Scientific Calendar Event

An ICTP hybrid meeting

Antimicrobial resistance is a global threat to modern medicine, whereby bacteria evolve resistance to (i.e the ability to not be killed by) antibiotics. Since bacteria are able to pass chunks of DNA between unrelated individuals, this allows them to pass around genes encoding resistance mechanisms - in other words they can give each other an evolutionary head-start, directly donating the ability to survive an antibiotic in a process called Horizontal Gene Transfer.

Plasmids are key players in Horizontal Gene Transfer, acting as vehicles of antimicrobial resistance (AMR) spread, able to transfer tens of genes, and therefore multidrug resistance, in one event. It is therefore critical that we understand their biology, ecology and epidemiology.

Recent technology developments (longread sequencing and targeted bioinformatic tools) have led to improved ability to observe these processes, making thorough investigation of plasmid-mediated AMR outbreaks possible.
However, it has also highlighted how complex plasmid evolution is, the uniqueness of plasmid eco-evolutionary processes and the unsuitableness of many chromosome-based methods like point-mutation- and tree- based phylogenetics. New models are needed to be able to understand the processes that genomics allows us to observe and to appreciate their clinical and epidemiological implications in the light of plasmid evolution.

Call for Contributed Abstracts: All applicants are encouraged to submit an abstract for a poster presentation and/or a contributed talk. Abstract templates are available below for download.

D. AANENSEN, University of Oxford, UK
F. BENZ, Institut Pasteur Paris, France
T. DAGAN, Christian-Albrechts University of Kiel, Germany
E. FEIL, University of Bath, UK
P. J. HALL, University of Liverpool, UK
J. HAWKEY, Monash University, Australia
O. KOSTERLITZ, University of Washington, USA
N. QUINONES-OLVERA, Harvard University, USA
A. ROBERTS, Liverpool School of Tropical Medicine, UK
E. ROCHA, Institut Pasteur Paris, France
L. P. SHAW, University of Oxford, UK
D. VAN TYNE, University of Pittsburgh, USA
Grants: A limited number of grants are available to support the attendance of selected participants, with priority given to participants from developing countries. There is no registration fee.

