ASM Microbe 2024
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Oxford Nanopore are sponsoring, exhibiting and presenting at this event. As the world’s largest microbial sciences conference, ASM Microbe is the best place to showcase your research, engage with global leaders and forge new connections with scientists, researchers and educators, just like you. Dive deep into groundbreaking discoveries across 8 scientific tracks and tailor your experience with a unique meeting-within-a-meeting format.
Members of the Oxford Nanopore team will be on hand throughout the ASM Microbe Annual Meeting 2024. Please contact events@nanoporetech.com ahead of the event if you would like to arrange a meeting. You will be able to find us at booth 517 throughout the conference - do stop by and say hello!
Please register below for our evening event on Friday, June 14th at 6:30 pm. Hear leading researchers present their latest work demonstrating the advantages and novel applications of nanopore sequencing.
See additional details below for our on-booth schedule of demos and Data for Breakfast.
Evening event
Celebrating a decade of DNA discoveries: 10 years of the MinION in microbiology
Date: Friday, June 14th, 2024
Time: 6:30 – 9:00 pm ET
Location: Omni Atlanta Hotel at Centennial Park, International Ballroom A/B/C
Join us for an insightful session as we mark the 10-year anniversary of the launch of the MinION and celebrate the journey of early pioneers and innovators of nanopore sequencing in the microbiology community. We will hear from distinguished speakers who have been trailblazers in developing and implementing nanopore sequencing over the years for a range of applications, from real-time outbreak response, to generating perfecting bacterial genome assemblies, to veterinary microbiome profiling, and expanding viral genomic surveillance capacity globally. Speakers will present key findings from their research, offering valuable insights into MinION's transformative role in microbiology. Following the presentations, we will engage in a panel discussion with live Q&A, where experts will share their experiences and perspectives on driving new sequencing methods and strategies over the years. Don't miss this opportunity to celebrate a decade of transformative DNA discoveries with nanopore sequencing.
Drinks and canapes will be served throughout the event. Please reach out to events@nanoporetech.com if you have any questions
Speakers
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Aaron Pomerantz, Associate Director of Global Segment Marketing, Oxford Nanopore TechnologiesAaron Pomerantz is the Associate Director of Global Segment Marketing at Oxford Nanopore, where he covers synthetic biology, microbiology and infectious disease. He received his PhD from UC Berkeley in the Department of Integrative Biology, employing genomics, genome editing, and bioimaging techniques in non-model organisms, as well as in-field nanopore sequencing in the Amazon rainforest. In his role as Segment Marketing Manager, he drives development of new areas in the research life sciences market.
From a 2014 hospital outbreak of Salmonella to the present day, Josh will look back at a decade of using nanopore sequencing for real-time outbreak reponse.
From a 2014 hospital outbreak of Salmonella to the present day, Josh will look back at a decade of using nanopore sequencing for real-time outbreak reponse.
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Josh Quick, UKRI Future Leaders Fellow, University of BirminghamIn 2016, ONT reads had an accuracy of only about 85%, and ONT-only assemblies were about 99% accurate. Today, simplex ONT reads have accuracies of over 99% and consensus sequences are approaching perfection. In this talk, I will describe how advancements in chemistry, basecalling and assembly algorithms now allow for the creation of error-free bacterial genomes using only ONT reads.
In 2016, ONT reads had an accuracy of only about 85%, and ONT-only assemblies were about 99% accurate. Today, simplex ONT reads have accuracies of over 99% and consensus sequences are approaching perfection. In this talk, I will describe how advancements in chemistry, basecalling and assembly algorithms now allow for the creation of error-free bacterial genomes using only ONT reads.
