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Deng L, Wang Q, Liu H, Jiang Y, Xu M, Xiang Y, Yang T, Yang S, Yan D, Li M, Zhao L, Zhao X, Wan K, He G, Mijiti X, Li G. Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China. Front Microbiol 2024; 15:1290227. [PMID: 38686109 PMCID: PMC11056549 DOI: 10.3389/fmicb.2024.1290227] [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: 09/07/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Tuberculosis (TB), mainly caused by Mycobacterium tuberculosis (Mtb), remains a serious public health problem. Increasing evidence supports that selective evolution is an important force affecting genomic determinants of Mtb phenotypes. It is necessary to further understand the Mtb selective evolution and identify the positively selected genes that probably drive the phenotype of Mtb. Methods This study mainly focused on the positive selection of 807 Mtb strains from Southern Xinjiang of China using whole genome sequencing (WGS). PAML software was used for identifying the genes and sites under positive selection in 807 Mtb strains. Results Lineage 2 (62.70%) strains were the dominant strains in this area, followed by lineage 3 (19.45%) and lineage 4 (17.84%) strains. There were 239 codons in 47 genes under positive selection, and the genes were majorly associated with the functions of transcription, defense mechanisms, and cell wall/membrane/envelope biogenesis. There were 28 codons (43 mutations) in eight genes (gyrA, rpoB, rpoC, katG, pncA, embB, gid, and cut1) under positive selection in multi-drug resistance (MDR) strains but not in drug-susceptible (DS) strains, in which 27 mutations were drug-resistant loci, 9 mutations were non-drug-resistant loci but were in drug-resistant genes, 2 mutations were compensatory mutations, and 5 mutations were in unknown drug-resistant gene of cut1. There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. The epitopes of T and B cells were both hyper-conserved, particularly in the T-cell epitopes. Conclusion This study revealed the ongoing selective evolution of Mtb. We found some special genes and sites under positive selection which may contribute to the advantage of MDR and L3 strains. It is necessary to further study these mutations to understand their impact on phenotypes for providing more useful information to develop new TB interventions.
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Affiliation(s)
- Lele Deng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Quan Wang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Haican Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yi Jiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Miao Xu
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yu Xiang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Ting Yang
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Shuliu Yang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- School of Public Health, University of South China, Hengyang, China
| | - Di Yan
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Machao Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lili Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiuqin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Kanglin Wan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Guangxue He
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaokaiti Mijiti
- Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Guilian Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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Feng Q, Zhang G, Chen L, Wu H, Yang Y, Gao Q, Asakawa T, Zhao Y, Lu S, Zhou L, Lu H. Roadmap for ending TB in China by 2035: The challenges and strategies. Biosci Trends 2024; 18:11-20. [PMID: 38325824 DOI: 10.5582/bst.2023.01325] [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: 02/09/2024]
Abstract
Tuberculosis (TB) is one of the top ten causes of death worldwide, taking the lives of over a million people annually. In addition to being a serious health issue, TB is also closely linked to eradicating poverty according to the Sustainable Development Goals (SDGs) of the United Nations (UN). All UN members have committed to ending the TB epidemic by 2030. China has one of the highest TB loads worldwide, ranking third in the world on many TB burden indices. The national strategy for TB control is aimed at creating a collaborative network and integrating TB treatment into the medical system. According to the WHO's global TB report, China is expected to have 748,000 new cases of TB in 2022 and an incidence of 52 cases per 100,000 people. Ending TB remains a huge challenge and requires comprehensive control strategies in China. In this work, we have discussed the challenges of TB prevention and control in China and proposed specific measures to end TB.
