outbreak investigations
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The document discusses the role of laboratories in outbreak investigations. It describes how laboratories can help establish the existence of an outbreak by verifying diagnoses and confirming the causative agent through tests like culture, PCR, and serology. Laboratories also aid epidemiological investigations by defining cases, conducting surveillance to identify additional cases, and comparing laboratory and environmental findings. Finally, laboratories play an important long-term role in monitoring for disease reservoirs, detecting silent outbreaks through surveillance data, and evaluating the success of prevention and control measures.
outbreak investigations
- 1. The Role of Laboratory in Outbreak investigations Dr. Iman M. Fawzy; MD. PhD Consultant of Clinical Pathology, Mansoura, Egypt
- 2. An outbreak • is the occurrence of more cases of disease than expected in a given area or among a specific group of people over a particular period of time.
- 4. Ways to recognize an outbreak – Routine surveillance activities – Reports from clinicians and laboratories – Reports from affected individuals
- 5. • Characterize a public health problem • Identify preventable risk factors • Provide new research insights into disease • Train health department staff in methods of public health investigations and emergency response Goals of an outbreak investigation
- 7. Steps of an outbreak investigation • Prepare for field work • Establish the existence of an outbreak • Verify the diagnosis and confirm the outbreak • Construct a working case definition • Find cases systematically and record information • Tabulate and orient data: time, place, person • Take immediate control measures
- 8. • Perform descriptive epidemiology • Formulate and test hypothesis • Plan and execute additional studies • Compare laboratory and/or environmental studies • Implement and evaluate control measures • Initiate or maintain surveillance • Communicate findings Steps of an outbreak investigation
- 10. Define a case and conduct case finding • Develop a specific case definition using: – Symptoms or laboratory results – Time period – Location • Conduct surveillance using case definition – Existing surveillance – Active surveillance (e.g. review medical records) • Interview case-patients
- 11. Define a case and conduct case finding
- 12. Define a case and conduct case finding Corona • Suspected case A person with one or more symptoms of acute respiratory tract infection ( e.g. fever ≥ 38°C, cough and difficulty in breathing) AND clinical and radiological evidence of pulmonary parenchymal disease AND need admission in the intensive care unit • Confirmed case – A person with laboratory confirmation of MERS-CoV infection1
- 13. Define a case and conduct case finding multiple case definitions are used e.g. • laboratory-confirmed case vs. clinical case; • definite vs. probable vs. possible case; • outbreak-associated case vs. nonoutbreak-associated case, • primary case vs. secondary case
- 14. Tabulate and orient data • Create line listing • Person – Who was infected? – What do the cases have in common? • Place – Where were they infected? – May be useful to draw a map • Time – When were they infected? – Create an epidemic curve
- 15. Take immediate control measures • If an obvious source of the contamination is identified…institute control measures immediately!
- 16. Formulate and test hypothesis • Develop hypotheses – literature reviews of previous outbreaks – interviews of several case-patients • Conduct an analytic study to test hypotheses – Retrospective cohort study – Case-control study
- 17. Plan and execute additional studies Environmental sampling – Collect appropriate samples – Allow epidemiological data to guide testing – If analytic study results are conclusive, don’t wait for positive samples before implementing prevention
- 18. Implement and evaluate control measures • Prevent further exposure and future outbreaks by eliminating or treating the source • Work with regulators, industry, and health educators to institute measures • Create mechanism to evaluate both short- and long-term success
- 19. Communicate findings • Interact with media and communicate progress and findings • Summarize investigation, make recommendations, and disseminate report to all participants
- 20. Laboratory-based surveillance data • Identification of cases for investigations and follow up
- 21. Laboratory-based surveillance data Estimate the magnitude of a health problem, follow trends in incidence and distribution
- 22. Laboratory-based surveillance data Evaluate prevention and control measures
- 23. Laboratory-based surveillance data Monitor changes in infectious agents (e.g. antibiotic resistance, clinical spectrum)
- 24. Laboratory-based surveillance data Facilitate epidemiologic and lab research
- 25. Laboratory-based surveillance data Facilitate epidemiologic and lab research
- 26. Laboratory-based surveillance data Formulate prevention and control strategies
- 27. Laboratory-based surveillance data Detect changes in health practice (e.g. impact of use of new diagnostic methods on case counts)
- 28. Laboratory-based surveillance data • Facilitate planning (policy development) • Detect outbreak to trigger intervention
- 29. Role of Lab in outbreak management • Prevention Reservoir monitoring • Early detection Survillance • Investigations Agent, source, transmission • Control Post- intervention agents eradication
- 30. Reservoir monitoring Outbreak prevention • Environment: Legionella water contamination • Food borne infection: Salmonella, Campylobacter in foodstaff • Healthcare associated infections: MRSA carrier in admitted patients
- 31. Agent, source and transmission • Distinguish outbreak cases from concurrent sporadic cases • Definition of confirmed cases • Confirm outbreak
- 32. Lab tools • Phenotypic methods – Biotyping – Serotyping – Phagetyping – Antimictobial susceptability • Genotypic methods – PCR – RFLP – Sequencing – Others
- 33. Respiratory tract outbreaks • Nasopharyngeal (NP) or nasal swab, and nasal wash or aspirate Samples • should be collected within the first 4 days of illness.
