ASM Conference on Rapid Applied Microbial Next-

Generation Sequencing and Bioinformatic Pipelines

December 7-11, 2020 • Online

Final Program

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Program Committee .........................................................................2

Acknowledgments .............................................................................2

General Information .........................................................................3

Program ..............................................................................................5

TABLE OF CONTENTS

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Duncan MacCannell - ChairCenters for Disease Control and Prevention, Atlanta, Ga.

Ruth Timme - Co-ChairU.S. Food and Drug AdministrationCollege Park, Md.

Marc AllardU.S. Food and Drug AdministrationCollege Park, Md.

Jennifer GardyBill & Melinda Gates FoundationSeattle, Wash.

Elodie GhedinNew York UniversityNew York, N.Y.

George GthinjiKEMRI/Wellcome TrustNairobi, Kenya

Dag HarmsenUniversity of MuensterMuenster, Germany

Paul KeimNorthern Arizona University and TGen North, Flagstaff, Ariz.

Adam PhillippyNational Institutes of Health, Bethesda, Md.

Torsten SeemannUniversity of Melbourne Melbourne, Australia

Sofonias TessemaAfrica CDCAddis Ababa, Ethiopia

PROGRAM COMMITTEE

ACKNOWLEDGMENTSThe 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

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General Information

NAVIGATING VIRTUAL ASM NGSAttendees will be able to access all conference sessions and materials, including abstracts, posters, session presentations, live after chats and con-ference surveys. Detailed directions to assist in navigating are included throughout the site.

SESSIONSAll General and Poster Sessions will be presented virtually on the date and time scheduled, and available on-demand for six months after the conference. Scheduled sessions are organized by day. To access a specific session, select the day in which the session takes place. You will then be able to join the session at its sched-uled start time.

ABSTRACTSTo view abstracts, visit https://asm.org/Events/ASM-NGS/Abstracts.

CERTIFICATE OF ATTENDANCECertificates of Attendance will be avail-able through the conference platform once all mandatory sessions are at-tended.

Please Note: Poster Session viewing is not required to receive a Certificate of Attendance.

PROTECTING THE SCIENCE — PHOTO POLICYTo protect the integrity of the science, taking photos of the screen or videos of projected images of any session, slide, or poster with any device is prohibited.

ASM EVENTS CODE OF CONDUCT The American Society for Microbiol-ogy (ASM) is the main forum for microbial sciences that considers and debates scientific issues in an orderly, respectful, and fair man-ner. ASM 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. ASM prohibits and will not tolerate any form of harassment or bullying at its events. For the full ASM Events Code of Conduct policy, please visit asm.org/codeofconduct.

SOCIAL MEDIA ETIQUETTEWhile attending any ASM meeting, as well as when interacting with ASM on social media, ASM expects that all attendees will contribute to the professional atmosphere of the meet-ing. ASM and the Program Committee reserve the right to remove, delete, or block any individuals or social media comments exhibiting behavior that detracts from or disrupts the scientific virtual environment.

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General Information

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Program

MONDAY, DECEMBER 7 3:30 p.m. – 3:50 p.m. Welcome Duncan MacCannell, Chair, Centers for Disease ControlandPrevention

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&MelindaGatesFoundation, Seattle,Wash.

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

Panelist Trevor Bedford, Fred Hutchinson Cancer ResearchCenter,Seattle,Wash.

Panelist Bronwyn MacInnis, BroadInstitute,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, United Kingdom

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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,LaboratoryCorporationof America, Burlington, N.C. UtilizationofWholeGenomeSequencingof SARS-CoV-2 for Public Health Response Heather M. Blankenship, Michigan Department of Health and Human Services, Lansing, Mich. NearReal-timeGenomicEpidemiologyofthe SARS-CoV-2PandemicinConnecticut,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:PipelinestoPixels:Bioinformatic Tools,Workflows,DataIntegrationand Visualization Session Chair: Jennifer Gardy

Keynote RealTimeTrackingforReal-lifePandemics: Nextstrain and SARS-CoV-2 Emma Hodcroft, University of Basel, Basel Switzerland

Keynote PreciselyPracticingMedicineforCOVID,froma QuarterMillionTestedPatientsandaTrillion Points of Data Atul Butte, University of California, San Francisco, San Francisco, Calif.

