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Bhanushali A, Atre S, Nair P, Thandaseery GA, Shah S, Kuruwa S, Zade A, Nikam C, Gomare M, Chatterjee A. Whole-genome sequencing of clinical isolates from tuberculosis patients in India: real-world data indicates a high proportion of pre-XDR cases. Microbiol Spectr 2024; 12:e0277023. [PMID: 38597637 PMCID: PMC11064594 DOI: 10.1128/spectrum.02770-23] [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: 08/08/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Treatment decisions for tuberculosis (TB) in the absence of full drug-susceptibility data can result in amplifying resistance and may compromise treatment outcomes. Genomics of Mycobacterium tuberculosis (M.tb) from clinical samples enables detection of drug resistance to multiple drugs. We performed whole-genome sequencing (WGS) for 600 clinical samples from patients with tuberculosis to identify the drug-resistance profile and mutation spectrum. We documented the reasons reported by clinicians for referral. WGS identified a high proportion (51%) of pre-extensively drug-resistant (pre-XDR) cases followed by multidrug-resistant tuberculosis (MDR-TB) (15.5%). This correlates with the primary reason for referral, as non-response to the first-line treatment (67%) and treatment failure or rifampicin resistance (14%). Multivariate analysis indicated that all young age groups (P < 0.05), male gender (P < 0.05), and Beijing strain (P < 0.01) were significant independent predictors of MDR-TB or MDR-TB+ [pre-extensively drug-resistant tuberculosis (XDR-TB) and XDR-TB]. Ser315Thr (72.5%) in the inhA gene and Ser450Leu in the rpoB gene (65.5%) were the most prevalent mutations, as were resistance-conferring mutations to pyrazinamide (41%) and streptomycin (61.33%). Mutations outside the rifampicin resistance-determining region (RRDR), Ile491Phe and Val170Phe, were seen in 1.3% of cases; disputed mutations in rpoB (Asp435Tyr, His445Asn, His445Leu, and Leu430Pro) were seen in 6% of cases, and mutations to newer drugs such as bedaquiline and linezolid in 1.0% and 7.5% of cases, respectively. This study on clinical samples highlights that there is a high proportion of pre-XDR cases and emerging resistance to newer drugs; ongoing transmission of these strains can cause serious threat to public health; and whole-genome sequencing can effectively identify and support precision medicine for TB. IMPORTANCE The current study is based on real-world data on the TB drug-resistance profile by whole-genome sequencing of 600 clinical samples from patients with TB in India. This study indicates the clinicians' reasons for sending samples for WGS, which is for difficult-to-treat cases and/or relapse and treatment failure. The study reports a significant proportion of cases with pre-XDR-TB strains that warrant policy makers' attention. It reflects the current iterative nature of the diagnostic tests under programmatic conditions that leads to delays in appropriate diagnosis and empirical treatment. India had an estimated burden of 2.95 million TB cases in 2020 and 135,000 multidrug-resistant cases. However, WGS profiles of M.tb from India remains disproportionately poorly represented. This study adds a significant body of data on the mutation profiles seen in M.tb isolated from patients with TB in India, mutations outside the RRDR, disputed mutations, and resistance-conferring mutations to newer drugs such as bedaquiline and linezolid.
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Affiliation(s)
| | - Sachin Atre
- Dr. D.Y. Patil Medical College Hospital and Research Centre, Pune, India
| | - Preethi Nair
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
| | | | - Sanchi Shah
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
| | | | - Amrutraj Zade
- HaystackAnalytics Pvt. Ltd., IIT Bombay, Mumbai, India
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Datta D, Jamwal S, Jyoti N, Patnaik S, Kumar D. Actionable mechanisms of drug tolerance and resistance in Mycobacterium tuberculosis. FEBS J 2024. [PMID: 38676952 DOI: 10.1111/febs.17142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 02/23/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Abstract
The emergence of antimicrobial resistance (AMR) across bacterial pathogens presents a serious threat to global health. This threat is further exacerbated in tuberculosis (TB), mainly due to a protracted treatment regimen involving a combination of drugs. A diversity of factors contributes to the emergence of drug resistance in TB, which is caused by the pathogen Mycobacterium tuberculosis (Mtb). While the traditional genetic mutation-driven drug resistance mechanisms operate in Mtb, there are also several additional unique features of drug resistance in this pathogen. Research in the past decade has enriched our understanding of such unconventional factors as efflux pumps, bacterial heterogeneity, metabolic states, and host microenvironment. Given that the discovery of new antibiotics is outpaced by the emergence of drug resistance patterns displayed by the pathogen, newer strategies for combating drug resistance are desperately needed. In the context of TB, such approaches include targeting the efflux capability of the pathogen, modulating the host environment to prevent bacterial drug tolerance, and activating the host anti-mycobacterial pathways. In this review, we discuss the traditional mechanisms of drug resistance in Mtb, newer understandings and the shaping of a set of unconventional approaches to target both the emergence and treatment of drug resistance in TB.