Go to day
  • Monday, 18 September 2023
    • 09:00 - 10:00
      • 09:00 Registration formalities 1h0'
        REGISTRATION: Upon arrival, Visitors not staying in the ICTP Guest Houses, are kindly requested to complete registration formalities at the Adriatico Guest House (Lower level). The Registration Desk will be open from 9.00 to 10.00.
    • 10:00 - 14:00
      • 10:00 Welcome remarks 15'
      • 10:15 Speed-dating style introduction 1h45'
      • 12:00 Working lunch and coffee 1h45' ( Adriatico Guesthouse Cafeteria )
      • 13:45 Posters 15'
    • 14:00 - 18:30 Session 1: What's in a plasmid?
      • 14:00 Unraveling the Taxonomic Diversity of Plasmids 20'
        Speaker: Fernando DE LA CRUZ CALAHORRA (University of Cantabria, Spain)
      • 14:20 Phage-plasmids connect and generate phages and plasmids 20'
        Speaker: Eduardo ROCHA (Institut Pasteur Paris, France)
        Material: Video
      • 14:40 Interaction between mobile genetic elements and plasmids drives the evolution of multidrug resistance plasmids 20'
        Speaker: Tal DAGAN (Christian-Albrechts University of Kiel, Germany)
      • 15:00 Insights into intracellular transfer of AMR associated MGEs 20'
        Speaker: Adam ROBERTS (Liverpool School of Tropical Medicine, UK)
        Material: Video
      • 15:20 Q&A 10'
      • 15:30 Coffee break 30'
      • 16:00 Diverse and abundant bacteriophages exploit conjugative plasmids 20'
        Speaker: Natalia QUINONES-OLVERA (Harvard University, USA)
        Material: Video
      • 16:20 Unmasking the Hidden Players: Unveiling the Conjugative Origins of Transfer 15'
        Speaker: Manuel ARES ARROYO (Institut Pasteur, France)
      • 16:35 Efficiency of restriction-modification systems against AMR plasmid conjugation 15'
        Speaker: Tatiana DIMITRIU (University of Exeter, UK)
        Material: Video
      • 16:50 Anti-Defense Systems on Plasmids 15'
        Speaker: Bruria SAMUEL (Tel Aviv University, Israel)
        Material: Video
      • 17:05 The role of intracellular competition in the fixation of novel plasmids 15'
        Speaker: Fernando WELKER SAPOJKIN ROSSINE (Harvard Medical School, USA)
        Material: Video
      • 17:20 Q&A 15'
      • 17:35 Presentation of the projects/discussion groups 55'
    • 19:00 - 21:30
      • 19:00 Campfire Session: interdisciplinary collaborations 2h30'
      • 19:00 Welcome reception 2h30' ( Adriatico Guesthouse - lower level )
        All participants are cordially invited to the Welcome reception.
  • Tuesday, 19 September 2023
    • 09:00 - 19:15 Session 2: How do plasmid evolve?
      • 09:00 How do plasmids evolve over epidemiological and evolutionary timescales 20'
        Speaker: Zamin IQBAL (EBI Cambridge, UK)
        Material: Video
      • 09:20 Evolutionary "crowdsourcing": distributed adaptation of horizontally transferred genes within bacterial communities 20'
        Speaker: Olivia KOSTERLITZ (University of Washington, USA)
        Material: Video
      • 09:40 Host-specific plasmid evolution explains the variable spread of clinical antibiotic-resistance plasmids 20'
        Speaker: Fabienne BENZ (Institut Pasteur Paris, France)
        Material: Video
      • 10:00 Megaplasmids as vehicles for resistance genes 20'
        Speaker: Jamie HALL (University of Liverpool, UK)
      • 10:20 Coffee break 40'
      • 11:00 Plasmid evolution and defence systems 20'
        Speaker: Liam SHAW (University of Oxford, UK)
        Material: Video
      • 11:20 Diverse evolutionary paths led plasmid adaptation to the antibiotic era 15'
        Speaker: Adrian CAZARES LOPEZ (European Bioinformatics Institute (EMBL-EBI), UK)
      • 11:35 Evolutionary interplay of chromosomal and plasmid-borne compensatory mutations 15'
        Speaker: Christopher WITZANY (ETH Zurich, Switzerland)
        Material: Video
      • 11:50 Q&A 25'
      • 12:15 Lunch break and personal time 3h0'
      • 15:15 Coffee and posters 30'
      • 15:45 Discussion/Projects 1h45'
      • 17:30 Personal time 1h0'
      • 18:30 Conjugative-killer plasmids, a novel antimicrobial alternative 5'
        Speaker: Luis Pedro DORADO-MORALES (Institut Pasteur Paris, France)
      • 18:35 Transference of antibiotic resistance genes through marine conjugative plasmids 5'
