Using bacteriophage to control Salmonella in pigs

Antimicrobial resistance (AMR) is a growing problem in many types of bacteria which cause disease (pathogens) in animals and humans. Salmonella is an important bacterial pathogen of both, and often causes gastrointestinal infections which may sometimes progress to more serious and life-threatening disease. It can spread from infected farm animals to humans through the food chain. Intensively farmed food animals such as poultry and pigs are an important source of Salmonella, and the use of antibiotics in these animals over many years has been associated with the development of new strains of this bacterium which are resistant to antibiotics. This means that infections in animals and humans are more difficult to treat, which may result in more serious infections occurring over time, particularly in vulnerable groups such as the elderly, or those with poor immunity. There is an urgent need to find alternatives to antibiotics which are more sustainable. This project will investigate the use of bacteriophage as a biological control against strains of Salmonella which infect pigs. Bacteriophage, often contracted to 'phage', are viruses which infect and kill bacteria. They are quite specific, only affecting the targeted bacterial species while leaving other bacteria, which may be beneficial, unharmed. Unlike other viruses, phages do not infect the cells of animals or humans and can be found widely in the environment. We plan to use phages to selectively kill strains of Salmonella strains which infect pigs and have the potential to be transmitted through the food chain to consumers. These phages, when used individually or in combination, have the potential to be a natural and sustainable alternative to antibiotics, and may also result in new treatments for antibiotic resistant bacterial infections in other animals and potentially humans as well. The effective application of phage therapy will require a thorough understanding of phage-bacteria interactions in a range of environments. This project will use laboratory experiments and computer simulations (machine learning) to build a comprehensive understanding of how phages infect Salmonella under different conditions. This information will then be used to design protocols for the optimal use of phage therapy to treat experimental Salmonella infections in pigs.

In this project we will use host-specific bacteriophage to target pathogenic strains of Salmonella Typhimurium which are clinically important, and currently circulating in the UK/EU swine population. This approach has the potential to be an effective and viable alternative to antibiotic treatment. The selection of suitable bacteriophage biocontrol candidates requires the in-depth characterisation of the phage and detailed analysis of how phages interact with their hosts in vitro and in vivo. We will isolate and characterise a library of phage which infect Salmonella Typhimurium. These phage will be screened individually and in combination in a phenotypic microarray against a panel of Salmonella strains to determine their host range and infection kinetics. These results will be used to build a machine learning tool which will predict and optimise the performance of different phage cocktails. The performance of these cocktails will be determined initially in an insect model (Galleria mellonella) and subsequently a pig model of Salmonella infection. In the pigs, we will assess the effect of phage treatment on the gut microbiome, and the expression of immune genes in a microfluidic qPCR platform. In addition to determining the effect of directly applying phage to treat Salmonella in pigs, we will also discover whether phage in the environment can protect pigs from subsequent Salmonella challenge.

The emergence of bacterial resistance to all classes of antibiotics is an increasing global health concern, with the annual death tolls worldwide predicted to reach 10 million by 2050. The associated economic, and social loss highlights the pressing need to develop alternative therapeutics. The identification and development of new antibiotics is slow, difficult and costly, and there is an urgent need to explore other viable alternatives. Our work is centred on developing a novel phage product against Salmonella, an important enteric pathogen in humans and animals worldwide, and where human infection strongly linked to animal consumption, particularly of poultry and swine. As Salmonella becomes more resistant to antibiotics in animals, it also becomes less treatable in humans. Indeed, it is increasingly becoming resistant to antibiotics, and multidrug resistant strains have been isolated from swine. There is therefore a need to develop novel therapeutics to prevent and treat infection in animals both in order to treat them per se, and to prevent infection in humans. Phage therapy has enormous potential to compliment antibiotics, but its development is not straight forward. We have identified the major steps needed and assembled a multidisciplinary team to address them.

Harnessing the lytic activity and specificity of phages offers a plausible alternative approach to treat MDR bacteria, and investment in development of this technology offers an opportunity to have a significant impact in the medium to long term on public health, animal health and welfare, and on the economy. Whilst in the short term, our research will reduce Salmonella in the farm environment and prevent it entering the human food chain, the longer-term future beneficiaries of this research will be much wider. The work will also benefit healthcare providers in the UK, and reduce the amount of time nationally that is lost to illness caused by Salmonella infection and subsequent gastrointestinal disorders known as Salmonellosis. Other beneficiaries of the research include the veterinary industry and farmers who are under increasing pressure to not prescribe antibiotics but need to treat their livestock, and doctors who are likewise coming under increasing pressure to reduce antibiotic prescriptions.

The proposed research will contribute to advances in knowledge and understanding of how the process of developing phage treatments can be optimised. This builds on recent technological advances in both hardware (robotics and high throughput screening), and software (machine learning) to solve this new, complex problem. The machine learning tool developed as an outcome of this project will be able to be adapted to other phage/bacterial combinations. Rather than being a standalone tool, it will be used as part of an adaptive process which will accommodate information about new phages introduced into the collection and reoptimise the phage cocktails as needed. This process will become more accurate and effective as number of phages assessed increases.

This project will directly impact the pig industry, as ultimately it will progress research to facilitate a new therapeutic option to treat animals infected by Salmonella. We will also identify how stable phages are in the lairage environment, and determine if they can protect against new infections, which again will inform on other bacterial-phage systems.

To summarise, our efforts to develop a phage product will be of benefit to food producers in the UK, and in academic and industrial researchers working on developing both prophylactic and therapeutic treatments for a wide range of gastrointestinal infections. Whilst our target country is the UK, we future work could extend the phage product development and make it accessible to other swine producers worldwide, such as China, and thus by funding this work the UK will be in a leading position to develop the technology worldwide.