1
|
Tafess K, Ng TTL, Tam KKG, Leung KSS, Leung JSL, Lee LK, Lao HY, Chan CTM, Yam WC, Wong SSY, Lau TCK, Siu GKH. Genetic mechanisms of co-emergence of INH-resistant Mycobacterium tuberculosis strains during the standard course of antituberculosis therapy. Microbiol Spectr 2024; 12:e0213323. [PMID: 38466098 PMCID: PMC10986572 DOI: 10.1128/spectrum.02133-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
The incidence of isoniazid (INH) resistant Mycobacterium tuberculosis is increasing globally. This study aimed to identify the molecular mechanisms behind the development of INH resistance in M. tuberculosis strains collected from the same patients during the standard course of treatment. Three M. tuberculosis strains were collected from a patient before and during antituberculosis (anti-TB) therapy. The strains were characterized using phenotypic drug susceptibility tests, Mycobacterial Interspersed Repeated Unit-Variable-Number Tandem Repeats (MIRU-VNTR), and whole-genome sequencing (WGS) to identify mutations associated with INH resistance. To validate the role of the novel mutations in INH resistance, the mutated katG genes were electroporated into a KatG-deleted M. tuberculosis strain (GA03). Three-dimensional structures of mutated KatG were modeled to predict their impact on INH binding. The pre-treatment strain was susceptible to INH. However, two INH-resistant strains were isolated from the patient after anti-TB therapy. MIRU-VNTR and WGS revealed that the three strains were clonally identical. A missense mutation (P232L) and a nonsense mutation (Q461Stop) were identified in the katG of the two post-treatment strains, respectively. Transformation experiments showed that katG of the pre-treatment strain restored INH susceptibility in GA03, whereas the mutated katG genes from the post-treatment strains rendered negative catalase activity and INH resistance. The protein model indicated that P232L reduced INH-KatG binding affinity while Q461Stop truncated gene transcription. Our results showed that the two katG mutations, P232L and Q461Stop, accounted for the co-emergence of INH-resistant clones during anti-TB therapy. The inclusion of these mutations in the design of molecular assays could increase the diagnostic performance.IMPORTANCEThe evolution of drug-resistant strains of Mycobacterium tuberculosis within the lung lesions of a patient has a detrimental impact on treatment outcomes. This is particularly concerning for isoniazid (INH), which is the most potent first-line antimycobacterial drug. However, the precise genetic factors responsible for drug resistance in patients have not been fully elucidated, with approximately 15% of INH-resistant strains harboring unknown genetic factors. This raises concerns about the emergence of drug-resistant clones within patients, further contributing to the global epidemic of resistance. In this study, we revealed the presence of two novel katG mutations, which emerged independently due to the stress exerted by antituberculosis (anti-TB) treatment on a parental strain. Importantly, we experimentally demonstrated the functional significance of both mutations in conferring resistance to INH. Overall, this research sheds light on the genetic mechanisms underlying the evolution of INH resistance within patients and provides valuable insights for improving diagnostic performance by targeting specific mutations.
Collapse
Affiliation(s)
- Ketema Tafess
- Department of Applied Biology, School of Applied Natural Sciences, Adama Science and Technology University, Adama, Ethiopia
- Institute of Pharmaceutical Sciences, Adama Science and Technology University, Adama, Ethiopia
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kenneth Siu-Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Samson Sai Yin Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Terrence Chi-Kwong Lau
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| |
Collapse
|
2
|
Wang Z, Tang Z, Heidari H, Molaeipour L, Ghanavati R, Kazemian H, Koohsar F, Kouhsari E. Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis. J Chemother 2023; 35:583-595. [PMID: 37211822 DOI: 10.1080/1120009x.2023.2214473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.
