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Genomic population structures of microbial pathogens
Scientific discussion meeting organised by Professor Mark Achtman FRS, Professor Kathryn Holt and Professor David Aanensen.
The comparative genomics of microbial pathogens from all domains of life has become a big data problem. Databases already contain >200,000 assembled genomes from single species but adequate tools to reveal population structures are in their infancy. This meeting brought together world-class bioinformaticians with experts on bacterial and viral genomes to illustrate multiple approaches to solving this challenge.
A related journal issue has been published in Philosophical Transactions of the Royal Society B.
Attending the event
This meeting has taken place. You can watch the recording here.
Enquiries: contact the Scientific Programmes team
Organisers
Schedule
Chair
Dr Alison Mather, Quadram Institute Bioscience, UK
Dr Alison Mather, Quadram Institute Bioscience, UK
Alison Mather is a Group Leader and Head of the Microbes in the Food Chain programme at Quadram Institute Bioscience, and a Food Standards Agency Fellow. Her research interests are to understand the origins, evolution, epidemiology and transmission of bacteria, with a focus on antimicrobial resistant and zoonotic bacteria. Her group are expert in the development and application of bioinformatics and statistical techniques to investigate these questions, using short-read, long-read and metagenome sequencing.
| 12:50 - 13:00 |
Open
Professor Mark Achtman FRS, University of Warwick, UK
Professor Mark Achtman FRS, University of Warwick, UKSince 1965, Achtman has founded four highly distinct areas of bacterial genetics: 1) bacterial conjugation involving the Escherichia coli F sex factor (1965-78), 2) E. coli neonatal meningitis (1979-86), 3) epidemic cerebrospinal meningitis caused by Neisseria meningitis (1983-2000). Since 1998 he has dedicated himself to the population genetics and genomics of bacterial pathogens. In each area he made seminal discoveries, resulting in global recognition, and is one of the globally most prominent bacterial population geneticists. In recent years, he was one of three co-inventors of multilocus sequence typing and has been at the forefront of comparative population genomics. He elucidated the historical associations of Helicobacter pylori with ancient human migrations, ancient global routes of transmission of historical plague, and has introduced dramatic changes to the practice of epidemiological typing of Salmonella enterica. More recently, he has been responsible for developing EnteroBase which provides access to 100,000s of assembled genomes from a variety of genera containing bacterial pathogens. Honours: main prize of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie, 2004; foreign member of the Norwegian Academy of Sciences and Letters, 2014, Fellow of the Royal Society, 2015, and the Pettenkofer Prize, 2018. |
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| 13:00 - 13:30 |
EnteroBase: Hierarchical clustering of >600,000 bacterial genomes
The number of sets of genomic short read sequences in the public domain has exploded since 2012. EnteroBase (https://enterobase.warwick.ac.uk/) has assembled >600,000 draft genomes from short reads (from SRA or uploaded by users), assigned allelic designations to sequences from the core genome (cgMLST), and clustered the resulting sequence types at multiple levels (hierarchical clustering; HierCC (PMID: 33823553) for the genera Salmonella, Escherichia/Shigella, Streptococcus, Clostridioides, Vibrio and Yersinia (PMID: 31809257, 32726198, 33055096, 33614977). One HierCC level is a complete replacement for classical taxonomy or ANI because it automatically and reliably identifies species/sub-species. In several genera, two other HierCC levels correspond to ST Complexes and Super-Lineages, which are the predominant population structures in these genera. HierCC levels with even higher resolution are proving useful for tracking transmissions and single-source outbreaks of gastrointestinal disease. HierCC topologies are also consistent with trees based on the presence or absence of all genes in the pan-genome. These conclusions will be illustrated with specialised case studies.
Professor Mark Achtman FRS, University of Warwick, UK
Professor Mark Achtman FRS, University of Warwick, UKSince 1965, Achtman has founded four highly distinct areas of bacterial genetics: 1) bacterial conjugation involving the Escherichia coli F sex factor (1965-78), 2) E. coli neonatal meningitis (1979-86), 3) epidemic cerebrospinal meningitis caused by Neisseria meningitis (1983-2000). Since 1998 he has dedicated himself to the population genetics and genomics of bacterial pathogens. In each area he made seminal discoveries, resulting in global recognition, and is one of the globally most prominent bacterial population geneticists. In recent years, he was one of three co-inventors of multilocus sequence typing and has been at the forefront of comparative population genomics. He elucidated the historical associations of Helicobacter pylori with ancient human migrations, ancient global routes of transmission of historical plague, and has introduced dramatic changes to the practice of epidemiological typing of Salmonella enterica. More recently, he has been responsible for developing EnteroBase which provides access to 100,000s of assembled genomes from a variety of genera containing bacterial pathogens. Honours: main prize of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie, 2004; foreign member of the Norwegian Academy of Sciences and Letters, 2014, Fellow of the Royal Society, 2015, and the Pettenkofer Prize, 2018. |
| 13:30 - 14:00 |
Analysing bacterial population structure from millions of genomes
In less than a decade, bacterial population genomics has progressed from the effort of sequencing dozens to thousands of strains in a single study. There are now >250,000 genomes available even for a single bacterial species and the number of genomes is expected to continue to increase rapidly given the advances in sequencing technology and widespread genomic surveillance initiatives. The biological insights enabled by population genomics are particularly important in evolutionary epidemiology, as the genome sequences provide high-resolution data for the estimation of transmission and evolutionary dynamics, including the horizontal transfer of virulence and resistance elements. Professor Corander will discuss statistical and computational techniques that are amenable to rapidly analysing population structure in data consisting of millions of whole genomes. 
Professor Jukka Corander, University of Oslo and Wellcome Sanger Institute, Norway and UK
Professor Jukka Corander, University of Oslo and Wellcome Sanger Institute, Norway and UKJukka Corander is Professor at the Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Norway, and an Associate Faculty member at the Wellcome Sanger Institute, Cambridge, UK. He has won two ERC grants, an ERC StG (2009-2014) from the mathematics and statistics panel and an ERC AdG (2017-2022) from the infection and immunity panel. Jukka’s main research interests are microbial evolution and transmission modeling, statistical machine learning, population genomics and inference algorithms. The statistical methods introduced by his research group have led to numerous discoveries on the evolution, resistance, virulence and transmission of pathogenic bacteria and viruses. |
| 14:00 - 14:30 |
Discussion
Dr Francesc Coll, London School of Hygiene & Tropical Medicine, UK
Dr Francesc Coll, London School of Hygiene & Tropical Medicine, UKFrancesc is a computational biologist with expertise in bacterial genomics, antibiotic resistance, and clinical microbiology. He is currently an Assistant Professor at the London School of Hygiene & Tropical Medicine (LSHTM) supported by an ISSF Fellowship. His research projects focus on the applications of whole-genome sequencing as a research, surveillance, and diagnostic tool for bacterial infections. Francesc joined LSHTM in July 2016 as a Postdoctoral Fellow in Professor Sharon Peacock's lab funded by a Sir Henry Wellcome Postdoctoral Fellowship. Since then, he’s worked on the application of genomic surveillance to track the transmission of antibiotic-resistant nosocomial pathogens; and in the application of GWAS to identify the genetic mechanisms mediating antibiotic susceptibility, host adaptation and disease presentation in pathogenic bacteria. In October 2014, he completed his PhD at the School under the supervision of Professor Taane Clark, which focused on strain genotyping and drug resistance in Mycobacterium tuberculosis using whole genome sequencing.
