Research Fellow | Milner Genomics Centre Manager
BSc (Hertfordshire, 2004)
DPhil (Sussex, 2008)
Research Fellow | Lecturer in Pathogen Genomics June 2016 – present
Using traditional microbiology techniques allied with modern microbial genomics, bioinformatics and a global network of collaborators I manage an active research portfolio, including research into Campylobacter global epidemiology, emergence of multi-drug resistant Campylobacter coli, Campylobacter ecology and evolution and Genome-wide identification of transmission and virulence traits. I am a research leader with proven leadership skills and the ability to design administer and articulate a clear research vision and strategy for effective delivery of successful projects. I have built a global network of collaborators which are vital to the success (or otherwise) of my chosen research topics.
I have setup and managed NGS sequencing facilities at Swansea University and the University of Bath. We sequenced over 4,000 microbial genomes in 3 years in Swansea with an annual turnover of ~£80,000pa. Since our move to Bath in May 2016 we have already sequenced over 6,000 microbial genomes, generated over £300,000 in income and expanded our repertoire to include low-complexity meta-genomic samples. I have helped foster and develop internal or external networks of benefit to the University. Our sequencing facility continues to provide an excellent opportunity for us to collaborate extensively and augment our research with a global perspective.
I have experience of leading research collaborations with international partners. I have led and supported collaborative efforts in different countries to expand our network of collaborators and augment our collections of pathogenic bacteria isolates and genomes. Supported by funding from British Council, the Newton Fund and MRC CLIMB I have led our research activity in Thailand (Chiang Mai University and Chulalongkorn University), Vietnam (the Oxford University Clinical Research Unit and the Biotechnology Centre in Ho Chi Minh), the Gambia (the MRC Unit @LSHTM), and Peru among others.
Finally, I have a track record of successful supervision of postdoctoral research staff and/or postgraduate students. I have supervised technical research staff, visiting researchers and undergraduate/ postgraduate students since 2012
I’m part of the MRC CLIMB consortium that provides high-performance computing infrastructure to UK microbiologists (2015 – present), which has included organizing workshops in Brazil, the Gambia, Vietnam and the UK.
Campylobacter global epidemiology
- Driven by collaborative projects in S. America, North Africa and SE Asia – where Campylobacter infection has serious implications for child health and malnutrition.
- Several smaller, individual collaborative projects in the Gambia, Burkina Faso, Ghana, Benin, Thailand, Peru, Vietnam, Egypt, China, USA, France and India.
- Honorary Research Fellow in the School of Allied Medical Studies (2016-present) and School of Veterinary Sciences (2020-present) at Chiang Mai University in Thailand.
- MRC grant awarded (Co-I) in collaboration with researchers from the MRC Unit in the Gambia, Burkina Faso and Ghana.
- UK lead on awarded NIH R01 grant led by Margaret Kosek (University of Virginia, USA).
- Pascoe B, Schiaffino F, […], Kosek M & Sheppard SK. (2020) Genomic epidemiology of Campylobacter jejuni associated with asymptomatic pediatric infection in the Peruvian Amazon. PloS NTD 14 (8) e0008533
- Dunn, S, […], Pascoe, B, Sheppard, SK, Manning, G & McNally, A (2018) Genomic Epidemiology of clinical Campylobacter spp. at a single health trust site. Microbial Genomics 4; doi: 10.1099/mgen.0.000227
- Florez-Cuadrado, D, […]., Pascoe, B, Sáez-Llorente, JL, Orozco, GL, Domínguez, L & Sheppard, SK (2017) Genome comparison of erythromycin resistant Campylobacter from turkey identifies hosts and pathways for horizontal spread of erm(B) genes Frontiers in Microbiology 8: 2240; DOI: 10.3389/fmicb.2017.02240
- Thépault, A., Méric, G., Rivoal, K., Pascoe, B, […], Chemaly, M., Sheppard, SK. (2017) Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni AEM 83 (7): e03085-16
Emergence of multi-drug resistant Campylobacter coli
- Ongoing study with collaborators in Peru who are part of the MAL-ED programme: a global network of researchers investigating child health, including gastrointestinal disease and malnutrition at several establish sites in LMICs.
- Hosted visiting researchers from India (2020), Peru (2019), Thailand (2016), Egypt (2018).
- Chaired session at the bi-annual CHRO conference on emerging trends in antimicrobial resistance.
- Conference presentations (poster / talk) at ASM Microbe, San Francisco (2019), Microbiology Society meeting, Belfast (2019), IAFP, Salt Lake City (2018), ECCMID-2019, Amsterdam, SMBE 2018, Leipzig, SMBE workshop 2018, Kyoto.
