lab guide – 2019 · salivary sputum except for patient on therapy in the tb unit and induced...

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Lab Guide – 2019 TB Section Lab Guide

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CLINICAL

MYCOBACTERIOLOGY (NATIONAL TB

REFERENCE LABORATORY)

SPECIMEN COLLECTION

GUIDE

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NATIONAL TB REFERENCE LAB – HGH SPECIMEN GUIDELINES

Critical value (CRIV) in TB Reference Lab

Mycobacteriology (TB) Test

Critical Result (Record the time of Identification)

Acid Fast Bacilli smear Smear positive result from direct specimen in TB Lab

First GeneXpert PCR test

First GeneXpert positive result, where smear results are negative

First TB Culture First culture positive result from direct specimens in TB lab, where GeneXpert and smear results are negative

For Collection guideline

CLINICAL MYCOBACTERIOLOGY SPECIMEN COLLECTION GUIDE

https://itawasol/EN/How%20We%20Work/Clinical_Services/Laboratory/MICROBIOLOGY/Documents/07%20March%202018/Clinical%20Mycobacteriology%20specimenn%20collection%20-%202018.docx

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1. Abscesses and aspirates

ITEM PROCESS

Cerner order AFB smear/AFB PCR/ C AFB.

Specimen requirement

Decontaminate the surface site with 70% alcohol.

Collect purulent material aseptically from an undrained

abscess using a sterile needle and syringe. Open abscess

(after incision and drainage) and collect the expressed

material with a needle and syringe.

Transfer 5-10 ml of aspirated fluid abscess material or Pus

aspirate in 50 ml sterile conical tube (leak proof without

fixative).

Pus aspirate is always superior to a swab specimen. Specify

anatomic Site.

Volume 5-10 ml. (Minimum 2 ml)

Transport Temperature As soon as possible. Refrigerate the specimen at 2-8 °C.

Days test performed Daily.

Turnaround Time

Microscopy and AFB PCR: 24 hr. and/or Next day

Exception: outpatient samples and extra pulmonary

specimens received on Thursday and weekends, will be

released on Sunday.

Culture: No specific Turnaround time, for negative

cultures 42 days; for positive culture, when culture

becomes positive the preliminary report is released within

24 hours of detection time. Final result for MTB sensitivity is

differing from case to case.

Method Microscopy: Auramine O and Ziehl-Neelsen.

Culture: BACTEC MGIT.

GeneXpert TB PCR.

Reference value Microscopy: Negative, No AFB seen.

Culture: No growth at 42 days.

PCR: Negative, MTB DNA not detected.

Interpretation

Microscopy: Average number of AFB / 100 fields, >100/field.

Culture: Growth of MTB complex with susceptibility to

primary drugs SIRE and PZA or Growth of MOTT.

PCR:

Positive, MTB DNA Detected Rif resistance Detected.

Positive, MTB DNA Detected Rif resistance Not Detected.

Rejection criteria Swab specimen (only smear done).

Swabs are a not suitable because they dry easily and because of the limited amount of material transferred.

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Swabs are not optimal for AFB culture and PCR.

Specimen for culture, submitted in un-sterile containers.

Leaking containers

Performing Lab Location National TB Reference Laboratory – Rumailah, Ext. # 6671 / 6675.

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2. Body Fluids

ITEM PROCESS

Cerner order AFB smear/ AFB PCR/ C AFB.


Disinfect site with 70% alcohol if collecting by needle and syringe. Aspirate fluid as much as possible optimal volume (10 ml desirable) in a 50 ml sterile conical tube leak proof container without fixative.

Specify anatomic site (Plural, Pericardial, Peritoneal, Abdominal, Amniotic, Ascites, Bile, Synovial, and OTHERS).

Volume Minimum 10-15 ml.



Turnaround Time




released on Sunday.

Culture: No specific Turnaround time, for negative cultures 42 days; for positive culture, when culture becomes positive the preliminary report is released within 24 hours of detection time. Final result for MTB sensitivity is differing from case to case.



GeneXpert TB PCR.


Culture: No growth at 42.


