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Whole Genome Sequencing Conference

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Purpose & Audience

The purpose of this conference is to offer a state-of-the-art seminar on the role of whole genome sequencing and advanced molecular biology to boost the epidemiology of infectious diseases and patient care.

The target audiences for Day 1 sessions are public health practitioners, clinicians, researchers, and students with an interest in infectious diseases and whole genome sequencing. The target audiences for the Day 2 workshop are Department of Health Epidemiologists and lab personnel, but all attendees are welcome. 

The conference is organized by the University of Houston College of Pharmacy and sponsored by the Texas Department of State Health Services.

Schedule Day 1 - Wednesday, July 26

MORNING SESSION: PUBLIC HEALTH INITIATIVES IN ID GENOMICS
Time Presentation Title Speaker
9-10 Moving Public Health, and Specifically the Battle against Antibiotic Resistance, Into the Era of Next Generation Sequencing (view/download PDF) Clifford McDonald, CDC
10-10:45 Historical overview of molecular biology and strain typing (view/download PDF) George Broukhanski, Public Health Ontario
10:45-11:15 BREAK
11:15-12:00 Texas-wide surveillance of C. difficile infection (view/download PDF) Kevin W. Garey, University of Houston
12:00-1:00 LUNCH
AFTERNOON SESSION: Use of ID Genomics
Time Presentation Title Speaker
1-1:45 Improving infectious diseases epidemiology through genomics (view/download PDF) Seth Walk, Montana State University
1:45-2:30 Phylogenomic Outbreak Analysis of Escherichia coli (view/download PDF) Dave Lacher, FDA
2:30-3:00 BREAK
3:00-3:45 Clinical impact of whole genome sequencing of bacterial isolates: lessons from the front line (view/download PDF) Sam Shelburne, MD Anderson Cancer Center
3:45-4:30 Population Genomics of bacteria from Outbreaks to Species Bill Hanage, Harvard University

Schedule Day 2 - Thursday, July 27

Day 2 will involve a workshop specifically designed for Department of Health Epidemiologists and lab personnel, but all conference attendees are welcome. 

MORNING SESSION: Overview of genomic analysis, data visualization and interpretation
Time Presentation Title Speaker
9:00-10:00 Overview of genomic analysis and data visualization Seth Walk, Montana State University
10:00-11:00 Combination genomic approaches / transition of the field George Broukhanski, Public Health Ontario
11:00-12:00 Overview of bionumerics and microbiological use (MLVA, Whole-genome Sequencing, Metagenomics) Eugenie Basseres & Brad Endres, University of Houston
12:00-1:00 LUNCH
AFTERNOON SESSION: Case studies and hands-on learning Data Analysis
Time Presentation Title Speaker
1:00-2:30 C diff outbreak case study All
2:30-4:00 Other outbreaks including Salmonella All
4:00-4:30 Concluding remarks All

Speaker: George Broukhanski, Ph.D., M.S.



George Broukhanski, Ph.D., M.S.
Assistant Professor, University of Toronto Molecular Specialist, Public Health Ontario Laboratories

Presentation Title: Historical overview of molecular biology and strain typing

Primary Research Area: Molecular epidemiology of infectious diseases Secondary Research Area: Bacterial pathogenomics

Research Statement: Initiate and implement research studies in molecular epidemiology of Clostridium difficile and other bacterial and viral pathogens; investigate biomarkers associated with strains causing outbreaks in hospitals, develop methods for detection and typing of this pathogen, supervise implementation of these methods for routine testing at the Public Health Ontario Laboratories for surveillance purposes, outbreak investigations and for identifying person-to-person transmission.

Speaker: William Hanage, Ph.D.



William Hanage, Ph.D.
Associate Professor of Epidemiology, Department of Epidemiology, Harvard University

Presentation Title: Population Genomics of bacteria from Outbreaks to Species

Bill Hanage is Associate Professor of Epidemiology based in the Center for Communicable Disease Dynamics at the Harvard T. H. Chan School of Public Health. He studied at Imperial College London and did postdoc work there and the University of Oxford, using methods like MLST while developing a more theoretical approach to bacterial population genetics. He has authored over 100 publications and book chapters on multiple pathogens, and has won the Fleming Prize and a Young Investigator award from ASM for his work.

