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Farhat M, Cox H, Ghanem M, Denkinger CM, Rodrigues C, Abd El Aziz MS, Enkh-Amgalan H, Vambe D, Ugarte-Gil C, Furin J, Pai M. Drug-resistant tuberculosis: a persistent global health concern. Nat Rev Microbiol 2024:10.1038/s41579-024-01025-1. [PMID: 38519618 DOI: 10.1038/s41579-024-01025-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2024] [Indexed: 03/25/2024]
Abstract
Drug-resistant tuberculosis (TB) is estimated to cause 13% of all antimicrobial resistance-attributable deaths worldwide and is driven by both ongoing resistance acquisition and person-to-person transmission. Poor outcomes are exacerbated by late diagnosis and inadequate access to effective treatment. Advances in rapid molecular testing have recently improved the diagnosis of TB and drug resistance. Next-generation sequencing of Mycobacterium tuberculosis has increased our understanding of genetic resistance mechanisms and can now detect mutations associated with resistance phenotypes. All-oral, shorter drug regimens that can achieve high cure rates of drug-resistant TB within 6-9 months are now available and recommended but have yet to be scaled to global clinical use. Promising regimens for the prevention of drug-resistant TB among high-risk contacts are supported by early clinical trial data but final results are pending. A person-centred approach is crucial in managing drug-resistant TB to reduce the risk of poor treatment outcomes, side effects, stigma and mental health burden associated with the diagnosis. In this Review, we describe current surveillance of drug-resistant TB and the causes, risk factors and determinants of drug resistance as well as the stigma and mental health considerations associated with it. We discuss recent advances in diagnostics and drug-susceptibility testing and outline the progress in developing better treatment and preventive therapies.
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Affiliation(s)
- Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Helen Cox
- Institute of Infectious Disease and Molecular Medicine, Wellcome Centre for Infectious Disease Research and Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa
| | - Marwan Ghanem
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Claudia M Denkinger
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Infection Research (DZIF), partner site Heidelberg University Hospital, Heidelberg, Germany
| | | | - Mirna S Abd El Aziz
- Division of Infectious Disease and Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Debrah Vambe
- National TB Control Programme, Manzini, Eswatini
| | - Cesar Ugarte-Gil
- School of Public and Population Health, University of Texas Medical Branch, Galveston, TX, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Madhukar Pai
- McGill International TB Centre, McGill University, Montreal, Quebec, Canada.
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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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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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Zhu C, Yang T, Yin J, Jiang H, Takiff HE, Gao Q, Liu Q, Li W. The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains. Microbiol Spectr 2023; 11:e0333922. [PMID: 37272796 PMCID: PMC10434187 DOI: 10.1128/spectrum.03339-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/23/2023] [Indexed: 06/06/2023] Open
Abstract
Strains of the Mycobacterium tuberculosis complex (MTBC) Beijing family aroused concern because they were often found in clusters and appeared to be exceptionally transmissible. However, it was later found that strains of the Beijing family were heterogeneous, and the transmission advantage was restricted to sublineage L2.3 or modern Beijing. In this study, we analyzed the previously published genome sequences of 7,896 L2.3 strains from 51 different countries. Using BEAST software to approximate the temporal emergence of L2.3, our calculations suggest that L2.3 initially emerged in northern East Asia during the early 15th century and subsequently diverged into six phylogenetic clades, identified as L2.3.1 through L2.3.6. Using terminal branch length and genomic clustering as proxies for transmissibility, we found that the six clades displayed distinct population dynamics, with the three recently emerged clades (L2.3.4 to L2.3.6) exhibiting significantly higher transmissibility than the older three clades (L2.3.1 to L2.3.3). Of the Beijing family strains isolated outside East Asia, 83.1% belonged to the clades L2.3.4 to L2.3.6, which were also associated with more cross-border transmission. This work reveals the heterogeneity in sublineage L2.3 and demonstrates that the global success of Beijing family strains is driven by the three recently emerged L2.3 clades. IMPORTANCE The recent population dynamics of the global tuberculosis epidemic are heavily shaped by Mycobacterium tuberculosis complex (MTBC) strains with enhanced transmissibility. The infamous Beijing family strain stands out because it has rapidly spread throughout the world. Identifying the strains responsible for the global expansion and tracing their evolution should help to understand the nature of high transmissibility and develop effective strategies to control transmission. In this study, we found that the L2.3 sublineage diversified into six phylogenetic clades (L2.3.1 to L2.3.6) with various transmission characteristics. Clades L2.3.4 to L2.3.6 exhibited significantly higher transmissibility than clades L2.3.1 to L2.3.3, which helps explain why more than 80% of Beijing family strains collected outside East Asia belong to these three clades. We conclude that the global success of L2.3 was not caused by the entire L2.3 sublineage but rather was due to the rapid expansion of L2.3.4 to L2.3.6. Tracking the transmission of L2.3.4 to L2.3.6 strains can help to formulate targeted TB prevention and control.
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Affiliation(s)
- Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | | | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Científicas, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Kim NY, Kim DY, Chu J, Jung SH. pncA Large Deletion is the Characteristic of Pyrazinamide-Resistant Mycobacterium tuberculosis belonging to the East Asian Lineage. Infect Chemother 2023; 55:247-256. [PMID: 37407242 DOI: 10.3947/ic.2023.0037] [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: 04/05/2023] [Accepted: 05/10/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Pyrazinamide (PZA) is often used as an add-on agent in the treatment of multidrug-resistant tuberculosis, regardless of phenotypic drug susceptibility testing (pDST) results. However, evaluating the effectiveness of PZA is challenging because of its low pH activity, which can result in unreliable pDST results. This study aimed to investigate the genomic characteristics associated with PZA resistance that can be used to develop genotypic DST. MATERIALS AND METHODS A publicly available whole genome sequencing (WGS) dataset of 10,725 Mycobacterium tuberculosis complex genomes (3,326 phenotypically PZA-resistant and 7,399 phenotypically PZA-susceptible isolates) were analyzed. RESULTS In total, 2,934 pncA non-silent mutations were identified in 2,880 isolates (26.9%). Detected mutations were found throughout the entire coding region of pncA in a scattered pattern, of which the most frequent mutation was p.Q10P (n = 278), followed by p.H57D (n = 167) and c.-11A>G (n = 122). The sensitivity and specificity of the group 1 or 2 mutations reported by the World Health Organization (WHO) mutational catalogue were 73.0% and 98.9%, respectively. We further identified 18 novel pncA mutations that were significantly associated with phenotypically PZA-resistant. In addition to these mutations, we identified 102 large deletions in the pncA gene, and all but two isolates were phenotypically resistant to PZA isolates. Notably, pncA deletions were mutually exclusive to pncA mutations, and more than half of the isolates with pncA large deletions belonged to the East Asian lineage (67.6%). The sensitivity, specificity, positive predictive value, and negative predictive value of the pooled variants (group 1 or 2 mutations, novel resistance-associated mutations, and large deletions of the pncA gene) were 79.0%, 98.9%, 97.0%, and 91.3%, respectively. The area under the curve (AUC) value for the pooled variants was significantly higher than the AUC value for the group 1 or 2 mutations (P <0.001), indicating that the pooled variants have a better discriminative ability for predicting PZA resistance. CONCLUSION Using WGS, we found that the pncA mutations are scattered without specific mutational hotspots, and large deletions associated with PZA resistance are more common in the East Asian lineage of M. tuberculosis isolates. Our data also demonstrated the reliability of group 1 or 2 mutations presented in the WHO mutation catalogue and the need for further investigation on group 3 mutations, contributing to the evaluation of the current knowledge base on mutations associated with the PZA-resistant M. tuberculosis complex.
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Affiliation(s)
- Na Yung Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Do Young Kim
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jiyon Chu
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Biochemistry, Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Integrated Research Center for Genomic Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea.
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6
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Ashton PM, Cha J, Anscombe C, Thuong NTT, Thwaites GE, Walker TM. Distribution and origins of Mycobacterium tuberculosis L4 in Southeast Asia. Microb Genom 2023; 9:mgen000955. [PMID: 36729036 PMCID: PMC9997747 DOI: 10.1099/mgen.0.000955] [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: 08/01/2022] [Accepted: 12/21/2022] [Indexed: 02/03/2023] Open
Abstract
Molecular and genomic studies have revealed that Mycobacterium tuberculosis Lineage 4 (L4, Euro-American lineage) emerged in Europe before becoming distributed around the globe by trade routes, colonial migration and other historical connections. Although L4 accounts for tens or hundreds of thousands of tuberculosis (TB) cases in multiple Southeast Asian countries, phylogeographical studies have either focused on a single country or just included Southeast Asia as part of a global analysis. Therefore, we interrogated public genomic data to investigate the historical patterns underlying the distribution of L4 in Southeast Asia and surrounding countries. We downloaded 6037 genomes associated with 29 published studies, focusing on global analyses of L4 and Asian studies of M. tuberculosis. We identified 2256 L4 genomes including 968 from Asia. We show that 81 % of L4 in Thailand, 51 % of L4 in Vietnam and 9 % of L4 in Indonesia belong to sub-lineages of L4 that are rarely seen outside East and Southeast Asia (L4.2.2, L4.4.2 and L4.5). These sub-lineages have spread between East and Southeast Asian countries, with no recent European ancestor. Although there is considerable uncertainty about the exact direction and order of intra-Asian M. tuberculosis dispersal, due to differing sampling frames between countries, our analysis suggests that China may be the intermediate location between Europe and Southeast Asia for two of the three predominantly East and Southeast Asian L4 sub-lineages (L4.2.2 and L4.5). This new perspective on L4 in Southeast Asia raises the possibility of investigating host population-specific evolution and highlights the need for more structured sampling from Southeast Asian countries to provide more certainty of the historical and current routes of dispersal.
