Molecular Diagnostics for Infectious Disease

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, now in its third year at the Molecular Med Tri-Conference, will describe, discuss, and debate the benefits and challenges in the latest advances in molecular testing technologies and approaches. We will focus on the latest advances in next generation sequencing as the path forward for this technology, including implementation and reimbursement. We will address the latest in rapid diagnostics for point-of-care testing, as well as challenges in diagnosing sepsis and CNS, GI, and respiratory infections. Special attention will be paid to the diagnosis of C. Difficile and questions surrounding molecular versus toxin testing. This year’s antimicrobial resistance section will focus on bacterial identification and antibiotic resistance profiling. A special session this year will focus on the next era of diagnostics: artificial intelligence and data science approaches to infectious disease diagnosis. Join esteemed colleagues, service and technology providers, and peers to discuss these topics and more.

10:30 am Conference Program Registration Open

NGS AND MOLECULAR TECHNOLOGIES: ADVANCES AND NEW APPLICATIONS

11:50 Chairperson’s Opening Remarks

Duncan MacCannell, Ph.D., CSO, OAMD, NCEZID, Centers for Disease Control and Prevention

12:00 pm Molecular Approaches to Diagnosing CNS Infections

Jennifer Dien Bard, Ph.D., D(ABMM), FCCM, Director Microbiology and Virology; Associate Professor of Clinical Pathology, Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; University of Southern California

Infections of the central nervous system (CNS) are associated with significant morbidity and mortality. Definitive identification of infectious etiology is imperative for appropriate patient management. Emerging molecular technologies have shifted the testing paradigm for CNS disease. This session will provide an overview of the current approaches to the laboratory diagnosis of CNS infections, with a focus on molecular technologies. Benefits and limitation will be highlighted.

12:30 Metagenomic NGS for Infectious Disease Diagnosis

Charles Chiu, M.D., Ph.D., Associate Professor, Laboratory Medicine and Medicine/Infectious Diseases, Director, UCSF-Abbott Viral Diagnostics and Discovery Center, Associate Director, UCSF Clinical Microbiology Laboratory, UCSF School of Medicine

We have validated an mNGS assay to identify infectious causes of meningitis and encephalitis from cerebrospinal fluid in a clinically licensed (CLIA) laboratory, which is now available as a clinical reference test for acutely ill hospitalized patients. We report the results of a multi-hospital, nationwide clinical study to evaluate the utility, performance, and cost-effectiveness of a Metagenomic next-generation sequencing (mNGS) assay relative to standard microbiological testing in diagnosis of these neurological infections. We will also describe new technologies and diagnostic approaches.

1:00 Session Break

1:10 Enjoy Lunch on Your Own

2:10 Session Break

NEXT-GENERATION SEQUENCING: THE PATH FORWARD

2:30 Chairperson’s Remarks

Jennifer Dien Bard, Ph.D., D(ABMM), FCCM, Director Microbiology and Virology; Associate Professor of Clinical Pathology, Pathology and Laboratory Medicine, Children’s Hospital Los Angeles; University of Southern California

2:40 Quality Control for Metagenomic NGS Testing in the Clinical Laboratory

Steve Miller, M.D., Ph.D., Associate Professor and Director, UCSF Clinical Microbiology Laboratory, University of California San Francisco

Metagenomic next-generation sequencing requires a highly complex workflow and is susceptible to analytical errors at several points. This talk will discuss potential pitfalls and quality control measures necessary for reliable pathogen detection using these methods.

3:10 Advanced Molecular Detection: Transforming Public Health

Duncan MacCannell, Ph.D., CSO, OAMD, NCEZID, Centers for Disease Control and Prevention

The CDC’s Advanced Molecular Detection program is helping to drive the coordinated and sustainable implementation of NGS and other emerging and innovative technologies in routine practice throughout the US public health laboratory system. The AMD program directly supports cross-cutting efforts, such as: building shared IT and laboratory capacity for genomics, proteomics, bioinformatics and next-generation diagnostic testing; developing training in bioinformatics and other essential skills; and supporting continued innovation and coordinated application of genomics and other emerging technologies to meet public health challenges.

