Foodborne Disease Outbreak Investigation Team Training: Module 6 – Laboratory Investigation Laboratory investigations Module Learning Objectives At the end of this module, you will be.
Download ReportTranscript Foodborne Disease Outbreak Investigation Team Training: Module 6 – Laboratory Investigation Laboratory investigations Module Learning Objectives At the end of this module, you will be.
Foodborne Disease Outbreak Investigation Team Training: Module 6 – Laboratory Investigation Laboratory investigations 1 Module Learning Objectives At the end of this module, you will be able to 1. Determine the likely causative agent for a foodborne outbreak based on clinical findings and/or suspect food. 2. List important considerations in the collection and submission of clinical and food specimens to the laboratory. 3. Interpret results from testing of clinical and food specimens. 4. Describe three ways subtyping of the causative agent can be used in an outbreak investigation. Laboratory investigations > Learning objectives 2 Determining Causative Agent • Laboratory testing Clues about causative agent can be gained from: • Clinical findings among ill persons • Suspected food, if known Laboratory investigations 3 Non-laboratory Methods for Determining Causative Agent Laboratory investigations 4 Useful Clinical Findings among Ill Persons • Predominant signs and symptoms • Incubation period (i.e., time from exposure to causative agent to onset of illness) • Duration and severity of illness Laboratory investigations > Non-laboratory methods 5 General Categories of Foodborne Illness • Illnesses caused by preformed toxins • Illnesses caused by infections with growth in the gastrointestinal tract with – Direct damage to tissues and/or – Release of toxins in the gut (enterotoxins) Laboratory investigations > Non-laboratory methods 6 Illnesses due to Preformed Toxins • Ingestion of food already contaminated by toxins • Common clinical findings – Short incubation period (minutes or hours) – Abrupt onset – Symptoms depend on toxin Vomiting common Fever and elevated white blood cells in peripheral blood rare Laboratory investigations > Non-laboratory methods 7 Sources of Preformed Toxins • Bacteria - Staphylococcus aureus, Bacillus cereus, Clostridium perfringens • Fish – Scombrotoxin (histamine fish poisoning), Tetrodotoxin (puffer fish) • Marine algae – Ciguatoxin, saxitoxin (paralytic shellfish poisoning) • Fungus – Aflatoxin, mushroom toxins • Chemicals – Heavy metals, pesticides Laboratory investigations > Non-laboratory methods 8 Illnesses due to Infections • Growth of microorganism in body with direct damage to tissues and/or release of toxins in the gut (enterotoxins) • Common clinical findings – Relatively long incubation period – Diarrhea, nausea, vomiting, abdominal pain – Fever, elevated white blood cells in peripheral blood, white blood cells and red blood cells in stool Laboratory investigations > Non-laboratory methods 9 General Types of Infections • Viruses – Norovirus, hepatitis A virus, rotavirus • Bacteria – Salmonella, Shigella, Shiga toxinproducing E. coli • Parasites – Cryptosporidium, Cyclospora cayetanensis, Giardia intestinalis, Trichinella • Other – prions Laboratory investigations > Non-laboratory methods 10 Generalizations by Infection Type Viruses Incubation Less than a day to 4 days period Vomiting, Possible symptoms diarrhea, (rarely bloody) abdominal pain, fever Signs Duration Bacteria Parasites Less than a day to a week 1-4 weeks Vomiting, diarrhea, (sometimes bloody), abdominal pain, fever Abdominal pain and diarrhea WBC; fecal WBC WBC;fecal WBC Several weeks Several days to a 2-5 days week Laboratory investigations > Non-laboratory methods 11 Class Question Twenty people became ill after attending a banquet. Onset of illness occurred (on average) about 4 hours after eating at the banquet (range 18 hours). All cases reported nausea and vomiting. Two reported diarrhea and none reported fever. No ill persons sought health care. All were well within 48 hours. Based on the clinical findings reported by cases, is the causative agent likely to be a preformed toxin or infection due to a virus, bacteria, or parasite? Answer: Preformed toxin. Laboratory investigations > Non-laboratory methods 12 Class Question 51 children and staff from a childcare center developed gastroenteritis following a field trip to a dairy farm. Symptoms included diarrhea (100%), bloody diarrhea (27%), fever (45%), and vomiting (45%). White blood cell counts were elevated for the 10 patients tested. The average incubation period among cases was 3.5 days (range: 2-10 d). Based on the