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Specimen Collection,
Handling, Transport and
Processing
1
Part 1:
Specimen Collection
Handling and Transport
2
Specimen Quality is Important
The results of tests, as they affect patient
diagnosis and treatment, are directly
related to the quality of the specimen
collected and delivered to the laboratory.
3
http://www.aphl.org/aphlprograms/infectious/tuberculosis/Pages/tbtool.aspx
Working with Healthcare Providers
• Laboratories must develop a good working relationship
with health care providers collecting patient specimens
• Laboratories should have a reference manual for
providers that includes:
– Specimen type and volume requirements
– Specimen collection, labeling, storage and transport
instructions
– Specimen rejection criteria
• Laboratories should provide specific feedback to
individual healthcare providers regarding problems with
the quality of specimens received and provide
recommendations for improvement
4
Specimen Types
I. Respiratory
• Sputum
(expectorated,
induced)
• Bronchoalveolar
lavage (BAL)
• Bronchial
wash/brush
• Transtracheal
aspirate
5
II. Non-respiratory
• Tissue
• Body fluids
• Blood
• Stool
• Gastric lavage
• Urine
Refer to the CLSI M48-A document, Laboratory Detection and
Identification of Mycobacteria
RESPIRATORY (PULMONARY)
SPECIMENS
Specimen Collection, Handling, Transport and Processing
6
Sputum
• Recently discharged material from the bronchial tree, with
minimal amounts of oral or nasal material
• Expectorated Sputum: Generated from a DEEP productive cough
• Induced Sputum: produced with hypertonic saline if patient is
unable to produce sputum on their own
• Indications for sputum collection
– To establish an initial diagnosis of TB
– To monitor the infectiousness of the patient
– To determine the effectiveness of treatment
7
Sputum Quality
• Specimens are thick and contain
mucoid or mucopurulent material.
• Ideally, 3–5 ml in volume, although
smaller quantities are acceptable if
the quality is satisfactory.
• Poor quality specimens are thin and
watery. Saliva and nasal secretions
are unacceptable.
• Laboratory requisition form should
indicate when a specimen is induced
to avoid the specimen being labeled
as “unacceptable” quality.
Clinical and Laboratory Standards Institute. Laboratory detection and identification of
mycobacteria; approved guideline. CLSI Document M48-A. Wayne, PA: CLSI; 2008.
http://www.stoptb.org/wg/gli/assets/documents/29_specimen_condition_transport.doc 8
Sputum Quality
Thick,
Mucopurulent
Hemoptysis
(Bloody
Sputum)
Watery
(acceptable if
induced)
Salivary
9
Indications for Sputum Collection
• Initial diagnosis of TB:
• Collect a series of three sputum specimens, 8-24 hours
apart, at least one of which is an early morning specimen
• Optimally, sputum should be collected before the initiation
of drug therapy
• For release from home isolation:
• If patient is smear positive and on treatment: Collect
sputum until 3 specimens are negative.
• Monitoring of therapy: Obtain sputum specimens for
culture at least monthly until cultures convert to
negative
Centers for Disease Control and Prevention. Guidelines for Preventing the Transmission of Mycobacterium
tuberculosis in Health-Care Settings, MMWR 2005:54, RR-17 10
Specimen Collection: All aerosol producing
procedures pose a risk of exposure
11
Whether collecting specimen via
sputum collection or bronchoscopy, if
a patient is suspected or confirmed
of have tuberculosis, airborne
precaution must be used.
Specimen Collection
• Suspect or confirmed TB patients should
be in a negative pressure room
• Specimen collection is an aerosol
generating procedure, anyone in the room
during specimen collection must wear a
particulate respirator type N-95 and be
part of the respirator protection plan
• All mycobacteria specimens are collected
into a sealed leak proof container
12
Storage and Transport of Sputum
Specimens
• Collection sites should refrigerate samples that
cannot be transported immediately to reduce
growth of contaminating organisms
• Specimens should be delivered to the laboratory
as soon as possible, within 24 hours of collection
is optimal (avoid batching)
• Laboratories may include a cold pack with
specimen transport materials
13
Pulmonary Specimens Other Than Sputum:
Collection Guidance
Specimen
Types
Collection Volume
Requirements
Transport
Bronchoalveolar
lavage (BAL)
Bronch brush or
washing
Endotracheal
aspirate
Transtracheal
aspirate
Collect washing
or aspirate in
sputum trap
Place the brush
in a sterile, leak-
proof container
with up to 5 ml
of sterile saline
Minimum volume
is 3 ml
50-ml conical tube or
other sterile container
Transport as soon as
possible at room
temperature
If transport is delayed
more than 1 hour,
refrigerate specimen.
14
• The doubling time for other common respiratory flora is 15 to 20 minutes
• The doubling time for M. tuberculosis is 12 to 24 hours
NON-RESPIRATORY
(EXTRAPULMONARY) SPECIMENS
Specimen Collection, Handling, Transport and Processing
15
Extrapulmonary Specimens
• The laboratory should expect to receive a variety
of extrapulmonary specimens which may be
divided into two groups
– specimens from non-sterile body sites
– specimens from normally sterile body sites
• Should be collected in a sterile leak-proof
container
• Should be transported as soon as possible
• Swabs are generally not acceptable
16
Extrapulmonary Specimen
Collection Guidance
Specimen
from Non-
Sterile Body
Sites
Recommended
Collection Time
Volume
Requirements
Collection
Frequency
Transport Recommended
for Isolation of
MTBC?
Gastric
Aspirate
Early morning
before patient
eats and while
still in bed
5–10 ml is
optimal;
maximum
volume is 15 ml
One specimen
per day on three
consecutive days
Room
temperature; if
delayed >1
hour, neutralize
with 100 mg
sodium
carbonate
Yes
Urine First morning
specimen (void
midstream)
10–15 ml
minimum;
prefer up to 40
ml
One specimen
per day on three
consecutive days
If delayed >1
hour, refrigerate
Yes
Stool No
recommendation
Minimum
volume is 1
gram
No
recommendation
Refrigerate if
delayed >1
hour, do not
freeze
Mainly for
diagnosis of
disseminated
MAC disease in
patients with
AIDS
17
Extrapulmonary Specimen
Collection Guidance
Specimen from
Normally Sterile Body
Sites
Volume Requirements Transport Recommended for
Isolation of MTBC?
