| 14/09/2022 | S1 | 13:00-15:00 | Metagenomics and Microbiomes |
| | Chairs: Natacha Couto (Bath, United Kingdom), Eric Claas (Leiden, Netherlands) |
| 13:00-13:30 | Metagenomics for pathogen surveillance at the human-animal interface - Marion Koopmans (Rotterdam, Netherlands) |
| 13:30-14:00 | Metagenomics in the surveillance of antimicrobial resistance - Ana Sofia Ribeiro Duarte (Lyngby, Denmark) This talk will be given virtually |
| 14:00-14:30 | Challenges of using metagenomics for clinical diagnostics and pathogen surveillance - Alexander L. Greninger (Seattle, United States) |
| 14:30-14:45 | Metagenomic monitoring of antimicrobial resistance in 101 countries using sewage reveals new diversity and geographical patterns in the global resistome - Patrick Munk (Kgs. Lyngby, Denmark) |
| 14:45-15:00 | A new genomic surveillance paradigm: Wastewater based epidemiology using metagenomics in Canada - Chrystal Landgraff (Winnipeg, Canada) |
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| S2 | 15:30-17:00 | “One Health or Public Health in the Case of AMR?” Round-table discussion and debate |
| | Chairs: Ana R. Freitas (Porto, Portugal), Guido Werner (Wernigerode, Germany) |
| 15:30-16:00 | Antibiotic resistances among hospital pathogens – is there a link to animals and the environment? - Hajo Grundmann (Freiburg, Germany) |
| 16:00-16:30 | Intersectoral spread of resistances to antibiotics of last resort - Stefan Schwarz (Berlin, Germany) |
| 16:30-17:00 | The riverine resistome – what should we be monitoring? - Liz Wellington (Coventry, United Kingdom) This talk will be given virtually |
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| S3 | 17:30-19:30 | Opening Ceremony |
| | Chairs: Sandra Reuter (Freiburg, Germany), Sam Sheppard (Bath, United Kingdom) |
| 17:30-17:40 | Welcome from ESCMID EC - Annelies Zinkernagel (Zurich, Switzerland) |
| 17:40-17:50 | Welcome from ESGEM chair - Guido Werner (Wernigerode, Germany) |
| 17:50-18:00 | Welcome from local committee - Lauren Cowley (Bath, United Kingdom) |
| 18:00-18:45 | If genomes are the answer, what is the question? - Bill Hanage (Harvard, United States) |
| 18:45-19:30 | Genomics in LMIC - Iruka Okeke (Ibadan, Nigeria) |
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| 15/09/2022 | S4 | 08:30-10:00 | Recognising and Naming Lineages |
| | Chairs: Sylvain Brisse (Paris, France), Kathryn Holt (London, United Kingdom) |
| 08:30-09:00 | Tracking the spread of SARS-CoV-2 with lineages - Aine O’Toole (Edinburgh, United Kingdom) |
| 09:00-09:30 | High risk Klebsiella pneumoniae clones: MDR, hypervirulence and convergence - Kelly Wyres (Melbourne, Australia) |
| 09:30-10:00 | Infamous clones and their boundaries: stories from E. coli and the pneumococcus - Rebecca Gladstone (Oslo, Norway) |
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| S5 | 10:30-12:30 | Challenges of Genome-based pathogen surveillance in LMICs |
| | Chairs: Silvia Argimon (Oxford, United Kingdom), Iruka Okeke (Ibadan, Nigeria) |
| 10:30-11:00 | How genomics has change pathogens surveillance in Argentina: the new challenges - Josefina Campos (Buenos Aires, Argentina) |
| 11:00-11:30 | Pathogen-based genomic surveillance in West Africa for epidemic preparedness and response - Martin Antonio (Serrekunda, Gambia) |
| 11:30-12:00 | NIHR Global Health Research Unit on Genomic Surveillance of AMR - David Aanensen (Oxford, United Kingdom) |
| 12:00-12:15 | Genomic Surveillance of Staphylococcus aureus Submitted to the Nigerian Antimicrobial Resistance Surveillance Network from 2013-2021 - Anderson Oaikhena (Ibadan, Nigeria) |
| 12:15-12:30 | A quinolone resistant outbreak of Salmonella enterica serovar Paratyphi A in Phnom Penh, Cambodia - Koen Vandelannoote (Phnom Penh, Cambodia) |
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| S6 | 13:30-15:00 | The Long and Short of It |
| | Chairs: Ângela Novais (Porto, Portugal), Sandra Reuter (Freiburg, Germany) |
| 13:30-14:00 | Utilising large datasets to investigate mobile genetic elements - Grace Blackwell (Sydney, Australia) |
| 14:00-14:30 | Plasmid dynamics in hospital patients - Alvaro San Millan (Madrid, Spain) |
| 14:30-14:45 | A novel approach for consistent typing and identification of Escherichia coli plasmids - Sergio Arredondo-Alonso (Oslo, Norway) |
