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Collecting Specimens in Outbreak Investigations

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Title: Collecting Specimens in Outbreak Investigations


1
Collecting Specimens in Outbreak Investigations
2
Goals
  • Define and describe animal and human clinical
    specimens.
  • Define and describe environmental specimens such
    as food, water, and fomites.
  • Discuss proper methods of human specimen
    collection and transportation

3
Outbreaks Involving Clinical Specimens
  • Human clinical specimens from case-patients
  • Blood
  • Serum
  • Urine
  • Type of specimen depends on the outbreak
  • Similar specimens from animals
  • Saliva
  • Hair
  • Feces

4
Clinical Specimen Example 1 Monkeypox
  • Midwestern United States more than 70
    individuals experienced febrile rash thought to
    be caused by monkeypox virus
  • Cases laboratory confirmed using blood, skin,
    lymph node, pharyngeal specimens
  • All lab-confirmed human cases associated with
    purchase of prairie dogs as pets
  • Samples from prairie dogs confirmed infection
  • Prairie dogs infected at animal distribution
    facility where housed/transported with exotic
    rodents from Africa

5
Clinical Specimen Example 2 Hantavirus
  • 1993, southwestern United States outbreak of a
    fatal unexplained pulmonary illness associated
    with previously unknown type of hantavirus
  • Rodents found near homes of case-patients trapped
    and tested
  • Same strain of hantavirus cultured from tissue of
    a deer mouse captured near home of a case-patient
    who had died from the hantavirus strain
  • Results of a case-control study consistent with
    hypothesis that the fatal pulmonary disease was
    associated with proximity to infected
    deer mice.

6
Outbreaks Involving Environmental Specimens
  • Environmental specimens may be collected to
    confirm a source food, water, fomites
  • Food/water samples often collected in food or
    waterborne outbreaks
  • Frequently collected in conjunction with human
    clinical samples
  • When clinical and environmental specimens yield
    same results, supports hypothesis that outbreak
    source is same as environmental specimen source

7
Environmental Specimen Example 1 Cholera
  • 1991, individual in Maryland tested positive for
    cholera while hospitalized for diarrhea and
    dehydration
  • Case-patient had not reported any common risk
    factors for cholera (raw shellfish, travel to
    foreign country, vaccination)
  • Attended party 2 days prior to hospitalization
    other attendees also experienced diarrhea, had
    laboratory evidence of cholera
  • All case-patients reported eating homemade rice
    pudding prepared with frozen coconut milk
    imported from Thailand
  • Lab professionals cultured unopened packages of
    the same brand used to prepare the rice pudding
  • Tested positive for several types of Vibrio
    cholerae, Aeromonas, Salmonella

8
Environmental Specimen Example 2 E. coli
  • 1998, more than 50 cases of Escherichia coli
    0157H7 were laboratory confirmed in Wisconsin
  • Case-control found association with consumption
    of fresh cheese curds produced by a particular
    cheese factory
  • Cheese samples from opened package of curds
    served at a party attended by several
    case-patients tested positive for E. coli 0157H7
  • Pulsed-field gel electrophoresis demonstrated
    that 42 of the 44 case-patient isolates were
    indistinguishable from the curd isolates and from
    each other
  • Batch of unpasteurized cheddar cheese
    inadvertently used to make fresh cheese curds and
    incorrectly sold as pasteurized cheese curds

9
Environmental Specimen Example 3 E. coli
  • 1993, widespread outbreak of acute watery
    diarrhea occurred among 403,000 residents of
    Milwaukee, WI
  • Performed laboratory tests for enteric pathogens,
    examined ice made during time of the outbreak for
    cryptosporidium oocyst
  • Surveyed residents with confirmed or probable
    cryptosporidium infections
  • Outbreak caused by cryptosporidium oocysts that
    passed through filtration system of city's
    water-treatment plant

10
Environmental Specimen Example 4 Anthrax
  • Anthrax investigation, 2001
  • Sampling of envelopes containing white powder
    confirmed suspicion of anthrax attack
  • Results from sampling of envelopes, postal
    facilities, clothing, news media offices,
    residences, and other sites used to evaluate
    presence and extent of anthrax contamination and
    guide decontamination process

11
Challenges to Detecting Infectious Agents in the
Environment
  • Infectious pathogens can be difficult to isolate
    and identify
  • Infectious enteric agents in water are
    particularly difficult to detect and quantify
    because concentration is more diluted than in
    clinical specimens
  • Only 13 of causative organisms of U.S.
    waterborne infectious disease outbreaks in 1991
    and 1992 were identified

12
Challenges to Detecting Infectious Agents in the
Environment
  • Some methods cannot determine viability or
    infectivity of the organisms
  • Identification of infectious agents in food also
    challenging because present in small quantities
  • Detection of infectious agents in both food and
    water may require costly specialized methods
  • 2004 survey of 56 state and territorial public
    health labs 18 reported testing food
    specimens for viral pathogens

