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Molecular Diagnostics for Infectious Disease

Novel molecular technologies continue to evolve and improve helping cut the time it takes to diagnose and treat infectious disease. The Molecular Diagnostics for Infectious Disease Conference now in its 8th year in Washington D.C. will continue to showcase emerging technologies presented from both the clinical and research perspectives. Regulatory aspects of getting ID tests through the FDA and emerging technologies, including NGS for detection of ID will be covered. The impact of rapid diagnostic tests on antimicrobial stewardship and antibiotic usage, as well as blood pathogen detection will be highlighted along with rapid diagnostics being developed for the zika virus.

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SC1: NGS Diagnostics: Technology, Regulation and Reimbursement

SC6: NGS Assay Development and Validation

SC9: Practical Considerations for NGS Data Analysis and Interpretation

*Separate registration required


10:30 Registration

11:15 PLENARY KEYNOTE SESSION: Click here for details  

12:50 pm Luncheon Presentation: Point-of-Care Molecular Diagnostics Enable Better Testing Compliance and Immediate Patient Management Decisions

Shana_KelleyShana Kelley, Founder & CTO, Xagenic Inc.

Ihor_BoszkoIhor Boszko, Vice President, Business Development, Xagenic Inc.

Recent availability of CLIA waived molecular diagnostic tests has enabled improved patient care at a lower cost to the healthcare system. Xagenic is entering this rapidly growing market by commercializing a combination chlamydia/gonorrhea test, allowing better compliance with USPSTF and CDC screening recommendations. The Xagenic X1™ platform will permit in-office molecular testing in <20 minutes using non-refrigerated cartridges. We will produce a menu of multiplexed infectious disease tests with greatest utility during first clinical presentation.


1:25 Ice Cream and Cookie Break in the Exhibit Hall with Poster Viewing


1:50 Chairperson’s Opening Remarks

Gerrit van Roekel, MSc, MBA, Senior Program Officer, Life Science Partnerships, The Bill and Melinda Gates Foundation

2:00 Establishing FDA-ARGOS for Regulation of Sequencing-Based Diagnostics for Infectious Diseases

Heike_SichtigHeike Sichtig, Ph.D., Medical Countermeasures / Multiplex, Microbiology Devices, Center for Devices (CDRH), FDA

Lack of clinical diagnostics for Infectious Diseases can have devastating consequences for public and global health as highlighted by the recent Ebola outbreak in West Africa. Supporting infrastructure needs to be developed to equip public and global health care providers with tools necessary to combat rising threats such as emerging pathogens and antimicrobial resistance. Microbial diagnostic devices based on High Throughput Sequencing (HTS) technologies are on the cusp of making it into clinical laboratories and hospitals. The presentation will outline studies to evaluate the use of sequencing-based devices as an aid in infectious disease diagnostics, and to gain a better understanding of potential HTS clinical implementation strategies. Regulatory use case scenarios utilizing the FDA-ARGOS database resource will be showcased. The information contained in the presentation concerning possible approaches for validation are suggested approaches open for feedback.

2:30 Emerging Assays for Infectious Diseases in Diagnosis and Outbreak Surveillance

Charles_ChiuCharles 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 California, San Francisco

Advances in technology, genomics, and bioinformatics and the vast increases in the size of reference databases has 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.

3:00 Viral Hemorrhagic Fever Detection: Challenges of Translating Research into Actionable Diagnostics

Tim_MinogueTimothy D. Minogue, Ph.D., Chief, Molecular Diagnostics Department, Diagnostic Systems Division, USAMRIID

The current Ebola outbreak highlights the need for effective/ rapid diagnostics in an outbreak situation. However, several highly pathogenic organisms present with similar pathology are endemic to similar regions and co-circulate with Ebola. Our group strives to provide research and development of diagnostics to affect time-to-answer, assay sensitivity, and ease of use to help diagnosis these types of diseases.

3:30 Quantitative Molecular Diagnostics in Less Than 12 Minutes for Point of Care and Decentralized Settings

Robert Juncosa, CEO, Thermal Gradient, Inc.

Walter Gilde, Business Development Manager, KMC Systems, Inc.

Thermal Gradient's POC CLIA-Waivable instrument and cartridge perform molecular diagnostic testing in under 12 minutes. Learn the fundamentals of enabling rapid PCR technology, the basis for the Flash MDx platform, which is portable and fully automated, and how the Flash platform addresses the need for rapid molecular POC solutions.