| 14:45-15:00 | First comprehensive reconstruction of the plasmidome of Enterococcus faecalis - Val F. Lanza (Madrid, Spain) |
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| S7 | 15:30-17:00 | Platforms for Molecular Epidemiology |
| | Chairs: Lauren Cowley (Bath, United Kingdom), Torsten Seemann (Melbourne, Australia) |
| 15:30-15:45 | Pathogenwatch - Silvia Argimon (Oxford, United Kingdom) |
| 15:45-16:00 | NextStrain - Richard Neher (Basel, Switzerland) |
| 16:00-16:15 | BIGSdb - Keith Jolley (Oxford, United Kingdom) |
| 16:15-16:30 | Enterobase - Nabil-Fareed Alikhan (Norwich, United Kingdom) |
| 16:30-17:00 | Discussion |
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| 16/09/2022 | S8 | 08:30-10:30 | Evolution and Drivers of Pathogen Emergence |
| | Chairs: Kristin Hegstad (Tromso, Norway), Sam Sheppard (Bath, United Kingdom) |
| 08:30-09:00 | Chlamydia trachomatis responses to diagnostic and selective pressures - Helena Seth-Smith (Basel, Switzerland) |
| 09:00-09:30 | Mutational signatures predict bacterial niches - Christopher Ruis (Cambridge, United Kingdom) |
| 09:30-10:00 | Evolution and dissemination of bacterial pathogens with a global burden - Claire Chewapreecha (Bangkok, Thailand) |
| 10:00-10:15 | Improved accuracy of antibiotic resistance determination from Enterococcus faecium whole-genome sequences - Francesc Coll (London, United Kingdom) |
| 10:15-10:30 | Within-patient evolution and global dynamics of Klebsiella pneumoniae ST17 - Marit Andrea Klokkhammer Hetland (Stavanger, Norway) |
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| S9 | 11:00-13:00 | Zoonotic Pathogen Transmission |
| | Chairs: Sally Jane Cutler (London, United Kingdom), Ed Feil (Bath, United Kingdom) |
| 11:00-11:30 | Do host specialisms help to mitigate zoonotic transmission?- Edward Feil (Bath, United Kingdom) |
| 11:30-12:00 | The ecological shift to pathogenicity and zoonosis in Streptococcus suis - Lucy Weinert (Cambridge, United Kingdom) |
| 12:00-12:30 | Public health contributions of arboviruses genomic surveillance in Brazil - Jaqueline Goes de Jesus (Salvador, Brazil) |
| 12:30-12:45 | Plasmid presence and diversity within and between Campylobacter species - Aldert Zomer (Utrecht, The Netherlands) |
| 12:45-13:00 | Comparative genomics of persistence mechanisms in Listeria monocytogenes - Clare Barker (London, United Kingdom) |
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| 17/09/2022 | S9.5 | 08:30-09:00 | Core or more? Novel approaches in bioinformatics |
| | Chairs: Ed Feil (Bath, United Kingdom), Natacha Couto (Bath, United Kingdom) |
| 08:30-08:45 | Variety, velocity, and volume: Molecular epidemiological surveillance and the challenges of big data - Eric Stevens (College Park, USA) |
| 08:45-09:00 | Alignment-free typing schemes for bacterial, viral and eukaryotic pathogens - John Lees (Cambridge, United Kingdom) |
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| S10 | 09:00-11:00 | Layering on new Data Types |
| | Chairs: Lauren Cowley (Bath, United Kingdom), Benjamin Howden (Parkville, Australia) |
| 09:00-09:30 | Spatial trends of emerging viruses in Latin America: a dossier on sampling intensity and complementing data - Bernardo Gutierrez Granja (Oxford, United Kingdom) |
| 09:30-10:00 | Influence of patient flows on the genetic population structure of MRSA - Tjibbe Donker (Freiburg, Germany) |
| 10:00-10:30 | Hierarchical machine learning predicts geographical origin of Salmonella within four minutes of sequencing - Sion Bayliss (Bath, United Kingdom) |
| 10:30-10:45 | EpiLinx, a software to visualize patient networks for outbreak detection - Henrik Hasman (Copenhagen S, Denmark) |
| 10:45-11:00 | Molecular surveillance for mobile populations - Caroline Buckee (Boston, United States) This talk will be given virtually |
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| | 11:30-11:45 | Prize announcements |
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| S11 | 11:45-13:15 | Lessons learned from COVID-19 |
| | Chairs: Nick Loman (Birmingham, United Kingdom), Lauren Cowley (Bath, United Kingdom) |
| | Speaker 1 Bill Hanage (Harvard, United States) |
| | Speaker 2 Jacob Moran-Gilad (Be’er Sheva, Israel) |
| | Speaker 3 Benjamin P. Howden (Parkville, Australia) |
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