13
Challenges to Detecting Infectious Agents in the
Environment
  • To ensure sample integrity and proper diagnosis
    and treatment, specimens need to be collected as
    quickly as possible once an outbreak is suspected
  • In a foodborne disease outbreak, the implicated
    food may be discarded or consumed in a matter of
    days

14
Sampling Onboard Ship The Vessel Sanitation
Program
  • Vessel Sanitation Program (VSP)
  • Jointly established by the CDC and cruise ship
    industry in 1970s
  • CDC inspects ships, performs surveillance of
    diarrheal illness, conducts outbreak
    investigations, offers sanitation training
    seminars to ship staff members

15
Sampling Onboard Ship The Vessel Sanitation
Program
  • Epidemiological aspect interviewing all crew
    members and passengers who are ill, collecting
    information (using standardized questionnaire)
    from all ship crew and passengers
  • Laboratory aspect collection of stool, blood,
    vomitus from ill persons (as well as non-ill
    persons for comparison)
  • Environmental health aspect examining and
    sampling potential outbreak sources such as
    on-board potable water, ice, food 

16
Sampling Onboard Ship The Vessel Sanitation
Program
  • Investigated 21 acute gastroenteritis outbreaks
    in 2001
  • Stool samples revealed 9 outbreaks caused by
    noroviruses, 3 caused by bacteria, 9 of unknown
    etiology
  • Laboratory results shaped recommendations
    developed by CDC to stop outbreaks and prevent
    future outbreaks on cruise ships

17
PulseNet and DNA Fingerprinting
  • PulseNet national network by CDC
  • State and local health departments
  • Federal agencies such as CDC, USDA/FSIS, FDA
  • Perform standardized molecular subtyping of
    foodborne disease-causing bacteria using
    pulsed-field gel electrophoresis
  • Submit DNA fingerprints electronically to
    comprehensive database at CDC
  • Enables rapid comparison of patterns
  • Permits early identification of common
    source outbreaks

18
Logistics of Human Clinical Specimen Collection
and Transportation
  • Most specimen collection during disease outbreak
    involves human clinical specimens
  • Laboratory confirmation of an etiologic agent is
    a ritical component of a successful outbreak
    investigation
  • Ability of a laboratory to successfully identify
    a pathogen depends on appropriate specimen
    collection and transportation

19
Planning for Human Clinical Specimen Collection
  • Clinical and epidemiological data used to narrow
    range of possible causative agents
  • Clinical specimens needed to make a
    laboratory-confirmed diagnosis determined
  • Laboratory selected to perform testing and
    analysis
  • May be determined by the test(s) needed

20
Planning for Human Clinical Specimen Collection
  • Each lab has specific guidelines for specimen
    collection all aspects should be discussed
    before collection begins
  • Sample type
  • Materials needed
  • Local or on-site processing
  • Transportation
  • Communication of results

21
Planning for Human Clinical Specimen Collection
  • Transportation details to discuss with lab
  • Timing and delivery of the collected samples
  • Required transport media
  • Transit route
  • Shipping requirements
  • Temperature requirements
  • Documentation
  • Packaging and transportation must comply with
    national regulations for transporting infectious
    material, should be reviewed with transport
    service

22
Collecting Human Clinical Specimens
  • Specimens should be collected as soon as possible
    once an outbreak has been identified
  • Human specimens obtained early, particularly
    before antimicrobials are given to the patient,
    are more likely to yield the pathogen
  • In certain situations, specimen collection after
    a person recovers from illness may be equally
    important
  • Presence of antibodies in serum samples after
    recovery can confirm whether an individuals
    illness or infection was related to the outbreak

23
Collecting Human Clinical Specimens
  • Before obtaining human clinical specimens,
    explain the purpose and procedure to the
    case-patient
  • Obtain an adequate amount of the specimen and
    handle with care
  • This may be the only opportunity to obtain a
    specimen during the outbreak
  • Sample must be collected properly to ensure that
    the pathogen or infectious agent can be recovered
    in a viable form

24
Collecting Human Clinical Specimens
  • Communication with the laboratory before specimen
    collection is critical to ensure appropriate
    collection technique, maintain the sample, and
    allow for proper diagnosis and treatment
    decisions
  • For example, not advisable to collect most fungal
    cultures with swabs because swab fibers can
    interfere with interpretation of results
  • Laboratory may reject the specimen for
    insufficient sample quantity or contamination
    from other body fluids

25
Labeling and Identification of Human Clinical
Specimens
  • Over 70 of information used to diagnose and
    treat a patient is derived from laboratory
    testing
  • Ensuring that specimens are accurately labeled at
    collection time is essential
  • Misidentification of a specimen leads to
    misidentification of a patient, can result in
    improper diagnosis and treatment