Dr Alison Mather, Quadram Institute Bioscience, UK
Dr Alison Mather, Quadram Institute Bioscience, UKAlison Mather is a Group Leader and Head of the Microbes in the Food Chain programme at Quadram Institute Bioscience, and a Food Standards Agency Fellow. Her research interests are to understand the origins, evolution, epidemiology and transmission of bacteria, with a focus on antimicrobial resistant and zoonotic bacteria. Her group are expert in the development and application of bioinformatics and statistical techniques to investigate these questions, using short-read, long-read and metagenome sequencing.
Professor Jukka Corander, University of Oslo and Wellcome Sanger Institute, Norway and UK
Professor Jukka Corander, University of Oslo and Wellcome Sanger Institute, Norway and UKJukka Corander is Professor at the Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Norway, and an Associate Faculty member at the Wellcome Sanger Institute, Cambridge, UK. He has won two ERC grants, an ERC StG (2009-2014) from the mathematics and statistics panel and an ERC AdG (2017-2022) from the infection and immunity panel. Jukka’s main research interests are microbial evolution and transmission modeling, statistical machine learning, population genomics and inference algorithms. The statistical methods introduced by his research group have led to numerous discoveries on the evolution, resistance, virulence and transmission of pathogenic bacteria and viruses.
Professor Mark Achtman FRS, University of Warwick, UK
Professor Mark Achtman FRS, University of Warwick, UKSince 1965, Achtman has founded four highly distinct areas of bacterial genetics: 1) bacterial conjugation involving the Escherichia coli F sex factor (1965-78), 2) E. coli neonatal meningitis (1979-86), 3) epidemic cerebrospinal meningitis caused by Neisseria meningitis (1983-2000). Since 1998 he has dedicated himself to the population genetics and genomics of bacterial pathogens. In each area he made seminal discoveries, resulting in global recognition, and is one of the globally most prominent bacterial population geneticists. In recent years, he was one of three co-inventors of multilocus sequence typing and has been at the forefront of comparative population genomics. He elucidated the historical associations of Helicobacter pylori with ancient human migrations, ancient global routes of transmission of historical plague, and has introduced dramatic changes to the practice of epidemiological typing of Salmonella enterica. More recently, he has been responsible for developing EnteroBase which provides access to 100,000s of assembled genomes from a variety of genera containing bacterial pathogens. Honours: main prize of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie, 2004; foreign member of the Norwegian Academy of Sciences and Letters, 2014, Fellow of the Royal Society, 2015, and the Pettenkofer Prize, 2018. |
Chair
Dr Nicholas Croucher, Imperial College London, UK
Dr Nicholas Croucher, Imperial College London, UK
Nicholas Croucher is a Sir Henry Dale fellow and Senior Lecturer in Bacterial Genomics in the MRC Centre for Global Infectious Disease Analysis at Imperial College London. His current work uses molecular biology and mathematical modelling to study the genomic epidemiology and evolutionary biology of pneumococcal populations under selection by polysaccharide conjugate vaccination and antibiotic consumption. This is a continuation of work undertaken as a Post-doctoral Research Fellow at the Centre for Communicable Disease Dynamics at the Harvard School of Public Health, from where he moved after completing his PhD in the Pathogen Sequencing Unit of the Wellcome Sanger Institute.
| 15:00 - 15:30 |
Beyond the S. aureus comet: what tree shapes occur in large bacterial genomic data?
When methicillin-resistant Staphylococcus aureus (MRSA) arose and disseminated widely, some phylogenetic trees of MRSA-containing types of staphylococcus aureus had a distinctive 'comet' shape, with a 'comet head' of recently-adapted resistant isolates in the context of a 'comet tail' that was predominantly drug sensitive. Placing an isolate in the context of such a 'comet' helped public health laboratories interpret local data within the broader setting of S aureus evolution. In this work Professor Colijn and her colleagues ask what other tree shapes, analogous to the MRSA comet, are present in bacterial WGS datasets. They extract trees from large bacterial genomic datasets, visualise them as images, and cluster the images. They find nine major groups of tree images, including the 'comet', star-like phylogenies, barbell' phylogenies and other shapes, and comment on the evolutionary and epidemiological stories these shapes might illustrate. 
Professor Caroline Colijn, Simon Fraser University, Canada
Professor Caroline Colijn, Simon Fraser University, CanadaDr Caroline Colijn works at the interface of mathematics, evolution, infection and public health, and leads the MAGPIE research group. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She has broad interests in applications of mathematics to questions in evolution and public health. |
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| 15:30 - 16:00 |
Genome-scale metabolic network reconstructions of hundreds of diverse Escherichia coli strains reveal strain-specific adaptations and evolutionary trajectories
Bottom-up approaches to systems biology rely on constructing a mechanistic basis for the biochemical and genetic processes that underlie cellular functions. Genome-scale network reconstructions of metabolism are built from all known metabolic reactions and metabolic genes in a target organism. A network reconstruction can be converted into a mathematical format and thus lend itself to mathematical analysis. Genome-scale models (GEMs) of enable a systems approach to characterise the pan and core metabolic capabilities of the E coli species. The models have been used to systematically analyze growth capabilities in more than 650 different growth-supporting environments as well as to predict strain-specific auxotrophies. In this work, genome-scale models were constructed for more than 300 representative strains of E coli across all 295 HC1100 levels. The models were used to study E coli metabolic diversity and speciation on a large scale. The results show that unique strain-specific metabolic capabilities correspond to pathotypes and environmental niches. Genome-scale analysis of multiple strains of a species can thus be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment. 
Dr Jonathan Monk, University of California San Diego, USA
Dr Jonathan Monk, University of California San Diego, USAJonathan received his PhD in Chemical Engineering from UC San Diego studying genome-scale network reconstructions of metabolism for microbial pathogens. He pioneered the use of these tools to study the diversity of metabolic capabilities in different strains of a species and has since applied them to several pathogenic organisms including E. coli, K. pneumonia, S. aureus, A. baumannii and C. difficile. He now works as an academic data scientist applying big-data analysis techniques to study the genetics and evolution of antimicrobial resistance and virulence in bacteria. |
| 16:00 - 16:30 |
New methods with high accuracy and scalability for large-scale phylogenetic estimation
The estimation of phylogenetic trees for individual genes or multi-locus datasets is a basic part of considerable biological research. In order to enable large trees to be computed, Disjoint Tree Mergers (DTMs) have been developed; these methods operate by dividing the input sequence dataset into disjoint sets, constructing trees on each subset, and then combining the subset trees (using auxiliary information) into a tree on the full dataset. DTMs have been used to advantage for multi-locus species tree estimation, enabling highly accurate species trees at reduced computational effort, compared to leading species tree estimation methods. The talk will show that DTMs can be used to improve the accuracy and speed of methods for species tree estimation methods (eg, ASTRAL) as well as for gene tree estimation (eg, RAxML), thus enabling these methods to run efficiently on much larger datasets than currently possible, and without the need for high performing computing platforms or massive parallelism. These methods are available in open source form on github. 