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Ryan Wick, Postdoctoral Bioinformatician, University of MelbourneWhy should we care about dog microbiomes? Because we care about our pets’ health and well-being and the microbiome has key roles in health and disease. Because we share not only spaces with our pets but also microbes. Because their microbiomes are good models for our microbiomes. We have been characterizing dog microbiomes for a while, and Nanopore sequencing has allowed us to make the most of our data. For the skin microbiome, amplicon strategies were our first choice since they are low biomass samples. We achieved greater taxonomic resolution (down to the species level) when using longer amplicons (e.g. full-length 16S rRNA). Using a culturomics approach, we delved deeper into the genome of Staphylococcus pseudintermedius, one of the main causal agents of skin pyoderma in dogs but also a common commensal. We have characterized the genomes of 130 bacterial isolates from healthy and diseased skin. Currently, we are also developing a rapid clinical metagenomics assay for dogs with skin diseases such as pyoderma. For the fecal microbiome, we make the most of our data using metagenomics, achieving highly contiguous genome assemblies (even single-contig, closed, circular genomes). In Shanghai pet dogs, we retrieved most of the diversity within the community as high-quality MAGs. Thus, we can locate antimicrobial resistance genes in their respective genomes, and identify potential pathogens.bacterial isolates from healthy and diseased skin. Currently, we are also developing a rapid clinical metagenomics assay for dogs with skin diseases such as pyoderma. For the fecal microbiome, we make the most of our data using metagenomics, achieving highly contiguous genome assemblies (even single-contig, closed, circular genomes). In Shanghai pet dogs, we retrieved most of the diversity within the community as high-quality MAGs. Thus, we can locate antimicrobial resistance genes in their respective genomes, and identify potential pathogens.
Why should we care about dog microbiomes? Because we care about our pets’ health and well-being and the microbiome has key roles in health and disease. Because we share not only spaces with our pets but also microbes. Because their microbiomes are good models for our microbiomes. We have been characterizing dog microbiomes for a while, and Nanopore sequencing has allowed us to make the most of our data. For the skin microbiome, amplicon strategies were our first choice since they are low biomass samples. We achieved greater taxonomic resolution (down to the species level) when using longer amplicons (e.g. full-length 16S rRNA). Using a culturomics approach, we delved deeper into the genome of Staphylococcus pseudintermedius, one of the main causal agents of skin pyoderma in dogs but also a common commensal. We have characterized the genomes of 130 bacterial isolates from healthy and diseased skin. Currently, we are also developing a rapid clinical metagenomics assay for dogs with skin diseases such as pyoderma. For the fecal microbiome, we make the most of our data using metagenomics, achieving highly contiguous genome assemblies (even single-contig, closed, circular genomes). In Shanghai pet dogs, we retrieved most of the diversity within the community as high-quality MAGs. Thus, we can locate antimicrobial resistance genes in their respective genomes, and identify potential pathogens.bacterial isolates from healthy and diseased skin. Currently, we are also developing a rapid clinical metagenomics assay for dogs with skin diseases such as pyoderma. For the fecal microbiome, we make the most of our data using metagenomics, achieving highly contiguous genome assemblies (even single-contig, closed, circular genomes). In Shanghai pet dogs, we retrieved most of the diversity within the community as high-quality MAGs. Thus, we can locate antimicrobial resistance genes in their respective genomes, and identify potential pathogens.
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Anna Cusco, Postdoctoral Researcher, Fudan UniversityInfluenza A virus and SARS-CoV-2 pose significant global health threats and necessitate robust surveillance systems for timely outbreak detection, risk assessment, and effective vaccine strain selection. Traditionally, a small number of high-capacity national public health laboratories within the Global Influenza Surveillance and Response System network have played the lead role in monitoring, sequencing, and reporting these viruses. However, this surveillance network can be greatly expanded by increasing the number of global laboratories that participate in this effort. To this end, the Centers for Disease Control and Prevention (CDC), in partnership with the World Health Organization Global Influenza Programme and the Association of Public Health Laboratories, has launched a training program to build and support local genomic surveillance capacity in countries that may be new to next-generation sequencing (NGS). We leveraged the proven track record of our influenza sequencing pipeline and developed a robust SARS-CoV-2 sequencing method targeting the S-gene. Our use of amplicon-based nanopore sequencing and stand-alone informatics has roots in portable, field-based sequencing, and is designed for low to moderate throughputs and ease of implementation. Our Docker-deployable software, MIRA, assembles reads into consensus genomes via CDC's in-house, viral genome assembler, IRMA. MIRA provides the user a graphical interface to perform NGS analysis, assesses the data for quality, and explains the critical thresholds required to produce accurate sequence. Implementing this program occurs in multiple stages: assessment of the laboratory’s existing wet-lab and informatics capacity to perform NGS, hands-on training of laboratory personnel, distribution of supplies via CDC’s International Reagent Resource, remote support, and monitoring of data uploads. To date, we have trained 136 participants from 84 countries during seven regional trainings, with additional trainings planned, and thousands of samples have already been uploaded to public repositories. This expanded genetic surveillance capacity enables us to monitor the evolution and circulation of genetic variants of influenza A virus and SARS-CoV-2 in a more robust and timely fashion, providing valuable data for outbreak preparedness and response. By empowering more national public health laboratories in existing surveillance networks, we hope to expand our collaborative relationships, increase the autonomy of those performing surveillance and, ultimately, ensure a more proactive and timely response to emerging threats.