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Affiliation(s)
- Dipanwita Datta
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Shaina Jamwal
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Nishant Jyoti
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Srinivas Patnaik
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Bhubaneswar, India
| | - Dhiraj Kumar
- Cellular Immunology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
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Huang CK, Yu MC, Hung CS, Lin JC. Emerging insight of whole genome sequencing coupled with protein structure prediction into the pyrazinamide-resistance signature of Mycobacterium tuberculosis. Int J Antimicrob Agents 2024; 63:107053. [PMID: 38081550 DOI: 10.1016/j.ijantimicag.2023.107053] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 11/11/2023] [Accepted: 12/04/2023] [Indexed: 02/25/2024]
Abstract
Pyrazinamide (PZA) is considered to be a pivotal drug to shorten the treatment of both drug-susceptible and drug-resistant tuberculosis, but its use is challenged by the reliability of drug-susceptibility testing (DST). PZA resistance in Mycobacterium tuberculosis (MTB) is relevant to the amino acid substitution of pyrazinamidase that is responsible for the conversion of PZA to active pyrazinoic acid (POA). The single nucleotide variants (SNVs) within ribosomal protein S1 (rpsA) or aspartate decarboxylase (panD), the binding targets of POA, has been reported to drive the PZA-resistance signature of MTB. In this study, whole genome sequencing (WGS) was used to identify SNVs within the pncA, rpsA and panD genes in 100 clinical MTB isolates associated with DST results for PZA. The potential influence of high-confidence, interim-confidence or emerging variants on the interplay between target genes and PZA or POA was simulated computationally, and predicted with a protein structure modelling approach. The DST results showed weak agreement with the identification of high-confidence variants within the pncA gene (Cohen's kappa coefficient=0.58), the analytic results of WGS coupled with protein structure modelling on pncA mutants (Cohen's kappa coefficient=0.524) or related genes (Cohen's kappa coefficient=0.504). Taken together, these results suggest the practicable application of a genotypic-coupled bioinformatic approach to manage PZA-containing regimens for patients with MTB.
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Affiliation(s)
- Chun-Kai Huang
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ming-Chih Yu
- Division of Pulmonary Medicine, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Pulmonary Research Centre, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ching-Sheng Hung
- Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
| | - Jung-Chun Lin
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Pulmonary Research Centre, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
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Purkan P, Hadi S, Retnowati W, Sumarsih S, Wahyuni DK, Piluharto B, Panjaitan TM, Ifada C, Nadila A, Nabilah BA. Exploring of pyrazinamidase recombinant activity from PZA-sensitive and resistant Mycobacterium tuberculosis expressed in Escherichia coli BL21 (DE3). BRAZ J BIOL 2024; 84:e278911. [PMID: 38422295 DOI: 10.1590/1519-6984.278911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/15/2024] [Indexed: 03/02/2024] Open
Abstract
The mutations of pncA gene encoding pyrazinamidase/PZase in Mycobacterium tuberculosis are often associated with pyrazinamide/PZA resistance. The H and R1 isolates showed significant phenotypic differences to PZA. The H isolate was PZA sensitive, but R1 was PZA resistant up to 100 ug/ml. The paper reports the pncA profile for both isolates and the activity of their protein expressed in Escherichia coli BL21(DE3). The 0.6 kb of each pncA genes have been subcloned successfully into the 5.4 kb pET30a vector and formed the pET30a-pncA recombinant with a size of 6.0 kb. The pncAR1 profile exhibited base mutations, but not for pncAH against to pncA from the PZA-sensitive M. tuberculosis H37RV published in Genbank ID: 888260. Three mutations were found in pncAR1, ie T41C, G419A, and A535G that subsequently changed amino acids of Cys14Arg, Arg140His and Ser179Gly in its protein level. The mutant PZase R1 that expressed as a 21 kDa protein in E. coli Bl21(DE3) lost 32% of its performance in activating PZA drug to pyrazinoic acid/POA compared to the wild-type PZase H. The mutation in the pncAR1 gene that followed by the decreasing of its PZase activity underlies the emergence of pyrazinamide resistance in the clinical isolate. Structural studies for the R1 mutant PZase protein should be further developed to reveal more precise drug resistance mechanisms and design more effective TB drugs.