Cerebral Spinal Fluid 10 ml is optimal;
minimum volume is 2-3
ml
As soon as possible at
room temperature; do not
refrigerate
Usually paucibacillary;
culture may have limited
sensitivity
Other Body Fluids
(pleural, peritoneal,
pericardial, synovial)
10-15 ml is optimal;
minimum volume is 10 ml
If delayed, refrigerate Yes
Tissues or Lymph Nodes As much as possible;
add 2-3 ml sterile saline
As soon as possible at
room temperature (no
formalin, preservatives, or
fixatives)
Yes
Blood 10ml preferred, minimum
5 ml. Collect in SPS or
heparin tube, no EDTA
At room temperature, do
not refrigerate or freeze
Mainly for diagnosis of
disseminated MAC
disease in patients with
AIDS
18
SUBOPTIMAL AND UNACCEPTABLE
SPECIMENS
Specimen Collection, Handling, Transport and Processing
19
Suboptimal and Unacceptable
Specimens
• Processing of suboptimal or poor quality
specimens is a burden on both financial and
personnel resources
• Results generated from processing inappropriate
specimens may not be reliable
• Each laboratory must develop its own specimen
rejection criteria and make these criteria readily
accessible to providers
• Clinicians should be notified when a specimen is
rejected and the reason for rejection should be
provided
• Specimens collected by invasive procedures
should not be rejected
20
Possible Rejection Criteria (1)
• Labeling of specimen does not match identifiers
on requisition form
• Insufficient volume
• Dried swabs
– Swabs in general are not optimal
• Provide limited material
• Hydrophobicity of mycobacterial cell envelope
inhibits transfer to media
• Pooled sputum or urine
• Sputum left at room temperature for 24 hours
21
Possible Rejection Criteria (2)
• Broken specimen containers or leaking
specimens
• Excessive delay between specimen collection
and receipt in the laboratory
• Blood specimens collected in EDTA might be
rejected for culture as these inhibit growth of
MTB
• Tissue or abscess material in formalin
• Gastric lavage fluid if pH not adjusted within 1
hour of collection
22
SPECIMEN TRANSPORT: REFERRAL OF
SPECIMENS WITHIN A LABORATORY
NETWORK
Specimen Collection, Handling, Transport, and Processing
23
Transport of Biological Substances
(Category B)
Basic triple packaging system
• (i) a leak-proof primary receptacle(s);
• (ii) a leak-proof secondary packaging containing
sufficient additional absorbent material shall be
used to absorb all fluid in case of breakage
• For cold transportation conditions, ice or dry ice shall be placed
outside the secondary receptacle. Wet ice shall be placed in a leak-
proof container.
• (iii) an outer packaging of adequate strength for
its capacity, mass and intended use.
24
Transport of Biological Substances
(Category B)
Biological Substance,
Category B
25
Sputum Collection Kit
An example from the Wisconsin
State Laboratory of Hygiene
• Insulated mailer with address label
• UN3373 marking and proper
shipping name “Biological
Substance, Category B”
• Sterile plastic conical tube with
label
• Sealable biohazard specimen
transport
• Cool pack
• Absorbent pad
• Instruction sheet
26
Transport of Biological Substances
• Transport of patient specimens is regulated by
both the Department of Transportation (DOT)
and by International Air Transport Association
(IATA) rules.
• Laboratories must have personnel trained in and
familiar with these regulations
• For details regarding these regulations, please
see the information provided in the next slide.
27
Packing and Shipping Guidance
• ASM website-Guidance: Packing and Shipping Infectious
Substances
• DOT guidance: Transporting Infectious Substances Safely
• More DOT Guidance: Infectious substances guide
• IATA website: FAQs | Infectious Substances
• FedEx Guidance: Clinical Samples, Biological Substances
Category B(UN 3373) and Environmental Test Samples
• UPS Guidance: Packing Hazardous Materials
28
ADDITIONAL INFORMATION
Specimen Collection, Handling, Transport and Processing
29
Instructions for Sputum Collection
• Healthcare providers should educate patients on proper specimen
production and collection
• Patients should also be informed of the possible infectious nature of
his or her secretions
• Specimens should be collected in appropriate tubes that are sterile,
clear, plastic, and leak-proof (50 ml screw capped centrifuge tubes
that can withstand 3000 x g are preferred)
• Proper labeling protocols should be put in place by the laboratories
• Work with TB program to provide instructions for submitters
30
Examples for Instructions for
Sputum Collection
Pennsylvania
Department of
Health 31
Part 2:
Specimen Processing
32
Principles of Specimen Processing
Respiratory specimens (and other specimens from non-
sterile sites) require digestion, decontamination, and
concentration:
• Digestion: Mucolytic agent used to liquefy sputum
specimens to release AFB and expose normal flora for
decontamination
• Decontamination: Toxic agent used to kill rapidly growing
normal flora that would otherwise overgrow slow growing
mycobacteria
• Centrifugation: Used to sediment bacteria following
digestion/decontamination
33
Effect of Processing Procedure
• Reagents used for digestion and decontamination, to
some extent, are toxic to mycobacteria
• Procedures must be precisely followed
– Time in contact with digestion/decontamination reagents is
critical
– Centrifugation procedures also affect mycobacteria recovery
rates and must be carefully followed
• Culture positivity rates and contamination rates should
be monitored to evaluate performance of processing
methods
34
Safety
• Many of the steps within the specimen processing
procedure are aerosol-generating
• The following activities should be performed in a
biological safety cabinet:
 Digestion and decontamination
 Preparation of concentrated smear
 Inoculation of culture media
• Do not disrupt airflow of the cabinet
• Avoid excess clutter inside the BSC
For more information on the biosafety practices in the Mycobacteriology
laboratory, please review the module on biosafety within this series 35
Aseptic Techniques: Getting Started
• Disinfect BSC, centrifuge, and tabletop with tuberculocidal
disinfectant (repeat after specimen and culture workup
complete)
• Perform all work on absorbent pad soaked with disinfectant to
absorb any droplets that may inadvertently occur
• When possible, leave an empty space in the rack between
each specimen tube
