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Santos-Júnior PFDS, Batista VDM, Nascimento IJDS, Nunes IC, Silva LR, Costa CACB, Freitas JDD, Quintans-Júnior LJ, Araújo-Júnior JXD, Freitas MEGD, Zhan P, Green KD, Garneau-Tsodikova S, Mendonça-Júnior FJB, Rodrigues-Junior VS, Silva-Júnior EFD. A consensus reverse docking approach for identification of a competitive inhibitor of acetyltransferase enhanced intracellular survival protein from Mycobacterium tuberculosis. Bioorg Med Chem 2024; 108:117774. [PMID: 38833750 DOI: 10.1016/j.bmc.2024.117774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/08/2024] [Accepted: 05/24/2024] [Indexed: 06/06/2024]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), which remains a significant global health challenge. The emergence of multidrug-resistant (MDR) Mtb strains imposes the development of new therapeutic strategies. This study focuses on the identification and evaluation of potential inhibitors against Mtb H37Ra through a comprehensive screening of an in-house chemolibrary. Subsequently, a promising pyrimidine derivative (LQM495) was identified as promising and then further investigated by experimental and in silico approaches. In this context, computational techniques were used to elucidate the potential molecular target underlying the inhibitory action of LQM495. Then, a consensus reverse docking (CRD) protocol was used to investigate the interactions between this compound and several Mtb targets. Out of 98 Mtb targets investigated, the enhanced intracellular survival (Eis) protein emerged as a target for LQM495. To gain insights into the stability of the LQM495-Eis complex, molecular dynamics (MD) simulations were conducted over a 400 ns trajectory. Further insights into its binding modes within the Eis binding site were obtained through a Quantum mechanics (QM) approach, using density functional theory (DFT), with B3LYP/D3 basis set. These calculations shed light on the electronic properties and reactivity of LQM495. Subsequently, inhibition assays and kinetic studies of the Eis activity were used to investigate the activity of LQM495. Then, an IC50 value of 11.0 ± 1.4 µM was found for LQM495 upon Eis protein. Additionally, its Vmax, Km, and Ki parameters indicated that it is a competitive inhibitor. Lastly, this study presents LQM495 as a promising inhibitor of Mtb Eis protein, which could be further explored for developing novel anti-TB drugs in the future.
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Affiliation(s)
| | - Vitoria de Melo Batista
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Igor José Dos Santos Nascimento
- Post-Graduation Program of Pharmaceutical Sciences, Pharmacy Department, State University of Paraíba, Campina Grande, Brazil
| | - Isabelle Cavalcante Nunes
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | - Leandro Rocha Silva
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - Johnnatan Duarte de Freitas
- Department of Chemistry, Federal Institute of Alagoas, Maceió campus, Mizael Domingues Street, 57020-600 Maceió, Alagoas, Brazil
| | - Lucindo José Quintans-Júnior
- Pharmaceutical Sciences Graduate Program (PPGCS), Federal University of Sergipe, São Cristóvão, Sergipe 49100-001, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Institute of Pharmaceutical Sciences, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil
| | | | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, United States
| | | | - Valnês S Rodrigues-Junior
- Department of Pharmaceutical Sciences, Federal University of Paraíba, João Pessoa, Brazil; Post-Graduation Program in Natural Products and Bioactive Synthetics, Federal University of Paraíba, João Pessoa, Brazil
| | - Edeildo Ferreira da Silva-Júnior
- Research Group of Biological and Molecular Chemistry, Institute of Chemistry and Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simões campus, 57072-970 Alagoas, Maceió, Brazil.