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Affiliation(s)
- Philip M. Ashton
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jaeyoon Cha
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Catherine Anscombe
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nguyen T. T. Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study. Antimicrob Agents Chemother 2022; 66:e0207521. [PMID: 35532237 DOI: 10.1128/aac.02075-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Point mutations in the rrs gene and the eis promoter are known to confer resistance to the second-line injectable drugs (SLIDs) amikacin (AMK), capreomycin (CAP), and kanamycin (KAN). While mutations in these canonical genes confer the majority of SLID resistance, alternative mechanisms of resistance are not uncommon and threaten effective treatment decisions when using conventional molecular diagnostics. In total, 1,184 clinical Mycobacterium tuberculosis isolates from 7 countries were studied for genomic markers associated with phenotypic resistance. The markers rrs:A1401G and rrs:G1484T were associated with resistance to all three SLIDs, and three known markers in the eis promoter (eis:G-10A, eis:C-12T, and eis:C-14T) were similarly associated with kanamycin resistance (KAN-R). Among 325, 324, and 270 AMK-R, CAP-R, and KAN-R isolates, 274 (84.3%), 250 (77.2%), and 249 (92.3%) harbored canonical mutations, respectively. Thirteen isolates harbored more than one canonical mutation. Canonical mutations did not account for 103 of the phenotypically resistant isolates. A genome-wide association study identified three genes and promoters with mutations that, on aggregate, were associated with unexplained resistance to at least one SLID. Our analysis associated whiB7 5'-untranslated-region mutations with KAN resistance, supporting clinical relevance for this previously demonstrated mechanism of KAN resistance. We also provide evidence for the novel association of CAP resistance with the promoter of the Rv2680-Rv2681 operon, which encodes an exoribonuclease that may influence the binding of CAP to the ribosome. Aggregating mutations by gene can provide additional insight and therefore is recommended for identifying rare mechanisms of resistance when individual mutations carry insufficient statistical power.
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Dohál M, Dvořáková V, Šperková M, Pinková M, Spitaleri A, Norman A, Cabibbe AM, Rasmussen EM, Porvazník I, Škereňová M, Solovič I, Cirillo DM, Mokrý J. Whole genome sequencing of multidrug-resistant Mycobacterium tuberculosis isolates collected in the Czech Republic, 2005-2020. Sci Rep 2022; 12:7149. [PMID: 35505072 PMCID: PMC9062869 DOI: 10.1038/s41598-022-11287-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/21/2022] [Indexed: 01/11/2023] Open
Abstract
The emergence and spread of resistant tuberculosis (TB) pose a threat to public health, so it is necessary to diagnose the drug-resistant forms in a clinically short time frame and closely monitor their transmission. In this study, we carried out a first whole genome sequencing (WGS)-based analysis of multidrug resistant (MDR) M. tuberculosis strains to explore the phylogenetic lineages diversity, drug resistance mechanisms, and ongoing transmission chains within the country. In total, 65 isolates phenotypically resistant to at least rifampicin and isoniazid collected in the Czech Republic in 2005-2020 were enrolled for further analysis. The agreement of the results obtained by WGS with phenotypic drug susceptibility testing (pDST) in the determination of resistance to isoniazid, rifampicin, pyrazinamide, streptomycin, second-line injectables and fluoroquinolones was more than 80%. Phylogenetic analysis of WGS data revealed that the majority of MDR M. tuberculosis isolates were the Beijing lineage 2.2.1 (n = 46/65; 70.8%), while the remaining strains belonged to Euro-American lineage. Cluster analysis with a predefined cut-off distance of less than 12 single nucleotide polymorphisms between isolates showed 19 isolates in 6 clusters (clustering rate 29.2%), located mainly in the region of the capital city of Prague. This study highlights the utility of WGS as a high-resolution approach in the diagnosis, characterization of resistance patterns, and molecular-epidemiological analysis of resistant TB in the country.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia.
| | - Věra Dvořáková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Miluše Šperková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Martina Pinková
- National Reference Laboratory for Mycobacteria, National Institute of Public Health, Praha, Czech Republic
| | - Andrea Spitaleri
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Mária Škereňová
- Department of Molecular Medicine and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
- Department of Clinical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
- Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Centre Martin, Jessenius Faculty of Medicine in Martin, Comenius University, Bratislava, Slovakia
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Yokobori N, López B, Ritacco V. The host-pathogen-environment triad: Lessons learned through the study of the multidrug-resistant Mycobacterium tuberculosis M strain. Tuberculosis (Edinb) 2022; 134:102200. [PMID: 35339874 DOI: 10.1016/j.tube.2022.102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
Multidrug-resistant tuberculosis is one of the major obstacles that face the tuberculosis eradication efforts. Drug-resistant Mycobacterium tuberculosis clones were initially disregarded as a public health threat, because they were assumed to have paid a high fitness cost in exchange of resistance acquisition. However, some genotypes manage to overcome the impact of drug-resistance conferring mutations, retain transmissibility and cause large outbreaks. In Argentina, the HIV-AIDS epidemics fuelled the expansion of the so-called M strain in the early 1990s, which is responsible for the largest recorded multidrug-resistant tuberculosis cluster of Latin America. The aim of this work is to review the knowledge gathered after nearly three decades of multidisciplinary research on epidemiological, microbiological and immunological aspects of this highly successful strain. Collectively, our results indicate that the successful transmission of the M strain could be ascribed to its unaltered virulence, low Th1/Th17 response, a low fitness cost imposed by the resistance conferring mutations and a high resistance to host-related stress. In the early 2000s, the incident cases due to the M strain steadily declined and stabilized in the latest years. Improvements in the management, diagnosis and treatment of multidrug-resistant tuberculosis along with societal factors such as the low domestic and international mobility of the patients affected by this strain probably contributed to the outbreak containment. This stresses the importance of sustaining the public health interventions to avoid the resurgence of this conspicuous multidrug-resistant strain.
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Affiliation(s)
- Noemí Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
| | - Beatriz López
- Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina.
| | - Viviana Ritacco
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
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10
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The Structural Basis of Mycobacterium tuberculosis RpoB Drug-Resistant Clinical Mutations on Rifampicin Drug Binding. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030885. [PMID: 35164151 PMCID: PMC8839920 DOI: 10.3390/molecules27030885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB), caused by the Mycobacterium tuberculosis infection, continues to be a leading cause of morbidity and mortality in developing countries. Resistance to the first-line anti-TB drugs, isoniazid (INH) and rifampicin (RIF), is a major drawback to effective TB treatment. Genetic mutations in the β-subunit of the DNA-directed RNA polymerase (rpoB) are reported to be a major reason of RIF resistance. However, the structural basis and mechanisms of these resistant mutations are insufficiently understood. In the present study, thirty drug-resistant mutants of rpoB were initially modeled and screened against RIF via a comparative molecular docking analysis with the wild-type (WT) model. These analyses prioritized six mutants (Asp441Val, Ser456Trp, Ser456Gln, Arg454Gln, His451Gly, and His451Pro) that showed adverse binding affinities, molecular interactions, and RIF binding hinderance properties, with respect to the WT. These mutant models were subsequently analyzed by molecular dynamics (MD) simulations. One-hundred nanosecond all-atom MD simulations, binding free energy calculations, and a dynamic residue network analysis (DRN) were employed to exhaustively assess the impact of mutations on RIF binding dynamics. Considering the global structural motions and protein-ligand binding affinities, the Asp441Val, Ser456Gln, and His454Pro mutations generally yielded detrimental effects on RIF binding. Locally, we found that the electrostatic contributions to binding, particularly by Arg454 and Glu487, might be adjusted to counteract resistance. The DRN analysis revealed that all mutations mostly distorted the communication values of the critical hubs and may, therefore, confer conformational changes in rpoB to perturb RIF binding. In principle, the approach combined fundamental molecular modeling tools for robust "global" and "local" level analyses of structural dynamics, making it well suited for investigating other similar drug resistance cases.
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Han Z, Li J, Sun G, Gu K, Zhang Y, Yao H, Jiang Y. Transmission of multidrug-resistant tuberculosis in Shimen community in Shanghai, China: a molecular epidemiology study. BMC Infect Dis 2021; 21:1118. [PMID: 34715793 PMCID: PMC8557015 DOI: 10.1186/s12879-021-06725-0] [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: 11/08/2020] [Accepted: 08/20/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) has become a major public health problem in China, with mounting evidence suggesting that recent transmission accounts for the majority of MDR-TB. Here we aimed to reveal the transmission pattern of an MDR-TB outbreak in the Jing'an District of Shanghai between 2010 and 2015. METHODS We used whole-genome sequencing (WGS) to conduct genomic clustering analysis along with field epidemiological investigation to determine the transmission pattern and drug resistance profile of a cluster with ten MDR-TB patients in combining field epidemiological investigation. RESULTS The ten MDR-TB patients with genotypically clustered Beijing lineage strains lived in a densely populated, old alley with direct or indirect contact history. The analysis of genomic data showed that the genetic distances of the ten strains (excluding drug-resistant mutations) were 0-20 single nucleotide polymorphisms (SNPs), with an average distance of 9 SNPs, suggesting that the ten MDR-TB patients were infected and developed the onset of illness by the recent transmission of M. tuberculosis. The genetic analysis confirmed definite epidemiological links between the clustered cases. CONCLUSIONS The integration of the genotyping tool in routine tuberculosis surveillance can play a substantial role in the detection of MDR-TB transmission events. The leverage of genomic analysis in combination with the epidemiological investigation could further elucidate transmission patterns. Whole-genome sequencing could be integrated into intensive case-finding strategies to identify missed cases of MDR-TB and strengthen efforts to interrupt transmission.