• Work in sets equivalent to one centrifuge load (e.g., 8
specimens at a time)
36
Aseptic Techniques: Processing
• Use a fresh individual, disposable, sterile pipette at every step to
avoid transfer of bacilli
• To avoid droplet aerosol cross-contamination, open and remove
caps from tubes one at a time
• Add diluent to centrifuge tubes from individual tubes without the lip
of the tube touching or creating an aerosol (do not use common
containers or carboys)
• Use aerosol-proof sealed centrifuge cups
• Discard supernatant from decontaminated specimens into splash-
proof container with disinfectant. Autoclave the discard container
daily
37
Digestion & Decontamination Methods
Several methods are available for digestion and
decontamination of clinical specimens:
• N-acetyl-L-cysteine-sodium hydroxide (NALC-
NaOH)
• Commercially available: Alpha-Tec NAC-PAC™, BD
MycoPrep™
• Oxalic acid
• Cetylpyridinium chloride (CPC)-sodium chloride
• NaOH method (Petroff’s method)
• Zephiran-trisodium phosphate (Z-TSP)
38
NALC-NaOH Method: Principle
• Most common and preferred method
• Rapid and relatively effective in reducing the number of
contaminants
• Addition of the mucolytic agent 2% NALC allows
effective decontamination with 1% NaOH (less harsh on
mycobacteria) (final concentrations)
• Sodium citrate also included in digestion mixture to bind
heavy metal ions in specimen that could inactivate N-
acetyl-L-cysteine 39
NALC-NaOH Method: Reagents
CLSI M-48A
Kent and Kubica
• NaOH and sodium citrate can be prepared and
combined in advance
• NALC should be prepared and added fresh daily
• Once NALC added, solution should be used within 24
hours
Volume of
digestant
needed
4% NaOH 2.9% sodium
citrate
dehydrate
Add NALC
(fresh)
50 ml 25 ml 25 ml 0.25 g
100 ml 50 ml 50 ml 0.50 g
500 ml 250 ml 250 ml 2.50 g
40
NALC-NaOH Method: Procedure for Sputum
1. Add equal volume of NALC-NaOH solution to 5-10 ml of sputum in
50 ml plastic screw cap centrifuge tube
2. Cap tube tightly. Invert the tube so that the NALC-NaOH solution
contacts all inside surfaces of the tube and cap and then mix the
contents for approximately 5-20 seconds with a Vortex mixer.
3. Allow mixture to stand for 15 minutes at room temperature with
occasional gentle shaking by hand.
4. Add sterile distilled water or sterile pH 6.8 phosphate buffer to the
50 ml mark on tube. Securely cap tube and mix by inversion
5. Centrifuge the tubes for 15 min at 3,000 x g using aerosol-proof
sealed centrifuge cups
41
NALC-NaOH Method: Procedure for Sputum
• After centrifugation, open centrifuge cups in BSC, slowly poor off
supernatant into splash-proof discard container containing
disinfectant
– Take care to not disturb or pour off sediment (pellet)
– Take care to avoid aerosol production and to prevent contamination of
the lip of the tube
• Wipe the lip of the tube with gauze soaked with disinfectant
• Resuspend sediment in 1-2 ml of saline solution or phosphate buffer
• Mix gently and proceed to culture inoculation and smear preparation
42
NaOH Concentration is Key
Amount of
NaOH in 100 ml
water
% NaOH % NaOH when
added to equal
volume Na
citrate
Final
concentration of
NaOH when
added to
specimen
4.0g 4.0% 2.0% 1.0%
6.0g 6.0% 3.0% 1.5%
8.0g 8.0% 4.0% 2.0%
CLSI M-48A
• Recommended final concentration is 1.0% NaOH
• Concentration of NaOH can be adjusted based on contamination
rate in individual laboratories
• NaOH at a FINAL concentration of ≥2.0% can be lethal to
mycobacteria (may see decrease culture sensitivity in smear
negative specimens)
43
Timing is CRITICAL
• 15 MINUTES
– Time in contact with NALC-NaOH is critical since the high
pH rapidly kills microorganisms in the specimen including
mycobacteria
• Over processing results in reduced recovery of
mycobacteria
• The importance of timing must be considered when
deciding how many specimens can be processed in
one run
44
Specimen Processing QC
• A Negative Processing Control (10 ml sterile
water or buffer) should be included with each
batch of specimens processed
• Negative control is put through entire specimen
processing procedure and inoculated to media
• Determines if contamination is introduced during
processing or culture handling
• Assures that isolates are coming from patients and
not from any other source
45
46
Definition of Cross Contamination
Cross contamination: the transfer of M.
tuberculosis complex bacilli (or other
mycobacteria) from one specimen to
another specimen that does not contain
viable bacilli, causing a false positive result.
– The phenomenon of misdiagnosis of tuberculosis due
to cross contamination has been widely reported and
has significant clinical and therapeutic impact on the
patient.
47
To reduce the possibility of Cross
Contamination:
• Use daily aliquots of processing reagents and buffers.
Any leftover should be discarded.
• Never use common beakers or flasks when processing.
• Keep the specimen tubes tightly closed and clean the
outside of the tube prior to vortexing or shaking.
• Pour decontamination reagents or buffers slowly on the
side of the tube without causing any splashing. Do not
touch the container of reagents to the lip of the tube at
any time during addition.
48
To reduce the possibility of Cross
Contamination:
• Open the specimen tubes very gently to avoid aerosol
generation.
• When adding reagents to the tube, open one tube at a
time. Do not keep all the tubes open at the same time.
• Do not place tubes too close to each other in the rack
• Change gloves often
• Avoid manipulation of PT specimens
• Disinfect biological safety cabinet work surfaces
routinely.
49
Specimen Processing Proficiency
• Digestion, decontamination, and conentration
procedures should only be performed byt rrained
laboratory staff.
• Mycobacteriology laboratories should participate in an
approved proficiency testing program.
• Proficiency in culture and identification of MTV may be
maintained by digestion and culture of 15-20 specimens
per week.
SPECIMENS FROM CYSTIC FIBROSIS
PATIENTS AND EXTRAPULMONARY SITES
Specimen Collection, Handling, Transport and Processing
50
Cystic Fibrosis (CF) Patients
• Specimens from CF patients are often heavily
contaminated with Pseudomonas aeruginosa.
• If it is known or discovered specimen is from a
patient with CF or notable media contamination
you can process concentrated sediment using
only the 5% oxalic acid method.
