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Davies-Bolorunduro OF, Jaemsai B, Ruangchai W, Phumiphanjarphak W, Aiewsakun P, Palittapongarnpim P. Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations. Sci Rep 2023; 13:13324. [PMID: 37587174 PMCID: PMC10432532 DOI: 10.1038/s41598-023-40152-2] [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: 04/11/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023] Open
Abstract
Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Center for Tuberculosis Research, Microbiology Department, Nigerian Institute of Medical Research, 6 Edmund Crescent, P.M.B 2013, Yaba, 101012, Lagos, Nigeria
| | - Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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Akimova NI, Bekker OB, Danilenko VN. Functional Significance of Mycolicibacterium smegmatis Toxin–Antitoxin Module in Resistance to Antibiotics and Oxidative Stress. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422050027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Lang J, Li Y, Yang W, Dong R, Liang Y, Liu J, Chen L, Wang W, Ji B, Tian G, Che N, Meng B. Genomic and resistome analysis of Alcaligenes faecalis strain PGB1 by Nanopore MinION and Illumina Technologies. BMC Genomics 2022; 23:316. [PMID: 35443609 PMCID: PMC9022240 DOI: 10.1186/s12864-022-08507-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background Drug-resistant bacteria are important carriers of antibiotic-resistant genes (ARGs). This fact is crucial for the development of precise clinical drug treatment strategies. Long-read sequencing platforms such as the Oxford Nanopore sequencer can improve genome assembly efficiency particularly when they are combined with short-read sequencing data. Results Alcaligenes faecalis PGB1 was isolated and identified with resistance to penicillin and three other antibiotics. After being sequenced by Nanopore MinION and Illumina sequencer, its entire genome was hybrid-assembled. One chromosome and one plasmid was assembled and annotated with 4,433 genes (including 91 RNA genes). Function annotation and comparison between strains were performed. A phylogenetic analysis revealed that it was closest to A. faecalis ZD02. Resistome related sequences was explored, including ARGs, Insert sequence, phage. Two plasmid aminoglycoside genes were determined to be acquired ARGs. The main ARG category was antibiotic efflux resistance and β-lactamase (EC 3.5.2.6) of PGB1 was assigned to Class A, Subclass A1b, and Cluster LSBL3. Conclusions The present study identified the newly isolated bacterium A. faecalis PGB1 and systematically annotated its genome sequence and ARGs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08507-7.
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Affiliation(s)
- Jidong Lang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yanju Li
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Wenjuan Yang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Ruyi Dong
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Yuebin Liang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Jia Liu
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Lanyou Chen
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Weiwei Wang
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Binbin Ji
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.,Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, People's Republic of China
| | - Nanying Che
- Department of Pathology, Beijing Key Laboratory for Drug Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, China.
| | - Bo Meng
- Geneis (Beijing) Co., Ltd, Beijing, 100102, China.
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Jia H, Chu H, Dai G, Cao T, Sun Z. Rv1258c acts as a drug efflux pump and growth controlling factor in Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 133:102172. [PMID: 35158297 DOI: 10.1016/j.tube.2022.102172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/27/2022]
Abstract
The possible role of efflux pump as a survival mechanism in Mycobacterium tuberculosis (M. tb) is gaining an increasing attention. Previously, Rv1258c (Tap) and its certain mutations confer the clinically relevant drug resistance. In this study, we found new mutations of Rv1258c in G195C, T297P and I328T. Effect of modulating T297P and I328T on the drug resistance by knockout and complement in M. tb H37Rv showed that M. tb ΔRv1258c showed a slightly lower MIC for rifampin, ethambutol, ofloxacin, amikacin, capreomycin and streptomycin than M. tb H37Rv WT and the complement. Rv1258c T297P and Rv1258c I328T showed an increased drug resistance to ethambutol and capreomycin than the complement of Rv1258c WT. Most importantly, M. tb ΔRv1258c exhibited a slow growth in the normal culture medium. TMT-based quantitative proteomics analysis of M. tb ΔRv1258c and WT showed that the knockout of Rv1258c greatly down-regulated the expression of the ribosome system and one of the special five type VII secretion systems, ESX-3, which impaired the bacterial growth. These results indicate that the newly found T297P and I328T mutations of Rv1258c contributed to an increased resistance to ethambutol and capreomycin, and Rv1258c as growth controlling factor influencing the growth of M. tb.
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Affiliation(s)
- Hongbing Jia
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Hongqian Chu
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Guangming Dai
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Tingming Cao
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China
| | - Zhaogang Sun
- Beijing Key Laboratory in Drug Resistant Tuberculosis Research, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China; Translational Medicine Center, Beijing Chest Hospital, Capital Medical University, Beijing, 101149, China.
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5
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Liu J, Shi W, Zhang S, Hao X, Maslov DA, Shur KV, Bekker OB, Danilenko VN, Zhang Y. Mutations in Efflux Pump Rv1258c (Tap) Cause Resistance to Pyrazinamide, Isoniazid, and Streptomycin in M. tuberculosis. Front Microbiol 2019; 10:216. [PMID: 30837962 PMCID: PMC6389670 DOI: 10.3389/fmicb.2019.00216] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/25/2019] [Indexed: 11/13/2022] Open
Abstract
Although drug resistance in Mycobacterium tuberculosis is mainly caused by mutations in drug activating enzymes or drug targets, there is increasing interest in the possible role of efflux in causing drug resistance. Previously, efflux genes have been shown to be upregulated upon drug exposure or implicated in drug resistance in overexpression studies, but the role of mutations in efflux pumps identified in clinical isolates in causing drug resistance is unknown. Here we investigated the role of mutations in efflux pump Rv1258c (Tap) from clinical isolates in causing drug resistance in M. tuberculosis. We constructed point mutations V219A and S292L in Rv1258c in the chromosome of M. tuberculosis and the point mutations were confirmed by DNA sequencing. The susceptibility of the constructed M. tuberculosis Rv1258c mutants to different tuberculosis drugs was assessed using conventional drug susceptibility testing in 7H11 agar in the presence and absence of efflux pump inhibitor piperine. A C14-labeled PZA uptake experiment was performed to demonstrate higher efflux activity in the M. tuberculosis Rv1258c mutants. Interestingly, the V219A and S292L point mutations caused clinically relevant drug resistance to pyrazinamide (PZA), isoniazid (INH), and streptomycin (SM), but not to other drugs in M. tuberculosis. While V219A point mutation conferred low-level drug resistance, the S292L mutation caused a higher level of resistance. Efflux inhibitor piperine inhibited INH and PZA resistance in the S292L mutant but not in the V219A mutant. The S292L mutant had higher efflux activity for pyrazinoic acid (the active form of PZA) than the parent strain. We conclude that point mutations in the efflux pump Rv1258c in clinical isolates can confer clinically relevant drug resistance, including PZA resistance, and could explain some previously unaccounted drug resistance in clinical strains. Future studies need to take efflux mutations into consideration for improved detection of drug resistance in M. tuberculosis and address their role in affecting treatment outcome in vivo.
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Affiliation(s)
- Jiayun Liu
- Department of Clinical Laboratory, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Wanliang Shi
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Shuo Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Xiaoke Hao
- Department of Clinical Laboratory, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Dmitry A Maslov
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Kirill V Shur
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olga B Bekker
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Valery N Danilenko
- Laboratory of Bacterial Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
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Shur KV, Bekker OB, Zaichikova MV, Maslov DA, Akimova NI, Zakharevich NV, Chekalina MS, Danilenko VN. Genetic Aspects of Drug Resistance and Virulence in Mycobacterium tuberculosis. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418120141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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