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Analysis. Answers. Action. www.aphl.org
Appropriate Collection and
Handling of Respiratory
Specimens
Analysis. Answers. Action. www.aphl.org
Specimen Collection
• Who collects specimens?
• Who will be collecting or has collected in the past?
• Who does not collect specimens?
Analysis. Answers. Action. www.aphl.org
Objectives
• PPE
• Specimen Collection (Timing)
• Specimen types
• Labeling
• Storage
• Package and shipping
• Examples
Analysis. Answers. Action. www.aphl.org
Specimen CollectionOverview: Points to Consider
• The time of specimen collection relative to symptom
onset and clinical presentation are very important
when considering what specimens to collect
• Maintain proper infection control when collecting
specimens
• Use approved collection methods and equipment
when collecting specimens
• Handle, store and ship specimens appropriately
Analysis. Answers. Action. www.aphl.org
• Gloves
• Mask (fitted N-95)
• Protective clothing
• Eye protection
• Sharps protection
Specimen CollectionPersonal Protective Equipment (PPE)Personal Protective Equipment (PPE)
Analysis. Answers. Action. www.aphl.org
• Respiratory specimens– Collect as soon as possible after symptoms
begin (ideally within 7 days)
– Ideally before antiviral medications are
administered
– Collect multiple specimens on multiple days
Specimen CollectionTimingTiming
Analysis. Answers. Action. www.aphl.org
• Serum for serology
– Paired serum samples are most useful
– Acute sample (within 7 days after symptom
onset)
– Convalescent sample (2 weeks or more after
acute sample)
Specimen CollectionTimingTiming
Analysis. Answers. Action. www.aphl.org
Virus
shedding
Antibody response
PCR
Antigen detection / Culture
Incubation Antibody detection
Days After Onset of Illness
Specimen CollectionTimingTiming
Analysis. Answers. Action. www.aphl.org
Rhinitis (common cold)
Pharyngitis/Tonsilitis
Laryngitis
Tracheitis
Laryngotraceobronchistis (croup)
Bronchitis
Bronchiolitis
Pneumonia
Specimen CollectionUpper and Lower Respiratory TractUpper & Lower Respiratory Tract
Analysis. Answers. Action. www.aphl.org
• URT specimens
– nasal swab (N)
– nasopharyngeal swab (NP)
– nasophyaryngeal wash or aspirate
(NW/NA)
– NW/NA > NP > N
– oropharyngeal (throat) swab or wash
Specimen CollectionTypes of Respiratory Tract SpecimensTypes of Respiratory Tract Specimens
http://www.anigenetics .com/products /images /2010-02-03(7).jpg
Analysis. Answers. Action. www.aphl.org
Specimen CollectionSwab Specimen CollectionSwab Specimen Collection
Analysis. Answers. Action. www.aphl.org
• LRT specimens
– sputum
– tracheal aspirates
– bronchoalveolar lavage (BAL)
– pleural fluid (sterile)
Specimen CollectionTypes of Respiratory Tract Specimens, Slide #2Types of Respiratory Tract Specimens, slide #2
Analysis. Answers. Action. www.aphl.org
Specimen CollectionClinical PresentationClinical Presentation
Analysis. Answers. Action. www.aphl.org
• Should be drayon, rayon, or polyester fiber swabs
• Select swabs with serrated shafts
• Do not use calciumalginate or cotton swabsnor ones with woodensticks; they may inhibit PCR
Specimen CollectionSwab SpecimensSwab Specimens
NP swab
OP swab
Analysis. Answers. Action. www.aphl.org
Hernes SS, et al. Eur J Clin Microbiol Infect Dis. 2011;30:159-65.
Munywoki PK, et al. J Clin Microbiol. 2011;49:3365-7.
Abu-Diab A, et al. J Clin Microbiol. 2008;46:2414-7.
Specimen CollectionFlocked SwabsFlocked Swabs
Analysis. Answers. Action. www.aphl.org
World Health Organization
Specimen CollectionViral Transport MediaViral Transport Media
Analysis. Answers. Action. www.aphl.org
• Specimen labeling
• Specimen documentation
• Specimen storage
• Specimen packaging/Shipping
Specimen Labeling, Storage, and
Transport
Analysis. Answers. Action. www.aphl.org
• Label all specimen containers with:
• Patient name
• Patient ID number Specimen type(s)
Date collected.