51
Oxalic Acid Processing Method for Specimens
from CF Patients
• Add an equal amount of 5% oxalic acid to:
- 5-10 ml of primary respiratory specimen or
- NALC-NaOH processed concentrated sediment
• Vortex specimen and allow to incubate at room temperature for 30
minutes, mixing every 10 minutes
• Neutralize with buffer solution
• Concentrate specimen by centrifugation for 15 minutes at ≥ 3000 x g
• Decant supernatant into splash-proof container and resuspend pellet
with buffer solution
• Inoculate media
52
Processing Gastric Lavage and Urine
• Centrifuge for 30 minutes at ≥ 3000 x g
• Discard supernatant carefully into splash-proof
container
• Re-suspend pellet in sterile distilled water
• Process suspension as for sputum (NALC-
NaOH)
53
Processing Aseptically Collected Fluids
• Cerebral spinal fluid (CSF), synovial,
pleural, peritoneal, pericardial
• No decontamination required
• Concentrate specimen to maximize the
yield of mycobacteria
• Inoculate directly to culture media
54
Processing Tissue Specimens
• Lymph node, lung tissue, biopsies
• Tissue submitted in formalin is unsatisfactory for culture
• No decontamination required
• Process tissue specimens using a sterile tissue grinder,
or mortar and pestle
• Inoculate directly to culture media
55
Processing Blood or Bone Marrow Aspirates
• Specimens inoculated directly into MYCO/F LYTIC
bottles or BacT/ALERT MB blood medium
• Direct inoculation of blood onto a solid medium is not
recommended
• If transport is necessary, sodium polyanethol sulfate,
heparin, or citrate may be used as anticoagulants
• Blood collected in EDTA and coagulated blood are not
acceptable
56
PRINCIPLES OF CENTRIFUGATION
Specimen Collection, Handling, Transport and Processing
57
Concentration of Specimens
• Since mycobacteria do not readily sediment, centrifugation force and
time are important for maximal concentration
• Specimens should be centrifuged for at least 15 minutes at 3000 x g
• Revolutions per minute (rpm) is a measure of speed for a particular
centrifuge head and not a measure of concentration efficiency or
relative centrifugal force (RCF)
• The relative centrifugal force is measured in units and is expressed
in multiples of the earth’s gravitational field abbreviated as g
• Use of a refrigerated centrifuge at 8 to 10°C may help to eliminate
heat build-up which could be lethal to mycobacteria
58
Calculation of Centrifugal Force
Formula for calculating a particular centrifugal force
is:
RCF = 1.12r (RPM/1000) 2
where r is the radius, which is the distance in
mm from the center of rotation to a point
within the rotor, and RPM (revolutions per
minute), which is the speed of rotation
• This information should be published in many of
the centrifuge manufacturers instruction manuals
59
Note: Nomogram attached in Resources section
QUALITY INDICATORS
Specimen Collection, Handling, Transport and Processing
60
Quality Indicators: Contamination Rate
• “Contamination” occurs when inoculated media is completely
compromised due to overgrowth with non-acid fast
organisms.
• Contamination Rate monitors specimen preparation and the
decontamination process
• Calculation of contamination rate in Liquid media:
– Numerator: number of inoculated broth cultures discarded or re-
decontaminated in 1 month due to contamination
– Denominator: total number of broth cultures inoculated in one month
• Calculation of contamination rate in Solid media:
– Numerator: number of inoculated solid media slants or plates discarded in 1
month due to contamination
– Denominator: total number of solid media slants or plates inoculated in one
month
61
Contamination Rates
• Acceptable overall rates of contamination
– Solid media (LJ) is 2-5%
– Liquid media (MGIT960) is 7-8%
– Contamination rates for the individual laboratory can be affected
by the type of media used (i.e. media containing antibiotics)
• A contamination rate less than that of the acceptable
rate indicates that processing methods are too harsh
– NaOH concentration too high
– Specimen exposure time to NALC-NaOH too long
• A contamination rate greater than that of the acceptable
rate could indicate a pre-analytical problem, an
inadequate decontamination process, or both
APHL, 2009, Assessing your Laboratory
62
Potential Causes of High Contamination Rates
CLSI M-48A
• Lack of appropriate sputum collection guidance for patients
• Delays in transport
• Lack of refrigeration prior to transport
• Inappropriate storage conditions or processing delays upon
receipt in the laboratory
• Decontamination process is ineffective
– NaOH concentration too low
– Specimen exposure time to NALC-NaOH too short
63
Quality Indicators: Positivity (Recovery) Rate
• Establishes a baseline for a given population or
geographic area
• Assists in identifying potential false positive or false
negative cultures (MTB)
• Assists in identifying environmental contamination
• Calculation of positivity rate:
– Numerator: number of cultures reported as MTB in one
month
– Denominator: total number of cultures reported (TB, NTM,
negative, contaminated) in one month.
64
Quality Indicators: Positivity (Recovery) Rate
• Expectation: Population/geographic region dependent
• Increases may be due to:
– Shift in patient population
– Cross contamination/false positives
– Contaminated reagents, media, water (NTM)
– Specimens contaminated during collection
• Decreases may be due to:
– Shift in patient population
– Problems with specimen quality
– Problems with specimen processing
– Problems with equipment or media
– Increase in contamination
65
What should I do if Quality Indicators or
Controls are out of range?
• Ensure quality specimens are being received in the laboratory
• Ensure quality reagents and media are being used
• Ensure water used for specimen processing is sterile and
filtered
• Ensure laboratory equipment (e.g. incubators, BSCs) is
functioning properly
• Ensure protocols are followed
• Ensure staff are trained and proficient
66
References
• Kent and Kubica, Public Health Mycobacteriology, A Guide for
the Level III Laboratory, US Public Health Service. 1985
• ASM Press, Manual of Clinical Microbiology, 10th edition.
Volume 1. James Versalovic, editor. 2011
• CLSI. Laboratory Detection & Identification of Mycobacteria;
Approved Guidelines. CLSI document M48-A. Wayne, PA:
Clinical & Laboratory Standards Institute; 2008.
• APHL/CDC. Mycobacterium tuberculosis: Assessing Your
Laboratory. 2009
67
References
• Centers for Disease Control and Prevention. Guidelines for Preventing the
Transmission of Mycobacterium tuberculosis in Health-Care Settings, 2005.
MMWR 2005;54(No. RR-17).
• Public Health Mycobacteriology. A Guide for the Level III Laboratory. U.S.
