• Users Online: 141
  • Home
  • Print this page
  • Email this page

 Table of Contents  
Year : 2020  |  Volume : 9  |  Issue : 1  |  Page : 29-33

Performance of Mali's biosafety level 3 laboratory in the external quality assessment in preparedness of laboratory accreditation and support to clinical trials

1 University Clinical Research Center-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
2 National Referral Laboratory of Mycobacteriology, National Institute of Public Health, INSP, Bamako, Mali
3 University Clinical Research Center-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali; Center for Global Health, Northwestern University, Chicago, IL, USA
4 Collaborative Clinical Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
5 Microbiology and Biotechnology Research Laboratory, Faculty of Sciences and Techniques, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali

Date of Submission01-Nov-2020
Date of Decision27-Jan-2020
Date of Acceptance28-Jan-2020
Date of Web Publication6-Mar-2020

Correspondence Address:
B Diarra
University Clinical Research Center-SEREFO-Laboratory, University of Sciences, Techniques and Technologies of Bamako, Bamako
Login to access the Email id

Source of Support: None, Conflict of Interest: None

DOI: 10.4103/ijmy.ijmy_5_20

Rights and Permissions

Background: The external quality assessment (EQA) or external quality control is an evaluation conducted by a certified external organization to inquire about the quality of the results provided by a laboratory. The primary role of EQA is to verify the accuracy of laboratory results. This is essential in research because research data should be published in international peer-reviewed journals, and laboratory results must be repeatable. In 2007, the University Clinical Research Center (UCRC's) biosafety level 3 (BSL-3) laboratory joined the EQA program with the College of American Pathologists in acid-fast staining and culture and identification of mycobacteria as per laboratory accreditation preparedness. Thus, after 11 years of participation, the goal of our study was to evaluate the performance of our laboratory during the different interlaboratory surveys. Methods: We conducted a descriptive retrospective study to evaluate the results of UCRC mycobacteriology laboratory from surveys conducted during 2007 and 2017. Results: Of the 22 evaluations, the laboratory had satisfactory (100% of concordance results) in 18 (81.8%) and good (80% of concordance results) in 4 (18.2%). Overall, the laboratory was above the commended/accepted limits of 75%. Conclusion: So far, UCRC's BSL-3 performed well during the first 11 years of survey participation, and efforts should be deployed to maintain this high quality in the preparedness for laboratory accreditation and support to clinical trials.

Keywords: External quality assessment, Mali, mycobacteriology

How to cite this article:
Coulibaly N, Kone B, Sanogo M, G Togo A C, Diarra B, Sarro Y S, Cisse A B, Kodio O, Coulibaly G, Kone M, Baya B, Maiga M, Dabitao D, Belson M, Dao S, Diallo S, Diakite M, Babana A H, Doumbia S. Performance of Mali's biosafety level 3 laboratory in the external quality assessment in preparedness of laboratory accreditation and support to clinical trials. Int J Mycobacteriol 2020;9:29-33

How to cite this URL:
Coulibaly N, Kone B, Sanogo M, G Togo A C, Diarra B, Sarro Y S, Cisse A B, Kodio O, Coulibaly G, Kone M, Baya B, Maiga M, Dabitao D, Belson M, Dao S, Diallo S, Diakite M, Babana A H, Doumbia S. Performance of Mali's biosafety level 3 laboratory in the external quality assessment in preparedness of laboratory accreditation and support to clinical trials. Int J Mycobacteriol [serial online] 2020 [cited 2020 Sep 20];9:29-33. Available from: http://www.ijmyco.org/text.asp?2020/9/1/29/280152

  Introduction Top

The external quality assessment (EQA), previously known as external quality control, is a verification by a certified external organism of the quality of the results provided by a laboratory on samples known to the external organism but unknown to the laboratory.[1] It is a retrospective control allowing interlaboratory confrontation in order to improve the quality of the work of all the participants.[1]

The College of American Pathologists (CAP) is a world leader proficiency testing and accreditation organism with more than 20,000 participating laboratories around the world.[2] From routine to more specialized samples, the program helps laboratories to stay at high-quality performance and accuracy in patient results.

