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2013 Archived Content

Molecular Diagnostics for Infectious Disease 

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7:30 am Problem Solving Breakout Discussions with Continental Breakfast


Table 1. Regulation of Emerging Technologies in Point-of-Care & ID  

Christine C. Ginocchio, Ph.D., M.T. (ASCP), Chief, Division of Infectious Disease Diagnostics, Department of Pathology and Laboratory Medicine Professor, Hofstra University North Shore-LIJ School of Medicine North Shore-LIJ Health System Laboratories

Table 2. Introducing NGS to a Clinical Microbiology Lab

• Which applications make the most sense now?
• What do I need to get started?
• How do I maintain NGS services?
• What is the outlook for the future of clinical microbiology?

Moderator: Patrick Tang, MD, PhD, FRCP(C), Medical Microbiologist, Program Head, Mycobacteriology/TB Laboratory, Program Head, Molecular Services Laboratory, B.C. Centre for Disease Control, Public Health Microbiology & Reference Laboratory, Clinical Assistant Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia

Table 3. Digital Microbiology: The Ultimate Frontier in Pre-Analytics

• What do I need to get started, which laboratories will automation fit in?
• How do laboratories address downtime, especially with staff reductions?
• What factors should be considered when justifying return on investment
• What should a laboratory do to verify the system meets stated performance characteristics?
• Is there a role for change management?
• What is the outlook for the future of clinical microbiology?
 Moderator: Nathan A. Ledeboer, Ph.D., Assistant Professor of Pathology, Medical College of Wisconsin 

Table 4: Molecular Diagnostics in Drug and Vaccine Development

• Will pathogen specific diagnostic testing drive drug development or will drug development drive pathogen specific diagnostic testing?
• Can point of care screening diagnostics be used to identify high-risk patients before they get sick? 
• Using single versus multiplexed diagnostics in antiviral, antibiotic and vaccine clinical trials. Do you really want to know?
• Examples of how commercial and custom diagnostics have been used and are being used in clinical trials for influenza, respiratory syncytial virus, C. difficile, P. aeruginosa and S. aureus drug and vaccine development will be discussed.

Moderator: Mark T. Esser, Ph.D., Director, Translational Medicine, Vaccines & Infectious Diseases, MedImmune Inc.





8:25 Chairperson’s Opening Remarks

Robin PatelRobin Patel, M.D., Chair, Clinical Microbiology; Consultant, Clinical Microbiology and Infectious Diseases; Professor, Microbiology and Medicine, College of Medicine, Mayo Clinic



8:30 The Impact of Emerging Diagnostic Laboratory Techniques and the Effects on Healthcare Outcome

Franklin R. CockerillFranklin R. Cockerill, III, M.D., Deptartment of Laboratory Medicine and Pathology, Mayo Clinic

The diagnosis and treatment of infectious diseases has been significantly facilitated by new testing methods, providing considerably faster and more accurate means for diagnosis of pathogens; and in some cases, have provided the first means for identification and quantification of pathogens, particularly viruses.  This lecture will include a historical and a high level technical review of newer diagnostic methods, and the impact these methods have had on the diagnosis and treatment of infectious disease.

8:55 Validation of Next-Generation Sequencing Assays for Pathogen Diagnosis in a CLIA Laboratory

Charles ChiuCharles Chiu, M.D., Ph.D., Assistant Professor, Departments of Laboratory Medicine and Medicine (Infectious Diseases), UCSF School of Medicine

Here we will discuss validation of an NGS-based assay for viral detection in the CLIA laboratory with a high degree of sensitivity and specificity; implementation of a flexible, automated, and cloud-compatible pipeline for pathogen detection in metagenomic NGS data; and applications of this system for microbial diagnosis and outbreak investigation in clinical and public health settings.

 9:20 Next-Generation Sequencing in a Public Health Laboratory 

Patrick TangPatrick Tang, M.D., Ph.D., FRCPC, Program Head, Molecular Microbiology and Genomics, BC Centre for Disease Control - Public Health Microbiology and Reference Laboratory

Clinical microbiology laboratories are now exploring the use of next-generation sequencing technology to replace or complement traditional methods for infectious disease diagnosis and epidemiology. Recent successes include the use of whole genome sequencing for communicable disease epidemiology.