Professor Tandy Warnow, University of Illinois, USA
Professor Tandy Warnow, University of Illinois, USATandy Warnow is the Grainger Distinguished Chair in Engineering, and Professor and Associate Head of Computer Science at the University of Illinois at Urbana-Champaign. Tandy received her PhD in Mathematics at University of California, Berkeley under the direction of Gene Lawler, and did postdoctoral training with Simon Tavaré and Michael Waterman at USC. Her research combines computer science, statistics, and discrete mathematics, focusing on developing improved models and algorithms for reconstructing complex and large-scale evolutionary histories in biology and historical linguistics. Her awards include the NSF Young Investigator Award (1994), the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2003), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the International Society for Computational Biology (ISCB) in 2017. |
| 16:30 - 17:00 |
Discussion
Dr Nicholas Croucher, Imperial College London, UK
Dr Nicholas Croucher, Imperial College London, UKNicholas Croucher is a Sir Henry Dale fellow and Senior Lecturer in Bacterial Genomics in the MRC Centre for Global Infectious Disease Analysis at Imperial College London. His current work uses molecular biology and mathematical modelling to study the genomic epidemiology and evolutionary biology of pneumococcal populations under selection by polysaccharide conjugate vaccination and antibiotic consumption. This is a continuation of work undertaken as a Post-doctoral Research Fellow at the Centre for Communicable Disease Dynamics at the Harvard School of Public Health, from where he moved after completing his PhD in the Pathogen Sequencing Unit of the Wellcome Sanger Institute. 
Dr John Lees, Imperial College London, UK
Dr John Lees, Imperial College London, UKJohn Lees is a Research Fellow at Imperial College London (at the MRC Centre for Global Disease Analysis), where he is part of the Bacterial Evolutionary Epidemiology Group. His research focuses on computational analyses of large microbial genome datasets, both to increase our understanding of infectious diseases, and to develop the efficient and easy-to-use methods required to perform these analyses. Much of his research has focused on Streptococcus pneumoniae, due to its importance as a global pathogen and the recent availability of large genomic datasets. He is particularly passionate about developing open source tools in bioinformatics, and widening access to genomic analysis of publicly funded data. 
Dr Cheryl P Andam, University at Albany, State University of New York, USA
Dr Cheryl P Andam, University at Albany, State University of New York, USADr Cheryl Andam is Assistant Professor at the University at Albany, State University of New York, USA. Research in her lab focuses on microbial population genomics, evolution and horizontal gene transfer as they apply to infectious diseases and public health. She completed her PhD Microbiology degree from the University of Connecticut. She was a Postdoctoral Fellow at Cornell University and the Harvard School of Public Health. Her research is supported by the National Science Foundation CAREER and National Institutes of Health MIRA awards.
Professor Caroline Colijn, Simon Fraser University, Canada
Professor Caroline Colijn, Simon Fraser University, CanadaDr Caroline Colijn works at the interface of mathematics, evolution, infection and public health, and leads the MAGPIE research group. She joined SFU's Mathematics Department in 2018 as a Canada 150 Research Chair in Mathematics for Infection, Evolution and Public Health. She has broad interests in applications of mathematics to questions in evolution and public health.
Dr Jonathan Monk, University of California San Diego, USA
Dr Jonathan Monk, University of California San Diego, USAJonathan received his PhD in Chemical Engineering from UC San Diego studying genome-scale network reconstructions of metabolism for microbial pathogens. He pioneered the use of these tools to study the diversity of metabolic capabilities in different strains of a species and has since applied them to several pathogenic organisms including E. coli, K. pneumonia, S. aureus, A. baumannii and C. difficile. He now works as an academic data scientist applying big-data analysis techniques to study the genetics and evolution of antimicrobial resistance and virulence in bacteria.
Professor Tandy Warnow, University of Illinois, USA
Professor Tandy Warnow, University of Illinois, USATandy Warnow is the Grainger Distinguished Chair in Engineering, and Professor and Associate Head of Computer Science at the University of Illinois at Urbana-Champaign. Tandy received her PhD in Mathematics at University of California, Berkeley under the direction of Gene Lawler, and did postdoctoral training with Simon Tavaré and Michael Waterman at USC. Her research combines computer science, statistics, and discrete mathematics, focusing on developing improved models and algorithms for reconstructing complex and large-scale evolutionary histories in biology and historical linguistics. Her awards include the NSF Young Investigator Award (1994), the David and Lucile Packard Foundation Award (1996), a Radcliffe Institute Fellowship (2003), and the John Simon Guggenheim Foundation Fellowship (2011). She was elected a Fellow of the Association for Computing Machinery (ACM) in 2015 and of the International Society for Computational Biology (ISCB) in 2017. |
Chair
Professor Edward Feil, University of Bath, UK
Professor Edward Feil, University of Bath, UK
Professor Feil’s research career has encompassed the evolution, population genomics and molecular epidemiology of a broad range of bacterial pathogens of humans and animals. He was involved with the development and implementation of Multilocus Sequence Typing, a key contribution being the eBURST clustering algorithm (J Bact 186(5):1518-30 2004). He was joint-first author of a publication in 2010 demonstrating proof of principal for the use of WGS for molecular epidemiology (Science 22;327(5964):469-74 2010). His current research focus on ‘One-Health’ questions of genome diversity, adaptation and AMR in the Enterobacteriaceae (https://www.biorxiv.org/content/10.1101/2021.08.05.455249v2).
| 12:00 - 12:30 |
Opening the door to studying nucleotide-resolution genetic variation in bacterial pan-genomes
When we study evolution of a bacterial species, we use different models, depending on what we want to achieve or infer. One approach is to reduce to single nucleotide polymorphism (SNP) variation in the 'core genome' (presumably inherited vertically) to study phylogeography or to study an outbreak. In focusing on SNPs (and invariant sites), it has been possible for researchers to build a range of sophisticated phylogenetic models. However once we try to incorporate genome organisation, chromosomal rearrangements, movement of plasmids, transposons or phage, then the modelling problem is far harder. The question of how to properly model bacterial genetic variation is wide open and extremely challenging. A prerequisite for any solution to this, is a decision on how to describe the variation in the first place – you cannot model variation until you represent it. Note that this is true even if you have perfect genome assemblies: even if it were possible to multiple sequence align them, this would not really help with how to notice that a SNP at one position in one genome is 'the same' as a SNP somewhere else in another. This talk will cover a solution to this representation problem, showing how it is possible to represent the pan genome of a species as a network of 'floating' graphs, representing the ensemble of known variation in orthology blocks (using genes and intergenic regions, but this could be done for mobile elements also). In doing so it becomes possible to discover and describe genetic variation at fine (SNP/indel) and coarse (gene order) level, and to compare diverse cohorts of genomes across the full pan-genome. 