Influenza A virus and SARS-CoV-2 pose significant global health threats and necessitate robust surveillance systems for timely outbreak detection, risk assessment, and effective vaccine strain selection. Traditionally, a small number of high-capacity national public health laboratories within the Global Influenza Surveillance and Response System network have played the lead role in monitoring, sequencing, and reporting these viruses. However, this surveillance network can be greatly expanded by increasing the number of global laboratories that participate in this effort. To this end, the Centers for Disease Control and Prevention (CDC), in partnership with the World Health Organization Global Influenza Programme and the Association of Public Health Laboratories, has launched a training program to build and support local genomic surveillance capacity in countries that may be new to next-generation sequencing (NGS). We leveraged the proven track record of our influenza sequencing pipeline and developed a robust SARS-CoV-2 sequencing method targeting the S-gene. Our use of amplicon-based nanopore sequencing and stand-alone informatics has roots in portable, field-based sequencing, and is designed for low to moderate throughputs and ease of implementation. Our Docker-deployable software, MIRA, assembles reads into consensus genomes via CDC's in-house, viral genome assembler, IRMA. MIRA provides the user a graphical interface to perform NGS analysis, assesses the data for quality, and explains the critical thresholds required to produce accurate sequence. Implementing this program occurs in multiple stages: assessment of the laboratory’s existing wet-lab and informatics capacity to perform NGS, hands-on training of laboratory personnel, distribution of supplies via CDC’s International Reagent Resource, remote support, and monitoring of data uploads. To date, we have trained 136 participants from 84 countries during seven regional trainings, with additional trainings planned, and thousands of samples have already been uploaded to public repositories. This expanded genetic surveillance capacity enables us to monitor the evolution and circulation of genetic variants of influenza A virus and SARS-CoV-2 in a more robust and timely fashion, providing valuable data for outbreak preparedness and response. By empowering more national public health laboratories in existing surveillance networks, we hope to expand our collaborative relationships, increase the autonomy of those performing surveillance and, ultimately, ensure a more proactive and timely response to emerging threats.
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Matthew Keller, PhD, Biologist, Centers for Disease Control and Prevention
Agenda
6:30 - 9:00 pm EDT | Agenda (subject to change) | |
|---|---|---|
6:30 - 7:00 pm | Networking reception | |
7:00 - 7:05 pm | Welcome and introductions | Aaron Pomerantz, Oxford Nanopore Technologies |
7:05 - 7:15 pm | A decade of nanopore sequencing for real-time outbreak response | Josh Quick, University of Birmingham |
7:15 - 7:25 pm | Perfect bacterial genomes from Nanopore reads alone | Ryan Wick, University of Melbourne |
7:25 - 7:35 pm | From fur to feces: exploring canine microbiomes (and beyond) using multiple Nanopore sequencing strategies | Anna Cusco, Big Data Biology Lab, Fudan University |
7:35 - 7:45 pm | Leveraging Portable Technology to Expand Global Influenza A Virus and SARS-CoV-2 Genetic Surveillance | Matthew Keller, Centers for Disease Control and Prevention |
7:45 - 8:05 pm | Q&A and audience discussion | Panel, facilitated by Aaron Pomerantz, Oxford Nanopore Technologies |
8:05 - 9:00 pm | Networking reception continued |
Booth demos
Demo title | Description | Date |
|---|---|---|
Flow cell loading/initiating a sequencing run | Learn how to load a flow cell and initiate a sequencing run using Oxford Nanopore technology. | Friday June 14th - 11:00 am Saturday June 15th - 4:00 pm Sunday June 16th - 1:00 pm |
Bacterial Genomes (NO-MISS) | Whole-genome sequencing of microbial isolates provides valuable information for public health, clinical microbiology research, food safety, and microbial ecology. Nanopore-only microbial isolate sequencing solution (NO-MISS) is a new rapid end-to-end workflow for the sequencing and analysis of bacterial isolates. Join our demo to learn how this workflow provides assembly, antimicrobial resistance and more in one easy to perform experiment! | Friday June 14th - 1:00 pm Saturday June 15th - 11:00 am Sunday June 16th - 3:30 pm |
ElysION: Streamlining sample-to-answer microbial sequencing | Effortlessly go from sample to ultra-rich sequencing data with a push of a button. Discover how our newest device, ElysION, accelerates your sequencing workflow, from extraction to analysis, ensuring rapid answers in labs of every size. Join our demo to see how ElysION transforms sample-to-answer Nanopore-only Microbial Isolate Sequencing (NO-MISS) into seamless, straightforward science. Leap into the future of automated genomics. | Friday June 14th - 4:00 pm Saturday June 15th - 1:00 pm Sunday June 16th - 11:00 am |
Visit booth 517 for Data for Breakfast.
