4th ASM Conference on Rapid Applied Microbial Next-Generation Sequencing and Bioinformatic Pipelines (ASM NGS)
- Important Information
- Schedule & Presentations [monday|tuesday|wednesday|thursday|friday]
- Code of Conduct
- Live Notes
- NCBI Preconference Workshop
- ASM NGS Hackathon
- About ASMNGS
Welcome to ASM NGS 2020! As with so many things, ASMNGS will be a bit different this year, but we're grateful that you could join us in this virtual conference format.
As in years past, we're trying to make this conference as open, accessible, and user-friendly as possible in the interest of open science. This repo will store slides, posters, and notes from the conference from those participants who are up for sharing their material, and it will also serve as another mechanism to receive realtime 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, gramming, tiktoking, or whatever, please use the hashtag #ASMNGS. 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 or email this year's meeting chairs – Ruth Timme (twitter | email) and Duncan MacCannell (twitter | email). You can also open a new issue in this repo, or you can contact the wonderful ASM Conferences team through the meeting website.
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. If we're missing important links or useful supplemental materials, please let us know (or feel free to submit a pull request). We'll try to stay on top of it over the course of this week.
Our default 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.
PRESENTERS If we don't have your Twitter profile linked, or if you'd like us to add a PDF copy of your slides (or URL!), please tag Duncan or Ruth at any time during the meeting!
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| 15:30-15:40 | Duncan MacCannell & Ruth Timme | Program Committee | Welcome to ASMNGS 2020 |
| 15:40-15:50 | Victor DiRita | American Society for Microbiology | Welcome on Behalf of ASM |
| 15:50-16:50 | Trevor Bedford, Bronwyn MacInnis, Yonatan Grad - Moderated by Jennifer Gardy | Fred Hutch, Broad Institute, Harvard University | OPENING PANEL DISCUSSION: Navigating high-profile investigations and activities in the time of COVID-19 |
| 16:50-17:00 | Planning Committee | Planning Committee | Thanks, closing and logistics for the week. |
Genomic sequencing and molecular epidemiology are indispensable tools for clinical reference diagnostics, public health surveillance outbreak detection and response. This session will discuss how sequencing is being used in clinical and public health microbiology, and the challenges and successes in implementing these technologies successfully in routine and standard practice.
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| 10:00-10:30 | Sharon Peacock | Public Health England | TBD |
| 10:30-11:00 | Mike Worobey | University of Arizona | TBD |
| 11:00-11:15 | Oral abstract | Mike Levandoski | Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States |
| 11:15-11:30 | Oral abstract | Heather Blankenship | Utilization of Whole Genome Sequencing of SARS-CoV-2 for Public Health Response |
| 11:30-11:45 | Oral abstract | Joseph Fauver | Near real-time genomic epidemiology of the SARS-CoV-2 pandemic in Connecticut, USA |
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| TBD | Featured Poster | Rebecca Rockett (USydney) | The Powerful Duo: Synthesis of SARS-CoV-2 Genome Sequencing and Epidemiological Data for Targeted Control of COVID-19 |
| TBD | Featured Poster | Jorge Cervantes (Texas Tech) | Genetic Identification and Drug-Resistance Characterization of Mycobacterium tuberculosis Using a Portable Sequencing Device |
| TBD | Featured Poster | Matthias Groeschel (Harvard) | GenTB: A user-friendly online tool to predict antibiotic resistance in Mycobacterium tuberculosisusing statistical machine learning models |
| TBD | Featured Poster | Chunxiao Liao (Rice) | VariPhyer: a Modular, Open-source Computational Platform for Verifying Microbial Phylogenetic and Variant Analyses |
| TBD | Featured Poster | Mustapha Gani (UGreenwich) | Comparative metagenomic analysis of crude oil polluted, remediated and unpolluted soil samples across the Niger Delta region in Nigeria |
Interpreting genomic data in the context of other data, like spatiotemporal or epidemiological data, is critical to translating genomic data into public health action. This session will explore approaches to and tools for integrating and visualizing data for use in decision-making.