Dr Zamin Iqbal, The European Bioinformatics Institute, UK
Dr Zamin Iqbal, The European Bioinformatics Institute, UKZamin Iqbal leads a computational genomics research group working on genetic variation in microbes, developing methods for representing and understanding complex genetic variation (eg surface antigens in P falciparum and the pan-genome in bacteria), and exploring surveillance and diagnostics for antimicrobial resistance. Zamin obtained his PhD in Mathematics from the University of Oxford, worked in the software industry for several years and returned to academia to work on the 1000 Genomes project. |
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| 12:30 - 13:00 |
How the interplay between mobile elements shapes bacterial genomes
Horizontal gene transfer driven by self-mobilisable genetic elements allows the acquisition of complex adaptive traits and their transmission to subsequent generations. Transfer speeds up evolutionary processes as exemplified by the acquisition of virulence traits in emerging infectious agents and by antibiotic resistance in many human pathogens. Transfer is also costly because the vectors of horizontal transfer compete within genomes, have their own mobile elements and are often deadly. As a result, genomes are repositories of multiple defense systems from hosts and from mobile elements that interact in complex ways to drive gene flow in communities. The combination of evolutionary genomics and sequence analysis is now opening up these processes to show how they bring into the genome a constant flux of novel genes that favour the establishment and the invention of novel functions. 
Dr Eduardo Rocha, Institut Pasteur & CNRS, France
Dr Eduardo Rocha, Institut Pasteur & CNRS, FranceEduardo Rocha studied Chemical Engineering and Applied Maths, did a PhD in Bioinformatics and an Habilitation in Biology. He is the director of the Genome & Genetics department at Pasteur Institute, where he heads the Microbial Evolutionary Genomics lab since 2008. He is a Specialist in comparative genomics, in particular in the use of bioinformatics and biostatistics to study microbial evolution. His research aims at understanding how and why genomes are organised, and how such organisational features evolve in respect to genome dynamics and bacterial adaptation. In the last decade, his work has focused on the role of mobile genetic elements in shaping gene repertoires and driving functional innovation. |
| 13:00 - 13:30 |
Diversification and adaptation of human skin bacteria during health and disease
Professor Tami Lieberman, Massachusetts Institute of Technology, USA
Professor Tami Lieberman, Massachusetts Institute of Technology, USATami Lieberman is an Assistant Professor at MIT, in the Institute for Medical Engineering and Sciences and the Department of Civil and Environmental Engineering. Dr Lieberman received a BA in Biological Sciences, with a minor in Mathematics from Northwestern University and a PhD in Systems Biology from Harvard University. As a graduate student in Roy Kishony’s laboratory, she studied bacterial evolution during human infections and developed experimental tools for understanding the evolution of antibiotic resistance. She then did a postdoc in Eric Alm’s laboratory at MIT, where she uncovered the first evidence that bacteria in the gut microbiome change via adaptive mutations, even during health. The Lieberman Lab continues to develop new tools to track and model within-person bacterial evolution, with a focus on the skin microbiome, towards revealing mechanistic understanding of community assembly in human microbiomes and the impact of in-microbiome mutations for health and disease. |
| 13:30 - 14:00 |
Discussion
Professor Edward Feil, University of Bath, UK
Professor Edward Feil, University of Bath, UKProfessor Feil’s research career has encompassed the evolution, population genomics and molecular epidemiology of a broad range of bacterial pathogens of humans and animals. He was involved with the development and implementation of Multilocus Sequence Typing, a key contribution being the eBURST clustering algorithm (J Bact 186(5):1518-30 2004). He was joint-first author of a publication in 2010 demonstrating proof of principal for the use of WGS for molecular epidemiology (Science 22;327(5964):469-74 2010). His current research focus on ‘One-Health’ questions of genome diversity, adaptation and AMR in the Enterobacteriaceae (https://www.biorxiv.org/content/10.1101/2021.08.05.455249v2).
Dr Eduardo Rocha, Institut Pasteur & CNRS, France
Dr Eduardo Rocha, Institut Pasteur & CNRS, FranceEduardo Rocha studied Chemical Engineering and Applied Maths, did a PhD in Bioinformatics and an Habilitation in Biology. He is the director of the Genome & Genetics department at Pasteur Institute, where he heads the Microbial Evolutionary Genomics lab since 2008. He is a Specialist in comparative genomics, in particular in the use of bioinformatics and biostatistics to study microbial evolution. His research aims at understanding how and why genomes are organised, and how such organisational features evolve in respect to genome dynamics and bacterial adaptation. In the last decade, his work has focused on the role of mobile genetic elements in shaping gene repertoires and driving functional innovation.
Dr Zamin Iqbal, The European Bioinformatics Institute, UK
Dr Zamin Iqbal, The European Bioinformatics Institute, UKZamin Iqbal leads a computational genomics research group working on genetic variation in microbes, developing methods for representing and understanding complex genetic variation (eg surface antigens in P falciparum and the pan-genome in bacteria), and exploring surveillance and diagnostics for antimicrobial resistance. Zamin obtained his PhD in Mathematics from the University of Oxford, worked in the software industry for several years and returned to academia to work on the 1000 Genomes project.
Professor Tami Lieberman, Massachusetts Institute of Technology, USA
Professor Tami Lieberman, Massachusetts Institute of Technology, USATami Lieberman is an Assistant Professor at MIT, in the Institute for Medical Engineering and Sciences and the Department of Civil and Environmental Engineering. Dr Lieberman received a BA in Biological Sciences, with a minor in Mathematics from Northwestern University and a PhD in Systems Biology from Harvard University. As a graduate student in Roy Kishony’s laboratory, she studied bacterial evolution during human infections and developed experimental tools for understanding the evolution of antibiotic resistance. She then did a postdoc in Eric Alm’s laboratory at MIT, where she uncovered the first evidence that bacteria in the gut microbiome change via adaptive mutations, even during health. The Lieberman Lab continues to develop new tools to track and model within-person bacterial evolution, with a focus on the skin microbiome, towards revealing mechanistic understanding of community assembly in human microbiomes and the impact of in-microbiome mutations for health and disease. |
Chair
Professor Ross Fitzgerald, Edinburgh Infectious Diseases and University of Edinburgh, UK
Professor Ross Fitzgerald, Edinburgh Infectious Diseases and University of Edinburgh, UK
Ross Fitzgerald is currently Director of Edinburgh Infectious Diseases and Professor of Molecular Bacteriology at The Roslin Institute, University of Edinburgh. After completing PhD and post-doctoral training in Trinity College, Dublin, and the NIH, USA he established a research group at the University of Edinburgh investigating the biology of major bacterial pathogens including Staphylococci and Legionella. His group is combining genomics and functional analyses to understand how new pathogens emerge, spread and cause disease. A major goal is the translation of fundamental discoveries into novel approaches to controlling infectious disease such as diagnostics and vaccines.
| 14:30 - 15:00 |
A scalable analytical approach from bacterial genomes to epidemiology
Recent years have seen a remarkable increase in the practicality of sequencing whole genomes from large numbers of bacterial isolates. The availability of this data source has huge potential to deliver new insights into the evolution and epidemiology of bacterial pathogens, but the analytical methodology has been lagging behind the sequencing technology. Here Professor Didelot presents a step-by-step approach for such genomic epidemiology analyses, from bacterial genomes to epidemiological interpretations. A central component of this approach is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. The construction of dated phylogenies from bacterial genomic data needs to account for the disruptive effect of recombination on phylogenetic relationships, and Professor Didelot describes how this can be achieved. Dated phylogenies can then be used to perform fine-scale or large-scale epidemiological analyses, depending on the proportion of cases for which genomes are available. A key feature of this approach is computational scalability, and in particular the ability to process hundreds or thousands of genomes within a matter of hours. This is a clear advantage of the step-by-step approach described here. Professor Didelot discusses other advantages and disadvantages of the approach, as well as potential improvements and avenues for future research. 