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Affiliation(s)
- Zhiying Han
- Department of Tuberculosis Prevention and Control, Jing'an District Center for Disease Control and Prevention, Shanghai, 200072, China.
| | - Jing Li
- Tuberculosis Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Guomei Sun
- Department of Tuberculosis Prevention and Control, Jing'an District Center for Disease Control and Prevention, Shanghai, 200072, China
| | - Kaikan Gu
- Department of Tuberculosis Prevention and Control, Jing'an District Center for Disease Control and Prevention, Shanghai, 200072, China
| | - Yangyi Zhang
- Tuberculosis Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China
| | - Hui Yao
- Second Shimen Road Community Health Center, Shanghai, China
| | - Yuan Jiang
- Tuberculosis Laboratory, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, 200036, China.
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Waturuocha UW, P. J. A, Singh KK, Malhotra V, Krishna MS, Saini DK. A high-frequency single nucleotide polymorphism in the MtrB sensor kinase in clinical strains of Mycobacterium tuberculosis alters its biochemical and physiological properties. PLoS One 2021; 16:e0256664. [PMID: 34529706 PMCID: PMC8445491 DOI: 10.1371/journal.pone.0256664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/11/2021] [Indexed: 11/19/2022] Open
Abstract
The DNA polymorphisms found in clinical strains of Mycobacterium tuberculosis drive altered physiology, virulence, and pathogenesis in them. Although the lineages of these clinical strains can be traced back to common ancestor/s, there exists a plethora of difference between them, compared to those that have evolved in the laboratory. We identify a mutation present in ~80% of clinical strains, which maps in the HATPase domain of the sensor kinase MtrB and alters kinase and phosphatase activities, and affects its physiological role. The changes conferred by the mutation were probed by in-vitro biochemical assays which revealed changes in signaling properties of the sensor kinase. These changes also affect bacterial cell division rates, size and membrane properties. The study highlights the impact of DNA polymorphisms on the pathophysiology of clinical strains and provides insights into underlying mechanisms that drive signal transduction in pathogenic bacteria.
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Affiliation(s)
- Uchenna Watson Waturuocha
- Department of Studies in Zoology, Manasagangotri, University of Mysore, Mysore, India
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Athira P. J.
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Krishna Kumar Singh
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
| | - Vandana Malhotra
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, Delhi, India
| | - M. S. Krishna
- Department of Studies in Zoology, Manasagangotri, University of Mysore, Mysore, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, India
- Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
- * E-mail:
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Ma P, Luo T, Ge L, Chen Z, Wang X, Zhao R, Liao W, Bao L. Compensatory effects of M. tuberculosis rpoB mutations outside the rifampicin resistance-determining region. Emerg Microbes Infect 2021; 10:743-752. [PMID: 33775224 PMCID: PMC8057087 DOI: 10.1080/22221751.2021.1908096] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Mycobacterium tuberculosis has been observed to develop resistance to the frontline anti-tuberculosis drug rifampicin, primarily through mutations in the rifampicin resistance-determining region (RRDR) of rpoB. While these mutations have been determined to confer a fitness cost, compensatory mutations in rpoA and rpoC that may enhance the fitness of resistant strains have been demonstrated. Recent genomic studies identified several rpoB non-RRDR mutations that co-occurred with RRDR mutations in clinical isolates without rpoA/rpoC mutations and may confer fitness compensation. In this study, we identified 33 evolutionarily convergent rpoB non-RRDR mutations through phylogenomic analysis of public genomic data for clinical M. tuberculosis isolates. We found that none of these mutations, except V170F and I491F, can cause rifampin resistance in Mycolicibacterium smegmatis. The compensatory effects of five representative mutations across rpoB were evaluated by an in vitro competition assay, through which we observed that each of these mutations can significantly improve the relative fitness of the initial S450L mutant (0.97–1.08 vs 0.87). Furthermore, we observed that the decreased RNAP transcription efficiency introduced by S450L was significantly alleviated by each of the five mutations. Structural analysis indicated that the fitness compensation observed for the non-RRDR mutations might be achieved by modification of the RpoB active centre or by changes in interactions between RNAP subunits. Our results provide experimental evidence supporting that compensatory effects are exerted by several rpoB non-RRDR mutations, which could be utilized as additional molecular markers for predicting the fitness of clinical rifampin-resistant M. tuberculosis strains.
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Affiliation(s)
- Pengjiao Ma
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Tao Luo
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Liang Ge
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Zonghai Chen
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Xinyan Wang
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Rongchuan Zhao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Wei Liao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Lang Bao
- Laboratory of Infection and Immunity, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [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: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Brandis G, Granström S, Leber AT, Bartke K, Garoff L, Cao S, Huseby DL, Hughes D. Mutant RNA polymerase can reduce susceptibility to antibiotics via ppGpp-independent induction of a stringent-like response. J Antimicrob Chemother 2021; 76:606-615. [PMID: 33221850 PMCID: PMC7879142 DOI: 10.1093/jac/dkaa469] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 10/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background Mutations in RNA polymerase (RNAP) can reduce susceptibility to ciprofloxacin in Escherichia coli, but the mechanism of transcriptional reprogramming responsible is unknown. Strains carrying ciprofloxacin-resistant (CipR) rpoB mutations have reduced growth fitness and their impact on clinical resistance development is unclear. Objectives To assess the potential for CipRrpoB mutations to contribute to resistance development by estimating the number of distinct alleles. To identify fitness-compensatory mutations that ameliorate the fitness costs of CipRrpoB mutations. To understand how CipRrpoB mutations reprogramme RNAP. Methods E. coli strains carrying five different CipRrpoB alleles were evolved with selection for improved fitness and characterized for acquired mutations, relative fitness and MICCip. The effects of dksA mutations and a ppGpp0 background on growth and susceptibility phenotypes associated with CipRrpoB alleles were determined. Results The number of distinct CipRrpoB mutations was estimated to be >100. Mutations in RNAP genes and in dksA can compensate for the fitness cost of CipRrpoB mutations. Deletion of dksA reduced the MICCip for strains carrying CipRrpoB alleles. A ppGpp0 phenotype had no effect on drug susceptibility. Conclusions CipRrpoB mutations induce an ppGpp-independent stringent-like response. Approximately half of the reduction in ciprofloxacin susceptibility is caused by an increased affinity of RNAP to DksA while the other half is independent of DksA. Stringent-like response activating mutations might be the most diverse class of mutations reducing susceptibility to antibiotics.
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Affiliation(s)
- Gerrit Brandis
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Susanna Granström
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Anna T Leber
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Katrin Bartke
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Douglas L Huseby
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Box 582, Biomedical Center, Uppsala University, Sweden
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Alame Emane AK, Guo X, Takiff HE, Liu S. Highly transmitted M. tuberculosis strains are more likely to evolve MDR/XDR and cause outbreaks, but what makes them highly transmitted? Tuberculosis (Edinb) 2021; 129:102092. [PMID: 34102584 DOI: 10.1016/j.tube.2021.102092] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Multi-Drug-Resistant strains of Mycobacterium tuberculosis (MDR-TB) are a serious obstacle to global TB eradication. While most MDR-TB strains are infrequently transmitted, a few cause large transmission clusters that contribute substantially to local MDR-TB burdens. Here we examine whether the known mutations in these strains can explain their success. Drug resistance mutations differ in fitness costs and strains can also acquire compensatory mutations (CM) to restore fitness, but some highly transmitted MDR strains have no CM. The acquisition of resistance mutations that maintain high transmissibility seems to occur by chance and are more likely in strains that are intrinsically highly transmitted and cause many cases. Modern Beijing lineage strains have caused several large outbreaks, but MDR outbreaks are also caused by ancient Beijing and lineage 4 strains, suggesting the lineage is less important than the characteristics of the individual strain. The development of fluoroquinolone resistance appears to represent another level of selection, in which strains must surmount unknown fitness costs of gyrA mutations. The genetic determinants of high transmission are poorly defined but may involve genes encoding proteins involved in molybdenum acquisition and the Esx systems. In addition, strains eliciting lower cytokine responses and producing more caseating granulomas may have advantages for transmission. Successful MDR/XDR strains generally evolve from highly transmitted drug sensitive parent strains due to selection pressures from deficiencies in local TB control programs. Until TB incidence is considerably reduced, there will likely be highly transmitted strains that develop resistance to any new antibiotic.