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 17:30-18:00 | Emma Hodcroft | University of Bern | Real-time Tracking for Real-Life Pandemics: Nextstrain & SARS-CoV-2 |
| 18:00-18:30 | [Atul Butte]((https://www.twitter.com/atulbutte) | UCSF | TBD |
| 18:30-18:45 | Oral abstract | Anthony Underwood (CGPS) | Informing public health intervention by linking and visualising SARS-CoV-2 genome sequences and COVID metadata |
| 18:45-19:00 | Oral abstract | Aaron Petkau (PHAC) | CARD:Live: A Dynamic Visualization of the Current State of Global Antimicrobial Resistance (AMR) |
Understanding microbial diversity as it exists in the natural world, on farms, and in the built environment is critical for understanding origins of contamination events, AMR, biocide resistance and other pathogen risks. This session will highlight genomic research in veterinary, food and environmental microbiology.
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| 10:00-10:30 | Nathan Grubaugh | Yale School of Public Health | TBD |
| 10:30-10:45 | Oral abstract | Eva Wagner | PathoSeq: A multidisciplinary project aiming to materialize the benefits of whole genome sequencing in the food processing industry |
| 10:45-11:00 | Oral abstract | Hanna Castro | Profiling of 553 Listeria monocytogenes genomes suggests different niche adaptations for food processing and dairy farm environments |
| 11:00-11:15 | Oral abstract | Enrique Delgado | Genomic surveillance of Salmonellaspp. in surface waters used in agriculture and aquaculture in Mexico |
| 11:15-11:30 | Oral abstract | Vincente Gomez-Alverez | Monitoring Your Building Water: implementing metagenomic approaches to understand the water microbiome |
Sequencing is providing important new insights in the emergence of antimicrobial resistance, and the risk that resistant organisms pose to humans, animals, agriculture and the environment. This session will explore new approaches for antimicrobial genotyping and the characterization of antimicrobial resistant microbial populations, and the development of new tools to improve their impact.
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| 15:30-16:00 | Ami Bhatt | Stanford | TBD |
| 16:00-16:15 | Oral abstract | Ines Mendes | Improving the Utility of Antimicrobial Resistance Gene Prediction Tools Using the PHA4GE AMR Output Specification Package |
| 16:15-16:30 | Oral abstract | Ivan Sserwadda | rMAP; Rapid microbial analysis pipeline for ESKAPE bacterial group whole-genome sequence data |
| 16:30-16:45 | Oral abstract | Rory Welsh | Genomic analysis from each of the four major Candida auris clades reveal chromosomal rearrangements and loss of subtelomeric adhesins in Clade II |
| 16:45-17:00 | Oral abstract | Hannah-Marie Martiny | Digging Deep for AMR: Monitoring Antimicrobial Resistance in 100k Host and Environmental Metagenomes |
Recent technology advances have made whole-genome sequencing and other sequencing-based assays ubiquitous in modern microbiology. However, this shift in techniques is generating huge volumes of data that require computational analysis. This session covers new analytical methods and bioinformatics tools designed to surf the growing wave of genomic data.
| Time | Speaker | Affiliation | Title |
|---|---|---|---|
| 08:30-09:00 | Aine O'Toole | University of Edinburgh | 200,001: A tree-space odyssey. Pandemic phylogenetics and reporting in 2020 |
| 09:00-09:30 | Yiming Bao | Beijing Institite of Genomics | TBD |
| 09:30-09:45 | Oral abstract | Sam Nicholls (UBirmingham) | MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance |
| 09:45-10:00 | Oral abstract | Francoise Thibaud-Nissen (NCBI) | Accelerate your research with RAPT, an assembly and gene annotation pipeline |
| 10:00-10:15 | Oral abstract | Derya Aytan-Atkug (DTU) | Predicting Antimicrobial Resistance Using Globally Aligned Partial Genomes |
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| TBD | Featured Poster | Emma Griffiths (UBC) | The DataHarmonizer: A fast, secure application for the harmonization of SARS-CoV-2 contextual data |
| TBD | Featured Poster | Mohammed Khalfan (NYU) | MAD: A Pipeline for Evaluating Minor Allele Detection Tools |
| TBD | Featured Poster | Daria van Tyne (UPitt) | Whole-genome sequencing surveillance to study the epidemiology of vancomycin-resistant enterococci at a tertiary care hospital over three years |
| TBD | Featured Poster | Sandra Montano-Salazar (UNColombia) | The microbiome as evolutionary trait of octocorals |
| TBD | Featured Poster | Tryna Tania (UIndonesia) | Whole genome sequencing analysis of multi-drug resistantMycobacterium tuberculosisfrom Java, Indonesia |
| Time (GMT-5) | Speaker | Affiliation | Title |
|---|---|---|---|
| 10:00-1030h | Sofonias Tessema | Africa CDC | The AfricaCDC Pathogen Genomics Initiative |
| 10:50-11:30 | Kim Pruitt (NCBI), Guy Cochrane (EBI), Takashi Gojoburi (DDBJ), Yiming Bao (BIG) - Moderated by David Lipman (Founding Director, NCBI) | NCBI, EBI, DDBJ and BIG | PANEL DISCUSSION: Open pathogen sequence data sharing and collaboration in public health, lessons from COVID-19 and directions for the future |
| 11:30-11:45 | Planning Committee | Planning Committee | Closing comments. |
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!
