ASM Conference on Rapid Applied Microbial Next- Generation Sequencing and Bioinformatic Pipelines

December 7-11, 2020 • Online

Final Program See sequencing in a new light

Explore the NextSeq™ 2000

www.illumina.com/NextSeq2000 For Research Use Only. Not for use in diagnostic procedures. © 2020 Illumina, Inc. All rights reserved. TABLE OF CONTENTS

Program Committee ...... 2

Acknowledgments ...... 2

General Information ...... 3

Program ...... 5

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1 PROGRAM COMMITTEE

Duncan MacCannell - Jennifer Gardy Paul Keim Chair Bill & Melinda Gates Northern Arizona Centers for Disease Foundation University and TGen Control and Prevention, Seattle, Wash. North, Flagstaff, Ariz. Atlanta, Ga. Elodie Ghedin Adam Phillippy Ruth Timme - Co-Chair New York University National Institutes of U.S. Food and Drug New York, N.Y. Health, Bethesda, Md. Administration College Park, Md. George Gthinji Torsten Seemann KEMRI/Wellcome Trust University of Melbourne Marc Allard Nairobi, Kenya Melbourne, Australia U.S. Food and Drug Administration Dag Harmsen Sofonias Tessema College Park, Md. University of Muenster Africa CDC Muenster, Germany Addis Ababa, Ethiopia

ACKNOWLEDGMENTS

The ASM NGS Program Committee and the American Society for Microbiology acknowledge the support of the Bill & Melinda Gates Foundation for selecting participants from low to middle- income countries.

Additionally, the following sponsors are acknowledged for their support of the conference. On behalf of our leadership and members, we thank them for their financial support:

Platinum

Gold

Bronze

2 General Information

NAVIGATING VIRTUAL ASM ASM EVENTS CODE OF NGS CONDUCT Attendees will be able to access all The American Society for Microbiol- conference sessions and materials, ogy (ASM) is the main forum for including abstracts, posters, session microbial sciences that considers presentations, live after chats and con- and debates scientific issues in an ference surveys. Detailed directions orderly, respectful, and fair man- to assist in navigating are included ner. ASM is committed to providing throughout the site. an environment that encourages the free expression and exchange SESSIONS of scientific ideas and promotes All General and Poster Sessions will equal opportunities and respectful be presented virtually on the date treatment for all participants. ASM and time scheduled, and available prohibits and will not tolerate any on-demand for six months after the form of harassment or bullying at conference. Scheduled sessions are its events. For the full ASM Events organized by day. To access a specific Code of Conduct policy, please visit session, select the day in which the asm.org/codeofconduct. session takes place. You will then be able to join the session at its sched- SOCIAL MEDIA ETIQUETTE uled start time. While attending any ASM meeting, as well as when interacting with ASM ABSTRACTS on social media, ASM expects that To view abstracts, visit https://asm. all attendees will contribute to the org/Events/ASM-NGS/Abstracts. professional atmosphere of the meet- ing. ASM and the Program Committee CERTIFICATE OF ATTENDANCE reserve the right to remove, delete, or Certificates of Attendance will be avail- block any individuals or social media able through the conference platform comments exhibiting behavior that once all mandatory sessions are at- detracts from or disrupts the scientific tended. virtual environment.

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4 Program

MONDAY, DECEMBER 7

3:30 p.m. – 3:50 p.m. Welcome Duncan MacCannell, Chair, Centers for Disease Control and Prevention

Ruth Timme, Co-Chair, U.S. Food and Drug Administration

3:50 p.m. – 5:00 p.m. Opening Panel Discussion

Moderator Jennifer Gardy, Bill & Melinda Gates Foundation, Seattle, Wash.

Panelist Yonatan Grad, Harvard School of Public Health, Boston, Mass.

Panelist Trevor Bedford, Fred Hutchinson Cancer Research Center, Seattle, Wash.

Panelist Bronwyn MacInnis, Broad Institute, Cambridge, Mass.

5:15 p.m. – 6:15 p.m. Opening Session Live Q/A

TUESDAY, DECEMBER 8

8:00 a.m. – 9:00 a.m. Featured Poster Session A

10:00 a.m. – 11:45 a.m. Session 1: Epidemiological Cues: Sequencing in Clinical and Public Health Microbiology Session Chair: Duncan MacCannell

Keynote SARS-CoV-2 Sequencing as a Public Health Tool Sharon Peacock, University of Cambridge, Cambridge,

5 Program

Keynote The Emergence of SARS-CoV-2 in Europe and North America Mike Worobey, University of Arizona, Tucson, Ariz.

Geographic and Temporal Mapping of the SARS-CoV-2 Pandemic in the United States Michael Levandoski, Laboratory Corporation of America, Burlington, N.C.

Utilization of Whole Genome Sequencing of SARS-CoV-2 for Public Health Response Heather M. Blankenship, Michigan Department of Health and Human Services, Lansing, Mich.

Near Real-time Genomic Epidemiology of the SARS-CoV-2 Pandemic in Connecticut, USA Joseph R. Fauver, Yale School of Public Health, New Haven, Conn.

3:30 p.m. – 4:30 p.m. Poster Session 1: Epidemiological Cues

5:30 p.m. – 7:00 p.m. Session 2: Pipelines to Pixels: Bioinformatic Tools, Workflows, Data Integration and Visualization Session Chair: Jennifer Gardy

Keynote Real Time Tracking for Real-life Pandemics: and SARS-CoV-2 Emma Hodcroft, University of Basel, Basel Switzerland

Keynote Precisely Practicing Medicine for COVID, from a Quarter Million Tested Patients and a Trillion Points of Data Atul Butte, University of California, San Francisco, San Francisco, Calif.