Interpretation

Microscopy: Report Average no. of AFB / 100 fields,>100/field.

Culture: Growth of MTB complex with susceptibility to primary drugs SIRE and PZA or Growth of MOTT.

PCR:



Rejection criteria

Swab dipped in fluid.


Leaking containers

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3. Bone marrow

ITEM PROCESS



MGIT BD tube obtained from TB lab.(Discards half of the

media and add the sample).

Or 10 ml yellow top collectors containing polyanethol

sulfonate (SPS).

Transport Temperature ≤ 2 hrs. as soon as possible at Room Temperature.

Do not refrigerate or freeze Bone marrow specimen.


Turnaround Time




released on Sunday.

Culture: No specific Turnaround time, for negative

cultures 42 days; for positive culture, when culture

becomes positive the preliminary report is released

within 24 hours of detection time. Final result for MTB

sensitivity is differing from case to case.



GeneXpert TB PCR.




Interpretation

Microscopy: Report Average no. of AFB / 100

fields,>100/field.


PCR:



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Rejection criteria

Bone marrow specimen sent in unsterile tube.

Bone marrow specimen in EDTA tube, plain tube or any other

tube than SPS tube.


Leaking containers


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4. Cerebrospinal fluid (CSF)

ITEM PROCESS


Specimen requirement Collect aseptically 2-3ml CSF Sterile leak-proof sterile tubes.

Volume 2 to 3 ml, optimal is upto10 ml.

Transport temperature ≤ 2 hrs, as soon as possible at room temperature.

Do not refrigerate or freeze CSF specimen.


Turnaround time




released on Sunday.

Culture: No specific Turnaround time, for negative cultures 42 days; for positive culture, when culture becomes positive the preliminary report is released within 24 hours of detection time. Final result for MTB sensitivity is differing from case to case.



GeneXpert TB PCR.




Interpretation


fields,>100/field.

Culture: Growth of MTB complex with susceptibility to primary

drugs SIRE and PZA or Growth of MOTT.

PCR:



Rejection criteria Specimen sent in unsterile tube.

Specimen in tube with preservative or additive.

Leaking containers


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5. Gastric wash or lavage

ITEM PROCESS



Collect three consecutive days in early morning before

patients eat and while are still in bed.

Perform lavage with 25 to 50 mL of chilled, sterile distilled

water. Recover sample and place in 50 mL conical sterile

tube.

Volume 25 to 50 mL (Recommended 15ml).



Turnaround Time




released on Sunday.

Culture: No specific Turnaround time, for negative cultures

42 days; for positive culture, when culture becomes positive

the preliminary report is released within 24 hours of

detection time. Final result for MTB sensitivity is differing

from case to case.



GeneXpert TB PCR.




Interpretation


fields,>100/field.


drugs SIRE AND PZA or Growth of MOTT.

PCR:



Rejection criteria Gastric lavage sent on swab.


Leaking containers

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6. Sputum specimens

ITEM PROCESS



Rinse mouth with water to remove food particles, debris,

mouthwash, or oral drugs, which may inhibit the growth of

Mycobacteria.

Collect sputum (for 2 consecutive days), have patient

breathe deeply and cough several times to achieve a deep

lower reparatory specimen. (not postnasal fluid) .

volume Collect 5-10 ml (minimum 3ml early morning specimen).

Transport temperature As soon as possible. Refrigerate the specimen at 2-8 °C.


Turnaround time




released on Sunday.





from case to case.



GeneXpert TB PCR.


Culture: No growth at 42. PCR: Negative, MTB DNA not detected.

Interpretation


fields,>100/field.


primary. Drugs SIRE AND PZA or Growth of MOTT.

PCR:



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Rejection criteria

Salivary sputum except for patient on therapy in the TB unit

and induced sputum.

Third consecutive sputum from the same patient, pooled

sputum.

Leaking specimens and swabs.




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7. Lower Respiratory specimens

ITEM PROCESS



Lower Respiratory Endo-tracheal, Trans-tracheal secretions,

Bronchoalveolar Lavage or Bronchial wash in a 50 ml sterile

conical tube leak proof container without fixative.

Induced sputum is collected by trained staff.

