1
|
Wang L, Lim DR, Phelan JE, Reyes LT, Palparan AG, Sanchez MGC, Asuncion LAA, Tujan MAA, Medado IAP, Daga CMA, Llames JHS, Mitarai S, Murase Y, Morishige Y, Ang CF, Malabad JCM, Montoya JC, Hafalla JC, Campino S, Hibberd ML, Ama CG, Basilio RP, La Paz EMCD, Clark TG. Whole genome sequencing analysis of Mycobacterium tuberculosis reveals circulating strain types and drug-resistance mutations in the Philippines. Sci Rep 2024; 14:19602. [PMID: 39179783 PMCID: PMC11344074 DOI: 10.1038/s41598-024-70471-x] [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: 02/27/2024] [Accepted: 08/16/2024] [Indexed: 08/26/2024] Open
Abstract
The Philippines is a high-incidence country for tuberculosis, with the increasing prevalence of multi- (MDR-TB) and extensively-drug (XDR-TB) resistant Mycobacterium tuberculosis strains posing difficulties to disease control. Understanding the genetic diversity of circulating strains can provide insights into underlying drug resistance mutations and transmission dynamics, thereby assisting the design of diagnostic tools, including those using next generation sequencing (NGS) platforms. By analysing genome sequencing data of 732 isolates from Philippines drug-resistance survey collections spanning from 2011 to 2019, we found that the majority belonged to lineages L1 (531/732; 72.5%) and L4 (European-American; n = 174; 23.8%), with the Manila strain (L1.2.1.2.1) being the most prominent (475/531). Approximately two-thirds of isolates were found to be at least MDR-TB (483/732; 66.0%), and potential XDR-TB genotypic resistance was observed (3/732; 0.4%), highlighting an emerging problem in the country. Genotypic resistance was highly concordant with laboratory drug susceptibility testing. By finding isolates with (near-)identical genomic variation, five major clusters containing a total of 114 isolates were identified: all containing either L1 or L4 isolates with at least MDR-TB resistance and spanning multiple years of collection. Closer inspection of clusters revealed transmission in prisons, some involving isolates with XDR-TB, and mutations linked to third-line drug bedaquiline. We have also identified previously unreported mutations linked to resistance for isoniazid, rifampicin, ethambutol, and fluoroquinolones. Overall, this study provides important insights into the genetic diversity, transmission and circulating drug resistance mutations of M. tuberculosis in the Philippines, thereby informing clinical and surveillance decision-making, which is increasingly using NGS platforms.
Collapse
Affiliation(s)
- Linfeng Wang
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Dodge R Lim
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Jody E Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Lorenzo T Reyes
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Alma G Palparan
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Maria Guileane C Sanchez
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Louella Abigail A Asuncion
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Ma Angelica A Tujan
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Inez Andrea P Medado
- Molecular Biology Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Chona Mae A Daga
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Jo-Hannah S Llames
- Philippine Genome Center, University of Philippines Diliman, Quezon City, Philippines
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yoshiro Murase
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Yuta Morishige
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Concepcion F Ang
- College of Medicine, University of the Philippines, Manila, Philippines
| | - John Carlo M Malabad
- Department of Science and Technology, DOST Compound, Bicutan, Taguig City, Philippine, Philippines
| | - Jaime C Montoya
- College of Medicine, University of the Philippines, Manila, Philippines
| | - Julius C Hafalla
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Martin L Hibberd
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Cecilia G Ama
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Ramon P Basilio
- National Tuberculosis Reference Laboratory, Research Institute for Tropical Medicine, Department of Health, Filinvest, Alabang, Muntinlupa City, Philippines
| | - Eva Maria Cutiongoco-De La Paz
- Philippine Genome Center, University of Philippines Diliman, Quezon City, Philippines
- College of Medicine, University of the Philippines, Manila, Philippines
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK.
