Low-cost Portable Molecular Diagnostic Platform for Rapid Detection of Poultry Infectious Pathogens (LMDP)

Lead Research Organisation: Brunel University
Department Name: Inst of Environment, Health & Societies

Abstract

The poultry industry in the Philippines accounts for 15% of the agricultural output, equating to 123.4 billion pesos per annum and is growing at a few percent per annum. One factor affecting growth is an inability to rapidly detect disease within the chicken population. There are a range of bacterial and viral pathogens which affect the poultry industry. Currently the diagnostic methodology is reliant on a drop in production performance, presence of clinical signs, pathological lesions and serological findings. As such the diagnostic time is quite long and this can affect the ability to implement control measures to limit the spread of the disease to adjacent poultry farms. Although the key disease pathogens are well known, Newcastle disease, infectious bursal disease virus (IBDV), avian infectious bronchitis (IB), Salmonellosis, Avian Pathogenic E. coli (APEC) and mycoplasma gallisepticum, It is unclear at this present time what the particular strain or strains are, which affect the Philippines or any information on the genetic diversity of these. When it is considered that a relatively small 1% increase or decrease in production can make a very large economic impact.
To address this, a multidisciplinary consortium from the UK (Brunel University London, Surrey University and the Pribright Institute) and the Philippines (College of Veterinary Medicine at the University of the Philippines Los Banos, College of Veterinary Medicine and Biomedical Sciences at Cavite State University and the College of Veterinary Medicine at the University of Eastern Philippines) has been formed. Using the complimentary skills of those involved the project proposes to develop and translate to the Philippines a rapid easy to use point of need molecular diagnostic test that can be used at the site of infection and test for the key viral and bacterial pathogens identified which are of current concern. The total test time will be under 1 hour (sample to result). The system will consist of a sample collection and preparation device and a small instrument approximately the size of a large matchbox which will be wirelessly connected to a smartphone. The smartphone app will run the assay and display the results. The results can also be sent wirelessly to a central store and used for surveillance purposes. The platform can be relatively easily adapted for any new and emerging strains of these pathogens. Once the system is laboratory validated it will be evaluated in the Philippines. In addition, agreements will be sought to transfer the technology to the Philippines for largescale manufacture thus providing for a secondary economic effect.
The consortium considers that this project meets the objectives of the BBSRC-Newton Fund call and will provide significant impact and economic benefit both from the perspective of poultry farming and from the development, manufacture and sale of test kit which will assist in the economic development of the Philippines.

Planned Impact

The poultry industry in Philippines provides a significant contribution to the growth of the agricultural sector and it has a share of about 15% of the total output of the country. Any disease outbreak of economically important poultry pathogens, especially in broiler chickens will adversely affect economic performance. In Philippines, poultry clinicians normally rely on production performance, clinical, pathological lesions and serological findings to make a diagnosis. Although, molecular diagnostic techniques for detecting viral and bacterial pathogens are fairly well advanced in the developed world, it is slow to be implemented in resource poor settings like in Philippines. Accurate and early diagnosis of poultry infections using molecular techniques may decrease the spread of disease and facilitate appropriate selection of more efficient management and treatment protocols. This project proses to develop a smartphone based diagnostic test and does not need expensive instrumentation to be available at the point-of-need in farms. Early detection will minimise the spread of disease within the country and hence avoid unnecessary mortality of poultry. Furthermore, early diagnosis of infections can also minimise any consequential zoonotic transmission within the farm workers as well as the population at large.

In either large or small-scale agribusiness, poultry farming promotes significant enhancement of Philippine's GDP and supports improved income for local poultry farmers. This research project would therefore, help the Philippine economy because rapid and accurate diagnoses of diseases in the farm means prompt and appropriate treatment. Once the technology transfer from the UK to Philippines is completed and a royalty sharing agreement has been signed with the IP generating consortium partners, this device can be mass produced cheaply for markets in other South Asian countries, which will generate significant income for Philippines. Cost-effective devices that can provide rapid and accurate results mean that diseases are addressed promptly through correct institution of treatment and biosecurity.