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Ding X, Wang Y, Gui Y, Yang C. Two-Stage Mixed-Dye-Based Isothermal Amplification with Ribonuclease-Cleavable Enhanced Probes for Dual-Visualization Detection of SARS-CoV-2 Variants of Interest. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401988. [PMID: 38829265 DOI: 10.1002/advs.202401988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/17/2024] [Indexed: 06/05/2024]
Abstract
Rapid and visual detection of SARS-CoV-2 variants is vital for timely assessment of variant transmission in resource-limited settings. Here, a closed-tube, two-stage, mixed-dye-based isothermal amplification method with ribonuclease-cleavable enhanced probes (REP), termed REP-TMAP, for dual-visualization detection of SARS-CoV-2 variants including JN.1, BA.2, BA.4/5, and Delta is introduced. The first stage of REP-TMAP is reverse transcription recombinase polymerase amplification and the second stage is dual-visualization detection synergistically mediated by the REP and the mixed dyes of cresol red and hydroxy naphthol blue. In REP-TMAP reaction, the color change under ambient light indicates SARS-CoV-2 infection, while the fluorescence change under blue light excitation specifies variant type. On detecting transcribed RNA of SARS-CoV-2 spike gene, this assay is rapid (within 40 min), highly sensitive (10-200 copies per reaction), and highly specific (identification of single-base mutations). Furthermore, the assay has been clinically validated to accurately detect JN.1, BA.2, and BA.4/5 variants from 102 human oropharyngeal swabs. The proposed assay therefore holds great potentials to provide a rapid, dual-visualization, sensitive, specific, point-of-care detection of SARS-CoV-2 variants and beyond.
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Affiliation(s)
- Xiong Ding
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Yaru Wang
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Yuxin Gui
- Key Laboratory of Environmental Medicine and Engineering, Ministry of Education, Department of Nutrition and Food Hygiene, School of Public Health, Southeast University, Nanjing, 210009, P. R. China
| | - Chuankun Yang
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, P. R. China
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3
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Zhao J, Qian C, Jiang Y, He W, Wu W. Drug-Resistant Characteristics, Genetic Diversity, and Transmission Dynamics of Multidrug-Resistant Mycobacterium tuberculosis in Jiangxi, China. Infect Drug Resist 2024; 17:2213-2223. [PMID: 38840971 PMCID: PMC11152055 DOI: 10.2147/idr.s460267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024] Open
Abstract
Purpose In this study, we aimed to determine the transmission pattern of multidrug-resistant tuberculosis (MDR-TB) isolates circulating in Jiangxi Province with whole-genome sequencing (WGS). In addition, we also sought to describe mutational resistome of MDR-TB isolates. Patients and Methods A total of 115 MDR-TB isolates determined by the phenotypic proportion method of drug susceptibility testing between January 2018 and December 2022 from provincial drug surveillance (DRS) in Jiangxi were included in our analysis. The demographic data and treatment history were extracted from the National TB Registry System. WGS was used to analyze the genotypic characteristics of drug resistance and transmissions. Results About 62.6% of MDR-TB strains were isolated from cases that received previous anti-tuberculosis treatment. According to the WGS results, 96.5% were genotypic MDR-TB, and more than half of MDR-TB isolates tested were also resistant to streptomycin (59.1%), ethambutol (56.5%), and fluroquinolones (53.0%), while resistance to cycloserine and linezolid was lowest, only in two (1.7%) and one (0.9%) isolate, respectively. Ser450Leu in rpoB (57.9%), Ser315Thr in katG (74.1%), Met306Val in embB (40.0%), Lys43Arg in rpsL (75.0%), Ala90Val in gyrA (32.8%) were predominant mutant types among the rifampin-, isoniazid-, ethambutol-, streptomycin-, fluoroquinolones-resistant isolates, respectively. Lineage 2 (East Asian genotype) occurred at the highest frequency with 97 cases (84.3%), followed by lineage 4 (Euro-American genotype) with 18 cases (15.7%). Additionally, 5 clusters consisting of 10 isolates were identified in the present study, demonstrating a clustering rate of 8.7%. Conclusion MDR/Rifampicin-Resistant (RR)-TB epidemic in this region is driven by lineage 2 clade that also show higher resistance to other anti-tuberculosis drugs. Lower cluster rates compared with a relatively higher proportion of new MDR-TB cases indicate that a considerable number of MDR-TB cases remain undiagnosed.