3:40 Road to Using NGS for Infectious Diseases as a Routine: Validation and Implementation of a 16S Metagenomics Assay in a Clinical Microbiology Laboratory

Shaun Yang, Ph.D., D(ABMM), Director of Molecular Microbiology, Infectious Disease, TriCore Reference Labs; Assistant Professor, Pathology, University of New Mexico

In our laboratory, we validated and implemented a quantitative 16S metagenomics assay for the identification of bacterial species in body fluids and tissues from patients with a wide spectrum of infections. This assay provides advantages including identification and quantification of polymicrobial infections and detection of culture-negative pathogens, especially in the setting of acute infections involving sterile body sites. We are working with ID specialists to make this test available as a routine test to maximally benefit patient care.

Seegene 4:10 Building A Comprehensive Syndromic Panel Menu using High Multiplex qPCR Technologies

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

Using proprietary DPO, TOCE and MuDT technologies, Seegene obtained a 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 on Thermo's QS5 as well as POC instruments.

4:40 Refreshment Break and Transition to Plenary Session

5:00 Plenary Keynote Session (click here for more details)

 

Precision for Medicine

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

7:30 Close of Day

Tuesday, February 13

7:30 am Registration Open and Morning Coffee

8:00 Plenary Keynote Session (click here for more details)

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

TECHNOLOGIES FOR BACTERIAL PROFILING AND ANTIBIOTIC SUSCEPTIBILITY TESTING

10:05 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

10:15 One-Step, Rapid Detection of Antibiotic Resistant Bacteria in Blood Stream Infections Using High Volume Droplet Blood 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

Antibiotic resistance represents a major global health threat. Lack of rapid diagnostics in the current paradigm of clinical microbiology, especially for bloodstream infections (BSIs), has resulted in use of inappropriate or unnecessarily broad-spectrum antibiotics, which are associated with significantly increased morbidity, mortality and healthcare cost as well as having the potential to select for resistant strains. In this presentation, we will discuss a new high throughput blood droplet PCR technology for rapid bacterial detection directly in blood samples without culture and sample processing.

10:45 Rapid Phenotypic Antibiotic Susceptibility Testing Directly from Clinical Samples Using Single-Molecule Counting

Rustem Ismagilov, Ph.D., Professor, Chemistry & Chemical Engineering, California Institute of Technology

Rapid antibiotic susceptibility testing (AST) is critical for delivering care and enabling antibiotic stewardship. Phenotypic AST is the gold standard, but is unacceptably slow, requiring pre-culture steps. Genotypic AST has not been sufficiently general to replace the gold standard (especially in Gram-negative organisms). We use SlipChip for digital single-molecule counting of pathogen-specific RNA and DNA to perform phenotypic AST directly from clinical samples in as fast as 30 minutes.

11:15 Developing Ultrasensitive Molecular Methods for Rapid Bacterial Identification and Antibiotic Resistance Profiling

Shana Kelley, Ph.D., Professor, Department of Pharmaceutical Sciences, University of Toronto

We are developing several different platforms for rapid bacterial analysis and the detection of antibiotic resistance. Devices that enable genetic analysis in heterogeneous samples will be described.

11:45 Presentation to be Announced  

12:15 pm Session Break

12:25 Enjoy Lunch on Your Own

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

POINT-OF-CARE AND RAPID DIAGNOSTICS

2:00 Chairperson’s Remarks

Nathan Ledeboer, Ph.D., Associate Professor of Pathology and Medical Director, Medical College of Wisconsin

2:10 Bringing Host-Based Biomarkers to Point-of-Care Instruments

Richard Schoske, Ph.D., MT (ASCP), Chief, Diagnostic and Detection, Chemical and Biological Technologies Department (J9CB), Defense Threat Reduction Agency

Many infections take days or weeks to appear, delaying treatment while the pathogen continues to invade the host. So what is needed to diagnose an exposure before the patient even realizes they are sick? Investigating early changes in cellular responses may provide host-based biomarkers that can help detect disease in humans by providing information on the presence or severity of disease prior to the onset of any symptoms.