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Affiliation(s)
- Qishun Feng
- 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, Guangdong, 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, Guangdong, China
| | - Liang Chen
- Guangdong Provincial Research Center for Public Health, Guangdong Provincial Center for Diseases Control and Prevention, Guangzhou, Guangdong, China
| | - Huizhong Wu
- Guangdong Provincial Center for Tuberculosis Control, Guangzhou, Guangdong, China
| | - Yingzhou Yang
- Shenzhen Center for Chronic Disease Control, Shenzhen, Guangdong, China
| | - Qian Gao
- 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, Guangdong, China
- School of Basic Medical Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tetsuya Asakawa
- 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, Guangdong, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuihua Lu
- 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, Guangdong, China
| | - Lin Zhou
- 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, Guangdong, China
- Guangdong Provincial People's Hospital, Guangzhou, Guangdong, China
| | - Hongzhou Lu
- 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, Guangdong, China
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Brunner VM, Fowler PW. Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis. Microb Genom 2024; 10:001187. [PMID: 38315172 PMCID: PMC10926696 DOI: 10.1099/mgen.0.001187] [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: 08/06/2023] [Accepted: 01/11/2024] [Indexed: 02/07/2024] Open
Abstract
Mutations in Mycobacterium tuberculosis associated with resistance to antibiotics often come with a fitness cost for the bacteria. Resistance to the first-line drug rifampicin leads to lower competitive fitness of M. tuberculosis populations when compared to susceptible populations. This fitness cost, introduced by resistance mutations in the RNA polymerase, can be alleviated by compensatory mutations (CMs) in other regions of the affected protein. CMs are of particular interest clinically since they could lock in resistance mutations, encouraging the spread of resistant strains worldwide. Here, we report the statistical inference of a comprehensive set of CMs in the RNA polymerase of M. tuberculosis, using over 70 000 M. tuberculosis genomes that were collated as part of the CRyPTIC project. The unprecedented size of this data set gave the statistical tests more power to investigate the association of putative CMs with resistance-conferring mutations. Overall, we propose 51 high-confidence CMs by means of statistical association testing and suggest hypotheses for how they exert their compensatory mechanism by mapping them onto the protein structure. In addition, we were able to show an association of CMs with higher in vitro growth densities, and hence presumably with higher fitness, in resistant samples in the more virulent M. tuberculosis lineage 2. Our results suggest the association of CM presence with significantly higher in vitro growth than for wild-type samples, although this association is confounded with lineage and sub-lineage affiliation. Our findings emphasize the integral role of CMs and lineage affiliation in resistance spread and increases the urgency of antibiotic stewardship, which implies accurate, cheap and widely accessible diagnostics for M. tuberculosis infections to not only improve patient outcomes but also prevent the spread of resistant strains.
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Affiliation(s)
| | - Philip W. Fowler
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford, UK
- Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, UK
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4
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Conkle-Gutierrez D, Ramirez-Busby SM, Gorman BM, Elghraoui A, Hoffner S, Elmaraachli W, Valafar F. Novel and reported compensatory mutations in rpoABC genes found in drug resistant tuberculosis outbreaks. Front Microbiol 2024; 14:1265390. [PMID: 38260909 PMCID: PMC10800992 DOI: 10.3389/fmicb.2023.1265390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Background Rifampicin (RIF) is a key first-line drug used to treat tuberculosis, a primarily pulmonary disease caused by Mycobacterium tuberculosis. RIF resistance is caused by mutations in rpoB, at the cost of slower growth and reduced transcription efficiency. Antibiotic resistance to RIF is prevalent despite this fitness cost. Compensatory mutations in rpoABC genes have been shown to alleviate the fitness cost of rpoB:S450L, explaining how RIF resistant strains harbor this mutation can spread so rapidly. Unfortunately, the full set of RIF compensatory mutations is still unknown, particularly those compensating for rarer RIF resistance mutations. Objectives We performed an association study on a globally representative set of 4,309 whole genome sequenced clinical M. tuberculosis isolates to identify novel putative compensatory mutations, determine the prevalence of known and previously reported putative compensatory mutations, and determine which RIF resistance markers associate with these compensatory mutations. Results and conclusions Of the 1,079 RIF resistant isolates, 638 carried previously reported putative and high-probability compensatory mutations. Our strict criteria identified 46 additional mutations in rpoABC for which no strong prior evidence of their compensatory role exists. Of these, 35 have previously been reported. As such, our independent corroboration adds to the mounting evidence that these 35 also carry a compensatory role. The remaining 11 are novel putative compensatory markers, reported here for the first time. Six of these 11 novel putative compensatory mutations had two or more mutation events. Most compensatory mutations appear to be specifically compensating for the fitness loss due to rpoB:S450L. However, an outbreak of 22 closely related isolates each carried three rpoB mutations, the rare RIFR markers D435G and L452P and the putative compensatory mutation I1106T. This suggests compensation may require specific combinations of rpoABC mutations. Here, we report only mutations that met our very strict criteria. It is highly likely that many additional rpoABC mutations compensate for rare resistance-causing mutations and therefore did not carry the statistical power to be reported here. These findings aid in the identification of RIF resistant M. tuberculosis strains with restored fitness, which pose a greater risk of causing resistant outbreaks.
