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Peng C, Cheng Y, Ma M, Chen Q, Duan Y, Liu S, Cheng H, Yang H, Huang J, Bu W, Shi C, Wu X, Chen J, Zheng R, Liu Z, Ji Z, Wang J, Huang X, Wang P, Sha W, Ge B, Wang L. Mycobacterium tuberculosis suppresses host antimicrobial peptides by dehydrogenating L-alanine. Nat Commun 2024; 15:4216. [PMID: 38760394 PMCID: PMC11101664 DOI: 10.1038/s41467-024-48588-4] [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: 09/18/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
Antimicrobial peptides (AMPs), ancient scavengers of bacteria, are very poorly induced in macrophages infected by Mycobacterium tuberculosis (M. tuberculosis), but the underlying mechanism remains unknown. Here, we report that L-alanine interacts with PRSS1 and unfreezes the inhibitory effect of PRSS1 on the activation of NF-κB pathway to induce the expression of AMPs, but mycobacterial alanine dehydrogenase (Ald) Rv2780 hydrolyzes L-alanine and reduces the level of L-alanine in macrophages, thereby suppressing the expression of AMPs to facilitate survival of mycobacteria. Mechanistically, PRSS1 associates with TAK1 and disruptes the formation of TAK1/TAB1 complex to inhibit TAK1-mediated activation of NF-κB pathway, but interaction of L-alanine with PRSS1, disables PRSS1-mediated impairment on TAK1/TAB1 complex formation, thereby triggering the activation of NF-κB pathway to induce expression of AMPs. Moreover, deletion of antimicrobial peptide gene β-defensin 4 (Defb4) impairs the virulence by Rv2780 during infection in mice. Both L-alanine and the Rv2780 inhibitor, GWP-042, exhibits excellent inhibitory activity against M. tuberculosis infection in vivo. Our findings identify a previously unrecognized mechanism that M. tuberculosis uses its own alanine dehydrogenase to suppress host immunity, and provide insights relevant to the development of effective immunomodulators that target M. tuberculosis.
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Affiliation(s)
- Cheng Peng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yuanna Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Mingtong Ma
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Qiu Chen
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Yongjia Duan
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Shanshan Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hongyu Cheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Hua Yang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jingping Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Wenyi Bu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Chenyue Shi
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Xiangyang Wu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianxia Chen
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruijuan Zheng
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhonghua Liu
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhe Ji
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China
| | - Jie Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaochen Huang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Peng Wang
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Sha
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Baoxue Ge
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Clinical Translation Research Center, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
| | - Lin Wang
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
- Department of Microbiology and Immunology, Tongji University School of Medicine, Shanghai, China.
- Shanghai Clinic and Research Center of Tuberculosis, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China.
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Xiong XS, Zhang XD, Yan JW, Huang TT, Liu ZZ, Li ZK, Wang L, Li F. Identification of Mycobacterium tuberculosis Resistance to Common Antibiotics: An Overview of Current Methods and Techniques. Infect Drug Resist 2024; 17:1491-1506. [PMID: 38628245 PMCID: PMC11020249 DOI: 10.2147/idr.s457308] [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: 01/14/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is an essential cause of tuberculosis treatment failure and death of tuberculosis patients. The rapid and reliable profiling of Mycobacterium tuberculosis (MTB) drug resistance in the early stage is a critical research area for public health. Then, most traditional approaches for detecting MTB are time-consuming and costly, leading to the inappropriate therapeutic schedule resting on the ambiguous information of MTB drug resistance, increasing patient economic burden, morbidity, and mortality. Therefore, novel diagnosis methods are frequently required to meet the emerging challenges of MTB drug resistance distinguish. Considering the difficulty in treating MDR-TB, it is urgently required for the development of rapid and accurate methods in the identification of drug resistance profiles of MTB in clinical diagnosis. This review discussed recent advances in MTB drug resistance detection, focusing on developing emerging approaches and their applications in tangled clinical situations. In particular, a brief overview of antibiotic resistance to MTB was present, referred to as intrinsic bacterial resistance, consisting of cell wall barriers and efflux pumping action and acquired resistance caused by genetic mutations. Then, different drug susceptibility test (DST) methods were described, including phenotype DST, genotype DST and novel DST methods. The phenotype DST includes nitrate reductase assay, RocheTM solid ratio method, and liquid culture method and genotype DST includes fluorescent PCR, GeneXpert, PCR reverse dot hybridization, ddPCR, next-generation sequencing and gene chips. Then, novel DST methods were described, including metabolism testing, cell-free DNA probe, CRISPR assay, and spectral analysis technique. The limitations, challenges, and perspectives of different techniques for drug resistance are also discussed. These methods significantly improve the detection sensitivity and accuracy of multidrug-resistant tuberculosis (MRT) and can effectively curb the incidence of drug-resistant tuberculosis and accelerate the process of tuberculosis eradication.
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Affiliation(s)
- Xue-Song Xiong
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Xue-Di Zhang
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Jia-Wei Yan
- Department of Laboratory Medicine, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Ting-Ting Huang
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
| | - Zhan-Zhong Liu
- Department of Pharmacy, Xuzhou Infectious Diseases Hospital, Xuzhou, Jiangsu Province, People’s Republic of China
| | - Zheng-Kang Li
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Liang Wang
- Department of Laboratory Medicine, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong Province, People’s Republic of China
| | - Fen Li
- Department of Laboratory Medicine, The Affiliated Huai’an Hospital of Yangzhou University, Huai’an, Jiangsu Province, People’s Republic of China
- Department of Laboratory Medicine, The Fifth People’s Hospital of Huai’an, Huai’an, Jiangsu Province, People’s Republic of China
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3
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Sao Emani C, Reiling N. The efflux pumps Rv1877 and Rv0191 play differential roles in the protection of Mycobacterium tuberculosis against chemical stress. Front Microbiol 2024; 15:1359188. [PMID: 38516013 PMCID: PMC10956863 DOI: 10.3389/fmicb.2024.1359188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/12/2024] [Indexed: 03/23/2024] Open
Abstract
Background It was previously shown that GlnA3sc enabled Streptomyces coelicolor to survive in excess polyamines. However, subsequent studies revealed that Rv1878, the corresponding Mycobacterium tuberculosis (M.tb) ortholog, was not essential for the detoxification of spermine (Spm), in M.tb. On the other hand, the multi-drug efflux pump Rv1877 was previously shown to enable export of a wide range of compounds, while Rv0191 was shown to be more specific to chloramphenicol. Rationale Therefore, we first wanted to determine if detoxification of Spm by efflux can be achieved by any efflux pump, or if that was dependent upon the function of the pump. Next, since Rv1878 was found not to be essential for the detoxification of Spm, we sought to follow-up on the investigation of the physiological role of Rv1878 along with Rv1877 and Rv0191. Approach To evaluate the specificity of efflux pumps in the mycobacterial tolerance to Spm, we generated unmarked ∆rv1877 and ∆rv0191 M.tb mutants and evaluated their susceptibility to Spm. To follow up on the investigation of any other physiological roles they may have, we characterized them along with the ∆rv1878 M.tb mutant. Results The ∆rv1877 mutant was sensitive to Spm stress, while the ∆rv0191 mutant was not. On the other hand, the ∆rv1878 mutant grew better than the wild-type during iron starvation yet was sensitive to cell wall stress. The proteins Rv1877 and Rv1878 seemed to play physiological roles during hypoxia and acidic stress. Lastly, the ∆rv0191 mutant was the only mutant that was sensitive to oxidative stress. Conclusion The multidrug MFS-type efflux pump Rv1877 is required for Spm detoxification, as opposed to Rv0191 which seems to play a more specific role. Moreover, Rv1878 seems to play a role in the regulation of iron homeostasis and the reconstitution of the cell wall of M.tb. On the other hand, the sensitivity of the ∆rv0191 mutant to oxidative stress, suggests that Rv0191 may be responsible for the transport of low molecular weight thiols.
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Affiliation(s)
- Carine Sao Emani
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Norbert Reiling
- Microbial Interface Biology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
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Sachan RK, Mistry V, Dholaria M, Rana A, Devgon I, Ali I, Iqbal J, Eldin SM, Mohammad Said Al-Tawaha AR, Bawazeer S, Dutta J, Karnwal A. Overcoming Mycobacterium tuberculosis Drug Resistance: Novel Medications and Repositioning Strategies. ACS OMEGA 2023; 8:32244-32257. [PMID: 37720746 PMCID: PMC10500578 DOI: 10.1021/acsomega.3c02563] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/10/2023] [Indexed: 09/19/2023]
Abstract
Mycobacterium tuberculosis, the bacterium responsible for tuberculosis, is a global health concern, affecting millions worldwide. This bacterium has earned a reputation as a formidable adversary due to its multidrug-resistant nature, allowing it to withstand many antibiotics. The development of this drug resistance in Mycobacterium tuberculosis is attributed to innate and acquired mechanisms. In the past, rifampin was considered a potent medication for treating tuberculosis infections. However, the rapid development of resistance to this drug by the bacterium underscores the pressing need for new therapeutic agents. Fortunately, several other medications previously overlooked for tuberculosis treatment are already available in the market. Moreover, several innovative drugs are under clinical investigation, offering hope for more effective treatments. To enhance the effectiveness of these drugs, it is recommended that researchers concentrate on identifying unique target sites within the bacterium during the drug development process. This strategy could potentially circumvent the issues presented by Mycobacterium drug resistance. This review primarily focuses on the characteristics of novel drug resistance mechanisms in Mycobacterium tuberculosis. It also discusses potential medications being repositioned or sourced from novel origins. The ultimate objective of this review is to discover efficacious treatments for tuberculosis that can successfully tackle the hurdles posed by Mycobacterium drug resistance.
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Affiliation(s)
| | - Vyoma Mistry
- C.