The pathogens that will be studied are of foremost public health importance and are considered to be one of the most important pathogens responsible for human food poisoning in the developed world and chicken products are widely acknowledged to be a significant reservoir for Salmonella spp.. For poultry viruses, Newcastle disease virus (NDV) may cause conjunctivitis in human and in high challenge areas such as in cases of an outbreak; NDV is an important health concern for farm workers. Hence, rapidly and accurately detecting these pathogens in poultry would help in the prevention of transmission of these diseases to humans.

The scientific findings and data that can be derived from these studies may serve as a guide for the authority to develop policy guidelines that are legally binding for the control of the spread of contagious poultry diseases. The database that will be developed to continuously monitor the spread of infection using wireless technology will be a valuable tool to predict, if a new strain of viral or bacterial pathogen develops in the future. The findings in the local poultry in the Philippines may serve as a reference for reproducibility of the developed technologies particularly to ASEAN neighbors whereby each member state shares lots of similarities in terms of ecological and socio-cultural characteristics.

The research findings will be published in both journals as well as at national and international conferences. A dedicated web site and other social media platforms will be set up maintained to continuously inform the public of the findings. Special seminars and workshops will be held to inform poultry farmers, government agencies to minimise the spread of disease as well as zoonotic effect.

Publications

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Betts JW (2018) Novel Antibacterials: Alternatives to Traditional Antibiotics. in Advances in microbial physiology

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Dimitrov KM (2019) Updated unified phylogenetic classification system and revised nomenclature for Newcastle disease virus. in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

 
Description A prototype of the proposed low-cost molecular diagnostic device was produced and used for experimental developments by partners. The feedback was used to develop a fully integrated beta-prototype of the same device and was used in a field visit to receive feedback from potential end users. A colorimetric LAMP assay for detection of Salmonella sp. was also developed and experimented on the platform. This assay setup together with the platform was demonstrated during the field visit to show the capability of the platform. Additionally, other colorimetric LAMP assays commercially available in Philippines were also tested on the device to show its flexibility and demonstrate it's platform nature. The feedback from potential end users was collected and it will be used in further development of the device to a scalable prototype.
Exploitation Route The findings were mainly feedback received from potential end users. Such feedback is fundamental in the development cycle as often they imply on product requirements. In addition to these, we also developed great understanding of the current infrastructure available in farms which also helps us develop products that seamlessly integrate into these infrastructures.
Sectors Agriculture, Food and Drink,Communities and Social Services/Policy,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description Currently the Philippine lacks the tools and infrastructure to effectively and rapidly diagnose and track poultry disease outbreaks. Diagnosis is currently reliant on a drop in production performance, presence of clinical signs, pathological lesions and serological findings. The aspect of routine monitoring with the focus on early detection and treatment is not a standard practice. During the field visit in February 2019, a fully functional prototype of the molecular diagnostic device was introduced and demonstrated to veterinarians, poultry farmers, farm managers, policy makers, standards authority and research professionals. These demonstrations sparked various discussions ranging from how Philippine poultry could adopt a monitoring approach as an alternative to the current system, where diagnosis is only performed when there is a known outbreak to how the government could utilise the platform for rapid in-farm detection of diseases during routine monitoring and outbreak events. Additionally, the discussions also included diversification of the device capability with more biochemical assays to detect diseases of other farm animals such as cattle and swine and also other poultry farming related issues such as antibiotic susceptibility.
First Year Of Impact 2019
Sector Agriculture, Food and Drink
Impact Types Cultural,Policy & public services

 
Description Chair of the Humanimal Trust
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Chair of the Veterinary Pathology SAC for the RCPath
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Participation in FSA ACSMF AMR committee
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
 
Title Alpha Prototype of a Diagnostic Device 
Description To fulfil the ultimate aim of a low-cost molecular diagnostic device, the research group produced a first prototype of the envisaged device. The device is capable of accepting a PCR-tube strip and provides the required temperature to perform isothermal amplification with LAMP reagents. Additionally, the device also performs periodic imaging during the amplification assay and stores the images internally. The embedded cloud connectivity allows easy transfer of data between collaborating research groups for further assay, device and software development. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? No  
Impact In its first functional form, the device enables the researchers to validate the intricate solutions that are used to make this device. This accelerates decision making in the device development process and also the connectivity solutions embedded in the device enables collaborating research groups to seamlessly access raw data for further developmental work. The main impact that this research tool has resulted in is the acceleration of research and development. 
 