- 34. Laboratory Confirmation Approved/Validated Tests • Standard culture for influenza virus, respiratory synctyial virus (RSV) and rhinovirus • Influenza, parainfluenza, RSV and adenovirus direct fluorescent antibody (DFA) antigen test • Influenza IgG serology tests • Nucleic acid amplification test (NAT) for influenza virus, RSV, rhinovirus/enterovirus, parainfluenza virus, adenovirus, human metapneumovirus, corona virus ribonucleic acid (RNA) • Rapid enzyme immunoassay (EIA) or immunochromatographic (ICT) test kits for influenza virus and RSV
- 35. Laboratory Confirmation Indications and Limitations • NAT primers and probes should be validated to detect the current strains of influenza, RSV, rhinovirus/enterovirus, parainfluenza virus, adenovirus, human metapneumovirus and coronavirus • A proportion of influenza isolates should be typed for strain identification, as appropriate, for epidemiological, public health and control purposes • Antigen testing for influenza virus and RSV is indicated only during the influenza season due to low positive predictive value.
- 36. Types of specimens for testing for the presence of novel coronavirus and advice on handling
- 38. Influenza virus outbreak H5N1 Preferred respiratory specimens • nasopharyngeal swab • nasal aspirate, wash or swab • endotracheal aspirate • bronchoalveolar lavage (BAL) • combined nasopharyngeal or nasal swab with oropharyngeal swab. Diagnosis • Rapid test, Immunofluorescence • RT-PCR (preffered) • Viral culture
- 39. Influenza virus outbreak H1N1 Preferred respiratory specimens • nasopharyngeal swab • nasal aspirate, wash or swab • endotracheal aspirate • bronchoalveolar lavage (BAL) • combined nasopharyngeal or nasal swab with oropharyngeal swab. Diagnosis • Rapid test, Immunofluorescence • RT-PCR (preffered) • Viral culture
- 40. Influenza virus outbreak • Seasonal Influenza (Flu)
- 41. Food borne Outbreaks • Salmonella: undercooked eggs, poultry ,دواجن meat products – Chicken – Salmonella Heidelberg – Raw Cheese - Salmonella Stanley – Pine Nuts والجوز الصنوبر Salmonella Enteritidis – Pistachios فستق Salmonella – Cantaloupes Salmonella Litchfield • undercooked or raw Ground Beef, raw milk – Escherichia coli O157:H7 مفروم لحم • Foods Dairy Products, deli meats باردة لحمة – Listeria monocytogenesاأللبان منتجات • Reheated rice Bacillus cereus
- 42. Food borne Outbreaks • raw and undercooked poultry, raw milk, and untreated waterCampylobacter jejuni • Shigella: person to person. • Raw Shellfish الخام المحار – Vibrio parahaemolyticus • Fresh Produce الطازجة المنتجات – Cyclospora • Frozen Food Products – Escherichia coli O121 • Clostridium botulinum: canned foods, restaurants, soil contamination ,serious deep wounds, Spores identified in honey • Coagulase-positive staphylococci: enterotoxin
- 43. Sample collection and transport in food born outbreak
- 44. Food borne Outbreaks Instructions for Collecting Stool Specimens Instructions Bacterial Parasitic ² Viral ³ Chemical When to collect During period of active diarrhea (preferably as soon as possible after onset of illness). Any time after onset of illness (preferably as soon as possible). Within 48-72 hours after onset of illness. Soon after onset of illness (preferably within 48 hours of exposure to contaminant). Method for collection Rectal swabs, transport medium bulk stool specimen Place fresh stool Collect urine, blood, or vomitus