clinical findings reported by cases, is the causative agent likely to be a preformed toxin or infection due to a virus, bacteria, or parasite? Answer: Illness likely due to an infection, specifically a bacterium Laboratory investigations > Non-laboratory methods 13 Clinical Findings • Always exceptions to the rules • Unique clinical findings can help pinpoint specific agent • Consult references Laboratory investigations > Non-laboratory methods 14 Suspect Foods • Certain causative agents are associated with certain foods because the foods – Derive from animal reservoirs of agent – Derive from plants/animals that produce or accumulate toxin – Provide adequate conditions for contamination, survival, and proliferation of agent • Common food-illness pairings Laboratory investigations > Non-laboratory methods 15 Foods and Commonly Associated Causative Agents Food Commonly associated causative agent Raw seafood Vibrio spp., hepatitis A virus, noroviruses Raw eggs Salmonella (particularly serotype Enteritidis) Undercooked meat or poultry Salmonella, Campylobacter, STEC, Clostridium perfringens Unpasteurized milk or juice Salmonella, Campylobacter, Yersinia, STEC Unpasteurized soft cheeses Salmonella, Campylobacter, Yersinia, Listeria, STEC Home-made canned goods Clostridium botulinum Raw hot dogs, deli meats Listeria spp. Mussels, clams, scallops Saxitoxin (paralytic shellfish poisoning); Tropical fish Ciguatera poisoning Shellfish Brevetoxin (neurotoxic shellfish poisoning) Mackerel, tuna, bluefish Scombrotoxin (histamine fish poisoning) Puffer fish Tetrodotoxin Wild mushrooms Mushroom poisoning Laboratory investigations > Non-laboratory methods 16 Class Question Which causative agents are commonly associated with each of these foods? Undercooked chicken Unpasteurized milk Shiga toxin-producing E.coli (STEC) Raw seafood Salmonella Raw eggs Hepatitis A virus Deli meats Listeria Norovirus Laboratory investigations > Non-laboratory methods 17 New Food Vehicles • • • • • • Bagged spinach Carrot juice Peanut butter Dog food Pot pies Broccoli powder on snack food • Canned chili sauce • Hot peppers • • • • • White pepper Raw cookie dough Whole, raw papaya Hazelnuts Pine nuts Laboratory investigations > Non-laboratory methods 18 Laboratory Methods for Determining Causative Agent Laboratory investigations 19 Laboratory Testing • “Laboratory responsibility” • Important role of other team members – Collect specimens – Package and store them – Transport them to the laboratory – Request proper test(s) – Provide information about illness and specimen Laboratory investigations 20 Diagnostic Specimens Need to have suspicion of likely causative agent because appropriate specimen differs by agent • Stool – Most infectious foodborne agents • Blood – Bacteria that cause invasive disease (bacteremia) • Serum – Hepatitis A virus and Trichinella • Urine/hair – Heavy metals • Vomitus, stool, suspected food – Preformed toxins Laboratory investigations > Diagnostic specimens 21 Guidance on Diagnostic Specimens • Testing laboratory • “Diagnosis and Management of Foodborne Illness: A Primer for Physicians” • CDC. “Guidelines for Confirmation of FoodborneDisease Outbreaks.” MMWR 2000; 49 (1): 54-62. (Table B) Laboratory investigations > Diagnostic specimens 22 Collection of Stool Specimens • Collect and submit as soon as possible • Typically from 5-10 cases not treated with antibiotics with illness characteristic of outbreak • Considerations that depend on suspected agent – Acceptability of rectal swabs – If more than one specimen is needed per patient – Use of preservative – Acceptability of freezing Photo source: S. Shiflett Laboratory investigations > Diagnostic specimens 23 Collection of Stool Specimens (cont’d) Suspected Agent Viruses Bacteria Parasites 10 cc bulk stool Bulk stool (rectal swab) 10 cc bulk stool Specimens per patient One One Preservative No** Cary Blair Amount Freezing No (only if RNA or Acceptable* antigen testing) Up to three 10% formalin, PVA No (only if RNA or antigen testing) *Freezing causes die off of Campylobacter jejuni. **Cary Blair acceptable in some laboratories but dilutes stool sample. Laboratory investigations > Diagnostic specimens 24 Class Question Using the references provided, what specimen would you collect if you suspect the following diseases? Are there any special considerations? Diagnostic Specimen Campylobacteriosis Stool, do not freeze Staphylococcal food poisoning Vomitus or food, not all labs accept vomitus Giardiasis Stool, do not freeze, multiple specimens might be necessary Listeriosis Blood or cerebrospinal fluid Laboratory investigations > Diagnostic