G. Bhakta Institute of Biotechnology, Uka
Tarsadia University, Bardoli 394350, Surat, India
| | - Mayuri Dholaria
- Naran
Lala College of Professional and Applied Sciences, Navsari 396450, Gujarat, India
| | - Abhishek Rana
- Jindal
Global Law School, OP Jindal Global University, Sonepat 131001, Haryana, India
| | - Inderpal Devgon
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Iftikhar Ali
- Center
for Plant Science and Biodiversity, University
of Swat, Charbagh 19120, Pakistan
- Department
of Genetics and Development, Columbia University
Irving Medical Center, New York, New York 10032, United States
| | - Javed Iqbal
- Department
of Botany, Bacha Khan University, Charsadda, 24420 Khyber Pakhtunkhwa, Pakistan
| | - Sayed M. Eldin
- Center
of Research, Faculty of Engineering, Future
University in Egypt, New Cairo 11835, Egypt
| | | | - Sami Bawazeer
- Faculty
of Pharmacy, Department of Pharmacognosy, Umm Al-Qura University, Makkah 4041-4152, Kingdom of Saudi Arabia
| | - Joydeep Dutta
- Lovely
Professional University, Phagwara 144411, Punjab, India
| | - Arun Karnwal
- Lovely
Professional University, Phagwara 144411, Punjab, India
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5
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Ansari MA, Shoaib S, Alomary MN, Ather H, Ansari SMA, Hani U, Jamous YF, Alyahya SA, Alharbi JN, Imran MA, Wahab S, Ahmad W, Islam N. Deciphering the emerging role of phytocompounds: Implications in the management of drug-resistant tuberculosis and ATDs-induced hepatic damage. J Infect Public Health 2023; 16:1443-1459. [PMID: 37523915 DOI: 10.1016/j.jiph.2023.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/05/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023] Open
Abstract
Tuberculosis is a disease of poverty, discrimination, and socioeconomic burden. Epidemiological studies suggest that the mortality and incidence of tuberculosis are unacceptably higher worldwide. Genomic mutations in embCAB, embR, katG, inhA, ahpC, rpoB, pncA, rrs, rpsL, gyrA, gyrB, and ethR contribute to drug resistance reducing the susceptibility of Mycobacterium tuberculosis to many antibiotics. Additionally, treating tuberculosis with antibiotics also poses a serious risk of hepatotoxicity in the patient's body. Emerging data on drug-induced liver injury showed that anti-tuberculosis drugs remarkably altered levels of hepatotoxicity biomarkers. The review is an attempt to explore the anti-mycobacterial potential of selected, commonly available, and well-known phytocompounds and extracts of medicinal plants against strains of Mycobacterium tuberculosis. Many studies have demonstrated that phytocompounds such as flavonoids, alkaloids, terpenoids, and phenolic compounds have antibacterial action against Mycobacterium species, inhibiting the bacteria's growth and replication, and sometimes, causing cell death. Phytocompounds act by disrupting bacterial cell walls and membranes, reducing enzyme activity, and interfering with essential metabolic processes. The combination of these processes reduces the overall survivability of the bacteria. Moreover, several phytochemicals have synergistic effects with antibiotics routinely used to treat TB, improving their efficacy and decreasing the risk of resistance development. Interestingly, phytocompounds have been presented to reduce isoniazid- and ethambutol-induced hepatotoxicity by reversing serum levels of AST, ALP, ALT, bilirubin, MDA, urea, creatinine, and albumin to their normal range, leading to attenuation of inflammation and hepatic necrosis. As a result, phytochemicals represent a promising field of research for the development of new TB medicines.
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Affiliation(s)
- Mohammad Azam Ansari
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441 Dammam, Saudi Arabia.
| | - Shoaib Shoaib
- Department Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India
| | - Mohammad N Alomary
- Advanced Diagnostic and Therapeutic Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Hissana Ather
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | | | - Umme Hani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia
| | - Yahya F Jamous
- Vaccine and Bioprocessing Center, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Sami A Alyahya
- Wellness and Preventive Medicine Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh 11442, Saudi Arabia
| | - Jameela Naif Alharbi
- Department of Epidemic Disease Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, 31441 Dammam, Saudi Arabia
| | - Mohammad Azhar Imran
- Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul 120752, Republic of Korea
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha 61421, Saudi Arabia
| | - Wasim Ahmad
- Department of Pharmacy, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Najmul Islam
- Department Biochemistry, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002, India.
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Bui VCB, Yaniv Z, Harris M, Yang F, Kantipudi K, Hurt D, Rosenthal A, Jaeger S. Combining Radiological and Genomic TB Portals Data for Drug Resistance Analysis. IEEE ACCESS : PRACTICAL INNOVATIONS, OPEN SOLUTIONS 2023; 11:84228-84240. [PMID: 37663145 PMCID: PMC10473876 DOI: 10.1109/access.2023.3298750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Tuberculosis (TB) drug resistance is a worldwide public health problem. It decreases the likelihood of a positive outcome for the individual patient and increases the likelihood of disease spread. Therefore, early detection of TB drug resistance is crucial for improving outcomes and controlling disease transmission. While drug-sensitive tuberculosis cases are declining worldwide because of effective treatment, the threat of drug-resistant tuberculosis is growing, and the success rate of drug-resistant tuberculosis treatment is only around 60%. The TB Portals program provides a publicly accessible repository of TB case data with an emphasis on collecting drug-resistant cases. The dataset includes multi-modal information such as socioeconomic/geographic data, clinical characteristics, pathogen genomics, and radiological features. The program is an international collaboration whose participants are typically under a substantial burden of drug-resistant tuberculosis, with data collected from standard clinical care provided to the patients. Consequentially, the TB Portals dataset is heterogenous in nature, with data representing multiple treatment centers in different countries and containing cross-domain information. This study presents the challenges and methods used to address them when working with this real-world dataset. Our goal was to evaluate whether combining radiological features derived from a chest X-ray of the host and genomic features from the pathogen can potentially improve the identification of the drug susceptibility type, drug-sensitive (DS-TB) or drug-resistant (DR-TB), and the length of the first successful drug regimen. To perform these studies, significantly imbalanced data needed to be processed, which included a much larger number of DR-TB cases than DS-TB, many more cases with radiological findings than genomic ones, and the sparse high dimensional nature of the genomic information. Three evaluation studies were carried out. First, the DR-TB/DS-TB classification model achieved an average accuracy of 92.4% when using genomic features alone or when combining radiological and genomic features. Second, the regression model for the length of the first successful treatment had a relative error of 53.5% using radiological features, 25.6% using genomic features, and 22.0% using both radiological and genomic features. Finally, the relative error of the third regression model predicting the length of the first treatment using the most common drug combination varied depending on the feature type used. When using radiological features alone, the relative error was 17.8%. For genomic features alone, the relative error increased to 19.9%. The model had a relative error of 19.0% when both radiological and genomic features were combined. Although combining radiological and genomic features did not improve upon the use of genomic features when classifying DR-TB/DS-TB, the combination of the two feature types improved the relative error of the predictive model for the length of the first successful treatment. Furthermore, the regression model trained on radiological features achieved the best performance when predicting the treatment length of the most common drug combination.
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Affiliation(s)
- Vy C B Bui
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Ziv Yaniv
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael Harris
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feng Yang
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Karthik Kantipudi
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Darrell Hurt
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alex Rosenthal
- Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stefan Jaeger
- Lister Hill National Center for Biomedical Communications, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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7
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Robbins L, Balaram A, Dejneka S, McMahon M, Najibi Z, Pawlowicz P, Conrad WH. Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model. Sci Rep 2023; 13:8551. [PMID: 37237156 DOI: 10.1038/s41598-023-35632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC-MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
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Affiliation(s)
- Laurel Robbins
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Ariane Balaram
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Stefanie Dejneka
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Matthew McMahon
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Zarina Najibi
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Peter Pawlowicz
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - William H Conrad
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA.
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8
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Mei YM, Zhang WY, Sun JY, Jiang HQ, Shi Y, Xiong JS, Wang L, Chen YQ, Long SY, Pan C, Luo T, Wang HS. Genomic characteristics of Mycobacterium tuberculosis isolates of cutaneous tuberculosis. Front Microbiol 2023; 14:1165916. [PMID: 37266022 PMCID: PMC10230547 DOI: 10.3389/fmicb.2023.1165916] [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: 02/14/2023] [Accepted: 04/19/2023] [Indexed: 06/03/2023] Open
Abstract
Objectives Cutaneous tuberculosis with various manifestations can be divided into several clinical types according to the host's immune status and infective route. However, the etiological factors of this disease remain unclear. The objective of this study is to investigate the pathogens associated with the occurrence and different types of cutaneous tuberculosis. Methods 58 Mycobacterium tuberculosis strains isolated from cutaneous tuberculosis over the last 20 years were sequenced and analyzed for genomic characteristics including lineage distribution, drug-resistance mutations, and mutations potentially associated with different sites of infection. Results The M. tuberculosis strains from four major types of cutaneous tuberculosis and pulmonary tuberculosis shared similar genotypes and genomic composition. The strains isolated from cutaneous tuberculosis had a lower rate of drug resistance. Phylogenic analysis showed cutaneous tuberculosis and pulmonary tuberculosis isolates scattered on the three. Several SNPs in metabolism related genes exhibited a strong correlation with different infection sites. Conclusions The different infection sites of TB may barely be affected by large genomic changes in M. tuberculosis isolates, but the significant difference in SNPs of drug resistance gene and metabolism-related genes still deserves more attention.
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Affiliation(s)
- You-Ming Mei
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Wen-Yue Zhang
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Ji-Ya Sun
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Hai-Qin Jiang
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Ying Shi
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Jing-Shu Xiong
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Le Wang
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Yan-Qing Chen
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Si-Yu Long
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Chun Pan
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Tao Luo
- Department of Pathogen Biology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hong-Sheng Wang
- Hospital of Skin Disease, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
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9
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Myers BK, Shin GY, Agarwal G, Stice SP, Gitaitis RD, Kvitko BH, Dutta B. Genome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum × Allium cepa hybrid. Front Microbiol 2023; 13:1094155. [PMID: 36817114 PMCID: PMC9933511 DOI: 10.3389/fmicb.2022.1094155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/30/2022] [Indexed: 02/05/2023] Open
Abstract
Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P. ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A. cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.
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Affiliation(s)
- Brendon K. Myers
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Gi Yoon Shin
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Gaurav Agarwal
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Shaun P. Stice
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Ronald D. Gitaitis
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States
| | - Brian H. Kvitko
- Department of Plant Pathology, The University of Georgia, Athens, GA, United States
| | - Bhabesh Dutta
- Department of Plant Pathology, The University of Georgia, Tifton, GA, United States,*Correspondence: Bhabesh Dutta, ✉
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10
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Naz S, Paritosh K, Sanyal P, Khan S, Singh Y, Varshney U, Nandicoori VK. GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis. eLife 2023; 12:75860. [PMID: 36695572 PMCID: PMC9876569 DOI: 10.7554/elife.75860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.
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Affiliation(s)
- Saba Naz
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
- Department of Zoology, University of DelhiDelhiIndia
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South CampusNew DelhiIndia
| | | | - Sidra Khan
- National Institute of ImmunologyNew DelhiIndia
| | | | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
| | - Vinay Kumar Nandicoori
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
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11
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Fichant A, Felten A, Gallet A, Firmesse O, Bonis M. Identification of Genetic Markers for the Detection of Bacillus thuringiensis Strains of Interest for Food Safety. Foods 2022; 11:foods11233924. [PMID: 36496733 PMCID: PMC9739007 DOI: 10.3390/foods11233924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Bacillus thuringiensis (Bt), belonging to the Bacillus cereus (Bc) group, is commonly used as a biopesticide worldwide due to its ability to produce insecticidal crystals during sporulation. The use of Bt, especially subspecies aizawai and kurstaki, to control pests such as Lepidoptera, generally involves spraying mixtures containing spores and crystals on crops intended for human consumption. Recent studies have suggested that the consumption of commercial Bt strains may be responsible for foodborne outbreaks (FBOs). However, its genetic proximity to Bc strains has hindered the development of routine tests to discriminate Bt from other Bc, especially Bacillus cereus sensu stricto (Bc ss), well known for its involvement in FBOs. Here, to develop tools for the detection and the discrimination of Bt in food, we carried out a genome-wide association study (GWAS) on 286 complete genomes of Bc group strains to identify and validate in silico new molecular markers specific to different Bt subtypes. The analyses led to the determination and the in silico validation of 128 molecular markers specific to Bt, its subspecies aizawai, kurstaki and four previously described proximity clusters associated with these subspecies. We developed a command line tool based on a 14-marker workflow, to carry out a computational search for Bt-related markers from a putative Bc genome, thereby facilitating the detection of Bt of interest for food safety, especially in the context of FBOs.