3:45 20-minute Multiplex PCR Detection of Antibiotic-Resistant Gram-Negative Bacteria: Utility of a Novel Random-Access Real-Time PCR System

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

Rapid testing strategies are needed to characterize antibiotic resistant organisms and improve antimicrobial stewardship programs. The Streck Zulu RT™ instrument, in combination with the ARM-D® line of real-time PCR kits, can screen samples for the presence of genes that mediate resistance in 20 minutes using 4 randomly accessible modules.

4:00 Refreshment Break in the Exhibit Hall with Poster Viewing

4:45 NGS for Diagnosis and Molecular Epidemiology in Clinical Laboratories: Experience and Challenges

Hank_WangGuiqing Wang, M.D., Ph.D., Chief of Labs, Pathology and Clinical Laboratories, Westchester Medical Center & New York Medical College

NGS has great potential for diagnosis of infectious diseases directly from primary clinical specimens and for molecular epidemiology in hospitals and public health setting. For diagnostic microbiology, various sample and library preparations and bioinformatics tools were explored for different types of clinical specimens. Also NGS was used to replace PFGE and MLST in hospital outbreak and nosocomial transmission investigations for improving infection control practice. Experience and challenges in the implementation and routine use of NGS in clinical laboratories will be addressed.

5:15 Standards for NGS-Based Microbial Identification and Quantitation

Jason_KraljJason Kralj, Ph.D., Staff Scientist, Complex Microbial Systems Group, Biosystems and Biomaterials Division, Material Measurements Laboratory, NIST

Increasingly, NGS-based platforms are being used for identifying clinical, environmental, and biothreat samples. As these continue to develop, it is clear that developers and end-users alike need standards to ensure compatibility between platforms, confidence in identification and limits of detection, and for competency testing for regulatory oversight. We explore how simple mixtures of well-characterized DNA materials can inform the process of sample identification, including how sequencing and informatics artifacts can be identified to improve confidence in analysis.

5:45 Clinical Metagenomics: A Next Generation Diagnostics Solution for Infectious Diseases

Nur_HasanNur Hasan, Ph.D., Adjunct Faculty, Center for Bioinformatics and Computational Biology, University of Maryland College Park, Leader Science Team, CosmosID

Next generation sequencing (NGS) based microbial genomics and metagenomics appears to be paramount to 21st century approaches to rapid microbial detection and precise sub-typing of pathogens —be it for identifying and characterizing infection-inducing agent (traditional, emerging, and advanced), polymicrobial community, and/or co-infections. Recent advancement in sequencing throughput and turnaround time, automation in nucleic acid extraction and library preparation, and significant advancement in developing ultrafast bioinformatics package (MetaGenID) and curated genome databases (GenBook) make this technology highly attractive for infectious disease detection, biosurveillance, and outbreak investigation. The presentation will describe various aspects of MetaGenID: ease and operational friendliness, data mining efficiency and processing speed, breadth, depth and curation of genome databases to deliver actionable results, flexibility to allow user incorporations of specific metadata and/or genome sequences, and ability to deploy such system in the field. The presentation will further demonstrate some valuable features that make this technology very attractive and powerful for simultaneous detection and characterization of infectious agents.

6:15 Close of Day

6:00 Dinner Short Course Registration


SC12: NGS for Infectious Disease Diagnostics

*Separate registration required

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7:30 am Problem-Solving Breakout Discussions with Continental Breakfast

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.

TABLE: Diagnostics to Combat Antibacterial Resistance

Ephraim L. Tsalik, M.D., Ph.D., Assistant Professor, Medicine, Duke University School of Medicine

  • Diagnostics to guide appropriate antibiotic use
  • Diagnostics to detect antimicrobial resistance (phenotypic vs. genotypic)
  • Changing practice following diagnostic testing (e.g., stewardship)

TABLE: Point-of-Care for ID

Nathan A. Ledeboer, Ph.D., Associate Professor of Pathology, Medical Director, Clinical Microbiology, Medical College of Wisconsin

  • Recent developments in rapid POC testing
  • The impact of technology in POC
  • Future directions for POC and rapid testing in ID

TABLE: NGS Clinical Dx for ID

Tom Slezak, Distinguished Member of the Technical Staff, Pathogen Bioinformatics, Lawrence Livermore National Laboratory

  • Reference databases
  • Targeted NGS


8:25 Chairperson’s Opening Remarks

Ihor Boszko, Vice President, Business Development, Xagenic, Inc.