Title LMDP 1.0 Diagnostic Platform 
Description A low-cost molecular diagnostic platform capable of performing isothermal nucleic acid amplification assays and detection through colorimetric techniques was produced. This second generation device was made with the focus on usability, cost reduction and improved functionality. The device is capable of accepting a PCR tube strip and has heating block and a lid, in which desired temperatures can be reached within 2 minutes. The device was used to perform colorimetric LAMP amplification directly from cultured Salmonella sp. cells. It was shown that the device is capable of performing LAMP amplification, perform imaging and transfer raw data to a central server for further analysis. Currently, this device is being further developed to produce a fully integrated scalable platform for molecular diagnostics. 
Type Of Technology Detection Devices 
Year Produced 2019 
Impact As a fully functional device, it was used in field visits in the Philippines to demonstrate how the final solution being produced will help end users detect poultry pathogens in farm settings. This demonstration also enabled us to receive constructive feedback on how to improve the functionality of the device and also greater input on the device requirements, such as the robustness level, size of the device and reduction of manual operations. 
 
Description AVS - Jan 2019 - AMR and biofilms - RVC -UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact A talk on AMR for the Association of Veterinary Students.
Year(s) Of Engagement Activity 2019
 
Description Organised microbiology Society Emerging Threats and AMR meeting 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Organised a Microbiology Society Surrey meeting on Emerging Threats and AMR.
Year(s) Of Engagement Activity 2018
 
Description Presentation at St George's hospital June 2018 - One health, Zoonoses and AMR 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Presentation at St George's hospital June 2018 - One health, Zoonoses and AMR
Year(s) Of Engagement Activity 2018
 
Description Press Release 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact A press release was made by Brunel University on the project which resulted in a number of requests from the general public, industry and academia for participation and involvement.
Year(s) Of Engagement Activity 2018
URL https://www.brunel.ac.uk/news-and-events/news/articles/Smartphone-to-help-farmers-test-for-poultry-i...
 
Description Research Workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Presented on the topic of Advanced Biosensors for Detecting Zoonotic Pathogens to a majority audience from non-engineering background. The purpose of the presentation was to provide an overview on emerging biosensing techniques and its applicability in veterinary and zoonotic pathogen detection. The presentation sparked a lot of discussion among participants regarding how advanced engineering solutions can be utilised successfully to address animal and public health.
Year(s) Of Engagement Activity 2019
 
Description Talk for the RCGP on AMR a veterinary perspective 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact A talk on AMR for the RCGP's
Year(s) Of Engagement Activity 2018
 
Description UK-Philippines Workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The organizers headed by Dr. Muhammad Munir of Lancaster University and Dr. Dennis V. Umali of the University of the Philippines Los Baños (UPLB), successfully conducted the "Newton Agham Researcher Links Workshop: Novel Vaccines and Diagnostic Technologies Against Emerging and Re-Emerging Veterinary Pathogens" held from 4 to 7 February 2019 at the Rizal Park Hotel Manila, Philippines. In the opening ceremonies, Dr. Jovencio Hubert A. Abalos, Assistant to the Dean and representing the dean of the College of Veterinary Medicine (CVM), UPLB welcomed the participants and wished them a fruitful workshop. He also mentioned that the topics to be covered in the workshop could bring out new topics for research for the dual Doctor of Philosophy programme being planned between UK universities and UPLB. Undersecretary Carol M. Yorobe representing the Department of Science and Technology (DOST), Philippines said that she hoped that the joint discussions will result in a collaborative network among UK and Philippine scientists. Mr. Norly Villar, Programme Manager, Newton Agham, British Council of the Philippines, also graced the occasion and welcomed the participants as well as inspiring and challenging them for a 4-day workshop.