        Speaker: Juan Manuel MEDINA MENDEZ (CSIC - University of Cantabria, Spain)
        Material: Video
      • 18:40 Capturing microbial genome diversity with pangenome graphs: the case of E. coli ST131 5'
        Speaker: Marco MOLARI (University of Basel, Switzerland)
        Material: Video
      • 18:45 Improved detection and classification of plasmids from circularized and fragmented assemblies 5'
        Speaker: Matias GIMENEZ MARTINEZ (Institut Pasteur Montevideo, Uruguay)
        Material: Video
      • 18:50 Can we use short-read data to monitor AMR markers in plasmids? 5'
        Speaker: Julio Felix DIAZ CABALLERO (University of Oxford, UK)
        Material: Video
      • 18:55 PlasBin-flow: A flow-based MILP algorithm for plasmid contigs binning 5'
        Speaker: Mahsa FAIZRAHNEMOON (Simon Fraser University, Canada)
        Material: Video
      • 19:00 Q&A 15'
    • 19:15 - 21:15
      • 19:15 Aperitivo dinner 2h0' ( Adriatico Guesthouse Cafeteria )
        All participants are cordially invited to the Aperitivo dinner.
  • Wednesday, 20 September 2023
    • 09:00 - 16:30 Session 3: How do plasmid spread in natural communities?
      • 09:00 Plasmids: pragmatic challenges for public health surveillance of AMR 20'
        Speaker: David AANENSEN (University of Oxford, UK)
        Material: Video
      • 09:20 Population genomics of Klebsiella pneumoniae plasmids 20'
        Speaker: Edward FEIL (University of Bath, UK)
        Material: Video
      • 09:40 Challenges of plasmid transmission analysis at the Alfred Hospital 20'
        Speaker: Jane HAWKEY (Monash University, Australia)
        Material: Video
      • 10:00 Q&A 15'
      • 10:15 Group photo 5'
        in person and online
      • 10:20 Coffee break 25'
      • 10:45 Antimicrobial resistance level and conjugation permissiveness shape plasmid distribution in clinical enterobacteria 20'
        Speaker: Alvaro SAN MILLAN CRUZ (CSIC Madrid, Spain)
        Material: Video
      • 11:05 Phylogemics adapted to pasmid evolution 20'
        Speaker: Alice LEDDA (UK Health Security Agency, UK)
        Material: Video
      • 11:25 Jaccard Index Network Analysis reveals the contribution of accessory genome to the recent diversification of Salmonella Typhi 15'
        Speaker: Arancha PENIL CELIS (Institute of Biomedicine and Biotechnology of Cantabria, Spain)
        Material: Video
      • 11:40 RoundHound: detecting plasmid transmission from short-read datasets 15'
        Speaker: Leah ROBERTS (Queensland University of Technology, Australia)
        Material: Video
      • 11:55 Approximating plasmid relatedness using Double Cut and Join Indel model 15'
        Speaker: Daria FROLOVA (European Bioinformatics Institute, UK)
        Material: Video
      • 12:10 Lunch break 1h20'
      • 13:30 Integrons on plasmids: the global genomic epidemiology of blaGES-5 15'
        Speaker: William MATLOCK (University Oxford, UK)
        Material: Video
      • 13:45 Detecting AMR plasmid variants in Shigella sonnei 15'
        Speaker: Sally PARTRIDGE (The Westmead Institute for Medical Research (WIMR), Australia)
        Material: Video
      • 14:00 Exploiting Short-Reads Plasmid Signature for Phenotypic Resistance Analysis: a bioinformatic methodology approach 5'
        Speaker: Federico DI MARCO (IRCCS San Raffaele Scientific Institute, Italy)
        Material: Video
      • 14:05 Accumulation of replicons carrying multiple copies of mcr and blaKPC-2 in Enterobacter kobei from Brazilian recreational coastal waters 5'
        Speaker: Gabriela BERGIANTE KRAYCHETE (Linköping University, Sweden)
      • 14:10 Aeromonas as a major host of antimicrobial resistance in wastewater settings 5'
        Speaker: David BALTRUS (University of Arizona, USA)
        Material: Video
      • 14:15 The emergence, context and impact of L3 lineage IncL plasmids on antimicrobial resistance dynamics 5'
        Speaker: Jose DELGADO BLAS (Complutense University of Madrid, Spain)
        Material: Video
      • 14:20 Three major Neisseria gonorrhoeae beta-lactamase plasmid variants are associated with TEM alleles and lineages 5'
        Speaker: Tabea ELSENER (Sir William Dunn School of Pathology, UK)
        Material: Video
      • 14:25 Integrated analysis of patient networks and plasmid genomes reveals a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes 5'