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Affiliation(s)
- Jingnan Zhao
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Chengyu Qian
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, People’s Republic of China
| | - Youqiao Jiang
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
- Young Scientific Research and Innovation Team, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, Jiangxi, 330029, People’s Republic of China
| | - Wangrui He
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
| | - Wenhua Wu
- Tuberculosis Control Department, Jiangxi Provincial Center for Disease Control and Prevention, Nanchang, 330029, People’s Republic of China
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Duffey M, Shafer RW, Timm J, Burrows JN, Fotouhi N, Cockett M, Leroy D. Combating antimicrobial resistance in malaria, HIV and tuberculosis. Nat Rev Drug Discov 2024; 23:461-479. [PMID: 38750260 DOI: 10.1038/s41573-024-00933-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/15/2024] [Indexed: 06/07/2024]
Abstract
Antimicrobial resistance poses a significant threat to the sustainability of effective treatments against the three most prevalent infectious diseases: malaria, human immunodeficiency virus (HIV) infection and tuberculosis. Therefore, there is an urgent need to develop novel drugs and treatment protocols capable of reducing the emergence of resistance and combating it when it does occur. In this Review, we present an overview of the status and underlying molecular mechanisms of drug resistance in these three diseases. We also discuss current strategies to address resistance during the research and development of next-generation therapies. These strategies vary depending on the infectious agent and the array of resistance mechanisms involved. Furthermore, we explore the potential for cross-fertilization of knowledge and technology among these diseases to create innovative approaches for minimizing drug resistance and advancing the discovery and development of new anti-infective treatments. In conclusion, we advocate for the implementation of well-defined strategies to effectively mitigate and manage resistance in all interventions against infectious diseases.
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Affiliation(s)
- Maëlle Duffey
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
- The Global Antibiotic Research & Development Partnership, Geneva, Switzerland
| | - Robert W Shafer
- Department of Medicine/Infectious Diseases, Stanford University, Palo Alto, CA, USA
| | | | - Jeremy N Burrows
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland
| | | | | | - Didier Leroy
- Medicines for Malaria Venture (MMV), R&D Department/Drug Discovery, ICC, Geneva, Switzerland.
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Otchere ID, Asante-Poku A, Akpadja KF, Diallo AB, Sanou A, Asare P, Osei-Wusu S, Onyejepu N, Diarra B, Dagnra YA, Kehinde A, Antonio M, Yeboah-Manu D. Opinion review of drug resistant tuberculosis in West Africa: tackling the challenges for effective control. Front Public Health 2024; 12:1374703. [PMID: 38827613 PMCID: PMC11141065 DOI: 10.3389/fpubh.2024.1374703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/29/2024] [Indexed: 06/04/2024] Open
Abstract
Drug-resistant (DR) tuberculosis (TB) is a major public health concern globally, complicating TB control and management efforts. West Africa has historically faced difficulty in combating DR-TB due to limited diagnostic skills, insufficient access to excellent healthcare, and ineffective healthcare systems. This has aided in the emergence and dissemination of DR Mycobacterium tuberculosis complex (MTBC) strains in the region. In the past, DR-TB patients faced insufficient resources, fragmented efforts, and suboptimal treatment outcomes. However, current efforts to combat DR-TB in the region are promising. These efforts include strengthening diagnostic capacities, improving access to quality healthcare services, and implementing evidence-based treatment regimens for DR-TB. Additionally, many West African National TB control programs are collaborating with international partners to scale up laboratory infrastructure, enhance surveillance systems, and promote infection control measures. Moreso, novel TB drugs and regimens, such as bedaquiline and delamanid, are being introduced to improve treatment outcomes for DR-TB cases. Despite these obstacles, there is optimism for the future of DR-TB control in West Africa. Investments are being made to improve healthcare systems, expand laboratory capacity, and support TB research and innovation. West African institutions are now supporting knowledge sharing, capacity building, and resource mobilization through collaborative initiatives such as the West African Network for TB, AIDS, and Malaria (WANETAM), the West African Health Organization (WAHO), and other regional or global partners. These efforts hold promise for improved diagnostics, optimized treatment regimens, and provide better patient outcomes in the future where drug-resistant TB in WA can be effectively controlled, reducing the burden of the disease, and improving the health outcomes of affected individuals.
