Dr Mohamed Elhadidy has been visiting the lab this month from Mansoura University in Egypt. Mohamed is an Associate Professor and in addition to enjoying the glorious summer weather in Bath, has been learning about our sequencing and analysis techniques with a view to building a relationship for collaboration. Everyone in the lab is looking forwards to working together in the future.
Jess, Mohamed and Ben
Our first paper has been published as part of what we hope will continue to be a fruitful collaboration with researchers at Chiang Mai University in Thailand. The manuscript focuses on identification of Salmonella Weltevrenden outbreak strains in the pork production chain in Chiang Mai. This Salmonella serovar was the dominant serovar found in the regions pork production 15 years ago, but has now been almost completely replaced by other, multi-drug resistant serovars. The Weltevrenden serovar rarely carries antimicrobial resistance genes, however the isolates we do find remaining in the region have began to acquire resistant genotypes. You can read the paper here.
We are glad to welcome Sylwia Banaszkiewicz to the lab, who is visiting as part of her PhD studies with Jacek Bania at the Faculty of Veterinary Medicine, Wrocław University of Environmental and Life Sciences in Poland. Sylwia will stay for 7 weeks, working on Staphylococcus pathogenicity island genomics.
Curry night in the Eastern Eye: Ben, Ed, Sion, Evangelos, Conrad, Jess, Sylwia & Sam
Sam, Ben and Evangelos enjoyed a productive collaboration meeting with Prof. David Kelly and Aidan Taylor at the University of Sheffield to discuss various aspects of Campylobacter genomics / biochemistry. Guillaume was also able to join us from Australia via Skype before he went to bed! Thanks again to David and Aidan for being excellent hosts and we have some exciting projects ahead.
After 6 years, 36 papers (and counting…) and 1 book Guillaume is leaving us for a new adventure in Australia. Everyone in the lab wishes him well in his new position in the Systems Genomics lab at the Baker Heart & Diabetes Institute.
Thanks to everyone for coming out to wish Guillaume well: Jean, Leo, Jess, Ben, Sam, Sion, Ed, Lyndsay, Nicola, Kay and especially Josie & Matt for coming all the way from Swansea.
Sheppard Lab was well represented at the recent Microbiology Society meeting in Birmingham with Ben, Evangelos and Jess all presenting work in the Bacterial zoonoses: ecology, epidemiology and evolution session chaired by Sam.
Ben Pascoe: Genetic bottlenecks in the evolution of an agriculture-associated disease causing clade of Streptococcus suis in SE Asia.
Jessica Calland: A microevolutionary approach using whole genome sequences to estimate the molecular clock in Campylobacter: a rapidly evolving zoonotic pathogen under purifying selection
Evangelos Mourkas: Host adaptation of Campylobacter jejuni in cattle
Yesterday, a fascinating lecture was given at the Bath Royal Literary and Scientific Institution (BRLSI) by Prof Mark Pagel FRS entitled: ‘The Evolution of Language – Darwin would approve’.
Prof Pagel contrasted animal communication with human language and how speech has evolved and adapted much like biological species. Bringing together concepts of hominid evolution and contemporary evidence Prof Pagel described how language led to the dominance of modern humans over our close ancestors the Neanderthals, the genetic traits that exist because of language, and the future for the many languages that are still spoken.
On 14th-16th December 2017, Prof. Sam Sheppard and Dr. Sion Bayliss from the Sheppard Lab (University of Bath) presented the MRC CLIMB project at the SMBE satellite meeting – “Evolution of microbes in natural and experimental populations”. The meeting was hosted by Dr. Siddartha Satapathy and Prof. Suvendra Ray (Tezpur University, Assam, India) in Kaziranga National Park, Assam, India.
During the MRC CLIMB session, Sam Sheppard and Sion Bayliss introduced the CLIMB project, described the infrastructure and detailed the VM provisioning model. Sion Bayliss gave an introduction to methodologies used in the analysis of whole genome sequence data for microbial genomics. Dr. Harry Thorpe (University of Bath) provided a video walk-through of a data analysis project, from raw data to phylogenetic tree, by way of a user testimonial for CLIMB.
Finally, a limited-over cricket game between India and the Rest of the World unsurprisingly resulted in a smashing win from our Indian hosts (by 6 wickets)!
Upcoming meeting about microbial evolution held next December 2017 in the Kaziranga National Park, Assam, India. For more information, click on the image below:
Ben Pascoe, Sion Bayliss and Radoslaw Poplawski have returned from a successful MRC CLIMB workshop in Vietnam. The two-day workshop introduced attendees to CLIMB and working with their own virtual machine. Participants used EDGE to assemble bacterial genomes, asses the quality of sequence reads and assemblies, identify contamination, define isolate phylogeny compared to selected reference genomes and identify common virulence and antimicrobial resistance genes. Many thanks to our hosts Guy Thwaits, Stephen Baker, Phil Ashton and Cate Anscome for inviting us to OUCRU and we hope to visit again soon.
The Sheppard Lab 
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