Specimen Labeling
Analysis. Answers. Action. www.aphl.org
• Each package with specimen(s ) should include line lis t :
Pa tient name
Patient ID number
Specimen type(s )
Date collected
Clinica l contact name, phone #, ema il
Clinica l submitte r, a ffla tion, phone #, ema il
Re levant clinica l informa tion (symptoms , da te of onse t, e tc.)
For deaths : pre liminary autopsy report
WHO specimen transport guidelines: http://www.who.int/csr/emc97_3.pdf
Specimen Documentation
Analysis. Answers. Action. www.aphl.org
• The shippe r – not the transport
company – is responsible for the
shipme nt until the package reaches
its destina tion.• Primary packaging
• Prima ry conta ine r must be water tight.
• Wrap multiple conta ine rs individua lly to prevent
breakage.
• Everything in the primary conta ine r, including
transport media , is cons ide red the infectious
substance.
Specimen Packaging
Analysis. Answers. Action. www.aphl.org
Specimen Packaging
WHO specimen transport guidelines: http://www.who.int/csr/emc97_3.pdf
Analysis. Answers. Action. www.aphl.org
• Specimens must be kept cool
• if transported ≤72 h, keep at 4oC
• if transported >72 h, keep at -70oC (ship on dry ice)
• Avoid repeated freeze/thaw cycles; do not use frost-free
freezers
• Sera may be stored at 4oC for up to one week; long term
storage at -20oC in non-frost-free freezer acceptable
• Prepare multiple aliquots of specimens
Specimen Storage
WHO specimen transport guidelines: http://www.who.int/csr/emc97_3.pdf
Analysis. Answers. Action. www.aphl.org
• Improperly identified specimens (specimen
container info and form do not match)
• No identification on specimen container or form
• Specimens with insufficient quantity for testing
• Improper specimen type sent
• Spillage or possibility of cross contamination
• Specimens shipped at improper temperature
• Excessive specimen transport time
Specimen CollectionUnacceptable SpecimensUnacceptable Specimens
Analysis. Answers. Action. www.aphl.org
MERS-CoV
• Who collects MERS samples?
• Correct sample types for MERS-CoV
Analysis. Answers. Action. www.aphl.org
Specimen CollectionMERS-CoV: Changes in Interim GuidelinesMERS-CoV: Changes in Interim Guidelines
Analysis. Answers. Action. www.aphl.org
Specimen CollectionMERS-CoV: Changes in Interim GuidelinesMERS-CoV: Changes in Interim Guidelines
Analysis. Answers. Action. www.aphl.org
Specimen CollectionMERS-CoV: Changes in Interim GuidelinesMERS-CoV: Changes in Interim Guidelines
Analysis. Answers. Action. www.aphl.org
• Lower respiratory tract specimens (sputum, trach
aspirate, BAL)
• Nasopharyngeal/Oropharyngeal (NP/OP) swabs
combined
• Serum and/or whole blood (PCR and serology)
• Use approved collection methods and equipment
when collecting specimens (BSL2 or BSL2+)
• Handle, store and ship specimens as per protocol
• Proper infection control when collecting specimens
NOTE: More sample and more specimen types collected on multiple days
may enhance MERS-CoV diagnosis.
Specimen CollectionMERS-CoV: Preferred SpecimensMERS-CoV: Changes in Interim Guidelines
Analysis. Answers. Action. www.aphl.org
Influenza (HPAI/LPAI)
• Who collects HPAI/LPAI samples?
• Correct sample types for HPAI/LPAI
Analysis. Answers. Action. www.aphl.org
URTI
• a nasopharyngeal swab, or
• a nasal aspira te or
• two swabs combine d (ex. NPS/OPS)
LRTI
• endotracheal aspira te
• bronchoa lve ola r la vage fluid (BAL)
NOTE: If possible, multiple specimens from different sites over 2 days
Specimen CollectionHPAI: Preferred SpecimensMERS-CoV: Changes in Interim Guidelines
Analysis. Answers. Action. www.aphl.org
• Use proper PPE
• Collected at the appropriate time
• Collect the appropriate specimen
• Use the proper collection equipment
• Label the specimen
• Proper storage
• Package and ship
Conclusions
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