Professor Xavier Didelot, University of Warwick, UK
Professor Xavier Didelot, University of Warwick, UKXavier Didelot is Professor of Statistical Epidemiology and Genomics at the University of Warwick. He studied for his doctorate in the Department of Statistics at the University of Oxford, and did postdoctoral work at the Universities of Warwick and Oxford. He also worked for many years in the Department of Infectious Disease Epidemiology at Imperial College before taking his current appointment. Xavier Didelot is the Director of the recently created Health Protection Research Unit in Genomics and Enabling Data which is funded by the National Institute for Health Research. This project is a collaboration between the University of Warwick, Public Health England, the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Xavier Didelot's research is concerned with understanding the way bacterial pathogens evolve, spread and cause disease. He has analysed both epidemiological and genomic data from a wide range of bacteria, especially those causing healthcare associated infections and gastrointestinal infections. A key aim is to develop new bioinformatics and statistical methods that can handle the very large amounts of data made available by novel high-throughput sequencing techniques. |
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| 15:00 - 15:30 |
Pathogenwatch and data tools to bridge genomics and epidemiology for public health
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UK
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UKDavid is Director of The Centre for Genomic Pathogen Surveillance housed between the Wellcome Sanger Institute and The Big Data Institute, University of Oxford. David and team focus on data flow and the use of genome sequencing for translational surveillance of microbial pathogens through a combination of web and software engineering, methods development for population genomics and large-scale structured pathogen surveys and sequencing of microbes with delivery of information for decision making. Working with major public health agencies such as the US CDC, the European CDC, Public Health England and the WHO, methods and systems are utilised to interpret and aid decision making for infection control. David is also Director of the NIHR funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance working with partners leading National AMR strategies in The Phillipines, Colombia, Nigeria and India to implement genomic surveillance and linking and processing routine phenotypic and epidemiological data for priority pathogens. http://pathogensurveillance.net http://ghru.pathogensurveillance.net
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| 15:30 - 16:00 |
Unlocking Typhi genomics data to inform public health policy
Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S Typhi). Antimicrobials are the mainstay of typhoid disease control, and effective antimicrobial therapy can reduce the rate of complications from 10–30% down to 1%. A new conjugate vaccine has recently been pre-qualified by WHO and national immunisation programs are currently being considered by many countries where the disease is endemic, however data on disease burden, pathogen populations and antimicrobial resistance (AMR) are scarce in most such settings. Where typhoid surveillance is undertaken, namely for routine surveillance of travel-related infections in high income countries and burden studies in low income countries, whole genome sequencing (WGS) has been widely adopted as the primary method for characterisation of S Typhi isolates. WGS data can provide insights into pathogen diversity and transmission dynamics, as well as the emergence, dissemination and prevalence of AMR, much of which has relevance to understanding disease in settings other than those directly sampled (including regional trends, and country-of-acquisition for travel cases). However the resulting data are not readily accessible to public health decision makers. To fill this gap we are developing an interactive dashboard (TyphiNET, http://typhi.net), which aims to provide a window into genome-derived surveillance information for non-genomics experts. The dashboard relies on critical infrastructure that is being developed alongside, including (i) a community-driven effort to publicly share S Typhi sequence and source data in a manner that facilitates downstream aggregation for public health surveillance (the Global Typhoid Genomics Consortium, https://www.typhoidgenomics.org/); (ii) the GenoTyphi genotyping scheme, which provides simple, stable, phylogenetically informative, nomenclature to facilitate reporting and communication about pathogen variants; and (iii) Typhi Pathogenwatch, a public genomic epidemiology platform that provides uniform identification of genotypes and AMR determinants from genome data (in addition to whole-genome-based clustering), which is then fed into the TyphiNET dashboard. 
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UK
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UKKat is a computational biologist specialising in infectious disease genomics, and is Professor of Microbial Systems Genomics at LSHTM’s Department of Infection Biology and an Adjunct Professor in the Department of Infectious Diseases at Monash University in Australia. She has a BA/BSc (Hons) majoring in Biochemistry, Applied Statistics and Philosophy (University of Western Australia); a Master of Epidemiology (University of Melbourne); and a PhD in Molecular Biology (University of Cambridge and Sanger Institute). Kat is currently Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics and a HHMI-Gates International Research Scholar. Kat’s research group uses computational genomics and sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study the evolution and transmission of bacterial pathogens, including tropical diseases such as typhoid, dysentery, E. coli diarrhoea and tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter. |
| 16:00 - 16:30 |
Discussion
Dr Yogesh Hooda, MRC Laboratory of Molecular Biology, UK
Dr Yogesh Hooda, MRC Laboratory of Molecular Biology, UKYogesh is currently working as a postdoctoral scientist at the MRC Laboratory of Molecular Biology (MRC-LMB), Cambridge, UK. He also works as an Adjunct Scientist at the Child Health Research Foundation (CHRF), Bangladesh. Yogesh did his PhD in Biochemistry at the University Toronto where he identified the Slam family of proteins in Gram-negative bacteria. Currently, he is working on developing tools to study assembly of membrane proteins at the MRC-LMB. He is also involved in whole genome sequencing projects on Salmonella Typhi and Paratyphi A at CHRF. In 2019, he identified the molecular basis of azithromycin resistance in typhoidal Salmonella. His interests include protein biogenesis, antimicrobial resistance, and genomic epidemiology.
Professor Ross Fitzgerald, Edinburgh Infectious Diseases and University of Edinburgh, UK
Professor Ross Fitzgerald, Edinburgh Infectious Diseases and University of Edinburgh, UKRoss Fitzgerald is currently Director of Edinburgh Infectious Diseases and Professor of Molecular Bacteriology at The Roslin Institute, University of Edinburgh. After completing PhD and post-doctoral training in Trinity College, Dublin, and the NIH, USA he established a research group at the University of Edinburgh investigating the biology of major bacterial pathogens including Staphylococci and Legionella. His group is combining genomics and functional analyses to understand how new pathogens emerge, spread and cause disease. A major goal is the translation of fundamental discoveries into novel approaches to controlling infectious disease such as diagnostics and vaccines.