Live notes have been an important ASM NGS for the past several meetings. For ASMNGS17 and 18, we used Mozilla's EtherPad platform, and unfortunately, I suspect that the notes were lost when Mozilla shuttered the platform in 2018. This time, we'll try Google Docs. The link to the ASMNGS20 collaborative live notes doc is right HERE. I have no idea how well this will work in an asynchronous virtual conference, but jump in and start contributing if you want to!
Update: Thanks to Matt Croxen for finding a PDF archive of the ASM2017 live notes!
The National Center for Biotechnology Information (NCBI) is hosting a virtual workshop entitled: "Introduction to NCBI Pathogen Detection and Google Cloud-Based Resources for Pathogen NGS Analysis". If interested in participating, please contact Bill Klimke by November 20th, 2020. More information can) be found in the PDF announcement linked here.
REGISTRATION IS CLOSED - THANKS FOR YOUR INTEREST.
This year, Boas van der Putten and Lee Katz are organizing what looks to be a wonderful ASM NGS Hackathon.
This year's objective is unit testing. Participants will learn by experience: unit testing, continuous integration, GitHub Actions, and everything else that goes with git.
In other words, each team will take on the task of choosing a bioinformatics software package, testing it in a standardized way, and reporting back to the group. A finished unit test will be represented by a shiny green badge on our site, indicating that the software works (or a red badge of shame if it doesn't). If successful, the site will serve as a certification that any given bioinformatics software works (or doesn't).
If interested in participating, please sign up here: https://forms.gle/rSSkQZv3pZXEAh3a7!
After signing up, please form teams via pull requests here: https://github.com/microbinfie-hackathon2020/CSIS/blob/main/TEAMS.md.
More information and the hackathon base of operations can be found here: https://github.com/microbinfie-hackathon2020/CSIS
Four teams developed unit tests and validation for common bioinformatic tools and workflows. Team Chewbbaca, Team SARS-CoV-2, Team All-The-Krakens and Team Assembly brought together dozens of beautiful nerds from across four (five?) continents! Running the hackathon was a learning experience, and all four teams made some really amazing hacks!
PUBLICATION: van der Putten, B. C. L., C. I. Mendes, B. M. Talbot, J. de Korne-Elenbaas, R. Mamede, P. Vila-Cerqueira, L. P. Coelho, et al. 2022. Software testing in microbial bioinformatics: a call to action. Microbial Genomics 8: 000790. link
CONGRATULATIONS TO ALL THAT PARTICIPATED, AND WE HOPE THAT THE HACKING CONTINUES ON!
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. Also in 2018, Ruth Timme (FDA) replaced Eric Brown on the organizing committee and the 2020 planning committee grew to include George Gthinji, Torsten Seemann, and Sofonias Tessema.
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 Ruth and Duncan - 149 were accepted, and 10 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, to ensure that ASM NGS continues to represent the full breadth, brightness and potential of our field.
Subsidized registration for participants from low and middle income countries (LMICs) is thanks to generous support from the Bill and Melinda Gates Foundation. You can apply for a subsidy here, or see if you are eligible.
We are grateful to all of our corporate sponsors this year, and look forward to a great conference.
Duncan MacCannell - Chair, Centers for Disease Control and Prevention, Atlanta
Ruth Timme - Co-Chair, U.S. Food and Drug Administration, College Park
Marc Allard U.S. Food and Drug Administration, College Park
Jennifer Gardy Bill and Melinda Gates Foundation, Seattle
Elodie Ghedin National Human Genome Research Institute, Bethesda
George Gthinji KEMRI/Wellcome Trust, Nairobi, Kenya
Dag Harmsen University of Muenster, Muenster, Germany
Paul Keim Northern Arizona University,Flagstaff
Adam Phillippy National Institutes of Health, Bethesda
Torsten Seemann University of Melbourne, Melbourne, Australia
Sofonias Tessema Africa CDC, Addis Ababa, Ethiopia