specimens 25 Submission of Stool Specimens • Label specimen clearly and maintain log. • Complete necessary laboratory forms. • Provide patient information: – Date of collection, – Date of onset, and – Signs and symptoms. Laboratory investigations > Diagnostic specimens 26 Testing of Stool Specimens • Routine stool culture – Salmonella, Shigella, STEC, Campylobacter jejuni/coli • Special requests – Vibrio, Yersinia, E. coli O157:H7*, other Campylobacter species – Viruses – detection of viral RNA by RT-PCR or visualization of virus under electron microscope – Most parasites – visualization by ova and parasite exam; Cryptosporidium or Cyclospora require special techniques *Most public health laboratories routinely test for E. coli O157:H7 Laboratory investigations > Diagnostic specimens 27 Interpretation of Stool Specimen Testing • Positive for certain agent – Patient’s illness caused by agent – Patient colonized with agent but illness not caused by agent – Contamination of specimen • Negative for certain agent – Patient’s illness not caused by agent (caused by another agent requiring different testing) – Collected too late in course of illness – Specimen handled improperly Laboratory investigations > Diagnostic specimens 28 Collection of Food Specimens • Collect as soon as possible and store. • Follow local policies on collection of foods from private homes. • Test when food implicated by other studies. • Check with laboratory on collection and storage. – Keep frozen foods frozen. – Refrigerate perishable foods. – If testing >48 hours after collection, consult laboratory about freezing. Laboratory investigations > Food specimens 29 Submission of Food Specimens • Label container and maintain log. • Complete necessary laboratory forms. • Provide sample information: – Date of collection, – When originally served, and – Handling since time of ingestion that caused illness. Laboratory investigations > Food specimens 30 Chain of Custody • Chronological written record that identifies who had control over specimen during what time • Includes all persons handling sample • Persons signing form – Are responsible for sample while in their possession – May be called to testify in criminal proceeding • Each agency has own form Laboratory investigations > Food specimens 31 Testing of Food Specimens • Challenging because – Food components can interfere with culture. – Food is not sterile. – Different methods are needed for different foods and causative agents. – Generally accepted procedures are not available. • Not all public health laboratories do food testing → May need to submit to reference laboratory • Consult with testing laboratory. Laboratory investigations > Food specimens 32 Interpretation of Food Specimen Testing • Positive for certain agent – Agent cause of outbreak (i.e., food is source) – Agent present but not the cause of the outbreak (e.g., contaminated after the fact) • Negative for certain agent – Agent not present (i.e., food not source) – Non-uniform contamination – Agent inactivated/killed during handling – Complexity of food product and testing procedures precluded detection of agent Laboratory investigations > Food specimens 33 Class Question An outbreak of gastroenteritis occurs following a wedding dinner reception. Ill persons reported diarrhea (100%), bloody diarrhea (25%), vomiting (80%), and fever (50%). The average incubation period for development of illness was 2 days. Stool specimens were collected from 10 ill persons. The dinner was catered by a local business. No foods from the dinner were available except raw chicken from a package used in the chicken Cordon Bleu. A sample was collected and submitted to the laboratory. Laboratory investigations 34 Class Question (cont’d) Eight of the 10 stool cultures were positive for Salmonella. How do you interpret the stool culture results? Answer: Symptoms among patients (i.e., diarrhea some of which is bloody, vomiting, and fever) and the incubation period (average of 2 days) are consistent with salmonellosis. A large number of stools are positive. Salmonella is likely to be the causative agent for this outbreak. Laboratory investigations 35 Class Question (cont’d) The raw chicken was also positive for Salmonella. How do you interpret the food test results, given the results of the stool cultures? Answer: The chicken could be the source of the outbreak but raw chicken is commonly contaminated with Salmonella. If chicken is properly prepared, Salmonella present will be killed. What information might help you interpret this information properly? Answer: Results from analytic epidemiologic studies, findings