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Vijay S, Bao NLH, Vinh DN, Nhat LTH, Thu DDA, Quang NL, Trieu LPT, Nhung HN, Ha VTN, Thai PVK, Ha DTM, Lan NH, Caws M, Thwaites GE, Javid B, Thuong NT. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study. eLife 2024; 13:RP93243. [PMID: 39250422 PMCID: PMC11383526 DOI: 10.7554/elife.93243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15-60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.
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Affiliation(s)
- Srinivasan Vijay
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | | | - Dao Nguyen Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | | | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
| | | | | | | | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Babak Javid
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, United States
| | - Nguyen Thuy Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh, Viet Nam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Vijay S, Bao NLH, Vinh DN, Nhat LTH, Thu DDA, Quang NL, Trieu LPT, Nhung HN, Ha VTN, Thai PVK, Ha DTM, Lan NH, Caws M, Thwaites GE, Javid B, Thuong NTT. Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates: an in-vitro longitudinal study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.22.568240. [PMID: 38045287 PMCID: PMC10690245 DOI: 10.1101/2023.11.22.568240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Antibiotic tolerance in Mycobacterium tuberculosis leads to less effective bacterial killing, poor treatment responses and resistant emergence. Therefore, we investigated the rifampicin tolerance of M. tuberculosis isolates, with or without pre-existing isoniazid-resistance. We determined the in-vitro rifampicin survival fraction by minimum duration of killing assay in isoniazid susceptible (IS, n=119) and resistant (IR, n=84) M. tuberculosis isolates. Then we correlated the rifampicin tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs) and isoniazid-resistant mutations. The longitudinal IR isolates collected from patients were analyzed for changes in rifampicin tolerance and associated emergence of genetic variants. The median duration of rifampicin exposure reducing the M. tuberculosis surviving fraction by 90% (minimum duration of killing-MDK90) increased from 1.23 (95%CI 1.11; 1.37) and 1.31 (95%CI 1.14; 1.48) to 2.55 (95%CI 2.04; 2.97) and 1.98 (95%CI 1.69; 2.56) days, for IS and IR respectively, during 15 to 60 days of incubation. This indicated the presence of fast and slow growing tolerant sub-populations. A range of 6 log 10 -fold survival fraction enabled classification of tolerance as low, medium or high and revealed IR association with increased tolerance with faster growth (OR=2.68 for low vs. medium, OR=4.42 for low vs. high, P -trend=0.0003). The high tolerance in IR isolates was specific to those collected during rifampicin treatment in patients and associated with bacterial genetic microvariants. Furthermore, the high rifampicin tolerant IR isolates have survival potential similar to multi-drug resistant isolates. These findings suggest that IR tuberculosis needs to be evaluated for high rifampicin tolerance to improve treatment regimen and prevent the risk of MDR-TB emergence.
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Qiao X, Ding L, Fang F, Fu C, Wei R, Chen Y, Zheng S, Wang X, Yan Y, Yang K, Xu N, Tao H, Yu K, Zhang L. An integrated meta-omics approach reveals the different response mechanisms of two anammox bacteria towards fluoroquinolone antibiotics. ENVIRONMENT INTERNATIONAL 2024; 185:108505. [PMID: 38394916 DOI: 10.1016/j.envint.2024.108505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/03/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024]
Abstract
The emerging fluoroquinolone antibiotics (FQs) are highly influential in nitrogen removal from livestock wastewater. However, beyond the capability of nitrogen removal, little is known about the molecular mechanisms (e.g., shift of core metabolism and energy allocation) of different anaerobic ammonium-oxidizing bacteria (AnAOB) under continuous FQ stress. This study investigated the effects of ciprofloxacin, ofloxacin and their mixture at concentrations detected in livestock wastewater on two key anammox species in membrane bioreactors. It was found 20 μg/L FQs promoted nitrogen removal efficiency and community stability, and42-51 % of FQs were removed simultaneously. Integrated meta-omics analysis revealed varied gene expression patterns between the two dominant AnAOB, Candidatus Brocadia sapporoensis (B AnAOB) and Candidatus Kuenenia stuttgartiensis (K AnAOB). The nitrogen metabolic processes were bolstered in B AnAOB, while those involved in anammox pathway of K AnAOB were inhibited. This difference was tentatively attributed to the up-regulation of reactive oxygen species scavenger genes (ccp and dxf) and FQ resistance gene (qnrB72) in B AnAOB. Importantly, most enhanced core biosynthesis/metabolism of AnAOB and close cross-feeding with accompanying bacteria were also likely to contribute to their higher levels of biomass yield and metabolism activity under FQ stress. This finding suggests that B AnAOB has the advantage of higher nitrogen metabolism capacity over K AnAOB in livestock wastewater containing FQs, which is helpful for efficient and stable nitrogen removal by the functional anammox species.
