J.6 - Example Key Elements.pdf

Attachment J.6 - Solicitation 75D301-20-R-67869

Study 31/ACTG 5349 Key Elements of Mycobacteriology Laboratory Procedures:

Towards Harmonization of Mycobacteriology in TB Trials

J.6 - Example Key Elements Page 1 of 9

Background

The proposed approach towards harmonization of Standard Operating Procedures (SOPs) across the Tuberculosis Trials Consortium (TBTC) and AIDS Clinical Trials Group (ACTG) Network Tuberculosis (TB) laboratories included, (1) identifying Key Elements in Mycobacteriology laboratory procedures that have the greatest impact on data quality and, (2) harmonizing those elements across all Mycobacteriology Laboratories in both networks. Rather than create new SOPS, Mycobacteriology Laboratory procedures should be reviewed for the presence or absence of the necessary Key Elements. Most clinical Mycobacteriology Laboratories already have SOPS and have either been accredited or are in the process of accreditation. Creating new SOPs would be burdensome in terms of time and resources, and would duplicate the efforts of other universal lab manuals that are currently available (e.g., GLI Mycobacteriology Laboratory Manual)

Cross-network harmonization and implementation of the Key Elements of Mycobacteriology Laboratory Procedures begins with TBTC Study 31, ACTG #5349, a multi-network phase three trial to evaluate safety and efficacy of shortened TB treatment regimens for acute pulmonary TB.

The Key Elements for TBTC Study 31, ACTG #5349 are detailed in Table 1 below. These are in agreement with the Key Elements developed by the ACTG Tuberculosis Transformative Science Group (TB TSG) Lab Core Team. Good Clinical Laboratory Practices (GCLP) and quality assessment (QA) activities are not considered as key elements but must be a part of the Mycobacteriology Laboratory procedures, and laboratory-specific Quality Management manuals. These Key Elements are directed towards Mycobacteriology results used as endpoints in TB drug trials; however, Key Elements of rapid drug susceptibility tests are included as the quality of these results and turnaround times are important in screening for subject eligibility. Likewise, quality indirect Drug Susceptibility Testing (DST) results are needed to ensure safety for subjects enrolled in the study.

How to Use Key Elements of Mycobacteriology Laboratory Procedures

1. Review the Key Elements for Mycobacteriology Laboratory Procedures

2. Ensure your laboratory SOPs for Mycobacteriology include each Key Element

3. Sign and return signature page to TBTCStudy31@cdc.gov, with subject line “Laboratory Key Elements”

4.

Title Study 31/ACTG 5349 Key Elements of Mycobacteriology Laboratory Procedures

Author(s) Anne Purfield (TBTC) Kathleen Eisenach (University of Arkansas for Medical Sciences)

Anne-Marie Demers (Desmond Tutu TB Centre, Stellenbosch University) Fatima Jones (Westat) Frances Whalen (Westat)

Version 1.9

Date 02-Jul-2015 mailto:TBTCStudy31@cdc.gov

Study 31/ACTG 5349 CLINICAL STUDY TEAM AND LABORATORY AGREEMENT SIGNATURE PAGE

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TBTC/ACTG Site _______ agrees that the Key Elements of Mycobacteriology Laboratory Procedures are included in SOPs that are performed for Study 31

Site Name: _______________________________________

Laboratory Name: __KEMRI/CDC TBLABORATORY_____________________________________

This agreement must be signed and dated prior to participant enrollment and reviewed annually thereafter until study is completed.

Principal Investigator Printed Name Signature Date

Annual review initial and date (month/year): _____/_____; _____/_____; _____/_____; _____/_____

Study Coordinator Printed Name Signature Date

Coordinator(s) Collecting Sputum Printed Name Signature Date

Laboratory Director Printed Name Signature Date

Mycobacteriologist* Printed Name Signature Date

Annual review initial and date: _____/_____; _____/_____; _____/_____; _____/_____

*The individual(s) completing TBTC Mycobacteriology (MB) Form

Table 1: Key Elements of Mycobacteriology Laboratory Procedures

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Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

1 Sputum Collection & Transport

Participant is to rinse mouth with boiled/sterile/bottled or distilled water prior to sputum collection

Quality of specimen

Sputum Collection SOP Version 1.0_01 Aug 2014

2 Sputum Collection & Transport

Collect at least 3 to 5 mL of sputum. If larger volumes cannot be obtained, a minimum of 1 mL is acceptablei

Quality of specimen

Sputum Collection SOP Version 1.0_01 Aug 2014

3 Sputum Collection & Transport

Transport sputum specimen to the laboratory in a cool box as soon as possible after collection. Store sputum in a refrigerator or cool box (2-8oC) if not received by to the laboratory within 1 hour of collectionii

Integrity of specimen

SOP# KEMRI/CDC

3003-RCP-1-06

6.2.3.