The EQA program in microbiology was initiated by the World Health Organization (WHO) in July 2002 with the support of the United States Agency for International Development and the Global Vaccine Alliance.[2] The Office of the WHO for the Africa Region, in collaboration with the National Institute for Communicable Diseases, set up this program to assess national laboratories' capacity to implement standardized methods, to improve their capacity for surveillance and response adapted to priority diseases. In 2005, malaria and tuberculosis (TB) became part of the EQA.[3]

TB remains a major public health problem with 10 million cases, 1.3 million of death around the world in 2018. The emergence of the human immunodeficiency virus (HIV) and anti-TB-resistant strains (480,000 multidrug-resistant cases) increases the threat.[4] It is a contagious disease caused by mycobacteria belonging to the Mycobacterium tuberculosis complex (MTBc) family.[4] Paradoxically, TB remains underdiagnosed and untreated in resource-limited setting, with only 57% of detection rate in Mali in 2017.[4] Its control aims to reduce the spread of infection[5],[6] by early diagnosing and treating pulmonary cases which are more infectious. Indeed, between 2000 and 2015, early diagnosis and adequate treatment of TB saved 49 million lives.[7] However, the diagnosis of TB is essentially based on smear microscopy.[8] The good quality of sputum smear remains one of the important components of the Directly Observed Treatment, Short-Course strategy which is highly recommended by the WHO for TB control. Laboratory results of a suspected patient are used by physicians to initiate or refute anti-TB treatment. In addition, as recommended in the WHO guidelines, treatment success monitoring is also followed by sputum smear examination using Ziehl–Neelsen or auramine (A/R) fluorescent microscopy (FM), in which conversion from smear positive to smear negative at 2 months is an important predictor of treatment success.[9],[10] Therefore, the laboratory becomes crucial in diagnosing and monitoring TB patients.

In Mali, EQA for clinical sample is very limited, and only TB program is trying to implement it. There is no national program for EQA.[11]

Since its creation in 2006, University Clinical Research Center (UCRC) biosafety level-3 (BSL-3), previously called SEREFO (HIV/TB Research and Training Center) laboratory program, has set up an EQA system with CAP. Thus, the purpose of this study was to evaluate the performance of UCRC BSL-3 TB laboratory after 11 years of participation in CAP microbiology proficiency testing.

  Materials and Methods Top

Study setting

The UCRC is a clinical research program created under the collaboration between Mali and the USA through their ministries of health. The UCRC's mission is to continuously improve the quality of health care nationally, regionally, and globally by facilitating excellent clinical research at international standards, strengthening research capacity, and providing training.[11] One of its composed laboratories is the BSL-3 where TB testing is conducted safely.

Study design

This was a cross-sectional study. The data were collected from BSL-3 Laboratory CAP's evaluation reports between 2007 and 2017.

Sample types and shipping to Bamako site

Samples received in the laboratory for analysis come from the CAP. These samples are usually a reconstituted human tissue, and the companies guarantee the quality, homogeneity, and stability of the samples. A total of five samples were well packed and marked with the infectious substances label before shipping to all laboratories participating in the survey (sites). The EQA for mycobacterial (Acid-Fast Staining and Mycobacterial Identification: Mycobacteriology Limited: E1-B Program under CAP) test is sent to the laboratory twice a year for testing. Each laboratory participating in the survey will perform 10 samples per year. Samples are coded so that the laboratory technician is blinded to the diagnosis by including undifferentiated positive and negative samples in the survey. In the laboratory, the samples should be performed like routine sample arriving for TB diagnosis in the laboratory by following standard operating procedures. The results are then reported on the CAP website using the codes on the tubes. The CAP assesses the results and scores from 0% to 100% of correct answer. The laboratory performance is considered acceptable when the survey scores are >75%.[2]

