing and biting fleece. Treatment relies on use of insecticides; however, resistance has developed against pyrethroid and other insect growth regulator lousicides. There is urgent need to develop cost-effective lice management to reduce the use of insecticides, with the application of insecticidal treatments only applied when an infestation is detected. However, the current detection method relies on fleece parting for detection of B. ovis which is highly dependent on the skill of the inspector, the number of sheep examined, and the prevalence and severity of the infestation. To improve B. ovis detection, a highly sensitive (5 × 10-8 ng/μL) and specific multiplex quantitative PCR which simultaneously detects sheep lice and sheep DNA was developed. In addition, a B. ovis loop-mediated isothermal amplification (LAMP) assay was developed for field use. The B. ovis LAMP (Bov-LAMP) assay was optimized to reliably detect B. ovis from wool samples down to 5 × 10-6 ng/μL, with time to positive (Tp) < 10 min. Both assays demonstrate high sensitivity and specificity, enabling rapid identification of B. ovis DNA from sheep fleece samples and have the capacity to be used for ongoing management and surveillance of B. ovis in Australian sheep flocks.

Standardization of loop-mediated isothermal amplification for detection of D. nodosus and F. necrophorum causing footrot in sheep and goats

The loop-mediated isothermal amplification (LAMP) was standardized for rapid detection of Dichelobacter nodosus and Fusobacterium necrophorum. A total of 250 foot swabs were screened from sheep (200) and goats (50) from different districts of Rayalaseema, viz., Chittoor, Nellore, Kadapa, and Anantapur. Out of 250 samples 75 (30.0%) and 85 (34.0%) were positive for D. nodosus and F. necrophorum, respectively. All the 250 samples were screened individually for both the organisms by LAMP. Among them, 104 (41.6%) were found to be positive for D. nodosus and 120 (48.0%) were positive for F. necrophorum. The efficacy of LAMP in terms of sample DNA detection limit was compared with the PCR by using standard dilutions of DNA extracted from D. nodosus and F. necrophorum cultures. The detection limit was found to be higher than PCR for both the organisms. The sensitivity of LAMP is compared with PCR by targeting 16S rRNA gene of D. nodosus and lktA gene of F. necrophorum. In case of D. nodosus, out of 250 samples, 75 (30.0%) were positive by PCR and 104 (41.6%) were positive by LAMP. Among 250 samples, 85 (34.0%) were positive by PCR and 120 (48.0%) were positive by LAMP in case of F. necrophorum. The LAMP was found to be more sensitive than PCR in detecting the organisms with high statistical significance.

Rapid Extraction and Detection of African Swine Fever Virus DNA Based on Isothermal Recombinase Polymerase Amplification Assay

African swine fever virus (ASFV) is the causative agent of a deadly disease in pigs and is spread rapidly across borders. Samples collected from suspected cases must be sent to the reference laboratory for diagnosis using polymerase chain reaction (PCR). In this study, we aimed to develop a simple DNA isolation step and real-time recombinase polymerase amplification (RPA) assay for rapid detection of ASFV. RPA assay based on the p72 encoding B646L gene of ASFV was established. The assays limit of detection and cross-reactivity were investigated. Diagnostic performance was examined using 73 blood and serum samples. Two extraction approaches were tested: silica-column-based extraction method and simple non-purification DNA isolation (lysis buffer and heating, 70 °C for 20 min). All results were compared with well-established real-time PCR. In a field deployment during a disease outbreak event in Uganda, 20 whole blood samples were tested. The assay’s analytical sensitivity was 3.5 DNA copies of molecular standard per µL as determined by probit analysis on eight independent assay runs. The ASFV RPA assay only detected ASFV genotypes. Compared to real-time PCR, RPA diagnostic sensitivity and specificity were 100%. Using the heating/lysis buffer extraction procedure, ASFV-RPA revealed better tolerance to inhibitors than real-time PCR (97% and 38% positivity rate, respectively). In Uganda, infected animals were identified before the appearance of fever. The ASFV-RPA assay is shown to be as sensitive and specific as real-time PCR. Moreover, the combination of the simple extraction protocol allows its use at the point of need to improve control measures.