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UK
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UKDavid is Director of The Centre for Genomic Pathogen Surveillance housed between the Wellcome Sanger Institute and The Big Data Institute, University of Oxford. David and team focus on data flow and the use of genome sequencing for translational surveillance of microbial pathogens through a combination of web and software engineering, methods development for population genomics and large-scale structured pathogen surveys and sequencing of microbes with delivery of information for decision making. Working with major public health agencies such as the US CDC, the European CDC, Public Health England and the WHO, methods and systems are utilised to interpret and aid decision making for infection control. David is also Director of the NIHR funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance working with partners leading National AMR strategies in The Phillipines, Colombia, Nigeria and India to implement genomic surveillance and linking and processing routine phenotypic and epidemiological data for priority pathogens. http://pathogensurveillance.net http://ghru.pathogensurveillance.net
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UK
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UKKat is a computational biologist specialising in infectious disease genomics, and is Professor of Microbial Systems Genomics at LSHTM’s Department of Infection Biology and an Adjunct Professor in the Department of Infectious Diseases at Monash University in Australia. She has a BA/BSc (Hons) majoring in Biochemistry, Applied Statistics and Philosophy (University of Western Australia); a Master of Epidemiology (University of Melbourne); and a PhD in Molecular Biology (University of Cambridge and Sanger Institute). Kat is currently Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics and a HHMI-Gates International Research Scholar. Kat’s research group uses computational genomics and sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study the evolution and transmission of bacterial pathogens, including tropical diseases such as typhoid, dysentery, E. coli diarrhoea and tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter.
Professor Xavier Didelot, University of Warwick, UK
Professor Xavier Didelot, University of Warwick, UKXavier Didelot is Professor of Statistical Epidemiology and Genomics at the University of Warwick. He studied for his doctorate in the Department of Statistics at the University of Oxford, and did postdoctoral work at the Universities of Warwick and Oxford. He also worked for many years in the Department of Infectious Disease Epidemiology at Imperial College before taking his current appointment. Xavier Didelot is the Director of the recently created Health Protection Research Unit in Genomics and Enabling Data which is funded by the National Institute for Health Research. This project is a collaboration between the University of Warwick, Public Health England, the Centre for Genomic Pathogen Surveillance and the University of Cambridge. Xavier Didelot's research is concerned with understanding the way bacterial pathogens evolve, spread and cause disease. He has analysed both epidemiological and genomic data from a wide range of bacteria, especially those causing healthcare associated infections and gastrointestinal infections. A key aim is to develop new bioinformatics and statistical methods that can handle the very large amounts of data made available by novel high-throughput sequencing techniques. |
Chair
Dr Sebastian Duchene, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Australia
Dr Sebastian Duchene, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Australia
Sebastian Duchene is an early career Research Fellow at the Peter Doherty Institute for Infection and Immunity, which he joined in 2019. He obtained his PhD in 2015 and conducted postdoctoral work at the University of Sydney. His work at the University of Sydney involved understanding the timescales over which viruses evolve. At present he is developing approaches to leverage genome data with epidemiological information in outbreaks of infectious microbes. This work has been applied to understand the COVID19 pandemic in different countries and to inform Australia’s response. Sebastian has been awarded several competitive fellowship and grant schemes, including a McKenzie fellowship from the University of Melbourne, a Discovery Early Career Award from the Australian Research Council, and grants from the National Health and Medical Research Council. He is an author of over 78 peer-reviewed articles and an editor of Virus Evolution.
| 07:00 - 07:30 |
Real-time to Real-life: Phylogenetics & SARS-CoV-2 Variant Tracking
Since the UK government announced a more transmissible variant of SARS-CoV-2 in December 2020, countries around the world have quickly committed resources to tracking the main variants of concern (VoC). But even variants without obvious changes in viral traits can give insight into how SARS-CoV-2 spreads, help track specific epidemics, and give clues about arising mutations. However, tracking variants can be challenging for scientists unfamiliar with huge numbers of sequences and complex phylogenetic trees – with over 2.5 million publicly available sequences, it is no small task to track and monitor emerging and existing variants. This talk will discuss significant variants and what we have observed about them, how we detect variants of concern and interest, and how both our methods and what we classify as 'variants worth watching' may change in the future. 
Dr Emma Hodcroft, Institute of Social and Preventive Medicine, University of Bern, Switzerland
Dr Emma Hodcroft, Institute of Social and Preventive Medicine, University of Bern, SwitzerlandDr Emma Hodcroft began working in molecular epidemiology, phylogenetics, and modelling in HIV at the University of Edinburgh, where she investigated the heritability of viral load and developed an agent-based model simulating HIV phylogenies. In 2017, she moved to Basel and joined the Nextstrain project, becoming a co-developer of the project. Prior to the pandemic, Dr Hodcroft worked on projects with tuberculosis, campylobacter, influenza, and RSV, but primarily studied Enterovirus D68, where she has formulated new hypotheses about its evolution and transmission patterns. Since February 2020, Dr Hodcroft has worked full-time on SARS-CoV-2, including identifying a key variant that dominated Europe in the summer of 2020 despite not being more transmissible. This work led to her website CoVariants.org (recognised as an SIB Remarkable Output), which tracks SARS-CoV-2 variants. Dr Hodcroft has also been very active in science communication during the pandemic, gaining over 65,000 twitter followers, and contributing to two BBC radio programmes every week. |
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| 07:30 - 08:00 |
Bayesian spatiotemporal reconstruction of SARS-CoV-2 spread
SARS-CoV-2 genome data has been crucial to track the rapidly changing COVID-19 epidemic. The accumulation of high data volumes over short time makes time-consuming Bayesian phylogenetic inference impractical for real-time analyses. However, SARS-CoV-2 genomes come with a number of other challenges that can be confronted by Bayesian phylodynamic approaches. Specifically, these methods can take advantage of data integration opportunities and result in more realistic spatiotemporal reconstruction of SARS-CoV-2 spread. This will be demonstrated through the incorporation of global mobility data, individual travel histories and upsampled diversity in phylogeographic reconstructions. Such approaches allow addressing important epidemiological questions, such as to what extent lineage persistence and new introductions contributed to the COVID-19 resurgence in Europe late summer 2020. Various ways of making Bayesian inference more efficient and scalable will be highlighted in different settings. 
Professor Philippe Lemey, KU Leuven, Belgium
Professor Philippe Lemey, KU Leuven, BelgiumPhilippe Lemey is a Professor at the Rega Institute, KU Leuven, where he leads a research team that investigates the evolutionary processes that shape viral genetic diversity, from large-scale epidemic processes to small-scale transmission histories and within-host evolutionary processes. He is the senior editor of the second edition of the Phylogenetic Handbook and a two-time ERC grant awardee. His team is part of the ARTIC consortium (http://artic.network) and contributes to BEAST (http://beast.community) software. |
| 08:00 - 08:30 |
The fitness advantage and effective reproductive number of SARS-CoV-2 variants
During the COVID-19 pandemic, the Stadler group has set up an extensive nation-wide sequencing effort, covering roughly 8% of all confirmed SARS-CoV-2 cases in Switzerland each week. In addition, the group has developed the method that is federally used to estimate the effective reproductive number of SARS-CoV-2 from a variety of case report data. During this talk, Jana will detail the group’s efforts to track SARS-CoV-2 variants in PCR samples and wastewater, as well as related work to estimate the effective reproductive number and fitness advantage of individual variants. 