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Affiliation(s)
- Arnaud Fichant
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
- Université Côte d’Azur, CNRS, INRAE, ISA, France
| | - Arnaud Felten
- Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 22440 Ploufragan, France
| | - Armel Gallet
- Université Côte d’Azur, CNRS, INRAE, ISA, France
| | - Olivier Firmesse
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
| | - Mathilde Bonis
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
- Correspondence:
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12
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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13
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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14
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Liu Q, Qiu B, Li G, Yang T, Tao B, Martinez L, Zhu L, Wang J, Mao X, Lu W. Tuberculosis reinfection and relapse in eastern China: A prospective study using whole-genome sequencing. Clin Microbiol Infect 2022; 28:1458-1464. [PMID: 35700940 DOI: 10.1016/j.cmi.2022.05.019] [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: 12/17/2021] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Tuberculosis recurrence after an initial successful treatment episode can occur from either reinfection or relapse. In a population-based sample and whole genome sequencing (WGS) in eastern China, we aimed to evaluate risk factors for tuberculosis recurrence, and assess the proportion of recurrence due to either reinfection or relapse. METHODS Successfully treated pulmonary tuberculosis patients with sputum culture positive results were recruited from five cities in Jiangsu Province from 2013-2015 and followed for two years for tuberculosis recurrence. Among patients developing a second tuberculosis episode, WGS was performed to distinguish relapse or reinfection through a distance threshold of 6-single-nucleotide polymorphisms (SNP). We analyzed risk factors for recurrence and epidemiological characteristics of different types of recurrent patients. RESULTS Of 1,897 successful treated tuberculosis patients, 7.4% (141/1879) developed recurrent tuberculosis. Compared with non-recurrent tuberculosis, patients were at higher risk of recurrence in older age (Adjusted Odds Ratio [AOR], 1.02 for each additional year; 95% CI, 1.01-1.03, P=0.003), patients previously treated for tuberculosis (AOR=2.22; 95% CI, 1.52-3.26, P<0.001), or with bilateral cavities (AOR, 1.56; 95% CI, 1.05-2.32, P=0.029). Among 27.0% (38/141) recurrent tuberculosis patients with successfully sequenced pairs, relapse was substantially more common than reinfection (71.1% versus 28.9%, P=0.014). CONCLUSIONS Endogenous relapse was significantly more common than exogenous reinfection in the first two years after treatment in eastern China. Prioritization of high-risk groups for recurrence, such as the elderly, with a previous tuberculosis diagnosis, or with bilateral cavities, may provide opportunities to reduce post-tuberculosis morbidity.
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Affiliation(s)
- Qiao Liu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Guoli Li
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Tingting Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shanghai, PR China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Leonardo Martinez
- Department of Epidemiology, School of Public Health, Boston University, Boston, Massachusetts, United States
| | - Limei Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Xuhua Mao
- Department of Clinical Laboratory, Affiliated Yixing People's Hospital, Jiangsu University, Wuxi, China.
| | - Wei Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, Jiangsu Province, PR China.
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15
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Rahman MM, Alam Tumpa MA, Zehravi M, Sarker MT, Yamin M, Islam MR, Harun-Or-Rashid M, Ahmed M, Ramproshad S, Mondal B, Dey A, Damiri F, Berrada M, Rahman MH, Cavalu S. An Overview of Antimicrobial Stewardship Optimization: The Use of Antibiotics in Humans and Animals to Prevent Resistance. Antibiotics (Basel) 2022; 11:667. [PMID: 35625311 PMCID: PMC9137991 DOI: 10.3390/antibiotics11050667] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Antimicrobials are a type of agent widely used to prevent various microbial infections in humans and animals. Antimicrobial resistance is a major cause of clinical antimicrobial therapy failure, and it has become a major public health concern around the world. Increasing the development of multiple antimicrobials has become available for humans and animals with no appropriate guidance. As a result, inappropriate use of antimicrobials has significantly produced antimicrobial resistance. However, an increasing number of infections such as sepsis are untreatable due to this antimicrobial resistance. In either case, life-saving drugs are rendered ineffective in most cases. The actual causes of antimicrobial resistance are complex and versatile. A lack of adequate health services, unoptimized use of antimicrobials in humans and animals, poor water and sanitation systems, wide gaps in access and research and development in healthcare technologies, and environmental pollution have vital impacts on antimicrobial resistance. This current review will highlight the natural history and basics of the development of antimicrobials, the relationship between antimicrobial use in humans and antimicrobial use in animals, the simplistic pathways, and mechanisms of antimicrobial resistance, and how to control the spread of this resistance.
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Affiliation(s)
- Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Mst. Afroza Alam Tumpa
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy Girls Section, Prince Sattam Bin Abdul Aziz University, Alkharj 11942, Saudi Arabia;
| | - Md. Taslim Sarker
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Yamin
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Rezaul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Md. Harun-Or-Rashid
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh; (M.A.A.T.); (M.T.S.); (M.Y.); (M.R.I.); (M.H.-O.-R.); (M.A.)
| | - Sarker Ramproshad
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Banani Mondal
- Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj 1400, Bangladesh; (S.R.); (B.M.)
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata 700073, India;
| | - Fouad Damiri
- Labortory of Biomolecules and Organic Synthesis (BioSynthO), Department of Chemistry, Faculty of Sciences Ben M’Sick, University Hassan II of Casablanca, Casablanca 20000, Morocco; (F.D.); (M.B.)
| | - Mohammed Berrada
- Labortory of Biomolecules and Organic Synthesis (BioSynthO), Department of Chemistry, Faculty of Sciences Ben M’Sick, University Hassan II of Casablanca, Casablanca 20000, Morocco; (F.D.); (M.B.)
| | - Md. Habibur Rahman
- Department of Global Medical Science, Wonju College of Medicine, Yonsei University, Wonju 26426, Korea
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania
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16
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Wu X, Shang Y, Ren W, Wang W, Wang Y, Xue Z, Li S, Pang Y. Minimum inhibitory concentration of cycloserine against Mycobacterium tuberculosis using the MGIT 960 system and a proposed critical concentration. Int J Infect Dis 2022; 121:148-151. [PMID: 35577251 DOI: 10.1016/j.ijid.2022.05.030] [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] [Received: 04/06/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES We aimed to determine the breakpoint of cycloserine (CS) susceptibility in MGIT and to describe the molecular characteristics of CS-resistant Mycobacterium tuberculosis (MTB) isolates. METHODS A total of 124 MTB isolates were recruited in our analysis. Minimum inhibitory concentration (MIC) was determined using the MGIT system. The mutations of MTB isolates within alr, ddl, ald, and cycA, potentially conferring CS resistance were analyzed by the whole-genome sequencing. RESULTS In vitro drug susceptibility testing of isolates with doubling concentrations of CS revealed that the modal MIC values was 4 mg/L for MGIT, accounting for 35.5% (44/124) of isolates tested. Seven isolates harbored mutations conferring CS resistance, consisting of five with alr mutations and two with ald mutations. On the basis of the MIC distributions of wild-type and resistotype populations, we proposed a tentative epidemiologic cut-off value of 16 mg/l. The proportion of CS resistance in extensively drug-resistant TB was significantly higher than that of multidrug-resistant TB. CONCLUSION In conclusion, we propose critical concentration for MGIT 960 to properly diagnose CS-resistant MTB and demonstrate that mutations in alr and ald genes are the major mechanism conferring CS resistance in clinical isolates.
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Affiliation(s)
- Xiao Wu
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Wei Wang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Yufeng Wang
- Innovation Alliance on Tuberculosis Diagnosis and Treatment, Beijing, People's Republic of China
| | - Zhongtan Xue
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, People's Republic of China.
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17
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Liu W, Li W, Zheng H, Kwok LY, Sun Z. Genomics divergence of Lactococcus lactis subsp. lactis isolated from naturally fermented dairy products. Food Res Int 2022; 155:111108. [DOI: 10.1016/j.foodres.2022.111108] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 12/13/2022]
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18
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Use of Whole-Genome Sequencing to Predict Mycobacterium tuberculosis Complex Drug Resistance from Early Positive Liquid Cultures. Microbiol Spectr 2022; 10:e0251621. [PMID: 35311541 PMCID: PMC9045259 DOI: 10.1128/spectrum.02516-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Our objective was to evaluate the performance of whole-genome sequencing (WGS) from early positive liquid cultures for predicting Mycobacterium tuberculosis complex (MTBC) drug resistance. Clinical isolates were obtained from tuberculosis patients at Shanghai Pulmonary Hospital (SPH). Antimicrobial susceptibility testing (AST) was performed, and WGS from early Bactec mycobacterial growth indicator tube (MGIT) 960-positive liquid cultures was performed to predict the drug resistance using the TB-Profiler informatics platform. A total of 182 clinical isolates were enrolled in this study. Using phenotypic AST as the gold standard, the overall sensitivity and specificity for WGS were, respectively, 97.1% (89.8 to 99.6%) and 90.4% (83.4 to 95.1%) for rifampin, 91.0% (82.4 to 96.3%) and 95.2% (89.1 to 98.4%) for isoniazid, 100.0% (89.4 to 100.0%) and 87.3% (80.8 to 92.1%) for ethambutol, 96.6% (88.3 to 99.6%) and 61.8% (52.6 to 70.4%) for streptomycin, 86.8% (71.9 to 95.6%) and 95.8% (91.2 to 98.5%) for moxifloxacin, 86.5% (71.2 to 91.5%) and 95.2% (90.3 to 98.0%) for ofloxacin, 100.0% (54.1 to 100.0%) and 67.6% (60.2 to 74.5%) for amikacin, 100.0% (63.1 to 100.0%) and 67.2% (59.7 to 74.2%) for kanamycin, 62.5% (24.5 to 91.5%) and 88.5% (82.8 to 92.8%) for ethionamide, 33.3% (4.3 to 77.7%) and 98.3% (95.1 to 99.7%) for para-aminosalicylic acid, and 0.0% (0.0 to 12.3%) and 100.0% (97.6 to 100.0%) for cycloserine. The concordances of WGS-based AST and phenotypic AST were as follows: rifampin (92.9%), isoniazid (93.4%), ethambutol (89.6%), streptomycin (73.1%), moxifloxacin (94.0%), ofloxacin (93.4%), amikacin (68.7%), kanamycin (68.7%), ethionamide (87.4%), para-aminosalicylic acid (96.2%) and cycloserine (84.6%). We conclude that WGS could be a promising approach to predict MTBC resistance from early positive liquid cultures. IMPORTANCE In this study, we used whole-genome sequencing (WGS) from early positive liquid (MGIT) cultures instead of solid cultures to predict drug resistance of 182 Mycobacterium tuberculosis complex (MTBC) clinical isolates to predict drug resistance using the TB-Profiler informatics platform. Our study indicates that WGS may be a promising method for predicting MTBC resistance using early positive liquid cultures.