2:40 Digital Universal High-Resolution Melt Rapidly Identifies Individual Bacteria in Blood

Stephanie Fraley, Ph.D., Assistant Professor, Bioengineering, University of California, San Diego

We report the development of an integrated microfluidic platform enabling the identification of individual bacterial pathogens in blood in less than four hours. The system incorporates a microfluidic chip and instrumentation to accomplish universal digital PCR amplification and High Resolution Melting (HRM) across 20,000 picoliter scale reactions. Image processing and machine learning algorithms identify bacterial pathogens and quantify absolute loads based on the HRM curves collected from each reaction, which originate from single genomes. Our results suggest that this device could have exciting implications in the clinical setting.

3:10 Multiplex Respiratory Pathogen Molecular Testing at the Point of Care: A Clinical Study

Omai Garner, Ph.D., D(ABMM), Assistant Professor, Pathology and Laboratory Medicine, University of California, Los Angeles

This clinical study involved the testing of the CLIA waived Biofire RP EZ platform in 3 urgent care centers at UCLA Health over the course of 6 months. We enrolled 100 patients and explored the clinical outcomes of POC multiplex respiratory pathogen molecular testing.

3:40 PANEL DISCUSSION: Challenges in Point-of-Care and Rapid Diagnostics from Technology to the Clinic

Session Speakers

 

  • What are some of the biggest challenges in developing point-of-care and rapid diagnostics?
  • Where are the new opportunities in technology?
  • What are the implementation challenges for the clinic?

 

4:10 Valentine’s Day Celebration 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.

The Impact of NGS on Clinical and Public Health Infectious Disease Laboratories

Duncan MacCannell, PhD, Chief Science Officer, OAMD, NCEZID, Centers for Disease Control and Prevention

 

  • Changing technical and workforce needs
  • CLIA compliance
  • The impact of CIDT on public health surveillance

 

Infectious Disease Diagnostics in Urgent Care and Emergency Settings

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

 

  • Discuss the unique challenges faced in emergency rooms and urgent care settings
  • Examine diagnostic needs and challenges in developing technologies for these settings
  • Share experiences and lessons learned

 

6:00 Close of Day

Wednesday, February 14

7:00 am Breakfast Presentation (Sponsorship Opportunity Available)  

7:30 Registration Open and Morning Coffee

8:00 Plenary Keynote Session (click here for more details)

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

BIG DATA AND TECHNOLOGY: NOVEL APPROACHES TO INFECTIOUS DISEASE DIAGNOSIS

10:50 Chairperson’s Remarks

Aydogan Ozcan, Ph.D., Professor, Electrical and Computer Engineering, Bioengineering, University or California, Los Angeles

11:00 The Rise of the Machines: Digital Image Analysis in Clinical Microbiology

Nathan Ledeboer, Ph.D., Associate Professor of Pathology and Medical Director, Medical College of Wisconsin

Technology is changing the field of clinical microbiology dramatically. The advent of artificial intelligence, laboratory automation, and mass spectrometry has changed every aspect of the clinical laboratory. The session will evaluate the prospects of this technology and specifically evaluate the potential for AI to be used in diagnostic microbiology

11:30 Leveraging Heterogeneity in Host Response for Diagnosis and Prognosis of Infectious Diseases

Timothy Sweeney, MD, PhD, CEO, Inflammatix

Current experiment and analysis paradigm in biomedical and biological research is to reduce heterogeneity in the data to ensure the conclusions are not confounded by biological, technological and demographic factors. However, this paradigm does not account for the real-world patient population heterogeneity, which in turn requires replication in multiple independent cohorts prior to translation into clinical practice. Consequently, biomedical research today is slow and expensive. I will describe an analytic framework that turns the current paradigm on its head. This talk will focus on how heterogeneity across independent experiments can lead to identification of disease signatures that are diagnostic, prognostic, therapeutic and mechanistic across a broad spectrum of diseases including infections, autoimmune diseases, cancer, and organ transplants. I will also discuss how biological and technical heterogeneity in publicly-available data can be leveraged to make translational medicine better, faster, and cheaper.

