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Laboratory Diagnostics, Specimen Collection, and Biosafety Issues

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Title: Laboratory Diagnostics, Specimen Collection, and Biosafety Issues


1
Laboratory Diagnostics, Specimen Collection,and
Biosafety Issues

May, 2007
2
Learning Objectives
  • Know the basic components of specimen collection
    kits for use with suspect avian influenza cases
  • Know what specimens to collect, how to collect
    them, store them, and transport them to the
    laboratory
  • Understand laboratory safety precautions
  • Discuss diagnostic tests and laboratory data
    management

3
Session Overview
  • Specimen collection
  • Specimen storage, handling, shipping
  • Safety precautions in the laboratory
  • Working with reference laboratories
  • Managing laboratory data

4
The Specimen Collection Kit
5
Specimen Collection Kit
  • Personal protective equipment
  • Collection vials with VTM
  • Polyester fiber-tipped applicators
  • Tongue depressors
  • Items for blood collection
  • Secondary container/ cooler
  • Ice packs
  • Suspect case forms
  • A pen or marker for labeling samples
  • Labels

6
Personal Protective Equipment
  • Gloves
  • Mask
  • Gown
  • Eye protection

7
Polyester Fiber-Tipped Applicator
  • Should be drayon, rayon, or polyester fiber
    swabs
  • Do not use calcium alginated or cotton swabs nor
    ones with wooden sticks they inhibit PCR

8
Viral Transport Media
Viral Transport Media
9
Phlebotomy Supplies
  • Tourniquet
  • Disposable needles
  • Vacuum tubes with EDTA
  • Plastic needle holder
  • Alcohol and iodine swabs
  • Gauze
  • Band-aids
  • Biohazard sharps container

10
How to Manage Kits
  • Store specimen collection kits in a dry, cool
    place
  • Store specimen collection kit where it will be
    accessible after hours and on weekends

11
How to Safely And Correctly Collect Specimens
Target regionfor seasonalinfluenza
Target region for H5N1 detection
Image obtained from www.nlm.nih.gov
12
Clinical Specimen Collection Responsibility
  • Usually a hospital staff function
  • May be a rapid responder function if hospital
    staff are unavailable
  • Designate at least one member of the team to be
    trained to collect specimens

13
When to Collect
  • CDC recommends laboratory testing for
  • Suspected cases
  • Symptoms consistent with influenza
  • Epidemiologic link to avian influenza A (H5N1)

14
Updated Interim Guidance for Laboratory Testing
of Persons with Suspected Infection with Avian
Influenza A (H5N1) Virus in the United States
  • Testing for avian influenza A (H5N1) virus
    infection is recommended for
  • a patient who has an illness that
  • requires hospitalization or is fatal AND
  • has or had a documented temperature of 100.4
    F AND
  • has radiographically confirmed pneumonia, acute
    respiratory distress syndrome (ARDS), or other
    severe respiratory illness for which an
    alternate diagnosis has not been established
    AND
  • has at least one of the following potential
    exposures within 10 days of symptom onset

15
A) History of travel to a country with influenza
H5N1 documented in poultry, wild birds, and/or
humans, AND had at least one of the following
potential exposures during travel direct
contact with (e.g., touching) sick or dead
domestic poultry direct contact with surfaces
contaminated with poultry feces consumption
of raw or incompletely cooked poultry or poultry
products direct contact with sick or
dead wild birds suspected or confirmed to
have influenza H5N1 close contact (approach
within 1 meter approx. 3 feet) of a person
who was hospitalized or died due to a severe
unexplained respiratory illness
16
B) Close contact (approach within 1 meter
approx. 3 feet) of an ill patient who was
confirmed or suspected to have H5N1 or C)
Worked with live influenza H5N1 virus in a
laboratory.
17
Case by Case Considerations!
  • Mild or atypical disease (hospitalized or
    ambulatory) with one of the exposures listed
    above
  • Severe or fatal respiratory disease whose
    epidemiological information is uncertain,
    unavailable, or otherwise suspicious but does not
    meet the criteria above

18
What to Collect
  • Preferred specimens
  • Oropharyngeal swabs
  • Lower respiratory tract specimens
  • Bronchoalveolar lavage or tracheal aspirates
  • Other specimens
  • Nasopharyngeal swabs
  • Nasal swabs and aspirates
  • Acute and convalescent sera
  • Sputum specimens
  • Collect samples on several different days

19
When to Collect Respiratory Specimens
  • As soon as possible after symptoms begin
  • Ideally before antiviral medications are
    administered
  • Collect multiple specimens on multiple days

