Cambridge Healthtech Institute’s 2nd Annual

Molecular Diagnostics for Infectious Disease

Advancing Molecular Diagnostics to Improve Detection and Patient Outcome

February 20-22, 2017 | Moscone North Convention Center | San Francisco, CA
Part of the 24th International Molecular Medicine Tri-Conference

 

With a growing number of technologies, tests, antibiotic-resistant bugs, and epidemics, molecular diagnostics are more important than ever for a wide range of infectious diseases. Molecular Diagnostics for Infectious Disease will outline, discuss, and debate these challenges. This year, we will highlight advances in current and emerging technologies, including next-generation sequencing, and discuss the challenges in integrating these technologies in clinical labs. We will address the latest in rapid diagnostics for point-of-care testing, as well as challenges in diagnosing sepsis and epidemics like Zika. This year, our discussion on antimicrobial resistance will focus on susceptibility testing, including emerging technologies for this use. We will again highlight novel approaches for infectious disease diagnostics, as well as key outcome studies.



Monday, February 20

10:30 am Conference Program Registration Open

NEXT GENERATION SEQUENCING FOR INFECTIOUS DISEASES

11:50 Chairperson’s Opening Remarks

Andrew Bryan, M.D., Ph.D., Acting Assistant Professor, Assistant Director, Clinical Microbiology, Department of Laboratory Medicine, University of Washington

12:00 pm Emerging Assays for Infectious Diseases in Diagnosis and Outbreak Surveillance

Charles Chiu, M.D., Ph.D., Associate Professor, Lab Medicine and Infectious Diseases; Director, UCSF-Abbott Viral Diagnostics and Discovery Center; Associate Director, Clinical Microbiology Laboratory, University of California, San Francisco

Advances in technology, genomics, and bioinformatics and the vast increases in the size of reference databases have made comprehensive diagnosis of infectious diseases practical. Here we will discuss the promise, challenges, and experience with clinical validation and implementation of a metagenomic next-generation sequencing (mNGS) assay for identification of pathogens in hospitalized patients. We will also discuss the use of new technologies, including nanopore sequencing and transcriptome profiling, for surveillance of epidemics such as the 2015-2016 Zika virus outbreak in the Americas.

12:30 Implementation of Metagenomic Next-Generation Sequencing for Pathogen Detection in the Clinical Laboratory

Samia Naccache, PhD, Clinical Microbiology Fellow, Pathology and Lab Medicine, Children’s Hospital Los Angeles

Metagenomic next-generation sequencing (mNGS) for pathogen detection allows for unbiased identification of infectious agent nucleic acid in clinical samples. We have implemented this assay in the UCSF clinical laboratory for diagnosis of meningitis / encephalitis using optimized library preparation and bioinformatics processing steps, with case discussion and decision support through the Microbial Sequencing Board. This talk will outline the mNGS assay performance, clinical utility and effect on patient management decisions.

1:00 Session Break

Fry_Labs1:15 Luncheon Presentation: Years On the Bench: Design and Implementation of a Microbial NGS Clinical Diagnostics System

Jeremy Ellis, Ph.D., Research Director, Laboratory Manager, Research & Development, Fry Laboratories, LLC

Translating research-based NGS methods into the clinical diagnostics laboratory poses several unique challenges. Experience with a microbial NGS diagnostics assay will be reviewed in addition to design requirements. Our system, RIDI™, will be used to explore challenges and opportunities.

2:10 Session Break

2:30 Chairperson’s Remarks

Jennifer Dien Bard, Director of the Clinical Microbiology Laboratory, Assistant Professor of Clinical Pathology, Keck School of Medicine of the University of Southern California

2:40 The Role of Deep Sequencing for Clinical Diagnoses of Polymicrobial Bacterial Infections

Andrew Bryan, M.D., Ph.D., Acting Assistant Professor, Assistant Director, Clinical Microbiology, Department of Laboratory Medicine, University of Washington

Bacterial identification and susceptibility testing in clinical microbiology laboratories relies on an array of diagnostic methods ranging from classic culture, rapid commercial molecular platforms, MALDI-TOF mass spectrometry, and sequencing methods. While each of these technologies brings valuable contributions to patient care, deep sequencing of polymicrobial bacterial infections has the potential to accurately de-convolute these complex infections and identify clinically significant organisms not detected by classical or Sanger-based sequencing methods.