Collapse
Affiliation(s)
- Zheming Wang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Zhihua Tang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | | | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Koohsar
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
| |
Collapse
|
3
|
Li R, Li Y, Chen X, Jia L, Yu H, Huang Y, Wu Q, Xiao M, Ge S, Zhang Y, Feng Z, Li Q, Xu Y, Shi W, Sun F, Zhang W. Ability of the MeltPro MTB/PZA Assay to Detect Susceptibility to Pyrazinamide in Rifampin-Resistant Tuberculosis Patients. Microbiol Spectr 2023; 11:e0483622. [PMID: 37162355 PMCID: PMC10269598 DOI: 10.1128/spectrum.04836-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023] Open
Abstract
Prediction of susceptibility to pyrazinamide (PZA) directly from sputum has been challenging. The MeltPro MTB/PZA assay, based on melting curve analysis, can simultaneously detect Mycobacterium tuberculosis and the resistance to PZA from sputum. We aimed to evaluate the MeltPro MTB/PZA assay to predict PZA resistance among rifampin-resistant tuberculosis (RR-TB) patients. We prospectively enrolled RR-TB patients in the registered trials, and their baseline sputum samples were obtained to perform the assay and culture. DNA sequencing of culture isolates was analyzed and used as the reference standard. Sanger sequencing was performed for samples with discrepant results between next-generation sequencing (NGS) and the investigational assay. The main analysis was conducted in the population of patients with interpretable results by both NGS and the assay. A total of 239 patients with RR-TB were screened, and 220 underwent the MeltPro MTB/PZA assay. The assay provided no information for 25 of 220 patients (11.4%). Among the remaining 195 patients, 13 had negative culture or insufficient raw NGS sequencing data, and 15 had indeterminate assay results. A total of 167 patients were included in the main analysis. Against DNA sequencing, the sensitivity, specificity, and negative predictive value of the assay for detecting resistance to PZA were 91.4% (95% confidence interval [CI], 87.1% to 95.6%), 89.9% (95% CI, 85.3% to 94.5%), and 95.2% (95% CI, 91.9% to 98.4%), respectively. In conclusion, the MeltPro MTB/PZA assay is a fast semiautomatic molecular platform to rapidly predict resistance to PZA from sputum and holds promise as a screening tool with satisfactory sensitivity. IMPORTANCE This study evaluated the accuracy of the MeltPro MTB/PZA assay at detecting the presence of PZA resistance through registered clinical trials. Compared to DNA sequencing, the assay had high sensitivity and negative predictive value, suggesting its potential utility as a screening tool in clinical practice. The assay could serve as an ideal primary screening tool in low PZA-resistant M. tuberculosis prevalence settings and could be used as an additional test to identify PZA resistance rapidly and initially in the RR-TB population.
Collapse
Affiliation(s)
- Rong Li
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinchang Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Lina Jia
- Department of Tuberculosis, Guiyang Public Health Clinical Center, Guiyang, China
| | - Hongying Yu
- Center for Infectious Diseases, The First People’s Hospital of Huaihua, Huaihua, Hunan, China
| | - Ya Huang
- Department of Tuberculosis, Ge Jiu Infectious Disease Hospital, Gejiu, China
| | - Qianhong Wu
- Department of Tuberculosis, Shaanxi Provincial Tuberculosis Prevention and Control Hospital, Xi’an, Shannxi, China
| | - Mingying Xiao
- Department of Tuberculosis, Baoshan People’s Hospital, Baoshan, China
| | - Shijia Ge
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yilin Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen Feng
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wenzhi Shi
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Feng Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
| |
Collapse
|
4
|
Modlin SJ, Mansjö M, Werngren J, Ejike CM, Hoffner SE, Valafar F. Pyrazinamide-resistant Tuberculosis Obscured From Common Targeted Molecular Diagnostics. Drug Resist Updat 2023; 68:100959. [PMID: 37043916 DOI: 10.1016/j.drup.2023.100959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/10/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023]
Abstract
Here, we describe a clinical case of pyrazinamide-resistant (PZA-R) tuberculosis (TB) reported as PZA-susceptible (PZA-S) by common molecular diagnostics. Phenotypic susceptibility testing (pDST) indicated PZA-R TB. Targeted Sanger sequencing reported wild-type PncA, indicating PZA-S TB. Whole Genome Sequencing (WGS) by PacBio and IonTorrent both detected deletion of a large portion of pncA, indicating PZA-R. Importantly, both WGS methods showed deletion of part of the primer region targeted by Sanger sequencing. Repeating Sanger sequencing from a culture in presence of PZA returned no result, revealing that 1) two minority susceptible subpopulations had vanished, 2) the PZA-R majority subpopulation harboring the pncA deletion could not be amplified by Sanger primers, and was thus obscured by amplification process. This case demonstrates how a small susceptible subpopulation can entirely obscure majority resistant populations from targeted molecular diagnostics and falsely imply homogenous susceptibility, leading to incorrect diagnosis. To our knowledge, this is the first report of a minority susceptible subpopulation masking a majority resistant population, causing targeted molecular diagnostics to call false susceptibility. The consequence of such genomic events is not limited to PZA. This phenomenon can impact molecular diagnostics' sensitivity whenever the resistance-conferring mutation is not fully within primer-targeted regions. This can be caused by structural changes of genomic context with phenotypic consequence as we report here, or by uncommon mechanisms of resistance. Such false susceptibility calls promote suboptimal treatment and spread of strains that challenge targeted molecular diagnostics. This motivates development of molecular diagnostics unreliant on primer conservation, and impels frequent WGS surveillance for variants that evade prevailing molecular diagnostics.