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| |
Collapse
|
2
|
Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
Collapse
Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| |
Collapse
|
3
|
Liu A, Liu S, Lv K, Zhu Q, Wen J, Li J, Liang C, Huang X, Gong C, Sun Q, Gu H. Rapid detection of multidrug resistance in tuberculosis using nanopore-based targeted next-generation sequencing: a multicenter, double-blind study. Front Microbiol 2024; 15:1349715. [PMID: 38495513 PMCID: PMC10940340 DOI: 10.3389/fmicb.2024.1349715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Background Resistance to anti-tuberculous drugs is a major challenge in the treatment of tuberculosis (TB). We aimed to evaluate the clinical availability of nanopore-based targeted next-generation sequencing (NanoTNGS) for the diagnosis of drug-resistant tuberculosis (DR-TB). Methods This study enrolled 253 patients with suspected DR-TB from six hospitals. The diagnostic efficacy of NanoTNGS for detecting Mycobacterium tuberculosis and its susceptibility or resistance to first- and second-line anti-tuberculosis drugs was assessed by comparing conventional phenotypic drug susceptibility testing (pDST) and Xpert MTB/RIF assays. NanoTNGS can be performed within 12 hours from DNA extraction to the result delivery. Results NanoTNGS showed a remarkable concordance rate of 99.44% (179/180) with the culture assay for identifying the Mycobacterium tuberculosis complex. The sensitivity of NanoTNGS for detecting drug resistance was 93.53% for rifampicin, 89.72% for isoniazid, 85.45% for ethambutol, 74.00% for streptomycin, and 88.89% for fluoroquinolones. Specificities ranged from 83.33% to 100% for all drugs tested. Sensitivity for rifampicin-resistant tuberculosis using NanoTNGS increased by 9.73% compared to Xpert MTB/RIF. The most common mutations were S531L (codon in E. coli) in the rpoB gene, S315T in the katG gene, and M306V in the embB gene, conferring resistance to rifampicin, isoniazid, and ethambutol, respectively. In addition, mutations in the pncA gene, potentially contributing to pyrazinamide resistance, were detected in 32 patients. Other prevalent variants, including D94G in the gyrA gene and K43R in the rpsL gene, conferred resistance to fluoroquinolones and streptomycin, respectively. Furthermore, the rv0678 R94Q mutation was detected in one sample, indicating potential resistance to bedaquiline. Conclusion NanoTNGS rapidly and accurately identifies resistance or susceptibility to anti-TB drugs, outperforming traditional methods. Clinical implementation of the technique can recognize DR-TB in time and provide guidance for choosing appropriate antituberculosis agents.
Collapse
Affiliation(s)
- Aimei Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Sang Liu
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Kangyan Lv
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingdong Zhu
- Department of Tuberculosis, The Fourth People's Hospital of Nanning, Nanning, Guangxi, China
| | - Jun Wen
- Department of Pulmonary Medicine, The Third People's Hospital of Guilin, Guilin, Guangxi, China
| | - Jianpeng Li
- Department of Pulmonary Medicine, The Third People's Hospital of Wuzhou, Wuzhou, Guangxi, China
| | - Chengyuan Liang
- Department of Infectious Diseases, The People's Hospital of Baise, Baise, Guangxi, China
| | - Xuegang Huang
- Department of Infectious Diseases, The First People's Hospital of Fangchenggang, Fangchenggang, Guangxi, China
| | - Chunming Gong
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Qingfeng Sun
- Department of Tuberculosis, Guangxi Zhuang Autonomous Region Chest Hospital, Liuzhou, Guangxi, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, China
| |
Collapse
|
4
|
Xiao YX, Liu KH, Lin WH, Chan TH, Jou R. Whole-genome sequencing-based analyses of drug-resistant Mycobacterium tuberculosis from Taiwan. Sci Rep 2023; 13:2540. [PMID: 36781938 PMCID: PMC9925824 DOI: 10.1038/s41598-023-29652-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) posed challenges to global TB control. Whole-genome sequencing (WGS) is recommended for predicting drug resistance to guide DR-TB treatment and management. Nevertheless, data are lacking in Taiwan. Phenotypic drug susceptibility testing (DST) of 12 anti-TB drugs was performed for 200 Mycobacterium tuberculosis isolates. WGS was performed using the Illumina platform. Drug resistance profiles and lineages were predicted in silico using the Total Genotyping Solution for TB (TGS-TB). Using the phenotypic DST results as a reference, WGS-based prediction demonstrated high concordance rates of isoniazid (95.0%), rifampicin (RIF) (98.0%), pyrazinamide (98.5%) and fluoroquinolones (FQs) (99.5%) and 96.0% to 99.5% for second-line injectable drugs (SLIDs); whereas, lower concordance rates of ethambutol (87.5%), streptomycin (88.0%) and ethionamide (84.0%). Furthermore, minimum inhibitory concentrations confirmed that RIF rpoB S450L, FQs gyrA D94G and SLIDs rrs a1401g conferred high resistance levels. Besides, we identified lineage-associated mutations in lineage 1 (rpoB H445Y and fabG1 c-15t) and predominant lineage 2 (rpoB S450L and rpsL K43R). The WGS-based prediction of drug resistance is highly concordant with phenotypic DST results and can provide comprehensive genetic information to guide DR-TB precision therapies in Taiwan.
