CUKPGP: Streptococcus suis in the pig meat supply chain: from genomics to control strategies.
Lead Research Organisation:
University of Cambridge
Department Name: Veterinary Medicine
Abstract
Streptococcus suis (SS) is an important zoonotic pathogen of pigs with global relevance to pig productivity and human health. Strategies for SS control are needed to protect human health andto reduce dependence of pig production on antimicrobials. This project aims to identify control points for the prevention of SS related disease in pigs and humans. Longitudinal studies in UK and Chinese farms and abattoirs (intensive and traditional systems), with whole genome sequencing of isolates, will provide guidance to new control points for disease prevention by shedding light on strain diversity, fitness, and antimicrobial resistance along the supply chain. Sequences will be compared to those obtained from pig meat products and those available from human isolates. Risk factors for carriage of SS on consumer-ready pig-meat will be investigated. We will identify avenues for environmental control of SS using transposon directed insertion site sequencing (TraDIS) to explore the genes that underpin environmental survival of SS in the farm, abattoir and meat product context.All partners (Cambridge University, Huazhong Agricultural University (HAU), and Wellcome Trust Sanger Institute (WTSI)) have strong track records in SS research. CU and HAU hold a China Partnering Award, and all 3 work together within the existing BBSRC Longer and Larger funded consortium, 'A single platform diagnostic and multivalent vaccine approach to bacterial respiratory diseases of pigs'.
Technical Summary
Streptococcus suis (SS) is an important zoonotic pathogen of pigs with global relevance to pig productivity and human health. Strategies for SS control are needed to protect human health andto reduce dependence of pig production on antimicrobials. This project aims to identify control points for the prevention of SS related disease in pigs and humans. Longitudinal studies in UK and Chinese farms and abattoirs (intensive and traditional systems), with whole genome sequencing of isolates, will provide guidance to new control points for disease prevention by shedding light on strain diversity, fitness, and antimicrobial resistance along the supply chain. Sequences will be compared to those obtained from pig meat products and those available from human isolates. Risk factors for carriage of SS on consumer-ready pig-meat will be investigated. We will identify avenues for environmental control of SS using transposon directed insertion site sequencing (TraDIS) to explore the genes that underpin environmental survival of SS in the farm, abattoir and meat product context.All partners (Cambridge University, Huazhong Agricultural University (HAU), and Wellcome Trust Sanger Institute (WTSI)) have strong track records in SS research. CU and HAU hold a China Partnering Award, and all 3 work together within the existing BBSRC Longer and Larger funded consortium, 'A single platform diagnostic and multivalent vaccine approach to bacterial respiratory diseases of pigs'.
Planned Impact
The outcome of this project, and associated impact, are as follows:
1. Longitudinal data on prevalence, and antimicrobial sensitivity profiles, of SS in pigs from weaning to slaughter in UK and intensive / traditional Chinese production systems. Information on longitudinal changes in SS sequence diversity within intensive and traditional farms, including number of sequence types and antimicrobial resistance. Sequence associations /features for strains found in pigs at slaughter and on consumer-ready pig meat. Sequence associations between published human isolates and those found in pigs at slaughter, or on consumer-ready pig meat.This data is of value to veterinarians to assist in planning and implementing of appropriate control programs for disease outbreaks, including antimicrobial strategies. Also of value to researchers developing diagnostic tools that can track important vs less important strains (e.g. those that make it through to slaughter and consumer ready foods, or those strains that appear in human populations.
2. Archived SS isolates for diversity studies (approx. 250 assuming a 50% carriage rate): An importnant resource for future studies in evolutionary microbiology.
3. Preliminary descriptive information for 15 pig production farms (5 in UK, 10 in China) of on-farm risk factors for cohort prevalence for SS carriage, individual pig carriage at weaning and slaughter, incidence of streptococcal disease on farm, and appearance of new AMR phenotypes: Importn information to assist in the planning of larger scale statistically robust risk factor analyses to identify novel control programs.
4. Prevalence estimates for SS carriage and load on different pig meat products sourced from intensive and traditional systems. Information on factors associated with prevalence and bacterial load of SS on consumer-ready pig meat products in China: Important data for planning managemental apporaches to reducing S suis prevalence on consumer-ready foods.