Department of Health and Human Services Public Health Service. Centers
for Disease Control, Atlanta, Georgia. 1985.
• D. Rickwood, T. Ford, and J. Steensgaard. Centrifugation, Essential Data.
John Wiley & Sons. Published in association with BIOS Scientific
Publishers Limited, 1994.
• Rickman TW, Moyer NP. Increased Sensitivity of Acid-Fast Smears.
Journal of Clinical Microbiology. 1980; 11:618-20.
• A Centrifuge Primer. Published by Spinco Division of Beckman Instruments,
Inc., Palo Alto, California. Copyright 1980, Beckman Instruments, Inc.
68

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TB_Specimen_Collection_thru_Processing_TrainerNotes.pdf

  • 3. Specimen Quality is Important The results of tests, as they affect patient diagnosis and treatment, are directly related to the quality of the specimen collected and delivered to the laboratory. 3 http://www.aphl.org/aphlprograms/infectious/tuberculosis/Pages/tbtool.aspx
  • 4. Working with Healthcare Providers • Laboratories must develop a good working relationship with health care providers collecting patient specimens • Laboratories should have a reference manual for providers that includes: – Specimen type and volume requirements – Specimen collection, labeling, storage and transport instructions – Specimen rejection criteria • Laboratories should provide specific feedback to individual healthcare providers regarding problems with the quality of specimens received and provide recommendations for improvement 4
  • 5. Specimen Types I. Respiratory • Sputum (expectorated, induced) • Bronchoalveolar lavage (BAL) • Bronchial wash/brush • Transtracheal aspirate 5 II. Non-respiratory • Tissue • Body fluids • Blood • Stool • Gastric lavage • Urine Refer to the CLSI M48-A document, Laboratory Detection and Identification of Mycobacteria
  • 6. RESPIRATORY (PULMONARY) SPECIMENS Specimen Collection, Handling, Transport and Processing 6
  • 7. Sputum • Recently discharged material from the bronchial tree, with minimal amounts of oral or nasal material • Expectorated Sputum: Generated from a DEEP productive cough • Induced Sputum: produced with hypertonic saline if patient is unable to produce sputum on their own • Indications for sputum collection – To establish an initial diagnosis of TB – To monitor the infectiousness of the patient – To determine the effectiveness of treatment 7
  • 8. Sputum Quality • Specimens are thick and contain mucoid or mucopurulent material. • Ideally, 3–5 ml in volume, although smaller quantities are acceptable if the quality is satisfactory. • Poor quality specimens are thin and watery. Saliva and nasal secretions are unacceptable. • Laboratory requisition form should indicate when a specimen is induced to avoid the specimen being labeled as “unacceptable” quality. Clinical and Laboratory Standards Institute. Laboratory detection and identification of mycobacteria; approved guideline. CLSI Document M48-A. Wayne, PA: CLSI; 2008. http://www.stoptb.org/wg/gli/assets/documents/29_specimen_condition_transport.doc 8
  • 10. Indications for Sputum Collection • Initial diagnosis of TB: • Collect a series of three sputum specimens, 8-24 hours apart, at least one of which is an early morning specimen • Optimally, sputum should be collected before the initiation of drug therapy • For release from home isolation: • If patient is smear positive and on treatment: Collect sputum until 3 specimens are negative. • Monitoring of therapy: Obtain sputum specimens for culture at least monthly until cultures convert to negative Centers for Disease Control and Prevention. Guidelines for Preventing the Transmission of Mycobacterium tuberculosis in Health-Care Settings, MMWR 2005:54, RR-17 10
  • 11. Specimen Collection: All aerosol producing procedures pose a risk of exposure 11 Whether collecting specimen via sputum collection or bronchoscopy, if a patient is suspected or confirmed of have tuberculosis, airborne precaution must be used.
  • 12. Specimen Collection • Suspect or confirmed TB patients should be in a negative pressure room • Specimen collection is an aerosol generating procedure, anyone in the room during specimen collection must wear a particulate respirator type N-95 and be part of the respirator protection plan • All mycobacteria specimens are collected into a sealed leak proof container 12
  • 13. Storage and Transport of Sputum Specimens • Collection sites should refrigerate samples that cannot be transported immediately to reduce growth of contaminating organisms • Specimens should be delivered to the laboratory as soon as possible, within 24 hours of collection is optimal (avoid batching) • Laboratories may include a cold pack with specimen transport materials 13
  • 14. Pulmonary Specimens Other Than Sputum: Collection Guidance Specimen Types Collection Volume Requirements Transport Bronchoalveolar lavage (BAL) Bronch brush or washing Endotracheal aspirate Transtracheal aspirate Collect washing or aspirate in sputum trap Place the brush in a sterile, leak- proof container with up to 5 ml of sterile saline Minimum volume is 3 ml 50-ml conical tube or other sterile container Transport as soon as possible at room temperature If transport is delayed more than 1 hour, refrigerate specimen. 14 • The doubling time for other common respiratory flora is 15 to 20 minutes • The doubling time for M. tuberculosis is 12 to 24 hours
  • 16. Extrapulmonary Specimens • The laboratory should expect to receive a variety of extrapulmonary specimens which may be divided into two groups – specimens from non-sterile body sites – specimens from normally sterile body sites • Should be collected in a sterile leak-proof container • Should be transported as soon as possible • Swabs are generally not acceptable 16
  • 17. Extrapulmonary Specimen Collection Guidance Specimen from Non- Sterile Body Sites Recommended Collection Time Volume Requirements Collection Frequency Transport Recommended for Isolation of MTBC? Gastric Aspirate Early morning before patient eats and while still in bed 5–10 ml is optimal; maximum volume is 15 ml One specimen per day on three consecutive days Room temperature; if delayed >1 hour, neutralize with 100 mg sodium carbonate Yes Urine First morning specimen (void midstream) 10–15 ml minimum; prefer up to 40 ml One specimen per day on three consecutive days If delayed >1 hour, refrigerate Yes Stool No recommendation Minimum volume is 1 gram No recommendation Refrigerate if delayed >1 hour, do not freeze Mainly for diagnosis of disseminated MAC disease in patients with AIDS 17
