- Important Information
- Schedule & Presentations
- Code of Conduct
- Live Notes (shortcut to the Etherpad)
- Social Events
- About ASMNGS18
Welcome to ASMNGS18! In the spirit of open science, we're trying to make this conference as open, accessible, and user-friendly as possible. This repo will store slides, posters, and notes from the conference from those participants who are up for sharing their material, and also serves as a mechanism to receive feedback in the form of issues (check this out if you're unsure how to create an issue).
The conference website contains all sorts of useful information, and if you're tweeting, please use the hashtag #ASMNGS18. You can tag @ASMicrobiology too.
If you need to get in touch with the organizers at any time, you have multiple options. You can tweet at the meeting chairs – @jennifergardy and @dmaccannell, you can email Jennifer or Duncan, you can create an issue in this repo, or you can talk to our ASM Meetings team, including Latonya Trower, at the Registration Desk.
We are encouraging speakers and poster presenters to make their materials available online. There are multiple avenues for doing so, including Google Drive, Slideshare, figshare, F1000 Posters, and many more. The schedule below will be updated with links to slides as they are made available, and below the schedule is a list of posters that authors have placed online. Speaker name links go to Twitter profiles; talk title links go to slide files.
Our social media policy is that anything said by a speaker is fair game for tweeting and live note-taking unless the speaker states otherwise. We encourage speakers to indicate which slides, if any, should not be tweeted about or noted in the online notes. If you are planning to tweet about a poster, please ask permission of the poster presenter first.
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 5:00-5:05 | Dag Harmsen | Program Committee | Welcome |
| 5:05-5:15 | Jennifer Gardy | Program Commitee | Conference Logistics |
| 5:15-6:00 | Kate Baker | University of Liverpool | Finding Private Cable and a Century of Dysentery |
| 6:00-6:45 | Peter Daszak | EcoHealth Alliance | Pandemic Forecasting |
| 7:00-8:30 | Opening reception |
Monday Morning: Epidemiological Cues: NGS in Clinical and Public Health Microbiology (chair: Duncan MacCannell)
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 9:00-9:45 | Varvara Kozyreva | California Department of Public Health | CLIA-Compliant Validation of WGS for Clinical Microbiological Applications: Experience of a State Public Health Reference Laboratory |
| 9:45-10:30 | Luke Meredith | University of Cambridge | Mobile Genomics Laboratories for Viral Outbreak Response |
| 10:30-11:00 | Coffee break & Meet the Journal of Clinical Microbiology Editor in Chief | ||
| 11:00-11:20 | Oral abstract | Matthew Keller | Deployable NGS for Influenza Virus Field Surveillance and Outbreak Response |
| 11:20-11:40 | Oral abstract | Georgia Lagoudas | One Week, One Thousand Bacterial Genomes: Microfluidics for Molecular Epidemiology and High-resolution Intra-patient Bacterial Evolution |
| 11:40-12:00 | Oral abstract | Justin O'Grady | Rapid diagnosis of lower respiratory infection using nanopore based metagenomic sequencing |
| 12:00-12:20 | Oral abstract | Rita Colwell | Translating Metagenomics into Clinical Reality |
| 12:30-2:00 | Lunch (Tysons Ballroom) | ||
| 2:00-3:30 | Poster Session A: Posters 1-84 (Ash Grove Ballroom) |
Monday Afternoon: Pipelines to Pixels: NGS Data Integration and Visualization session (chair: Jennifer Gardy)
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 3:45-4:30 | Maia Majumder | MIT | Digital Disease Data for Outbreak Surveillance |
| 4:30-5:15 | Tom Schenk Jr. | KPMG | Predictive Analytics, Cities and Public Health |
| 5:15-5:30 | Oral abstract | Richard Goater | Pathogenwatch: A Global Platform for Genomic Surveillance |
| 5:30-5:45 | Oral abstract | Anamaria Crisan | A Method for Systematically Surveying Data Visualizations in Infectious Disease Genomic Epidemiology |
| 5:45-6:00 | Oral abstract | James Davis | Using Machine Learning to Predict Antimicrobial Minimum Inhibitory Concentrations and Associated Genomic Features for Nontyphoidal Salmonella |
Tuesday Morning: Farm-to-Table: NGS in Veterinary, Food, and Environmental Microbiology (chair: Ruth Timme)