Randox Pharma Services9:45 Multiplex Respiratory Pathogen Detection: Combining Speed with Accuracy to Enhance Clinical Decision Making  

Scott McKeown, Ph.D., Molecular Diagnostics Business Manager, Randox Laboratories Ltd.   

Respiratory tract infections (RTI) are a leading cause of mortality and morbidity worldwide and are the most common ailments dealt with in primary care.  Symptoms from RTIs are similar but can be caused by a heterogeneous range of viral and bacterial pathogens, leading to difficulty in accurate diagnosis.  We describe the Respiratory Multiplex Array (Randox Laboratories Ltd), a biochip assay developed for simultaneous detection of 22 respiratory pathogens (15 viruses and 7 bacteria) in up to 54 patient samples in one run.  Based on a combination of multiplex PCR, probe hybridization and chemiluminescence detection, this array offers laboratories a cost effective, rapid and high throughput IVD assay, allowing severely infected patients to be treated quickly and appropriately, while facilitating the reduction of unnecessary antibiotic use.

Evogen10:00 HyBeacons as a New Approach to RT-PCR Based on Melt Curve Differentiation

Richard St.Clair, Vice President, Commercialization, Evogen, Inc.

HyBeacons probes have been developed as a new tool for rapid sequence detection and discrimination and can be used for a variety of real-time PCR applications because of their sensitivity and specificity. Multiplex and SNP assays can be designed for identification of multiple targets due melt curve differentiation for DNA and RNA targets.

10:15 Coffee Break in the Exhibit Hall with Poster Viewing


10:45 Automated, Cloud-Enabled Bioinformatics Pipeline for Whole-Genome Sequencing-Based Pathogen Diagnostics

W. Florian FrickeW. Florian Fricke, Assistant Professor, Microbiology & Immunology, Institute for Genome Sciences, University of Maryland School of Medicine

WGS-based diagnostic tools promise to provide increased resolution for isolate typing, phenotype prediction, and epidemiological analyses. In order to facilitate the transition of WGS-based diagnostics into the clinic, standardized, bioinformatic analysis protocols are needed. We demonstrate the feasibility of building an automated, cloud computing-enabled diagnostic pipeline to support reproducible WGS analysis for microbial isolate typing, virulence, and antimicrobial resistance profiling.

11:15 The Next Generation of Outbreak Investigation: Identification of Known Viruses in New Places and an Unknown Virus in the US

Laura McMullanLaura McMullan, Ph.D., Molecular Pathogenesis and Antiviral Section, Virus Special Pathogens Branch, Centers for Disease Control

Outbreaks require diagnostic assays that rapidly identify the pathogen. We have developed a metagenomics approach of pathogen discovery that has identified a new arenavirus in Zambia, Yellow Fever virus in Uganda, and a novel phlebovirus in the USA.


11:45 A Tsunami of Change, Automation in Clinical Microbiology

Nathan A. LedeboerNathan A. Ledeboer, Ph.D., Assistant Professor of Pathology, Medical College of Wisconsin

Since inception, clinical microbiology has required a highly technical and skilled workforce with limited automation. Clinical staff have complained of poor turnaround, while the laboratory awaits microbial growth. However, with increasing specimen volumes and fewer available skilled workers, laboratories are increasingly seeking automated solutions.


AdvanDx12:15 pm A History of FISHing with PNA: Always Reliable, Now Quicker and Easier Than Ever 

Margie_MorganMargie A. Morgan, Ph.D., Department of Pathology & Laboratory Medicine, Cedars-Sinai Medical Center

In the 10 years since peptide nucleic acid fluorescent in situ hybridization, PNA FISH, was introduced to the clinical microbiology laboratory for the rapid (1.5hours ) identification of select pathogens in positive blood cultures, a renewed interest in antimicrobial stewardship and escalating pressures to control hospital costs made the appropriate use of PNA FISH a desirable and cost-efficient alternative to conventional microbiological blood culture identification methods.  Today, QuickFISH  positions the clinician to receive the fastest (20 minutes)  identification of bloodborne pathogens, even when compared to each of the many rapid molecular identification methods recently introduced to the market.  This presentation discusses the merits of using PNA FISH and QuickFISH in the microbiology laboratory to effectively and rapidly identify blood culture pathogens, improve patient care, strengthen antimicrobial stewardship efforts, and decrease hospital costs.

