Future Directions Unknowns:

Slides:

Advertisements

Similar presentations

1Surveillance and outbreak detection Foodborne Disease Outbreak Investigation Team Training: Module 2 – Foodborne Disease Surveillance and Outbreak Detection.

Advertisements

Non-O157 Shiga toxin-producing Escherichia coli: Isolation and detection challenges Cheryl Bopp, M.S., Chief, Epidemic Investigations Laboratory Unit,

Prevalence of Enterohemorrhagic E. coli (EHEC) Marler and Clark Retail Ground Beef Baseline Study: Phase 3.

Role of the laboratory in disease surveillance

1 Don L. Zink, Ph.D. Center for Food Safety and Applied Nutrition U.S. Food & Drug Administration College Park, MD The Challenge of Emerging Foodborne.

WHO Global Salm-Surv: A Global Salmonella Surveillance Network World Health Organization, Geneva Centers for Disease Control and Prevention, Atlanta Danish.

Dissertation work in Functional Genomics Naim Rashid 4 th Year PhD, Biostatistics.

1 Feel free to contact us at

Richard H. Scheuermann, Ph.D. Department of Pathology Division of Biomedical Informatics U.T. Southwestern Medical Center Standardizing Metadata Associated.

Standardizing Metadata Associated with NIAID Genome Sequencing Center Projects and their Implementation in NIAID Bioinformatics Resource Centers Richard.

Bioinformatics Core Facility Ernesto Lowy February 2012.

Molecular Surveillance of Foodborne Infections Peter Gerner-Smidt, MD, PhD Chief of PulseNet USA CDC

Food Industry Perspective on Non-O157 STEC Jenny Scott Vice President, Food Safety Programs Grocery Manufacturers/Food Products Association.

Genomic walking (1) To start, you need: -the DNA sequence of a small region of the chromosome -An adaptor: a small piece of DNA, nucleotides long.

Global Foodborne Infections Network (GFN) Building capacity to detect, control and prevent foodborne and other enteric infections from farm to table National.

The Power of New Information in Risk-Based Decision Making Don L. Zink, Ph.D. Center for Food Safety and Applied Nutrition U.S. Food and Drug Administration.

Molecular Techniques in Microbiology These include 9 techniques (1) Standard polymerase chain reaction Kary Mullis invented the PCR in 1983 (USA)Kary.

Whole Genome Sequencing aka “WGS” - utility in foodborne illness outbreak detection and investigations Dan Rice FDA ORA – Pacific Regional Lab Northwest.

Non-O157 STEC: New Challenges / Practical Limitations / Next Steps Robert L. Buchanan HHS Food and Drug Administration Center for Food Safety and Applied.

100K Genome Project By: Amanda Crichton and Laura Henkel.

The PulseNet USA WebBoard – A Rapid Alert and Information Sharing System Peter Gerner-Smidt CDC, Atlanta, USA 5th Annual Meeting PulseNet America Latina,

The Whole Genome Sequencing Revolution Martin Wiedmann Gellert Family Professor of Food Safety Department of Food Science Cornell University, Ithaca, NY.

Liberia Field Epidemiology Training Programme (LFETP)Liberia Field Epidemiology Training Programme LFETP) FIELD WORK 2 -Expanded Surveillance Report- -Measles.

Antimicrobial resistance and virulence genes among Streptococcus suis serotype 2 isolates from pig-derived products  Streptococcus suis is an emerging.

Other uses of DNA microarrays

Severe Acute Respiratory Syndrome (SARS) AA Model for Preparedness for Emerging Diseases Finding and Filling Gaps.

Jean B. Patel, PhD, D(ABMM) Division of Healthcare Quality Promotion National Center for Emerging and Zoonotic Infectious Disease Centers for Disease Control.

MODULE 2 – FOODBORNE DISEASE SURVEILLANCE AND OUTBREAK DETECTION FOODBORNE DISEASE OUTBREAK INVESTIGATION TEAM TRAINING.