Collapse
Affiliation(s)
- Yu-Xin Xiao
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Kuang-Hung Liu
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Wan-Hsuan Lin
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Tai-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C..
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C..
| |
Collapse
|
5
|
Xia H, Song Y, Zheng Y, Wang S, Zhao B, He W, Liu D, Ou X, Zhou Y, Zhao Y. Detection of Mycobacterium tuberculosis Rifampicin Resistance Conferred by Borderline rpoB Mutations: Xpert MTB/RIF is Superior to Phenotypic Drug Susceptibility Testing. Infect Drug Resist 2022; 15:1345-1352. [PMID: 35378895 PMCID: PMC8976515 DOI: 10.2147/idr.s358301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Dongxin Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Correspondence: Yanlin Zhao, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, People’s Republic of China, Tel +86 10-58900517, Email
| |
Collapse
|
6
|
Reevaluating Rifampicin Breakpoint Concentrations for Mycobacterium tuberculosis Isolates with Disputed rpoB Mutations and Discordant Susceptibility Phenotypes. Microbiol Spectr 2022; 10:e0208721. [PMID: 35107324 PMCID: PMC8809345 DOI: 10.1128/spectrum.02087-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, rifampicin resistance breakpoints based on MICs of disrupted rpoB mutants of Mycobacterium tuberculosis (MTB) were explored using the Mycobacteria Growth Indicator Tube (MGIT) system and microplate alamarBlue assay (MABA). Sixty-one MTB isolates with disputed low-level rifampicin resistance-associated rpoB mutations and 40 RIF-susceptible wild-type isolates were included. Among the 61 resistant isolates, 25 (41.0%) had MICs ≥2.0 mg/L via MABA, while 16 (26.2%) were identified as RIF resistant via MGIT. Epidemiological cut-off (ECOFF) values obtained using MABA and MGIT were 0.25 and 0.125 mg/L, respectively. Based on 0.125 mg/L as a tentative critical concentration (CC), MABA RIF resistance-detection sensitivity was 93.4%, prompting the reduction of the MGIT CC to 0.125 mg/L, given that only a single isolate (1.6%) with the borderline mutation would be misclassified as susceptible to RIF based on this CC. Based on DNA sequencing of RRDR as the gold standard, the diagnostic accuracy of MGIT (99.0%) was significantly higher than that of MABA (91.1%). MICs of Leu511Pro mutant isolates were negatively correlated with time to liquid culture positivity (TTP) in our analysis (R = 0.957, P < 0.01). In conclusion, our results demonstrated missed detection of a high proportion of rifampicin-resistant isolates based on the WHO-endorsed CC. Such missed detections would be avoided by reducing the optimal MGIT RIF CC to 0.125 mg/L. In addition, MGIT based on reduced CC outperformed MABA in detecting borderline RIF resistance, with MABA MIC results obtained for isolates with the same mutation correlating with MTB growth rate. IMPORTANCE Tuberculosis (TB) is still one of the world's leading infectious disease killers. The early and accurate diagnosis of RIF resistance is necessary to deliver timely and appropriate treatment for TB patients and improve their clinical outcome. Actually, a proportion of MTB isolates with disputed rpoB mutations present a diagnostic dilemma between Xpert and phenotypical drug susceptibility testing (pDST). Recently, WHO reported a pragmatic approach by lowering critical concentration (CC) to boost sensitivity of resistance detection of pDST. Therefore, a detailed analysis of the association between RIF susceptibility and disrupted mutations within rpoB gene would lay a foundation to assess the diagnostic accuracy of pDST with lowering RIF CC. In this study, we aim to determine the MICs of MTB isolates with disrupted mutations by MGIT and microplate alamarBlue assay (MABA). We also aimed to determine the optimal breakpoints for MTB isolates with these mutations.
Collapse
|