Feasibility, Ease-of-Use, and Operational Characteristics of World Health Organization–Recommended Moderate-Complexity Automated Nucleic Acid Amplification Tests for the Detection of Tuberculosis and Resistance to Rifampicin and Isoniazid

Abstract

Four moderate-complexity automated nucleic acid amplification tests for the diagnosis of tuberculosis are reported as having laboratory analytical and clinical performance similar to that of the Cepheid Xpert MTB/RIF assay. These assays are the Abbott RealTime MTB and RealTime MTB RIF/INH Resistance, Becton Dickinson MAX MDR-TB, the Hain Lifescience/Bruker FluoroType MTBDR, and the Roche cobas MTB and MTB RIF/INH assays. The study compared feasibility, ease of use, and operational characteristics of these assays/platforms. Manufacturer input was obtained for technical characteristics. Laboratory operators were requested to complete a questionnaire on the assays’ ease of use. A time-in-motion analysis was also undertaken for each platform. For ease-of-use and operational requirements, the BD MAX MDR-TB assay achieved the highest scores (86% and 90%) based on information provided by the user and manufacturer, respectively, followed by the cobas MTB and MTB-RIF/INH assay (68% and 86%), the FluoroType MTBDR assay (67% and 80%), and the Abbott RT-MTB and RT MTB RIF/INH assays (64% and 76%). The time-in-motion analysis revealed that for 94 specimens, the RealTime MTB assay required the longest processing time, followed by the cobas MTB assay and the FluoroType MTBDR assay. The BD MAX MDR-TB assay required 4.6 hours for 22 specimens. These diagnostic assays exhibited different strengths and weaknesses that should be taken into account, in addition to affordability, when considering placement of a new platform. Four moderate-complexity automated nucleic acid amplification tests for the diagnosis of tuberculosis are reported as having laboratory analytical and clinical performance similar to that of the Cepheid Xpert MTB/RIF assay. These assays are the Abbott RealTime MTB and RealTime MTB RIF/INH Resistance, Becton Dickinson MAX MDR-TB, the Hain Lifescience/Bruker FluoroType MTBDR, and the Roche cobas MTB and MTB RIF/INH assays. The study compared feasibility, ease of use, and operational characteristics of these assays/platforms. Manufacturer input was obtained for technical characteristics. Laboratory operators were requested to complete a questionnaire on the assays’ ease of use. A time-in-motion analysis was also undertaken for each platform. For ease-of-use and operational requirements, the BD MAX MDR-TB assay achieved the highest scores (86% and 90%) based on information provided by the user and manufacturer, respectively, followed by the cobas MTB and MTB-RIF/INH assay (68% and 86%), the FluoroType MTBDR assay (67% and 80%), and the Abbott RT-MTB and RT MTB RIF/INH assays (64% and 76%). The time-in-motion analysis revealed that for 94 specimens, the RealTime MTB assay required the longest processing time, followed by the cobas MTB assay and the FluoroType MTBDR assay. The BD MAX MDR-TB assay required 4.6 hours for 22 specimens. These diagnostic assays exhibited different strengths and weaknesses that should be taken into account, in addition to affordability, when considering placement of a new platform. Despite significant progress in the fight against tuberculosis (TB), the disease remains one of the top 10 causes of death worldwide and second only to coronavirus disease 2019 as a leading cause of death from a single infectious agent, ranking above HIV/AIDS.1World Health Organization. Global tuberculosis report 2021. WHO, Geneva, Switzerland2021https://www.who.int/publications/i/item/9789240037021Date accessed: April 7, 2022Google Scholar The most recent threat to the TB cascade of care is the coronavirus disease 2019 pandemic, which re-directed resources, resulting in an approximately 18% decline in the number of patients newly diagnosed with TB and reported compared with 2019.1World Health Organization. Global tuberculosis report 2021. WHO, Geneva, Switzerland2021https://www.who.int/publications/i/item/9789240037021Date accessed: April 7, 2022Google Scholar Of the other gaps and weaknesses identified in the management of TB,2Subbaraman R. Nathavitharana R.R. Mayer K.H. Satyanarayana S. Chadha V.K. Arinaminpathy N. Pai M. Constructing care cascades for active tuberculosis: a strategy for program monitoring and identifying gaps in quality of care.PLoS Med. 2019; 16: e1002754Crossref PubMed Scopus (90) Google Scholar one of the biggest challenges remains the lack of diagnostic and drug resistance detection tools appropriate for different laboratory settings. The introduction of the Xpert MTB/RIF (Xpert) (Cepheid, Sunnyvale, CA), Xpert MTB/RIF Ultra (Xpert Ultra), and the Truenat MTB, MTB Plus, and MTB-RIF Dx