20
Serological Samples
  • Paired serum samples are most useful
  • Acute sample
  • Within 7 days after symptom onset
  • Convalescent sample
  • 2 to 4 weeks after acute sample

21
Personal Protective Equipment
  • Masks (N-95 or N/P/R-100)
  • Gloves
  • Protective eyewear (goggles)
  • Hair covers
  • Boot or shoe covers
  • Protective clothing (gown or apron)

22
Collecting Specimens
23
Suspect Case Form
  • Patient name
  • Unique identification number
  • Patient symptoms and date of onset
  • Specimens and collection date
  • Whether or not patient is hospitalized
  • Patient contact information
  • Patient demographic information

24
(No Transcript)
25
Specimen Tracking System
  • Maintain a database to track
  • Identification number
  • Subject information
  • Type of specimen
  • Specimen collection date
  • Specimen collection location
  • Date of laboratory receipt of specimen
  • Date tested
  • Diagnostic test results

26
Nasopharyngeal Swab
  • Insert dry swab into nostril and back to
    nasopharynx
  • Leave in place for a few seconds
  • Slowly remove swab while slightly rotating it

27
Nasopharyngeal Swabcontinued
  • Use a different swab for the other nostril
  • Put tip of swab into vial containing VTM,
    breaking applicators stick

28
Oropharyngeal Swab
  • Ask the subject to open his or her mouth
  • Depress the tongue
  • Swab the posterior pharynx
  • Avoid the tonsils

29
Nasopharyngeal AspirateCollection Process
  • Attach mucus trap to vacuum source
  • Place catheter into nostril parallel to palate
  • Apply vacuum
  • Slowly remove catheter while slightly rotating it
  • Repeat with other nostril using the same catheter
  • After collection, flush catheter with 3 ml VTM
    and return VTM to a plastic vial

30
Blood Collection for Serology
  • Only by trained persons
  • Collect red-top tubes
  • Freeze sera separated from cells at -20º C

31
How to Label Samples
  • Use pre-printed barcode labels
  • On the specimen container
  • On the field data collection form
  • On the log book
  • Label each specimen with
  • Subjects name
  • Subjects unique identification number

32
Specimen Storage, Handling, and Transportation
33
How to Store Respiratory Specimens
  • For specimens in VTM
  • Transport to laboratory as soon as possible
  • Store specimens at 4 C before and during
    transportation within 48 hours
  • Store specimens at -70 C beyond 48 hours
  • Do not store in standard freezer keep on dry
    ice or in refrigerator
  • Avoid freeze-thaw cycles
  • Better to keep on ice for a week than to have
    repeat freeze and thaw

34
Handling Infectious Materials in the Field
  • Always wear personal protective equipment
  • Be careful with sharp objects
  • Treat all clinical samples as potentially
    infected with avian influenza

35
Packing Specimens for Transportation
  • Use three packaging layers
  • First layer should be water tight
  • Use absorbent material in all layers
  • No more than 500 mL should be in the specimen
    container

36
Packing Specimens for Transportation
  • Keep specimens at 4 ºC
  • Fill a cooler with ice packs or coolant packs
  • Double-bag specimens if you use dry ice
  • Include an itemized list of specimens with
    identification numbers and laboratory
    instructions

37
Transporting Specimens
  • Initial testing at State Public Health Laboratory
  • Call CDC Hotline before sending specimens for
    reference testing
  • 770-488-7100
  • Send overnight or using appropriate means based
    on recommendations from the State Department of
    health or CDC
  • Include inventory sheet and CDC case ID number
  • Coordinate with the laboratory

38
Laboratory Biosafety
  • Laboratory testing of suspected novel influenza
    viruses should be conducted in biosafety level 3
    (BSL-3) laboratories
  • Infectious agents that may be transmitted via the
    airborne route
  • PPE for laboratory personnel may include
    respirators

39
Managing Laboratory Data
40
Data Management Rules
  • Double check data entry accuracy
  • Include unique identification numbers
  • Keep subject names confidential
  • Track testing dates and results
  • Back up the database

41
Computer Software
  • Epi-info (CDC)
  • Free, at http//www.cdc.gov/epiinfo/
  • Microsoft Excel and Access
  • Oracle
  • MySQL
  • Filemaker Pro

42
Data Analysis Measures
  • Prevalence
  • The number of cases divided by the size of the
    population
  • Sensitivity
  • The number of cases identified by the test
    divided by the number of true positives which
    were identified by the gold standard technique
  • Specificity
  • The number of non-cases identified by the test
    divided by the number of true negatives that were
    identified by the gold standard technique

43
How to Present Results
  • Report
  • Time and place of the outbreak
  • Prevalence of infection
  • Clinical information about cases
  • Epidemic curve
  • Share results with local, state and federal
    health officials.

