Cambridge Healthtech Institute’s Second Annual
Advances in Microbiome Diagnostics
New Research and Developments for Utilizing the Microbiome in Diagnostics
August 18, 2017 | Grand Hyatt Washington | Washington, DC
The microbiome continues to prove itself as fertile ground for advances in understanding disease, therapeutics, and diagnostics. The challenge in microbiome diagnostics lies in developing diagnostic methods and tests that provide accurate assessment of the taxonomic compositions of microbiomes associated with complex samples. Cambridge Healthtech Institute’s 2nd Annual Advances in Microbiome Diagnostics symposium will highlight the latest research regarding microbiome mechanisms, biomarker discovery, and cutting-edge technologies. Special attention will be paid to novel approaches for diagnostics, as well as challenges and questions in funding, reimbursement, and commercialization. Join venture capitalists, regulatory agencies, and test developers to discuss these topics and more.
Final Agenda
Recommended Short Course(s)*
SC18: Novel Technologies for Exploring the Human Microbiome
*Separate registration required
FRIDAY, AUGUST 18
8:00 am Registration & Morning Coffee
8:25 Chairperson’s Opening Remarks
Katrine Whiteson, Assistant Professor, Molecular Biology & Biochemistry/Pediatrics, University of California, Irvine
8:30 KEYNOTE PRESENTATION: The Human Skin Microbiome: Diagnostics to Therapeutics
Julia Oh, Ph.D., Assistant Professor, The Jackson Laboratory for Genomic Medicine
Metagenomic analyses of the human skin demonstrate that contrasting forces of the skin’s biogeography and individuality shape the skin microbiome and its temporal dynamics. Striking changes in the skin’s microbiome are observed in skin disease and other host factors like age or immunodeficiency. This talk will address the potential for using the skin’s microbiome as a diagnostic as well as using it to design targeted therapies that spare the healthy microbiota.
9:00 Toward Microbial Disease Diagnosis Using Metagenomics: A Case of the Runs
Kostas Konstantinidis, Ph.D., Associate Professor, School of Civil & Environmental Engineering and School of Biological Sciences (Adjunct), Georgia Institute of Technology
Diagnosis of foodborne infections currently relies on culture-based methods, which are not rapid enough for real-time disease surveillance and frequently fail to identify the causative agents. Culture-independent metagenomic analyses of stool could overcome these limitations. I will summarize our recent efforts to validate metagenomics for outbreak characterization, and develop appropriate bioinformatics pipelines for metagenomic data analysis.
9:30 Metabolites, Germs and People: Eavesdropping on Human Microbial Communities
Katrine Whiteson, Assistant Professor, Molecular Biology & Biochemistry/Pediatrics, University of California, Irvine
The Whiteson lab uses culture-independent metagenomics, metabolomics, and ecological statistics along with hypothesis-driven, reductionist microbiology to answer questions about how bacteria and viruses affect human health. Several recent research projects will be presented from 1) healthy humans, 2) premature infants from Children’s Hospital Orange County, and 3) Cystic Fibrosis patients.
10:00 Opportunities and Roadblocks in Developing Microbiome Diagnostics
Session speakers
Panelists will discuss the following topics: What current research and knowledge tells us about the microbiome now – and which directions the field can take to develop diagnostics? Scientific roadblocks in developing diagnostics: what more do we need to know? Where the greatest diagnostic potential lies: is it companion diagnostics or direct diagnostics?
10:30 Coffee Break with Poster Viewing
11:00 Precision Metagenomics Identifies Colonization, Invasion, and Transmission of Antibiotic Resistant Bacteria
David Haslam, M.D., Associate Professor, Pediatric Infectious Diseases, Cincinnati Children’s Hospital
Using shotgun metagenomic sequencing (MSS) of samples from high risk patients we find a high rate of intestinal domination by antibiotic resistant pathogens. MSS allows identification to the strain level, enabling the ability to track strains that transition from colonization to invasive infection. Further, MSS is able to identify episodes of presumed patient-to-patient transmission. MSS will be a valuable screening test to identify patients at highest risk of infection.
11:30 Microbiome Sequencing in the Cystic Fibrosis Lung Detects Poor Response to Suboptimal Antibiotic Therapy
Andrea Hahn, MD, Assistant Professor, Infectious Diseases, Children’s National Health System
Next-generation sequencing of the cystic fibrosis lung microbiome detects changes in microbial communities in response to antibiotic treatment for pulmonary exacerbations. The lung microbiome of three CF patients with cultured antibiotic resistant gram negative pulmonary infections were evaluated pre and post antibiotic therapy. Shannon diversity decreased with antibiotic exposure (3.498 vs 2.558, p=0.087). The proportion of reads attributed to the cultured pathogen was significantly higher post-antibiotics compared to pre-antibiotics (49.6% vs 25%, p<0.001). These findings suggest that suboptimal antibiotic therapy preferentially targets commensal microbes, leading to a further dominance of the pathogenic organism.
12:00 pm Microbiome-Based Diagnosis of Pneumonia in the Intensive Care Unit
Georgios Kitsios, M.D., Ph.D., Instructor of Medicine; Post-Doctoral Scholar, Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh Medical Center
Limitations of microbiologic cultures for diagnosis of pneumonia in critically-ill patients result in “one-size-fits-all” antibiotic prescriptions, which can be harmful for individual patients and promote antibiotic resistance. We are examining the clinical utility of next-generation sequencing techniques of microbial DNA for the development of more accurate and faster diagnostics of pneumonia, with the goal of accomplishing precision antibiotic management in critically-ill patients.
12:30 Sponsored Presentation (Opportunity Available)
1:00 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own
1:30 Session Break
2:00 Chairperson’s Remarks
Keith Batchelder, M.D., CEO & Founder, Genomic Healthcare Strategies
2:05 The Human Virome: Current Understanding and Its Role in Microbiome Research
Lori Holtz, M.D., MSPH, Assistant Professor, Pediatrics, Washington University School of Medicine
We will define the virome, broadly discuss how it is studied, review our current understanding of the human infant gut virome and how it might interact with the bacterial microbiome, and discuss potential future directions for the virome.
2:35 Microbiome Disruption Indices: Harnessing the Human Microbiome for Human Health
Alison Laufer Halpin, Team Lead, Metagenomics and Molecular Biology Team, Clinical and Environmental Branch, Division of Healthcare Quality Promotion, CDC
This talk will cover previous and current work completed and funded by CDC as well as a discussion of the potential applications of microbiome measures to human health and infection control in the healthcare setting.
3:05 Refreshment Break with Poster Viewing
3:35 PANEL DISCUSSION: Challenges in Commercialization of Microbiome Diagnostics
Moderator:
Keith Batchelder, M.D., CEO & Founder, Genomic Healthcare Strategies
This panel discussion will touch on key challenges in commercializing microbiome diagnostics. What are the differences in diagnostic development between microbiome diagnostics and more traditional tests? What challenges do startups face in securing VC funding? What challenges and roadblocks face venture capitalists when developing these companies and their diagnostics?
Panelists:
Alison Laufer Halpin, Team Lead, Metagenomics and Molecular Biology Team, Clinical and Environmental Branch, Division of Healthcare Quality Promotion, CDC
Rita Colwell, Ph.D., Founder and Chair, CosmosID
4:35 Close of Symposia Programs