Quanterix12:45 Luncheon Presentation I: Immunoassay Technology with Sensitivity of Nucleic Acid Testing: p24 Case Study

David Duffy, Ph.D., Vice President, Research, R&D, Quanterix

This presentation will describe the application of an ultra-sensitive single-molecule digital immunoassay to HIV detection, using a single molecule array (Simoa) to count individual molecules of p24 capsid protein in the blood, which indicates the presence of HIV virus. Results showed 3,000 times greater analytical sensitivity than conventional immunoassays, and comparable to the gold standard of nucleic acid testing.

1:15 Luncheon Presentation II (Sponsorship Opportunity Available)

1:45 Session Break


2:00 Chairperson’s Remarks

Pietro ScalfaroPietro Scalfaro, M.D., MBA, Consultant, Molecular Personalized Medicine, FMH Paediatrics & Intensive Care





2:05 Rapid Detection of Bloodstream Infections

Donna M. WolkDonna M. Wolk, MHA, Ph.D., D(ABMM), System Director, Clinical Microbiology, Geisinger Health System, Department of Laboratory Medicine

This program will describe and review existing and future technologies that can improve the microbiology laboratory’s ability to rapidly identify bloodstream pathogens and provide pivotal results for escalation or de-escalation of antimicrobials. Current and potential applications of technologies in diagnostic clinical microbiology laboratories will be discussed.

2:35 Panel Discussion: Improving Pathogen Detection & Monitoring the Host Response in Sepsis Detection & Management

Moderator: Pietro Scalfaro, M.D., MBA, Consultant, Molecular Personalized Medicine, FMH Paediatrics & Intensive Care

Panelists: Steven Michael Opal, M.D., Professor of Medicine, Infectious Disease Division, Brown Medical School

Roslyn A. Brandon, Ph.D., Co-Founder, President & CEO, Immunexpress

Bert K. Lopansri, M.D. Division of Infectious Diseases and Clinical Epidemiology Intermountain Medical Center and LDS Hospital, Medical Director, UCR Clinical Microbiology Laboratory

John P. Burke, M.D., Chief, Division of Clinical Epidemiology & Infectious Diseases, Intermountain Medical Center and LDS Hospital, & Professor of Internal Medicine at the University of Utah

Teresa Raich, Ph.D., Vice President, Clinical & Scientific Affairs, Nanosphere, Inc.

3:35 Spotlight Presentation: Application of Digital PCR to Clinical Viral Load Testing

Randall T. HaydenRandall T. Hayden, M.D., Director, Clinical and Molecular Microbiology, Member, Department of Pathology, St. Jude Children’s Research Hospital

Viral load testing has become integral to clinical care, but is often limited by poor standardization and precision. Digital PCR offers a means of direct quantitative measurement that may improve both accuracy and precision over current methods. This session will describe the theory behind digital PCR, as well as some initial studies evaluating its use for viral load testing in clinical samples.

4:05 A Novel, 2nd Generation Device for Ambient Storage and Transportation for Downstream Infectious Disease Testing: ViveSTTM

Anita M. McClernonAnita M. McClernon, MSc, Director of Laboratory Services, bioMONTR® Labs

Infectious disease monitoring often requires collection sites to ship patient samples to reference laboratories, requiring careful temperature control and special packaging.  Here we report data evaluating the stability and reproducibility of infectious plasma specimens stored on ViveST analyzed with RT-PCR and Sequencing Technolgies.  ViveST can offer a global solution and enhance access to healthcare and significantly reduce the burden associated with shipping frozen samples.

4:35 Close of Conference

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