3:10 Challenges and Approaches for Assuring the Quality of Next-Generation Sequencing in Clinical Laboratories Sequencing Human or Pathogen DNA

Ira M. Lubin, Ph.D., FACMG, Division of Laboratory Systems/CSELS, Office of Public Health Scientific Service, The Centers for Disease Control and Prevention

The Centers for Disease Control and Prevention published practice recommendations developed by multidisciplinary workgroups for the integration of next-generation sequencing into clinical laboratory settings. Although targeted at the analysis of human genomic DNA, general principles were identified relevant to the analysis of pathogens. Common challenges and approaches faced by laboratories, whether sequencing human or pathogen DNA, will be discussed.

3:40 Panel Discussion: Challenges in Implementing and Using NGS in Clinical Laboratories

Moderator: Andrew Bryan, M.D., Ph.D., Acting Assistant Professor, Assistant Director, Clinical Microbiology, Department of Laboratory Medicine, University of Washington

Panelists: Session Speakers

 

  • Challenges in implementing NGS in a network of clinical labs
  • Developing standards and workflows
  • Putting NGS into clinical practice and seeing benefits in patient management

 

 

4:40 Refreshment Break and Transition to Plenary Session

5:00 Plenary Keynote Session

6:00 Grand Opening Reception in the Exhibit Hall with Poster Viewing

7:30 Close of Day

Tuesday, February 21

7:30 am Registration Open and Morning Coffee

8:00 Plenary Keynote Session

9:00 Refreshment Break in the Exhibit Hall with Poster Viewing

MOLECULAR DIAGNOSTICS FOR ZIKA

10:05 Chairperson’s Remarks

Gerrit Van Roekel, Senior Program Officer, Business Development, Bill & Melinda Gates Foundation

10:15 Rapid Development and Implementation of Hospital-Based Molecular Diagnostics of Emerging Infectious Agents: An Ongoing Unmet Need

James M. Musser, MD, PhD, Director, Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute; Professor of Pathology and Laboratory Medicine, Weill Cornell Medical College of Cornell University

Epidemics, like Zika, caused by microbial pathogens can wreak havoc on our citizens, economy and food supply. These epidemics can occur as rapid bursts of devastation or languid or unrecognized waves. Hospitals nationwide are the primary front lines in caring for patients with life-threatening infections. Despite the billions of dollars spent on infectious diseases emergency preparedness, very few hospitals have the capacity to develop and implement rapid molecular diagnostics and respond effectively to these threats. Some of our experiences in this area, particularly around the Zika virus, will be discussed.

10:45 Minimally-Instrumented, Point-of-Care Molecular Detection of Zika Virus

Changchun Liu, Ph.D., Research Assistant Professor, Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania

Zika virus (ZIKV) is currently causing a large outbreak in the Americas. Rapid and reliable diagnostics for ZIKV are vital. Since immunoassays lack adequate sensitivity and selectivity, molecular diagnostics is an effective means to detect ZIKV soon after infection and throughout pregnancy. In this talk, I will present our recent effort towards the development of an inexpensive minimally-instrumented smart cup for molecular detection of ZIKV at the point-of-care.

POINT-OF-CARE TESTING FOR INFECTIOUS DISEASE: A NEW PARADIGM

11:15 A New Paradigm in Infectious Disease Testing: Molecular Point-of-Care Testing

Omai Garner, Ph.D., D(ABMM), Assistant Professor, Pathology and Laboratory Medicine, UCLA

Point-of-care testing for infectious disease has always suffered from poor sensitivity due to the usage of lateral flow based assays. Recently, the FDA has made a couple of molecular based influenza diagnostics CLIA waived. This talk will detail the sensitivity and specificity of these new tests as compared to in-lab molecular diagnostics, and will discuss the many challenges involved in implementing molecular testing within a physician’s office.

 Thermal Gradient11:45 FlashDirect - 12 min (or less) Sample-to-Answer Molecular Diagnostics

Robert Juncosa, CEO, Thermal Gradient, Inc.

Thermal Gradient will introduce its rapid sample prep and quantitative PCR technology and three instrument systems capable of full very rapid sample-to-answer molecular diagnostics. The FlashDirect instruments and disposable cartridges support a wide variety of specimens and nucleic acid targets.