Program

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CAREER CONNECTIONS

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InformingPublicHealthInterventionby LinkingandVisualisingSARS-CoV-2Genome SequencesandCOVIDMetadata Anthony P. Underwood, Centre for Genomic Pathogen Surveillance, Cambridge, United Kingdom CARD:Live:ADynamicVisualizationofthe CurrentStateofGlobalAntimicrobial 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,FoodandEnvironmental Microbiology Session Chair: Ruth Timme

Keynote WestNile4K:CollaborativeNetworkto Uncover Virus Emergence and Spread Nathan Grubaugh, Yale University, New Haven, Conn.

PathoSeq:AMultidisciplinaryProjectAiming toMaterializetheBenefitsofWholeGenome SequencingintheFoodProcessingIndustry Eva Wagner,Nofima-NorwegianInstituteof Food, Fisheries and Aquaculture Research, Ås, Norway Profilingof553Listeriamonocytogenes GenomesSuggestsDifferentNiche AdaptationsforFoodProcessingandDairy Farm Environments Hanna Castro, University of Helskinki, Helsinki, Finland

Program

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Genomic Surveillance of Salmonella spp. in Surface Waters Used in Agriculture and Aquaculture in Mexico Enrique Delgado Suarez,NationalAutonomous University of Mexico, Ciudad de Mexico, Mexico MonitoringYourBuildingWater:Implementing Metagenomic Approaches to Understand the Water Microbiome Vicente Gomez-Alvarez, U.S. Environmental ProtectionAgency,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. ImprovingtheUtilityofAntimicrobial ResistanceGenePredictionToolsUsingthe PHA4GEAMROutputSpecificationPackage 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 AdhesinsinCladeII Rory Welsh, Centers for Disease Control, Atlanta, Ga.

Program

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Program

Digging Deep for AMR: Monitoring AntimicrobialResistancein100kHostand Environmental Metagenomes Hannah-Marie Matiny, NationalFoodInstitute, Technical University of Denmark, Kongens Lyngby, Denmark

5:30 p.m. – 6:30 p.m. Next-generationSequencing(NGS)Applications forSARS-CoV-2DetectionandSurveillance Sponsored by Illumina Kelly Hoon,IlluminaExecutiveSalesSpecialist, MicrobiologyandInfectiousDisease

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. Session5:PipeDreams:Analytical Methods,BioinformaticTools and Pipelines Session Chair: Adam Phillippy

Keynote 200,0001:ATree-SpaceOdyssey,Outbreak Investigation in 2020 Aine O’Toole, University of Edinburgh, Edinburgh, United Kingdom Keynote DatabaseandToolsatthe2019Novel Coronavirus Resource Yiming Bao, NationalGenomicsData Center, Bejing, China

MAJORA:ContinuousIntegration SupportingDecentralisedSequencing for SARS-CoV-2 Genomic Surveillance Samuel M. Nicholls, University of Birmingham, Birmingham, United Kingdom

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Program

AccelerateYourResearchwithRAPT, anAssemblyandGeneAnnotation Pipeline Francoise Thibaud-Nissen, NCBI/NLM/NIH/DHHS, Bethesda, Md. PredictingAntimicrobialResistance UsingGloballyAlignedPartial Genomes Derya Aytan-Aktug, Technical University of Denmark, Kgs. Lyngby, Denmark

10:30 a.m. – 11:30 a.m. PosterSession5:PipeDreams

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

5:30 p.m. – 6:30 p.m. NetworkingSpeakerandSponsorChats

FRIDAY, DECEMBER 11 8:00 a.m. – 9:00 a.m. PosterSession6:NewTools

10:00 a.m. – 11:30 a.m. Closing Panel Discussion Keynote AfricaPathogenGenomicsInitiative(AfricaPGI) Sofonias Tessema, African Union, Addis Ababa, Ethiopia Panelist Kim Pruitt,NationalCenterforBiotechnology Information,Bethesda,Md.

Panelist Guy Cochrane,EuropeanNucleotide Archive, Cambridgeshire, United Kingdom

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Panelist Takahashi Gojoburi, DNA Data Bank of Japan, Japan

Panelist Yiming Bao,NationalGenomicsData Center, Beijing, China Panelist David Lipman,NationalCenterfor BiotechnologyInformation,Bethesda, Md.

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