Development and clinical evaluation of a new multiplex PCR assay for a simultaneous diagnosis of tuberculous and nontuberculous mycobacteria

Yeya dit Sadio Sarro; Matthew A Butzler; Fanta Sanogo; Ousmane Kodio; Mohamed Tolofoudie; Mariam S Goumane; Bocar Baya; Seydou Diabate; Ibrahim Boubacar Diallo; Djakaridja Daniogo; Bindongo PP Dembele; Issiaka Camara; Alisha Kumar; Etienne Dembele; Bourahima Kone; Chad J Achenbach; Grant Theron; Khadidia Ouattara; Yacouba Toloba; Bassirou Diarra; Seydou Doumbia; Babafemi Taiwo; Jane L Holl; Robert L Murphy; Souleymane Diallo; Sally M McFall; Mamoudou Maiga

EBioMedicine (Aug 2021)

Development and clinical evaluation of a new multiplex PCR assay for a simultaneous diagnosis of tuberculous and nontuberculous mycobacteria

Yeya dit Sadio Sarro,
Matthew A Butzler,
Fanta Sanogo,
Ousmane Kodio,
Mohamed Tolofoudie,
Mariam S Goumane,
Bocar Baya,
Seydou Diabate,
Ibrahim Boubacar Diallo,
Djakaridja Daniogo,
Bindongo PP Dembele,
Issiaka Camara,
Alisha Kumar,
Etienne Dembele,
Bourahima Kone,
Chad J Achenbach,
Grant Theron,
Khadidia Ouattara,
Yacouba Toloba,
Bassirou Diarra,
Seydou Doumbia,
Babafemi Taiwo,
Jane L Holl,
Robert L Murphy,
Souleymane Diallo,
Sally M McFall,
Mamoudou Maiga

Affiliations

Yeya dit Sadio Sarro: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Matthew A Butzler: Northwestern University, Chicago, Illinois, USA
Fanta Sanogo: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Ousmane Kodio: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Mohamed Tolofoudie: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Mariam S Goumane: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Bocar Baya: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Seydou Diabate: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Ibrahim Boubacar Diallo: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Djakaridja Daniogo: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Bindongo PP Dembele: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Issiaka Camara: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Alisha Kumar: Northwestern University, Chicago, Illinois, USA
Etienne Dembele: Northwestern University, Chicago, Illinois, USA
Bourahima Kone: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Chad J Achenbach: Northwestern University, Chicago, Illinois, USA
Grant Theron: Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
Khadidia Ouattara: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Yacouba Toloba: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Bassirou Diarra: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Seydou Doumbia: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Babafemi Taiwo: Northwestern University, Chicago, Illinois, USA
Jane L Holl: University of Chicago, Chicago, Illinois, USA
Robert L Murphy: Northwestern University, Chicago, Illinois, USA
Souleymane Diallo: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
Sally M McFall: Northwestern University, Chicago, Illinois, USA; Corresponding authors at: University of Sciences, Techniques and Technologies of Bamako (USTTB), 2145 Sheridan Rd., Tech Institute E-310, Evanston, IL, 60208, USA.
Mamoudou Maiga: University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali; Northwestern University, Chicago, Illinois, USA; Corresponding authors at: University of Sciences, Techniques and Technologies of Bamako (USTTB), 2145 Sheridan Rd., Tech Institute E-310, Evanston, IL, 60208, USA.

Journal volume & issue: Vol. 70
p. 103527

Abstract

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Background: The prevalence of non-tuberculous mycobacteria (NTM) has been increasing worldwide in both developed and developing countries. NTM infection is clinically indistinguishable from tuberculosis and therefore poses significant challenges in patient management, especially in patients chronically treated for pulmonary TB. In this study, we evaluated a new highly sensitive Multiplex MTB/NTM assay that can differentiate M. tuberculosis complex (MTBC) from all NTM, including the treatable and most common NTM, M. avium complex (MAC). Methods: We developed and optimized a new open- Multiplex MTB/NTM assay with two gene-targets for MTBC (IS6110/senX3-regX3) and two targets for MAC (IS1311/DT1) with samples spiked with stored strains and testing 20 replicates. Patients with presumptive TB and NTM were enrolled at the Respiratory Disease Department of The University Teaching Hospital of Point G, in Mali. Findings: In the development stage, the new assay showed a high analytic performance with 100% detections of MTBC and MAC at only 5 colony forming units (CFUs). Overall, without the treatment failure cases, the Multiplex assay and the Xpert showed a sensitivity, specificity, PPV and NPV of 83·3% [66·4-92·6], 96·6% [88·6-99·0], 92·5% [82·3-96·5] and 92·2% [82·7-96·5] and the Xpert had values of 96·7% [83·3-99·4], 80·0% [68·2-88·1], 70·7 [55·5-82·3] and 97·9% [89·3-99·6], respectively. The Multiplex assay successfully detected all (5/5) the MAC cases. Interpretation: Our new Multiplex assay demonstrates better specificity than Xpert for all group studied, in addition to detecting potential NTM cases. The assay could therefore complement the widely used Xpert assay and enhance discrimination of TB and NTM infections. Funding: This work was supported by the National Institutes of Health (R03AI137674, U54EB027049, D43TW010350 and UM1AI069471) and Northwestern University's Institute for Global Health Catalyzer Fund.

Published in EBioMedicine

ISSN: 2352-3964 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Medicine: Medicine (General)
Website: http://www.journals.elsevier.com/ebiomedicine/

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