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Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection. Proc Natl Acad Sci U S A 2022; 119:e2113600119. [PMID: 35452305 PMCID: PMC9173582 DOI: 10.1073/pnas.2113600119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
SignificancePrevious attempts to identify the action of natural selection in the Mycobacterium tuberculosis complex (MTBC) were limited by sample size and averaging across time and lineages. We investigate changes in selective pressures across time for every single gene of the MTBC. We developed a methodology to analyze temporal signals of selection in a large dataset (∼5,000 complete genomes) and showed that 1) almost half of the genes seem to have been under positive selection at some point in time; 2) experimentally confirmed epitopes tend to accumulate more mutations in deeper branches than in external branches; and 3) temporal signals identify genes that were conserved in the past but under positive selection in the present, suggesting ongoing adaptation to the host.
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20
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Wei W, Qiao J, Jiang X, Cai L, Hu X, He J, Chen M, Yang M, Cui T. Dehydroquinate Synthase Directly Binds to Streptomycin and Regulates Susceptibility of Mycobacterium bovis to Streptomycin in a Non-canonical Mode. Front Microbiol 2022; 13:818881. [PMID: 35516432 PMCID: PMC9063660 DOI: 10.3389/fmicb.2022.818881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/22/2022] [Indexed: 12/02/2022] Open
Abstract
Antimicrobial resistance (AMR) represents one of the main challenges in Tuberculosis (TB) treatment. Investigating the genes involved in AMR and the underlying mechanisms holds promise for developing alternative treatment strategies. The results indicate that dehydroquinate synthase (DHQS) regulates the susceptibility of Mycobacterium bovis BCG to first-line anti-TB drug streptomycin. Perturbation of the expression of aroB encoding DHQS affects the susceptibility of M. bovis BCG to streptomycin. Purified DHQS impairs in vitro antibacterial activity of streptomycin, but did not hydrolyze or modify streptomycin. DHQS directly binds to streptomycin while retaining its own catalytic activity. Computationally modeled structure analysis of DHQS–streptomycin complex reveals that DHQS binds to streptomycin without disturbing native substrate binding. In addition, streptomycin treatment significantly induces the expression of DHQS, thus resulting in DHQS-mediated susceptibility. Our findings uncover the additional function of DHQS in AMR and provide an insight into a non-canonical resistance mechanism by which protein hijacks antibiotic to reduce the interaction between antibiotic and its target with normal protein function retained.
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Affiliation(s)
- Wenping Wei
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junjie Qiao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaofang Jiang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Luxia Cai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaomin Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jin He
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Min Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Min Yang,
| | - Tao Cui
- Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
- Tao Cui,
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21
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Ponnusamy N, Arumugam M. Interaction of Host Pattern Recognition Receptors (PRRs) with Mycobacterium Tuberculosis and Ayurvedic Management of Tuberculosis: A Systemic Approach. Infect Disord Drug Targets 2022; 22:e130921196420. [PMID: 34517809 DOI: 10.2174/1871526521666210913110834] [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: 11/20/2020] [Revised: 04/15/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb), infects the lungs' alveolar surfaces through aerosol droplets. At this stage, the disease progression may have many consequences, determined primarily by the reactions of the human immune system. However, one approach will be to more actively integrate the immune system, especially the pattern recognition receptor (PRR) systems of the host, which notices pathogen-associated molecular patterns (PAMPs) of Mtb. Several types of PRRs are involved in the detection of Mtb, including Toll-like receptors (TLRs), C-type lectin receptors (CLRs), Dendritic cell (DC) -specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN), Mannose receptor (MR), and NOD-like receptors (NLRs) related to inflammasome activation. In this study, we focus on reviewing the Mtb pathophysiology and interaction of host PPRs with Mtb as well as adverse drug effects of anti-tuberculosis drugs (ATDs) and systematic TB treatment via Ayurvedic medicine.
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Affiliation(s)
- Nirmaladevi Ponnusamy
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
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22
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The Neglected Contribution of Streptomycin to the Tuberculosis Drug Resistance Problem. Genes (Basel) 2021; 12:genes12122003. [PMID: 34946952 PMCID: PMC8701281 DOI: 10.3390/genes12122003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
The airborne pathogen Mycobacterium tuberculosis is responsible for a present major public health problem worsened by the emergence of drug resistance. M. tuberculosis has acquired and developed streptomycin (STR) resistance mechanisms that have been maintained and transmitted in the population over the last decades. Indeed, STR resistant mutations are frequently identified across the main M. tuberculosis lineages that cause tuberculosis outbreaks worldwide. The spread of STR resistance is likely related to the low impact of the most frequent underlying mutations on the fitness of the bacteria. The withdrawal of STR from the first-line treatment of tuberculosis potentially lowered the importance of studying STR resistance. However, the prevalence of STR resistance remains very high, could be underestimated by current genotypic methods, and was found in outbreaks of multi-drug (MDR) and extensively drug (XDR) strains in different geographic regions. Therefore, the contribution of STR resistance to the problem of tuberculosis drug resistance should not be neglected. Here, we review the impact of STR resistance and detail well-known and novel candidate STR resistance mechanisms, genes, and mutations. In addition, we aim to provide insights into the possible role of STR resistance in the development of multi-drug resistant tuberculosis.
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23
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Tamilzhalagan S, Shanmugam S, Selvaraj A, Suba S, Suganthi C, Moonan PK, Surie D, Sathyanarayanan MK, Gomathi NS, Jayabal L, Sachdeva KS, Selvaraju S, Swaminathan S, Tripathy SP, Hall PJ, Ranganathan UD. Whole-Genome Sequencing to Identify Missed Rifampicin and Isoniazid Resistance Among Tuberculosis Isolates-Chennai, India, 2013-2016. Front Microbiol 2021; 12:720436. [PMID: 34880835 PMCID: PMC8645853 DOI: 10.3389/fmicb.2021.720436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/12/2021] [Indexed: 11/15/2022] Open
Abstract
India has a high burden of drug-resistant tuberculosis (DR TB) and many cases go undetected by current drug susceptibility tests (DSTs). This study was conducted to identify rifampicin (RIF) and isoniazid (INH) resistance associated genetic mutations undetected by current clinical diagnostics amongst persons with DR TB in Chennai, India. Retrospectively stored 166 DR TB isolates during 2013–2016 were retrieved and cultured in Löwenstein-Jensen medium. Whole genome sequencing (WGS) and MGIT DST for RIF and INH were performed. Discordant genotypic and phenotypic sensitivity results were repeated for confirmation and the discrepant results considered final. Further, drug resistance-conferring mutations identified through WGS were analyzed for their presence as targets in current WHO-recommended molecular diagnostics. WGS detected additional mutations for rifampicin and isoniazid resistance than WHO-endorsed line probe assays. For RIF, WGS was able to identify an additional 10% (15/146) of rpoB mutant isolates associated with borderline rifampicin resistance compared to MGIT DST. WGS could detect additional DR TB cases than commercially available and WHO-endorsed molecular DST tests. WGS results reiterate the importance of the recent WHO revised critical concentrations of current MGIT DST to detect low-level resistance to rifampicin. WGS may help inform effective treatment selection for persons at risk of, or diagnosed with, DR TB.
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Affiliation(s)
| | | | - Ashok Selvaraj
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Sakthi Suba
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | | | - Patrick K Moonan
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Diya Surie
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | | | | | - Sriram Selvaraju
- ICMR-National Institute for Research in Tuberculosis, Chennai, India
| | - Soumya Swaminathan
- ICMR-National Institute for Research in Tuberculosis, Chennai, India.,World Health Organization, Geneva, Switzerland
| | | | - Patricia J Hall
- U.S. Centers for Disease Control and Prevention, Atlanta, GA, United States
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Maeda T, Kawada M, Sakata N, Kotani H, Furusawa C. Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles. Sci Rep 2021; 11:15136. [PMID: 34302035 PMCID: PMC8302736 DOI: 10.1038/s41598-021-94645-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/14/2021] [Indexed: 11/09/2022] Open
Abstract
Drug-resistant tuberculosis (TB) is a growing public health problem. There is an urgent need for information regarding cross-resistance and collateral sensitivity relationships among drugs and the genetic determinants of anti-TB drug resistance for developing strategies to suppress the emergence of drug-resistant pathogens. To identify mutations that confer resistance to anti-TB drugs in Mycobacterium species, we performed the laboratory evolution of nonpathogenic Mycobacterium smegmatis, which is closely related to Mycobacterium tuberculosis, against ten anti-TB drugs. Next, we performed whole-genome sequencing and quantified the resistance profiles of each drug-resistant strain against 24 drugs. We identified the genes with novel meropenem (MP) and linezolid (LZD) resistance-conferring mutation, which also have orthologs, in M. tuberculosis H37Rv. Among the 240 possible drug combinations, we identified 24 pairs that confer cross-resistance and 18 pairs that confer collateral sensitivity. The acquisition of bedaquiline or linezolid resistance resulted in collateral sensitivity to several drugs, while the acquisition of MP resistance led to multidrug resistance. The MP-evolved strains showed cross-resistance to rifampicin and clarithromycin owing to the acquisition of a mutation in the intergenic region of the Rv2864c ortholog, which encodes a penicillin-binding protein, at an early stage. These results provide a new insight to tackle drug-resistant TB.