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Affiliation(s)
- Derek Conkle-Gutierrez
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
| | - Sarah M. Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
| | - Bria M. Gorman
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
| | - Afif Elghraoui
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
| | - Sven Hoffner
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
- Department of Global Public Health, Karolinska Institute, Stockholm, Sweden
| | - Wael Elmaraachli
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of California, San Diego, San Diego, CA, United States
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, CA, United States
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Morey-León G, Mejía-Ponce PM, Granda Pardo JC, Muñoz-Mawyin K, Fernández-Cadena JC, García-Moreira E, Andrade-Molina D, Licona-Cassani C, Berná L. A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools. PLoS One 2023; 18:e0294670. [PMID: 38051742 DOI: 10.1371/journal.pone.0294670] [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: 03/18/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
INTRODUCTION Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen's kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. IMPORTANCE Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.
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Affiliation(s)
- Gabriel Morey-León
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Universidad de la República, Montevideo, Uruguay
- University of Guayaquil, Guayaquil, Ecuador
| | - Paulina M Mejía-Ponce
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Nuevo León, México
| | - Juan Carlos Granda Pardo
- Centro de Referencia Nacional de Micobacterias, Instituto Nacional de Investigación en Salud Pública Dr Leopoldo Izquieta Perez, INSPI-LIP, Guayaquil, Ecuador
| | - Karen Muñoz-Mawyin
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | | | - Derly Andrade-Molina
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Jeon SM, Park S, Lim NR, Lee N, Jung J, Sung N, Kim S. Molecular Analysis of Anti-Tuberculosis Drug Resistance of Mycobacterium tuberculosis Isolated in the Republic of Korea. Antibiotics (Basel) 2023; 12:1324. [PMID: 37627744 PMCID: PMC10451913 DOI: 10.3390/antibiotics12081324] [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: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Rapid and accurate detection of tuberculosis (TB) drug resistance is critical for the successful treatment and control of TB. Here, we investigated resistance to anti-TB drugs and genetic variations in 215 drug-resistant Mycobacterium tuberculosis isolates in Korea. Genetic variations were observed in rpoB Ser531Leu, katG Ser315Thr, and gyrA Asp94Gly; however, the minimum inhibitory concentrations varied, which can be attributed to other resistance mechanisms. Examination of genetic relatedness among drug-resistant isolates revealed that the cluster size of resistant bacteria was less than six strains, suggesting no evidence of a large-scale epidemic caused by a specific strain. However, rpoC mutants of the rifampicin-resistant isolates were composed of five types of clusters, suggesting that these compensatory mutations advance propagation. In the present study, more than 90% of the resistance mechanisms to major anti-TB drugs were identified, and the effect of each mutation on drug resistance was estimated. With the clinical application of recent next-generation sequencing-based susceptibility testing, the present study is expected to improve the clinical utilization of genotype-based drug susceptibility testing for the diagnosis and treatment of patients with drug-resistant TB.
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Affiliation(s)
- Se-Mi Jeon
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Sanghee Park
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Na-Ra Lim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
| | - Noori Lee
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Jihee Jung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Nackmoon Sung
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon-si 51755, Republic of Korea; (N.L.); (J.J.); (N.S.)
| | - Seonghan Kim
- Division of Bacterial Disease Research, Korea National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju-si 28159, Republic of Korea; (S.-M.J.); (S.P.); (N.-R.L.)