Laboratory methods for culture and identification

Specimen samples were digested and decontaminated using the standard N-acetyl-L-cysteine/4% NaOH solution, concentrated by centrifugation (4500 rpm), and inoculated on both liquid (Mycobacterium Growth Incubator Tube [BBL™ MGIT™ Becton Dickinson, Sparks, MD, USA]), and solid (Middlebrook 7H11 Agar and Selective 7H11 Agar) media. Simultaneously, an aliquot of concentrated specimen was prepared for indirect commercial A/R staining (BBL™ Becton Dickinson, Sparks, MD, USA). Speciation of positive mycobacterial cultures was based on acid-fast bacilli (AFB) positivity in FM and colony morphology on solid medium and was confirmed by nucleic acid probes (AccuProbe® Gen-Probe, San Diego, CA, USA), or Capilia™ TB-Neo assay, TAUNS Laboratories, Inc., Futaba-Cho, Numazu, Shizuoka, Japan.

Fluorescent auramine staining protocol and grading of smear microscopy

A/R staining protocol is a very old staining technic used in the TB diagnosis and its treatment follow-up. The property of acid-fastness is based on the presence of mycolic acids in the mycobacterial cell wall. The primary stain (A/R) binds strongly to the mycolic acids of the cell wall. Intense decolorization (strong acids, alcohol) does not release primary stain from the cell wall and the mycobacterial retain the fluorescent bright yellow color of A/R. Potassium permanganate or TB methylene blue is used to quench the fluorescence in the background.

The grading of sputum smear microscopy was done following the International Union against Tuberculosis and Lung Diseases grading criteria as negative (no AFB seen or 0), few AFB seen (10–99 AFB seen in 100 fields or 1+), moderate AFB seen (1–10 AFB seen per field or 2+), and many AFB seen (>10 AFB seen per field or 3+).[12] Following these tests, the results were reported on the CAP website for evaluation.

Statistical analysis

The data were collected from the result sheets (CAP Evaluation report or Annex-4) sending to the laboratory by CAP program and entered into the Excel sheet. The data were analyzed using the SPSS Software version 21.0 (IBM SPSS, Armonk, New York: IBM Corporation) to evaluate laboratory performance.

  Results Top

Number of samples received during the 11 years of survey participation

In total, 90 sample tests in 22 surveys were received for EQA between 2007 and 2017 in UCRC's BSL-3 laboratory [Table 1]. Overall, we obtained satisfactory (100% of concordance) results in 18 (81.8%) surveys and good (80% of concordance) results in 4 (18.2%) surveys [Figure 1].
Table 1: Overall participation of the University Clinical Research Center in the different surveys between 2007 and 2017 with the corresponding number of samples received and teste

Click here to view
Figure 1: Comparison of University Clinical Research Center biosafety level-3 laboratory score to the score of other laboratories as for microscopy reading

Click here to view

Smear and culture results

Between 2007 and 2017, a total of 529 laboratories participated to the CAP's EQA survey for smear microscopy for AFB identification. Except the years 2011 and 2015, our results were 100% of concordance with expected results and above the global average of other participating laboratories [Figure 2] and [Figure 3].
Figure 2: University Clinical Research Center biosafety level-3 laboratory score compared to the score of the other laboratories according to the culture technique

Click here to view
Figure 3: Performance of University Clinical Research Center biosafety level-3 laboratory in the external quality assessment between 2007 and 2017

Click here to view

During the same period, 480 laboratories performing culture and identification of mycobacteria were participating in the survey. Our score was 100% in all the 22 surveys except for the years 2011 and 2015 [Figure 2] and [Figure 3].

Performance of University Clinical Research Center personnel

During the 2-year period 2016 and 2017, we evaluated the performance of our personnel, and we had 100% of sensitivity, specificity, positive, and negative predictive values in smear microscopy and culture of mycobacteria [Table 2].
Table 2: Performance of the trainer compares to that of a trainee at the microscopy and culture for the identification of Mycobacterium tuberculosis complex in 2016 and 2017

