Bringing together experts in the fields of bacterial genomics, evolution, population biology, network analysis and modelling.

Purpose of the Workshop

Understanding how pathogens evolve is central to understanding how they cause disease and how they are transmitted amongst host and non-host niches. The research environment has rapidly undergone a major change in following three central respects:
  1. The basic epidemiological workhorse, Multilocus Sequence Typing (MLST), has been replaced by whole-genome sequencing.
  2. Novel modeling and algorithmic approaches to analysis of complex evolutionary processes have emerged, such as Approximate Bayesian Computation (ABC) and various pangenome analysis tools.
  3. Realization of the extraordinary levels of horizontal gene transfer happening in numerous major pathogens, which provides them with enormous evolutionary potential.
To foster knowledge dissemination and exchange of novel ideas maximizing the potential on elucidating the evolutionary mechanisms in pathogens, we are holding a workshop focused on three evolutionary microbiology topics:
  1. Whole genomes and their evolution.
  2. Statistical and computational tools, such as ABC and genome-wide association studies
  3. Reconstructing evolutionary history, understanding phenotypes from genotypes and the uses of phylogenies together with modeling of pangenome evolution.

Organising Committee

Stephen Bentley

Principal Scientist

Wellcome Trust Sanger Institute


Sarah Cobey

Principal Investigator

Department of Ecology and Evolution

University of Chicago

Caroline Colijn

Faculty of Natural Sciences

Imperial College London


Jukka Corander

Professor Jukka Corander

Department of Mathematics


Ed Feil


Department of Biology & Biochemistry

University of Bath

Alison Mather

University of Glasgow


Time Speaker Topic
16:00 - 17:30 Welcome reception and poster session 1
17:30 - 18:05 Tetsuya Hayashi Nation-wide high-resolution phylogenomic analysis of Rickettsia japonica in Japan
18:05 - 18:40 Susan Holmes Using all the data for analyses of the Human Microbiome
19:00 DINNER

Time Speaker Topic
8:30 - 9:05 Nigel French Incursion, evolution and transmission of zoonotic pathogens in an isolated ecosystem: three tales from New Zealand
9:05 - 9:40 Stephen Beres Population pathogenomics of a current ongoing Streptococcus pyogenes invasive disease epidemic
9:40 - 10:15 Hattie Chung Selection and migration timescales that shape the spatial diversity of a pathogen in the human lung
10:15 - 10:45 BREAK
10:45 - 11:20 Denise Kühnert Phylodynamic analysis of (rapidly) evolving pathogens
11:20 - 11:55 Jennifer Gardy Genomics in the public health TB lab: what have we done, where are we going, and why does evolution keep screwing everything up?
17:00 - 17:35 Ashlee Earl Rewinding the clock on drug resistant tuberculosis
17:35 - 18:10 Christophe Fraser Transmission and genetic paraphyly
18:10 - 18:45 Alan McNally Pan-genome analysis provides an unprecedented resolution view of an emerging bacterial pathogen
18:45 - 19:15 BREAK
19:15 - 19:50 Yonatan Grad Using within-host RSV and population-level influenza viral diversity to explore the impact of host selective pressure on viral evolutionary dynamics
19:50 - 20:25 Edward Feil How much should we care about the variation in intergenic sites?
20:30 DINNER

Time Speaker Topic
8:30 - 9:05 Nobuto Takeuchi Gene-specific selective sweeps in bacteria and archaea caused by negative frequency- dependent selection
9:05 - 9:40 Jukka Corander Whole-genome linkage analysis reveals co-evolutionary mechanisms of antibiotic resistance in the pneumococcus
9:40 - 10:15 Vegard Eldholm Out of Africa? A phylodynamic analysis of TB transmission within a large immigrant group in Norway
10:15 - 10:45 BREAK
10:45 - 11:20 Caitlin Pepperell Adaptation of the Type VII secretion system
11:20 - 11:55 Bill Hanage Evolution in the short term - the potential and the limits for studying transmission
16:00 - 16:35 Tami Lieberman Intrapatient pathogen diversity reveals past selective pressures and patterns of within- host dissemination
16:35 - 17:10 Paul Rainey Untangling the origins of a plant disease outbreak
17:10 - 17:45 Caroline Colijn Two flavours of tree comparisons with applications
17:45 - 18:15 BREAK
18:15 - 18:50 Steve Baker A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure
18:50 - 19:25 Stephen Bentley Increased incidence and increased virulence of listeria monocytogenes sequence type 6 meningitis explained through pathogen population genomics
19:30 - 21:00 DINNER
21:00 - 22:00 Poster session 2