Dr. Muhammad Munir, Lecturer, Lancaster University and one of the organizers, presented the mechanics of the activities ahead. He stated the objectives and expected outcomes, which are identification of research gaps, establishment of collaborations, identify potential threats to livestock and poultry and production of a white paper to be presented to policy makers and funding bodies.

The workshop was conducted for four days. On the first day, there were 9 papers presented, divided into 3 sessions. Each paper was read for 30 to 40 minutes, then a 10-minute open forum followed after each session. On the second day, there were 6 papers in 2 sessions, followed by two interactive sessions (workshops). On the third day, there were 6 papers in 2 sessions, followed by an interactive session (field trip), which included a cultural dinner. On the fourth day, there were 4 papers in one session. In summary, there were 25 technical papers and 3 interactive sessions. In general, the papers and workshops had a common goal, that of controlling and preventing infectious diseases of farm animals. Most of the papers focused on molecular techniques for the production of diagnostic kits and vaccines.

The abstracts of all the papers were published as proceedings and distributed to all participants before the workshop while the highlights of each paper, workshop outputs of Interactive Sessions 1 and 2, and the powerpoint presentations are attached as Appendices A, B, C and D, respectively. In Interactive Session 3 (Networking and Outdoor Activities), the participants had a field trip at the Philippine Genome Center (PGC) situated at the University of the Philippines Diliman, Quezon City. Selected staff of the facility welcomed them warmly and immediately proceeded in conducting a guided tour. The group visited the Shared Genomics Core Laboratory (SGCL) of the PGC, which primarily aims to build the capacity of local researchers to perform top-of-the-line genomics research. Also visited was the DNA Sequencing and Bioinformatics Facility (DSBF) of the PGC, which offers training packages in Basic Molecular Biology, Sanger Sequencing, Next Generation Sequencing and Bioinformatics. The activity provided everyone a glimpse of the capability of the center as well as giving an opportunity for potential collaborations, networking and information exchanges. Part of the interactive session was the cultural dinner at the Barbara's Heritage Restaurant in historic Intramuros, Manila. The cultural show composed of songs and dances featured the rich Filipino culture while providing a venue for strengthening British-Filipino camaraderie among the participants.

In the Closing Ceremony, Mr. Norly Villar, Programme Manager of the Newton Agham, British Council of the Philippines, presented the current programs and research opportunities offered by the British Council. He reported that there are 21 ongoing scholars and the first batch is expected to return in 2019 or 2020. He encouraged everyone to visit the Newton Agham Programme website for more details. Dr. Synan S. Baguio, Supervising Science Research Specialist and Officer-in-Charge, Livestock Research Division, Philippine Council for Agriculture, Aquatic and Natural Resources Research Development (PCAARRD), DOST delivered an inspirational message. He thanked everyone for a successful workshop and hoped that the shared information would be put to practical use and continue the collaboration among the participants. Dr. Rio John T. Ducusin, a professor of the College of Veterinary Medicine, UPLB who served as rapporteur during the entire workshop, read the agreement (Appendix E), which is one of the outputs of the workshop. He mentioned that hopefully, in the not-so-distant future, the items listed in the above document would be realized. The agreement was duly signed by the participants. The closing remarks were delivered by Dr. Jovencio Hubert A. Abalos, Assistant to the Dean of the College of Veterinary Medicine, UPLB. He thanked the organizers, sponsors, participants and everyone who contributed to the success of the workshop. He wished everyone a safe travel going back home.
Year(s) Of Engagement Activity 2019
URL http://uk-philippines-workshop.com/
 
Description Visit to the Pirbright Institute 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Visit to the Pirbright Institute to discuss future collaborative work on developing engineering solutions for animal health and welfare
Year(s) Of Engagement Activity 2019