The authors provide an overview of different techniques and conclude that phage diagnostics have been proven as a rapid non-culture-based solution for detection of viable bacterial infection, including Listeria monocytogenes, Salmonella, and Escherichia coli as well as various species of mycobacteria, the causal agents of diseases including bovine tuberculosis (bTB) and Johne’s disease (MAP).
Culture-based detection is currently considered to be the gold standard for detection and identification of bacterial pathogens within the agricultural supply chain. However, for identifying mycobacterial diseases, culture-based approaches are notoriously insensitive and unreliable. Mycobacteria can take several weeks to grow, rendering them susceptible to contamination and making culture impractical as a detection tool to ensure animal health and welfare, and food security.
Culture-based work is also time-consuming, labour-intensive, and requires level 2 or level 3 containment laboratories (depending on the organism being grown). Additionally, further confirmatory tests such as polymerase chain reaction (PCR) are required, adding to the time, cost, and labour required to positively identify an organism.
As a result, non-culture molecular methods are gaining in popularity. However, direct PCR can be expensive, sensitive to inhibition and cannot discriminate between viable or dead cells. This is a particular issue when measuring the efficacy of food processing methods designed to reduce the viable pathogens.
Immunological methods such as ELISAs use antibodies to detect proteins or antigens developed in response to a pathogen so that pathogens and associated toxins can be identified. These also have limitations, particularly in sensitivity.
For Mycobacterium bovis (M. bovis) the Single Intradermal Comparative Cervical Tuberculin (SICCT) test is most widely used test in the UK. The SICCT test, although excellent as a screening tool at herd level, is extremely poor at an individual level. A lack of sensitivity means that infections in herds can persist for a long time on farms.
Furthermore, both PCR and antibody diagnostic methods require a high level of skill and a laboratory infrastructure.
Meanwhile, Whole-Genome Sequencing (WGS) is an exciting prospect in detection markets. However, the routine use of WGS as a detection tool, especially in agriculture, is prohibitively expensive for food sector industries and currently relies on culture of the organism.
It is clear that alternative detection methods are needed which are rapid, specific, and can differentiate between active and past infections. Phage-based detection methods have been developed that fulfil these requirements while keeping costs low.
Phages have evolved to infect and propagate within specific bacterial hosts, replicating at a faster rate than their host, resulting in lysis, efficiently releasing mycobacterial DNA from viable cells. This allows detection using PCR while overcoming one of the major limitations of this technique.
The authors conclude that phage-based detection methods are low cost, portable, and accessible to a wide range of users, without the need for extensive training or equipment. As such, phage-based methods have the potential to be used throughout the agricultural supply chain—from farm-to-fork—to revolutionize the detection of bacterial pathogens.
The paper: The Application of Bacteriophage Diagnostics for Bacterial Pathogens in the Agricultural Supply Chain: From Farm-to-Fork ; Helen J. Jones, Christopher G. Shield, and Benjamin M.C. Swift Published in PHAGE: Therapy, Applications, and Research Volume 1, Number 4, 2020