8:30 Automated Plate Reading and Interpretation: Fact or Fiction?

Nathan_LedeboerNathan A. Ledeboer, Ph.D., Associate Professor of Pathology, Medical Director, Clinical Microbiology, Medical College of Wisconsin

Automation in clinical chemistry and hematology laboratories has been widely available for years, but only recently in microbiology. The initial goal of automation in microbiology was to standardized plating, incubation, and imaging of colonies with technologists interpreting the results of the images. Further advancement in colony and color recognition have led to development of reading algorithms allowing the instruments to identify the presence of colonies on a plate and distinguish between different colors, such as those found on chromogenic agars. Following development of an automated reading algorithm, we evaluated its performance for identification of MRSA and VRE from chromogenic media and apply performance of the algorithm to recognize and quantitate colonies from a blood agar plates.

9:00 Axiom MDA – A High-Throughput Pan-Microbial Microarray

Tom_SlezakTom Slezak, Distinguished Member of the Technical Staff, Pathogen Bioinformatics, Lawrence Livermore National Laboratory

The Lawrence Livermore Microbial Detection Array (LLMDA) has evolved since 2007 to now be able to identify over 12,000 unique species (all sequenced bacteria, viruses, fungi, archaea, and protozoa as of the design date). It has recently been commercialized on the Affymetrix Axiom platform which processes 24 or 96 samples in parallel, each with 1.4M probes covering the 12,000+ species. We will briefly discuss the history of how the LLMDA has been used on prior platforms and data from the new Axiom MDA format.

9:30 A Multiplexed Platform for Precision Medicine at the Point of Care Applied to Sepsis Diagnostics

Chris_MyattChris Myatt, CEO, MBio Diagnostics, Inc.

Optical waveguide sensors combined with fluorescent detection enable sensitive and multiplexed tests for point of care use. We will detail a simple disposable cartridge and portable reader design that enables fast measurements of host response signatures. We detail examples of risk stratification and rapid classification of infection for sepsis.

9:45 Rapid Point-of-Care Molecular Diagnostics for Sexually Transmitted Infections

John_ClarksonJohn Clarkson, Ph.D., CEO, Atlas Genetics

Atlas Genetics is an innovative MDx Company focused on POC testing through its fully-automated, ultra-rapid platform providing lab quality molecular tests. Up to 24 genetic targets can be detected from multiple sample types. CE Mark was awarded January 2016 for a Chlamydia trachomatis test, with CT/NG in the near-term pipeline.

Celsee Diagnostics10:00 Coffee Break in the Exhibit Hall with Poster Viewing

10:50 The Host Response as a Diagnostic Target for Infectious Disease

Ephraim_TsalikEphraim L. Tsalik, M.D., Ph.D., Assistant Professor, Medicine, Duke University School of Medicine

Infection represents a maladaptive interaction between pathogen and host. Diagnostics have largely focused on pathogen identification although this approach has limitations. A focus on the host response offers a complementary diagnostic strategy. Biomarkers may derive both from biology-informed candidates as well as unbiased ‘omic methodologies. Advances in modeling and technology are now converging, creating new opportunities for host-response diagnostics in infectious diseases.

11:20 Validation and Implementation of the Biofire GI Panel

Julie_RibesJulie A. Ribes, M.D., Ph.D., Director, Clinical Microbiology, Associate Director, Hospital Laboratories, UK HealthCare Chandler Hospital

UK HealthCare went live with the FDA-approved Biofire GI FilmArray early in 2015. The intent of this implementation was to replace the 3-4 day routine stool culture with a test that is completed in about an hour. This talk will cover how the film array works, how to validate the panel, and issues encountered with implementation, and 1 year’s experience.


11:50 Molecular Detection of Pathogens and Mechanisms of Resistance in Patients with Sepsis

Julie_RibesJulie A. Ribes, M.D., Ph.D., Director, Clinical Microbiology, Associate Director, Hospital Laboratories, UK HealthCare Chandler Hospital

UK HealthCare implemented the Nanosphere Gram positive and Gram negative Blood culture panels in the fall of 2014, and the Biofire Sepsis panel in 2016. The intent of these implementations was to provide the patient with the right drug at the right time. This talk will discuss the evaluation of Nanosphere and BioFire platforms, their implementation and post-go live experience.