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Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

4 Sputum Receipt Storage

Store sputum specimen in a refrigerator or cool box (2-8°C) if not processed within 1 hour of receipt at the laboratory

Integrity of specimen

SAMPLE TRANSPORTATION

AND RECEPTION IN THE

LABORATORY

SOP# 3003-RCP-1-06

6.2.5

5 Sputum Processing

Decontaminate sputum specimen with a final sodium hydroxide (NaOH) concentration of 1.0 to 1.5% for 15 to 20 minutes prior to adding phosphate buffered saline (PBS) (pH 6.8)

Isolation of MTB SPECIMEN PROCESSING, CULTURE, INNOCULATION, SMEAR PREPARATION

SOP# 3003-MCD-2-04

6.6.3.2

6 Sputum Processing

Centrifuge specimen with a relative centrifugal force (RCF) of 3000xg, for at least 15 minutesiii

Isolation of MTB SPECIMEN PROCESSING, CULTURE, INNOCULATION, SMEAR PREPARATION

SOP# 3003-MCD-2-04

6.6.3.10

7 Sputum Processing

Re-suspend the digested decontaminated specimen to final volume of 1.5 to 2.0 mL with PBS (pH 6.8)iv

Comparability of results

SPECIMEN PROCESSING,

CULTURE, INNOCULATION,

SMEAR PREPARATION

SOP# 3003-MCD-2-04

6.6.3.13

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Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

8 Sputum Processing

Include positive controls at least once per week or with each participant batch, and negative controls daily or with each participant batch

Isolation of MTB and Detect Cross- Contamination

SPECIMEN PROCESSING,

CULTURE, INNOCULATION,

SMEAR PREPARATION

SOP# 3003-MCD-2-04

6.6.2

9 Smear Microscopy

Positive and negative control slides must be included with every batch of participant slides

Quality of smear results

ZIEHL NIELSON STAINING

TECHNIQUE AND

MICROSCOPY

SOP# 3003-MCD-6-04

AURAMINE STAINING

TECHNIQUE AND

MICROSCOPY # 3003-MCD-

0-03

7.1

10 Smear Microscopy

Report results according to

WHO/IUATLD

grading scale as per the Global Laboratory Initiative (StopTB Partnership) Sputum Microscopy Handbookv

Comparability of results

ZIEHL NIELSON STAINING

TECHNIQUE AND

MICROSCOPY

SOP# 3003-MCD-6-04

AURAMINE STAINING

TECHNIQUE AND

MICROSCOPY # 3003-MCD-

0-03

6.2.27

6.3.9

J.6 - Example Key Elements Page 6 of 9

Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

11 Rapid Molecular Testing

Perform rapid molecular test (e.g., GeneXpert) according to the manufacturer's product insert

Comparability of results

MOLECULAR DETECTION OF

MTB IN CLINICAL SPECIMEN

USING GENEXPERT MTB/RIF

# 3003-GXP-1-05

6.0

12 Rapid Molecular Testing and Smear Microscopy

Report results of screening tests used for subject eligibility to clinic staff within 48 to 72 h of sputum specimen receipt

Turnaround time TB laboratory quality indicators- #3003-QMS-

17-00

6.7.2.7

13 Solid Media Culture

Inoculate solid media (slant or plate) with

0.2 mL of re-suspended sputum sedimentvi

Comparability of results

INNOCULATION AND

FOLLOW UP OF PROCESSED

SPECIMENS ON

MIDDLEBROOK 7H11S

MEDIA #30030MCD-21

6.2.3

14 Solid Media Culture

Incubate solid media for at least 6 weeks before reporting a negative result; or at least 8 weeks for drug resistant TB trials

Isolation of MTB INNOCULATION AND

FOLLOW UP OF PROCESSED

SPECIMEN INTO

LOWENSTEIN JENSEN

MEDIA #3003-MCD-04-04

6.4.5

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Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

15 Solid Media Culture

Test appropriate controls before media is used, regardless if purchased commercially or prepared in-housevii

Isolation of MTB Internal Quality Control-

3003-QMS-12-00

6.6

16 MGIT Culture Inoculate each MGIT tube with 0.5 mL of the re-suspended sputum sediment

Comparability of results

MGIT PREPARION

INOCULATION AND

FOLLOW UP IN MGIT

960 #3003-MCD-4-03

6.2.5.4.

