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.

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.

3. Types of Outbreaks

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

6. Outbreak
investigations
Epidemiologic
investigations
Laboratory
investigations
Environmental
investigations

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

37. Algorhythm for MERS-CoVby
RT-PCR

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 waterCampylobacter 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