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Affiliation(s)
- Tomoya Maeda
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan. .,Laboratory of Microbial Physiology, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan.
| | - Masako Kawada
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Natsue Sakata
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Hazuki Kotani
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan
| | - Chikara Furusawa
- RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furuedai, Suita, Osaka, 565-0874, Japan.,Universal Biology Institute, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
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25
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Roy TK, Chatterjee K, Khatri J, Schwaab G, Havenith M. Stepwise Microhydration of Isoxazole: Infrared Spectroscopy of Isoxazole-(Water)n≤2 Clusters in Helium Nanodroplets. J Phys Chem A 2021; 125:4766-4774. [DOI: 10.1021/acs.jpca.1c01974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tarun Kumar Roy
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Kuntal Chatterjee
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Jai Khatri
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, 44801 Bochum, Germany
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26
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da Silva PB, Araújo VHS, Fonseca-Santos B, Solcia MC, Ribeiro CM, da Silva IC, Alves RC, Pironi AM, Silva ACL, Victorelli FD, Fernandes MA, Ferreira PS, da Silva GH, Pavan FR, Chorilli M. Highlights Regarding the Use of Metallic Nanoparticles against Pathogens Considered a Priority by the World Health Organization. Curr Med Chem 2021; 28:1906-1956. [PMID: 32400324 DOI: 10.2174/0929867327666200513080719] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/11/2020] [Accepted: 03/20/2020] [Indexed: 11/22/2022]
Abstract
The indiscriminate use of antibiotics has facilitated the growing resistance of bacteria, and this has become a serious public health problem worldwide. Several microorganisms are still resistant to multiple antibiotics and are particularly dangerous in the hospital and nursing home environment, and to patients whose care requires devices, such as ventilators and intravenous catheters. A list of twelve pathogenic genera, which especially included bacteria that were not affected by different antibiotics, was released by the World Health Organization (WHO) in 2017, and the research and development of new antibiotics against these genera has been considered a priority. The nanotechnology is a tool that offers an effective platform for altering the physicalchemical properties of different materials, thereby enabling the development of several biomedical applications. Owing to their large surface area and high reactivity, metallic particles on the nanometric scale have remarkable physical, chemical, and biological properties. Nanoparticles with sizes between 1 and 100 nm have several applications, mainly as new antimicrobial agents for the control of microorganisms. In the present review, more than 200 reports of various metallic nanoparticles, especially those containing copper, gold, platinum, silver, titanium, and zinc were analyzed with regard to their anti-bacterial activity. However, of these 200 studies, only 42 reported about trials conducted against the resistant bacteria considered a priority by the WHO. All studies are in the initial stage, and none are in the clinical phase of research.
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Affiliation(s)
- Patricia Bento da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | - Bruno Fonseca-Santos
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Mariana Cristina Solcia
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Renata Carolina Alves
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Andressa Maria Pironi
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | | | | | - Mariza Aires Fernandes
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Paula Scanavez Ferreira
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Gilmar Hanck da Silva
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Fernando Rogério Pavan
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
| | - Marlus Chorilli
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences, Araraquara-SP, Brazil
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27
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Liu X, Ma Y, Wang J. Genetic variation and function: revealing potential factors associated with microbial phenotypes. BIOPHYSICS REPORTS 2021; 7:111-126. [PMID: 37288143 PMCID: PMC10235906 DOI: 10.52601/bpr.2021.200040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/09/2021] [Indexed: 06/09/2023] Open
Abstract
Innovations in sequencing technology have generated voluminous microbial and host genomic data, making it possible to detect these genetic variations and analyze the function influenced by them. Recently, many studies have linked such genetic variations to phenotypes through association or comparative analysis, which have further advanced our understanding of multiple microbial functions. In this review, we summarized the application of association analysis in microbes like Mycobacterium tuberculosis, focusing on screening of microbial genetic variants potentially associated with phenotypes such as drug resistance, pathogenesis and novel drug targets etc.; reviewed the application of additional comparative genomic or transcriptomic methods to identify genetic factors associated with functions in microbes; expanded the scope of our study to focus on host genetic factors associated with certain microbes or microbiome and summarized the recent host genetic variations associated with microbial phenotypes, including susceptibility and load after infection of HIV, presence/absence of different taxa, and quantitative traits of microbiome, and lastly, discussed the challenges that may be encountered and the apparent or potential viable solutions. Gene-function analysis of microbe and microbiome is still in its infancy, and in order to unleash its full potential, it is necessary to understand its history, current status, and the challenges hindering its development.
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Affiliation(s)
- Xiaolin Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Ma
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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28
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Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
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Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
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29
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Gaikwad NB, Afroz P, Ahmad MN, Kaul G, Shukla M, Nanduri S, Dasgupta A, Chopra S, Yaddanapudi VM. Design, synthesis, in vitro and in silico evaluation of new 3-phenyl-4,5-dihydroisoxazole-5-carboxamides active against drug-resistant mycobacterium tuberculosis. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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30
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Wang G, Jiang G, Jing W, Zong Z, Yu X, Chen S, Li W, Huang H. Prevalence and molecular characterizations of seven additional drug resistance among multidrug-resistant tuberculosis in China: A subsequent study of a national survey. J Infect 2021; 82:371-377. [PMID: 33556430 DOI: 10.1016/j.jinf.2021.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/08/2020] [Accepted: 02/02/2021] [Indexed: 11/26/2022]
Abstract
The drug resistance prevalence data facilitates selection of the initial drug for treating multidrug-resistant tuberculosis (MDR-TB). The aim of this study was to investigate the prevalence and molecular characterization of seven additional types of drug resistances among MDR-TB isolates collected from the first/only nationwide drug resistance surveillance in China. A total of 391 out of the 401 MDR-TB strains were successfully recovered by Löwenstein-Jensen medium. Drug susceptibility testing was performed against moxifloxacin (Mfx), bedaquiline (Bdq), linezolid (Lzd), clofazimine (Cfz), cycloserine (Cs), delamanid (Dlm) and pyrazinamide (PZA). The strains were subjected to whole-genome sequencing for the analysis corresponding drug resistant genes and their profiles. 269 (68.80%) were simple MDR-TB, 28 (7.16%) were extensively drug-resistant tuberculosis (XDR-TB) and 94 (24.04%) were pre-XDR-TB. Dlm, Lzd, Cfz and Bdq presented the lowest drug resistant rates i.e. 3.32% (13/391), 3.84% (15/391),6.65% (26/391) and 7.16% (28/391), respectively. Mfx (17.39%, 68/391) and CS (13.55%, 53/391) also demonstrated strong potencies against the MDR strains, whereas PZA (38.36%, 150/391) presented much higher resistant rate. 54.41% (37/68) Mfx-resistant strains carried mutations located within gyrA or gyrB. 70.15% (94/134) PZA-resistant strains had pncA mutations. Two of the 26 Cfz-resistant isolates had mutation in Rv0678 were also resistant to Bdq. Dlm, Lzd, Cfz and Bdq exhibited excellent activity against MDR-TB, including XDR-TB. These data highlighted the necessity of a timely, feasible and reliable DST, while genotypic DST for Mfx and PZA is promising at this moment.
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Affiliation(s)
- Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Guanglu Jiang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Wei Jing
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Zaojing Zong
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Xia Yu
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Suting Chen
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Weimin Li
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China.
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31
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Srivastava S, Chapagain M, van Zyl J, Deshpande D, Gumbo T. Potency of vancomycin against Mycobacterium tuberculosis in the hollow fiber system model. J Glob Antimicrob Resist 2021; 24:403-410. [PMID: 33508482 DOI: 10.1016/j.jgar.2021.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/11/2020] [Accepted: 01/05/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES To determine whether an inhaled vancomycin formulation resulting in high intrapulmonary 24-h area under the concentration-time curve (AUC0-24) could be optimised for tuberculosis treatment. We also explored vancomycin synergy and antagonism with d-cycloserine and benzylpenicillin. METHODS We determined MICs of two Mycobacterium tuberculosis (Mtb) laboratory strains (H37Ra and H37Rv) and two drug-susceptible and nine multidrug resistant clinical strains. Second, in the hollow fiber system model of TB [HFS-TB] using Mtb H37Ra strain, we recapitulated vancomycin intrapulmonary pharmacokinetics of eight doses administered twice daily over 28 days, mimicking a 6-h half-life. Using the HFS-TB, vancomycin was tested in combination with d-cycloserine and benzylpenicillin to determine synergy or antagonism between drugs targeting the same pathway. RESULTS Vancomycin MICs were 12 and 48 mg/L in drug-susceptible clinical isolates but >96 mg/L in all MDR isolates.In the HFS-TB, vancomycin killed 3.9 ± 0.6 log10 CFU/mL Mtb. The EC50 was calculated as AUC0-24/MIC of 184.6 ± 106.5. Compared with day 0, 1.0 and 2.0 log10 CFU/mL kill was achieved by AUC0-24/MIC of 168 and 685, respectively. Acquired vancomycin resistance developed to all vancomycin doses tested in the HFS-TB. In the HFS-TB, vancomycin was antagonistic to benzylpenicillin, which works downstream to glycopeptides in peptidoglycan synthesis, but synergistic with d-cycloserine, which inhibits upstream d-Ala-d-Ala ligase and alanine racemase. CONCLUSION Our proof-of-concept studies show that vancomycin optimal exposure target for Mtb kill could be achieved via inhalational drug delivery. Addition of drugs synergistic with vancomycin, e.g. d-cycloserine, may lower the vancomycin concentrations required to kill Mtb.
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Affiliation(s)
- Shashikant Srivastava
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Moti Chapagain
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Quantitative Preclinical and Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA
| | - Johanna van Zyl
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Devyani Deshpande
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Tawanda Gumbo
- Department of Pulmonary Immunology, University of Texas Health Science Center at Tyler, Tyler, TX, USA; Quantitative Preclinical and Clinical Sciences Department, Praedicare Inc., Dallas, TX, USA; Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa.
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32
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Integron gene cassettes harboring novel variants of D-alanine-D-alanine ligase confer high-level resistance to D-cycloserine. Sci Rep 2020; 10:20709. [PMID: 33244063 PMCID: PMC7691350 DOI: 10.1038/s41598-020-77377-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/10/2020] [Indexed: 11/08/2022] Open
Abstract
Antibiotic resistance poses an increasing threat to global health. To tackle this problem, the identification of principal reservoirs of antibiotic resistance genes (ARGs) plus an understanding of drivers for their evolutionary selection are important. During a PCR-based screen of ARGs associated with integrons in saliva-derived metagenomic DNA of healthy human volunteers, two novel variants of genes encoding a d-alanine-d-alanine ligase (ddl6 and ddl7) located within gene cassettes in the first position of a reverse integron were identified. Treponema denticola was identified as the likely host of the ddl cassettes. Both ddl6 and ddl7 conferred high level resistance to d-cycloserine when expressed in Escherichia coli with ddl7 conferring four-fold higher resistance to D-cycloserine compared to ddl6. A SNP was found to be responsible for this difference in resistance phenotype between the two ddl variants. Molecular dynamics simulations were used to explain the mechanism of this phenotypic change at the atomic scale. A hypothesis for the evolutionary selection of ddl containing integron gene cassettes is proposed, based on molecular docking of plant metabolites within the ATP and d-cycloserine binding pockets of Ddl.