Click here to view

  Discussion Top

EQA is an essential component of quality control and is an effective way to identify problems and verify laboratory performance against other laboratories using external agencies.[13],[14],[15] In this study, we assessed the overall performance of UCRC BSL-3 after 11 years of proficiency testing under CAP. We found that our laboratory results in smear microscopy and culture of mycobacteria are in good agreement and have good sensitivity and specificity with CAP's expected results [Table 2]. Therefore, we demonstrate the continuous efficacy and efficiency of the personnel.[16] EQA programs are increasingly needed and essential for increasing confidence in the laboratory results that must be used in the diagnosis, treatment, or epidemiological surveillance of certain diseases.[17],[18] Moreover, it appears necessary for each Biomedical Analysis Laboratory (BAL) to be enrolled in EQA programs in order to improve their services and their result reliability. Research laboratory also requires this kind of EQA for their research or clinical trial result validation.[19],[20],[21],[22],[23]

Given the pivotal role of accurate diagnosis of TB by direct examination, culture and molecular techniques,[24] and mainly in resource-limited countries with an increased number of underdiagnosed patients,[25] strategies to initiate EQA implementation should be encouraged in these regions even only at one laboratory. An example is Mali, where the north of the country suffers from instability due to terrorist groups, despite the presence of peacekeeping forces since 2013. Thus, TB diagnostic services in such a setting are especially challenging, as no supervision visits by the national TB program can be conducted to the north of the country. Therefore we cannot guarantee good results from those laboratories. In our study, the number of participating laboratories was 529 for the microscopy survey and 480 for the culture. This implies that several laboratories are participating in CAP program and confirmed that our results were more discussed and valued. With smear results, we had 100% agreement of the laboratory results with those expected from CAP during a period of 8 years out of 11 years of participation, thus demonstrating the accuracy of our results. These results are identical to that of Ssengooba et al. in Uganda in 2015.[26] However, the concordance results during the years 2011 and 2015 were 75% and 80%, respectively. These results could be explained by the hiring of new technicians in the laboratory in 2011 followed by a poor orientation training and by the burden of laboratory work in 2015 with the advent of the Ebola virus disease (EVD) epidemic in our country.[27]

During the EVD epidemic, in addition to suspected Ebola sample testing, the team was continuing working on TB samples. However, the scores were still within the allowed limit which is 75% of concordance.[28] The culture is the gold standard in TB diagnosis because it is based on the capacity of bacilli to grow on specific culture media and to demonstrate their viability. We had the same performance in smear and culture.

High sensitivity and specificity are highly recommended for all diagnostic tests mainly for TB. In our study, we obtained 100% of concordance in 8 years demonstrating the efficacy and efficiency of the laboratory for the identification of MTBc. Due to laboratory certification and maintenance of the BSL-3, we missed one complete year of participation. Thus, we should identify alternative backup in such a situation. The high scores obtained by the laboratory during the 11 years were attributable to the continuous training and skill acquired over the years. UCRC leadership should continue monitoring the training record of the personnel so that they maintain and try to upgrade the gap in this record in order for the laboratory to maintain high quality. Moreover, the laboratory application for accreditation will be the most important step to follow.

Our desire to implement high-quality standardized laboratory results obliged us to register and participate in the WHO survey since 2018. These are 20 unknown samples prepared and shipped from the Institute of Tropical Medicine, Antwerp, Belgium, for culture and identification of mycobacteria and drug susceptibility testing (DST). So far, our results are in good concordance with expected results. This is crucial in this era of antimycobacterial drug resistance. In addition, the WHO portfolio will complete the capacity of a resource-limited TB laboratory with smear microscopy, culture, identification, and DST which are the most tests required with regard to laboratory accreditation and clinical trials.

The strengths of our study include the continuous performance over the 11-year period despite the movement of personnel and new tests within the laboratory. Thus, we were able to maintain a standard quality control test for a long period of time, in addition to our regular protocol works.

Our study has some limitations. First, we were not able to perform all the samples received due to laboratory shutdown for certification, but we failed also in identify some samples. Second, this is just smear, culture, and identification, and it will be interesting to have good performance in DST with CAP and WHO.

  Conclusion Top

UCRC BSL-3 mycobacteriology laboratory performed very well over 11-year participation in CAP EQA for smear and culture and must continue as well. This performance is of great importance to maintain high-quality work in diagnosing TB. These results should be used as proof to initiate the accreditation of the laboratory and to initiate clinical trials.


