Time: 16:00 22 April 2020 (UTC)
Zoom link: https://cdc.zoomgov.com/j/1613270485
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Video: https://www.youtube.com/watch?v=hQY1t4CcaN8
In October 2010, cholera appeared in Haiti for the first time in over 150 years, and after the initial epidemic waves, cholera may now be endemic in Haiti. Spread of cholera in the midst of an epidemic is largely driven by direct transmission from person to person, although it is well recognized that V. cholerae is also capable of growth and long-term survival in aquatic ecosystems. While prior studies have shown that aquatic reservoirs are important in persistence of the disease in the Indian subcontinent, an epidemiological view postulating that locally evolving environmental V. cholerae contribute to outbreaks outside Asia remains debated. We investigated the phylogeography of both clinical and aquatic toxigenic V. cholerae O1 isolates and show robust evidence of the establishment of aquatic reservoir, as well as ongoing evolution of V. cholerae isolates from aquatic sites. Novel environmental lineages emerged from sequential population bottlenecks, carrying mutation potentially involved in adaptation to the aquatic ecosystem. Based on such empirical data, we developed a mixed transmission dynamic model of V. cholerae, where aquatic reservoirs actively contribute to genetic diversification and epidemic emergence, which underscores the complexity of transmission pathways in epidemic and endemic settings, and the need for long-term investments in cholera control at both human and environmental levels. Then in 2015, Inaba became the dominant serotype circulating in Haiti, surpassing the number of cases caused from original Ogawa serotype. With the data our group generated, we wanted to assess the evolutionary dynamics that are occurring in the V. cholerae genome that caused the switch in serotype. Our results propose that the V. cholerae strains circulating in Haiti have evolved from the single-source introduction of the Ogawa serotype to the new, unintroduced Inaba serotype. The circulation of different serotypes is indicative of a separate introduction in many parts of the world, but our results promote that the Inaba serotype in Haiti is the outcome of the initial Ogawa serotype evolving to Inaba. These conclusions suggest that Haiti is becoming a source for toxigenic V. cholerae in the Caribbean and may lead to cholera outbreaks throughout the region. The single-source introduction of toxigenic V. cholerae in Haiti, one of the largest outbreaks occurring this century with 812,586 suspected cases and 9,606 deaths reported through July 2018, provides a unique opportunity to evaluate the role of aquatic reservoirs, the switch from Ogawa to Inaba, and to assess bacterial transmission dynamics of the environmental and serotype factors driving V. cholerae to persist in Haiti.
I am a PhD Candidate studying the phylodynamics of Vibrio cholerae. I received by bachelor’s degree in Biology from Florida State University. My current projects include studying the evolution of V. cholerae in Haiti and the Democratic Republic of Congo. I am interested in studying computational techniques and methods to help conduct phylodynamic analysis on whole genomes of infectious disease pathogens. In my free time I enjoy your typical nerd activities, such as discussing Game of Thrones at great lengths and playing video games too late into the night (only on the weekends of course). I also enjoy practicing yoga and being anywhere on the water in Florida. Also, I love my cats, Arya and Hamilton.
Github: https://github.com/taylorpaisie
Twitter: https://twitter.com/tpaisie
Linkedin: https://www.linkedin.com/in/taylorpaisie/
Video: https://www.youtube.com/watch?v=hQY1t4CcaN8
Sanitation practices are essential to reduce the risk of Listeria monocytogenes (Lm) contaminations along the food chain, yet the outstanding tolerance of some strains to biocides challenges food safety. This study aims to apply hybrid tools, implementing a combination of continuous phenotypes, statistical and phylogenomic methods, to characterize the Lm genomic determinants increasing tolerance to biocides used in the food industry at the pangenomic scale. A genome-wide association study (GWAS) was performed on 188 strains isolated from ready-to-eat foods, wild and farm animals/environments. These strains were accurately selected from the wide collection of the research project LISTADAPT to encompass the genomic diversity of Lm clonal complexes (CC) observed in Europe. Generalized linear models with advanced correction for population structure considering homologous recombination events from the coregenome were used to test for associations between pangenomic orthologous genes (POG) and minimum inhibitory concentrations (MIC) of eight biocides. Strong causal associations (lrt-pvalue<4.69E-05 – Bonferroni correction at 5%) for benzalkonium chloride (BC) were identified in clusters of POGs depicting mobile genomic elements (MGE) like the Tn6188 transposon and pLMST6 plasmid. Increased tolerance to BC was previously described in Lm strains harbouring these MGEs. Visually inflated quantile-quantile plots from GWAS pointed to a cluster of 24 POGs, part of large plasmids known to be involved in Lm survival to food-processing stress, also associated to BC-tolerance at less stringent significance levels (lrt-pvalue<1.61E-04). Below this genome-wide significance level, the pLMST6 was also associated with didecyldimethylammonium chloride (DDAC), a quaternary ammonium compound (QAC) with bactericidal action similar to BC. As expected, no POGs were associated with chemically reactive biocides (e.g. hydrogen peroxide) and biocides that cause cytoplasmic proteins denaturation and cell contents coagulation (e.g. alcohol). Accessory genomic determinants for increased MICs to BC and DDAC mainly characterized food strains from phylogenetically distant CCs collected across Europe, suggesting that these MGEs represent pleiotropic key-markers promoting and spreading QACs tolerance in Lm populations. Screening these MGEs could assist in improving decision-making for monitoring biocide-tolerant genotypes throughout the food chain.
