The Second SMBE Satellite Workshop on

Genome Evolution in Pathogen Transmission and Disease

Kyoto, Japan
4-7 November 2018

2018 Workshop

Three Days of Leading-Edge Science
November 4-7
Kyoto, Japan

Building on the success of the 2016 SMBE Satellite Workshop on Genome Evolution in Pathogen Transmission and Disease, we are delighted to announce that the second edition of this popular workshop will be held in November, 2018 in Kyoto, Japan!

New technologies and novel modeling and algorithmic methods are dramatically transforming the microbial pathogenomics and molecular epidemiology landscapes, allowing us to explore pathogen evolution in the context of human health in a way that has never before been possible. Through invited talks and attendee presentations, this workshop will explore the leading edge of pathogen evolution, including: the use of new long-read technologies for pathogen surveillance; the emerging area of genome-wide association studies in bacterial and viral populations; the role of evolutionary analysis in emerging infectious diseases such as Ebola and Zika and established pathogens; the link between genotype and phenotypic virulence and antibiotic resistance; new tools for evolutionary analysis; and the union of evolutionary and epidemic modelling for inferring outbreak and epidemic dynamics.

The 2018 workshop is proudly brought to you by Stephen Bentley, Caroline Colijn, Jukka Corander, Jennifer Gardy, Tetsuya Hayashi, and Kat Holt, with the support of the Society for Molecular Biology and Evolution, the University of Oslo, Kyushu University, and the journal Microbial Genomics.

 

Agenda & Location

Agenda
All sessions at Room B, 5/F, Mielparque Kyoto unless otherwise noted.
Sunday, November 4
  • 18:30-21:30 Opening remarks and social

Monday, November 5
  • 09:30-10:00 Thibault Jombart: When are pathogen genome sequences useful in outbreak analytics?

  • 10:00-10:30 Anne Cori: A graph-based evidence synthesis approach to detecting outbreak clusters: an application to dog rabies

  • 10:30-11:00 Aaron Darling: Real-time sequencing, real-time outbreak surveillance. Fake-time phylogenetics?

  • 11:00-11:15 Break

  • 11:15-12:00 Lightning Talks

  • 12:00-17:00 Free time in Kyoto

  • 17:00-17:30 Richard Neher: Tracking pathogenic bacteria and AMR at the plasmid, genome, and pan-genome level

  • 17:30-18:00 Martha Cloakie: Using genome based approaches to develop global bacteriophage products as antimicrobials to treat antibiotic resistant bacteria

  • 18:00-19:00 Lightning Talks

Tuesday, November 6
  • 09:30-10:00 Trevor Bedford: Forecasting strain turnover in influenza and dengue viruses

  • 10:00-10:30 Katia Koelle: Using viral sequence data to infer transmission dynamics and bottlenecks

  • 10:30-11:00 Charles Agoti: Is RSV transmission in households tractable using genomics?

  • 11:00-11:15 Break

  • 11:15-12:00 Lightning Talks

  • 12:00-17:00 Free time in Kyoto

  • 17:00-17:30 Brian Arnold: Landscape of selection and admixture in Neisseria gonorrhoeae

  • 17:30-18:00 Kate Baker: Horizontal gene transfer among Shigella species

  • 18:00-18:30 Claire Chewapreecha: Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

  • 18:30-19:00 Lightning Talks

Wednesday, November 7
  • 09:30-10:00 John Lees: Expanding variables in bacterial GWAS: multi-locus and multi-trait approaches

  • 10:00-10:30 Ed Feil: AMR, transmission and population genomics of the Klebsiella genus: Preliminary results from the SpARK project

  • 10:30-11:00 Yonatan Grad: Acquiring and maintaining antibiotic resistance in Neisseria gonorrhoeae

  • 11:00-11:15 Break

  • 11:15-12:00 Lightning Talks

  • 12:00-15:00 Free time in Kyoto

  • 15:00-15:30 Claire Jenkins: Evolution and transmission of Shiga toxin–producing Escherichia coli (STEC) in England (1983 to 2018)

  • 15:30-16:00 Caitlin Pepperell:

  • 16:00-16:30 Wataru Iwasaki: Generalist species drive microbial dispersion and evolution

  • 16:30-17:00 Lightning Talks

  • 17:30-20:00 Closing Dinner at the New Miyako Hotel

Location & Accommodation

All scientific sessions will take place in Room B, 5/F, Mielparque Kyoto.

Mielparque Kyoto is a short, one-minute walk from Kyoto Station. For more information on travelling to Kyoto by plane and train, check Inside Kyoto. There are a number of hotels within walking distance of the venue; we recommend the New Miyako, located a ten-minute walk from the conference site.

 

Speakers

Confirmed speakers:
  • Charles Agoti: Tracking transmission of endemic respiratory and enteric viral infections in Kenya using sequence data

  • Brian Arnold: Landscape of selection and admixture in Neisseria gonorrhoeae

  • Kate Baker: Horizontal gene transfer among Shigella species 

  • Trevor Bedford: Forecasting strain turnover in influenza and dengue viruses

  • Claire Chewapreecha: Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

  • Martha Cloakie: Using genome based approaches to develop global bacteriophage products as antimicrobials to treat antibiotic resistant bacteria

  • Anne Cori: A graph-based evidence synthesis approach to detecting outbreak clusters: an application to dog rabies

  • Aaron Darling: Real-time sequencing, real-time outbreak surveillance. Fake-time phylogenetics?

  • Ed Feil: AMR, transmission and population genomics of the Klebsiella genus: Preliminary results from the SpARK project

  • Yonatan Grad: Acquiring and maintaining antibiotic resistance in Neisseria gonorrhoeae

  • Wataru Iwasaki: Generalist species drive microbial dispersion and evolution

  • Claire Jenkins: Evolution and transmission of Shiga toxin–producing Escherichia coli (STEC) in England (1983 to 2018)

  • Thibault Jombart: When are pathogen genome sequences useful in outbreak analytics?

  • Katia Koelle: Using viral sequence data to infer transmission dynamics and bottlenecks

  • John Lees: Expanding variables in bacterial GWAS: multi-locus and multi-trait approaches

  • Richard Neher: Tracking pathogenic bacteria and AMR at the plasmid, genome, and
    pan-genome level

  • Caitlin Pepperell

  • Marc Suchard: High-performance phylodynamic inference

 
 

Register

Registration ($400USD) includes access to the scientific sessions, the opening social, and the conference dinner. A discounted registration fee ($200USD) is available for students currently enrolled in a degree program. 
Because we aim to keep this workshop small and collaborative, only 55 places are available in our first ticket release; register ASAP to ensure you can join us. A further 10-15 places will be made available to waitlisted individuals following the close of the first ticket release. If you want to attend the workshop but are concerned about not receiving travel approval in time to secure one of the 50 early release spots, please email us so we can work out an arrangement!

For more information, contact smbegeptdworkshop@gmail.com

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