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 8:00-8:45 | Jack Gilbert | University of Chicago | Breakfast Seminar sponsored by Illumina: Human and Environmental Microbial Health: A Global Perspective |
| 9:00-9:45 | Yu Wang | FDA | The Genetic Diversity of Salmonella and Listeria Isolates from Food Facilities |
| 9:45-10:30 | Nikki Shariat | Gettysburg College | CRISPR-SeroSeq: A Novel Amplicon-based Tool For Probing Salmonella Serovar Diversity |
| 10:30-11:00 | Coffee break | ||
| 11:00-11:20 | Oral abstract | Caroline Baretto | A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica |
| 11:20-11:40 | Oral abstract | Arthur Pightling | Measuring the Influences of Contamination on Whole-Genome Sequence Analyses of Foodborne Pathogens |
| 11:40-12:00 | Oral abstract | Chao Jiang | Dynamic Human Environmental Exposome Revealed by Longitudinal Personal Monitoring |
| 12:00-12:20 | Oral abstract | Mushal Allam | Whole-genome Sequencing Analyses to Investigate a Nationwide Outbreak of Listeriosis Caused by Ready-to-Eat Processed Meat Products, South Africa, 2017-2018 |
| 12:30-2:00 | Lunch (Tysons Ballroom) | ||
| 2:00-3:30 | Poster Session B: Posters 85-169 (Ash Grove Ballroom) |
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 3:45-4:30 | Blake Hanson | UTHealth | Nanopore Sequencing to Understand AMR |
| 4:30-5:15 | Mike Feldgarden | NCBI | AMR Resources at NCBI’s Pathogen Portal |
| 5:15-5:30 | Oral abstract | Emily Snavely | Development and Validation of a Clinical Whole-Genome Sequencing Pipeline for the Detection of Antimicrobial Resistance Genes in Bacterial Isolates |
| 5:30-5:45 | Oral abstract | David Rasko | Diversity Among blaKPC-containing Plasmids in Escherichia coli and Other Bacterial Species Isolated from the Same Patients |
| 5:45-6:00 | Oral abstract | Finlay Maguire | AMRtime: Rapid Accurate Identification of Antimicrobial Resistance Determinants from Metagenomic Data |
| 6:00-8:00 | Dinner (on your own) | ||
| 8:00-10:00 | Games Night social event |
Wednesday Morning: Pipe Dreams: Analytical Methods, Bioinformatics Tools, and Pipelines (chair: Adam Phillippy)
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 9:00-9:45 | Torsten Seemann | University of Melbourne | How to Write Bioinformatics Software no one will use |
| 9:45-10:30 | Beth Neuhaus | CDC | The CDC Domestic Influenza Surveillance System: From Pipe Dream to High-Performance Reality |
| 10:30-11:00 | Coffee break | ||
| 11:00-11:10 | Oral abstract | Anders Goncalves da Silva | AusTrakka: Enabling Data Sharing for Surveillance --- or Why Your Parents Were Right |
| 11:10-11:20 | Oral abstract | Brian Ondov | Mash Screen: Fast Sequence Containment Estimation Using MinHash |
| 11:20-11:30 | Oral abstract | Sam Minot | Gene-level metagenomic analysis identifies microbial genes reproducibly associated with IBD and CRC across independent clinical cohorts |
| 11:30-11:40 | Oral abstract | Ivan Liachko | From Contigs to Chromosomes: A Hi-C Based Graph Assembly Tool Significantly Improves Metagenome Contiguity and -Cfree Metagenomic Deconvolution |
| 11:40-11:50 | Oral abstract | Karin Lagesen | ORION - One health surRveillance Initiative on harmOnization of Data Collection and interpretatioN |
| 11:50-12:00 | Oral abstract | Dmitry Antipov | Plasmid Detection and Assembly in Genomic and Metagenomic Datasets |
| 12:00-12:10 | Oral abstract | Daniel Baker | Dash: Efficient Genomic Set Operations Using HyperLogLogs |
| 12:10-12:45 | Q&A for presenters |
ASM and the ASMNGS team is committed to providing an environment that encourages the free expression and exchange of scientific ideas and promotes equal opportunities and respectful treatment for all participants. All participants are expected to treat others with respect and consideration, follow venue rules, and alert ASM staff or security of any dangerous situations or anyone in distress.
ASM prohibits and will not tolerate any form of harassment or bullying at its events. Harassment is unwanted and unwelcome attention or other conduct that creates an environment where a reasonable person would feel unwelcome, intimidated, excluded, or abused. Harassment based on gender, race, religion, national origin, age, marital status, personal appearance, sexual orientation, gender identity or expression, family responsibilities, genetic information, disability, matriculation, political affiliation, and any other personal characteristic is strictly prohibited.