During my Master degree in Food Science and Technology (2011-2014), I specialised in molecular typing of bacterial pathogens applied to Food Safety at the Department of Agriculture and Food Science of the University of Bologna (Italy). In my PhD (2014-2018), I trained in microbial genomics and bioinformatics, which became the main tools of my research activities. I, therefore, carried out international research projects within the objectives of the European project COMPARE (WP4 and 7) and in collaboration with the research team supported by the INNUENDO project under the supervision of Prof. Mirko Rossi. My thesis focused on the surveillance and persistence investigations of foodborne pathogens (e.g. Listeria monocytogenes and Salmonella enterica) along the food chain, in particular Italian swine chain and rabbit meat cutting plant, combining phenotypic and genomics methods. During my postdoctoral fellowships (2018-present) at the French agency for food safety (Maisons-Alfort lab, ANSES), I continued to apply advanced microbial genomic methods for (i) assessing the persistence and cold adaption of L. monocytogenes from ready-to-eat industries (ii) designing genome databases for the source attribution of monophasic S. Typhimurium (iii) implementing logistic regression models for source attribution based on accessory genes, and (iv) rapidly detecting outbreak-related foodborne pathogens using non-parametric tests. I currently manage collaborative research projects within the WP4 of the One Health EJP LISTADAPT focusing on the discovery of genomic features associated with antimicrobial resistance of L. monocytogenes combining phenotypic traits, phylogenomic and pangenome-wide association study. https://orcid.org/0000-0002-7865-961X
Video: https://www.youtube.com/watch?v=kQNYFcaxxao
Neisseria gonorrhoeae is a major public health threat due to increasing incidence and antimicrobial resistance. Mathematical modelling and genomic analyses are powerful methods for investigating transmission dynamics of N. gonorrhoeae; however, both approaches often make the implicit assumption that N. gonorrhoeae isolates at different anatomical sites within the same patient are the same strain, which may confound accurate assessment of evolution and transmission dynamics. This study examined a collection of N. gonorrhoeae isolates from 2011-2019 from patients that had N. gonorrhoeae detected at multiple anatomical sites. We used whole genome sequencing (WGS) and a variety of bioinformatic approaches (e.g. differing reference genomes and filtering of SNPs in repeats, mobile genetic elements and recombinant regions) to determine the within-host genetic diversity. Thirty-seven patients had cultured N. gonorrhoeae from two or more anatomical sites (urogenital, anorectal or oropharyngeal), with a final dataset of 105 isolates. In 35/37 (95%) patients, infections were the same strain, with identical MLST and NG-MAST profiles. Pairwise comparisons of the core-genome SNP alignment indicated that the median intra-patient SNP distance was zero SNPs, with a range of 0-18. Additionally, there were four groups of patient isolates that clustered together with identical MLST and a maximum pairwise SNP distances ≤18 SNPs, which was within the same range as the maximum within-host diversity, indicating the likelihood that patients within each cluster were involved in the same transmission network. Our data demonstrates that in most cases, the same strain of N. gonorrhoeae causes infection at multiple sites, however WGS data alone cannot differentiate between the same infecting strain or reinfections from the same transmission network.
Dr Melinda Ashcroft was awarded her PhD from the University of Queensland, Australia in early 2019, investigating the roles of mobile genetic elements, antimicrobial resistance and DNA methylation in the evolution of Escherichia coli lineages. Melinda is now a Postdoctoral Research Fellow in Microbial Bioinformatics at the Peter Doherty Institute for Infection and Immunity at the University of Melbourne, Australia. Her work focuses on genomic epidemiology, transmission, evolution and antimicrobial resistance of pathogenic Neisseria spp. Melinda is also passionate about science communication and is a current Australian Society of Microbiology Communications Ambassador.
Video: https://youtu.be/dLAgLgY6teg