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

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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

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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.

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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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 

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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

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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

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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

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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.

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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.

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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.