Collapse
|
5
|
Wu MH, Hsiao HC, Chu PW, Chan HH, Lo HY, Jou R. Surveillance of multidrug-resistant tuberculosis in Taiwan, 2008-2019. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2023; 56:120-129. [PMID: 35995668 DOI: 10.1016/j.jmii.2022.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Drug-resistant tuberculosis (DR-TB) is a major contributor to global cases of antimicrobial resistance and remains a public health challenge. To understand the extent and trend of DR-TB under an enhanced multidrug-resistant TB (MDR-TB) management program, we conducted a population-based retrospective study of 1511 Taiwanese MDR-TB cases reported from 2008 to 2019. METHODS We obtained patient demographics and clinical and bacteriological information from the National TB Registry and the Infectious Disease Notification System. RESULTS Of the 1511 MDR-TB patients, 941 were new cases, 485 were previously treated, and 85 had an unknown history of treatment. The male to female ratio was 2.75, and the median age of the patients was 57 years (IQR: 45-72). We observed a significant decline in MDR-TB cases, with annual percentage change (APC) of -4.17%. However, new and previously treated MDR-TB cases had APCs of -1.41% and -9.18%, respectively. The rates of MDR-TB resistance to ethambutol, streptomycin and pyrazinamide were 47.2%, 42.4% and 28.9%, respectively, whereas the rates of resistance to fluoroquinolones and second-line injectable drugs (SLIDs) were 4.1-7.1%, 9.0-14.1%; and the rate of extensively drug-resistant TB was 1.9%, respectively. Furthermore, we observed a decreasing trend of resistance to SLIDs (APCs -7.0% to -8.2%) in new cases and a significant decreasing trend of resistance to moxifloxacin (-24.6%) and levofloxacin (-23.3%) in previously treated cases. CONCLUSION The decreasing trend of MDR-TB and resistance to second-line drugs suggested that our programmatic management of TB was effective and that the impact on TB control was profound.
Collapse
Affiliation(s)
- Mei-Hua Wu
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare Taipei, Taiwan; Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare Taipei, Taiwan; Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Po-Wei Chu
- Chronic Infectious Disease Division, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hsin-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare Taipei, Taiwan; Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hsiu-Yun Lo
- Chronic Infectious Disease Division, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare Taipei, Taiwan; Reference Laboratory of Mycobacteriology, Taiwan Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan; Institute of Microbiology and Immunology, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| |
Collapse
|
6
|
Dookie N, Ngema SL, Perumal R, Naicker N, Padayatchi N, Naidoo K. The Changing Paradigm of Drug-Resistant Tuberculosis Treatment: Successes, Pitfalls, and Future Perspectives. Clin Microbiol Rev 2022; 35:e0018019. [PMID: 36200885 PMCID: PMC9769521 DOI: 10.1128/cmr.00180-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) remains a global crisis due to the increasing incidence of drug-resistant forms of the disease, gaps in detection and prevention, models of care, and limited treatment options. The DR-TB treatment landscape has evolved over the last 10 years. Recent developments include the remarkable activity demonstrated by the newly approved anti-TB drugs bedaquiline and pretomanid against Mycobacterium tuberculosis. Hence, treatment of DR-TB has drastically evolved with the introduction of the short-course regimen for multidrug-resistant TB (MDR-TB), transitioning to injection-free regimens and the approval of the 6-month short regimens for rifampin-resistant TB and MDR-TB. Moreover, numerous clinical trials are under way with the aim to reduce pill burden and shorten the DR-TB treatment duration. While there have been apparent successes in the field, some challenges remain. These include the ongoing inclusion of high-dose isoniazid in DR-TB regimens despite a lack of evidence for its efficacy and the inclusion of ethambutol and pyrazinamide in the standard short regimen despite known high levels of background resistance to both drugs. Furthermore, antimicrobial heteroresistance, extensive cavitary disease and intracavitary gradients, the emergence of bedaquiline resistance, and the lack of biomarkers to monitor DR-TB treatment response remain serious challenges to the sustained successes. In this review, we outline the impact of the new drugs and regimens on patient treatment outcomes, explore evidence underpinning current practices on regimen selection and duration, reflect on the disappointments and pitfalls in the field, and highlight key areas that require continued efforts toward improving treatment approaches and rapid biomarkers for monitoring treatment response.
Collapse
Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Senamile L. Ngema
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
| | - Rubeshan Perumal
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nikita Naicker
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council–CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| |
Collapse
|
7
|
Rajendran A, Palaniyandi K. Mutations Associated with Pyrazinamide Resistance in Mycobacterium tuberculosis: A Review and Update. Curr Microbiol 2022; 79:348. [PMID: 36209317 DOI: 10.1007/s00284-022-03032-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 09/06/2022] [Indexed: 11/03/2022]
Abstract
Pyrazinamide (PZA) has remained a keystone of tuberculosis (TB) therapy, and it possesses high imperative sterilizing action that can facilitate reduction in the present chemotherapy regimen. The combination of PZA works both with first- and second-line TB drugs, notably fluoroquinolones, clofazimine, bedaquiline, delamanid and pretomanid. Pyrazinamide inhibits various targets that are involved in different cellular processes like energy production (pncA), trans-translation (rpsA) and pantothenate/coenzyme A (panD) which are required for persistence of the pathogen. It is well known that pncA gene encoding pyrazinamidase is involved in the transition of PZA into the active form of pyrazinoic acid, which implies that mutation in the pncA gene can develop PZA resistance in Mycobacterium tuberculosis (M. tuberculosis) strain leading to a major clinical and public health concern. Therefore, it is very crucial to understand its resistance mechanism and to detect it precisely to help in the management of the disease. Scope of this review is to have a deep understanding of molecular mechanism of PZA resistance with its multiple targets which would help study the association of mutations and its resistance in M. tuberculosis. This will in turn help learn about the resistance of PZA and develop more accurate molecular diagnostic tool for drug-resistant TB in future TB therapy.