Ms Jana S Huisman, ETH Zurich, Switzerland
Ms Jana S Huisman, ETH Zurich, SwitzerlandOriginally from the Netherlands, Jana Huisman studied physics and math in Bonn, DE, before moving to the Technical University Denmark (DTU) to obtain her Masters in physics and nanotechnology. During her PhD, Jana studied the role of plasmids in the spread of antibiotic resistance with Tanja Stadler and Sebastian Bonhoeffer at the Swiss Federal Institute of Technology (ETH). Since March 2020, she has played a key role in the public health response to COVID-19 in Switzerland, developing the official method to estimate the effective reproductive number of SARS-CoV-2 from case reports and RNA concentrations in wastewater. |
| 08:30 - 09:00 |
Discussion
Dr Sebastian Duchene, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Australia
Dr Sebastian Duchene, Peter Doherty Institute for Infection and Immunity, University of Melbourne, AustraliaSebastian Duchene is an early career Research Fellow at the Peter Doherty Institute for Infection and Immunity, which he joined in 2019. He obtained his PhD in 2015 and conducted postdoctoral work at the University of Sydney. His work at the University of Sydney involved understanding the timescales over which viruses evolve. At present he is developing approaches to leverage genome data with epidemiological information in outbreaks of infectious microbes. This work has been applied to understand the COVID19 pandemic in different countries and to inform Australia’s response. Sebastian has been awarded several competitive fellowship and grant schemes, including a McKenzie fellowship from the University of Melbourne, a Discovery Early Career Award from the Australian Research Council, and grants from the National Health and Medical Research Council. He is an author of over 78 peer-reviewed articles and an editor of Virus Evolution.
Dr Emma Hodcroft, Institute of Social and Preventive Medicine, University of Bern, Switzerland
Dr Emma Hodcroft, Institute of Social and Preventive Medicine, University of Bern, SwitzerlandDr Emma Hodcroft began working in molecular epidemiology, phylogenetics, and modelling in HIV at the University of Edinburgh, where she investigated the heritability of viral load and developed an agent-based model simulating HIV phylogenies. In 2017, she moved to Basel and joined the Nextstrain project, becoming a co-developer of the project. Prior to the pandemic, Dr Hodcroft worked on projects with tuberculosis, campylobacter, influenza, and RSV, but primarily studied Enterovirus D68, where she has formulated new hypotheses about its evolution and transmission patterns. Since February 2020, Dr Hodcroft has worked full-time on SARS-CoV-2, including identifying a key variant that dominated Europe in the summer of 2020 despite not being more transmissible. This work led to her website CoVariants.org (recognised as an SIB Remarkable Output), which tracks SARS-CoV-2 variants. Dr Hodcroft has also been very active in science communication during the pandemic, gaining over 65,000 twitter followers, and contributing to two BBC radio programmes every week.
Ms Jana S Huisman, ETH Zurich, Switzerland
Ms Jana S Huisman, ETH Zurich, SwitzerlandOriginally from the Netherlands, Jana Huisman studied physics and math in Bonn, DE, before moving to the Technical University Denmark (DTU) to obtain her Masters in physics and nanotechnology. During her PhD, Jana studied the role of plasmids in the spread of antibiotic resistance with Tanja Stadler and Sebastian Bonhoeffer at the Swiss Federal Institute of Technology (ETH). Since March 2020, she has played a key role in the public health response to COVID-19 in Switzerland, developing the official method to estimate the effective reproductive number of SARS-CoV-2 from case reports and RNA concentrations in wastewater.
Professor Philippe Lemey, KU Leuven, Belgium
Professor Philippe Lemey, KU Leuven, BelgiumPhilippe Lemey is a Professor at the Rega Institute, KU Leuven, where he leads a research team that investigates the evolutionary processes that shape viral genetic diversity, from large-scale epidemic processes to small-scale transmission histories and within-host evolutionary processes. He is the senior editor of the second edition of the Phylogenetic Handbook and a two-time ERC grant awardee. His team is part of the ARTIC consortium (http://artic.network) and contributes to BEAST (http://beast.community) software. |
Chair
Professor Julian Parkhill FRS FMedSci, University of Cambridge, UK
Professor Julian Parkhill FRS FMedSci, University of Cambridge, UK
Julian is currently a Professor in the Department of Veterinary Medicine at the University of Cambridge. His research interests are focused on the evolution of bacterial pathogens, and his group uses large-scale genomics to understand their origin and transmission, and how they adapt to selective pressures such as antibiotics and vaccines. Over the last few years his group has identified the global origin and routes of spread of many human and animal pathogens, and discovered mechanisms of resistance to antibiotics and evasion of vaccines. They are also interested in bacterial communities, and have studied the microbiota of key body sites including the lung and the gut, to uncover associations with health and disease. Before moving to Cambridge in 2019, he worked at the Wellcome Sanger Institute for 20 years.
| 09:30 - 10:00 |
Evolutionary and ecological dynamics of emerging viruses
Professor Oliver Pybus, University of Oxford and Royal Veterinary College London, UK
Professor Oliver Pybus, University of Oxford and Royal Veterinary College London, UKOliver Pybus is Professor of Evolution & Infectious Disease at the University of Oxford and Professor of Infectious Diseases at the Royal Veterinary College London. He is co-Director of the Oxford Martin School Program for Pandemic Genomics and Chief Editor of the journal Virus Evolution. He researches the evolutionary and ecological dynamics of infectious diseases, particularly rapidly-evolving RNA viruses, and helped to establish the field of phylodynamics. |
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| 10:00 - 10:30 |
Within and between host pathogen genetics as a unique window into transmission and evolution
Pathogen genomics provides insight into the structure of epidemics, providing a disaggregated view of the epidemic, resolving transmission into clusters. Phylogenetic reconstruction enables the inference of the history of transmission. A particularity of pathogen genetics is that different pathogens within the same infection can be genetically distinct, either because the individual was infected more than once, or more usually because the pathogen has replicated and differentiated during the course of infection. This talk will review advances that allow improved characterisation of within and between host pathogen genetic diversity. Applications for viruses and bacteria will be shown. Improvements in the resolution of transmission will be highlighted. The talk will finish with a research agenda focused on characterising the transmission interface as a key area for improving intervention that limit infection and disease. 
Professor Christophe Fraser, Nuffield Department of Medicine, University of Oxford, UK
Professor Christophe Fraser, Nuffield Department of Medicine, University of Oxford, UKChristophe Fraser a Senior Group Leader in Pathogen Dynamics at the Big Data Institute, and Professor in the Nuffield Department of Medicine. He is interested in the population dynamics and epidemiology of pathogens, and translating this knowledge to public health. The primary tools used in his group are mathematical modelling and pathogen genomics. He trained in theoretical particle physics, and converted to mathematical biology after his PhD, in 1998. He was Royal Society URF and then Professor in the Department of Infectious Disease Epidemiology at Imperial College before joining the BDI at Oxford in 2016. In recent years he has focused on HIV in sub-Saharan Africa, using genomics and modelling to discover the structural drivers of the epidemic. During COVID, his group and collaborators provided modelling, genomics, and Christophe led the scientific deployment of contact tracing apps, working with the NHS, with Google and with Apple. |
| 10:30 - 11:00 |
Discussion
Daniel Falush, Institute Pasteur Shanghai, China
Daniel Falush, Institute Pasteur Shanghai, ChinaDaniel Falush is a statistical geneticist who has developed algorithms for human and bacterial genetics, including STRUCTURE, fineSTRUCTURE and ClonalFrame and applied them to address a variety of evolutionary questions. After many years as an academic wanderer, he recently set up a research group in Institute Pasteur, Shanghai. Currently a principle focus are human pathogenic bacteria Helicobacter pylori and Vibrio parahaemolyticus. These organisms are characterised by high recombination rates and approximate linkage equilibrium within populations. Professor Falush is using these organisms to investigate patterns of coadaptation between genes in natural populations using genomic data analysis and now laboratory work. 