44
Laboratory Tests
45
Laboratory Diagnosis for Influenza
  • Tests for respiratory samples
  • PCR-based techniques
  • Virus isolation
  • Immunofluorescence
  • Rapid antigen detection
  • Blood used for
  • Measurement of specific antibodies (Most common
    for influenza, sera is used)
  • Viral isolation (whole blood if viremia is a
    consideration)
  • PCR-based techniques (sera)

46
PCR-based Techniques
  • Examples nested reverse transcriptase polymerase
    chain reaction (RT-PCR) and real-time RT-PCR
  • Sensitivity depends on the particular test, the
    influenza strain, and the type of specimen used

47
Virus Isolation
  • Allows identification of virus and test for drug
    susceptibilities
  • Technically difficult and requires BSL-3
    laboratory with enhancements
  • Not recommended for diagnostic use for avian
    influenza A (H5N1)
  • Reserved for specially designated laboratories

48
Immunofluorescence
  • Works best on clinical specimens collected
    immediately after symptoms begin
  • Results will tell you whether a particular
    influenza virus is present
  • Sensitivity and specificity not established

49
Indirect IF Staining of Cells From Tracheal
Aspirate
Anti-H5
Anti-H3
Anti-A/NP
Anti-B
Taken from World Bank Training by Alexander
Klimov, CDC
50
Rapid Antigen Tests
  • Detects influenza A and B virus
  • Detects human strains of influenza
  • Limitations
  • Not used to test for avian influenza because of
    reduced sensitivity and inability to distinguish
    H5 from seasonal influenza
  • Specificity and sensitivity not yet established

51
Serology Tests
  • Used to confirm infection because it takes
    several weeks to get results
  • Useful when the sample is taken too late for
    other methods
  • Collect both acute and convalescent serum samples

52
Serology Tests
  • Types
  • Haemagglutination inhibition test
  • Enzyme immunoassay
  • Virus neutralization test
  • Western Blot

53
When Single Samples are Appropriate
  • 1. Convalescent samples collected in outbreak
    investigations of novel viruses (such as H7 or
    H9)
  • Single samples collected in convalescent phase
    are compared to age-matched controls

54
How to Avoid Misinterpretations
  • Use positive and negative controls
  • Make sure you understand what the test is
    identifying
  • Use multiple tests to confirm results

55
Summary
  • When handling infectious materials in the
    laboratory or in the field, take safety
    precautions.
  • Proper specimen storage, handling, and shipping
    are vital to successful laboratory tests.
  • Maintain adequately stocked specimen collection
    kits and store them properly when they are not in
    use.

56
Summary
  • Oropharyngeal swabs and lower respiratory
    specimens are the best specimens to collect for
    avian influenza A (H5N1).
  • Collect multiple specimens (respiratory and
    blood) on multiple days.
  • Keep track of information on the specimens
    collected in a database or logbook.
  • Properly dispose of any infectious material.

57
Summary
  • Most states will be able to perform some basic
    influenza identification tests on a clinical
    specimen, but more specific testing may need to
    be done at a higher level national or regional
    laboratory. Results should be confirmed by the
    CDC.
  • When you report on the progress of an outbreak
    investigation, share investigation results with
    local, regional, and federal health officials.

58
Laboratory Practice Exercise
59
Glossary
  • Centrifuge
  • A machine that uses high-speed rotation to
    separate materials with different densities.
  • Culture
  • The growing of microorganisms in a nutrient-rich
    medium.
  • Nucleic acid
  • A component genetic material such as DNA or RNA
    found in all cells in humans, animals, bacteria,
    and viruses. Every species and organism has a
    unique pattern.

60
Glossary
  • Pipette
  • A glass or plastic tube used to measure or
    transfer small amounts of liquid.
  • Saline
  • A liquid solution made of salt and water.
  • Viral Transport Medium (VTM)
  • The preservative liquid in which specimens are
    stored until they are tested.

61
References and Resources
  • Recommended laboratory tests to identify avian
    influenza A virus in specimens from humans. World
    Health Organization, June, 2005.
    http//www.who.int/csr/disease/avian_influenza/gui
    delines/avian_labtests2.pdf
  • WHO guidelines for the collection of human
    specimens for laboratory diagnosis of avian
    influenza infection, 12 January 2005.
    http//www.who.int/csr/disease/avian_influenza/gui
    delines/humanspecimens/en/index.html
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