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Affiliation(s)
- Amel Kevin Alame Emane
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Xujun Guo
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Howard E Takiff
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China; Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75015, France; Laboratorio de Genética Molecular, CMBC, IVIC, Km. 11 Carr. Panamericana, Caracas, Venezuela.
| | - Shengyuan Liu
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
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18
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Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics 2021; 36:100471. [PMID: 34256273 DOI: 10.1016/j.epidem.2021.100471] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 01/14/2020] [Accepted: 05/17/2021] [Indexed: 11/22/2022] Open
Abstract
As multi-drug resistant tuberculosis (MDR-TB) continues to spread, investigating the transmission potential of different drug-resistant strains becomes an ever more pressing topic in public health. While phylogenetic and transmission tree inferences provide valuable insight into possible transmission chains, phylodynamic inference combines evolutionary and epidemiological analyses to estimate the parameters of the underlying epidemiological processes, allowing us to describe the overall dynamics of disease spread in the population. In this study, we introduce an approach to Mycobacterium tuberculosis (M. tuberculosis) phylodynamic analysis employing an existing computationally efficient model to quantify the transmission fitness costs of drug resistance with respect to drug-sensitive strains. To determine the accuracy and precision of our approach, we first perform a simulation study, mimicking the simultaneous spread of drug-sensitive and drug-resistant tuberculosis (TB) strains. We analyse the simulated transmission trees using the phylodynamic multi-type birth-death model (MTBD, (Kühnert et al., 2016)) within the BEAST2 framework and show that this model can estimate the parameters of the epidemic well, despite the simplifying assumptions that MTBD makes compared to the complex TB transmission dynamics used for simulation. We then apply the MTBD model to an M. tuberculosis lineage 4 dataset that primarily consists of MDR sequences. Some of the MDR strains additionally exhibit resistance to pyrazinamide - an important first-line anti-tuberculosis drug. Our results support the previously proposed hypothesis that pyrazinamide resistance confers a transmission fitness cost to the bacterium, which we quantify for the given dataset. Importantly, our sensitivity analyses show that the estimates are robust to different prior distributions on the resistance acquisition rate, but are affected by the size of the dataset - i.e. we estimate a higher fitness cost when using fewer sequences for analysis. Overall, we propose that MTBD can be used to quantify the transmission fitness cost for a wide range of pathogens where the strains can be appropriately divided into two or more categories with distinct properties.
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Singh P, Jamal S, Ahmed F, Saqib N, Mehra S, Ali W, Roy D, Ehtesham NZ, Hasnain SE. Computational modeling and bioinformatic analyses of functional mutations in drug target genes in Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:2423-2446. [PMID: 34025934 PMCID: PMC8113780 DOI: 10.1016/j.csbj.2021.04.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/09/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022] Open
Abstract
MycoTRAP-DB, a database of mutations and their impact on normal functionality of protein in M.tb genes. Several secondary mutations were identified with significant impact on protein structure and function. Comprehensive information gives insight for screening of suspected hotspots in advance to combat drug resistant TB.
Tuberculosis (TB) continues to be the leading cause of deaths due to its persistent drug resistance and the consequent ineffectiveness of anti-TB treatment. Recent years witnessed huge amount of sequencing data, revealing mutations responsible for drug resistance. However, the lack of an up-to-date repository remains a barrier towards utilization of these data and identifying major mutations-associated with resistance. Amongst all mutations, non-synonymous mutations alter the amino acid sequence of a protein and have a much greater effect on pathogenicity. Hence, this type of gene mutation is of prime interest of the present study. The purpose of this study is to develop an updated database comprising almost all reported substitutions within the Mycobacterium tuberculosis (M.tb) drug target genes rpoB, inhA, katG, pncA, gyrA and gyrB. Various bioinformatics prediction tools were used to assess the structural and biophysical impacts of the resistance causing non-synonymous single nucleotide polymorphisms (nsSNPs) at the molecular level. This was followed by evaluating the impact of these mutations on binding affinity of the drugs to target proteins. We have developed a comprehensive online resource named MycoTRAP-DB (Mycobacterium tuberculosis Resistance Associated Polymorphisms Database) that connects mutations in genes with their structural, functional and pathogenic implications on protein. This database is accessible at http://139.59.12.92. This integrated platform would enable comprehensive analysis and prioritization of SNPs for the development of improved diagnostics and antimycobacterial medications. Moreover, our study puts forward secondary mutations that can be important for prognostic assessments of drug-resistance mechanism and actionable anti-TB drugs.
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Affiliation(s)
- Pooja Singh
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Salma Jamal
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Faraz Ahmed
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Najumu Saqib
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Seema Mehra
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Waseem Ali
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110062, India
| | - Deodutta Roy
- Department of Environmental and Occupational Health, Florida International University, Miami 33029, USA
| | - Nasreen Z Ehtesham
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, India
| | - Seyed E Hasnain
- Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida 201301, India.,Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Delhi (IIT-D), Hauz Khas, New Delhi 110016, India
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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21
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Chen X, He G, Lin S, Wang S, Sun F, Chen J, Zhang W. Analysis of Serial Multidrug-Resistant Tuberculosis Strains Causing Treatment Failure and Within-Host Evolution by Whole-Genome Sequencing. mSphere 2020; 5:e00884-20. [PMID: 33361124 PMCID: PMC7763549 DOI: 10.1128/msphere.00884-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/20/2020] [Indexed: 11/20/2022] Open
Abstract
The cure rate of multidrug-resistant tuberculosis (MDR-TB) is relatively low in China. The reasons for the treatment failure and within-host evolution during treatment have not been sufficiently studied. All MDR-TB patients receiving standard treatment from January 2014 to September 2016 at a designated TB Hospital in Zhejiang Province were retrospectively included and grouped according to their known treatment outcome. Clinical information was collected. Baseline strains of all patients and serial strains of treatment-failure patients were revived. Drug susceptibility tests (DSTs) of 14 drugs and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were performed. The genetic distance and within-host evolution were investigated based on SNPs. In total, 20 treatment failure patients and 74 patients who succeeded in treatment were included. The number of effective drugs for patients who failed treatment was no more than three. Eighteen (90.0%) treatment-failure patients were characterized by a continuous infection of the primary strain, of which 14 patients (77.8%) developed phenotypic or genotypic acquired drug resistance under ineffective treatment. Acquired resistance to amikacin and moxifloxacin (2.0 mg/ml) was detected most frequently, in 5 and 4 patients, respectively. The insufficient number of effective drugs in the combined treatment regimen was the main reason for MDR-TB treatment failure. The study emphasizes the importance of DST for second-line drugs when implementing the second-line drug regimen in MDR-TB patients. For patients with risk factors for MDR-TB, DST of second-line antituberculosis drugs should be performed at initiation of treatment. Second-line drugs should be selected based on the results of DST to avoid acquired resistance. WGS detects low-frequency resistance mutations and heterogeneous resistance with high sensitivity, which is of great significance for guiding clinical treatment and preventing acquired resistance.IMPORTANCE Few studies have focused on the reasons for the low cure rate of multidrug-resistant tuberculosis in China and within-host evolution during treatment, which is of great significance for improving clinical treatment regimens. Acquired resistance events were common during the ineffective treatment, among which resistance to amikacin and high-level moxifloxacin were the most common. The main reason for the treatment failure of MDR-TB patients was insufficient effective drugs, which may lead to higher levels of drug resistance in MDR-TB strains. Therefore, the study emphasizes the importance of DST in the development of second-line treatment regimen when there is a risk of MDR. By performing whole-genome sequencing of serial strains from patients with treatment failure, we found that WGS can detect low-frequency resistance mutations and heterogeneous resistance with high sensitivity. It is thus recommended to conduct drug susceptibility tests at the beginning of treatment and repeat the DST when the sputum bacteria remain positive.
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Affiliation(s)
- Xinchang Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Guiqing He
- Department of Infectious Diseases, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, China
| | - Siran Lin
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Shiyong Wang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Feng Sun
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, School of Life Science, 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) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
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22
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Perdigão J, Silva C, Maltez F, Machado D, Miranda A, Couto I, Rabna P, Florez de Sessions P, Phelan J, Pain A, McNerney R, Hibberd ML, Mokrousov I, Clark TG, Viveiros M, Portugal I. Emergence of multidrug-resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. Emerg Microbes Infect 2020; 9:1342-1353. [PMID: 32538300 PMCID: PMC7473242 DOI: 10.1080/22221751.2020.1774425] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/17/2020] [Accepted: 05/14/2020] [Indexed: 11/22/2022]
Abstract
The Beijing genotype comprises a highly disseminated strain type that is frequently associated with multidrug resistant (MDR) tuberculosis (TB) and increased transmissibility but, countries such as Portugal and Guinea-Bissau fall outside the regions phylogeographically associated with this specific genotype. Nevertheless, recent data shows that this genotype might be gradually emerging in these two countries as an underlying cause of primary MDR-TB. Here, we describe the emergence of Mycobacterium tuberculosis Beijing strains associated with MDR-TB in Portugal and Guinea-Bissau demonstrating the presence of the well described superclusters 100-32 and 94-32 in Portugal and Guinea-Bissau, respectively. Genome-wide analysis and comparison with a global genomic dataset of M. tuberculosis Beijing strains, revealed the presence of two genomic clusters encompassing isolates from Portugal and Guinea-Bissau, GC1 (n = 121) and GC2 (n = 39), both of which bore SNP signatures compatible with the 100-32/B0/W148 and 94-32/Central Asia Outbreak clades, respectively. Moreover, GC2 encompasses a cross-border cluster between Portugal, Guinea-Bissau and Brazil thus supporting migration-associated introduction of MDR-TB and subsequent clonal expansion at the community-level. The comparison with global Beijing datasets demonstrates the global reach of the disease and its complex dissemination across multiple countries while in parallel there are clear microevolutionary trajectories towards extensively drug resistant TB.