  • 18. Extrapulmonary Specimen Collection Guidance Specimen from Normally Sterile Body Sites Volume Requirements Transport Recommended for Isolation of MTBC? Cerebral Spinal Fluid 10 ml is optimal; minimum volume is 2-3 ml As soon as possible at room temperature; do not refrigerate Usually paucibacillary; culture may have limited sensitivity Other Body Fluids (pleural, peritoneal, pericardial, synovial) 10-15 ml is optimal; minimum volume is 10 ml If delayed, refrigerate Yes Tissues or Lymph Nodes As much as possible; add 2-3 ml sterile saline As soon as possible at room temperature (no formalin, preservatives, or fixatives) Yes Blood 10ml preferred, minimum 5 ml. Collect in SPS or heparin tube, no EDTA At room temperature, do not refrigerate or freeze Mainly for diagnosis of disseminated MAC disease in patients with AIDS 18
  • 19. SUBOPTIMAL AND UNACCEPTABLE SPECIMENS Specimen Collection, Handling, Transport and Processing 19
  • 20. Suboptimal and Unacceptable Specimens • Processing of suboptimal or poor quality specimens is a burden on both financial and personnel resources • Results generated from processing inappropriate specimens may not be reliable • Each laboratory must develop its own specimen rejection criteria and make these criteria readily accessible to providers • Clinicians should be notified when a specimen is rejected and the reason for rejection should be provided • Specimens collected by invasive procedures should not be rejected 20
  • 21. Possible Rejection Criteria (1) • Labeling of specimen does not match identifiers on requisition form • Insufficient volume • Dried swabs – Swabs in general are not optimal • Provide limited material • Hydrophobicity of mycobacterial cell envelope inhibits transfer to media • Pooled sputum or urine • Sputum left at room temperature for 24 hours 21
  • 22. Possible Rejection Criteria (2) • Broken specimen containers or leaking specimens • Excessive delay between specimen collection and receipt in the laboratory • Blood specimens collected in EDTA might be rejected for culture as these inhibit growth of MTB • Tissue or abscess material in formalin • Gastric lavage fluid if pH not adjusted within 1 hour of collection 22
  • 23. SPECIMEN TRANSPORT: REFERRAL OF SPECIMENS WITHIN A LABORATORY NETWORK Specimen Collection, Handling, Transport, and Processing 23
  • 24. Transport of Biological Substances (Category B) Basic triple packaging system • (i) a leak-proof primary receptacle(s); • (ii) a leak-proof secondary packaging containing sufficient additional absorbent material shall be used to absorb all fluid in case of breakage • For cold transportation conditions, ice or dry ice shall be placed outside the secondary receptacle. Wet ice shall be placed in a leak- proof container. • (iii) an outer packaging of adequate strength for its capacity, mass and intended use. 24
  • 25. Transport of Biological Substances (Category B) Biological Substance, Category B 25
  • 26. Sputum Collection Kit An example from the Wisconsin State Laboratory of Hygiene • Insulated mailer with address label • UN3373 marking and proper shipping name “Biological Substance, Category B” • Sterile plastic conical tube with label • Sealable biohazard specimen transport • Cool pack • Absorbent pad • Instruction sheet 26
  • 27. Transport of Biological Substances • Transport of patient specimens is regulated by both the Department of Transportation (DOT) and by International Air Transport Association (IATA) rules. • Laboratories must have personnel trained in and familiar with these regulations • For details regarding these regulations, please see the information provided in the next slide. 27
  • 28. Packing and Shipping Guidance • ASM website-Guidance: Packing and Shipping Infectious Substances • DOT guidance: Transporting Infectious Substances Safely • More DOT Guidance: Infectious substances guide • IATA website: FAQs | Infectious Substances • FedEx Guidance: Clinical Samples, Biological Substances Category B(UN 3373) and Environmental Test Samples • UPS Guidance: Packing Hazardous Materials 28
  • 29. ADDITIONAL INFORMATION Specimen Collection, Handling, Transport and Processing 29
  • 30. Instructions for Sputum Collection • Healthcare providers should educate patients on proper specimen production and collection • Patients should also be informed of the possible infectious nature of his or her secretions • Specimens should be collected in appropriate tubes that are sterile, clear, plastic, and leak-proof (50 ml screw capped centrifuge tubes that can withstand 3000 x g are preferred) • Proper labeling protocols should be put in place by the laboratories • Work with TB program to provide instructions for submitters 30
  • 31. Examples for Instructions for Sputum Collection Pennsylvania Department of Health 31
  • 33. Principles of Specimen Processing Respiratory specimens (and other specimens from non- sterile sites) require digestion, decontamination, and concentration: • Digestion: Mucolytic agent used to liquefy sputum specimens to release AFB and expose normal flora for decontamination • Decontamination: Toxic agent used to kill rapidly growing normal flora that would otherwise overgrow slow growing mycobacteria • Centrifugation: Used to sediment bacteria following digestion/decontamination 33
  • 34. Effect of Processing Procedure • Reagents used for digestion and decontamination, to some extent, are toxic to mycobacteria • Procedures must be precisely followed – Time in contact with digestion/decontamination reagents is critical – Centrifugation procedures also affect mycobacteria recovery rates and must be carefully followed • Culture positivity rates and contamination rates should be monitored to evaluate performance of processing methods 34
  • 35. Safety • Many of the steps within the specimen processing procedure are aerosol-generating • The following activities should be performed in a biological safety cabinet:  Digestion and decontamination  Preparation of concentrated smear  Inoculation of culture media • Do not disrupt airflow of the cabinet • Avoid excess clutter inside the BSC For more information on the biosafety practices in the Mycobacteriology laboratory, please review the module on biosafety within this series 35