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Affiliation(s)
- Isaac Darko Otchere
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Adwoa Asante-Poku
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Awa Ba Diallo
- Biological Sciences Department, Faculty of Pharmacy at Cheikh Anta Diop University, Dakar, Senegal
| | - Adama Sanou
- Centre Muraz, Institut National de Santé Publique, Bobo-Dioulasso, Burkina Faso
| | - Prince Asare
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nneka Onyejepu
- Microbiology Department, Center for Tuberculosis Research Laboratory, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | - Aderemi Kehinde
- Department of Medical Microbiology and Parasitology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Martin Antonio
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, Gambia
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Epidemic Preparedness and Response, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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He P, Zhao B, He W, Song Z, Pei S, Liu D, Xia H, Wang S, Ou X, Zheng Y, Zhou Y, Song Y, Wang Y, Cao X, Xing R, Zhao Y. Impact of MSMEG5257 Deletion on Mycolicibacterium smegmatis Growth. Microorganisms 2024; 12:770. [PMID: 38674714 PMCID: PMC11052289 DOI: 10.3390/microorganisms12040770] [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: 02/04/2024] [Revised: 04/07/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Mycobacterial membrane proteins play a pivotal role in the bacterial invasion of host cells; however, the precise mechanisms underlying certain membrane proteins remain elusive. Mycolicibacterium smegmatis (Ms) msmeg5257 is a hemolysin III family protein that is homologous to Mycobacterium tuberculosis (Mtb) Rv1085c, but it has an unclear function in growth. To address this issue, we utilized the CRISPR/Cas9 gene editor to construct Δmsmeg5257 strains and combined RNA transcription and LC-MS/MS protein profiling to determine the functional role of msmeg5257 in Ms growth. The correlative analysis showed that the deletion of msmeg5257 inhibits ABC transporters in the cytomembrane and inhibits the biosynthesis of amino acids in the cell wall. Corresponding to these results, we confirmed that MSMEG5257 localizes in the cytomembrane via subcellular fractionation and also plays a role in facilitating the transport of iron ions in environments with low iron levels. Our data provide insights that msmeg5257 plays a role in maintaining Ms metabolic homeostasis, and the deletion of msmeg5257 significantly impacts the growth rate of Ms. Furthermore, msmeg5257, a promising drug target, offers a direction for the development of novel therapeutic strategies against mycobacterial diseases.
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Affiliation(s)
- Ping He
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Bing Zhao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Wencong He
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Zexuan Song
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Shaojun Pei
- School of Public Health, Peking University, Haidian District, Beijing 100871, China;
| | - Dongxin Liu
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Hui Xia
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Shengfen Wang
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Xichao Ou
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yang Zheng
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yang Zhou
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yuanyuan Song
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yiting Wang
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Xiaolong Cao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Ruida Xing
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
| | - Yanlin Zhao
- Chinese Center for Disease Control and Prevention, Changping District, Beijing 102206, China; (P.H.); (B.Z.); (W.H.); (Z.S.); (D.L.); (H.X.); (S.W.); (X.O.); (Y.Z.); (Y.Z.); (Y.S.); (Y.W.); (X.C.); (R.X.)
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Chitwood MH, Colijn C, Yang C, Crudu V, Ciobanu N, Codreanu A, Kim J, Rancu I, Rhee K, Cohen T, Sobkowiak B. The recent rapid expansion of multidrug resistant Ural lineage Mycobacterium tuberculosis in Moldova. Nat Commun 2024; 15:2962. [PMID: 38580642 PMCID: PMC10997638 DOI: 10.1038/s41467-024-47282-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024] Open
Abstract
The projected trajectory of multidrug resistant tuberculosis (MDR-TB) epidemics depends on the reproductive fitness of circulating strains of MDR M. tuberculosis (Mtb). Previous efforts to characterize the fitness of MDR Mtb have found that Mtb strains of the Beijing sublineage (Lineage 2.2.1) may be more prone to develop resistance and retain fitness in the presence of resistance-conferring mutations than other lineages. Using Mtb genome sequences from all culture-positive cases collected over two years in Moldova, we estimate the fitness of Ural (Lineage 4.2) and Beijing strains, the two lineages in which MDR is concentrated in the country. We estimate that the fitness of MDR Ural strains substantially exceeds that of other susceptible and MDR strains, and we identify several mutations specific to these MDR Ural strains. Our findings suggest that MDR Ural Mtb has been transmitting efficiently in Moldova and poses a substantial risk of spreading further in the region.