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Affiliation(s)
- João Perdigão
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carla Silva
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Fernando Maltez
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral-CHLC, Lisboa, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Isabel Couto
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Paulo Rabna
- Instituto Nacional de Saúde Pública/Projecto de Saúde de Bandim (INASA/PSB), Bissau,Guiné-Bissau
| | | | - Jody Phelan
- London School of Hygiene & Tropical Medicine, London, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St Petersburg Pasteur Institute, St Petersburg, Russia
| | - Taane G. Clark
- London School of Hygiene & Tropical Medicine, London, UK
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Isabel Portugal
- iMed.ULisboa – Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
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23
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HIV Coinfection Is Associated with Low-Fitness rpoB Variants in Rifampicin-Resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:AAC.00782-20. [PMID: 32718966 PMCID: PMC7508592 DOI: 10.1128/aac.00782-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
We analyzed 312 drug-resistant genomes of Mycobacterium tuberculosis isolates collected from HIV-coinfected and HIV-negative TB patients from nine countries with a high tuberculosis burden. We found that rifampicin-resistant M. tuberculosis strains isolated from HIV-coinfected patients carried disproportionally more resistance-conferring mutations in rpoB that are associated with a low fitness in the absence of the drug, suggesting these low-fitness rpoB variants can thrive in the context of reduced host immunity.
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24
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Grandjean L, Monteserin J, Gilman R, Pauschardt J, Rokadiya S, Bonilla C, Ritacco V, Vidal JR, Parkhill J, Peacock S, Moore DA, Balloux F. Association between bacterial homoplastic variants and radiological pathology in tuberculosis. Thorax 2020; 75:584-591. [PMID: 32546574 PMCID: PMC7361023 DOI: 10.1136/thoraxjnl-2019-213281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Understanding how pathogen genetic factors contribute to pathology in TB could enable tailored treatments to the most pathogenic and infectious strains. New strategies are needed to control drug-resistant TB, which requires longer and costlier treatment. We hypothesised that the severity of radiological pathology on the chest radiograph in TB disease was associated with variants arising independently, multiple times (homoplasies) in the Mycobacterium tuberculosis genome. METHODS We performed whole genome sequencing (Illumina HiSeq2000 platform) on M. tuberculosis isolates from 103 patients with drug-resistant TB in Lima between 2010 and 2013. Variables including age, sex, HIV status, previous TB disease and the percentage of lung involvement on the pretreatment chest radiograph were collected from health posts of the national TB programme. Genomic variants were identified using standard pipelines. RESULTS Two mutations were significantly associated with more widespread radiological pathology in a multivariable regression model controlling for confounding variables (Rv2828c.141, RR 1.3, 95% CI 1.21 to 1.39, p<0.01; rpoC.1040 95% CI 1.77 to 2.16, RR 1.9, p<0.01). The rpoB.450 mutation was associated with less extensive radiological pathology (RR 0.81, 95% CI 0.69 to 0.94, p=0.03), suggestive of a bacterial fitness cost for this mutation in vivo. Patients with a previous episode of TB disease and those between 10 and 30 years of age also had significantly increased radiological pathology. CONCLUSIONS This study is the first to compare the M. tuberculosis genome to radiological pathology on the chest radiograph. We identified two variants significantly positively associated with more widespread radiological pathology and one with reduced pathology. Prospective studies are warranted to determine whether mutations associated with increased pathology also predict the spread of drug-resistant TB.
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Affiliation(s)
- Louis Grandjean
- Department of Medicine, Imperial College London, London, UK .,Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Institute of Child Health, UCL Division of Infection and Immunity, London, UK
| | - Joha Monteserin
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Robert Gilman
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Julia Pauschardt
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru
| | - Sakib Rokadiya
- Faculty of Medicine, Imperial College London, London, UK
| | - Cesar Bonilla
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Julia Rios Vidal
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sharon Peacock
- Faculty of Medicine, University of Cambridge, Cambridge, UK
| | - David Aj Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK
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25
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Vargas AP, Rios AA, Grandjean L, Kirwan DE, Gilman RH, Sheen P, Zimic MJ. Determination of potentially novel compensatory mutations in rpoc associated with rifampin resistance and rpob mutations in Mycobacterium tuberculosis Clinical isolates from peru. Int J Mycobacteriol 2020; 9:121-137. [PMID: 32474533 PMCID: PMC10022416 DOI: 10.4103/ijmy.ijmy_27_20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Rifampicin (RIF) resistance in Mycobacterium tuberculosis is frequently caused by mutations in the rpoB gene. These mutations are associated with a fitness cost, which can be overcome by compensatory mutations in other genes, among which rpoC may be the most important. We analyzed 469 Peruvian M. tuberculosis clinical isolates to identify compensatory mutations in rpoC/rpoA associated with RIF resistance. Methods The M. tuberculosis isolates were collected and tested for RIF susceptibility and spoligotyping. Samples were sequenced and aligned to the reference genome to identify mutations. By analyzing the sequences and the metadata, we identified a list of rpoC mutations exclusively associated with RIF resistance and mutations in rpoB. We then evaluated the distribution of these mutations along the protein sequence and tridimensional structure. Results One hundred and twenty-five strains were RIF susceptible and 346 were resistant. We identified 35 potential new compensatory mutations, some of which were distributed on the interface surface between rpoB and rpoC, arising in clusters and suggesting the presence of hotspots for compensatory mutations. Conclusion This study identifies 35 putative novel compensatory mutations in the β' subunit of M. tuberculosis RNApol. Six of these (S428T, L507V, A734V, I997V, and V1252LM) are considered most likely to have a compensatory role, as they fall in the interaction zone of the two subunits and the mutation did not lead to any change in the protein's physical-chemical properties.
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Affiliation(s)
- Ana Paula Vargas
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Angela A. Rios
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louis Grandjean
- Department of Paediatric Infectious Diseases, Imperial College, University of London, London, England
| | - Daniela E. Kirwan
- Infection and Immunity Research Institute, St. George’s, University of London, London, England
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Patricia Sheen
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko J. Zimic
- Department of Cellular and Molecular Sciences, Laboratory of Bioinformatics and Molecular Biology, Faculty of Science and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
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26
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Choudhury A, Fenster JA, Fankhauser RG, Kaar JL, Tenaillon O, Gill RT. CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli. Mol Syst Biol 2020; 16:e9265. [PMID: 32175691 PMCID: PMC7073797 DOI: 10.15252/msb.20199265] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/14/2023] Open
Abstract
Deep mutational scanning can provide significant insights into the function of essential genes in bacteria. Here, we developed a high-throughput method for mutating essential genes of Escherichia coli in their native genetic context. We used Cas9-mediated recombineering to introduce a library of mutations, created by error-prone PCR, within a gene fragment on the genome using a single gRNA pre-validated for high efficiency. Tracking mutation frequency through deep sequencing revealed biases in the position and the number of the introduced mutations. We overcame these biases by increasing the homology arm length and blocking mismatch repair to achieve a mutation efficiency of 85% for non-essential genes and 55% for essential genes. These experiments also improved our understanding of poorly characterized recombineering process using dsDNA donors with single nucleotide changes. Finally, we applied our technology to target rpoB, the beta subunit of RNA polymerase, to study resistance against rifampicin. In a single experiment, we validate multiple biochemical and clinical observations made in the previous decades and provide insights into resistance compensation with the study of double mutants.
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Affiliation(s)
- Alaksh Choudhury
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- IAMEINSERMUniversité de ParisParisFrance
| | - Jacob A Fenster
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Joel L Kaar
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
| | | | - Ryan T Gill
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderCOUSA
- Renewable & Sustainable Energy InstituteUniversity of ColoradoBoulderCOUSA
- Novo Nordisk Foundation Center for BiosustainabilityDanish Technical UniversityCopenhagenDenmark
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27
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Wang S, Zhou Y, Zhao B, Ou X, Xia H, Zheng Y, Song Y, Cheng Q, Wang X, Zhao Y. Characteristics of compensatory mutations in the rpoC gene and their association with compensated transmission of Mycobacterium tuberculosis. Front Med 2020; 14:51-59. [PMID: 31938981 DOI: 10.1007/s11684-019-0720-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/07/2019] [Indexed: 11/26/2022]
Abstract
The aim of this study was to characterize rpoC gene mutations in Mycobacterium tuberculosis (MTB) and investigate the factors associated with rpoC mutations and the relation between rpoC mutations and tuberculosis (TB) transmission. A total of 245 MTB clinical isolates from patients with TB in six provinces and two municipalities in China were characterized based on gene mutations through DNA sequencing of rpoC and rpoB genes, phenotyping via standard drug susceptibility testing, and genotypic profiling by mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. Approximately 36.4% of the rifampin-resistant isolates harbored nonsynonymous mutations in the rpoC gene. Twenty-nine nonsynonymous single mutations and three double mutations were identified. The rpoC mutations at locus 483 (11.3%) were predominant, and the mutations at V483G, W484G, I491V, L516P, L566R, N698K, and A788E accounted for 54.5% of the total detected mutations. Fifteen new mutations in the rpoC gene were identified. Rifampin resistance and rpoB mutations at locus 531 were significantly associated with rpoC mutations. MIRU-VNTR genotype results indicated that 18.4% of the studied isolates were clustered, and the rpoC mutations were not significantly associated with MIRU-VNTR clusters. A large proportion of rpoC mutation was observed in the rifampicin-resistant MTB isolates. However, the findings of this study do not support the association of rpoC mutation with compensated transmissibility.