5. Information on genes and pathways related to environmental fitness of SS in zoonotic and animal transmission contexts. Valuable information for development of novel approaches to infection control.
1. Longitudinal data on prevalence, and antimicrobial sensitivity profiles, of SS in pigs from weaning to slaughter in UK and intensive / traditional Chinese production systems. Information on longitudinal changes in SS sequence diversity within intensive and traditional farms, including number of sequence types and antimicrobial resistance. Sequence associations /features for strains found in pigs at slaughter and on consumer-ready pig meat. Sequence associations between published human isolates and those found in pigs at slaughter, or on consumer-ready pig meat.This data is of value to veterinarians to assist in planning and implementing of appropriate control programs for disease outbreaks, including antimicrobial strategies. Also of value to researchers developing diagnostic tools that can track important vs less important strains (e.g. those that make it through to slaughter and consumer ready foods, or those strains that appear in human populations.
2. Archived SS isolates for diversity studies (approx. 250 assuming a 50% carriage rate): An importnant resource for future studies in evolutionary microbiology.
3. Preliminary descriptive information for 15 pig production farms (5 in UK, 10 in China) of on-farm risk factors for cohort prevalence for SS carriage, individual pig carriage at weaning and slaughter, incidence of streptococcal disease on farm, and appearance of new AMR phenotypes: Importn information to assist in the planning of larger scale statistically robust risk factor analyses to identify novel control programs.
4. Prevalence estimates for SS carriage and load on different pig meat products sourced from intensive and traditional systems. Information on factors associated with prevalence and bacterial load of SS on consumer-ready pig meat products in China: Important data for planning managemental apporaches to reducing S suis prevalence on consumer-ready foods.
5. Information on genes and pathways related to environmental fitness of SS in zoonotic and animal transmission contexts. Valuable information for development of novel approaches to infection control.
Publications
Baig A
(2015)
Whole genome investigation of a divergent clade of the pathogen Streptococcus suis.
in Frontiers in microbiology
Hadjirin NF
(2021)
Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis.
in BMC biology
Hernandez-Garcia J
(2017)
Patterns of antimicrobial resistance in Streptococcus suis isolates from pigs with or without streptococcal disease in England between 2009 and 2014.
in Veterinary microbiology
Weinert LA
(2015)
Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis.
in Nature communications
Wileman TM
(2019)
Pathotyping the Zoonotic Pathogen Streptococcus suis: Novel Genetic Markers To Differentiate Invasive Disease-Associated Isolates from Non-Disease-Associated Isolates from England and Wales.
in Journal of clinical microbiology
| Description | 1. New data on S suis prevalence in pig meat supply chains: S. suis is essentially ubiquitous in the Chinese and UK pig meat supply chains. We showed that Chinese pigs were more likely to carry stains of S suis (SS) that are associated with disease in pigs and / or humans than were pigs in the UK. We showed that the prevalence of carriage was increased during warmer weather and also that the diversity of strains within an individual pig was likely to be greater during warm weather. In addition we found that antibiotic resistance was widespread in the UK and Chinese isolates, with a greater prevalence of resistance genes in Chinese pigs. There was a tendency for the isolates collected from 20 weeks old pigs to carry more resistances/isolate than those isolates collected from 5 week old pigs. The data generated will be presented at the International Pig Veterinary Congress in 2016 and will be published in peer reviewed literature. 2. Prevalence load and risk factors for carriage of SS on retail meat products: This work involved quantitative analysis of SS on meat and liver samples collected from abattoirs, supermarkets and wet markets during summer and winter seasons. Temperature was a significant factor (P=0.033), and the effect of temperature did not depend on Sites and Tissues. In winter at the slaughter house, the S.suis level of meat was significant higher than that of Liver collected at the same location (P<0.05). The S.suis level of meat in the slaughter house was significantly higher than that of Supermarket and wet market. The most important outcome of this work was to show that temperature was the most significant factor, of those tested, influencing carriage of SS on meat or pig-derived products. 3. Genes and pathways impacting on environmental fitness of S. suis: We used a library of 10,000 individual mutants of SS, together with high throughput sequencing (transposon directed insertion site sequencing) to study the fitness of individual mutants under different environmental conditions representing chilling or freezing of meat (food borne transmission), survival in water (environmental survival in cleaned pig pens between batches) and on intact or damaged pig skin (as a surrogate for occupational transmission to people, with or without abrasions, working with pigs). Our findings indicated particular importance of pathways associated with carbohydrate metabolism and should form the basis for future studies aimed at indentifying new targets for next-generation disinfectants. We also found that the mutation of certain genes (for example mutY - involved in repair of mutated bacterial DNA) resulted in increased fitness in the environment (across our test conditions), emphasising the importance of short term benefits for environmental survival where SS is able to mutate and adapt to more demanding environments. The data generated are being prepared for publication in peer reviewed literature. |