assays (Molbio Diagnostics, Goa, India), and their subsequent endorsement by the World Health Organization (WHO, https://www.who.int/news/item/08-12-2010-who-endorses-new-rapid-tuberculosis-test, last accessed April 7, 2022; WHO, https://www.who.int/news/item/25-03-2017-next-generation-xpert-mtb-rif-ultra-assay-recommended-by-who, last accessed April 7, 2022; and FIND, https://www.finddx.org/newsroom/pr-02jul20, last accessed August 1, 2022), represented a substantial improvement in the rapid diagnosis of TB; however, these assays are limited by only providing a rifampicin (Rif) resistance profile. Rif resistance has been considered a reliable indicator of multidrug-resistant TB (MDR-TB) since the WHO estimated that in 2014, only 1.1% of patients with TB worldwide had Rif mono-resistance.3World Health Organization. Global tuberculosis report 2015. Geneva, Switzerland: WHO, 2015. Available at: https://apps.who.int/iris/handle/10665/191102 (accessed April 7, 2022).Google Scholar However, in the last few years, there has been increasing evidence that Rif-resistant TB may not be a reliable predictive marker of MDR-TB, especially in countries where higher rates of Rif mono-resistance are being reported.4Liu Z. Dong H. Wu B. Zhang M. Zhu Y. Pang Y. Wang X. Is rifampin resistance a reliable predictive marker of multidrug-resistant tuberculosis in China: a meta-analysis of findings.J Infect. 2019; 79: 349-356Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar,5Mvelase N.R. Balakrishna Y. Lutchminarain K. Mlisana K. Evolving rifampicin and isoniazid mono-resistance in a high multidrug-resistant and extensively drug-resistant tuberculosis region: a retrospective data analysis.BMJ Open. 2019; 9: e031663Crossref PubMed Scopus (8) Google Scholar The new Xpert MTB/XDR (Cepheid) assay may mitigate this limitation because the assay offers isoniazid (INH) resistance detection in addition to the second-line injectable drugs and fluoroquinolones.6Chakravorty S. Roh S.S. Glass J. Smith L.E. Simmons A.S. Lund K. Lokhov S. Liu X. Xu P. Zhang G. Via L.E. Shen Q. Ruan X. Yuan X. Zhu Zhu H. Viazovkina E. Shenai S. Rowneki M. Lee J.S. Barry C.E.I.I.I. Gao Q. Persing D. Kwiatkawoski R. Jones M. Gall A. Alland D. Detection of isoniazid-, fluoroquinolone-, amikacin-, and kanamycin-resistant tuberculosis in an automated, multiplexed 10-color assay suitable for point-of-care use.J Clin Microbiol. 2016; 55: 183-198Crossref PubMed Scopus (36) Google Scholar,7Penn-Nicholson A. Georghiou S. Ciobanu N. Kazi M. Bhalla M. David A. Conradie F. Ruhwald M. Crudu V. Rodrigues C. Myneedu V.P. Scott L. Denkinger C.M. Schumacher S.G. Xpert XDR Trial ConsortiumDetection of isoniazid, fluoroquinolone, ethionamide, amikacin, kanamycin, and capreomycin resistance by the Xpert MTB/XDR assay: a cross-sectional multicentre diagnostic accuracy study.Lancet Infect Dis. 2022; 22: 242-249Abstract Full Text Full Text PDF PubMed Scopus (38) Google Scholar However, the lack of Rif and INH resistance detection on a single cartridge is still a disadvantage. The RealTime MTB (RT-MTB) and RealTime MTB RIF/INH Resistance (RT MTB RIF/INH) assays (Abbott Molecular, Des Plaines, IL),8Berhanu R.H. David A. da Silva P. Shearer K. Sanne I. Stevens W. Scott L. Performance of Xpert MTB/RIF, Xpert Ultra, and Abbott RealTime MTB for the diagnosis of pulmonary tuberculosis in a high-HIV-burden setting.J Clin Microbiol. 2018; 56: e00560-18Crossref PubMed Scopus (40) Google Scholar BD MAX MDR-TB assay (Becton, Dickinson and Company, Sparks, MD),9Shah M. Paradis S. Betz J. Beylis N. Bharadwaj R. Caceres T. Gotuzzo E. Joloba M. Mave V. Nakiyingi L. Nicol M.P. Pradhan N. King B. Armstrong D. Knecht D. Maus C.E. Cooper C.K. Dorman S.E. Manabe Y.C. Multicenter study of the accuracy of the BD MAX multidrug-resistant tuberculosis assay for detection of Mycobacterium tuberculosis complex and mutations associated with resistance to rifampin and isoniazid.Clin Infect Dis. 2019; 71: 1161-1167Crossref Scopus (28) Google Scholar FluoroType MTBDR (FluoroType) assay (Hain Lifescience/Bruker, Nehren, Germany),10de Vos M. Derendinger B. Dolby T. Simpson J. van Helden P.D. Rice J.E. Wangh L.J. Theron G. Warren R.M. Diagnostic accuracy and utility of FluoroType MTBDR, a new molecular assay for multidrug-resistant tuberculosis.J Clin Microbiol. 2018; 56: e00531-18Crossref PubMed Scopus (32) Google Scholar and cobas MTB and MTB RIF/INH assays (Roche, Basel, Switzerland)11Scott L. David A. Govender L. Furrer J. Rakgokong M. Waja Z. Martinson N. Eisenberg G. Marlowe E. Stevens W. Performance of the Roche cobas MTB assay for the molecular diagnosis of pulmonary tuberculosis in a high HIV burden setting.J Mol Diagn. 