26
Labeling and Identification of Human Clinical
Specimens
  • Laboratories may have different requirements
  • Labels affixed to the specimen container should
    include
  • Patients name (first and last)
  • Unique identification number
  • Date, hour, place of collection
  • Type of sample
  • Specific anatomic culture site (to validate the
    specimen and help select appropriate medium)
  • Name of specimen collector
  • Specimens known to contain a dangerous pathogen
    should be clearly marked

27
Labeling and Identification of Human Clinical
Specimens
  • Case investigation form with matching information
    should be completed for each specimen at time of
    collection, retained by investigation team for
    reference
  • All information should be printed legibly

28
Storage and Transport of Human Clinical Specimens
  • Specimens must be stored appropriately to
    preserve integrity
  • Environmental conditions can affect maintenance
    and survival
  • If they multiply or die during collection,
    transport, or storage, they no longer accurately
    represent the disease process 
  • Storage in appropriate medium and maintenance of
    proper temperature is critical

29
Storage and Transport of Human Clinical Specimens
  • Requirements depend on type of specimen and
    sample, should be determined before specimen
    collection begins
  • Most specimens (exception of feces) need to be
    transported in sterile containers
  • Specimens transported in incorrect containers may
    be rejected by the lab
  • Specimen containers should be closed tightly
  • Labs may reject a specimen for signs of leakage
    or seepage, since this could expose
    laboratory personnel to contents 

30
Storage and Transport of Human Clinical Specimens
  • Packaging must comply with postal and commercial
    regulations for transport of infectious materials
  • Regulations depend on type of transport (ground
    or air delivery)
  • Should be determined in consultation with lab and
    carrier prior to specimen collection
  • Receiving laboratory should be notified of
    pending shipment before transport

31
Summary
  • This issue touched on ways in which clinical and
    environmental specimens can provide valuable
    information to an outbreak investigation, and
    importance of appropriate and timely specimen
    collection
  • Next issues of FOCUS will discuss what happens
    after a specimen is sent to the lab and what
    types of laboratory diagnostics may be used to
    help identify an agent suspected in an outbreak

32
Resources
  • World Health Organization. Guidelines for the
    collection of clinical specimens during field
    investigations of outbreaks, 2000.
    http//www.who.int/csr/resources/publications/
    surveillance/WHO_CDS_CSR_EDC_2000_4/en/
  • CDC. Guidelines for specimen collection.
    http//www.cdc.gov/foodborneoutbreaks/
    guide_sc.htm.
  • State health department websites

33
References
  • Centers for Disease Control and Prevention.
    Update multistate outbreak of Monkeypox ---
    Illinois, Indiana, Kansas, Missouri, Ohio and
    Wisconsin, 2003. MMWR Morb Mort Wkly Rep. 2003
    52642-626.
  • Centers for Disease Control and Prevention. All
    about hantaviruses. Available at
    http//www.cdc.gov/ncidod/ diseases/hanta/hps/nofr
    ames/outbreak.htm. Accessed December 12, 2006.
  • Centers for Disease Control and Prevention.
    Cholera associated with imported frozen coconut
    milk - Maryland, 1991. MMWR Morb Mort Wkly Rep.
    199140844-845.
  • Centers for Disease Control and Prevention.
    Outbreak of Escherichia coli O157H7 infection
    associated with eating fresh cheese curds ---
    Wisconsin, June 1998. MMWR Morb Mort Wkly Rep.
    200041911-913.

34
References
  • MacKenzie WR, Hoxie NJ, Proctor ME, et al. A
    massive outbreak in Milwaukee of cryptosporidium
    infection transmitted through the public water
    supply. N Engl J Med. 1994331161-167.
  • Jernigan DB, Raghunathan PL, Bell BP, et al.
    Investigation of bioterrorism-related anthrax,
    United States, 2001 Epidemiologic findings.
    Emerg Infect Dis. 200281019-1028.
  • Moe CL. Waterborne Transmission of infectious
    agents. In Hurst CJ, Crawford RL, Knudsen GR,
    McInerney MJ, Stetzenbach LD, eds. Manual of
    Environmental Microbiology. 2nd ed. Washington,
    DC ASM Press 2002136-152.
  • Majkowski J. Strategies for rapid response to
    emerging foodborne microbial hazards. Emerg
    Infect Dis. 19973551-554.

35
References
  • Association of Public Health Laboratories. State
    Public Health Laboratory Food Safety Capacity,
    September 2004. Available at http//www.aphl.org/
    docs/Food Safety Issue Brief 9-14-04.pdf.
    Accessed December 12, 2006.
  • Miller, JM. A Guide to Specimen Management in
    Clinical Microbiology. 2nd ed. Washington, DC
    ASM Press 1996.
  • Dock, B. Improving accuracy of specimen labeling.
    Clin Lab Sci. 2005 18210.
  • Last JM, ed. A Dictionary of Epidemiology. 3rd
    ed. New York, NY Oxford University Press, Inc.
    2001.
  • Kendrew J, ed. The Encyclopedia of Molecular
    Biology. Oxford, England Blackwell Science 1994.
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