ASM will investigate all complaints of harassment, and investigations will be conducted in an unbiased manner. Violation of this code of conduct may result in the participant being asked to leave the event at which the incident occurred, without warning or refund; being barred from attending ASM events in the future; and, if relevant, being barred from or revocation of membership in the ASM. Event security and local police may be contacted in the event violators pose an imminent threat to others or are disrupting the event. If an ASM Staff member is found to be in violation, the ASM Headquarters Employment Policy (Prohibition against Sexual and Other Harassment and Discrimination) will be followed. Action regarding an ASM staff member may result in termination of employment.
This policy applies to all attendees, speakers, exhibitors, contractors, volunteers, and guests at ASM events. If a participant experiences or witnesses harassment, he/she should contact ASM staff (ASM staff are identifiable by their ASM Staff name badge) as soon as possible or contact security if they feel unsafe. All complaints will be responded to promptly and treated seriously and, to the extent possible, confidentially. Complaints that require broader investigation will be handled by ASM’s Ethics Committee. ASM expressly forbids any retaliation against individuals for reporting harassment.
In the event that an individual knowingly provides false information regarding a harassment situation, ASM may take similar disciplinary action.
If a participant experiences or witnesses harassment as described in ASM’s Events Code of Conduct, they should contact ASM staff (identifiable by ASM staff badge) to report the incident. If at any time a participant feels unsafe, they should contact meeting venue security immediately. If the participant is unsure that the incident was in violation of the ASM’s Events Code of Conduct, they may inquire first from an ASM staff member before filing a formal complaint.
The following information should be provided when reporting a harassment incident:
- Name and contact information of participant
- Name and contact information of any witnesses
- Identifying information (e.g. name, badge number, physical appearance) of the individual(s) who are accused of the harassment
- The specific action or behavior that was in violation of the ASM Events Code of Conduct
- The date and approximate time of the incident
- The location and circumstances surrounding the incident
ASM will accept and investigate all complaints of harassment and investigations will be conducted in an unbiased manner. All complaints will be responded to promptly and treated seriously and, to the extent possible, confidentially.
Thank you for helping to make this a welcoming, friendly space for all!
At ASMNGS17, we started using the EtherPad platform for live, collaborative note-taking - the 2017 notes can be found here. We're doing it again for ASMNGS18 - jump in and start taking notes at https://tinyurl.com/asmngs18 and feel free to tweet the link so others can follow along from wherever they are. This Etherpad will stay up as long as Mozilla keeps that instance alive. We'll also archive a version to figshare after the meeting.
Thanks to both ASM and our wonderful sponsors, we are able to host a number of social events during the meeting:
- Sunday 7:00-8:30pm is our opening reception, hosted by ASM and included in your registration
- Monday 7:00-11:00pm is a party hosted off-site by one of our conference sponsors, Oxford Nanopore. Registration for this free event is required - register here.
- Tuesday 8:00-8:45am is a breakfast seminar hosted by one of our conference sponsors, Illumina. Registration is not required.
- Tuesday 8:00pm will feature a conference games night social for all attendees, organized by ASM and made possible through sponsorship. Mini-golf, bean-bag toss, and drinks!
ASMNGS began in 2015 (if you're feeling nostalgic, the program is available here), organized by Dag Harmsen (University of Muenster), Marc Allard (FDA), and Eric Brown (FDA). In 2017, the program committee was co-chaired by Dag and Jennifer Gardy (BCCDC), and also included Marc, Eric, and new committee members Elodie Ghedin (NYU), Paul Keim (TGen), Duncan MacCannell (CDC), Adam Phillippy (NHGRI). In order to both coincide with the GenomeTrakr annual meeting and to not conflict with ABPHM, the committee decided to move the meeting to even years beginning in 2018. This year's meeting has been co-chaired by Jennifer and Duncan, and Ruth Timme (FDA) replaced Eric Brown on the organizing committee. The pre-conference workshop was organized by Dag.
Keynote speakers were selected by soliciting ideas from the organizing committee, who then arrived at our top choices through an email discussion. Submitted abstracts were reviewed by Jennifer and Duncan - 194 were accepted, and 22 were declined. Reasons for declining abstracts included a topic not consistent with the conference's scope, or inadequate/inappropriate/insufficient methods/results/conclusions. All accepted abstracts were reviewed by the organizing committee, and six committee members cast votes for that they felt merited oral presentation. Votes were tallied, and abstracts selected for oral presentation accordingly. We also looked for diversity in our presenters, though we acknowledge gender diversity was hard to achieve in the Tools and Pipelines section. Travel awards for trainees were also allocated using the committee's votes.
All program committee members have funded their own travel and registration costs for the meeting. Invited keynote speakers have been reimbursed according to ASM guidelines. All sponsorship money raised has gone towards the cost of hosting the meeting, including social events.