12:15 pm Session Break

12:25 Luncheon Presentation: Portable System for Mulitplexed Immunoassays in Complex Sample Matrices

Michael Lochhead, Ph.D., CTO, MBio Diagnostics, Inc.

MBio Diagnostics has developed a portable assay system that enables multiplexed, quantitative immunoassays using a disposable cartridge and simple fluorescence reader. This presentation will focus on demonstrations of MBio's unique ability to run complex sample matrices without pre-processing.

1:25 Refreshment Break in the Exhibit Hall with Poster Viewing

POINT-OF-CARE TESTING FOR INFECTIOUS DISEASE: A NEW PARADIGM (CONT.)

2:00 Chairperson’s Remarks

Gerrit Van Roekel, Senior Program Officer, Business Development, Bill & Melinda Gates Foundation

2:10 PANEL DISCUSSION: Point-of-Care Molecular Diagnostics Platforms in Global Health – Does Current Technology Meet the Needs?

Moderator: Gerrit Van Roekel, Senior Program Officer, Business Development, Bill & Melinda Gates Foundation

Panelists: Mickey S. Urdea, Ph.D., Founder, Partner, Halteres Associates, LLC 

Bernhard H. Weigl, Principal Investigator, Flow Based Diagnostics, Intellectual Ventures/Global Good, Affiliate Professor, Department of Bioengineering, University of Washington

Judi Tilghman, Ph.D., Vice President, Technology Assessment, Quidel

We’ll see a plethora of sample-to-answer point-of-care diagnostics platforms come online in the coming years, which should help to address the need for diagnostic testing in global health settings, and emerging markets for diagnostic testing in low and middle income countries are projected to grow exponentially. But does the current technology adequately address global health needs? In this panel we will feature presentations on the need for diagnostics in global health settings and the technologies addressing those needs, followed by Q&A with the panelists.

3:10 Research Developments in Point-of-Care Testing for the DoD Chem/Bio Defense Program

Richard Schoske, GS-15, Ph.D., Chief, Diagnostics, Detection and Threat Surveillance Div (CBA), Chemical and Biological Technologies Department (J9/CB), Defense Threat Reduction Agency

The Chem/Bio Defense Program is developing prototype Point-of-Care devices and assays for the identification of biological threat agents for the multiplex identification of pathogens and the determination of host biomarkers of early warning of exposure using Molecular and Immuno-diagnostic methods. The underlying design goal is the development of tools for the differential diagnosis of syndromic panels for diseases for which the initial symptoms and presentation is generic that are: sensitive and specific, CLIA-waiver compatible, robust for use in austere environments, rapid, and cost-effective.

3:40 20-Minute Genetic ID of Resistant Bacteria to Improve Surveillance and Antimicrobial Stewardship

Michael van Waes, Ph.D., Director, Molecular Products, Molecular Technology, Streck

Rapid testing strategies characterize antibiotic resistant organisms and improve antimicrobial stewardship programs. The Streck Zulu RT instrument, in combination with the ARM-D real-time PCR kits, can screen samples for the presence of genes that mediate resistance in 20 minutes.

3:55 High Multiplex qPCR Technologies and Syndromic PanelsSeegene  

Helen Cha Roberts, Ph.D., President, Seegene Technologies

Using proprietary DPO, TOCE and MuDT technologies, Seegene obtained 510(k) clearance for its HSV types 1 & 2 assay and is focused on developing a comprehensive menu of high multiplex qPCR assay panels for clinical research and additional FDA submissions.

4:10 Hollywood Oscar Dessert Reception in the Exhibit Hall with Poster Viewing

5:00 Breakout Discussions in the Exhibit Hall

These interactive discussion groups are open to all attendees, speakers, sponsors, & exhibitors. Participants choose a specific breakout discussion group to join. Each group has a moderator to ensure focused discussions around key issues within the topic. This format allows participants to meet potential collaborators, share examples from their work, vet ideas with peers, and be part of a group problem-solving endeavor. The discussions provide an informal exchange of ideas and are not meant to be a corporate or specific product discussion. Pre-registration to sign up for one of the topics will occur a week or two prior to the Event via the App.

Rapid Susceptibility Testing

Jennifer Dien Bard, Director of the Clinical Microbiology Laboratory, Assistant Professor of Clinical Pathology, Keck School of Medicine of the University of Southern California

  • What are current susceptibility testing practices?
  • What are the benefits of phenotypic versus genotypic testing?
  • What are the emerging technologies currently available for rapid susceptibility testing?