The Oxford Nanopore team will present on Saturday June 15th and Sunday June 16th at 10:30 am on EPI2ME: Oxford Nanopore data analysis for anyone. Breakfast and coffee will be provided.
Friday, June 14th
Assessing carbapenemase-producing bacteria in wastewater samples in New York State: A pilot study
Time: 10:00 am - 5:00 pm
Session #: AES-P-019
Poster #: 738
Presenter: Kailee Cummings, Wadsworth Center NYSDOH
A dynamic adaptive sampling approach enriches antimicrobial genes in microbial communities
Time: 10:00 am - 5:00 pm
Session #: AES-P-010
Poster #: 780
Presenter: Danielle Wrenn, University of Alaska Fairbanks
Nanopore metagenomic sequencing for systemic bloodstream infection diagnostics evaluated in a prospective observational study
Time: 10:00 am - 5:00 pm
Session #: CPHM-P-032
Poster #: 301
Presenter: Morten Nielsen, Aalborg University
Clinical performance of real-time nanopore metagenomic sequencing for rapid identification of bacterial pathogens in cerebrospinal fluid
Time: 10:00 am - 5:00 pm
Session #: CPHM-P-032
Poster #: 302
Presenter: Young Kyung Yoon, Korea University Anam Hospital
Nanopore direct RNA sequencing reveals virus-induced changes in m6A patterns in human bronchial epithelial cells
Time: 10:00 am - 5:00 pm
Session #: HMB-P-013
Poster #: 951
Presenter: Dongyu Wang, University of Oklahoma
Does long-read sequencing technology produce superior viral genome assemblies
Time: 10:00 am - 5:00 pm
Session #: MBP-P-030
Poster #: 651
Presenter: Corina Tabron, American Type Culture Collection
Saturday, June 15th
Rapid species ID and AST direct from whole blood: initial results from a feasibility study in patients with suspected blood stream infection
Time: 10:00 am - 5:00 pm
Session #: CPHM-P-008
Poster #: 230
Presenter: Nicole Billings, Day Zero Diagnostics
Returning to full length sequencing of 16s rRNA for community profiling: evaluating sequencing quality and universal primer sets for use with nanopore long reads
Time: 10:00 am - 5:00 pm
Session #: MBP-P-028
Poster #: 651
Presenter: Kendra Maas, University of Connecticut
Sunday, June 16th
Surveillance of Neisseria meninigitidis drug resistance in New York State
Time: 10:00 am - 4:00 pm
Session #: AAR-P-003
Poster #: 415
Presenter: Andrew Peifer, Wadsworth Center
Implementation of diagnostic whole genome sequencing for identification of Non-Tuberculous Mycobacteria (NTM) in a reference public health laboratory: Evaluation of different analytical approaches and validation of a novel taxonomic marker, TlyC, for NTM speciation
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-014
Poster #: 259
Presenter: Varvara Kozyreva, Mycotic and Parasitic Diseases Section, California Department of Public Health
Optimization of a nanopore based detection method for 17 foodborne pathogens
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-034
Poster #: 304
Presenter: Doo Won Seo, National Institute of Food and Drug Safety Evaluation
Multiple approaches to genomic sequencing of Monkeypox Virus during the 2022-2023 outbreak
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-034
Poster #: 306
Presenter: Crystal Gigante, Centers for Disease Control and Prevention
Evaluation of agnostic RNA sequencing for biothreat and emerging infectious disease detection
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-034
Poster #: 308
Presenter: Anthony Kappell, Signature Science, LLC
SISPA-based metagenomics for the detection of respiratory pathogens
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-034
Poster #: 314
Presenter: Kelvin To, University of Hong Kong
High-accuracy, long-read sequencing of microbial isolates and standards enables AMR profiling, methylation detection, and taxonomic annotation