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Affiliation(s)
- Melanie H Chitwood
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University, 8888 University Drive West, Burnaby, BC, Canada
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, No. 132 Outer Ring East Road, Guangzhou University Town Guangdong, Guangdong, PR China
| | - Valeriu Crudu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Alexandru Codreanu
- Phthisiopneumology Institute, Strada Constantin Vârnav 13, Chisinau, Republic of Moldova
| | - Jaehee Kim
- Department of Computational Biology, Cornell University, 237 Tower Road, Ithaca, NY, USA
| | - Isabel Rancu
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
| | - Kyu Rhee
- Department of Medicine, Weill Cornell Medicine, 1300 York Ave, New York, NY, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA.
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Disease, Yale School of Public Health, 60 College Street, New Haven, CT, USA
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8
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Eckartt KA, Delbeau M, Munsamy-Govender V, DeJesus MA, Azadian ZA, Reddy AK, Chandanani J, Poulton NC, Quiñones-Garcia S, Bosch B, Landick R, Campbell EA, Rock JM. Compensatory evolution in NusG improves fitness of drug-resistant M. tuberculosis. Nature 2024; 628:186-194. [PMID: 38509362 PMCID: PMC10990936 DOI: 10.1038/s41586-024-07206-5] [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: 09/30/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024]
Abstract
Drug-resistant bacteria are emerging as a global threat, despite frequently being less fit than their drug-susceptible ancestors1-8. Here we sought to define the mechanisms that drive or buffer the fitness cost of rifampicin resistance (RifR) in the bacterial pathogen Mycobacterium tuberculosis (Mtb). Rifampicin inhibits RNA polymerase (RNAP) and is a cornerstone of modern short-course tuberculosis therapy9,10. However, RifR Mtb accounts for one-quarter of all deaths due to drug-resistant bacteria11,12. We took a comparative functional genomics approach to define processes that are differentially vulnerable to CRISPR interference (CRISPRi) inhibition in RifR Mtb. Among other hits, we found that the universally conserved transcription factor NusG is crucial for the fitness of RifR Mtb. In contrast to its role in Escherichia coli, Mtb NusG has an essential RNAP pro-pausing function mediated by distinct contacts with RNAP and the DNA13. We find this pro-pausing NusG-RNAP interface to be under positive selection in clinical RifR Mtb isolates. Mutations in the NusG-RNAP interface reduce pro-pausing activity and increase fitness of RifR Mtb. Collectively, these results define excessive RNAP pausing as a molecular mechanism that drives the fitness cost of RifR in Mtb, identify a new mechanism of compensation to overcome this cost, suggest rational approaches to exacerbate the fitness cost, and, more broadly, could inform new therapeutic approaches to develop drug combinations to slow the evolution of RifR in Mtb.
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Affiliation(s)
- Kathryn A Eckartt
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Madeleine Delbeau
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | | | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Zachary A Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Abhijna K Reddy
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Robert Landick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA.
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9
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Lan Y, Crudu V, Ciobanu N, Codreanu A, Chitwood MH, Sobkowiak B, Warren JL, Cohen T. Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model. EBioMedicine 2024; 102:105085. [PMID: 38531172 PMCID: PMC10987885 DOI: 10.1016/j.ebiom.2024.105085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Multidrug resistant tuberculosis (MDR-TB) represents a major public health concern in the Republic of Moldova, with an estimated 31% of new and 56% of previously treated TB cases having MDR disease in 2022. A recent genomic epidemiology study of incident TB occurring in 2018 and 2019 found that 92% of MDR-TB was the result of transmission. The MDR phenotype was concentrated among two M. tuberculosis (Mtb) lineages: L2.2.1 (Beijing) and L4.2.1 (Ural). METHODS We developed and applied a hierarchical Bayesian multinominal logistic regression model to Mtb genomic, spatial, and epidemiological data collected from all individuals with diagnosed TB in Moldova in 2018 and 2019 to identify locations in which specific Mtb strains are being transmitted. We then used a logistic regression model to estimate locality-level factors associated with local transmission. FINDINGS We found differences in the spatial distribution and degree of local concentration of disease due to specific strains of Beijing and Ural lineage Mtb. Foci of transmission for four strains of Beijing lineage Mtb, predominantly of the MDR-TB phenotype, were located in several regions, but largely concentrated in Transnistria. In contrast, transmission of Ural lineage Mtb had less marked patterns of spatial aggregation, with a single strain (also of the MDR phenotype) spatially clustered in southern Transnistria. We found a 30% (95% credible interval 2%-80%) increase in odds of a locality being a transmission cluster for each increase of 100 persons per square kilometer, while higher local tuberculosis incidence and poverty were not associated with a locality being a transmission focus. INTERPRETATION Our results identified localities where specific Mtb transmission networks were concentrated and quantified the association between locality-level factors and focal transmission. This analysis revealed Transnistria as the primary area where specific Mtb strains (predominantly of the MDR-TB phenotype) were locally transmitted and suggests that targeted intensified case finding in this region may be an attractive policy option. FUNDING Funding for this work was provided by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.