 

Developing New Infectious Disease Diagnostics

Weian Zhao, PhD, Assistant Professor, Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, University of California–Irvine

  • What is the biggest challenge in your project?
  • What are the major hurdles to bring new infectious disease Dx to the market?
  • What is the next big thing in next 10-20 years?

 

Rapid molecular diagnostics for infectious diseases in the emergency department

Larissa May, MD, MS, Associate Professor and Director of Emergency Department Antibiotic Stewardship, University of California-Davis Medical Center, Sacramento, CA

  • What are the unique challenges and opportunities for molecular diagnostics in the ED setting?
  • How can rapid molecular diagnostics be effectively implemented and effectiveness measured in the acute care setting?
  • What is the role of diagnostic testing in antibiotic stewardship in acute care settings?

 

6:00 Close of Day

Wednesday, February 22

7:00 am Registration Open

7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Plenary Keynote Session

10:00 Refreshment Break and Poster Competition Winner Announced in the Exhibit Hall

ANTIMICROBIAL RESISTANCE AND SUSCEPTIBILITY TESTING

10:50 Chairperson’s Remarks

Weian Zhao, Ph.D., Assistant Professor, Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, University of California–Irvine

11:00 Emerging Technologies for Rapid Susceptibility Testing

Jennifer Dien Bard, Director of the Clinical Microbiology Laboratory, Assistant Professor of Clinical Pathology, Keck School of Medicine of the University of Southern California

Despite significant advances in the approaches to pathogen identification directly from clinical specimens, antimicrobial susceptibility testing is mainly performed by conventional methods, delaying results by 2-5 days. There is an unmet need for rapid, phenotypic approaches to susceptibility testing directly from clinical specimens. The current multiplexed molecular panels available identify organisms directly from positive blood cultures and detect the presence of resistance markers. This session will summarize the current and emerging technologies for rapid phenotypic susceptibility testing.

11:30 Sizing Up Your Enemy: The Use of Molecular Tests to Predict Antimicrobial Resistance in Neisseria Gonorrhoeae

Peera Hemarajata, M.D., Ph.D., D(ABMM), Clinical Instructor, Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA

Neisseria gonorrhoeae has become a serious threat due to high prevalence of antimicrobial resistance. Prospective susceptibility testing enables physicians to use antimicrobials other than those recommended for empirical treatment, and could potentially delay emergence of resistance to recommended antibiotics. Few laboratories routinely perform culture and susceptibility testing for N. gonorrhoeae. We will discuss molecular assays that may be able to predict susceptibility directly from specimens without the need for culture.

12:00 pm Insights into Antimicrobial Resistance Learned from NGS

Susan Butler-Wu, Ph.D., D(ABMM), Associate Professor of Clinical Pathology, Keck School of Medicine of the University of Southern California, Director, Clinical Microbiology, LAC+USC Medical Center

12:30 Session Break

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:10 Refreshment Break in the Exhibit Hall and Last Chance for Poster Viewing

SEPSIS DIAGNOSTICS

1:50 Chairperson’s Remarks

Matthew Faron, PhD, Research Scientist, Clinical Microbiology, Medical College of Wisconsin

2:00 Next-Generation Sequencing Diagnostics of Blood Stream Infections

Kai Sohn, Ph.D., Group Leader, MBT, Fraunhofer IGB

Bloodstream infections remain one of the major challenges in intensive care units leading to sepsis or septic shock. Due to the lack of timely diagnostic approaches with sufficient sensitivity, mortality rates of sepsis are still unacceptably high. We describe the establishment of a complete diagnostic workflow for the identification of infectious microorganisms from seven septic patients based on unbiased sequence analyses of free circulating DNA from plasma by next-generation sequencing.

2:25 Performance of PCR-REBA Assay for Screening and Identifying Pathogens Directly in Whole Blood of Patients with Suspected Sepsis

Hyeyong Lee, Ph.D., Professor, Biomedical Laboratory Science, Yonsei University, Wonju Campus

The present study investigated blood samples from 882 patients who matched the criteria of systemic inflammatory response syndrome with suspected bacterial or fungal infection. In brief, the results from this study showed that the concordance rate of blood culture and PCR-REBA was 83.0% (95% confidence interval [CI], 79.8-84.8, p<0.0001). The results also showed that PCR-REBA positive patients had higher CRP or PCT levels than PCR-REBA negative and blood culture negative patients.