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Affiliation(s)
- Shengfen Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Zhou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yang Zheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yuanyuan Song
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Qian Cheng
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinyang Wang
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
- Department of Microbiology, Basic Medicine College, Harbin Medical University, Harbin, 150081, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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28
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2019; 113:336-351. [PMID: 31903874 PMCID: PMC7006823 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- MI Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - JG Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - MI Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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29
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Black AT, Hamblion EL, Buttivant H, Anderson SR, Stone M, Casali N, Drobniewski F, Nwoguh F, Marshall BG, Booth L. Tracking and responding to an outbreak of tuberculosis using MIRU-VNTR genotyping and whole genome sequencing as epidemiological tools. J Public Health (Oxf) 2019; 40:e66-e73. [PMID: 29106587 DOI: 10.1093/pubmed/fdx075] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/13/2017] [Indexed: 11/13/2022] Open
Abstract
Background We describe an outbreak that contributed to a near doubling of the incidence of tuberculosis in Southampton, UK. We examine the importance of 24 locus mycobacterial interspersed repetitive unit variable number tandem repeat (MIRU-VNTR) genotyping in its identification and management and the role of whole genome sequencing (WGS) in tracing the spread of the strain. Methods Outbreak cases were defined as those diagnosed between January and December 2011 with indistinguishable 24 locus-MIRU-VNTR genotypes or, cases linked epidemiologically. A cluster questionnaire was administered by TB nurses to identify contacts and social settings. Results Overall, 25 patients fulfilled the case definition. No cases with this MIRU-VNTR genotype had been detected in the UK previously. Connections were found between all cases through household contacts or social venues including a football club, Internet cafe and barber's shop. Public health actions included extended contact tracing, venue screening and TB awareness-raising. The outbreak resulted in a high rate of transmission and high incidence of clinical disease among contacts. Conclusions This outbreak illustrates the value of combining active case-finding with prospective MIRU-VNTR genotyping to identify settings to undertake public health action. In addition WGS revealed that the VNTR-defined cluster was a single outbreak and that active TB transmission not reactivation was responsible for this outbreak in non-UK born individuals.
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Affiliation(s)
- Anne T Black
- Public Health England Wessex Centre, Whiteley, Hampshire, UK
| | - Esther L Hamblion
- Public Health England, Field Epidemiology Service (Victoria), London, UK
| | - Helen Buttivant
- Health Education Wessex, Wessex School of Public Health, Winchester, Hampshire, UK
| | - Sarah R Anderson
- Public Health England, Field Epidemiology Service (Victoria), London, UK
| | | | - Nicola Casali
- National Mycobacterium Reference Laboratory, London, UK
| | | | | | - Ben G Marshall
- University Hospital of Southampton, Faculty of Southampton, Life Sciences Building, Highfield Campus, University of Southampton, Southampton, UK
| | - Linda Booth
- Public Health England Wessex Centre, Whiteley, Hampshire, UK
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30
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Dara M, Ehsani S, Mozalevskis A, Vovc E, Simões D, Avellon Calvo A, Casabona I Barbarà J, Chokoshvili O, Felker I, Hoffner S, Kalmambetova G, Noroc E, Shubladze N, Skrahina A, Tahirli R, Tsertsvadze T, Drobniewski F. Tuberculosis, HIV, and viral hepatitis diagnostics in eastern Europe and central Asia: high time for integrated and people-centred services. THE LANCET. INFECTIOUS DISEASES 2019; 20:e47-e53. [PMID: 31740252 DOI: 10.1016/s1473-3099(19)30524-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022]
Abstract
Globally, high rates (and in the WHO European region an increasing prevalence) of co-infection with tuberculosis and HIV and HIV and hepatitis C virus exist. In eastern European and central Asian countries, the tuberculosis, HIV, and viral hepatitis programmes, including diagnostic services, are separate vertical structures. In this Personal View, we consider underlying reasons for the poor integration for these diseases, particularly in the WHO European region, and how to address this with an initial focus on diagnostic services. In part, this low integration has reflected different diagnostic development histories, global funding sources, and sample types used for diagnosis (eg, typically sputum for tuberculosis and blood for HIV and hepatitis C). Cooperation between services improved as patients with tuberculosis needed routine testing for HIV and vice versa, but financial, infection control, and logistical barriers remain. Multidisease diagnostic platforms exist, but to be used optimally, appropriate staff training and sensible understanding of different laboratory and infection control risks needs rapid implementation. Technically these ideas are all feasible. Poor coordination between these vertical systems remains unhelpful. There is a need to increase political and operational integration of diagnostic and treatment services and bring them closer to patients.
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Affiliation(s)
- Masoud Dara
- Communicable Diseases Department, Division of Health Emergencies and Communicable Diseases, Regional Office for Europe, World Health Organization, Copenhagen, Denmark.
| | - Soudeh Ehsani
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Antons Mozalevskis
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Elena Vovc
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Daniel Simões
- EPI Unit, Institute of Public Health, University of Porto, Porto, Portugal
| | - Ana Avellon Calvo
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | - Jordi Casabona I Barbarà
- Center for Epidemiological Studies on STI and AIDS in Catalonia and Research Network on Biomedical Research, Epidemiology and Public Health, Catalan Agency of Public Health, Badalona, Spain
| | - Otar Chokoshvili
- Infectious diseases and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Irina Felker
- Scientific department, Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | | | - Ecatarina Noroc
- National AIDS Programme, Dermatology and Communicable Diseases Hospital, Chisinau, Moldova
| | - Natalia Shubladze
- National Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Alena Skrahina
- Clinical department, Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Rasim Tahirli
- Laboratory for Medical Service, Specialized Treatment Institution, Main Medical Department, Ministry of Justice, Baku, Azerbaijan
| | - Tengiz Tsertsvadze
- Infectious Diseases and Clinical Immunology Research Center, Tbilisi State University, Tbilisi, Georgia
| | - Francis Drobniewski
- Global Health and Tuberculosis, Imperial College London, London, UK; WHO European Laboratory Initiative on Tuberculosis, HIV and Viral hepatitis, WHO Regional Office of Europe, Copenhagen, Denmark
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31
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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32
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Rutaihwa LK, Menardo F, Stucki D, Gygli SM, Ley SD, Malla B, Feldmann J, Borrell S, Beisel C, Middelkoop K, Carter EJ, Diero L, Ballif M, Jugheli L, Reither K, Fenner L, Brites D, Gagneux S. Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing Into Africa Over Centuries. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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33
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Brandis G, Hughes D. Mechanisms of fitness cost reduction for rifampicin-resistant strains with deletion or duplication mutations in rpoB. Sci Rep 2018; 8:17488. [PMID: 30504835 PMCID: PMC6269455 DOI: 10.1038/s41598-018-36005-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/09/2018] [Indexed: 12/22/2022] Open
Abstract
Rifampicin resistance (RifR) is caused by mutations in rpoB, encoding the β-subunit of RNA polymerase. RifR mutations generally incur a fitness cost and in resistant isolates are frequently accompanied by compensatory mutations in rpoA, rpoB or rpoC. Previous studies of fitness compensation focused on RifR caused by amino acid substitutions within rpoB. RifR is also caused by deletion and duplication mutations in rpoB but it is not known whether or how such mutants can ameliorate their fitness costs. Using experimental evolution of Salmonella carrying RifR deletion or duplication mutations we identified compensatory amino acid substitution mutations within rpoA, rpoB or rpoC in 16 of 21 evolved lineages. Additionally, we found one lineage where a large deletion was compensated by duplication of adjacent amino acids (possibly to fill the gap within the protein structure), two lineages where mutations occurred outside of rpoABC, and two lineages where a duplication mutant reverted to the wild-type sequence. All but the two revertant mutants maintained the RifR phenotype. These data suggest that amino acid substitution mutations are the major compensatory mechanism regardless of the nature of the primary RifR mutation.
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Affiliation(s)
- Gerrit Brandis
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, 75123, Sweden
| | - Diarmaid Hughes
- Uppsala University, Department of Medical Biochemistry and Microbiology, Uppsala, 75123, Sweden.
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34
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Merker M, Barbier M, Cox H, Rasigade JP, Feuerriegel S, Kohl TA, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Nübel U, Supply P, Wirth T, Niemann S. Compensatory evolution drives multidrug-resistant tuberculosis in Central Asia. eLife 2018; 7:38200. [PMID: 30373719 PMCID: PMC6207422 DOI: 10.7554/elife.38200] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 10/02/2018] [Indexed: 12/21/2022] Open
Abstract
Bacterial factors favoring the unprecedented multidrug-resistant tuberculosis (MDR-TB) epidemic in the former Soviet Union remain unclear. We utilized whole genome sequencing and Bayesian statistics to analyze the evolutionary history, temporal emergence of resistance and transmission networks of MDR Mycobacterium tuberculosis complex isolates from Karakalpakstan, Uzbekistan (2001-2006). One clade (termed Central Asian outbreak, CAO) dating back to 1974 (95% HPD 1969-1982) subsequently acquired resistance mediating mutations to eight anti-TB drugs. Introduction of standardized WHO-endorsed directly observed treatment, short-course in Karakalpakstan in 1998 likely selected for CAO-strains, comprising 75% of sampled MDR-TB isolates in 2005/2006. CAO-isolates were also identified in a published cohort from Russia (2008-2010). Similarly, the presence of mutations supposed to compensate bacterial fitness deficits was associated with transmission success and higher drug resistance rates. The genetic make-up of these MDR-strains threatens the success of both empirical and standardized MDR-TB therapies, including the newly WHO-endorsed short MDR-TB regimen in Uzbekistan.