  • 36. Aseptic Techniques: Getting Started • Disinfect BSC, centrifuge, and tabletop with tuberculocidal disinfectant (repeat after specimen and culture workup complete) • Perform all work on absorbent pad soaked with disinfectant to absorb any droplets that may inadvertently occur • When possible, leave an empty space in the rack between each specimen tube • Work in sets equivalent to one centrifuge load (e.g., 8 specimens at a time) 36
  • 37. Aseptic Techniques: Processing • Use a fresh individual, disposable, sterile pipette at every step to avoid transfer of bacilli • To avoid droplet aerosol cross-contamination, open and remove caps from tubes one at a time • Add diluent to centrifuge tubes from individual tubes without the lip of the tube touching or creating an aerosol (do not use common containers or carboys) • Use aerosol-proof sealed centrifuge cups • Discard supernatant from decontaminated specimens into splash- proof container with disinfectant. Autoclave the discard container daily 37
  • 38. Digestion & Decontamination Methods Several methods are available for digestion and decontamination of clinical specimens: • N-acetyl-L-cysteine-sodium hydroxide (NALC- NaOH) • Commercially available: Alpha-Tec NAC-PAC™, BD MycoPrep™ • Oxalic acid • Cetylpyridinium chloride (CPC)-sodium chloride • NaOH method (Petroff’s method) • Zephiran-trisodium phosphate (Z-TSP) 38
  • 39. NALC-NaOH Method: Principle • Most common and preferred method • Rapid and relatively effective in reducing the number of contaminants • Addition of the mucolytic agent 2% NALC allows effective decontamination with 1% NaOH (less harsh on mycobacteria) (final concentrations) • Sodium citrate also included in digestion mixture to bind heavy metal ions in specimen that could inactivate N- acetyl-L-cysteine 39
  • 40. NALC-NaOH Method: Reagents CLSI M-48A Kent and Kubica • NaOH and sodium citrate can be prepared and combined in advance • NALC should be prepared and added fresh daily • Once NALC added, solution should be used within 24 hours Volume of digestant needed 4% NaOH 2.9% sodium citrate dehydrate Add NALC (fresh) 50 ml 25 ml 25 ml 0.25 g 100 ml 50 ml 50 ml 0.50 g 500 ml 250 ml 250 ml 2.50 g 40
  • 41. NALC-NaOH Method: Procedure for Sputum 1. Add equal volume of NALC-NaOH solution to 5-10 ml of sputum in 50 ml plastic screw cap centrifuge tube 2. Cap tube tightly. Invert the tube so that the NALC-NaOH solution contacts all inside surfaces of the tube and cap and then mix the contents for approximately 5-20 seconds with a Vortex mixer. 3. Allow mixture to stand for 15 minutes at room temperature with occasional gentle shaking by hand. 4. Add sterile distilled water or sterile pH 6.8 phosphate buffer to the 50 ml mark on tube. Securely cap tube and mix by inversion 5. Centrifuge the tubes for 15 min at 3,000 x g using aerosol-proof sealed centrifuge cups 41
  • 42. NALC-NaOH Method: Procedure for Sputum • After centrifugation, open centrifuge cups in BSC, slowly poor off supernatant into splash-proof discard container containing disinfectant – Take care to not disturb or pour off sediment (pellet) – Take care to avoid aerosol production and to prevent contamination of the lip of the tube • Wipe the lip of the tube with gauze soaked with disinfectant • Resuspend sediment in 1-2 ml of saline solution or phosphate buffer • Mix gently and proceed to culture inoculation and smear preparation 42
  • 43. NaOH Concentration is Key Amount of NaOH in 100 ml water % NaOH % NaOH when added to equal volume Na citrate Final concentration of NaOH when added to specimen 4.0g 4.0% 2.0% 1.0% 6.0g 6.0% 3.0% 1.5% 8.0g 8.0% 4.0% 2.0% CLSI M-48A • Recommended final concentration is 1.0% NaOH • Concentration of NaOH can be adjusted based on contamination rate in individual laboratories • NaOH at a FINAL concentration of ≥2.0% can be lethal to mycobacteria (may see decrease culture sensitivity in smear negative specimens) 43
  • 44. Timing is CRITICAL • 15 MINUTES – Time in contact with NALC-NaOH is critical since the high pH rapidly kills microorganisms in the specimen including mycobacteria • Over processing results in reduced recovery of mycobacteria • The importance of timing must be considered when deciding how many specimens can be processed in one run 44
  • 45. Specimen Processing QC • A Negative Processing Control (10 ml sterile water or buffer) should be included with each batch of specimens processed • Negative control is put through entire specimen processing procedure and inoculated to media • Determines if contamination is introduced during processing or culture handling • Assures that isolates are coming from patients and not from any other source 45
  • 46. 46 Definition of Cross Contamination Cross contamination: the transfer of M. tuberculosis complex bacilli (or other mycobacteria) from one specimen to another specimen that does not contain viable bacilli, causing a false positive result. – The phenomenon of misdiagnosis of tuberculosis due to cross contamination has been widely reported and has significant clinical and therapeutic impact on the patient.
  • 47. 47 To reduce the possibility of Cross Contamination: • Use daily aliquots of processing reagents and buffers. Any leftover should be discarded. • Never use common beakers or flasks when processing. • Keep the specimen tubes tightly closed and clean the outside of the tube prior to vortexing or shaking. • Pour decontamination reagents or buffers slowly on the side of the tube without causing any splashing. Do not touch the container of reagents to the lip of the tube at any time during addition.
  • 48. 48 To reduce the possibility of Cross Contamination: • Open the specimen tubes very gently to avoid aerosol generation. • When adding reagents to the tube, open one tube at a time. Do not keep all the tubes open at the same time. • Do not place tubes too close to each other in the rack • Change gloves often • Avoid manipulation of PT specimens • Disinfect biological safety cabinet work surfaces routinely.
  • 49. 49 Specimen Processing Proficiency • Digestion, decontamination, and conentration procedures should only be performed byt rrained laboratory staff. • Mycobacteriology laboratories should participate in an approved proficiency testing program. • Proficiency in culture and identification of MTV may be maintained by digestion and culture of 15-20 specimens per week.