Collapse
Affiliation(s)
- Ananthi Rajendran
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, #1, Mayor Sathyamoorthy Road, Chetpet, Chennai, 600031, India
| | - Kannan Palaniyandi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, #1, Mayor Sathyamoorthy Road, Chetpet, Chennai, 600031, India.
| |
Collapse
|
8
|
Leung KSS, Tam KKG, Ng TTL, Lao HY, Shek RCM, Ma OCK, Yu SH, Chen JX, Han Q, Siu GKH, Yam WC. Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens. Front Microbiol 2022; 13:974428. [PMID: 36160212 PMCID: PMC9505518 DOI: 10.3389/fmicb.2022.974428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/02/2022] [Indexed: 12/02/2022] Open
Abstract
An in-house-developed target amplicon sequencing by next-generation sequencing technology (TB-NGS) enables simultaneous detection of resistance-related mutations in Mycobacterium tuberculosis (MTB) against 8 anti-tuberculosis drug classes. In this multi-center study, we investigated the clinical utility of incorporating TB-NGS for rapid drug-resistant MTB detection in high endemic regions in southeast China. From January 2018 to November 2019, 4,047 respiratory specimens were available from patients suffering lower respiratory tract infections in Hong Kong and Guangzhou, among which 501 were TB-positive as detected by in-house IS6110-qPCR assay with diagnostic sensitivity and specificity of 97.9 and 99.2%, respectively. Preliminary resistance screening by GenoType MTBDRplus and MTBDRsl identified 25 drug-resistant specimens including 10 multidrug-resistant TB. TB-NGS was performed using MiSeq on all drug-resistant specimens alongside 67 pan-susceptible specimens, and demonstrated 100% concordance to phenotypic drug susceptibility test. All phenotypically resistant specimens with dominating resistance-related mutations exhibited a mutation frequency of over 60%. Three quasispecies were identified with mutation frequency of less than 35% among phenotypically susceptible specimens. They were well distinguished from phenotypically resistant cases and thus would not complicate TB-NGS results interpretations. This is the first large-scale study that explored the use of laboratory-developed NGS platforms for rapid TB diagnosis. By incorporating TB-NGS with our proposed diagnostic algorithm, the workflow would provide a user-friendly, cost-effective routine diagnostic solution for complicated TB cases with an average turnaround time of 6 working days. This is critical for timely management of drug resistant TB patients and expediting public health control on the emergence of drug-resistant TB.
Collapse
Affiliation(s)
- Kenneth Siu-Sing Leung
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kingsley King-Gee Tam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Timothy Ting-Leung Ng
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hiu-Yin Lao
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Raymond Chiu-Man Shek
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | | | - Shi-Hui Yu
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Guangzhou, China
| | | | - Qi Han
- Guangzhou KingMed Diagnostics Group, Guangzhou, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Wing-Cheong Yam
- Department of Microbiology, Queen Mary Hospital, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- *Correspondence: Wing-Cheong Yam,
| |
Collapse
|
9
|
Hoffmann AM, Wolke M, Rybniker J, Plum G, Fuchs F. In vitro Activity of Repurposed Nitroxoline Against Clinically Isolated Mycobacteria Including Multidrug-Resistant Mycobacterium tuberculosis. Front Pharmacol 2022; 13:906097. [PMID: 35721137 PMCID: PMC9198898 DOI: 10.3389/fphar.2022.906097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/10/2022] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial treatment options for mycobacterial infections are limited due to intrinsic resistance and the emergence of acquired resistance in Mycobacterium tuberculosis. Isolates resisting first- and second line drugs are raising concerns about untreatable infections and make the development of new therapeutic strategies more pressing. Nitroxoline is an old oral antimicrobial that is currently repurposed for the treatment of urinary tract infection (UTI). In this study, we report the in vitro activity of nitroxoline against 18 clinical isolates of M. tuberculosis complex (MTBC) (M. tuberculosis N = 16, M. bovis BCG N = 1, M. bovis sp. bovis N = 1). Since nitroxoline achieves high concentrations in the urinary tract, we included all MTBC-isolates from urinary samples sent to our laboratory between 2008 and 2021 (University Hospital of Cologne, Germany). Isolates from other sources (N = 7/18) were added for higher sample size and for inclusion of drug-resistant M. tuberculosis isolates (N = 4/18). Based on our clinical routine the fluorescence-based liquid media system BACTEC MGIT 960 was used for susceptibility testing of nitroxoline and mainstay antitubercular drugs. Nitroxoline yielded a MIC90 of 4 mg/L for MTBC. In all M. tuberculosis isolates nitroxoline MICs were at least two twofold dilutions below the current EUCAST susceptibility breakpoint of ≤16 mg/L (limited to E. coli and uncomplicated UTI). In vitro activity of nitroxoline can be considered excellent, even in multidrug-resistant isolates. Future studies with in vivo models should evaluate a potential role of nitroxoline in the treatment of tuberculosis in the era of drug resistance.