- Panel discussion @ IAFP2018, Salt Lake City: Invited to sit on a panel of experts to discuss future directions in Campylobacter source attribution research.
Publications in preparation with collaborators in Egypt and Vietnam.
- Jehanne Q, Pascoe B, Bénéjat L, Ducournau A, Buissonnière A, Mourkas E, Mégraud F, Bessède E, Sheppard SK & Lehours P. (2020) Determination of Campylobacter coli host-segregating SNPs and their use for source attribution of clinical isolates. AEM doi: 10.1128/AEM.01787-20
- Mourkas E*, Florez-Cuadrado D*, Pascoe B, […], Sheppard SK (2019) Gene pool transmission of multidrug resistance among Campylobacter from livestock, sewage and human disease in Environmental Microbiology doi:10.1111/1462-2920.14760
Campylobacter ecology and evolution
My work also focusses on the underlying genetics of the organism and how differences in ecology can affect disease.
- Grant submitted to the NIH/NSF/UKRI (US: UK) joint call on the Ecology and evolution of infectious diseases (Co-I, UK-lead) with collaborators from the US into the genetics of Campylobacter from wild bird species.
- Calland JK, Pascoe B, […], Falush D & Sheppard SK (2020) Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages. bioRxiv doi: 10.1101/2020.12.02.407999
- Mouftah S*, Cobo-Diaz JF*, […], Pascoe B, Sheppard SK & Elhadidy M. (2020) Stress-resistance is associated with multi‐host transmission and enhanced biofilm formation among hyper-aerotolerant generalist Campylobacter jejuni. Food Microbiology (In press)
- Mourkas E, Taylor AJ, Méric G, Bayliss SC, Pascoe B, […], Sheppard SK* (2020) Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni. PNAS 117 (20) 11018-11028; doi: 10.1073/pnas.1917168117
- Pascoe, B.; Méric, G., Yahara K., […], Didelot, X., Parker, CT. & Sheppard, SK. (2017) Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations Molecular Ecology 26 (17): 4497-4508
Identifying evidence of human adaptation in bacterial pathogens
Projects in Campylobacter and the human host restricted pathogen, Helicobacter pylori, where a rapidly evolving genome with high levels of horizontal gene transfer allows the reconstruction of recent human migrations to the extent that genetic admixture among the bacteria reflects interactions among human populations. Recent publication and current projects investigating evidence of human ancestry on H. pylori genomes from South America (with collaborators from across South America).
- Muñoz-Ramirez ZY, Pascoe B, […], Sheppard SK, Thorell K* & Torres J* (2020) A five-hundred year tale of co-evolution, adaptation and virulence: Helicobacter pylori in the Americas. The ISME Jornal (In press) doi: 10.1038/s41396-020-00758-0
- Méric, G., McNally, A., Pessia, A., Mourkas, E., Pascoe, B., […], & Sheppard, SK. (2018) Convergent amino acid signatures in paraphyletic Campylobacter jejuni sub-populations suggest human niche tropism Genome Biology & Evolution 10 (3): 763-774
- Dearlove B, Cody A, Pascoe B, Méric G, Wilson D, Sheppard SK (2016) Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections. The ISME Journal 10 (3): 721-9
Genome-wide identification of transmission and virulence traits
Multiple projects in several species: Campylobacter, Helicobacter pylorii, Listeria monocytogens, Ecoli and Salmonella.
- Méric, G.*, Mageiros, M.*, Pensar, J., Laabei, M., Yahara, K., Pascoe, B., […], Corander, J. & Sheppard, SK. (2018) A pathogen in plain sight: disease-causing genotypes of the commensal skin bacterium Staphylococcus epidermidis. Nature Communications 9:5034; doi: 10.1038/s41467-018-07368-7
- Berthenet, E., Yahara, K., Thorell, K., Pascoe, B., […] Falush, D. & Sheppard, SK. (2018) A GWAS on Helicobacter pylori strains points to genetic variants associated with gastric cancer risk. BMC Biology 16:84
- Yahara, K., Méric, G., Taylor, AJ., de Vries, SPW., Murray, S., Pascoe, B., […] Kelly, DJ., Sheppard, SK. (2016) Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork. Environmental Microbiology 19(1):361-380; doi:10.1111/1462-2920.13628 [PeerJ preprint: doi.org/10.7287]
- Pascoe B, Méric G, Murray S, Yahara K, […], Lappin-Scott HM, Asakura H, Sheppard SK (2015) Enhanced biofilm formation and multi-host transmission evolve from divergent genetic backgrounds in Campylobacter jejuni. Environmental Microbiology 17:(11) 4779–4789