from an environmental health assessment of the chicken preparation, subtyping of isolates from cases and the chicken Laboratory investigations 36 Subtyping of Causative Agents Laboratory investigations 37 Subtyping of Causative Agent • Characterization of microorganisms below the species level using characteristics that – Differ between strains – Are same among isolates with common origin • Variety of subtyping methods (e.g., serotyping, phage typing, antibiotic susceptibility, pulsed field gel electrophoresis [PFGE], multiple-locus variable number tandem repeat analysis [MLVA]), not all of which are available for all organisms • Not all methods equally discriminatory Laboratory investigations > Subtyping of causative agent 38 Uses of Subtyping in Outbreak Investigation • Usefulness in outbreaks based on presumption – Isolates in an outbreak have a common origin – Single strain will be the culprit in most outbreaks • Uses – Link cases together – Link foods with outbreaks – Refine case definition decreasing misclassification in epidemiologic studies – Link outbreaks in different locations Laboratory investigations > Subtyping of causative agent 39 Pulsed Field Gel Electrophoresis (PFGE) • Separation of DNA fragments in a gel using a pulsing electric field • Creates visual banding pattern unique for isolate • Different DNA composition different PFGE • Indistinguishable patterns suggest similar origin of isolates Cluster of indistinguishable patterns Laboratory investigations > Subtyping of causative agent 40 PulseNet Laboratory Network Participating Laboratories Standardized testing of • E. coli O157:H7, • Salmonella, • Shigella, • Listeria, and • Campylobacter PFGE Patterns Patterns uploaded by testing laboratory PulseNet National Database (CDC) • Monitors for similar patterns • Notifies foodborne epidemiologists of clusters • State labs can query Laboratory investigations > Subtyping of causative agent 41 PulseNet Participants PulseNet headquarters Regional laboratories Local and secondary state laboratories Federal laboratories Laboratory investigations > Subtyping of causative agent 42 E. coli O157:H7 and Hazelnuts • December 2010, cluster of 8 cases of E. coli O157:H7 identified through PulseNet • Follow-up interviews revealed in-shell hazelnuts consumed by all cases • Outbreak strain isolated from hazelnuts • Traceback led to common distributor • Product recalled March 2011 Laboratory investigations > Subtyping of causative agent 43 Subtyping Issues • Matching of subtypes not proof of common exposure • Association of multiple subtypes with one outbreak • Need for routine subtyping (in real time) • Limited ability of available methods to distinguish between strains • Patient isolate not available if rapid diagnostic testing used Laboratory investigations > Subtyping of causative agent 44 No Smoking Gun? • Most convincing evidence about the source of an outbreak is isolation of causative agent from suspected vehicle (i.e., food) • Causative agent isolated from food vehicle in only 14% of outbreaks with a confirmed etiology • Importance of epidemiologic and environmental health studies Laboratory investigations 45 Quick Quiz Laboratory investigations 46 Quick Quiz 1. Which of the following causative agents tend to have the longest incubation period? A. Preformed toxins B. Viruses C. Bacteria D. Parasites Laboratory investigations 47 Quick Quiz 2. Most foods can be associated with a variety of causative agents. A. True B. False Laboratory investigations 48 Quick Quiz 3. The following are true statements about stool specimens collected during a foodborne disease outbreak EXCEPT A. Stool is the specimen of choice for most causative agents. B. Routine stool cultures cover the most common foodborne disease causative agents. C. The method of collection and handling depend on the suspected causative agent. D. Freezing of stool specimens can interfere with detection of some causative agents. Laboratory investigations 49 Quick Quiz 4. Which of the following is a possible interpretation of a negative result on a routine stool culture? A. The patient’s illness was not caused by agents detected through routine cultures. B. The specimen was collected too late in the course of illness. C. The specimen was handled improperly, killing any causative agents present. D. All of the above Laboratory investigations 50 Quick Quiz 5. Subtyping of isolates from cases of the same disease can be used for all of the following EXCEPT A. Link cases together B. Link outbreaks in different geographic locations C. Link foods with cases D. As sole proof of an outbreak Laboratory investigations 51