 Paratus Diagnotstics
12:20 pm Integrated Sample-Prep and Immunoassay Array Platform for High-Sensitivity, Low-Complexity Multiplexed POC Diagnostics

John C. Carrano, Ph.D., CEO, Paratus Diagnostics

Here we report on a disposable device that utilizes our Specimen Delivery System (Paratus SDS®) and attaches to a smartphone for multiplexed detection of infectious diseases. Operation involves inserting the specimen containing swab directly into the sensing cartridge where the biomarkers elute downstream for subsequent detection through a chemiluminescent immunoassay.

Randox_Biosciences12:35 pm A Fluidic Card Multiplex Array for Quick Point-Of-Care Detection of Sepsis

Claire Huguet, Ph.D., Head, Biomarker Services, Biosciences, Randox Biosciences

Severe sepsis is a leading cause of death worldwide, requiring fast germ identification techniques. We describe a 45-plex, molecular assay using a disposable fluidic biochip format for use with a POC platform at patient bedside. Accurate germ ID is obtained in 2 hours, covering a mix of bacteria’s and fungi.

12:50 Luncheon Presentation: TB Testing at Hennepin in a Diverse Inner City Population

Glen Hansen, Ph.D., Medical Director, Clinical Microbiology and Molecular Diagnostics, Hennepin County Medical Center

An overview of TB testing platforms from one institute's experience.

1:20 Session Break


2:00 Chairperson’s Remarks

Thomas M. File, Jr., M.D., MSc, MACP, FIDSA, FCCP, Chair, Infectious Disease Division Summa Health System Akron; Professor, Internal Medicine, Northeast Ohio Medical University (NEOMED)

2:05 Multi-Cohort Analysis and Robust Host Gene Markers in Diagnosis and Prognosis of Infectious Disease

Tim_SweeneyTimothy E. Sweeney, M.D., Ph.D., Research Associate, Institute for Immunity, Transplantation and Infections, Stanford University

By integrating data from multiple study cohorts, we have found highly robust, parsimonious gene sets for the diagnosis of infectious diseases, such as acute bacterial or viral infections, or pulmonary TB. Similarly, promising work has shown the potential to risk-stratify patients with sepsis based on host biomarkers, potentially enabling a precision medicine approach to the septic patient.


2:35 Mass Spectrometry-Based Multiplexing Assays for Direct Detection and Absolute Quantitation of Flaviviral Proteins - A Tale of Two Flaviviruses: Dengue Virus and Zika Virus

Francois_JeanFrancois Jean, Ph.D., Associate Professor, Microbiology and Immunology; Scientific Director, Facility for Infectious Disease and Epidemic Research (FINDER), University of British Columbia

My talk will be directed at the critical need for molecular diagnosis of flavivirus infection - in particular with the current challenges associated with the co-infection of Zika virus (ZIKV) and Dengue virus (DENV) in the Americas.


3:05 Impact of Rapid Diagnostic Tests on Antimicrobial Stewardship

Thomas_FileThomas M. File, Jr., M.D., MSc, MACP, FIDSA, FCCP, Chair, Infectious Disease Division Summa Health System Akron; Professor, Internal Medicine, Northeast Ohio Medical University (NEOMED)

Antimicrobial resistance is a serious health threat that affects the clinical outcome of patients, as well as results in higher rates of adverse events and healthcare costs. Antibiotic misuse is the most important modifiable factor, which leads to antimicrobial resistance. Antimicrobial stewardship programs (ASP) have proven highly successful in improving antibiotic use. The availability of more rapid molecular tests for infectious disease has the potential to enable better pathogen-directed therapy, avoid antimicrobial overuse, and result in improved antimicrobial stewardship.

3:35 The Importance of Rapid Diagnostics in Antimicrobial Stewardship

Debbie_GoffDebra Goff, Pharm.D., FCCP Infectious Disease Specialist,The Ohio State University Wexner Medical Center

Our work involves a review of clinical applications of rapid diagnostic tests and the practical applications to stewardship, in support of early diagnosis for appropriate antimicrobial therapy.

4:05 Close of Conference

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