2020; 22: 1225-1237Abstract Full Text Full Text PDF PubMed Scopus (8) Google Scholar are therefore attractive options offering Mycobacterium tuberculosis complex (MTBC) detection, as well as Rif and INH resistance detection, on a single sputum specimen. An evaluation of these assays involving a laboratory analytical head-to-head comparison12World Health Organization. Accuracy of centralized assays for TB detection and detection of resistance to rifampicin and isoniazid: WHO Technical Expert Consultation Report. WHO, Geneva, Switzerland2019https://apps.who.int/iris/bitstream/handle/10665/329388/WHO-CDS-TB-2019.14-eng.pdf?ua=1Date accessed: April 7, 2022Google Scholar revealed comparable performance of the assays with the Xpert assay for MTBC detection, and with the GenoType MTBDRplus assay (Hain Lifescience/Bruker) for Rif and INH resistance detection. Similar clinical performance was reported in a meta-review performed by Kohli et al.13Kohli M. MacLean E. Pai M. Schumacher S. Denkinger C. Diagnostic accuracy of centralised assays for TB detection and detection of resistance to rifampicin and isoniazid: a systematic review and meta-analysis.Eur Respir J. 2021; 4: 2000747Crossref Scopus (11) Google Scholar These moderate-complexity automated nucleic acid amplification tests have also been endorsed by the WHO for MTBC and resistance detection (Rif and INH) on respiratory samples.14World Health Organization. WHO consolidated guidelines on tuberculosis: module 3: diagnosis, rapid diagnostics for tuberculosis detection. WHO, Geneva, Switzerland2021https://www.who.int/publications/i/item/9789240029415Date accessed: April 9, 2022Google Scholar In addition to assay workflow, several considerations need to be taken into account for laboratory placement. These include: power and space requirements, training and competency, specimen type (raw sputum, sputum pellet, and extrapulmonary specimens), maintenance, quality control and quality assessment, waste disposal, calibration (operator and manufacturer), in-country support, and connectivity (laboratory information systems). To assess these considerations, in addition to the performance data reported,15de Vos M. Scott L. David A. Trollip A. Hoffmann H. Georghiou S.B. Carmona S. Ruhwald M. Stevens W. Denkinger C.M. Schumacher S.G. Comparative analytical evaluation of four centralized platforms for the detection of Mycobacterium tuberculosis complex and resistance to rifampicin and isoniazid.J Clin Microbiol. 2021; 59: e02168-20Crossref PubMed Scopus (11) Google Scholar the feasibility, ease of use, and operational characteristics of these centralized molecular platforms are reported. For the study, retrospectively collected TB-negative sputum was pooled and homogenized and provided frozen to the study site in 10 mL aliquots. The sputum was spiked with two inactivated, well-characterized MTBC strains in defined stock concentrations (5 × 107 genomes/mL) for the study. These included a high number MTBC and a number Mycobacterium were in a were not provided by the manufacturer, the sputum was as a and Diagnostics, was as a control The feasibility, ease of use, and operational evaluation was performed in the clinical laboratory of the of and of the on each was performed as and and is in was provided by from each of the was as and provided study A questionnaire on technical of the assay was provided to each on the specimen and were by technical for each and by a on information each was a of to be the assays and a of to be and scores were for each study each was requested to complete a for each BD MAX BD Hain Lifescience/Bruker and amplification and detection and Roche cobas A was for each to their of with each and The was performed by two operators for each and an was for each An for each was In a time-in-motion analysis was performed for each platform. operational specimen and and and and of specimens), were that should be were the study. on the the for and the for detection and was and an was For this study, the was the provided by the the and are from The required that be to the and and the addition of an control in the amplification to the the of was not to the the on the the as an and of the the was MTBC was and be for resistance the an specimen on the the was to the specimen to the on the specimen and the a processing that not processing and the on the For the and causes and the most be in the which was on the and However, the the to the was and had to be from the from the were to the a of training was required on the BD MAX and an was two to For each specimen required and amplification the and were included in the was The and for the assay had to be into the which approximately The the specimen as well as the was into the the the BD MAX control was provided by For to were on a single two were required for a of specimens. MTBC detection and resistance and were performed the nucleic acid and amplification was for a of specimens, the of be for processing