Collapse
Affiliation(s)
- Ada Marie Hoffmann
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Martina Wolke
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn Cologne, Cologne, Germany
| | - Georg Plum
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Frieder Fuchs
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, Cologne, Germany
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, Koblenz, Germany
- *Correspondence: Frieder Fuchs, , orcid.org/0000-0001-7075-5378
| |
Collapse
|
10
|
Wang Z, Sun R, Mu C, Wang C, Zhao H, Jiang L, Ju H, Dai W, Zhang F. Characterization of Fluoroquinolone-Resistant and Multidrug-Resistant Mycobacterium tuberculosis Isolates Using Whole-Genome Sequencing in Tianjin, China. Infect Drug Resist 2022; 15:1793-1803. [PMID: 35444430 PMCID: PMC9013706 DOI: 10.2147/idr.s361635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/02/2022] [Indexed: 11/23/2022] Open
Abstract
Objective Methods Results Conclusion
Collapse
Affiliation(s)
- Zhirui Wang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Rui Sun
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Cheng Mu
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Chunhua Wang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Hui Zhao
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Lina Jiang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Hanfang Ju
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Wenxi Dai
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
| | - Fan Zhang
- Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, Tianjin, People’s Republic of China
- Correspondence: Fan Zhang, Tuberculosis Reference Laboratory, Tianjin Center for Tuberculosis Control, No. 124, Chifeng Road, Heping District, Tianjin, 300041, People’s Republic of China, Tel +86-22-27124491, Fax +86-22-27117595, Email
| |
Collapse
|
11
|
Liu P, Wang X, Liang J, Dong Q, Zhang J, Liu D, Wang S, Bi J, Liu W, Wang Z, Chen L, Liu L, Huang X, Zhang G. A Recombinase Polymerase Amplification-Coupled Cas12a Mutant-Based Module for Efficient Detection of Streptomycin-Resistant Mutations in Mycobacterium tuberculosis. Front Microbiol 2022; 12:796916. [PMID: 35069497 PMCID: PMC8770913 DOI: 10.3389/fmicb.2021.796916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a serious public health problem and threat to global TB prevention and control. Streptomycin (STR) is the earliest and classical anti-TB drug, and it is the earliest drug that generated resistance to anti-TB treatment, which limits its use in treating TB and impedes TB control efforts. The rapid, economical, and highly sensitive detection of STR-resistant TB may help reduce disease transmission and morbimortality. CRISPR/CRISPR-associated protein (Cas) is a new-generation pathogen detection method that can detect single-nucleotide polymorphisms with high sensitivity and good specificity. In this study, a Cas12a RR detection system that can recognize more non-traditional protospacer-adjacent motif-targeting sequences was developed based on Cas12a combined with recombinase polymerase amplification technology. This system detects 0.1% of the target substance, and the entire detection process can be completed within 60 min. Its sensitivity and specificity for detecting clinical STR-resistant Mycobacterium tuberculosis were both 100%. Overall, the Cas12 RR detection system provides a novel alternative for the rapid, simple, sensitive, and specific detection of STR-resistant TB, which may contribute to the prompt treatment and prevention of disease transmission in STR-resistant TB.