The authors thank the Division of Clinical Research of the National Institute of Health and Allergic Diseases (Bethesda, MD, USA). We are also grateful to Brehima Traore, Dr. Anou M Somboro, Dr. Amadou Somboro, Dr. Mohamed Tolofoudie, Ms. Fanta Sanogo, Ms. Fatimata Diallo, Ms. Mariam H Diallo, Mahamadou Kone, Ms. Mariam Goumane, Ms. Hawa B Drame, Mr. Boureima Degoga, and all SEREFO/UCRC personnel for their help and assistance for the study recruitment and laboratory tests.

Financial support and sponsorship

This work was done at the UCRC of the University of Sciences, Techniques and Technologies of Bamako (USTTB), Mali, and was partially funded by the USTTB through NIH/R01 grant R01AI110386 and NIH/FIC D71 TWO10428-01A1 and the Northwestern University (Chicago, IL, USA) through NIH/FIC D43 TW10350. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names and commercial products, or organizations imply endorsement by the U.S. Government. B.D. was supported by a TDR fellowship, TIMS ID B40072, the special program for research and training in tropical diseases, cosponsored by UNICEF, UNDP, World Bank, and WHO.

Conflicts of interest

There are no conflicts of interest.

  References Top

World Health Organization (WHO), General Information on Quality Control in Clinical Biology and the Proper Use of Probioqual Quality Control Results. Available from: www.probioqual.com. [Last accessed on 2016 Feb 25].  Back to cited text no. 1
Proficiency Testing – College of American Pathologists. Available from: https://www.cap.org/laboratory-improvement/proficiency-testing2. [Last accessed on 2019 Dec 16].  Back to cited text no. 2
World Health Organization. Principles and Procedures of the WHO/NICD External Quality Assessment Program. Available from: http://www.who.int/csr/ ihr/lyon/Policy. [Last accessed on 2016 May 14].  Back to cited text no. 3
World Health Organization (2018). Global Tuberculosis Reports 2018.   Back to cited text no. 4
Alexander KA, Laver PN, Michel AL, Williams M, Helden van PD, Warren RM, et al. Novel Mycobacterium tuberculosis Pathogen Complex, M. mungi. Emerg Infect Dis 2010;16:1296-9.  Back to cited text no. 5
World Health Organization (WHO). Global TB Report 2016. Available from: www.who.int/tb/publications/global report 2016. [Last accessed on 2017 Feb 28].  Back to cited text no. 6
World Health Organization (WHO) Global TB Report 2014. Available from: www.who.int/tb/publications/global report 2014. [Retrieved on 2016 Jun 10].  Back to cited text no. 7
Van Deun A, Portaels F. Limitations and requirements for quality control of sputum smear microscopy for fast-acid bacilli [Planning and Practice]. Int J Tuberc Lung Dis 1998;2:756-65.  Back to cited text no. 8
World Health Organization (WHO)/Tuberculosis. Aide memoire. Available on the website: www.who.int/mediacentre/. [Last accessed: 2017 Feb 28].  Back to cited text no. 9
Dembele SM, Ouedraogo HZ, Combary A, et al. Conversion rate at two-month follow-up of smear-positive tuberculosis patients in Burkina Faso. Int J Tuberc Lung Dis 2007;11:1339-44.  Back to cited text no. 10
Ministry of Health: Quality Plan in Mali. Available from: Globe-network.org/sites/default/files/documents/public/resaolab/plan-qualite-mali. [Last retrieved on 2017 Feb 12].  Back to cited text no. 11
International Union Against Tuberculosis and Lung Disease. Sputum Examination for Tuberculosis by Direct Microscopy in Low Income Countries. 2000; Fifth Edition.  Back to cited text no. 12
Morandi PA. External Quality Evaluation Programs: Retrospective Study of the Evolution of the Quality of the Results of Clinical Biology Analyzes in Three European Countries. University Claude Bernard-Lyon I; 2010. Available from: https://tel.archives-ouvertes.fr/tel-00846678. [Last accessed on 2016 May 14].  Back to cited text no. 13