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33
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Gallagher LA, Shears RK, Fingleton C, Alvarez L, Waters EM, Clarke J, Bricio-Moreno L, Campbell C, Yadav AK, Razvi F, O'Neill E, O'Neill AJ, Cava F, Fey PD, Kadioglu A, O'Gara JP. Impaired Alanine Transport or Exposure to d-Cycloserine Increases the Susceptibility of MRSA to β-lactam Antibiotics. J Infect Dis 2020; 221:1000-1016. [PMID: 31628459 DOI: 10.1093/infdis/jiz542] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 10/14/2019] [Indexed: 12/29/2022] Open
Abstract
Prolonging the clinical effectiveness of β-lactams, which remain first-line antibiotics for many infections, is an important part of efforts to address antimicrobial resistance. We report here that inactivation of the predicted d-cycloserine (DCS) transporter gene cycA resensitized methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics. The cycA mutation also resulted in hypersusceptibility to DCS, an alanine analogue antibiotic that inhibits alanine racemase and d-alanine ligase required for d-alanine incorporation into cell wall peptidoglycan. Alanine transport was impaired in the cycA mutant, and this correlated with increased susceptibility to oxacillin and DCS. The cycA mutation or exposure to DCS were both associated with the accumulation of muropeptides with tripeptide stems lacking the terminal d-ala-d-ala and reduced peptidoglycan cross-linking, prompting us to investigate synergism between β-lactams and DCS. DCS resensitized MRSA to β-lactams in vitro and significantly enhanced MRSA eradication by oxacillin in a mouse bacteremia model. These findings reveal alanine transport as a new therapeutic target to enhance the susceptibility of MRSA to β-lactam antibiotics.
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Affiliation(s)
- Laura A Gallagher
- School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Rebecca K Shears
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Claire Fingleton
- School of Natural Sciences, National University of Ireland, Galway, Ireland
| | - Laura Alvarez
- Molecular Infection Medicine, Sweden, Molecular Biology Department, Umeå University, Umeå, Sweden
| | - Elaine M Waters
- School of Natural Sciences, National University of Ireland, Galway, Ireland.,Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Jenny Clarke
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - Laura Bricio-Moreno
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | | | - Akhilesh K Yadav
- Molecular Infection Medicine, Sweden, Molecular Biology Department, Umeå University, Umeå, Sweden
| | - Fareha Razvi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Eoghan O'Neill
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Connolly Hospital, Dublin, Ireland
| | - Alex J O'Neill
- Antimicrobial Research Centre, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Felipe Cava
- Molecular Infection Medicine, Sweden, Molecular Biology Department, Umeå University, Umeå, Sweden
| | - Paul D Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Aras Kadioglu
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, United Kingdom
| | - James P O'Gara
- School of Natural Sciences, National University of Ireland, Galway, Ireland
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34
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Khawbung JL, Nath D, Chakraborty S. Drug resistant Tuberculosis: A review. Comp Immunol Microbiol Infect Dis 2020; 74:101574. [PMID: 33249329 DOI: 10.1016/j.cimid.2020.101574] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) was announced as a global emergency in 1993. There was an alarming counter attack of TB worldwide. However, when it was known that TB can be cured completely, the general public became ignorant towards the infection. The pathogenic organism Mycobacterium tuberculosis continuously evolved to resist the antagonist drugs. This has led to the outbreak of resistant strain that gave rise to "Multi Drug Resistant-Tuberculosis" and "Extensively Drug Resistant Tuberculosis" that can still be cured with a lower success rate. While the mechanism of resistance proceeds further, it ultimately causes unmanageable totally drug resistant TB (TDR-TB). Studying the molecular mechanisms underlying the resistance to drugs would help us grasp the genetics and pathophysiology of the disease. In this review, we present the molecular mechanisms behind Mycobacterium tolerance to drugs and their approach towards the development of multi-drug resistant, extremely drug resistant and totally drug resistant TB.
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Affiliation(s)
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
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35
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Sertbas M, Ulgen KO. Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. Front Cell Dev Biol 2020; 8:566702. [PMID: 33251208 PMCID: PMC7673413 DOI: 10.3389/fcell.2020.566702] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 09/30/2020] [Indexed: 12/14/2022] Open
Abstract
Pathogens give rise to a wide range of diseases threatening global health and hence drawing public health agencies' attention to establish preventative and curative solutions. Genome-scale metabolic modeling is ever increasingly used tool for biomedical applications including the elucidation of antibiotic resistance, virulence, single pathogen mechanisms and pathogen-host interaction systems. With this approach, the sophisticated cellular system of metabolic reactions inside the pathogens as well as between pathogen and host cells are represented in conjunction with their corresponding genes and enzymes. Along with essential metabolic reactions, alternate pathways and fluxes are predicted by performing computational flux analyses for the growth of pathogens in a very short time. The genes or enzymes responsible for the essential metabolic reactions in pathogen growth are regarded as potential drug targets, as a priori guide to researchers in the pharmaceutical field. Pathogens alter the key metabolic processes in infected host, ultimately the objective of these integrative constraint-based context-specific metabolic models is to provide novel insights toward understanding the metabolic basis of the acute and chronic processes of infection, revealing cellular mechanisms of pathogenesis, identifying strain-specific biomarkers and developing new therapeutic approaches including the combination drugs. The reaction rates predicted during different time points of pathogen development enable us to predict active pathways and those that only occur during certain stages of infection, and thus point out the putative drug targets. Among others, fatty acid and lipid syntheses reactions are recent targets of new antimicrobial drugs. Genome-scale metabolic models provide an improved understanding of how intracellular pathogens utilize the existing microenvironment of the host. Here, we reviewed the current knowledge of genome-scale metabolic modeling in pathogen cells as well as pathogen host interaction systems and the promising applications in the extension of curative strategies against pathogens for global preventative healthcare.
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Affiliation(s)
- Mustafa Sertbas
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.,Department of Chemical Engineering, Istanbul Technical University, Istanbul, Turkey
| | - Kutlu O Ulgen
- Department of Chemical Engineering, Bogazici University, Istanbul, Turkey
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36
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Hicks ND, Giffen SR, Culviner PH, Chao MC, Dulberger CL, Liu Q, Stanley S, Brown J, Sixsmith J, Wolf ID, Fortune SM. Mutations in dnaA and a cryptic interaction site increase drug resistance in Mycobacterium tuberculosis. PLoS Pathog 2020; 16:e1009063. [PMID: 33253310 PMCID: PMC7738170 DOI: 10.1371/journal.ppat.1009063] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/15/2020] [Accepted: 10/09/2020] [Indexed: 01/26/2023] Open
Abstract
Genomic dissection of antibiotic resistance in bacterial pathogens has largely focused on genetic changes conferring growth above a single critical concentration of drug. However, reduced susceptibility to antibiotics-even below this breakpoint-is associated with poor treatment outcomes in the clinic, including in tuberculosis. Clinical strains of Mycobacterium tuberculosis exhibit extensive quantitative variation in antibiotic susceptibility but the genetic basis behind this spectrum of drug susceptibility remains ill-defined. Through a genome wide association study, we show that non-synonymous mutations in dnaA, which encodes an essential and highly conserved regulator of DNA replication, are associated with drug resistance in clinical M. tuberculosis strains. We demonstrate that these dnaA mutations specifically enhance M. tuberculosis survival during isoniazid treatment via reduced expression of katG, the activator of isoniazid. To identify DnaA interactors relevant to this phenotype, we perform the first genome-wide biochemical mapping of DnaA binding sites in mycobacteria which reveals a DnaA interaction site that is the target of recurrent mutation in clinical strains. Reconstructing clinically prevalent mutations in this DnaA interaction site reproduces the phenotypes of dnaA mutants, suggesting that clinical strains of M. tuberculosis have evolved mutations in a previously uncharacterized DnaA pathway that quantitatively increases resistance to the key first-line antibiotic isoniazid. Discovering genetic mechanisms that reduce drug susceptibility and support the evolution of high-level drug resistance will guide development of biomarkers capable of prospectively identifying patients at risk of treatment failure in the clinic.
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Affiliation(s)
- Nathan D. Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Samantha R. Giffen
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Peter H. Culviner
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Michael C. Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Charles L. Dulberger
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jessica Brown
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Jaimie Sixsmith
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Ian D. Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Evidence for Expanding the Role of Streptomycin in the Management of Drug-Resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:AAC.00860-20. [PMID: 32540971 DOI: 10.1128/aac.00860-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/06/2020] [Indexed: 01/09/2023] Open
Abstract
In 2019, the WHO tuberculosis (TB) treatment guidelines were updated to recommend only limited use of streptomycin, in favor of newer agents or amikacin as the preferred aminoglycoside for drug-resistant Mycobacterium tuberculosis However, the emergence of resistance to newer drugs, such as bedaquiline, has prompted a reanalysis of antitubercular drugs in search of untapped potential. Using 211 clinical isolates of M. tuberculosis from South Africa, we performed phenotypic drug susceptibility testing (DST) to aminoglycosides by both critical concentration and MIC determination in parallel with whole-genome sequencing to identify known genotypic resistance elements. Isolates with low-level streptomycin resistance mediated by gidB were frequently misclassified with respect to streptomycin resistance when using the WHO-recommended critical concentration of 2 μg/ml. We identified 29 M. tuberculosis isolates from South Africa with low-level streptomycin resistance concomitant with high-level amikacin resistance, conferred by gidB and rrs 1400, respectively. Using a large global data set of M. tuberculosis genomes, we observed 95 examples of this corresponding resistance genotype (gidB-rrs 1400), including identification in 81/257 (31.5%) of extensively drug resistant (XDR) isolates. In a phylogenetic analysis, we observed repeated evolution of low-level streptomycin and high-level amikacin resistance in multiple countries. Our findings suggest that current critical concentration methods and the design of molecular diagnostics need to be revisited to provide more accurate assessments of streptomycin resistance for gidB-containing isolates. For patients harboring isolates of M. tuberculosis with high-level amikacin resistance conferred by rrs 1400, and for whom newer agents are not available, treatment with streptomycin may still prove useful, even in the face of low-level resistance conferred by gidB.