17 MGIT Culture Work up all MGIT cultures (positive and negative) according to the FIND MGIT Manual and MGIT culture algorithms/flow charts included in the study-specific laboratory reference manualviii

Isolation/Detection of MTB

MGIT PREPARION

INOCULATION AND

FOLLOW UP IN MGIT

960 #3003-MCD-4-03

6.4.

18 Identification of

MTB

Confirm the presence of M. tuberculosis complex (MTBC) vs.

non-MTBC at each trial time point when culture is positiveix

Isolation of MTB IDENTIFICATION OF

M.TUBERCULOSIS

COMPLEX BY CAPILIA TB-

NEO

#3003-IDT-1-03

6.2.6.

6.2.7.

J.6 - Example Key Elements Page 8 of 9

Laboratory Procedure

Key Element in Procedure

Potential effect/ Impact

What laboratory SOP document(s) has this key element been incorporated into? (name and SOP number)?

How will you address this element if it is not already in your current SOPs?

Please provide a short description of how this Key Element is implemented in your laboratory.

What part/section of the laboratory SOP reflects this key element?

19 Identification of

MTB

Include positive and negative controls at least once per week or with each batch of participant specimens and with each new lot or shipment of testing kits/reagents

Accuracy of MTB

ID

IDENTIFICATION OF

M.TUBERCULOSIS

COMPLEX BY CAPILIA TB-

NEO

#3003-IDT-1-03

7.3

20 Drug Susceptibility Testing (DST)

Include a drug susceptible quality control (QC) strain at least once per week or with each batch of participant specimens

Quality of DST results

DRUG SUSCEPTIBILITY

TESTING FOR SIRE

# 3003-MCD-9-03

7.1.

i If not possible to collect at least 1 mL expectorate sputum, use local procedures for sputum induction, when necessary ii When the distance between the clinic and laboratory is great (i.e., the clinic ships the specimen to a regional laboratory), the specimen should be maintained on cold chain and received at the laboratory no more than three to five days after collection.

iii Use of a refrigerated centrifuge is preferred.

iv For guidance on how to achieve accurate and precise resuspension volumes, please see Study 31/ACTG 5349 Mycobacteriology Laboratory Reference Manual.

v See Section 9, “Acid-fast Bacilli Microscopy (AFB) Examination”, from Global Laboratory Initiative Stop TB Partnership. Laboratory Diagnosis of

Tuberculosis by Sputum Microscopy – The Handbook 2013. Available from:

http://www.stoptb.org/wg/gli/assets/documents/TBLabDiagnosisSputum%20Microscopy_Handbook.pdf.

http://www.stoptb.org/wg/gli/assets/documents/TBLabDiagnosisSputum%20Microscopy_Handbook.pdf

J.6 - Example Key Elements Page 9 of 9 vi If using slants or plates where 0.2 mL of inoculum would overwhelm the surface area of the media, inoculate additional slants or plates so that the total volume of resuspended sputum sediment cultured on solid media is 0.2 mL. See Study 31/ACTG 5349 Mycobacteriology Laboratory Reference Manual.

vii See Section 16, “Quality Assurance”, from Global Laboratory Initiative Stop TB Partnership: Mycobacteriology Laboratory Manual. First edition, April

2014. Available from: http://www.stoptb.org/wg/gli/assets/documents/gli_mycobacteriology_lab_manual_web.pdf viii See Study 31/ACTG 5349 Mycobacteriology Laboratory Reference Manual.

ix At least one positive culture (e.g., AFB-positive MGIT) at each time point for each participant should be identified as M. tuberculosis or otherwise, depending on the laboratory resources. See Study 31/ACTG 5349 Mycobacteriology Laboratory Reference Manual.

http://www.stoptb.org/wg/gli/assets/documents/gli_mycobacteriology_lab_manual_web.pdf