| Exploitation Route | We planned to hold stakeholder meetings to discuss outcomes of our work in the UK and China. Because of budget limitations we instead used engagement opportunities including European, Cjinese and International Pig Veterinary Society Congresses to disseminate our findings to the professional pig veterinary communities in China, UK, and globally. Parallel projects in our lab on Strep suis have led to breakthroughs in vaccine-based approaches for control of Strep suis. We plan to present our integrated findings on diversity and risk factors for Strp suis plus vaccine based control strategies at the International Workshop on Strep suis in Germany later in 2016. We anticipate at least 5 peer reviewed manuscripts will be submitted from this project in 2016. |
| Sectors | Agriculture Food and Drink Healthcare |
| Description | There were two significant non-academic impacts of this project: 1. Information on antibiotic susceptibility of Strep. sis isolates from UK and China. The project collected a large amount of data on antibiotic sensitivity from more than 130 isolates of Streptococcus suis in the UK and more than 150 isolates in China. This data was shared with diagnostic labs in the UK (APHA) and China (Huazhong Ag Univ diagnostic lab) to assist in future selection of antibiotics for sensitivity testing of isolates arising from diagnostic samples. In addition the UK data is currently being drafted into a manuscript and, in addition, will be presented in an oral presentation confirmed for the International Pig Veterinary Society, June 2016. 2. Advice on diagnostic sampling to permit more effective diagnosis and management of outbreaks of S. suis disease. An oral presentation was made at the 2015 European Symposium for Pig Health Management in Nates, France that described the diversity of S. suis isolates obtained from tonsil sampling. A separate oral presentation was made at the UK Pig Veterinary Society in 2014 describing current best practices for sampling and planning evidence based antibiotic control programs for S. suis disease. Two papers were published in 2018 describing outputs from this project - in terms of antibiotic resistance profiles of S susses isolates from the UK, and also describing diversity and prevalence of S. suis carriage among slaughter pigs in China and UK - with notable new data indicating ambient temperature as being an important factor affecting these parameters. |
| Sector | Agriculture, Food and Drink |
| Impact Types | Policy & public services |
| Description | Adviser on Global Pig Health |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Advisory Committee on Microbiological Safety of Food |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | BPEX Technical Committee |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Description | Membership of FSA's Advisory Committee on Microbiological Safety of Food |
| Geographic Reach | National |
| Policy Influence Type | Membership of a guideline committee |
| Impact | ACMSF and its subgroups provides advice and recommendation the FSA Board. In turn the FSA contributes to the evolution of UK food safety legislation and its implementation. |
| Description | KTN CASE Studentship |
| Amount | £163,520 (GBP) |
| Organisation | Knowledge Transfer Network |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 09/2013 |
| End | 09/2017 |
| Description | Zoonosis in Emerging Livestock Systems |
| Amount | £1,600,000 (GBP) |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2015 |
| End | 12/2020 |
| Title | Sampling approaches for Streptococcus suis in healthy pigs |
| Description | We identified that individual pigs may carry multiple different isolates of S. suis in their tonsil. Previously, researchers had selected only a single colony for subsequent culture and characterisation but our work confirmed that up to 5 unique isolates may be present in a single animal. So, for studies of diversity it is essential that multiple colonies are selected from each primary culture. |
| Type Of Material | Biological samples |
| Year Produced | 2014 |
| Provided To Others? | Yes |
| Impact | A manuscript is under preparation. |
| Title | Additional file 1 of Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis |
| Description | Additional file 1: Table S1. The 678 isolates in our collection with meta data, MIC values and candidate determinant presence/absence. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Large-scale_genomic_analys... |
| Title | Additional file 1 of Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis |
| Description | Additional file 1: Table S1. The 678 isolates in our collection with meta data, MIC values and candidate determinant presence/absence. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_1_of_Large-scale_genomic_analys... |
| Title | Additional file 3 of Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis |
| Description | Additional file 3: Table S3 -The 401 additional isolates used to estimate population structure with their genetic BAPs cluster and their data availability. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Large-scale_genomic_analys... |
| Title | Additional file 3 of Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis |
| Description | Additional file 3: Table S3 -The 401 additional isolates used to estimate population structure with their genetic BAPs cluster and their data availability. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2021 |
| Provided To Others? | Yes |
| URL | https://springernature.figshare.com/articles/dataset/Additional_file_3_of_Large-scale_genomic_analys... |
| Description | Huazhong Agricultural University, College of Veterinary Medicine. |
| Organisation | Huazhong Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Collaboration on several projects and in training and academic exchange. |
| Collaborator Contribution | Provided additional funding to support Chinese post doc placements in UK. Provided funding to assist support of UK PhD students in China. |
| Impact | Student exchange. Post doc exchange. |
| Start Year | 2013 |
| Description | European Symposium on Pig Health Management 2013 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | This was an invited lecture to discuss the interaction between bacterial pathogens (Strep suis) environment and host susceptibility. Sparked questions and further invitations to speak at subsequent international meetings. None specific |
| Year(s) Of Engagement Activity | 2013 |
| Description | European Symposium on Pig Health Management 2015 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | We presented data on diagnostic approaches for Streptococcus suis and antimicrobial susceptibility data. |
| Year(s) Of Engagement Activity | 2015 |
| Description | International Pig Veterinary Society 2016 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Outcomes of the project will be presented in oral and poster presentations, confirmed as accepted for publication: including antibiotic susceptibility; prevalence and diversity of Strep suis carriage in UK and China and the impact of temperature. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Norfolk, Suffolk, Essex, Cambs Pig Discussion Groups |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation to vet practitioners on best practices for diagnosis, treatment and prevention of S. suis disease in laughter pig production systems. Follow-up phone discussions, changes in vaccination strategies, and herd management methods. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Nottingham University Seminar |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Professional Practitioners |
| Results and Impact | A seminar on natural history of Streptococcus suis in the pig meat supply chain was given at Nottingham University The audience comprise academics and also members of policy making committees in government. There was active discussion and a subsequent meeting to plan future research collaborations. |
| Year(s) Of Engagement Activity | 2015 |
| Description | PIC China Symposium |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The PI (Tucker) gave a presentation at the PIC China Symposium on the management and prevention of infectious diseases of pigs, including Streptococcus suis. |
| Year(s) Of Engagement Activity | 2015 |
| URL | http://www.wattagnet.com/articles/24751-pic-chinas-2015-symposium-highlights-value-components |
| Description | Scottish pig producer group 2014 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Talk stimulated reflection of effectiveness of respiratory disease control in group members' pig production units. Further phone discussions. Triggered change in diagnostics and vaccination programme. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Streptococcus suis Workshop 2016: The dynamics of Streptococcus suis carriage in recently weaned and slaughter-aged pigs in China and UK |
| 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 workshop was attended by around 80 global specialist researchers, medics and veterinarians with interest in Streptococcus suis associated disease management. |
| Year(s) Of Engagement Activity | 2016 |
| Description | UK Pig Vet Soc 2014 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk sparked questions and discussion Interest expressed in new diagnostic methodologies arising from our work. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Update on Streptococcus suis: epidemiology, diagnosis and control |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Research updates were provided to members of the UK Animal and Plant Health Agency's Pig Expert Group. Specifically progress on new vaccine development, diagnostic approaches and non-antimicrobial control strategies. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Vet Public Health Assoc conference 2014 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Lecture sparked questions and discussion. Nothing major. |
| Year(s) Of Engagement Activity | 2014 |
| Description | Wuhan Pig Veterinary Congress, 2013 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | Yes |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Talk sparked questions and discussion on diagnosis and management of Streptococcal diseases in pigs. None specific |
| Year(s) Of Engagement Activity | 2013 |