Collapse
Affiliation(s)
- Peng Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Xinjie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Juan Liang
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, China
| | - Qian Dong
- Department of Laboratory Medicine, Zhongshan Hospital of Sun Yat-sen University, Zhongshan, China
| | - Jinping Zhang
- Intensive Care Unit, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dongxin Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Shuai Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Jing Bi
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Wenqi Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhaoqin Wang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Liang Chen
- Guangdong Center for Tuberculosis Control, Guangzhou, China
| | - Lei Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| |
Collapse
|
12
|
Sodja E, Koren S, Toplak N, Truden S, Žolnir-Dovč M. Next-generation sequencing to characterize pyrazinamide resistance in Mycobacterium tuberculosis isolates from two Balkan countries. J Glob Antimicrob Resist 2021; 29:507-512. [PMID: 34818592 DOI: 10.1016/j.jgar.2021.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Next-generation sequencing (NGS) provide a comprehensive analysis of the genetic alterations that are most commonly linked with pyrazinamide (PZA) resistance. There are no studies reporting molecular background of PZA resistance in TB isolates from Balkan Peninsula. We aimed to examine the feasibility of full-length analysis of a gene linked with PZA resistance, pncA, using Ion Torrent technology in comparison to phenotypic BACTEC MGIT 960 DST in clinical TB isolates from two countries of the Balkan Peninsula. METHODS Between 1996 and 2017, we retrospectively selected 61 TB isolates. To identify gene variants related to drug resistance in genomic DNA extracted from TB isolates, AmpliSeq libraries were generated automatically using the AmpliSeq™ Kit for Chef DL8 and the Ion AmpliSeq TB Research Panel. RESULTS Of all 61 TB isolates included, 56 TB were phenotypically resistant to any antibiotic. Among them, 38/56 (67.9%) TB isolates were phenotypically resistant to pyrazinamide and pncA mutations were detected in 33/38 cases (86.8%). A mutation in the pncA promoter region was the most prevalent genetic alteration, detected in eight TB isolates. Comparison of NGS to conventional BACTEC MGIT 960 DST revealed very strong agreement (90.2%) between the two methods in identifying PZA resistance, with high sensitivity (89.5%) and specificity (95.7%) for NGS. CONCLUSIONS Detection of PZA resistance using NGS seems to be a valuable tool for surveillance of TB drug resistance also in the Balkan Peninsula, with great potential to provide useful information at least one weak earlier than is possible with phenotypic DST.
Collapse
Affiliation(s)
- Eva Sodja
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia.
| | | | | | - Sara Truden
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| | - Manca Žolnir-Dovč
- University Clinic of Respiratory and Allergic Diseases Golnik, Golnik, Slovenia
| |
Collapse
|
13
|
Campelo TA, Cardoso de Sousa PR, Nogueira LDL, Frota CC, Zuquim Antas PR. Revisiting the methods for detecting Mycobacterium tuberculosis: what has the new millennium brought thus far? Access Microbiol 2021; 3:000245. [PMID: 34595396 PMCID: PMC8479963 DOI: 10.1099/acmi.0.000245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/17/2021] [Indexed: 01/07/2023] Open
Abstract
Tuberculosis (TB) affects around 10 million people worldwide in 2019. Approximately 3.4 % of new TB cases are multidrug-resistant. The gold standard method for detecting Mycobacterium tuberculosis, which is the aetiological agent of TB, is still based on microbiological culture procedures, followed by species identification and drug sensitivity testing. Sputum is the most commonly obtained clinical specimen from patients with pulmonary TB. Although smear microscopy is a low-cost and widely used method, its sensitivity is 50-60 %. Thus, owing to the need to improve the performance of current microbiological tests to provide prompt treatment, different methods with varied sensitivity and specificity for TB diagnosis have been developed. Here we discuss the existing methods developed over the past 20 years, including their strengths and weaknesses. In-house and commercial methods have been shown to be promising to achieve rapid diagnosis. Combining methods for mycobacterial detection systems demonstrates a correlation of 100 %. Other assays are useful for the simultaneous detection of M. tuberculosis species and drug-related mutations. Novel approaches have also been employed to rapidly identify and quantify total mycobacteria RNA, including assessments of global gene expression measured in whole blood to identify the risk of TB. Spoligotyping, mass spectrometry and next-generation sequencing are also promising technologies; however, their cost needs to be reduced so that low- and middle-income countries can access them. Because of the large impact of M. tuberculosis infection on public health, the development of new methods in the context of well-designed and -controlled clinical trials might contribute to the improvement of TB infection control.
Collapse
Affiliation(s)
- Thales Alves Campelo
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | | | - Lucas de Lima Nogueira
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Paulo Renato Zuquim Antas
- Laboratório de Imunologia Clínica, Instituto Oswaldo Cruz, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| |
Collapse
|
14
|
Bagheri M, Pormohammad A, Fardsanei F, Yadegari A, Arshadi M, Deihim B, Hajikhani B, Turner RJ, Khalili F, Mousavi SMJ, Dadashi M, Goudarzi M, Dabiri H, Goudarzi H, Mirsaeidi M, Nasiri MJ. Diagnostic Accuracy of Pyrazinamide Susceptibility Testing in Mycobacterium tuberculosis: A Systematic Review with Meta-Analysis. Microb Drug Resist 2021; 28:87-98. [PMID: 34582723 DOI: 10.1089/mdr.2021.0048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: Pyrazinamide (PZA) susceptibility testing plays a critical role in determining the appropriate treatment regimens for multidrug-resistant tuberculosis. We conducted a systematic review and meta-analysis to evaluate the diagnostic accuracy of sequencing PZA susceptibility tests against culture-based susceptibility testing methods as the reference standard. Methods: We searched the MEDLINE/PubMed, Embase, and Web of Science databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures (i.e., sensitivity and specificity) were pooled with a random-effects model. All statistical analyses were performed with Meta-DiSc (version 1.4, Cochrane Colloquium, Barcelona, Spain), STATA (version 14, Stata Corporation, College Station, TX), and RevMan (version 5.3, The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark) software. Results: A total of 72 articles, published between 2000 and 2019, comprising data for 8,701 isolates of Mycobacterium tuberculosis were included in the final analysis. The pooled sensitivity and specificity of the PZA sequencing test against all reference tests (the combination of BACTEC mycobacteria growth indicator tube 960 (MGIT 960), BACTEC 460, and proportion method) were 87% (95% CI: 85-88) and 94.7% (95% CI: 94-95). The positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and the area under the curve estimates were found to be 12.0 (95% CI: 9.0-16.0), 0.17 (95% CI: 0.13-0.21), 106 (95% CI: 71-158), and 96%, respectively. Deek's test result indicated a low likelihood for publication bias (p = 0.01). Conclusions: Our analysis indicated that PZA sequencing may be used in combination with conventional tests due to the advantage of the time to result and in scenarios where culture tests are not feasible. Further work to improve molecular tests would benefit from the availability of standardized reference standards and improvements to the methodology.