For induced sputum, use sterile hypertonic saline. Avoid

sputum contamination with nebulizer reservoir water.

Saprophytic Mycobacteria in tap water may produce false-

positive culture or smear results. Indicate on test order if

specimen is induced sputum, as these watery specimens

resemble saliva and risk rejection as inadequate.

Avoid contaminating bronchoscope with tap water when

collecting Bronchoalveolar Lavage or Bronchial washing.

volume Collect 5-10 ml (minimum 3ml early morning specimen).

Transport temperature As soon as possible. Refrigerate the specimen at 2-8 °C.


Turnaround time




released on Sunday.





from case to case.



GeneXpert TB PCR.


Culture: No growth at 42. PCR: Negative, MTB DNA not detected.

Interpretation


fields,>100/field.


primary. Drugs SIRE AND PZA or Growth of MOTT.

PCR:



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Rejection criteria

Third consecutive pulmonary samples from the same patient.

Leaking specimens and swabs.




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8. Stool

ITEM PROCESS



Collect specimen in a clean bed pan or use plastic wrap

placed between the toilet seat and the bowl. Do not submit

feces contaminated with urine or toilet water.

Stool specimen in clean leak proof wide mouth container

without preservative. (Preferably 50 ml conical tube).

Utility of culturing stool for acid-fast bacilli remains

controversial and should be discouraged; however, stool

samples from immunocompromised and HIV patients may be

submitted, mainly to detect MOTT.

The stool specimen from patient other than mentioned above

requires prior consultation with TB Lab.

Volume 10-20 gm (minimum 1g).



Turnaround Time




released on Sunday.





from case to case.



GeneXpert TB PCR.


Culture: No grow at 42 days.


Interpretation

Microscopy: Report Average no of AFB / 100 fields,>100/field.


PCR:



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Rejection criteria

Stool in transport medium or preservatives.

Stool samples from NON immunocompromised and HIV patient.


Leaking containers


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9. Tissue / biopsy

ITEM PROCESS



Tissue collection is an invasive procedure and requires a

trained physician. Include material from both the center and

the edge of the lesion.

Aseptically collected tissues in 50 ml sterile containers

without fixatives or preservatives.

Specify anatomic site.

Volume > 1 ml or >1g (submit as much as possible).



Turnaround Time




released on Sunday.





from case to case.



GeneXpert TB PCR.




Interpretation

Microscopy: Report of Average no. of AFB / 100

fields,>100/field.



PCR:


Positive, MTB DNA Detected Rif resistance Not Detected

Rejection criteria

Tissue specimen sent in fixatives like formalin.

Swab specimen. Swabs are not optimal for AFB culture and

PCR.


Leaking containers


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10. Urine for AFB

ITEM PROCESS



First morning specimen in sterile container (midstream is

never advised). Organisms accumulate in bladder overnight,

so first void morning specimen provides best yield.

Specimens collected at other times are dilute and are not

optimal.

Collect urine specimen on 3 consecutive days.

Volume 15-20 ml (prefer up to 40 ml).



Turnaround Time




released on Sunday.





from case to case.



GeneXpert TB PCR.




Interpretation


fields,>100/field.


drugs SIRE and PZA or growth of MOTT.

PCR:



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Rejection criteria

24 h pooled specimen AND small volume.

Urine from bag.

Urine received in Boric acid container.


Leaking containers


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11. Wound specimen

ITEM PROCESS



Collect Tissue or pus aseptically in 50 ml sterile conical tube in leak proof without fixative and avoid indigenous microbiota.

Select caseous portion if available as the majority of organisms will be found in the periphery of a caseous lesion. Do not wrap in gauze. Freezing decreases yield.

Specify anatomic site.

Volume > 1 ml or > 1 gm.



Turnaround Time




released on Sunday.





from case to case.



GeneXpert TB PCR.




Interpretation


fields,>100/field.



PCR:



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Rejection criteria

Specimens in fixatives or preservatives e.g. tissue specimen

submitted in formalin.


Leaking containers

One swab for multiple requests, for example, for various

organisms (bacteria, AFB Fungi, Virus etc.)