  • 50. SPECIMENS FROM CYSTIC FIBROSIS PATIENTS AND EXTRAPULMONARY SITES Specimen Collection, Handling, Transport and Processing 50
  • 51. Cystic Fibrosis (CF) Patients • Specimens from CF patients are often heavily contaminated with Pseudomonas aeruginosa. • If it is known or discovered specimen is from a patient with CF or notable media contamination you can process concentrated sediment using only the 5% oxalic acid method. 51
  • 52. Oxalic Acid Processing Method for Specimens from CF Patients • Add an equal amount of 5% oxalic acid to: - 5-10 ml of primary respiratory specimen or - NALC-NaOH processed concentrated sediment • Vortex specimen and allow to incubate at room temperature for 30 minutes, mixing every 10 minutes • Neutralize with buffer solution • Concentrate specimen by centrifugation for 15 minutes at ≥ 3000 x g • Decant supernatant into splash-proof container and resuspend pellet with buffer solution • Inoculate media 52
  • 53. Processing Gastric Lavage and Urine • Centrifuge for 30 minutes at ≥ 3000 x g • Discard supernatant carefully into splash-proof container • Re-suspend pellet in sterile distilled water • Process suspension as for sputum (NALC- NaOH) 53
  • 54. Processing Aseptically Collected Fluids • Cerebral spinal fluid (CSF), synovial, pleural, peritoneal, pericardial • No decontamination required • Concentrate specimen to maximize the yield of mycobacteria • Inoculate directly to culture media 54
  • 55. Processing Tissue Specimens • Lymph node, lung tissue, biopsies • Tissue submitted in formalin is unsatisfactory for culture • No decontamination required • Process tissue specimens using a sterile tissue grinder, or mortar and pestle • Inoculate directly to culture media 55
  • 56. Processing Blood or Bone Marrow Aspirates • Specimens inoculated directly into MYCO/F LYTIC bottles or BacT/ALERT MB blood medium • Direct inoculation of blood onto a solid medium is not recommended • If transport is necessary, sodium polyanethol sulfate, heparin, or citrate may be used as anticoagulants • Blood collected in EDTA and coagulated blood are not acceptable 56
  • 57. PRINCIPLES OF CENTRIFUGATION Specimen Collection, Handling, Transport and Processing 57
  • 58. Concentration of Specimens • Since mycobacteria do not readily sediment, centrifugation force and time are important for maximal concentration • Specimens should be centrifuged for at least 15 minutes at 3000 x g • Revolutions per minute (rpm) is a measure of speed for a particular centrifuge head and not a measure of concentration efficiency or relative centrifugal force (RCF) • The relative centrifugal force is measured in units and is expressed in multiples of the earth’s gravitational field abbreviated as g • Use of a refrigerated centrifuge at 8 to 10°C may help to eliminate heat build-up which could be lethal to mycobacteria 58
  • 59. Calculation of Centrifugal Force Formula for calculating a particular centrifugal force is: RCF = 1.12r (RPM/1000) 2 where r is the radius, which is the distance in mm from the center of rotation to a point within the rotor, and RPM (revolutions per minute), which is the speed of rotation • This information should be published in many of the centrifuge manufacturers instruction manuals 59 Note: Nomogram attached in Resources section
  • 60. QUALITY INDICATORS Specimen Collection, Handling, Transport and Processing 60
  • 61. Quality Indicators: Contamination Rate • “Contamination” occurs when inoculated media is completely compromised due to overgrowth with non-acid fast organisms. • Contamination Rate monitors specimen preparation and the decontamination process • Calculation of contamination rate in Liquid media: – Numerator: number of inoculated broth cultures discarded or re- decontaminated in 1 month due to contamination – Denominator: total number of broth cultures inoculated in one month • Calculation of contamination rate in Solid media: – Numerator: number of inoculated solid media slants or plates discarded in 1 month due to contamination – Denominator: total number of solid media slants or plates inoculated in one month 61
  • 62. Contamination Rates • Acceptable overall rates of contamination – Solid media (LJ) is 2-5% – Liquid media (MGIT960) is 7-8% – Contamination rates for the individual laboratory can be affected by the type of media used (i.e. media containing antibiotics) • A contamination rate less than that of the acceptable rate indicates that processing methods are too harsh – NaOH concentration too high – Specimen exposure time to NALC-NaOH too long • A contamination rate greater than that of the acceptable rate could indicate a pre-analytical problem, an inadequate decontamination process, or both APHL, 2009, Assessing your Laboratory 62
  • 63. Potential Causes of High Contamination Rates CLSI M-48A • Lack of appropriate sputum collection guidance for patients • Delays in transport • Lack of refrigeration prior to transport • Inappropriate storage conditions or processing delays upon receipt in the laboratory • Decontamination process is ineffective – NaOH concentration too low – Specimen exposure time to NALC-NaOH too short 63
  • 64. Quality Indicators: Positivity (Recovery) Rate • Establishes a baseline for a given population or geographic area • Assists in identifying potential false positive or false negative cultures (MTB) • Assists in identifying environmental contamination • Calculation of positivity rate: – Numerator: number of cultures reported as MTB in one month – Denominator: total number of cultures reported (TB, NTM, negative, contaminated) in one month. 64
  • 65. Quality Indicators: Positivity (Recovery) Rate • Expectation: Population/geographic region dependent • Increases may be due to: – Shift in patient population – Cross contamination/false positives – Contaminated reagents, media, water (NTM) – Specimens contaminated during collection • Decreases may be due to: – Shift in patient population – Problems with specimen quality – Problems with specimen processing – Problems with equipment or media – Increase in contamination 65
  • 66. What should I do if Quality Indicators or Controls are out of range? • Ensure quality specimens are being received in the laboratory • Ensure quality reagents and media are being used • Ensure water used for specimen processing is sterile and filtered • Ensure laboratory equipment (e.g. incubators, BSCs) is functioning properly • Ensure protocols are followed • Ensure staff are trained and proficient 66
  • 67. References • Kent and Kubica, Public Health Mycobacteriology, A Guide for the Level III Laboratory, US Public Health Service. 1985 • ASM Press, Manual of Clinical Microbiology, 10th edition. Volume 1. James Versalovic, editor. 2011 • CLSI. Laboratory Detection & Identification of Mycobacteria; Approved Guidelines. CLSI document M48-A. Wayne, PA: Clinical & Laboratory Standards Institute; 2008. • APHL/CDC. Mycobacterium tuberculosis: Assessing Your Laboratory. 2009 67
  • 68. References • Centers for Disease Control and Prevention. Guidelines for Preventing the Transmission of Mycobacterium tuberculosis in Health-Care Settings, 2005. MMWR 2005;54(No. RR-17). • Public Health Mycobacteriology. A Guide for the Level III Laboratory. U.S. Department of Health and Human Services Public Health Service. Centers for Disease Control, Atlanta, Georgia. 1985. • D. Rickwood, T. Ford, and J. Steensgaard. Centrifugation, Essential Data. John Wiley & Sons. Published in association with BIOS Scientific Publishers Limited, 1994. • Rickman TW, Moyer NP. Increased Sensitivity of Acid-Fast Smears. Journal of Clinical Microbiology. 1980; 11:618-20. • A Centrifuge Primer. Published by Spinco Division of Beckman Instruments, Inc., Palo Alto, California. Copyright 1980, Beckman Instruments, Inc. 68