Time: 10:00 am - 4:00 pm
Session #: CPHM-P-034
Poster #: 325
Presenter: Lynn Ly, Oxford Nanopore Technologies
Friday, June 14th
Impact of Arctic thaw on soil microbial communities and emerging environmental health risks
Time: 11:45 am - 12:30 pm
Session #: AES-RF-001
Location: AES Track Hub
Presenter: Devin Drown, University of Alaska Fairbanks
Microbial ecology of PCB-contaminated sediments as part of an course-based undergraduate research experience (CURE)
Time: 11:45 am - 12:30 pm
Session #: POM-RF-001
Location: POM Track Hub
Presenter: Katrina Twing, Weber State University
Advancing antimicrobial resistance management in preterm infants
Time: 3:00 pm - 3:15 pm
Session #: AAR-IDS-005
Location: A315
Presenter: Amanda Ojeda, University of Florida
Direct-from-blood predictive AST from clinical samples
Time: 2:00 pm - 3:00 pm
Session #: LB-003
Location: Lounge & Learn 3
Presenter: Jason Wittenbach, Day Zero Diagnostics
Saturday, June 15th
Precision metagenomic testing: the next frontier
Time: 12:45 pm - 1:05 pm
Session #: CIV-TH-008
Location: CIV Track Hub
Presenter: Charles Chiu, University of California San Francisco
Treatment-emergent cefiderocol resistance in carbapenem-resistant Acinetobacter baumannii is associated with insertion sequence ISAba36 in the Siderophore receptor PirA
Time: 2:45 pm - 3:00 pm
Session #: AAR-IDS-008
Location: A311
Presenter: Sun Hee Moon, University of Arkansas for Medical Sciences
Characterization of microbial populations throughout the multiple parallel fermentation process of Makgeolli brewing
Time: 3:00 pm - 3:15 pm
Session #: AES-IDS-006
Location: B401
Presenter: Daniel Negrón, Noblis, Inc.
Isolation of novel dehalogenating bacteria from marine sponges
Time: 3:15 pm - 3:30 pm
Session #: AES-IDS-010
Location: B402
Presenter: Lauren Hall, Rutgers University
Next-generation sequencing is not rocket science, but genomic science. It is time for microbiology laboratories to implement routine AFB identification by NGS
Time: 3:05 pm - 3:20 pm
Session #: CPHM-IDS-012
Location: A411
Presenter: Jose Alexander, AdventHealth
Sequential collection of Bronchoalveolar Lavage specimens to monitor Pseudomonas aeruginosa adaptation in the human lung
Time: 3:00 pm - 3:15 pm
Session #: HMB-IDS-012
Location: B308
Presenter: Sophia Nozick, Northwestern University
Sunday, June 16th
Advancing wastewater-based genomics through the National Wastewater Surveillance System (NWSS)
Time: 8:15 am - 8:45 am
Session #: AES-IDS-003
Location: B401
Presenter: Jeffrey Mercante, Decatur, GA
From pandemics to phage therapy: Unlocking the capabilities of wastewater genomic epidemiology
Time: 8:45 am - 9:15 am
Session #: AES-IDS-003
Location: B401
Presenter: Smruthi Karthikeyan, California Institute of Technology
Evaluating the feasibility of influenza virus surveillance in wastewater
Time: 9:15 am - 9:30 am
Session #: AES-IDS-003
Location: B401
Presenter: Matthew Keller, Centers for Disease Control and Prevention
Metagenomics to decipher the dynamic of Carbapenem-Resistant Enterobacteriaceae in raw vs treated hospital wastewater
Time: 9:30 am - 9:45 am
Session #: AES-IDS-003
Location: B401
Presenter: Yaovi Hounmanou, University of Copenhagen
Evaluating the efficacy of wastewater testing programs in monitoring the prevalence of sexually transmitted infections
Time: 9:45 am - 10:00 am
Session #: AES-IDS-003
Location: B401
Presenter: Avnish Mistry, University of Nevada
Rapid detection and quantification of microorganisms by multiplexing nanopore sequencing for in-field application
Time: 10:00 am - 10:15 am
Session #: AES-IDS-003
Location: B401
Presenter: Kaiqin Bian, Georgia Institute of Technology