Time Speaker Topic
8:30 - 9:05 Kelly Wyres Exploring Klebsiella capsule diversity through analysis of whole-genome sequences
9:05 - 9:40 Lucy Weinert Replicated transitions from carriage to disease is associated with genome reduction in a zoonotic pathogen
9:40 - 10:15 Nick Croucher 'Intragenomic conflict' and the evolution of bacterial transformation
10:15 - 10:45 BREAK
10:45 - 11:20 Danny Wilson Within-host evolution of Staphylococcus aureus during asymptomatic carriage and invasive disease
11:20 - 11:55 Ben Cooper Reconstructing transmission trees for multiply antibiotic-resistant bacteria using densely sampled genomic data
17:00 - 17:35 Koji Yohara Methods for studying recombination hot regions and population structure in bacteria
17:35 - 18:10 Nadia El-Mabrouk Detection of codon reassignment and tRNA shift of function -Application to Bacillus genomes
18:10 - 18:45 Kathryn Holt Genomic insights into the evolution and transmission of drug resistant Acinetobacter baumannii
18:45 - 19:15 BREAK
19:15 - 19:50 Craig Winstanley Use of genomics to study the evolution of Pseudomonas aeruginosa populations
19:50 - 20:25 Alison Mather Investigating long-term and short-term transmission using genomics
20:30 DINNER


Speaker Topic
Siouxsie Wiles Evolution in Action: in vivo experimental evolution of the pathogenic bacterium Citrobacter rodentium
Michael Gutmann Fast Likelihood-Free Inference via Bayesian Optimization
Tadasuke Ooka Genomic diversity and evolutionary insights of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli
Claire Gorrie Asymptomatic carriage of K. pneumoniae and its role in hospital acquired infection
Yoshitoshi Ogura Identification of high Stx2-producing Escherichia coli O157 clades by WGS-based phylogenetic analysis
Yasuhiro Gotoh Explosive amplification of MITEs and a possible genome evolution pathway of Treponema phagedenis
Minna Vehkala Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

Speaker Topic
Rene Niehus Migration and horizontal gene transfer divide microbial genomes into multiple niches
Ken-ichi Lee Diffuse outbreak investigation in enterohemorrhagic Escherichia coli O121 by whole genome sequencing
Takayuki Wada Estimation of transmission routes of Mycobacterium tuberculosis based on genotypic and genomic analysis of a local prefectural surveillance in Japan
Sayaka Mino Genetic structure and spatial distribution pattern of chemolithoautotrophic Epsilonproteobacteria from deep-sea hydrothermal vents
Takahiko Shiba Dissimilarities of functional keystone species in co-occurrence network enable discrimination of intractable polymicrobial infectious diseases
Fumito Maruyama A hot-region promoting intraspecific divergence by shift of genetic elements related to defense systems against invading DNA
Iwamoto Tomotada Dynamic changes in genomic architecture of Mycobacterium avium in accordance with its phylogenetic diversification

  • Potential participants should pay registration fee only after receiving a confirmation of acceptance of their abstract.
  • All participants need to make their travel arrangements by themselves. Everyone except the invited speakers need to also book their own accommodation.

    The Shiga Lake hotel has a reserved number of rooms for the workshop delegates so please mention SMBE workshop when booking. If the reserved rooms are sold out, accommodation may also be booked in the nearby hotels, however, the organizers do not guarantee availability so please ensure that accommodation will be available before making your final travel arrangements.

    Confirmed participants will be provided an accommodation booking form which they should email to the Shiga Lake hotel to make room reservation .

Abstract Submission

Send Abstract

Abstract Submission

If you wish to participate in the meeting and give either a an oral or a poster presentation, please register below and send proposed title and short abstract to Indicate your preference of the presentation format and eventual restrictions regarding availability for presentation in case you cannot attend the whole duration of the meeting.

Send Abstract


Pay & Register


Fees: €250

Below link will take you to the payment site where you can pay and automatically register for the workshop. Please change the language on the site if necessary.

Pay & Register


Book your room

Accommodation Shiga Lake Hotel

Rooms have been reserved at the Shiga Lake Hotel and can be booked.

Confirmed participants will be provided an accommodation booking form which they should email to the Shiga Lake hotel to make room reservation.

In case the rooms reserved to workshop delegates are sold out, please check availability from the neighboring hotels before making further travel arrangements.

Below are some links to nearby hotels.

Prince Hotels

Shiga Kanko Hotel

Hotel Shirakabaso


Tokyo airport to Nagano by train:

There are two train lines out of Narita Airport. The JR company lines take you right into Tokyo. It can be quicker to use the Keisei Skyliner service to Ueno and pick up the JR Shinkansen from there.

This is a more direct route, but involves buying two lots of tickets and changing stations at Ueno (a 5 minute walk). A great website to see times for trains in Japan is Highly recommended as it shows transfer walking times, prices etc too.

Use Shinkansen train (about 90 minutes journey time, 2-3 trains per hour, 8200 Yen for a non-reserved seat, seat reservation costs around 700 Yen)

Nagano to Hasuike stop (close to the Lake Hotel): Bus (70 min, 1 run /hr, 1700 JPY)