12:00 pm Mobile Microscopy, Sensing and Diagnostics for Point-of-Care Medicine and Global Health

Aydogan Ozcan, Ph.D., Professor, Electrical and Computer Engineering, Bioengineering, University or California, Los Angeles

In this presentation, I will discuss some of the emerging applications and the future opportunities/challenges created by the use of mobile phones and other consumer electronics devices for the development of next-generation microscopy, sensing, and diagnostics tools for example, point-of-care medicine and global health applications.

12:30 Session Break

12:40 Enjoy Lunch on Your Own

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

MOLECULAR TESTING FOR DIAGNOSIS OF C. DIFFICILE

1:50 Chairperson’s Remarks

Rosemary She, M.D., Associate Professor, Clinical Pathology, Keck School of Medicine, University of Southern California

2:00 Nuclear Magnetic Resonance to Detect Analytes from Clinical Specimens: Toxigenic Clostridium difficile As An Example

Rosemary She, M.D., Associate Professor, Clinical Pathology, Keck School of Medicine, University of Southern California

A novel method employing nuclear magnetic resonance with the potential to detect nucleic acids or other targets from biological matrices is presented. Target molecules form binary complexes with magnetic nanoparticles. T2 relaxation times of surrounding water molecules, which depend on presence or absence of target, are measured after application of a magnetic field. This approach can detect concentrations at the femtomolar level with a dynamic range of up to 8-log.

2:30 Diagnostic Dilemmas in C. difficile Diagnostic Testing

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

3:00 Novel and Complementary Diagnostic Approaches to Reduce Healthcare-Associated Clostridium difficile Infection

Niaz Banaei, M.D., Associate Professor of Pathology and Medicine (Infectious Diseases & Geographic Medicine); Medical Director, Stanford Health Care Clinical Microbiology Laboratory Director, Stanford Clinical Microbiology, Stanford University

Inclusion of C. difficile infection (CDI) on the list of quality measures affecting hospital reimbursement has encouraged administrators, microbiologists, and epidemiologists to work creatively together to optimize C. difficile testing to reduce CDI rates. This session presents two complementary approaches on (i) real-time electronic patient data tracking to enable verification of C. difficile clinical testing criteria and (ii) toxin testing to reduce CDI rates.

3:30 Session Break

MOLECULAR TESTING FOR DIAGNOSIS OF C. DIFFICILE (CONT.)

3:40 Chairperson’s Remarks

Kimberly Hanson, M.D., MHS, Associate Professor, Medicine and Pathology, University of Utah

3:45 Upcoming New Guidelines for Management of C. difficile

Stuart Johnson, M.D., Professor, Infectious Disease, Loyola Medicine, Hines VA Hospital

Since publication of the IDSA/SHEA guidelines for C. difficile infection (CDI) in Adults in 2010, substantial changes have occurred in the diagnosis and treatment of CDI. In the U.S., there has been widespread adoption of molecular diagnostic assays. In addition, fidaxomicin was approved for treatment of CDI based on improved sustained responses compared to vancomycin. The updated guidelines will address these changes and include recommendations for children as well.

MOLECULAR DIAGNOSTICS FOR INFECTIOUS DISEASE IN TRANSPLANT PATIENTS

4:15 Diagnosing Infectious Disease in Transplant Patients: Rapid Molecular Tests

Kimberly Hanson, M.D., MHS, Associate Professor, Medicine and Pathology, University of Utah

This presentation will review recent developments in rapid diagnostics for opportunistic infections.

4:45 Next-Generation Diagnostics for Meningitis and Encephalitis in Transplant Patients

Michael Wilson, M.D., MAS, Assistant Professor, Neurology, UCSF School of Medicine

Dr. Wilson’s talk will summarize the potential for metagenomic next-generation sequencing to transform how we identify infections in patients with neuroinflammatory diseases like meningitis and encephalitis and, in particular, how this could impact the care of transplant patients and screening of potential organ donors.

5:15 Close of Conference Program


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