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Affiliation(s)
- Yu Lan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | | | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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10
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Dheda K, Mirzayev F, Cirillo DM, Udwadia Z, Dooley KE, Chang KC, Omar SV, Reuter A, Perumal T, Horsburgh CR, Murray M, Lange C. Multidrug-resistant tuberculosis. Nat Rev Dis Primers 2024; 10:22. [PMID: 38523140 DOI: 10.1038/s41572-024-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Tuberculosis (TB) remains the foremost cause of death by an infectious disease globally. Multidrug-resistant or rifampicin-resistant TB (MDR/RR-TB; resistance to rifampicin and isoniazid, or rifampicin alone) is a burgeoning public health challenge in several parts of the world, and especially Eastern Europe, Russia, Asia and sub-Saharan Africa. Pre-extensively drug-resistant TB (pre-XDR-TB) refers to MDR/RR-TB that is also resistant to a fluoroquinolone, and extensively drug-resistant TB (XDR-TB) isolates are additionally resistant to other key drugs such as bedaquiline and/or linezolid. Collectively, these subgroups are referred to as drug-resistant TB (DR-TB). All forms of DR-TB can be as transmissible as rifampicin-susceptible TB; however, it is more difficult to diagnose, is associated with higher mortality and morbidity, and higher rates of post-TB lung damage. The various forms of DR-TB often consume >50% of national TB budgets despite comprising <5-10% of the total TB case-load. The past decade has seen a dramatic change in the DR-TB treatment landscape with the introduction of new diagnostics and therapeutic agents. However, there is limited guidance on understanding and managing various aspects of this complex entity, including the pathogenesis, transmission, diagnosis, management and prevention of MDR-TB and XDR-TB, especially at the primary care physician level.
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Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fuad Mirzayev
- Global Tuberculosis Programme, WHO, Geneva, Switzerland
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital & Research Center, Mumbai, India
| | - Kelly E Dooley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kwok-Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong, SAR, China
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anja Reuter
- Sentinel Project on Paediatric Drug-Resistant Tuberculosis, Boston, MA, USA
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Megan Murray
- Department of Epidemiology, Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Paediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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11
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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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12
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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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13
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Liu B, Gao J, Liu XF, Rao G, Luo J, Han P, Hu W, Zhang Z, Zhao Q, Han L, Jiang Z, Zhou M. Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing. J Clin Microbiol 2023; 61:e0061723. [PMID: 37823665 PMCID: PMC10662344 DOI: 10.1128/jcm.00617-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/17/2023] [Indexed: 10/13/2023] Open
Abstract
Carbapenem resistance is a major concern in the management of antibiotic-resistant Pseudomonas aeruginosa infections. The direct prediction of carbapenem-resistant phenotype from genotype in P. aeruginosa isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in P. aeruginosa make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622 P. aeruginosa isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in P. aeruginosa, including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in P. aeruginosa from clinical samples by the key gene features selected and prediction models constructed, 72 P. aeruginosa-positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72 P. aeruginosa-positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive P. aeruginosa were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of P. aeruginosa, the carbapenem resistance of P. aeruginosa could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant P. aeruginosa.