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7
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Goig GA, Menardo F, Salaam-Dreyer Z, Dippenaar A, Streicher EM, Daniels J, Reuter A, Borrell S, Reinhard M, Doetsch A, Beisel C, Warren RM, Cox H, Gagneux S. Effect of compensatory evolution in the emergence and transmission of rifampicin-resistant Mycobacterium tuberculosis in Cape Town, South Africa: a genomic epidemiology study. THE LANCET. MICROBE 2023; 4:e506-e515. [PMID: 37295446 PMCID: PMC10319636 DOI: 10.1016/s2666-5247(23)00110-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/26/2023] [Accepted: 03/01/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Experimental data show that drug-resistance-conferring mutations are often associated with a decrease in the replicative fitness of bacteria in vitro, and that this fitness cost can be mitigated by compensatory mutations; however, the role of compensatory evolution in clinical settings is less clear. We assessed whether compensatory evolution was associated with increased transmission of rifampicin-resistant tuberculosis in Khayelitsha, Cape Town, South Africa. METHODS We did a genomic epidemiological study by analysing available M tuberculosis isolates and their associated clinical data from individuals routinely diagnosed with rifampicin-resistant tuberculosis in primary care and hospitals in Khayelitsha, Cape Town, South Africa. Isolates were collected as part of a previous study. All individuals diagnosed with rifampicin-resistant tuberculosis and with linked biobanked specimens were included in this study. We applied whole-genome sequencing, Bayesian reconstruction of transmission trees, and phylogenetic multivariable regression analysis to identify individual and bacterial factors associated with the transmission of rifampicin-resistant M tuberculosis strains. FINDINGS Between Jan 1, 2008, and Dec 31, 2017, 2161 individuals were diagnosed with multidrug-resistant or rifampicin-resistant tuberculosis in Khayelitsha, Cape Town, South Africa. Whole-genome sequences were available for 1168 (54%) unique individual M tuberculosis isolates. Compensatory evolution was associated with smear-positive pulmonary disease (adjusted odds ratio 1·49, 95% CI 1·08-2·06) and a higher number of drug-resistance-conferring mutations (incidence rate ratio 1·38, 95% CI 1·28-1·48). Compensatory evolution was also associated with increased transmission of rifampicin-resistant disease between individuals (adjusted odds ratio 1·55; 95% CI 1·13-2·12), independent of other patient and bacterial factors. INTERPRETATION Our findings suggest that compensatory evolution enhances the in vivo fitness of drug-resistant M tuberculosis genotypes, both within and between patients, and that the in vitro replicative fitness of rifampicin-resistant M tuberculosis measured in the laboratory correlates with the bacterial fitness measured in clinical settings. These results emphasise the importance of enhancing surveillance and monitoring efforts to prevent the emergence of highly transmissible clones capable of rapidly accumulating new drug resistance mutations. This concern becomes especially crucial at present, because treatment regimens incorporating novel drugs are being implemented. FUNDING Funding for this study was provided by a Swiss and South Africa joint research award (grant numbers 310030_188888, CRSII5_177163, and IZLSZ3_170834), the European Research Council (grant number 883582), and a Wellcome Trust fellowship (to HC; reference number 099818/Z/12/Z). ZS-D was funded through a PhD scholarship from the South African National Research Foundation and RMW was funded through the South African Medical Research Council.
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Affiliation(s)
- Galo A Goig
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland.
| | - Fabrizio Menardo
- Department of Plant and Microbial Biology, University of Zürich, Zürich, Switzerland
| | - Zubeida Salaam-Dreyer
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Anzaan Dippenaar
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Elizabeth M Streicher
- Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Johnny Daniels
- Médecins Sans Frontières, Khayelitsha, Cape Town, South Africa
| | - Anja Reuter
- Médecins Sans Frontières, Khayelitsha, Cape Town, South Africa
| | - Sonia Borrell
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Anna Doetsch
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Christian Beisel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Zürich, Swizterland
| | - Robin M Warren
- Department of Science and Innovation - National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Stellenbosch, South Africa; South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Helen Cox
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, Cape Town, South Africa
| | - Sebastien Gagneux
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
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8
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Kurepina N, Chudaev M, Kreiswirth BN, Nikiforov V, Mustaev A. Mutations compensating for the fitness cost of rifampicin resistance in Escherichia coli exert pleiotropic effect on RNA polymerase catalysis. Nucleic Acids Res 2022; 50:5739-5756. [PMID: 35639764 PMCID: PMC9177976 DOI: 10.1093/nar/gkac406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 04/28/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
The spread of drug-resistant bacteria represents one of the most significant medical problems of our time. Bacterial fitness loss associated with drug resistance can be counteracted by acquisition of secondary mutations, thereby enhancing the virulence of such bacteria. Antibiotic rifampicin (Rif) targets cellular RNA polymerase (RNAP). It is potent broad spectrum drug used for treatment of bacterial infections. We have investigated the compensatory mechanism of the secondary mutations alleviating Rif resistance (Rifr) on biochemical, structural and fitness indices. We find that substitutions in RNAP genes compensating for the growth defect caused by βQ513P and βT563P Rifr mutations significantly enhanced bacterial relative growth rate. By assaying RNAP purified from these strains, we show that compensatory mutations directly stimulated basal transcriptional machinery (2-9-fold) significantly improving promoter clearance step of the transcription pathway as well as elongation rate. Molecular modeling suggests that compensatory mutations affect transcript retention, substrate loading, and nucleotidyl transfer catalysis. Strikingly, one of the identified compensatory substitutions represents mutation conferring rifampicin resistance on its own. This finding reveals an evolutionary process that creates more virulent species by simultaneously improving the fitness and augmenting bacterial drug resistance.