Collapse
Affiliation(s)
- Mohammad Bagheri
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ali Pormohammad
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Fatemeh Fardsanei
- Medical Microbiology Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Ali Yadegari
- School of Medicine, Mazandaran University of Medical Sciences, Mazandaran, Iran
| | - Maniya Arshadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Behnaz Deihim
- Department of Bacteriology and Virology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ray J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Canada
| | - Farima Khalili
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Dabiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, College of Medicine-Jacksonville, University of Florida, Jacksonville, FL, USA
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| |
Collapse
|
15
|
Amini S, Kardan-Yamchi J, Kazemian H, Nasiri MJ, Hamzehloo G, Hoffner S, Feizabadi MM. The 7H11 Agar Medium Supplemented with Calf Bovine Serum for Susceptibility Testing of Mycobacterium tuberculosis Isolates Against Pyrazinamide. Microb Drug Resist 2021; 27:1652-1657. [PMID: 34077245 DOI: 10.1089/mdr.2020.0509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Despite its importance, pyrazinamide (PZA) is a blind spot in drug susceptibility testing in tuberculosis laboratories. The aim of this study was to set up a reliable agar-based proportion method for detection of PZA-resistant phenotypes using Middlebrook 7H11 agar supplemented with calf bovine serum (CBS) compared with albumin/dextrose/catalase (ADC) enrichment and pncA/rpsA sequencing results. The 7H11 agar medium supplemented with 10% ADC or 10% CBS (pH 6.2) and 100 μg/mL PZA was used to detect PZA resistance among 64 Mycobacterium tuberculosis isolates. Sanger sequencing and whole-genome sequencing were performed to track mutations in the pncA, rpsA, and their upstream regions. A total of 43 rifampicin/multidrug-resistant, 20 drug-susceptible, and 1 isoniazid mono-resistant M. tuberculosis isolates were investigated. The 7H11+ADC and 7H11+CBS could detect 22 and 23 PZA-resistant strains, respectively. With the same specificity, the sensitivity and accuracy of 7H11+CBS was found to be a little greater than 7H11+ADC in PZA resistance detection compared with sequencing results. Twenty-four mutant strains were found to have different mutations in pncA-upstream, pncA and rpsA genes, in which Gly97Asp was the most dominant mutation. The results obtained from 7H11+CBS were comparable to the results of 7H11+ADC. Therefore, the 7H11 agar proportion method would be a less-expensive test using CBS and produces reliable results.
Collapse
Affiliation(s)
- Sirus Amini
- Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalil Kardan-Yamchi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Kazemian
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Gholamreza Hamzehloo
- Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran, Iran
| | - Sven Hoffner
- Department of Global Public Health (GPH), Karolinska Institute, Stockholm, Sweden
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
16
|
Shi J, Su R, Zheng D, Zhu Y, Ma X, Wang S, Li H, Sun D. Pyrazinamide Resistance and Mutation Patterns Among Multidrug-Resistant Mycobacterium tuberculosis from Henan Province. Infect Drug Resist 2020; 13:2929-2941. [PMID: 32903869 PMCID: PMC7445508 DOI: 10.2147/idr.s260161] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE This study was designed to identify the phenotypic and genotypic characteristics of pyrazinamide (PZA) resistance among multidrug-resistant Mycobacterium tuberculosis (MDR-TB) from Henan and to evaluate the efficacy of pncA, rpsA, and panD mutations in predicting PZA resistance. MATERIALS AND METHODS A total of 152 MDR strains were included in this study. The Bactec MGIT system was used to determine PZA susceptibility for all strains. The pncA, rpsA, and panD genes were sequenced to identify any mutations, and the sequences were then aligned with the sequence of standard strain H37Rv. Moreover, the correlations between PZA-resistant phenotypes and treatment outcomes were analysed. RESULTS Of the152 strains, 105 had a PZA-resistant phenotype, and 102 harboured the pncA mutation. The PZA resistance rate was higher in the strains with resistance to all four first-line drugs and those that were pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR). A total of 100 different pncA mutation patterns were identified, including 80 point mutations and 20 insertions/deletions, and 32 new pncA mutation patterns were detected. In this study, 13 strains had multiple mutations. Of the11 PZA-resistant strains without pncA mutations, two harboured the rpsA mutation, and one harboured the panD mutation. With PZA susceptibility results as the reference, single-gene pncA sequencing had sensitivity of 89.52% and specificity of 89.36%. With the combination of rpsA and panD, the sensitivity increased to 92.38%, and the specificity remained the same. No significant differences were observed in the sputum smear/culture conversion rate between PZA-resistant patients and PZA-sensitive patients. However, PZA resistance was related to the time to sputum smear/culture conversion (P = 0.018). CONCLUSION The combination of pncA, rpsA, and panD was beneficial for the timely diagnosis of PZA resistance and could provide a laboratory basis for customizing treatment regimens for MDR-TB patients.