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Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Maxime Barbier
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Helen Cox
- Division of Medical Microbiology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Jean-Philippe Rasigade
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France.,CIRI INSERM U1111, University of Lyon, Lyon, France
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Thomas Andreas Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vladyslav Nikolayevskyy
- Imperial College London, London, United Kingdom.,Public Health England, London, United Kingdom
| | - Sönke Andres
- Division of Mycobacteriology, National Tuberculosis Reference Laboratory, Research Center Borstel, Borstel, Germany
| | - Ulrich Nübel
- Microbial Genome Research, Leibniz-Institut DSMZ- Deutsche Sammlung von Mikroorganismen und Zellkulturen, Braunschweig, Germany.,German Center for Infection Research, Braunschweig, Germany
| | - Philip Supply
- Université de Lille, CNRS UMR 8204, Inserm U1019, CHU de Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France.,Centre National de la Recherche Scientifique, Unité Mixte de Recherche, Center for Infection and Immunity of Lille, Lille, France.,Center for Infection and Immunity of Lille, Université de Lille Nord de France, Lille, France.,Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Thierry Wirth
- Laboratoire Biologie Intégrative des Populations, Evolution Moléculaire, Ecole Pratique des Hautes Etudes, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, UMR-CNRS 7205, Muséum National d'Histoire Naturelle, Université Pierre et Marie Curie, Ecole Pratique des Hautes Etudes, Sorbonne Universités, Paris, France
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Germany
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35
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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36
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Hicks ND, Yang J, Zhang X, Zhao B, Grad YH, Liu L, Ou X, Chang Z, Xia H, Zhou Y, Wang S, Dong J, Sun L, Zhu Y, Zhao Y, Jin Q, Fortune SM. Clinically prevalent mutations in Mycobacterium tuberculosis alter propionate metabolism and mediate multidrug tolerance. Nat Microbiol 2018; 3:1032-1042. [PMID: 30082724 PMCID: PMC6233875 DOI: 10.1038/s41564-018-0218-3] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 07/09/2018] [Indexed: 01/09/2023]
Abstract
The global epidemic of drug-resistant tuberculosis is a catastrophic example of how antimicrobial resistance is undermining the public health gains made possible by combination drug therapy. Recent evidence points to unappreciated bacterial factors that accelerate the emergence of drug resistance. In a genome-wide association study of Mycobacterium tuberculosis isolates from China, we find mutations in the gene encoding the transcription factor prpR enriched in drug-resistant strains. prpR mutations confer conditional drug tolerance to three of the most effective classes of antibiotics by altering propionyl-CoA metabolism. prpR-mediated drug tolerance is carbon-source dependent, and while readily detectable during infection of human macrophages, is not captured by standard susceptibility testing. These data define a previously unrecognized and clinically prevalent class of M. tuberculosis variants that undermine antibiotic efficacy and drive drug resistance.
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Affiliation(s)
- Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaobing Zhang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yonatan H Grad
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Liguo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhili Chang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jie Dong
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, and Centre for Tuberculosis, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
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37
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Xu Y, Liu F, Chen S, Wu J, Hu Y, Zhu B, Sun Z. In vivo evolution of drug-resistant Mycobacterium tuberculosis in patients during long-term treatment. BMC Genomics 2018; 19:640. [PMID: 30157763 PMCID: PMC6116439 DOI: 10.1186/s12864-018-5010-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/14/2018] [Indexed: 11/20/2022] Open
Abstract
Background In the current scenario, the drug-resistant tuberculosis is a significant challenge in the control of tuberculosis worldwide. In order to investigate the in vivo evolution of drug-resistant M. tuberculosis, the present study envisaged sequencing of the draft genomes of 18 serial isolates from four pre-extensively drug-resistant (pre-XDR) tuberculosis patients for continuous genetic alterations. Results All of the isolates harbored single nucleotide polymorphisms (SNPs) ranging from 1303 to 1309 with M. tuberculosis H37Rv as the reference. SNPs ranged from 0 to 12 within patients. The evolution rates were higher than the reported SNPs of 0.5 in the four patients. All the isolates exhibited mutations at sites of known drug targets, while some contained mutations in uncertain drug targets including folC, proZ, and pyrG. The compensatory substitutions for rescuing these deleterious mutations during evolution were only found in RpoC I491T in one patient. Many loci with microheterogeneity showed transient mutations in different isolates. Ninety three SNPs exhibited significant association with refractory pre-XDR TB isolates. Conclusions Our results showed evolutionary changes in the serial genetic characteristics of the pre-XDR TB patients due to accumulation of the fixed drug-resistant related mutations, and the transient mutations under continuous antibiotics pressure over several years. Electronic supplementary material The online version of this article (10.1186/s12864-018-5010-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuhui Xu
- Institute of Chinese Materia medica, China Academy of Chinese Medical Science, Beijing, 100700, China.,National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Fei Liu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Suting Chen
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.,Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Jiannan Wu
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.,Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yongfei Hu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China
| | - Baoli Zhu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Science, Beijing, 100101, China.
| | - Zhaogang Sun
- National Tuberculosis Clinical Laboratory, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China. .,Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
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38
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Bainomugisa A, Duarte T, Lavu E, Pandey S, Coulter C, Marais BJ, Coin LM. A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions. Microb Genom 2018; 4. [PMID: 29906261 PMCID: PMC6113869 DOI: 10.1099/mgen.0.000188] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A better understanding of the genomic changes that facilitate the emergence and spread of drug-resistant Mycobacterium tuberculosis strains is currently required. Here, we report the use of the MinION nanopore sequencer (Oxford Nanopore Technologies) to sequence and assemble an extensively drug-resistant (XDR) isolate, which is part of a modern Beijing sub-lineage strain, prevalent in Western Province, Papua New Guinea. Using 238-fold coverage obtained from a single flow-cell, de novo assembly of nanopore reads resulted into one contiguous assembly with 99.92 % assembly accuracy. Incorporation of complementary short read sequences (Illumina) as part of consensus error correction resulted in a 4 404 064 bp genome with 99.98 % assembly accuracy. This assembly had an average nucleotide identity of 99.7 % relative to the reference genome, H37Rv. We assembled nearly all GC-rich repetitive PE/PPE family genes (166/168) and identified variants within these genes. With an estimated genotypic error rate of 5.3 % from MinION data, we demonstrated identification of variants to include the conventional drug resistance mutations, and those that contribute to the resistance phenotype (efflux pumps/transporter) and virulence. Reference-based alignment of the assembly allowed detection of deletions and insertions. MinION sequencing provided a fully annotated assembly of a transmissible XDR strain from an endemic setting and showed its utility to provide further understanding of genomic processes within Mycobacterium tuberculosis.
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Affiliation(s)
- Arnold Bainomugisa
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia.,2Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Tania Duarte
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Evelyn Lavu
- 3Central Public Health Laboratory, Port Moresby, Papua New Guinea
| | - Sushil Pandey
- 4Queensland Mycobacteria Reference Laboratory, Brisbane, Australia
| | - Chris Coulter
- 4Queensland Mycobacteria Reference Laboratory, Brisbane, Australia
| | - Ben J Marais
- 5Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Lachlan M Coin
- 1Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
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39
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Have compensatory mutations facilitated the current epidemic of multidrug-resistant tuberculosis? Emerg Microbes Infect 2018; 7:98. [PMID: 29872078 PMCID: PMC5988693 DOI: 10.1038/s41426-018-0101-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/26/2018] [Accepted: 04/29/2018] [Indexed: 01/13/2023]
Abstract
Compensatory mutations have been suggested to promote multidrug-resistant tuberculosis (MDR-TB) transmission, but their role in facilitating the recent transmission of MDR-TB is unclear. To investigate the epidemiological significance of compensatory mutations, we analyzed a four-year population-based collection of MDR-TB strains from Shanghai (the most populous city in China) and 1346 published global MDR-TB strains. We report that MDR-TB strains with compensatory mutations in the rpoA, rpoB, or rpoC genes were neither more frequently clustered nor found in larger clusters than those without compensatory mutations. Our results suggest that compensatory mutations are not a major contributor to the current epidemic of MDR-TB.
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40
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Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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41
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A 10-Year Comparative Analysis Shows that Increasing Prevalence of Rifampin-Resistant Mycobacterium tuberculosis in China Is Associated with the Transmission of Strains Harboring Compensatory Mutations. Antimicrob Agents Chemother 2018; 62:AAC.02303-17. [PMID: 29378712 DOI: 10.1128/aac.02303-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/20/2018] [Indexed: 11/20/2022] Open
Abstract
In this work, we conducted bacterial population profile studies to assess trends of rifampin (RIF) resistance of Mycobacterium tuberculosis isolates collected across China from 2005 to 2015. Totals of 273 and 269 randomly selected M. tuberculosis isolates from 2005 and 2015, respectively, were analyzed. The rates of RIF resistance (36.4%), isoniazid resistance (39.0%), and levofloxacin resistance (25.7%) in 2015 were significantly higher than those in 2005 (28.2%, 30.0%, and 15.4%, respectively; P < 0.05). Genotypic data revealed 256 (95.2%) Beijing-type isolates in 2015, a rate significantly higher than that in 2005 (86.4%) (P < 0.01). A higher proportion of mutations was identified within the rifampin resistance-determining region (RRDR) of rpoB in isolates from 2015 (99.0%) than in 2005 isolates (85.7%, P < 0.01). In addition, a significantly higher proportion of RIF-resistant isolates carrying compensatory mutations was observed in 2015 (31.6%) than in 2005 (7.8%). Notably, the great majority of these compensatory mutations (91.9%) were observed in isolates that harbored a mutation of codon 531 of the rpoB gene. In conclusion, our data demonstrate that resistance to RIF, isoniazid, and levofloxacin has become significantly more prevalent during the past decade. In addition, the prevalence of the Beijing genotype significantly increased from 2005 to 2015. Notably, a significantly increased frequency of strains with mutations in rpoC or rpoA is observed among those that have codon 531 mutations, which suggests that they may be compensatory and may play a role in facilitating transmission.