        Speaker: Yu WAN (Imperial College London, UK)
        Material: Video
      • 14:30 Coffee and posters 30'
      • 15:00 Discussion/Projects 1h30'
    • 17:30 - 20:00
      • 17:30 Hike (optional) and Social Dinner 2h30'
        All participants are cordially invited to the dinner.
  • Thursday, 21 September 2023
    • 10:15 - 14:30
      • 10:15 Coffee and posters 30'
      • 10:45 Discussion/Projects 1h45'
      • 12:30 Lunch break and personal time 1h30'
      • 14:00 Posters 30'
    • 14:30 - 18:15 Session 4: Plasmids and AMR - do we have a problem?
      • 14:30 Sharing is caring: Mobile genetic element spread among multidrug-resistant bacteria in the hospital 20'
        Speaker: Daria VAN TYNE (University of Pittsburgh, USA)
        Material: Video
      • 14:50 The challenges of Plasmid Antibiotic Resistance Surveillance 20'
        Speaker: Teresa COQUE (IRYCIS, Spain)
      • 15:10 Break 20'
      • 15:30 Experimentally exploring the role of codon usage in determining the immediate and evolutionary success of the horizontal transfer of an antibiotic resistance gene 15'
        Speaker: Stephanie BEDHOMME (Centre for Evolutionary and Functional Ecology, France)
        Material: Video
      • 15:45 Using in vitro experimental epidemiology to compare the effectiveness of multi-drug treatment strategies to reduce plasmid-borne antibiotic resistance 15'
        Speaker: Sebastian BONHOEFFER (ETH Zurich, Switzerland)
        Material: Video
      • 16:00 Coffee break 30'
      • 16:30 Identifying plasmid transconjugants in the rare biosphere of the barley rhizosphere using Hi-C and target enrichment 15'
        Speaker: Thibault STALDER (University of Idaho, USA)
        Material: Video
      • 16:45 blaNDM-1-bearing plasmid transmission between Klebsiella pneumoniae strains in biofilm and planktonic lifestyle 15'
        Speaker: Michelle BUCKNER (University of Birmingham, UK)
        Material: Video
      • 17:00 The invasion success by antibiotic-resistant plasmid-bacterium associations in human-associated communities is determined by the interplay between intrinsic and environmental factors 15'
        Speaker: Ricardo LEON-SAMPEDRO (ETH Zurich, Switzerland)
        Material: Video
      • 17:15 Plasmid spread from carbapenemase producing Enterobacter hormaechei ST79 present on contaminated Dicillin capsules sold in Denmark 15'
        Speaker: Henrik HASMAN (Henrik Statens Serum Institut, Denmark)
        Material: Video
      • 17:30 Break 15'
      • 17:45 Investigation of the extent of clonal and multiple acquisition in OXA-48 plasmids in UK hospitals 5'
        Speaker: Toby NONNENMACHER (UK Health Security Agency, UK)
        Material: Video
      • 17:50 In silico investigation of the plasmid composition of over 400 Enterobacteriaceae strains held by the National Collection of Type Cultures 5'
        Speaker: Jake TURNBULL (UKHSA, UK)
        Material: Video
      • 17:55 Genomic Epidemiologic Investigation of a Hospital Outbreak of NDM-5-Producing Gram-Negative Enterobacterales Infections 5'
        Speaker: Nathan RAABE (University of Pittsburgh, USA)
        Material: Video
      • 18:00 IncC plasmids in the emergent genotype ST213 of Salmonella Typhimurium: Phenotypic analyses of plasmid-cured mutant strains and comparative genomics 5'
        Speaker: Marco PEREZ (Universidad Nacional Autonoma de Mexico, Mexico)
        Material: Video
      • 18:05 Ecology & evolution of a clinical plasmid population 5'
        Speaker: Celia SOUQUE (Harvard Medical School, USA)
        Material: Video
      • 18:10 Genomic dissection of plasmids driving AMR and hypervirulence convergence in Klebsiella pneumoniae 5'
        Speaker: Margaret LAM (Monash University, Australia)
        Material: Video
    • 19:15 - 20:15
      • 19:15 Get-together drink 1h0' ( Adriatico Guesthouse Cafeteria )
        All participants are cordially invited to the Get-together drink.
    • 20:15 - 21:15
      • 20:15 Campfire session: women in science 1h0'
        Speaker: Tal DAGAN (Christian-Albrechts University of Kiel, Germany)
  • Friday, 22 September 2023
    • 09:00 - 12:00
      • 09:00 Presentations from discussion groups and hand on 1h30'
      • 10:30 Coffee break 30'
      • 11:00 Sum up and goodbyes 1h0'