Bacterial populations exhibit varying degrees of genetic diversity, some being almost completely uniform while others are a riot of different clones, each characterized by different combinations of mutations and genes. The goal of the Hanage lab is to understand the evolutionary pressures that produce this observed variation, and to link it to transmission, virulence or other traits such as drug resistance. This means looking at how variation arises over different evolutionary timescales, from the origins of bacterial species to the very recent transmission that occurs in outbreaks. This perspective is informed by working on many different species, with the goal of finding general patterns.

We can now rapidly and economically determine genome sequences for hundreds or thousands of bacterial isolates, and members of the lab work to combine this information with mathematical and computational models of evolution, to understand how the pathogen populations we see have come to be. The hope is that by better understanding what has happened in the past, we can better intervene in the future to limit the burden of infection.

Speaker: David Lacher, Ph.D.



David Lacher, Ph.D.
Research Microbiologist, FDA, DHHS, CSFAN, OFVM, OARSA, MGB, Food and Drug Administration's Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment

Presentation Title: Phylogenomic Outbreak Analysis of Escherichia coli

Dr. Lacher is a research microbiologist with the Food and Drug Administration's Center for Food Safety and Applied Nutrition in the Office of Applied Research and Safety Assessment, Division of Molecular Biology. His research interests include the evolutionary genetics of virulence and the molecular subtyping of bacterial pathogens. He is currently pursuing these interests by examining the genetic diversity present within Escherichia coli and Shigella spp.

Speaker: L. Clifford McDonald, M.D.



L. Clifford McDonald, M.D.
Food and Drug Administration's Center for Food Safety and Applied Nutrition, Office of Applied Research and Safety Assessment

Presentation Title: Moving Public Health, and Specifically the Battle against Antibiotic Resistance, Into the Era of Next Generation Sequencing

Dr. McDonald graduated from Northwestern University Medical School, completed his Internal Medicine Residency at Michigan State University, and an Infectious Diseases Fellowship at the University of South Alabama, following which he completed a fellowship in Medical Microbiology at Duke University. Past positions have included Associate Investigator at the National Health Research Institutes in Taiwan and Assistant Professor in the Division of Infectious Diseases at the University of Louisville.

Dr. McDonald is a former officer in the Epidemic Intelligence Service and former Chief of the Prevention and Response Branch in the Division of Healthcare Quality Promotion at the CDC where he currently serves as the Senior Advisor for Science and Integrity in the same division. He is the author or co-author of over 100 peer-reviewed publications with his main interests in the epidemiology and prevention of healthcare-associated infections, especially Clostridium difficile infections, and the prevention of antimicrobial resistance. Dr. McDonald is a Fellow of the American College of Physicians and the Society for Healthcare Epidemiology of America, and a member of the Infectious Diseases Society of America and American Society for Microbiology.

Speaker: Sam Shelburne, M.D., Ph.D.



Sam Shelburne, M.D., Ph.D.
Associate Professor, Department of Genomic Medicine, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX

Presentation Title: Clinical impact of whole genome sequencing of bacterial isolates: lessons from the front line

The research in Dr. Shelburne’s laboratory focuses on understanding the molecular basis of bacterial infections in humans. From a pathogen standpoint, the laboratory seeks to understand the interaction between basic metabolic processes and bacterial virulence, using group A streptococcus as a model organism. In addition, the laboratory investigates the molecular basis of viridans group streptococcal infections and antimicrobial resistance in streptococci. Finally, the laboratory seeks to understand how host genetics, microbiome, and pathogen genetics contribute to susceptibility and infection outcomes in patients with malignancy.

Speaker: Seth Walk, Ph.D.



Seth Walk, Ph.D.
Assistant Professor, Department of Microbiology and Immunology, Montana State University

Presentation Title: Improving infectious diseases epidemiology through genomics

The Walk Lab studies microbes of human importance. We have projects ranging from how pathogens circulate in hospitals to how microbial communities improve human health. We also study how environmental factors influence human-microbe interactions and how host-associated microbes transition between hosts. We broadly develop and apply theories of microbial ecology and evolution to help improve human and animal health and decrease disease. We are lucky to be part of the Department of Microbiology & Immunology at Montana State University, located in the beautiful Gallatin Valley in Bozeman, Montana.