OUTCOME STUDIES

2:50 Designing Studies to Evaluate How Infectious Disease Diagnostics Affect Patient Care and Outcomes

Christopher R. Polage, M.D., MAS, Director, Clinical Microbiology Laboratory, Associate Professor of Clinical Pathology and Infectious Diseases, Pathology and Laboratory Medicine, University of California, Davis Health System

Molecular tests for infectious diseases are increasingly used for patient care but few studies investigate their impact on patient care and outcomes. This presentation examines selected clinical outcome studies to identify characteristics of successful and unsuccessful tests and studies with the goal of providing a road map to designing studies to accurately evaluate and maximize the impact of new tests on patient care.

3:10 A First In, First Out (FIFO) Respiratory Virus Testing Algorithm Significantly Impacts ICU Patient Outcomes

Raquel Marie Martinez, Ph.D., D(ABMM), Director, Clinical and Molecular Microbiology, Laboratory Medicine, Geisinger Health System

Nucleic acid amplification and detection of respiratory virus (RV) pathogens is rapid and sensitive, but multiplex methods can be costly. Implementation of molecular methods can promote improvements in laboratory workflow; however, few studies assess the impact of rapid results on downstream patient outcomes. The purpose of this study was to assess the impact of rapid multiplex RV testing for an ICU patient population.

3:30 Session Break

NOVEL APPROACHES TO INFECTIOUS DISEASE DIAGNOSIS

3:40 Chairperson’s Remarks

Raquel Marie Martinez, Ph.D., D(ABMM), Director, Clinical and Molecular Microbiology, Laboratory Medicine, Geisinger Health System

3:45 Automated Plate Reading and Quantitation: Can a Computer that Learns Replace Human Plate Reading?

Matthew Faron, PhD, Research Scientist, Clinical Microbiology, Medical College of Wisconsin

Digital imaging in microbiology has revolutionized the microbiology laboratory and significantly reduced turnaround of culture results. Most recently, we have partnered to developed software that can automatically read plates and interpret chromogenic media, only requiring human intervention for positive specimens and reducing the hands-on time for plate reading by 80%. We now report on the ability to read blood plates and quantify the number of colonies present on a plate.

4:10 Accelerating Diagnosis and Therapy of Infectious Diseases Using Public Heterogeneous Data

Purvesh Khatri, Ph.D., Assistant Professor, Medicine, Stanford University

Public availability of large amounts of heterogeneous molecular data for infectious diseases presents unprecedented opportunities for identifying novel diagnostic and prognostic markers, while accounting for the real world patient population heterogeneity observed across the world. I will discuss a novel framework and results obtained using the framework for diagnosis and prognosis of multiple infectious diseases including TB, dengue, influenza, and sepsis.

4:35 Digital Detection of Infectious Agents in Unprocessed Blood Using Blood Droplet PCR

Weian Zhao, Ph.D., Assistant Professor, Department of Pharmaceutical Sciences, Sue and Bill Gross Stem Cell Research Center, Chao Family Comprehensive Cancer Center, Edwards Lifesciences Center for Advanced Cardiovascular Technology, Department of Biomedical Engineering, University of California–Irvine

Rapid detection of infectious agents in blood remains an unmet challenge. The current systems are often not sensitive enough to detect low-abundance pathogens. Moreover, these techniques usually require culture and sample processing steps that are not suited for routine testing. I will present a new method that integrates droplet digital detection and direct blood PCR, which allows us to rapidly detect target cells at single cell sensitivity in unprocessed samples.

4:55 What Is Life? Real-Time Molecular Assessment of Microbial Viability and Growth in Samples

Gerard Cangelosi, Ph.D., Professor, Environmental and Occupational Health Sciences, University of Washington

Viable pathogen cells are usually more significant to human health than dead ones. Similarly, normally harmless commensal microorganisms can cause disease when they begin to proliferate unchecked. These distinctions are important but challenging for molecular and clinical microbiologists who rely on nucleic acid-based testing methods. This presentation describes new PCR-based methods that differentiate viable from inactivated microbial cells, and related methods that assess ongoing microbial growth in samples.

5:15 Close of Conference Program


Stay on for these Tri-Conference Symposium, taking place at February 23-24, 2017 at Moscone South Convention Center


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