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38
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Huang H, Ding N, Yang T, Li C, Jia X, Wang G, Zhong J, Zhang J, Jiang G, Wang S, Zong Z, Jing W, Zhao Y, Xu S, Chen F. Cross-sectional Whole-genome Sequencing and Epidemiological Study of Multidrug-resistant Mycobacterium tuberculosis in China. Clin Infect Dis 2020; 69:405-413. [PMID: 30321294 PMCID: PMC6637280 DOI: 10.1093/cid/ciy883] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/09/2018] [Indexed: 11/29/2022] Open
Abstract
Background The increase in multidrug-resistant tuberculosis (MDR-TB) severely hampers tuberculosis prevention and control in China, a country with the second highest MDR-TB burden globally. The first nationwide drug-resistant tuberculosis surveillance program provides an opportunity to comprehensively investigate the epidemiological/drug-resistance characteristics, potential drug-resistance mutations, and effective population changes of Chinese MDR-TB. Methods We sequenced 357 MDR strains from 4600 representative tuberculosis-positive sputum samples collected during the survey (70 counties in 31 provinces). Drug-susceptibility testing was performed using 18 anti-tuberculosis drugs, representing the most comprehensive drug-resistance profile to date. We used 3 statistical and 1 machine-learning methods to identify drug-resistance genes/single-nucleotide polymorphisms (SNPs). We used Bayesian skyline analysis to investigate changes in effective population size. Results Epidemiological/drug-resistance characteristics showed different MDR profiles, co-resistance patterns, preferred drug combination/use, and recommended regimens among 7 Chinese administrative regions. These factors not only reflected the serious multidrug co-resistance and drug misuse but they were also potentially significant in facilitating the development of appropriate regimens for MDR-TB treatment in China. Further investigation identified 86 drug-resistance genes/intergenic regions/SNPs (58 new), providing potential targets for MDR-TB diagnosis and treatment. In addition, the effective population of Chinese MDR-TB displayed a strong expansion during 1993–2000, reflecting socioeconomic transition within the country. The phenomenon of expansion was restrained after 2000, likely attributable to the advances in diagnosis/treatment technologies and government support. Conclusions Our findings provide an important reference and improved understanding of MDR-TB in China, which are potentially significant in achieving the goal of precision medicine with respect to MDR-TB prevention and treatment.
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Affiliation(s)
- Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Nan Ding
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics
| | - Tingting Yang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics.,University of Chinese Academy of Sciences
| | - Cuidan Li
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics.,University of Chinese Academy of Sciences
| | - Xinmiao Jia
- Central Research Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Jun Zhong
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics
| | - Ju Zhang
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics
| | - Guanglu Jiang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Shuqi Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Zhaojing Zong
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Wei Jing
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute
| | - Yongliang Zhao
- University of Chinese Academy of Sciences.,Chinese Academy of Sciences Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics
| | - Shaofa Xu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute.,National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Prevention and Control, Beijing
| | - Fei Chen
- Chinese Academy of Sciences Key Laboratory of Genome Sciences & Information, Beijing Institute of Genomics.,University of Chinese Academy of Sciences.,Collaborative Innovation Center for Genetics and Development, Shanghai, China
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A biochemically-interpretable machine learning classifier for microbial GWAS. Nat Commun 2020; 11:2580. [PMID: 32444610 PMCID: PMC7244534 DOI: 10.1038/s41467-020-16310-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
Current machine learning classifiers have successfully been applied to whole-genome sequencing data to identify genetic determinants of antimicrobial resistance (AMR), but they lack causal interpretation. Here we present a metabolic model-based machine learning classifier, named Metabolic Allele Classifier (MAC), that uses flux balance analysis to estimate the biochemical effects of alleles. We apply the MAC to a dataset of 1595 drug-tested Mycobacterium tuberculosis strains and show that MACs predict AMR phenotypes with accuracy on par with mechanism-agnostic machine learning models (isoniazid AUC = 0.93) while enabling a biochemical interpretation of the genotype-phenotype map. Interpretation of MACs for three antibiotics (pyrazinamide, para-aminosalicylic acid, and isoniazid) recapitulates known AMR mechanisms and suggest a biochemical basis for how the identified alleles cause AMR. Extending flux balance analysis to identify accurate sequence classifiers thus contributes mechanistic insights to GWAS, a field thus far dominated by mechanism-agnostic results. Current machine learning classifiers have been applied to whole-genome sequencing data to identify determinants of antimicrobial resistance, but they lack interpretability. Here the authors present a metabolic machine learning classifier that uses flux balance analysis to estimate the biochemical effects of alleles.
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40
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He G, Li Y, Chen X, Chen J, Zhang W. Prediction of treatment outcomes for multidrug-resistant tuberculosis by whole-genome sequencing. Int J Infect Dis 2020; 96:68-72. [PMID: 32339719 DOI: 10.1016/j.ijid.2020.04.043] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) has been proposed to be a powerful tool to predict drug resistance for antitubercular drugs. However, the feasibility of WGS in predicting final treatment outcomes for multidrug-resistant tuberculosis (MDR-TB) patients remains unclear PATIENTS AND METHODS: In this prospective observational study conducted from January 2014 to September 2016, MDR-TB patients were enrolled consecutively. Genotypic drug sensitivity testing was performed via WGS using culture isolates. Patients were followed for two years to determine the treatment outcomes. Multivariate analysis was used to identify the association between information provided by WGS and the final treatment outcomes RESULTS: A total of 123 patients with MDR-TB were included in this study. The overall favorable treatment outcome rate was 60.2%. Multivariate analysis showed that independent risk factors associated with unfavorable treatment outcome including high-level moxifloxacin phenotypic resistance (OR, 4.362; 95%CI, 1.364-13.950; p=0.013), cycloserine phenotypic resistance (OR, 7.457; 95%CI, 1.644-33.819; p=0.009), mutations causing high-level fluoroquinolones resistance (OR, 3.947; 95%CI, 1.195-13.034; p=0.024), and ethA mutation (OR, 3.817; 95% CI, 1.154-12.823; p=0.028). WGS costs for each patient are ¥450 ($63), and the average turnaround time was one week CONCLUSIONS: In summary, WGS showed promising feasibility in predicting treatment outcomes for MDR-TB patients within a clinically relevant time frame.
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Affiliation(s)
- Guiqing He
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yang Li
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xinchang Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, 200040, China; State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai, 200438, China; National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China; Key Laboratory of Medical Molecular Virology (MOE/MOH) and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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41
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Saund K, Lapp Z, Thiede SN, Pirani A, Snitkin ES. prewas: data pre-processing for more informative bacterial GWAS. Microb Genom 2020; 6. [PMID: 32310745 PMCID: PMC7371116 DOI: 10.1099/mgen.0.000368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior to their use in bacterial genome-wide association studies (bGWAS). Three nuances of variant pre-processing that impact downstream identification of genetic associations include the separation of variants at multiallelic sites, separation of variants in overlapping genes, and referencing of variants relative to ancestral alleles. Here we demonstrate the importance of these variant pre-processing steps on diverse bacterial genomic datasets and present prewas, an R package, that standardizes the pre-processing of multiallelic sites, overlapping genes, and reference alleles before bGWAS. This package facilitates improved reproducibility and interpretability of bGWAS results. prewas enables users to extract maximal information from bGWAS by implementing multi-line representation for multiallelic sites and variants in overlapping genes. prewas outputs a binary SNP matrix that can be used for SNP-based bGWAS and will prevent the masking of minor alleles during bGWAS analysis. The optional binary gene matrix output can be used for gene-based bGWAS, which will enable users to maximize the power and evolutionary interpretability of their bGWAS studies. prewas is available for download from GitHub.
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Affiliation(s)
- Katie Saund
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie N Thiede
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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Stothard P, Grant JR, Van Domselaar G. Visualizing and comparing circular genomes using the CGView family of tools. Brief Bioinform 2020; 20:1576-1582. [PMID: 28968859 PMCID: PMC6781573 DOI: 10.1093/bib/bbx081] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/14/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022] Open
Abstract
Graphical genome maps are widely used to assess genome features and sequence characteristics. The CGView (Circular Genome Viewer) software family is a popular collection of tools for generating genome maps for bacteria, organelles and viruses. In this review, we describe the capabilities of the original CGView program along with those of subsequent companion applications, including the CGView Server and the CGView Comparison Tool. We also discuss GView, a graphical user interface-enabled rewrite of CGView, and the GView Server, which offers several integrated analyses for identifying shared or unique genome regions relative to a collection of comparison genomes. We conclude with some remarks about our current development efforts related to CGView aimed at adding new functionality while increasing ease of use.
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Affiliation(s)
- Paul Stothard
- Corresponding author: Paul Stothard, Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton AB T6G2P5, Canada. Tel.: 780-492-5242; Fax:780-248-1900; E-mail:
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Model-based integration of genomics and metabolomics reveals SNP functionality in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2020; 117:8494-8502. [PMID: 32229570 DOI: 10.1073/pnas.1915551117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human tuberculosis is caused by members of the Mycobacterium tuberculosis complex (MTBC) that vary in virulence and transmissibility. While genome-wide association studies have uncovered several mutations conferring drug resistance, much less is known about the factors underlying other bacterial phenotypes. Variation in the outcome of tuberculosis infection and diseases has been attributed primarily to patient and environmental factors, but recent evidence indicates an additional role for the genetic diversity among MTBC clinical strains. Here, we used metabolomics to unravel the effect of genetic variation on the strain-specific metabolic adaptive capacity and vulnerability. To define the functionality of single-nucleotide polymorphisms (SNPs) systematically, we developed a constraint-based approach that integrates metabolomic and genomic data. Our model-based predictions correctly classify SNP effects in pyruvate kinase and suggest a genetic basis for strain-specific inherent baseline susceptibility to the antibiotic para-aminosalicylic acid. Our method is broadly applicable across microbial life, opening possibilities for the development of more selective treatment strategies.
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Mycobacterial Cell Wall: A Source of Successful Targets for Old and New Drugs. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10072278] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Eighty years after the introduction of the first antituberculosis (TB) drug, the treatment of drug-susceptible TB remains very cumbersome, requiring the use of four drugs (isoniazid, rifampicin, ethambutol and pyrazinamide) for two months followed by four months on isoniazid and rifampicin. Two of the drugs used in this “short”-course, six-month chemotherapy, isoniazid and ethambutol, target the mycobacterial cell wall. Disruption of the cell wall structure can enhance the entry of other TB drugs, resulting in a more potent chemotherapy. More importantly, inhibition of cell wall components can lead to mycobacterial cell death. The complexity of the mycobacterial cell wall offers numerous opportunities to develop drugs to eradicate Mycobacterium tuberculosis, the causative agent of TB. In the past 20 years, researchers from industrial and academic laboratories have tested new molecules to find the best candidates that will change the face of TB treatment: drugs that will shorten TB treatment and be efficacious against active and latent, as well as drug-resistant TB. Two of these new TB drugs block components of the mycobacterial cell wall and have reached phase 3 clinical trial. This article reviews TB drugs targeting the mycobacterial cell wall in use clinically and those in clinical development.