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Affiliation(s)
- Natalia Kurepina
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Maxim Chudaev
- Public Health Research Institute, and Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Vadim Nikiforov
- Public Health Research Institute, and Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Arkady Mustaev
- Public Health Research Institute, and Department of Microbiology, Biochemistry & Molecular Genetics, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
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Rodríguez-Beltrán É, López GD, Anzola JM, Rodríguez-Castillo JG, Carazzone C, Murcia MI. Heterogeneous fitness landscape cues, pknG low expression, and phthiocerol dimycocerosate low production of Mycobacterium tuberculosis ATCC25618 rpoB S450L in enriched broth. Tuberculosis (Edinb) 2021; 132:102156. [PMID: 34891037 DOI: 10.1016/j.tube.2021.102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 11/23/2021] [Accepted: 11/26/2021] [Indexed: 10/19/2022]
Abstract
Multidrug-resistant tuberculosis (isoniazid/rifampin[RIF]-resistant TB) ravages developing countries. Fitness is critical in clinical outcomes. Previous studies on RIF-resistant TB (RR-TB) showed competitive fitness gains and losses, with rpoB-S450L as the most isolated/fit mutation. This study measured virulence/resistance genes, phthiocerol dimycocerosate (PDIM) levels and their relationship with rpoB S450L ATCC25618 RR-TB strain fitness. After obtaining 10 different RR-TB GenoType MTBDRplus 2.0-genotyped isolates (with nontyped, S441, H445 and S450 positions), only one S450L isolate (R9, rpoB-S450L ATCC 25618, RR 1 μg/mL) was observed, with H445Y being the most common. A competitive fitness in vitro assay with wild-type (wt) ATCC 25618: R9 1:1 in 50 mL Middlebrook 7H9/OADC was performed, and generation time (G) in vitro and relative fitness were obtained. mRNA and PDIM were extracted on log and stationary phases. Fitness decreased in rpoB S450L and H445Y strains, with heterogeneous fitness cues in three biological replicas of rpoB-S450L: one high and two low fitness replicas. S450L strain had significant pknG increase. Compared with S450L, wt-rpoB showed increased polyketide synthase ppsA expression and high PDIM peak measured by HPLC-MS in log phase compared to S450L. This contrasts with previously increased PDIM in other RR-TB isolates.
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Affiliation(s)
- Édgar Rodríguez-Beltrán
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia
| | - Gerson-Dirceu López
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, CR 1 18A-12, Bogotá, D.C, 111711, Colombia
| | - Juan Manuel Anzola
- Corpogen, CR 4 20-41, Bogotá, D.C, 110311, Colombia; Universidad Central, CR 5 21-38, Bogotá, D.C, 110311, Colombia
| | - Juan Germán Rodríguez-Castillo
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia
| | - Chiara Carazzone
- Laboratory of Advanced Analytical Techniques in Natural Products (LATNAP), Chemistry Department, Universidad de los Andes, CR 1 18A-12, Bogotá, D.C, 111711, Colombia
| | - Martha I Murcia
- MicobacUN Group, Microbiology Department, The National University of Colombia (NUC) School of Medicine, AV CR 30 45-03, Bogotá, D.C, 111321, Colombia.
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Zhao Y, Liu J. Facing the Challenge of Tuberculosis: Towards "End TB in China by 2035". China CDC Wkly 2021; 3:243-246. [PMID: 34594858 PMCID: PMC8392954 DOI: 10.46234/ccdcw2021.070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/05/2022] Open
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