World Health Organization (WHO) Manual on the Quality Management System at the laboratory. Available at: http://apps.who.int/iris/bitstream/. [Last accessed on 2017 March 02].  Back to cited text no. 14
DINA DOHA. External Quality Assessment in Parasitology – Mycology: State of the Art and Perspectives. Thesis in Pharmacy Rabat. Morocco; 2014. Availble form: http://ao.um5.ac.ma/jspui/handle/123456789/14612. [Last accessed on 2016 Apr 27].  Back to cited text no. 15
Home - College of American Pathologists. Available from: http://www.cap.org/. [Cited 2018 Jul 11]. [Last accessed 2018 Jul 11].   Back to cited text no. 16
Lapointe S. TM: Quality control in medical biology laboratories: The winning conditions: Review of medical technologists. World Health Organization 2011. 2011;1:7-12.  Back to cited text no. 17
Zima T, MD, DSc. Technical Guide for Quality Control Accreditation in Medical Biology COFRAC. J Med Biochem 2017;36:231-7. Published online 2017 Jul 14. doi: 10.1515/jomb-2017-0025 PMCID: PMC6287213.  Back to cited text no. 18
Lewis SM. International System for External Evaluation of Quality in Hematology organized by WHO, Bull World Health Organ 1988;66;435-42.  Back to cited text no. 19
World Health Organization: Preliminary External Evaluation of the Quality of Transfusion Biology Practices. Available at: http://www.who.int/Blood safety/quality/external assessment/. [Last accessed 2016 Apr 11].  Back to cited text no. 20
World Health Organization. Laboratory Biosafety Manual. 3rd ed. Geneva: WHO. Available from: http://www.who.int/csr/resources/ publications/biosafety/en/Biosafety7.pdf. [Last accessed on 2016 May 14].  Back to cited text no. 21
Afnor NF. In ISO 15189: 2012. Laboratories of analysis of medical biology. Requirement concerning quality and competence; 2012.  Back to cited text no. 22
COFRAC, Human Health Section.SH REFO2. Recueil specific requirements for the accreditation of medical biology laboratories according to the NF standard in ISO 15189: 2012. Revision 4. 2013. Available at: http://www.cofrac.fr/documentation/sh.ref.02. [Visited on 2016 Dec 20].  Back to cited text no. 23
Piersimoni C, Scarparo C. Relevance of Commercial Amplification Methods for Direct Detection of Mycobacterium Tuberculosis Complex in Clinical Samples. J Clin Microbiol 2003;41:5355-65.  Back to cited text no. 24
AV Rie, Fitzgerald D, Kabuya G, Deun AV, Tabala M, Jarret N, et al. Sputum Smear Microscopy: Evaluation of Impact of Training, Microscope Distribution, and Use of External Quality Assessment Guidelines for Resource-Poor Settings. J ClinMicrobiol 2008;46:897-901.  Back to cited text no. 25
Ssengooba W, Gelderbloem SJ, Mboowa G, Wajja A, Namaganda C, Musoke P, et al. Feasibility of establishing a tuberculosis biosafety level 3.  Back to cited text no. 26
Diarra B, Safronetz D, Sadio Sarro Y dit, Kone A, Sanogo M, Tounkara S, Antieme C, Togo G, et al. Laboratory Response to 2014 Ebola Virus Outbreak in Mali. S164• JID 2016:214 (Suppl 3). PMID: 27707892.  Back to cited text no. 27
APHL/CDC/IUATLD/KNCV/RIT/WHO: External quality assessment for AFB smears microscopy. Washington, DC: APHL; 2002.  Back to cited text no. 28


  [Figure 1], [Figure 2], [Figure 3]

  [Table 1], [Table 2]


Similar in PUBMED
   Search Pubmed for
   Search in Google Scholar for
 Related articles
Access Statistics
Email Alert *
Add to My List *
* Registration required (free)

  In this article
Materials and Me...
Article Figures
Article Tables

 Article Access Statistics
    PDF Downloaded52    
    Comments [Add]    

Recommend this journal