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Merker M, Kohl TA, Barilar I, Andres S, Fowler PW, Chryssanthou E, Ängeby K, Jureen P, Moradigaravand D, Parkhill J, Peacock SJ, Schön T, Maurer FP, Walker T, Köser C, Niemann S. Phylogenetically informative mutations in genes implicated in antibiotic resistance in Mycobacterium tuberculosis complex. Genome Med 2020; 12:27. [PMID: 32143680 PMCID: PMC7060619 DOI: 10.1186/s13073-020-00726-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A comprehensive understanding of the pre-existing genetic variation in genes associated with antibiotic resistance in the Mycobacterium tuberculosis complex (MTBC) is needed to accurately interpret whole-genome sequencing data for genotypic drug susceptibility testing (DST). METHODS We investigated mutations in 92 genes implicated in resistance to 21 anti-tuberculosis drugs using the genomes of 405 phylogenetically diverse MTBC strains. The role of phylogenetically informative mutations was assessed by routine phenotypic DST data for the first-line drugs isoniazid, rifampicin, ethambutol, and pyrazinamide from a separate collection of over 7000 clinical strains. Selected mutations/strains were further investigated by minimum inhibitory concentration (MIC) testing. RESULTS Out of 547 phylogenetically informative mutations identified, 138 were classified as not correlating with resistance to first-line drugs. MIC testing did not reveal a discernible impact of a Rv1979c deletion shared by M. africanum lineage 5 strains on resistance to clofazimine. Finally, we found molecular evidence that some MTBC subgroups may be hyper-susceptible to bedaquiline and clofazimine by different loss-of-function mutations affecting a drug efflux pump subunit (MmpL5). CONCLUSIONS Our findings underline that the genetic diversity in MTBC has to be studied more systematically to inform the design of clinical trials and to define sound epidemiologic cut-off values (ECOFFs) for new and repurposed anti-tuberculosis drugs. In that regard, our comprehensive variant catalogue provides a solid basis for the interpretation of mutations in genotypic as well as in phenotypic DST assays.
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Affiliation(s)
- Matthias Merker
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany.
| | - Thomas A Kohl
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Ivan Barilar
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Erja Chryssanthou
- Department of Clinical Microbiology, Karolinska University Hospital, Solna, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Kristian Ängeby
- Department of Clinical Science and Education, Emergency Medicine, Stockholm South General Hospital, Karolinska Institute, Stockholm, Sweden
| | | | - Danesh Moradigaravand
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Thomas Schön
- Department of Infectious Diseases and Clinical Microbiology, Kalmar County Hospital, Kalmar, Sweden
- Department of Clinical and Experimental Medicine, Division of Medical Microbiology, Linköping University, Linköping, Sweden
| | - Florian P Maurer
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
- Institute of Medical Microbiology, Virology and Hospital Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timothy Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Claudio Köser
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Stefan Niemann
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
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Saber MM, Shapiro BJ. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes. Microb Genom 2020; 6:e000337. [PMID: 32100713 PMCID: PMC7200059 DOI: 10.1099/mgen.0.000337] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWASs) have the potential to reveal the genetics of microbial phenotypes such as antibiotic resistance and virulence. Capitalizing on the growing wealth of bacterial sequence data, microbial GWAS methods aim to identify causal genetic variants while ignoring spurious associations. Bacteria reproduce clonally, leading to strong population structure and genome-wide linkage, making it challenging to separate true 'hits' (i.e. mutations that cause a phenotype) from non-causal linked mutations. GWAS methods attempt to correct for population structure in different ways, but their performance has not yet been systematically and comprehensively evaluated under a range of evolutionary scenarios. Here, we developed a bacterial GWAS simulator (BacGWASim) to generate bacterial genomes with varying rates of mutation, recombination and other evolutionary parameters, along with a subset of causal mutations underlying a phenotype of interest. We assessed the performance (recall and precision) of three widely used single-locus GWAS approaches (cluster-based, dimensionality-reduction and linear mixed models, implemented in plink, pyseer and gemma) and one relatively new multi-locus model implemented in pyseer, across a range of simulated sample sizes, recombination rates and causal mutation effect sizes. As expected, all methods performed better with larger sample sizes and effect sizes. The performance of clustering and dimensionality reduction approaches to correct for population structure were considerably variable according to the choice of parameters. Notably, the multi-locus elastic net (lasso) approach was consistently amongst the highest-performing methods, and had the highest power in detecting causal variants with both low and high effect sizes. Most methods reached the level of good performance (recall >0.75) for identifying causal mutations of strong effect size [log odds ratio (OR) ≥2] with a sample size of 2000 genomes. However, only elastic nets reached the level of reasonable performance (recall=0.35) for detecting markers with weaker effects (log OR ~1) in smaller samples. Elastic nets also showed superior precision and recall in controlling for genome-wide linkage, relative to single-locus models. However, all methods performed relatively poorly on highly clonal (low-recombining) genomes, suggesting room for improvement in method development. These findings show the potential for multi-locus models to improve bacterial GWAS performance. BacGWASim code and simulated data are publicly available to enable further comparisons and benchmarking of new methods.
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Affiliation(s)
- Morteza M. Saber
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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Kardan-Yamchi J, Kazemian H, Battaglia S, Abtahi H, Rahimi Foroushani A, Hamzelou G, Cirillo DM, Ghodousi A, Feizabadi MM. Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran. J Clin Med 2020; 9:jcm9020465. [PMID: 32046149 PMCID: PMC7073636 DOI: 10.3390/jcm9020465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.
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Affiliation(s)
- Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Hamidreza Abtahi
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Gholamreza Hamzelou
- Tehran Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
- Correspondence: (A.G.); (M.M.F.)
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Correspondence: (A.G.); (M.M.F.)
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The Small Protein CydX Is Required for Cytochrome bd Quinol Oxidase Stability and Function in Salmonella enterica Serovar Typhimurium: a Phenotypic Study. J Bacteriol 2020; 202:JB.00348-19. [PMID: 31659011 DOI: 10.1128/jb.00348-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/21/2019] [Indexed: 01/12/2023] Open
Abstract
Cytochrome bd quinol oxidases, which have a greater affinity for oxygen than heme-copper cytochrome oxidases (HCOs), promote bacterial respiration and fitness in low-oxygen environments, such as host tissues. Here, we show that, in addition to the CydA and CydB subunits, the small protein CydX is required for the assembly and function of the cytochrome bd complex in the enteric pathogen Salmonella enterica serovar Typhimurium. Mutant S Typhimurium lacking CydX showed a loss of proper heme arrangement and impaired oxidase activity comparable to that of a ΔcydABX mutant lacking all cytochrome bd subunits. Moreover, both the ΔcydX mutant and the ΔcydABX mutant showed increased sensitivity to β-mercaptoethanol and nitric oxide (NO). Cytochrome bd-mediated protection from β-mercaptoethanol was not a result of resistance to reducing damage but, rather, was due to cytochrome bd oxidase managing Salmonella respiration, while β-mercaptoethanol interacted with the copper ions necessary for the HCO activity of the cytochrome bo-type quinol oxidase. Interactions between NO and hemes in cytochrome bd and cytochrome bd-dependent respiration during nitrosative stress indicated a direct role for cytochrome bd in mediating Salmonella resistance to NO. Additionally, CydX was required for S Typhimurium proliferation inside macrophages. Mutants deficient in cytochrome bd, however, showed a significant increase in resistance to antibiotics, including aminoglycosides, d-cycloserine, and ampicillin. The essential role of CydX in cytochrome bd assembly and function suggests that targeting this small protein could be a useful antimicrobial strategy, but potential drug tolerance responses should also be considered.IMPORTANCE Cytochrome bd quinol oxidases, which are found only in bacteria, govern the fitness of many facultative anaerobic pathogens by promoting respiration in low-oxygen environments and by conferring resistance to antimicrobial radicals. Thus, cytochrome bd complex assembly and activity are considered potential therapeutic targets. Here we report that the small protein CydX is required for the assembly and function of the cytochrome bd complex in S Typhimurium under stress conditions, including exposure to β-mercaptoethanol, nitric oxide, or the phagocytic intracellular environment, demonstrating its crucial function for Salmonella fitness. However, cytochrome bd inactivation also leads to increased resistance to some antibiotics, so considerable caution should be taken when developing therapeutic strategies targeting the CydX-dependent cytochrome bd.
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New potential drug leads against MDR-MTB: A short review. Bioorg Chem 2019; 95:103534. [PMID: 31884135 DOI: 10.1016/j.bioorg.2019.103534] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 11/26/2019] [Accepted: 12/20/2019] [Indexed: 12/25/2022]
Abstract
Multidrug resistant Mycobacterium tuberculosis (MDR-MTB) infections have created a critical health problem globally. The appalling rise in drug resistance to all the current therapeutics has triggered the need for identifying new antimycobacterial agents effective against multidrug-resistant Mycobacterium tuberculosis. Structurally unique chemical entities with new mode of action will be required to combat this pressing issue. This review gives an overview of the structures and outlines on various aspects of in vitro pharmacological activities of new antimycobacterial agents, mechanism of action and brief structure activity relationships in the perspective of drug discovery and development. This review also summarizes on recent reports of new antimycobacterial agents.
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A Metabolic Dependency for Host Isoprenoids in the Obligate Intracellular Pathogen Rickettsia parkeri Underlies a Sensitivity to the Statin Class of Host-Targeted Therapeutics. mSphere 2019; 4:4/6/e00536-19. [PMID: 31722991 PMCID: PMC6854040 DOI: 10.1128/msphere.00536-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism. Gram-negative bacteria in the order Rickettsiales have an obligate intracellular growth requirement, and some species cause human diseases such as typhus and spotted fever. The bacteria have evolved a dependence on essential nutrients and metabolites from the host cell as a consequence of extensive genome reduction. However, it remains largely unknown which nutrients they acquire and whether their metabolic dependency can be exploited therapeutically. Here, we describe a genetic rewiring of bacterial isoprenoid biosynthetic pathways in the Rickettsiales that has resulted from reductive genome evolution. Furthermore, we investigated whether the spotted fever group Rickettsia species Rickettsia parkeri scavenges isoprenoid precursors directly from the host. Using targeted mass spectrometry, we found that infection caused decreases in host isoprenoid products and concomitant increases in bacterial isoprenoid metabolites. Additionally, we report that treatment of infected cells with statins, which inhibit host isoprenoid synthesis, prohibited bacterial growth. We show that growth inhibition correlates with changes in bacterial size and shape that mimic those caused by antibiotics that inhibit peptidoglycan biosynthesis, suggesting that statins lead to an inhibition of cell wall synthesis. Altogether, our results describe a potential Achilles’ heel of obligate intracellular pathogens that can potentially be exploited with host-targeted therapeutics that interfere with metabolic pathways required for bacterial growth. IMPORTANCE Obligate intracellular pathogens, which include viruses as well as certain bacteria and eukaryotes, are a subset of infectious microbes that are metabolically dependent on and unable to grow outside an infected host cell because they have lost or lack essential biosynthetic pathways. In this study, we describe a metabolic dependency of the bacterial pathogen Rickettsia parkeri on host isoprenoid molecules that are used in the biosynthesis of downstream products, including cholesterol, steroid hormones, and heme. Bacteria make products from isoprenoids, such as an essential lipid carrier for making the bacterial cell wall. We show that bacterial metabolic dependency can represent a potential Achilles’ heel and that inhibiting host isoprenoid biosynthesis with the FDA-approved statin class of drugs inhibits bacterial growth by interfering with the integrity of the cell wall. This work supports the potential to treat infections by obligate intracellular pathogens through inhibition of host biosynthetic pathways that are susceptible to parasitism.
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