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Affiliation(s)
- Bing Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Jianpeng Gao
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Xue Fei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Jiajie Luo
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Weiting Hu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Ze Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Qianqian Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Lizhong Han
- Department of Clinical Microbiology,, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi Jiang
- Genskey Medical Technology Co., Ltd., Beijing, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
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14
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Coluzzi C, Guillemet M, Mazzamurro F, Touchon M, Godfroid M, Achaz G, Glaser P, Rocha EPC. Chance Favors the Prepared Genomes: Horizontal Transfer Shapes the Emergence of Antibiotic Resistance Mutations in Core Genes. Mol Biol Evol 2023; 40:msad217. [PMID: 37788575 PMCID: PMC10575684 DOI: 10.1093/molbev/msad217] [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: 07/04/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/05/2023] Open
Abstract
Bacterial lineages acquire novel traits at diverse rates in part because the genetic background impacts the successful acquisition of novel genes by horizontal transfer. Yet, how horizontal transfer affects the subsequent evolution of core genes remains poorly understood. Here, we studied the evolution of resistance to quinolones in Escherichia coli accounting for population structure. We found 60 groups of genes whose gain or loss induced an increase in the probability of subsequently becoming resistant to quinolones by point mutations in the gyrase and topoisomerase genes. These groups include functions known to be associated with direct mitigation of the effect of quinolones, with metal uptake, cell growth inhibition, biofilm formation, and sugar metabolism. Many of them are encoded in phages or plasmids. Although some of the chronologies may reflect epidemiological trends, many of these groups encoded functions providing latent phenotypes of antibiotic low-level resistance, tolerance, or persistence under quinolone treatment. The mutations providing resistance were frequent and accumulated very quickly. Their emergence was found to increase the rate of acquisition of other antibiotic resistances setting the path for multidrug resistance. Hence, our findings show that horizontal gene transfer shapes the subsequent emergence of adaptive mutations in core genes. In turn, these mutations further affect the subsequent evolution of resistance by horizontal gene transfer. Given the substantial gene flow within bacterial genomes, interactions between horizontal transfer and point mutations in core genes may be a key to the success of adaptation processes.
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Affiliation(s)
- Charles Coluzzi
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Martin Guillemet
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Fanny Mazzamurro
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Marie Touchon
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Maxime Godfroid
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Guillaume Achaz
- SMILE Group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Philippe Glaser
- Institut Pasteur, Université de Paris Cité, CNRS, UMR6047, Unité EERA, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
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15
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Lempens P, Van Deun A, Aung KJM, Hossain MA, Behruznia M, Decroo T, Rigouts L, de Jong BC, Meehan CJ. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microb Genom 2023; 9:001109. [PMID: 37750750 PMCID: PMC10569737 DOI: 10.1099/mgen.0.001109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 09/18/2023] [Indexed: 09/27/2023] Open
Abstract
The spread of multidrug-resistant tuberculosis (MDR-TB) is a growing problem in many countries worldwide. Resistance to one of the primary first-line drugs, rifampicin, is caused by mutations in the Mycobacterium tuberculosis rpoB gene. So-called borderline rpoB mutations confer low-level resistance, in contrast to more common rpoB mutations which confer high-level resistance. While some borderline mutations show lower fitness in vitro than common mutations, their in vivo fitness is currently unknown. We used a dataset of 394 whole genome sequenced MDR-TB isolates from Bangladesh, representing around 44 % of notified MDR-TB cases over 6 years, to look at differences in transmission clustering between isolates with borderline rpoB mutations and those with common rpoB mutations. We found a relatively low percentage of transmission clustering in the dataset (34.8 %) but no difference in clustering between different types of rpoB mutations. Compensatory mutations in rpoA, rpoB, and rpoC were associated with higher levels of transmission clustering as were lineages two, three, and four relative to lineage one. Young people as well as patients with high sputum smear positive TB were more likely to be in a transmission cluster. Our findings show that although borderline rpoB mutations have lower in vitro growth potential this does not translate into lower transmission potential or in vivo fitness. Proper detection of these mutations is crucial to ensure they do not go unnoticed and spread MDR-TB within communities.
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Affiliation(s)
- Pauline Lempens
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | - Tom Decroo
- Unit of HIV and TB, Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Bouke C. de Jong
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, UK
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