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Affiliation(s)
- P Purkan
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - S Hadi
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - W Retnowati
- Airlangga University, Faculty of Medicine, Department of Microbiology, Surabaya, Indonesia
| | - S Sumarsih
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - D K Wahyuni
- Airlangga University, Faculty of Science and Technology, Department of Biology, Surabaya, Indonesia
| | - B Piluharto
- Jember University, Faculty of Mathematic and Natural Sciences, Department of Chemistry, Jember, Indonesia
| | - T M Panjaitan
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - C Ifada
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - A Nadila
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
| | - B A Nabilah
- Airlangga University, Faculty of Science and Technology, Department of Chemistry, Surabaya, Indonesia
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Dong S, Shao G, Davies Forsman L, Wang S, Wang S, Cao J, Bao Z, Bruchfeld J, Alffenaar JWC, Liu J, Hu Y, Wu M. Drug Exposure and Susceptibility of Pyrazinamide Correlate with Treatment Response in Pyrazinamide-Susceptible Patients with Multidrug-Resistant Tuberculosis. Pharmaceutics 2024; 16:144. [PMID: 38276514 PMCID: PMC10820138 DOI: 10.3390/pharmaceutics16010144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/13/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024] Open
Abstract
Exploring the influence of pyrazinamide exposure and susceptibility on treatment response is crucial for optimizing the management of multidrug-resistant tuberculosis (MDR-TB). This study aimed to investigate the association between pyrazinamide exposure, susceptibility, and response to MDR-TB treatment, as well as find clinical thresholds for pyrazinamide. A prospective multi-center cohort study of participants with MDR-TB using pyrazinamide was conducted in three TB-designated hospitals in China. Univariate and multivariate analyses were applied to investigate the associations. Classification and Regression Tree (CART) analysis was used to identify clinical thresholds, which were further evaluated by multivariate analysis and receiver operating characteristic (ROC) curves. The study included 143 patients with MDR-TB. The exposure/susceptibility ratio of pyrazinamide was associated with two-month culture conversion (adjusted risk ratio (aRR), 1.1; 95% confidence interval (CI), 1.07-1.20), six-month culture conversion (aRR, 1.1; 95% CI, 1.06-1.16), treatment success (aRR, 1.07; 95% CI, 1.03-1.10), as well as culture conversion time (adjusted hazard ratio (aHR) 1.18; 95% CI,1.14-1.23). The threshold for optimal improvement in sputum culture results at the sixth month of treatment was determined to be a pyrazinamide AUC0-24h/MIC ratio of 7.8. In conclusion, the exposure/susceptibility ratio of pyrazinamide is associated with the treatment response of MDR-TB, which may change in different Group A drug-based regimens.
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Affiliation(s)
- Shulan Dong
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Ge Shao
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Lina Davies Forsman
- Department of Medicine, Division of Infectious Diseases, Karolinska Institutet Solna, 171 77 Stockholm, Sweden; (L.D.F.); (J.B.)
- Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Sainan Wang
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Shanshan Wang
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Jiayi Cao
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Ziwei Bao
- Department of Infectious Diseases, The Fifth People’s Hospital of Suzhou, Suzhou 215007, China; (Z.B.); (M.W.)
| | - Judith Bruchfeld
- Department of Medicine, Division of Infectious Diseases, Karolinska Institutet Solna, 171 77 Stockholm, Sweden; (L.D.F.); (J.B.)
- Department of Infectious Diseases, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Jan-Willem C. Alffenaar
- School of Pharmacy, Faculty of Medicine and Health, University of Sydney, Sydney 2006, Australia;
- Westmead Hospital, Sydney 2145, Australia
- Sydney Infectious Diseases Institute, University of Sydney, Sydney 2006, Australia
| | - Jia Liu
- Department of Infectious Diseases, The Fifth People’s Hospital of Suzhou, Suzhou 215007, China; (Z.B.); (M.W.)
| | - Yi Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety, Fudan University, Shanghai 201203, China; (S.D.); (G.S.); (S.W.); (S.W.); (J.C.)
| | - Meiying Wu
- Department of Infectious Diseases, The Fifth People’s Hospital of Suzhou, Suzhou 215007, China; (Z.B.); (M.W.)
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