Ovine footrot: A review of current knowledge

Footrot is a contagious foot disease mainly affecting sheep. It is caused by the Gram-negative anaerobic bacterium Dichelobacter nodosus. Warm, wet environmental conditions favour development of footrot, and under perfect conditions, it takes just 2-3 weeks from infection to manifestation of clinical signs. Affected sheep show lameness of various degrees and often graze while resting on their carpi. Local clinical signs vary in severity and extent from interdigital inflammation (benign footrot) to underrunning of the complete horn shoe in advanced stages of virulent footrot. Laboratory diagnosis ideally involves collection of four-foot interdigital swab samples followed by competitive real time PCR, allowing for detection of the presence of D. nodosus and differentiation between benign and virulent strains. Laboratory-based diagnostics at the flock level based on risk-based sampling and pooling of interdigital swab samples are recommended. The list of treatment options of individual sheep includes careful removal of the loose undermined horn, local or systemic administration of antimicrobials, systemic administration of non-steroidal anti-inflammatories (NSAIDs) and disinfectant footbathing. Strategies for control at the flock level are manifold and depend on the environmental conditions and the procedures traditionally implemented by the respective country. Generally, measures consist of treatment/culling of infected sheep, vaccination and prevention of reinfection of disease-free flocks. Gaining deeper insight into the beneficial effects of NSAIDs, screening for eco-friendly footbath solutions, developing better vaccines, including the development of a robust, reproducible infection model and elucidation of protective immune responses, as well as the elaboration of effective awareness training programs for sheep farmers, are relevant research gaps.

Hendra virus: Epidemiology dynamics in relation to climate change, diagnostic tests and control measures

Hendra virus (HeV) continues to pose a serious public health concern as spillover events occur sporadically. Terminally ill horses can exhibit a range of clinical signs including frothy nasal discharge, ataxia or forebrain signs. Early signs, if detected, can include depression, inappetence, colic or mild respiratory signs. All unvaccinated ill horses in areas where flying foxes exist, may potentially be infected with HeV, posing a significant risk to the veterinary community. Equivac® HeV vaccine has been fully registered in Australia since 2015 (and under an Australian Pesticides and Veterinary Medicines Authority special permit since 2012) for immunization of horses against HeV and is the most effective and direct solution to prevent disease transmission to horses and protect humans. No HeV vaccinated horse has tested positive for HeV infection. There is no registered vaccine to prevent, or therapeutics to treat, HeV infection in humans. Previous equine HeV outbreaks tended to cluster in winter overlapping with the foaling season (August to December), when veterinarians and horse owners have frequent close contact with horses and their bodily fluids, increasing the chance of zoonotic disease transmission. The most southerly case was detected in 2019 in the Upper Hunter region in New South Wales, which is Australia's Thoroughbred horse breeding capital. Future spillover events are predicted to move further south and inland in Queensland and New South Wales, aligning with the moving distribution of the main reservoir hosts. Here we (1) review HeV epidemiology and climate change predicted infection dynamics, (2) present a biosecurity protocol for veterinary clinics and hospitals to adopt, and (3) describe diagnostic tests currently available and those under development. Major knowledge and research gaps have been identified, including evaluation of vaccine efficacy in foals to assess current vaccination protocol recommendations.

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Hendra virus (HeV) continues to pose a serious public health threat to the equine and veterinary industries.

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HeV cases are likely to expand further south and inland due to climate change.

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Strict HeV specific biosecurity protocols should be implemented to protect veterinary staff.

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Research into HeV vaccination protocols in foals is required for evidence-based recommendations.

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Point-of-care and other diagnostic tests for HeV are currently under development.

Development of a Portable LAMP Assay for Detection of Neofabraea perennans in Commercial Apple Fruit

Bull's eye rot (BER) is a major economic postharvest disease of apple and pear that can be caused by four Neofabraea species: N. perennans, N. alba, N. malicorticis, and N. kienholzii. In Central Washington, BER is predominantly caused by N. perennans. The fungus infects fruit preharvest, and because of the dry growing season in the region, infections remain latent with symptoms expressed only after 3 to 4 months of storage, when BER incidences as high as 20% can been seen, especially in rainy seasons and on susceptible cultivars. To ensure early and efficient infection detections before BER symptoms become visible at point-of-care locations, a portable diagnostic tool based on loop-mediated isothermal amplification (LAMP) was developed using the β-tubulin gene. The LAMP assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of N. perennans and seven other fungal species. The results showed that the selected LAMP primer set was specific to N. perennans and highly sensitive as it detected DNA concentrations as low as 0.001 ng/µl after only 10 min. The assay was validated for N. perennans detection on artificially inoculated apples using a portable thermocycler, Genie II, without the need for DNA extraction. The LAMP assay detected N. perennans on apples inoculated with spore suspensions 3 weeks prior to harvest at concentrations of 10³ spores/ml or higher. The assay was further validated using commercial Piñata apples from organic and conventional orchards, demonstrating the ability of this technique to amplify N. perennans from asymptomatic fruit in a commercial setting 3 months before commercial maturity. The LAMP assay developed for N. perennans detection can be easily expanded to detect the other BER causal species. LAMP has potential to be used in orchards and at point-of-care facilities to better inform on BER management at different fruit growth stages, and it has potential to be utilized to better understand the epidemiology of Neofabraea spp.