6 Why Publish with ASM? DAYS From final decision to publication. ASM Journals has 19 a policy of expedited reviews. Learn more at journals.asm.org

ASM’s Job Board CAREER CONNECTIONS

Search for and apply to microbiology jobs, upload your resume/CV, set up e-mail notifcations, and more! www.asmcareerconnections.org

7 Program

Informing Public Health Intervention by Linking and Visualising SARS-CoV-2 Genome Sequences and COVID Metadata Anthony P. Underwood, Centre for Genomic Pathogen Surveillance, Cambridge, United Kingdom

CARD: Live: A Dynamic Visualization of the Current State of Global Antimicrobial Resistance (AMR) Aaron Petkau, Public Health Agency of Canada, Winnipeg, Manitoba

7:30 p.m. – 8:30 p.m. Poster Session 2: Pipelines to Pixels

WEDNESDAY, DECEMBER 9

10:00 a.m. – 11:30 a.m. Session 3: Farm to Table: Sequencing in Veterinary, Food and Environmental Microbiology Session Chair: Ruth Timme

Keynote West Nile 4K: Collaborative Network to Uncover Virus Emergence and Spread Nathan Grubaugh, Yale University, New Haven, Conn.

PathoSeq: A Multidisciplinary Project Aiming to Materialize the Benefits of Whole Genome Sequencing in the Food Processing Industry Eva Wagner, Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås,

Profiling of 553 Listeria monocytogenes Genomes Suggests Different Niche Adaptations for Food Processing and Dairy Farm Environments Hanna Castro, University of Helskinki, Helsinki, Finland

8 Program

Genomic Surveillance of Salmonella spp. in Surface Waters Used in Agriculture and Aquaculture in Mexico Enrique Delgado Suarez, National Autonomous University of Mexico, Ciudad de Mexico, Mexico

Monitoring Your Building Water: Implementing Metagenomic Approaches to Understand the Water Microbiome Vicente Gomez-Alvarez, U.S. Environmental Protection Agency, Cincinnati, Ohio

12:00 p.m. – 1:00 p.m. Poster Session 3: Farm to Table

3:30 p.m. – 5:00 p.m. Session 4: Drugs and Thugs: Sequencing to Combat AMR Session Chair: Elodie Ghedin

Keynote From Precision Microbial Genomics to Precision Medicine Ami Bhatt, Stanford University, Stanford, Calif.

Improving the Utility of Antimicrobial Resistance Gene Prediction Tools Using the PHA4GE AMR Output Specification Package Catarina I. Mendes, Universidade de Lisboa, Lisboa, Portugal

rMAP: Rapid Microbial Analysis Pipeline for ESKAPE Bacterial Group Whole-Genome Sequence Data Ivan Sserwadda, Makerere University, Kampala, Uganda

Genomic Analysis From Each of the Four Major Candida auris Clades Reveal Chromosomal Rearrangements and Loss of Subtelomeric Adhesins in Clade II Rory Welsh, Centers for Disease Control, Atlanta, Ga.

9 Program

Digging Deep for AMR: Monitoring Antimicrobial Resistance in 100k Host and Environmental Metagenomes Hannah-Marie Matiny, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark

5:30 p.m. – 6:30 p.m. Next-generation Sequencing (NGS) Applications for SARS-CoV-2 Detection and Surveillance Sponsored by Illumina Kelly Hoon, Illumina Executive Sales Specialist, Microbiology and Infectious Disease

7:00 p.m. – 8:00 p.m. Poster Session 4: Drugs and Thugs

THURSDAY, DECEMBER 10

8:30 a.m. – 10:15 a.m. Session 5: Pipe Dreams: Analytical Methods, Bioinformatic Tools and Pipelines Session Chair: Adam Phillippy

Keynote 200,0001: A Tree-Space Odyssey, Outbreak Investigation in 2020 Aine O’Toole, , Edinburgh, United Kingdom

Keynote Database and Tools at the 2019 Novel Coronavirus Resource Yiming Bao, National Genomics Data Center, Bejing, China

MAJORA: Continuous Integration Supporting Decentralised Sequencing for SARS-CoV-2 Genomic Surveillance Samuel M. Nicholls, University of Birmingham, Birmingham, United Kingdom

10 Program

Accelerate Your Research with RAPT, an Assembly and Gene Annotation Pipeline Francoise Thibaud-Nissen, NCBI/NLM/NIH/DHHS, Bethesda, Md.

Predicting Antimicrobial Resistance Using Globally Aligned Partial Genomes Derya Aytan-Aktug, Technical University of Denmark, Kgs. Lyngby, Denmark

10:30 a.m. – 11:30 a.m. Poster Session 5: Pipe Dreams

3:30 p.m. – 4:30 p.m. Featured Poster Session B

5:30 p.m. – 6:30 p.m. Networking Speaker and Sponsor Chats

FRIDAY, DECEMBER 11

8:00 a.m. – 9:00 a.m. Poster Session 6: New Tools

10:00 a.m. – 11:30 a.m. Closing Panel Discussion

Keynote Africa Pathogen Genomics Initiative (Africa PGI) Sofonias Tessema, African Union, Addis Ababa, Ethiopia

Panelist Kim Pruitt, National Center for Biotechnology Information, Bethesda, Md.

Panelist Guy Cochrane, European Nucleotide Archive, Cambridgeshire, United Kingdom

11 Panelist Takahashi Gojoburi, DNA Data Bank of Japan, Japan

Panelist Yiming Bao, National Genomics Data Center, Beijing, China

Panelist David Lipman, National Center for Biotechnology Information, Bethesda, Md.

11:30 a.m. – 11:45 a.m. Conference Wrap Up

12