- 45. Incubation, infectious periods and exclusion criteria
- 46. Waterborne Disease • typhoid fever • typhoid fever characterized by intestinal perforations • Naegleria fowleri infection –Primary amebic meningoencephalitis • cholera – • Guinea Worm Disease – • Acanthamoeba keratitis (AK) • Cryptosporidium • Giardia
- 47. MRSA outbreak • Methicillin-resistant Staphylococcus aureus outbreaks. E.g. – Surgical Unit Outbreak – Medical Unit Outbreak – ICU Outbreak – Hematology Unit Outbreak – Orthopedic unit Outbreak – Community acquired outbreak
- 48. ESBL outbreak • Klebsiella • E coli
- 49. Viral hepatitis outbreaks Outbreak-associated HBV and HCV infections Those with epidemiologic evidence of: • healthcare related transmission and include patients/residents • identified with acute infection, or previously undiagnosed chronic infections with epidemiologic evidence indicating that these were likely outbreak-related incident cases that progressed from acute to chronic.
- 50. Viral hepatitis outbreaks Outbreak-associated HBV and HCV infections HCV infection epidemiologic evidence along with a new finding of hepatitis C antibody and/or RNA positivity in a person not previously known positive
- 51. Viral hepatitis outbreaks HBV, HCV: • fingerstick devices for >1 resident • blood glucose meter for >1 resident (obsolete now) without cleaning and disinfection • HBV-infected orthopedic surgeon with high viral load performing exposure-prone procedures on patients • Drug diversion by radiology technologist
- 52. Viral hemorrhagic fevers • Variable incubation (2-21 days) • Flu-like symptoms with high fever • Increased vascular permeability causes: – hemorrhage in GI tract and mucous membranes – petechial or ecchymotic rash – edema – hypotension • Rapid progression to shock and death
- 53. Laboratory Testing • No widely available rapid tests • Government labs can provide nucleic acid assays • Routine labs reveal clotting abnormalities: – elevated PT and PTT, decreased platelets
- 54. Burkholderia pseudomallei – Aerobic, gram-negative, motile bacillus – Found in water and moist soil – Opportunistic pathogen – Produces exotoxins – Can survive in phagocytic cells • Latent infections common MELIOIDOSIS
- 55. disease of rice farmers endemic in tropics and subtropics: Southeast Asia, Australia, the Middle East, India, China, Caribbean U.S. and EU cases linked with travel abroad SYNDROMIC PRESENTATION MELIOIDOSIS
- 56. Clinical disease uncommon in endemic areas – antibodies in 5-20% of agricultural workers – no history of disease Seasonal increase (wet season) – heavy rainfall – high humidity or temperature SYNDROMIC PRESENTATION Epidemiology
- 57. WOUND INFECTION – Contact with contaminated soil or water INGESTION – Contaminated water INHALATION – Dust/ contaminated soil RARELY – Person-to-person – Animal-to-person SYNDROMIC PRESENTATION MELIOIDOSIS
- 58. INCUBATION PERIOD: 1-21 days (~ 9 days) up to 30 years MODE OF TRANSMISSION INDUCES DIFFERENT CLINICAL FORMS: INOCULATION =>Focal (wound) infection INHALATION => Acute pulmonary infection Both can result in secondary SEPTICEMIA CNS involvement is rare SYNDROMIC PRESENTATION MELIOIDOSIS
- 59. DIAGNOSIS: Clinical suspicion => travel to endemic areas low budget, outdoor travel=> occupational exposure medical, military Microbiology=> Isolation of organism => Various serological tests SYNDROMIC PRESENTATION MELIOIDOSIS
- 60. THANK YOU