Links to recorded talk videos available
on the dedicated YouTube channel (see individual links below)
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Subtitles are available (English for all for talks and Arabic for some talks)
To change the language from English to Arabic where available, click on the Settings button ⚙ > Subtitles/CC > Arabic. Where no curated Arabic subtitles have been produced by our team, you can still access automatic translation provided by YouTube by clicking on the Settings button ⚙ > Subtitles/CC > Auto-translate > Arabic.
Please post questions you would like to ask to the speakers
in the comments section of the YouTube video, or in this form:
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Speakers will answer your questions during the live session on 18th October 15:00 GMT+3
Presentations on Zoom during live session on 17th October 15:00 GMT+3
Khaled Almoayed
Epidemiology of Cholera / Cholera outbreaks response and control
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Nick Thomson
What is a genome?
Alyce Taylor-Brown
Introduction to Comparative Genomics
In this module I will take you through the process of what to do once you have sequenced a bacterial genome (or several). We touch on why you might carry out whole genome sequencing in the first place, and the different approaches you could take to analyse your data depending on your research question. This is not a protocol, but rather an overview of the steps, some commonly used tools, and an introduction to the concepts (genomic structure, assembly, read-mapping, pangenome) that will arise throughout the symposium.
Link to presentation on YouTube: https://youtu.be/eQ9qghLu9sY
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Florent Lassalle
Genomic epidemiology of cholera: [1] Background & methodology
Cholera is caused by the bacteria belonging to the species Vibrio cholerae, an organism native of brackish water environments such as river estuaries. This bacterial species is genomically diverse; however, the pathogen causing cholera is not. Indeed, only strains that carry the CTX toxin genes can cause genuine cholera i.e. the acute watery diarrhoea disease. Toxigenic (CTX+) strains are most often found within those that carry the LPS O-antigen of the serogroup O1. More specifically, the large majority of recent cholera outbreaks were caused by a single lineage that spread worldwide, called 7th pandemic El-Tor (7PET), which has very limited genomic diversity. This clonal pathogen has shown its very high capacity to spread from human to human and to cause epidemics, as well as being transmitted across large geographical distances; it is indeed the single cause of the 7th cholera pandemic, started in 1961. However, other strains from this bacterial species can cause disease, including intestinal disease, even though not genuine cholera. These strains belong to diverse lineages and are often found to be endemic strains living in the environment, from which food or drinking water can sporadically get contaminated and lead to infection, but this rarely leads to an outbreak.
Epidemiological surveillance must therefore account for both these aspects of V. cholerae-associated disease: the epidemic pathogen of lineage 7PET, causing cholera; and the endemic strains belonging to other lineages, causing sporadic disease. Culture-based detection of V. cholerae cannot differentiate between those two categories, and thus may fail to accurately document the start of an outbreak of the epidemic strain. Instead, sequencing the genome of V. cholerae bacterial isolates allows unambiguous typing. In addition, this approach allows to predict the phenotypic properties of the isolate (virulence, antibiotic resistance …) and to track its spread through the phylogenetic reconstruction of clonal relationships of various isolates. In this talk, we describe the background and methodologies for genomic epidemiology of V. cholerae, with a specific approach for each of these two types of V. cholerae.
Link to presentation on YouTube: https://youtu.be/Q66P8IWxMJE
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Francois-Xavier Weill
Genomics for tracing the cholera epidemic in Africa
Link to presentation on YouTube: https://youtu.be/O7Nmoety2BY
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Matt Dorman
Cholera in Latin America
Link to presentation on YouTube: https://youtu.be/Pp0Pkb8tkMo
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Florent Lassalle
Genomic epidemiology of cholera: [2] Study of the cholera outbreak in Yemen
The humanitarian crisis in Yemen led in 2016 to the biggest cholera outbreak documented in modern history, with more than 2.5 million suspected cases to date. In late 2018, epidemiological surveillance showed that V. cholerae isolated from cholera patients had turned multi-drug resistant (MDR). We generated genomes from 260 isolates sampled in Yemen between 2018 and 2019 to identify a possible shift in circulating genotypes. 84% of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sublineage T13 – same as in 2016 and 2017 – while the remaining 16% of strains were non-toxigenic and belonged to divergent lineages, likely reflecting sporadic gut colonisation by endemic strains. Phylogenomic analysis reveals a succession of T13 clones, with 2019 dominated by a clone that carried an IncC-type plasmid harbouring an MDR pseudo-compound transposon (PCT). Identical copies of these mobile elements were found independently in several unrelated lineages, suggesting exchange and recombination between endemic and epidemic strains. Treatment of severe cholera patients with macrolides in Yemen from 2016 to early 2019 coincides with the emergence of the plasmid-carrying T13 clone. This genotype is the first where an SXT ICE and an IncC plasmid are shown to stably coinhabit and its success durably reduced options for epidemic cholera case management. We advocate a heightened genomic epidemiology surveillance of cholera to help prevent further spread of this highly-transmissible, MDR clone.
Link to presentation on YouTube: https://youtu.be/3iQBiBOV3TE
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Avril Coghlan
Genomic epidemiology surveillance of cholera with Pathogen.watch
Since the first complete Vibrio cholerae was fully sequenced in 2000, advances in whole-genome sequencing technologies have led to sequencing of the genomes of thousands of V. cholerae isolates, in particular from the pathogenic 7PET lineage. We explain here how the Pathogen.watch website can be used to easily analyse this V. cholerae genomic data, as well as new genome sequences, in order to carry out analyses in order to understand the relationships between isolates, identify virulence genes and predict antimicrobial resistance.
Link to presentation on YouTube: https://youtu.be/ABk7eejX9lE