Dr Kate Baker, University of Liverpool, UK
Dr Kate Baker, University of Liverpool, UKKate Baker is a Senior Lecturer at the University of Liverpool where she leads an applied microbial genomics group that integrates genomics, epidemiology, wet laboratory experimentation, and mathematical modelling to understand the emergence of infectious disease and antimicrobial resistance. Having trained as a veterinarian she completed a One Health doctorate on the evolutionary and transmission dynamics of zoonotic virus spill over at the University of Cambridge and Zoological Society of London. She was then a postdoctoral fellow at the Wellcome Trust Sanger Institute where she began her work on the genomic epidemiology of enteric pathogens and antimicrobial resistance, collaborating closely with public health agencies. She has held two personal fellowships from the Wellcome Trust, major grants from UKRI, AMS, and NIHR, is on the editorial board of Microbial genomics, and was seconded to the Scientific Advisory Group for Emergencies during the COVID-19 pandemic.
Professor Julian Parkhill FRS FMedSci, University of Cambridge, UK
Professor Julian Parkhill FRS FMedSci, University of Cambridge, UKJulian is currently a Professor in the Department of Veterinary Medicine at the University of Cambridge. His research interests are focused on the evolution of bacterial pathogens, and his group uses large-scale genomics to understand their origin and transmission, and how they adapt to selective pressures such as antibiotics and vaccines. Over the last few years his group has identified the global origin and routes of spread of many human and animal pathogens, and discovered mechanisms of resistance to antibiotics and evasion of vaccines. They are also interested in bacterial communities, and have studied the microbiota of key body sites including the lung and the gut, to uncover associations with health and disease. Before moving to Cambridge in 2019, he worked at the Wellcome Sanger Institute for 20 years.
Professor Christophe Fraser, Nuffield Department of Medicine, University of Oxford, UK
Professor Christophe Fraser, Nuffield Department of Medicine, University of Oxford, UKChristophe Fraser a Senior Group Leader in Pathogen Dynamics at the Big Data Institute, and Professor in the Nuffield Department of Medicine. He is interested in the population dynamics and epidemiology of pathogens, and translating this knowledge to public health. The primary tools used in his group are mathematical modelling and pathogen genomics. He trained in theoretical particle physics, and converted to mathematical biology after his PhD, in 1998. He was Royal Society URF and then Professor in the Department of Infectious Disease Epidemiology at Imperial College before joining the BDI at Oxford in 2016. In recent years he has focused on HIV in sub-Saharan Africa, using genomics and modelling to discover the structural drivers of the epidemic. During COVID, his group and collaborators provided modelling, genomics, and Christophe led the scientific deployment of contact tracing apps, working with the NHS, with Google and with Apple.
Professor Oliver Pybus, University of Oxford and Royal Veterinary College London, UK
Professor Oliver Pybus, University of Oxford and Royal Veterinary College London, UKOliver Pybus is Professor of Evolution & Infectious Disease at the University of Oxford and Professor of Infectious Diseases at the Royal Veterinary College London. He is co-Director of the Oxford Martin School Program for Pandemic Genomics and Chief Editor of the journal Virus Evolution. He researches the evolutionary and ecological dynamics of infectious diseases, particularly rapidly-evolving RNA viruses, and helped to establish the field of phylodynamics. |
| 11:00 - 11:15 |
Final comments and close
Professor Mark Achtman FRS, University of Warwick, UK
Professor Mark Achtman FRS, University of Warwick, UKSince 1965, Achtman has founded four highly distinct areas of bacterial genetics: 1) bacterial conjugation involving the Escherichia coli F sex factor (1965-78), 2) E. coli neonatal meningitis (1979-86), 3) epidemic cerebrospinal meningitis caused by Neisseria meningitis (1983-2000). Since 1998 he has dedicated himself to the population genetics and genomics of bacterial pathogens. In each area he made seminal discoveries, resulting in global recognition, and is one of the globally most prominent bacterial population geneticists. In recent years, he was one of three co-inventors of multilocus sequence typing and has been at the forefront of comparative population genomics. He elucidated the historical associations of Helicobacter pylori with ancient human migrations, ancient global routes of transmission of historical plague, and has introduced dramatic changes to the practice of epidemiological typing of Salmonella enterica. More recently, he has been responsible for developing EnteroBase which provides access to 100,000s of assembled genomes from a variety of genera containing bacterial pathogens. Honours: main prize of the Deutsche Gesellschaft fuer Hygiene und Mikrobiologie, 2004; foreign member of the Norwegian Academy of Sciences and Letters, 2014, Fellow of the Royal Society, 2015, and the Pettenkofer Prize, 2018.
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UK
Professor Kathryn Holt, London School of Hygiene and Tropical Medicine, UKKat is a computational biologist specialising in infectious disease genomics, and is Professor of Microbial Systems Genomics at LSHTM’s Department of Infection Biology and an Adjunct Professor in the Department of Infectious Diseases at Monash University in Australia. She has a BA/BSc (Hons) majoring in Biochemistry, Applied Statistics and Philosophy (University of Western Australia); a Master of Epidemiology (University of Melbourne); and a PhD in Molecular Biology (University of Cambridge and Sanger Institute). Kat is currently Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics and a HHMI-Gates International Research Scholar. Kat’s research group uses computational genomics and sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study the evolution and transmission of bacterial pathogens, including tropical diseases such as typhoid, dysentery, E. coli diarrhoea and tuberculosis; and hospital associated pathogens such as Klebsiella and Acinetobacter.
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UK
Professor David Aanensen, University of Oxford and Wellcome Sanger Institute, UKDavid is Director of The Centre for Genomic Pathogen Surveillance housed between the Wellcome Sanger Institute and The Big Data Institute, University of Oxford. David and team focus on data flow and the use of genome sequencing for translational surveillance of microbial pathogens through a combination of web and software engineering, methods development for population genomics and large-scale structured pathogen surveys and sequencing of microbes with delivery of information for decision making. Working with major public health agencies such as the US CDC, the European CDC, Public Health England and the WHO, methods and systems are utilised to interpret and aid decision making for infection control. David is also Director of the NIHR funded Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance working with partners leading National AMR strategies in The Phillipines, Colombia, Nigeria and India to implement genomic surveillance and linking and processing routine phenotypic and epidemiological data for priority pathogens. http://pathogensurveillance.net http://ghru.pathogensurveillance.net
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