Further development of a reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of foot-and-mouth disease virus and validation in the field with use of an internal positive control

Foot-and-mouth disease (FMD) is a highly contagious viral disease of cloven-hooved animals. Global outbreaks have highlighted the significant economic, trade, psychosocial and animal welfare impacts that can arise from the detection of disease in previously 'FMD-free' countries. Rapid and early diagnosis provides significant advantages in disease control and minimization of deleterious consequences. We describe the process of further development and validation of a reverse-transcription loop-mediated isothermal amplification foot-and-mouth disease virus (RT-LAMP-FMDV) test, using a published LAMP primer set, for use in the field. An internal positive control (IPC) was designed and introduced for use with the assay to mitigate any intrinsic interference from the unextracted field samples and avoid false negatives. Further modifications were included to improve the speed and operability of the test, for use by non-laboratory trained staff operating under field conditions, with shelf-stable reaction kits which require a minimum of liquid handling skills. Comparison of the assay performance with an established laboratory-based real-time reverse transcriptase PCR (rRT-PCR) test targeting the 3D region of FMD virus (Tetracore Inc) was investigated. LAMP has the potential to complement current laboratory diagnostics, such as rRT-PCR, as a preliminary tool in the investigation of FMD. We describe a strategic approach to validation of the test for use in the field using extracted RNA samples of various serotypes from Thailand and then finally unextracted field samples collected from FMD-suspected animals (primarily oral lesion swabs) from Bhutan and Australia. The statistical approach to validation was performed by Frequentist and Bayesian latent class methods, which both confirmed this new RT-LAMP-FMDV test as fit-for-purpose as a herd diagnostic tool with diagnostic specificity >99% and sensitivity 79% (95% Bayesian credible interval: 65, 90%) on unextracted field samples (oral swabs).

A LAMP at the end of the tunnel: A rapid, field deployable assay for the kauri dieback pathogen, Phytophthora agathidicida

The root rot causing oomycete, Phytophthora agathidicida, threatens the long-term survival of the iconic New Zealand kauri. Currently, testing for this pathogen involves an extended soil bioassay that takes 14–20 days and requires specialised staff, consumables, and infrastructure. Here we describe a loop-mediated isothermal amplification (LAMP) assay for the detection of P. agathidicida that targets a portion of the mitochondrial apocytochrome b coding sequence. This assay has high specificity and sensitivity; it did not cross react with a range of other Phytophthora isolates and detected as little as 1 fg of total P. agathidicida DNA or 116 copies of the target locus. Assay performance was further investigated by testing plant tissue baits from flooded soil samples using both the extended soil bioassay and LAMP testing of DNA extracted from baits. In these comparisons, P. agathidicida was detected more frequently using the LAMP test. In addition to greater sensitivity, by removing the need for culturing, the hybrid baiting plus LAMP approach is more cost effective than the extended soil bioassay and, importantly, does not require a centralised laboratory facility with specialised staff, consumables, and equipment. Such testing will allow us to address outstanding questions about P. agathidicida. For example, the hybrid approach could enable monitoring of the pathogen beyond areas with visible disease symptoms, allow direct evaluation of rates and patterns of spread, and allow the effectiveness of disease control to be evaluated. The hybrid LAMP bioassay also has the potential to empower local communities to evaluate the pathogen status of local kauri stands, providing information for disease management and conservation initiatives.

