Philip Bronstein, Ph.D.Food Safety and Inspection Service

Office of Public Health Science

July 29, 2013

Pathogen Testing in a Public Health Setting: FSIS Perspective

• The Food Safety and Inspection Service (FSIS) is the public health agency in the U.S. Department of Agriculture responsible for ensuring that the nation's commercial supply of meat, poultry, and egg products is safe, wholesome, and correctly labeled and packaged.

• ~ 10,000 total personnel

Protecting Public Health through Food Safety and Food Defense

Food Safety and Inspection Service

Pre-PFGE era

• 1906 – organoleptic inspection

• 1960’s – laboratory testing to identify

economic adulteration (e.g., added water)

• 1970’s – routine microbiological testing

• 1988 – testing of ready-to-eat meat and poultry for Listeria monocytogenes

• 1994 – testing of ground beef for E. coli O157:H7

PFGE era: 1996 - Present

• FSIS resources and reliance on culture-based methods and isolate subtyping

• Regulatory testing, baseline surveys, and foodborne illness investigations

• Policy and actions based on culture confirmation (presence and absence), serotype, and PFGE

• FSIS contributes isolates to VetNet, PulseNet, and NARMS

FSIS Laboratories

Labs conduct routine monitoring, follow-up, and baseline study programs: Athens, Georgia

Executive AssociateEFSL-routine/other testingLQAD-quality assuranceFERN- biosecurity

St. Louis, MissouriMWFSL-routine testing

Alameda, CaliforniaWFSL-routine testing

ISO 17025 accredited by the American Association of Laboratory Accreditation (A2LA)

PFGE – FSIS Investment and Reliance

• PFGE is culture-dependent and requires an isolate

• Outbreaks Section of the Eastern Laboratory (OSEL)• PulseNet certified by CDC in 1996

• 10 employees - characterize strains, monitor PulseNet SharePoint site, provide lab support during investigations and evaluations of harborage

• 8 Bio-Rad Chef Mapper® systems, each generate 11 patterns per day

• E. coli STEC, Lm, and Salmonella isolate PFGE patterns are generated and uploaded to PulseNet (over 1000 uploads last year)

• Health department laboratories upload bacterial isolate PFGE patterns from clinical specimens (STEC, Lm, Salmonella)

• PFGE data support epidemiologic investigation by suggesting distinction between infections likely to be from a single source versus sporadic infections (case definition)

• 2009 – 2011: 71 foodborne illness investigations possibly associated with FSIS-regulated products a portion of which result in recalls

• 37 E. coli (STEC)

• 28 Salmonella spp.

• 5 Listeria monocytogenes

• 1 Clostridium perfringens

PFGE Data and Foodborne Illness Investigation

Foodborne Illness Investigations• Salmonella enterica serovar Chester infections

• Rare serotype with a new PFGE pattern in PulseNet • 43 case-patients in 18 states and food samples • June 17, 2010 - recall of Cheesy Chicken and Rice frozen meals in

commerce• Shiga toxin-producing E. coli (STEC) O26

• 3 case-patients from 2 states with indistinguishable PFGE• Leftover ground beef from the case-patient’s home tested positive for

E. coli O26 with indistinguishable PFGE pattern• August 28, 2010 - first U.S. recall of ground beef for non-O157 STEC

• Salmonella enterica serovar Enteritidis infections• 46 case-patients in 9 states and food samples • PFGE pattern and MLVA in case-patients and food samples were

indistinguishable• July 11, 2011 - recall of over 29,000 pounds raw ground beef products

Culture Isolate: Dependence to Independence

– With in context of FSIS’s legal framework and public health mission:• Methods must be -DEPENDABLE

• Results should be -DEFINITIVE, and

• Actions must be -DEFENSIBLE

– Reliance on culture has enabled FSIS to make progress in improving public health

– How will culture-independent diagnostics impact the existing paradigm?

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O45eae-stx-

O145eae+stx+

O13eae-stx-

O145eae+stx+

O13eae-stx-

Non-CultureResult

FSIS MLG Results

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Bacterial Population of Sample Screen Confirmation

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+Distributed virulence factors

Non-viable pathogen

Viable pathogen

FSIS Concerns for the Lack of Clinical Isolates

• Impacts - FSIS pathogen detection methods

• Impacts - FSIS enforcement activities

• Impacts - FSIS investigative process– Trace back

– Outbreak cluster identification

• No culture isolates for further characterization– Emerging pathogen/virulence factors detection

– Evaluation of new detection technologies

– Genomic studies

FSIS – beyond the PFGE Era Non-culture approach

• Cost, need, and technology will drive future innovation

• In this era FSIS will need help from our public health partners

– To demonstrate the 3Ds for FSIS before implementing these approaches

– To develop technologies and analyses to better understand virulence , adaptation mechanisms, and the complex ecology of food pathogens

100K Foodborne Pathogen Genome Project

FSIS has committed to contributing pathogen isolates from our regulatory sampling programs for this project.

Consortium of federal, academic and industry partners. The goals:

Sequence 100,000 genomes of foodborne pathogens anddeposit genomes along with meta-data into an open access database

Thank you!