BBSRC United States Partnering Award: Advancement of (meta) genomic tools to study the transmission of Campylobacter and other low abundance pathogens
Lead Research Organisation:
QUADRAM INSTITUTE BIOSCIENCE
Department Name: Microbes in the Food Chain
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Publications
Djeghout B
(2024)
Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool.
in Microbial genomics
| Description | Expert Advice to Food Standards Agency |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| URL | https://www.food.gov.uk/research/foodborne-pathogens/the-third-study-of-infectious-intestinal-diseas... |
| Description | Expert Advice to UK Government (FSA) |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Title | Utilisation of (meta) genomes in low abundance pathogen samples |
| Description | Development of HMW DNA extraction, purification and sample optimisation techniques coupled with sequencing and bioinformatic pipelines specifically optiomised for this biological dataset with researh partners. |
| Type Of Material | Biological samples |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | Impacts will be realised in 2024-25 for this dataset and method. |
| Title | Advances in metagenomic analysis for Campylobacter carriage in stool |
| Description | A set of mother, infant and animal metagenomes comprises of a rich dataset to apply advanced metagenomic tools to assess campylobacter presence and characteristics. The comparison between Kraken and Metaphlan have resulted in optimising bioinformatic pipelines. The research and analysis is ongoing. |
| Type Of Material | Data analysis technique |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | This subset and pipeline enables the same to be conducted on a wider dataset with substantial impact to the biology of Campylobacter, epidemiology and how advancement in molecular and bioinformatic tools provides greater resolution to sequenced data. |
| Title | Use of hybrid assembly to characterise Campylobacter genomes |
| Description | This bioinformatic technique was used for approx 800 genomes from my research collection of Campylobacter genomes in support of genomic characterisation |
| Type Of Material | Data analysis technique |
| Year Produced | 2023 |
| Provided To Others? | No |
| Impact | This dataset is the base for further method development to understand population diversity of Campylobacter using novel techniques |
| Description | Bioinformatic pipelines for Campylobacter population structure |
| Organisation | Utrecht University |
| Department | Institute for Risk Assessment Sciences |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | This partnership is a shared interest in the population structure and strain level difference in Campylobacter. We have contributed >1,000 genomes for shared analysis and testing of novel bioinformatic pipeline approaches. |
| Collaborator Contribution | Our Risk Assessment Institute, Utrecht University |
| Impact | Outcomes thus far have been the appointment of a Master's student (Utrecht University) to the project and monthly progress meetings |
| Start Year | 2022 |
| Description | Collaboration with Amira Roess - Dept of Global Health, George Washington University |
| Organisation | George Washington University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | This collaboration stems from a successful Gates foundation grant that Amira Roess (George Mason University) is a PI for and John Wain (QIB) a Co-I titled Transmission of Campylobacter in rural Bangladesh. I, as part of the QIB research team aided in building a sequencing laboratory infrastructure fo Oxford Nanopore Technologies sequencing for genomes and metagenomes in Dhaka, Bangladesh. During 2020-2021 we have leveraged that infrastructure to build further capacity within the Dhaka laboratory to sequence SARS-CoV-2. |
| Collaborator Contribution | The collaboration, led by Amira Roess, GMU has progressed to further capacity building in the Bangladesh laboratories. This collaboration is leading to new grant application opportunities and further work on global health. |
| Impact | This collaboration is interdisciplinary with microbiologist, bioinformatiticians, field epidemiologist and molecular biologist working together on assessing the routes of transmission of Campylobacter in rural Bangladesh. |
| Start Year | 2019 |
| Description | George Mason University, USA Genomics and Epidemiology Partnering |
| Organisation | George Mason University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | My research team has provided analysis, expertise, training and methodology development of lab and bioinformatics. I have attended in person networking events to develop further strategic projects with the MicroBiome Analysis Centre, Centre for Infectious Disease Research, Institute for Biohealth Innovation and the Centre for Applied Proteomics and Molecular Medicine, GMU, Washington, DC, USA |
| Collaborator Contribution | The collaborators have hosted a seminar series and event titled: Expanding Collaborations between UK, Bangladeshi, and Mason Scientists and Students to provide early career researchers with opportunities to network with scientists from across the globe. |
| Impact | 1. Multi-disciplinary seminar event (Jan 2024) consisting of bioinformaticians, molecular biologists, microbiologists, epidemiologists, early career researchers 2. Grant submissions to UKRI, NIH by collaborative multi-disciplinary team 3. Training of early career researchers 4. Hybrid seminar and strategic grant writing event (Feb 2025) consisting of bioinformatician, epidemiologist, microbiologist from the partnering team |
| Start Year | 2023 |
| Description | Global Health Challenges in Bangladesh: CHRF-QIB partnership |
| Organisation | Child Health Research Foundation |
| Country | Bangladesh |
| Sector | Charity/Non Profit |
| PI Contribution | My research team has provided laboratory and bioinformatic testing and analysis, while I have provided expertise, writing of reports, grants and manuscripts. |
| Collaborator Contribution | The CHRF team has provided expertise in field epidemiology, data analysis, samples, metadata and contributions to writing of reports, grants and manuscripts. |
| Impact | Outputs include 4 grant submissions, reporting, and knowledge exchange in Bangladesh, UK and USA. |
| Start Year | 2019 |
| Description | QIB-Utrech University (Dallman) |
| Organisation | Utrecht University |
| Country | Netherlands |
| Sector | Academic/University |
| PI Contribution | This partnership has resulted in three master's student projects at Utrecht University contributing to data analysis and benefiting from training of this partnering award in the area of bioinformatics, visualisation, Campylobacter epidemiology |
| Collaborator Contribution | Tim Dallman (Collaborator) has substantially contributed by training three students on the advanced metagenomic pipelines and analysis for pathogen detection and characterisation as part of the partnering award. Tim and the students have collated data, analysed and submitted reports. This has advanced the understanding of how metagenomic methods can be utilised for pathogen detection as well as compared software for taxonomic classification to identify limitations between sequencing data and biological probability. Data has been presented at seminars in Utrecht University and to the international partnering team. |
| Impact | To date there have been multiple outputs as a result of this collaboration. The interdisciplinary team consisting of bioinformatician, statistician, microbiologist, molecular biologist and epidemiologist inform fundamental biology of the pathogens of interest, computational sciences in pipelines and methods and applied sciences. |
| Start Year | 2023 |
| Description | Poster talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Other audiences |
| Results and Impact | This engagement was at the Microbiology Society Annual meeting where a poster on the characterisation of Campylobacter, the most prevalent foodborne bacterial pathogen in the UK, using metagenomic approaches. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Seminar presentation |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Third sector organisations |
| Results and Impact | The hybrid Seminar event, hosted by George Mason University Science and Technology Campus included approx 55 participants across higher education staff from senior management, academics, post graduate and undergraduate students, post doctoral staff and researchers. The topic of discussion was the application of metagenomics in understanding complex transmission dynamics of zoonotic pathogens. This was followed by round table discussions with students and early career researchers. |
| Year(s) Of Engagement Activity | 2024 |
| Description | UKHSA-QIB "Afternoon of Campy" Seminar Talk |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | The day long seminar and facility visit was attended by QIB researchers and UKHSA staff. I presented on Campylobacter trends and characterisation methodology research as well as conducted meetings with gastroenterics reference laboratory staff at UKHSA. |
| Year(s) Of Engagement Activity | 2024 |