A pilot evaluation of alternative procedures to simplify LAMP-based malaria diagnosis in field conditions

Highly-sensitive and field-friendly diagnostic tools are needed for accurate detection of low-density malaria infections. Although loop-mediated isothermal amplification (LAMP) fulfills these conditions, operational challenges are still encountered during pilot population screenings in remote settings when employing Loopamp™ MALARIA Pan/Pf detection kit (Eiken Chemical Co.). This study evaluates different procedures for the simplification of sample preparation and result reading steps of current LAMP protocols. The reference 'Boil & Spin' (B&S) pre-amplification procedure was compared to three alternative methods, along with a colorimetric staining protocol based on malachite green. Results suggested that the B&S supernatant transference step may be omitted without an impact on test performance, even when colorimetry was incorporated to facilitate results visualization. Procedures skipping centrifugation and/or heat-incubation were proved to be compatible with LAMP-based malaria DNA detection, but resulted in a low-to-moderate decrease in sensitivity and ambiguous result interpretation for the most straightforward protocol. Nevertheless, all simplified LAMP methods could still reach lower limits of detection than the currently used tools for malaria mass-screening (i.e. microscopy and rapid tests), indicating that these alternative strategies may deserve further consideration. This evaluation, therefore, demonstrates the feasibility of skipping some of the main procedural bottlenecks of LAMP-malaria protocols, a much-needed achievement to make point-of-care implementation of molecular diagnostics a reality.

Evaluation of loop-mediated isothermal amplification (LAMP) assay for detection of aprV2 positive Dichelobacter nodosus in-field by secondary users

OBJECTIVE

Dichelobacter nodosus is the primary aetiological agent of footrot in sheep. Ovine footrot causes considerable economic losses and substantial animal welfare issues in the Australian sheep industry. Current methods for detecting D. nodosus are difficult, laborious and time-consuming. Recently, we developed a robust LAMP assay (VDN LAMP) that was able to identify aprV2 positive D. nodosus in-field. A major advantage of LAMP technology is the ability of the assay to be performed by non-specialists with minimal training. We aimed to assess the performance of the VDN LAMP in-field in comparison to a laboratory-based aprV2/aprB2 rtPCR when used by secondary users after training by the authors.

RESULTS

Two animal health officers (termed secondary users) from Department of Primary Industries and Regions, South Australia (PIRSA) were trained in the use of VDN LAMP, before carrying out in-field testing on several locations in South Australia. The performance of VDN LAMP assay by secondary user 1 was shown to successfully detect 73.91% (n = 53) aprV2 positive samples, while secondary user 2 detected 37.93% (n = 30) aprV2 positive samples. Overall, the ability to identify virulent D. nodosus by VDN LAMP by secondary users was mixed for various reasons, however, this could be rectified by additional training and commercial production of the LAMP kits to increase stability. We envisaged in the future VDN LAMP will able to be used by non-specialists to aid control programs.

Optimization of a Loop Mediated Isothermal Amplification (LAMP) Assay for In-Field Detection of Dichelobacter nodosus With aprV2 (VDN LAMP) in Victorian Sheep Flocks

Dichelobacter nodosus is the primary etiological agent of footrot in sheep and has a variety of virulence factors. Of these, AprV2, an extracellular protease, has been shown to be capable of causing severe or “virulent” disease symptoms under the right conditions. Due to this, a loop-mediated isothermal amplification (LAMP) assay for the detection of aprV2-positive D. nodosus (VDN LAMP) was developed and evaluated for field use. A sample of 19 sheep flocks (309 sheep) in Victoria, Australia, were tested to determine the optimum conditions for in-field VDN LAMP assay use and sampling, for detecting aprV2-positive D. nodosus infected sheep. VDN LAMP performance was compared to a validated rtPCR that detects aprV2 and the benign strain counterpart, aprB2, using biologically duplicate samples to determine sensitivity and specificity. Flocks were sampled either in winter-spring (moist) or early summer (dry) conditions and had a range of clinical expressions of the disease ovine footrot. Variables considered for optimizing field performance were: sample collection method, sample preparation, clinical expression of disease, and nature of the feet when sampled (moist vs. dry, clean vs. soiled). The test was found to perform best when sheep were sampled with moist, clean feet, using a dry swab with the sample prepared in alkaline polyethylene glycol, pH 13.0, as the collection buffer. A sensitivity of 89% and specificity of 97% was seen when used in-field under these conditions, when compared to aprV2 detection by rtPCR, with “very good” agreement to rtPCR results. This study shows the VDN LAMP test is easy to use in-field to identify the presence of aprV2-positive D. nodosus in sheep flocks.