Collapse
Affiliation(s)
- Jie Shi
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Ruyue Su
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Danwei Zheng
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Yankun Zhu
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Xiaoguang Ma
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Shaohua Wang
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Hui Li
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| | - Dingyong Sun
- Henan Province Center for Disease Control and Prevention, Zhengzhou, Henan Province, People’s Republic of China
| |
Collapse
|
17
|
Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
Collapse
Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| |
Collapse
|
18
|
Pettengill MA. Hindsight Is 2019-the Year in Clinical Microbiology. ACTA ACUST UNITED AC 2020; 42:87-92. [PMID: 32461708 PMCID: PMC7241978 DOI: 10.1016/j.clinmicnews.2020.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Much changed in clinical microbiology in 2019, and, like the organisms, we, as clinical microbiologists, are responsible to detect, characterize, and teach others about our discipline. Also, it is important for us to adapt to changes in the field. In this review, I highlight some of the papers, practices, and regulatory issues that defined 2019 for our field, from my perspective.
Collapse
Affiliation(s)
- Matthew A Pettengill
- Thomas Jefferson University, Department of Pathology, Anatomy, and Cell Biology, Philadelphia, Pennsylvania
| |
Collapse
|
19
|
Lu Z, Jiang W, Zhang J, Lynn HS, Chen Y, Zhang S, Ma Z, Geng P, Guo X, Zhang H, Zhang Z. Drug resistance and epidemiology characteristics of multidrug-resistant tuberculosis patients in 17 provinces of China. PLoS One 2019; 14:e0225361. [PMID: 31751390 PMCID: PMC6874064 DOI: 10.1371/journal.pone.0225361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 11/02/2019] [Indexed: 11/18/2022] Open
Abstract
As China is one of high MDR-TB burden countries, it is important to determine the drug resistant pattern and clinical characteristics of multidrug resistant tuberculosis (MDR-TB). We conducted a comprehensive and nationwide study on MDR-TB in 17 provinces for the period from June 2009 to June 2015, and a total of 1154 cases of MDR-TB were finally investigated. The study sought to assess the clinical features and contrast drug susceptibility profiles of MDR-TB patients in China. Cavitary disease, young age, and long duration of TB disease among MDR-TB patients were important predictors. A high resistance proportion of first-line drugs was observed in Beijing, Shanghai and Tianjin. Resistant proportions of second-line anti-TB drugs in western region for amikacin, aminosalicylic acid, and levofloxacin were higher than eastern and central regions. High levels of drug resistance were seen in earlier cases (before 2011) and outpatients. We found high levels of resistance to 1st- and 2nd-line drugs in all settings, with considerable variabilities in terms of different Directly Observed Treatment Short Course (DOTS) programme, level of economic development(eastern, central and western regions) and patient source (inpatients and outpatients). Timely drug susceptibility testing (DST) and effective management are necessary to ensure an early detection of MDR-TB and its proper treatment.
Collapse
Affiliation(s)
- Zhenhui Lu
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Wenhan Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Xuhui District, Shanghai, People’s Republic of China
| | - Jing Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Xuhui District, Shanghai, People’s Republic of China
| | - Henry S. Lynn
- Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Xuhui District, Shanghai, People’s Republic of China
| | - Yue Chen
- School of Epidemiology, Public Health and Preventive Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Shaoyan Zhang
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Zifeng Ma
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Peihua Geng
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Xiaoyan Guo
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Huiyong Zhang
- Department of Respiratory, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
- * E-mail: (HZ); (ZZ)
| | - Zhijie Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Fudan University, Xuhui District, Shanghai, People’s Republic of China
- * E-mail: (HZ); (ZZ)
| |
Collapse
|