on the an the cause of the was on the and be the were in of an on the of the for a of four had to be a was a the processing of the for the specimens. of the and platforms required of and an was to the control was provided in the amplification required for nucleic acid were provided in and had to be in appropriate to to on the platform. The the required for the number of to be were provided in a for which required the addition of an control in the amplification an on the the the the and the to the be from the were to the a on the platform. The also had the of a the had Hain Lifescience/Bruker was the only that an of waste to of the approximately hours because and were and with and from a The of the was as The cobas MTB and MTB RIF/INH assays required for training the cobas and an was to four The was the most complex of assays the for and for and above the are from an was with the specimen the the specimen was from the which the to the to to The was by the the had been to the for had to be resistance Rif and INH) was information was not provided in the and the had to be each the an a processing on the cobas the had to be be required a Roche to The was not provided by an in-country 94 and two and are in a acid are provided in of and amplification are provided in of were were and not in amplification be for of (RT MTB to RT MTB RIF/INH to second use, the being by of the by the was the and platforms as the amplification had to be to the and was on the was was The RT assay reported on the of resistance a in the was in the a in the was in the for INH this was in addition to the in the of an the that the was not in the of a Rif-resistant The the to a and of the the a calibration by the to being the of the a to be to the is a 22 and two and are in a tests were on a cartridge be on subsequent 10 was was The BD MAX MDR-TB report a Rif and INH resistance information on the was The the waste and of four platforms and a and calibration by the Hain Lifescience/Bruker was the only that provided and for training and The was the only by an and the training 94 and two and are in a was was the of not be to the laboratory information The report the Rif and INH and the by the the and an and the also calibration by the 94 and two and are in a a of be in a approximately to 94 specimens. The report for Rif and INH information on the was The the to be performed on on that the had to that the specimen had been the The for of to of the specimen was the most for for the cobas assays The a on the the cobas was also reported to have the most is an and a may not the similar The an and calibration by the The BD MAX MDR-TB assay achieved the highest for each and based on information provided by the The Abbott RT-MTB and RT MTB RIF/INH assays achieved the scores to associated with specimen and of on by the specimen type 1, sputum and mL may be frozen and to processing is similar for different specimen specimen be for is required in is to may be performed are required for the assay not need to be the each drug assay not and TB drug not need to be provided by user not from a be the Abbott this to the a single space and is performed by a for and is performed are provided in and only on is only the is for of of the user not need to a user not need to data connectivity is for technical is in be a laboratory are required to are required to calibration is performed by the calibration is provided by the is for assays be on the and is provided is training is provided only are to of was the being was and a of was for a Becton laboratory information power For the Abbott this to the in a new A of was the being was and a of was for a Becton laboratory information power A is to the by the The the to most provided by the The BD MAX MDR-TB was the most of the four with the Abbott being the as by MTB and MTB on the and of on the of the on the of the of report and the specimen is an from of specimen the for is an from to of of and of the the of of the user of of the of of for a specimen of a specimen of of is an from of and of of of of is an from of the in the is an from of the of and for of is an from and of and was to assess the for each as and 1, not The is an from The is an from to The is an from in a new A was to assess the for each as and 1, not assays required similar processing with in the the and for each were and are in The Abbott RT-MTB assay required approximately hours for 94 specimens, with an hours required for resistance The BD MAX MDR-TB assay required 4.6 hours for processing 22 specimens. In of to 94 specimens, the Roche cobas MTB and MTB RIF/INH required the Hain Lifescience/Bruker FluoroType MTBDR required and the Abbott RT MTB and RT MTB RIF/INH assays required The to 22 on the BD MAX MDR-TB required diagnosis of TB and the detection of drug resistance are in of tests that be in care are the in the the diagnostic has the Cepheid and several molecular assays for in have been and have been by the Health Organization. WHO consolidated guidelines on tuberculosis: module 3: diagnosis, rapid diagnostics for tuberculosis detection. WHO, Geneva, Switzerland2021https://www.who.int/publications/i/item/9789240029415Date accessed: April 9, 2022Google Vos M. Scott L. David A. Trollip A. Hoffmann H. Georghiou S.B. Carmona S. Ruhwald M. Stevens W. Denkinger C.M. Schumacher S.G. Comparative analytical evaluation of four centralized platforms for the detection of Mycobacterium tuberculosis complex and resistance to rifampicin and isoniazid.J Clin Microbiol. 