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42
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Gygli SM, Borrell S, Trauner A, Gagneux S. Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives. FEMS Microbiol Rev 2018; 41:354-373. [PMID: 28369307 DOI: 10.1093/femsre/fux011] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/17/2017] [Indexed: 11/12/2022] Open
Abstract
Antibiotic-resistant Mycobacterium tuberculosis strains are threatening progress in containing the global tuberculosis epidemic. Mycobacterium tuberculosis is intrinsically resistant to many antibiotics, limiting the number of compounds available for treatment. This intrinsic resistance is due to a number of mechanisms including a thick, waxy, hydrophobic cell envelope and the presence of drug degrading and modifying enzymes. Resistance to the drugs which are active against M. tuberculosis is, in the absence of horizontally transferred resistance determinants, conferred by chromosomal mutations. These chromosomal mutations may confer drug resistance via modification or overexpression of the drug target, as well as by prevention of prodrug activation. Drug resistance mutations may have pleiotropic effects leading to a reduction in the bacterium's fitness, quantifiable e.g. by a reduction in the in vitro growth rate. Secondary so-called compensatory mutations, not involved in conferring resistance, can ameliorate the fitness cost by interacting epistatically with the resistance mutation. Although the genetic diversity of M. tuberculosis is low compared to other pathogenic bacteria, the strain genetic background has been demonstrated to influence multiple aspects in the evolution of drug resistance. The rate of resistance evolution and the fitness costs of drug resistance mutations may vary as a function of the genetic background.
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Affiliation(s)
- Sebastian M Gygli
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Department of Medical Parasitology and Infection Biology, 4002 Basel, Switzerland.,University of Basel, Basel, Switzerland
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43
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Hughes D, Andersson DI. Environmental and genetic modulation of the phenotypic expression of antibiotic resistance. FEMS Microbiol Rev 2018; 41:374-391. [PMID: 28333270 PMCID: PMC5435765 DOI: 10.1093/femsre/fux004] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Antibiotic resistance can be acquired by mutation or horizontal transfer of a resistance gene, and generally an acquired mechanism results in a predictable increase in phenotypic resistance. However, recent findings suggest that the environment and/or the genetic context can modify the phenotypic expression of specific resistance genes/mutations. An important implication from these findings is that a given genotype does not always result in the expected phenotype. This dissociation of genotype and phenotype has important consequences for clinical bacteriology and for our ability to predict resistance phenotypes from genetics and DNA sequences. A related problem concerns the degree to which the genes/mutations currently identified in vitro can fully explain the in vivo resistance phenotype, or whether there is a significant additional amount of presently unknown mutations/genes (genetic ‘dark matter’) that could contribute to resistance in clinical isolates. Finally, a very important question is whether/how we can identify the genetic features that contribute to making a successful pathogen, and predict why some resistant clones are very successful and spread globally? In this review, we describe different environmental and genetic factors that influence phenotypic expression of antibiotic resistance genes/mutations and how this information is needed to understand why particular resistant clones spread worldwide and to what extent we can use DNA sequences to predict evolutionary success.
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Affiliation(s)
- Diarmaid Hughes
- Corresponding author: Department of Medical Biochemistry and Microbiology, Biomedical Center (Box 582), Uppsala University, S-751 23 Uppsala, Sweden. Tel: +46 18 4714507; E-mail:
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44
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Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C. Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru. PLoS One 2017; 12:e0189838. [PMID: 29281674 PMCID: PMC5744980 DOI: 10.1371/journal.pone.0189838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software. RESULTS High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology. CONCLUSION Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.
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Affiliation(s)
- Louis Grandjean
- University College London, Institute of Child Health, London, United Kingdom
- Academic Health Sciences Centre, Imperial College, London, United Kingdom
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robert H. Gilman
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Tomatada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Chuo-ku, Kobe, Japan
| | - Claudio U. Köser
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Coronel
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - Mirko Zimic
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - M. Estee Török
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Diepreye Ayabina
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Michelle Kendall
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Diseases Epidemiology, Imperial College, London, United Kingdom
| | - Simon Harris
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sharon J. Peacock
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - David A. J. Moore
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - Caroline Colijn
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
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45
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Tan JL, Ng KP, Ong CS, Ngeow YF. Genomic Comparisons Reveal Microevolutionary Differences in Mycobacterium abscessus Subspecies. Front Microbiol 2017; 8:2042. [PMID: 29109707 PMCID: PMC5660101 DOI: 10.3389/fmicb.2017.02042] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/06/2017] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus, a rapid-growing non-tuberculous mycobacterium, has been the cause of sporadic and outbreak infections world-wide. The subspecies in M. abscessus complex (M. abscessus, M. massiliense, and M. bolletii) are associated with different biologic and pathogenic characteristics and are known to be among the most frequently isolated opportunistic pathogens from clinical material. To date, the evolutionary forces that could have contributed to these biological and clinical differences are still unclear. We compared genome data from 243 M. abscessus strains downloaded from the NCBI ftp Refseq database to understand how the microevolutionary processes of homologous recombination and positive selection influenced the diversification of the M. abscessus complex at the subspecies level. The three subspecies are clearly separated in the Minimum Spanning Tree. Their MUMi-based genomic distances support the separation of M. massiliense and M. bolletii into two subspecies. Maximum Likelihood analysis through dN/dS (the ratio of number of non-synonymous substitutions per non-synonymous site, to the number of synonymous substitutions per synonymous site) identified distinct genes in each subspecies that could have been affected by positive selection during evolution. The results of genome-wide alignment based on concatenated locally-collinear blocks suggest that (a) recombination has affected the M. abscessus complex more than mutation and positive selection; (b) recombination occurred more frequently in M. massiliense than in the other two subspecies; and (c) the recombined segments in the three subspecies have come from different intra-species and inter-species origins. The results lead to the identification of possible gene sets that could have been responsible for the subspecies-specific features and suggest independent evolution among the three subspecies, with recombination playing a more significant role than positive selection in the diversification among members in this complex.
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Affiliation(s)
- Joon L Tan
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Kee P Ng
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Chia S Ong
- Faculty of Information Science and Technology, Multimedia University, Melaka, Malaysia
| | - Yun F Ngeow
- Department of Pre-clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Petaling Jaya, Malaysia
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46
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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47
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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48
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Rodríguez-Castillo JG, Pino C, Niño LF, Rozo JC, Llerena-Polo C, Parra-López CA, Tauch A, Murcia-Aranguren MI. Comparative genomic analysis of Mycobacterium tuberculosis Beijing-like strains revealed specific genetic variations associated with virulence and drug resistance. INFECTION GENETICS AND EVOLUTION 2017; 54:314-323. [PMID: 28734764 DOI: 10.1016/j.meegid.2017.07.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 12/30/2022]
Abstract
Isolates of the Mycobacterium tuberculosis lineage 2/East-Asian are considered one of the most successful strains due to their increased pathogenicity, hyper-virulence associated with drug resistance, and high transmission. Recent studies in Colombia have shown that the Beijing-like genotype is associated with multidrug-resistance and high prevalence in the southwest of the country, but the genetic basis of its success in dissemination is unknown. In contribution to this matter, we obtained the whole sequences of six genomes of clinical isolates assigned to the Beijing-like genotype. The genomes were compared with the reference genome of M. tuberculosis H37Rv and 53 previously published M. tuberculosis genomes. We found that the six Beijing-like isolates belong to a modern Beijing sub-lineage and share specific genomic variants: i.e. deletion in the PPE8 gene, in Rv3806c (ubiA) responsible of high ethambutol resistance and in Rv3862c (whiB6) which is involved in granuloma formation and virulence, are some of them. Moreover, each isolated has exclusively single nucleotide polymorphisms (SNPs) in genes related with cell wall processes and cell metabolism. We identified polymorphisms in genes related to drug resistance that could explain the drug-resistant phenotypes found in the six isolates from Colombia. We hypothesize that changes due to these genetic variations contribute to the success of these strains. Finally, we analyzed the IS6110 insertion sequences finding very low variance between them, suggesting that SNPs is the major cause of variability found in Beijing-like strains circulating in Colombia.
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Affiliation(s)
- Juan Germán Rodríguez-Castillo
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Camilo Pino
- Facultad de Ingeniería, Grupo BioLISI, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Luis Fernando Niño
- Facultad de Ingeniería, Grupo BioLISI, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Juan Carlos Rozo
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali 760031, Colombia
| | | | - Carlos A Parra-López
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Andreas Tauch
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, 33615 Bielefeld, Germany
| | - Martha Isabel Murcia-Aranguren
- Departamento de Microbiología, Grupo MICOBACUN, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
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49
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Nusrath Unissa A, Hanna LE. Molecular mechanisms of action, resistance, detection to the first-line anti tuberculosis drugs: Rifampicin and pyrazinamide in the post whole genome sequencing era. Tuberculosis (Edinb) 2017; 105:96-107. [DOI: 10.1016/j.tube.2017.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/02/2017] [Accepted: 04/20/2017] [Indexed: 12/11/2022]
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50
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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