October 4, 2004 Building Steps for Canada’s New Integrated Enteric Pathogen Surveillance Program 12th Annual APHEO Conference October 4, 2004 Niagara Falls,

Outbreak Investigation

TB Genotyping and Whole Genome Sequencing in California

2. Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA

Whole Genome Sequencing for Epidemiologists – A Brief Introduction

CIFOR Guidelines for Foodborne Disease Outbreak Response and the CIFOR Toolkit: Focus Area 7: Epidemiology Investigation New York Integrated Center of.

Metro-Nashville and Tennessee NEARS

Steffany Cavallo, MPH (Tennessee) Carlota Medus, PhD, MPH (Minnesota)

Martin Wiedmann Cornell University

CIFOR Guidelines for Foodborne Disease Outbreak Response and the CIFOR Toolkit: Focus Area 5: Pathogen-Specific Surveillance New York Integrated Center.

CIFOR Toolkit: An Overview of Focus Area 2 – Necessary Resources

Laboratory investigation for clonality of a foodborne outbreak due to

Epidemiologist Supervisor Foodborne Diseases Unit

Drivers and Constraints – application of molecular typing in surveillance of foodborne diseases in EU/EEA Johanna Takkinen, on behalf of ECDC FWD team.

Whole genome sequencing: New methods for traceback investigations

Team-Building Tactics Which C-Executives Should Know.

The Use of Molecular Epidemiology and

Surveillance of Foodborne Enteropathogen in Brazil

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Genomics of medical importance

Genomics of epidemic pathogens

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

The Human Genome Project and beyond

Outbreak Investigation

Structure and Terminology

Education Jurisdiction

“Bug of the month “ Pseudomonas aeruginosa (Gram negative bacilli)

Israel Center for Excellence through Education Israel Arts and Science Academy.

Laboratory Investigation

Using Whole Genome Sequencing Analysis in California

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

Communication Department

Education Jurisdiction

Division of Tuberculosis Elimination

Perspectives from Los Angeles County Tuberculosis Control Program

Laura Lane, Epidemiologist

KEY CONCEPT Entire genomes are sequenced, studied, and compared.

ITS rRNA gene locus. ITS rRNA gene locus. Schematic of the eukaryotic ribosomal gene cluster. The SILVA database contains sequences of the 18S gene, while.

Francois Balloux, Ola Brønstad Brynildsrud, Lucy van Dorp, Liam P

CIFOR Guidelines for Foodborne Disease Outbreak Response and the CIFOR Toolkit: Focus Area 6: Initial Steps of an Investigation New York Integrated Center.

From Prediction Tools to Shiny App

Presentation transcript:

Future Directions Unknowns: What should we consider a cluster for other Salmonella serotypes and other pathogens or when using a different reference genome- i.e., how closely related do case-isolates have to be for us to investigate as a possible outbreak? Flexibility! How will lab and epi communicate? What should we consider a cluster for other Salmonella serotypes and other pathogens or when using a different reference genome- i.e., how closely related do case-isolates have to be for us to investigate as a possible outbreak? We need to get used to being flexible How will lab and epi communicate? It’s important to meet with your lab early on and discuss a plan-who will be responsible for identifying clusters, and how will the data be communicated

Future Directions In the near future: PulseNet (BioNumerics) More easily analyze our sequencing data at the state level wgMLST Nomenclature Beyond cluster detection: Salmonella serotyping, STEC virulence factors, presence of antimicrobial resistance genes… In the near future: We should be able to more easily analyze our sequencing data at the state level using BioNumerics. We’ll likely start using wgMLST for most pathogens, although SNP analysis will still be available. Using wgMLST will allow us to have a naming system, which should make it easier to communicate results and across jurisdictional lines. The use of WGS will go beyond cluster detection: WGS can be and will be used for Salmonella serotyping, for identifying STEC virulence factors, identify the presence of antimicrobial resistance genes…

As we move forward in implementing WGS, if you need help with training or discussion specifically for your state, if you have questions or if you want to discuss an outbreak you are working on, feel free to contact your regional Center of Excellence- we’ll be able to help you or refer you to a COE that can.

Questions? Thank you! Any questions or comments?