2021; 59: e02168-20Crossref PubMed Scopus (11) Google Scholar the of the placement of these platforms the of point-of-care to the and cobas platforms are to a The BD MAX to be the of a In of compared with the Xpert MTB/RIF spiked sputum, the Abbott RT MTB, BD MAX MDR-TB, and Roche cobas MTB assays analytical the Hain Lifescience/Bruker FluoroType assay a analytical Vos M. Scott L. David A. Trollip A. Hoffmann H. Georghiou S.B. Carmona S. Ruhwald M. Stevens W. Denkinger C.M. Schumacher S.G. Comparative analytical evaluation of four centralized platforms for the detection of Mycobacterium tuberculosis complex and resistance to rifampicin and isoniazid.J Clin Microbiol. 2021; 59: e02168-20Crossref PubMed Scopus (11) Google Scholar four assays accuracy comparable to that of the GenoType MTBDRplus assay for the detection of Rif and INH Vos M. Scott L. David A. Trollip A. Hoffmann H. Georghiou S.B. Carmona S. Ruhwald M. Stevens W. Denkinger C.M. Schumacher S.G. Comparative analytical evaluation of four centralized platforms for the detection of Mycobacterium tuberculosis complex and resistance to rifampicin and isoniazid.J Clin Microbiol. 2021; 59: e02168-20Crossref PubMed Scopus (11) Google Scholar study a head-to-head on feasibility, ease of use, and operational characteristics of the four new TB diagnostic the platforms each has and which are in the The required for the cobas assays is a the to the of the CA), this is the for operators a for specimen The of may processing however, for the of this study, only one was An of the cobas is that of approximately the need to each For resistance the specimen be provided that is The BD and the cobas assays the of the being performed on a single platform. The BD assay is also because and required for are the with the of the the and However, have to be for the BD which to the The cobas is the only one in which has to be resistance is which have and in with a high of For the Abbott a single be The BD and FluoroType assays MTBC and resistance in the which is an in with a high of The Abbott assays are the only assays in which may a number of is not as is not the However, this not a for of the Abbott has an The of the cobas into a number of being in a of on the cobas and on the cobas in an The of this have been reported by et G. S. E. A. molecular diagnostic of the to Mol Diagn. 2019; PubMed Scopus Google Scholar The cobas is the only that other to a specimen is being However, the cobas has the longest of the The BD MAX a to be specimen the of in a and a second of to with nucleic acid the is being These the an attractive for MDR-TB diagnosis, the of the is only 22 specimens, compared with the other which 94 The FluoroType assay has the processing the and the a to be the has which is a The Abbott assays have the longest processing of the platforms the to is that four platforms are of and of assays be performed on the Health Organization. diagnostic for the management of TB and other Geneva, accessed: April 9, 2022Google Scholar The cobas platforms the space and have requirements, which are The BD MAX achieved the most scores for ease of and operational because of BD MAX platforms be in a single this have of the FluoroType assay are that an of is which has space and and is of to the amplification to the waste by the disposal, which has is which is an for in a The Abbott and platforms be in the which a to with space is and of an calibration is required for calibration of the The cobas and BD assays not information on the mutations on the FluoroType provided the most information compared with the other For the Abbott of a which is not for on the a is an is required to the For Rif the of a from the is reported of an The number of that on platforms was for the cobas which a high number of was to the required to by the was reported to be the most complex on this platform. In addition to performance and as the ease of use, operational requirements, assay and of the assay and are when is being study that each has strengths and laboratory therefore a in the placement of a centralized molecular for MTBC and resistance

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