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Affiliation(s)
- Xuejiao Qiao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Lingyun Ding
- College of Health Science and Environmental Engineering, Shenzhen Technology University, Shenzhen 518118, China
| | - Fang Fang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Chenkun Fu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ruqian Wei
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yizhen Chen
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Sihan Zheng
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Xisong Wang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yan Yan
- State Key Laboratory of Isotope Geochemistry, CAS Center for Excellence in Deep Earth Science, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510000, China
| | - Kai Yang
- China MCC5 Group Corporation Limited, Chengdu 610023, China
| | - Nan Xu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Huchun Tao
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ke Yu
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| | - Lijuan Zhang
- Key Laboratory for Heavy Metal Pollution Control and Reutilization, School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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Vijay S, Nair RR, Sharan D, Jakkala K, Ajitkumar P. Percoll discontinuous density gradient centrifugation method for the fractionation of the subpopulations of Mycobacterium smegmatis and Mycobacterium tuberculosis from in vitro cultures. MethodsX 2023; 11:102344. [PMID: 37711139 PMCID: PMC10498404 DOI: 10.1016/j.mex.2023.102344] [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: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 09/16/2023] Open
Abstract
Bacterial populations in the in vitro laboratory cultures, environment, and patients contain metabolically different subpopulations that respond differently to stress agents, including antibiotics, and emerge as stress tolerant or resistant strains. To contain the emergence of such strains, it is important to study the features of the metabolic status and response of the subpopulations to stress agents. For this purpose, an efficient method is required for the fractionation and isolation of the subpopulations from the cultures. Here we describe in detail the manual setting up of a simple, easy-to-do, reproducibly robust Percoll discontinuous density gradient centrifugation for the fractionation of subpopulations of short-sized cells (SCs) and normal/long-sized cells (NCs) from Mycobacterium smegmatis and Mycobacterium tuberculosis cultures, which we had reported earlier. About 90-98% enrichment was obtained respectively for SCs and NCs for M. smegmatis and 69-67% enrichment was obtained respectively for the SCs and NCs for M. tuberculosis.•The Percoll discontinuous density gradient centrifugation helps the fractionation and isolation of mycobacterial subpopulations that differ in density.•The method offers a consistently reproducible high enrichment of the subpopulations of SCs and NCs from the in vitro cultures of M. smegmatis and M. tuberculosis.•Our earlier reports on the consistency in the differential response of the subpopulations, enriched using the method, to oxidative, nitrite, and antibiotic stress proves its validity.
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Affiliation(s)
- Srinivasan Vijay
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
- Cluster of Excellence Balance of the Microverse, Theoretical Microbial Ecology Group, Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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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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Mishra S, Saito K. Clinically encountered growth phenotypes of tuberculosis-causing bacilli and their in vitro study: A review. Front Cell Infect Microbiol 2022; 12:1029111. [PMID: 36439231 PMCID: PMC9684195 DOI: 10.3389/fcimb.2022.1029111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 07/11/2024] Open
Abstract
The clinical manifestations of tuberculosis (TB) vary widely in severity, site of infection, and outcomes of treatment-leading to simultaneous efforts to individualize therapy safely and to search for shorter regimens that can be successfully used across the clinical spectrum. In these endeavors, clinicians and researchers alike employ mycobacterial culture in rich media. However, even within the same patient, individual bacilli among the population can exhibit substantial variability in their culturability. Bacilli in vitro also demonstrate substantial heterogeneity in replication rate and cultivation requirements, as well as susceptibility to killing by antimicrobials. Understanding parallels in clinical, ex vivo and in vitro growth phenotype diversity may be key to identifying those phenotypes responsible for treatment failure, relapse, and the reactivation of bacilli that progresses TB infection to disease. This review briefly summarizes the current role of mycobacterial culture in the care of patients with TB and the ex vivo evidence of variability in TB culturability. We then discuss current advances in in vitro models that study heterogenous subpopulations within a genetically identical bulk culture, with an emphasis on the effect of oxidative stress on bacillary cultivation requirements. The review highlights the complexity that heterogeneity in mycobacterial growth brings to the interpretation of culture in clinical settings and research. It also underscores the intricacies present in the interplay between growth phenotypes and antimicrobial susceptibility. Better understanding of population dynamics and growth requirements over time and space promises to aid both the attempts to individualize TB treatment and to find uniformly effective therapies.
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Affiliation(s)
- Saurabh Mishra
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, United States
| | - Kohta Saito
- Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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Parbhoo T, Mouton JM, Sampson SL. Phenotypic adaptation of Mycobacterium tuberculosis to host-associated stressors that induce persister formation. Front Cell Infect Microbiol 2022; 12:956607. [PMID: 36237425 PMCID: PMC9551238 DOI: 10.3389/fcimb.2022.956607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis exhibits a remarkable ability to interfere with the host antimicrobial response. The pathogen exploits elaborate strategies to cope with diverse host-induced stressors by modulating its metabolism and physiological state to prolong survival and promote persistence in host tissues. Elucidating the adaptive strategies that M. tuberculosis employs during infection to enhance persistence is crucial to understanding how varying physiological states may differentially drive disease progression for effective management of these populations. To improve our understanding of the phenotypic adaptation of M. tuberculosis, we review the adaptive strategies employed by M. tuberculosis to sense and coordinate a physiological response following exposure to various host-associated stressors. We further highlight the use of animal models that can be exploited to replicate and investigate different aspects of the human response to infection, to elucidate the impact of the host environment and bacterial adaptive strategies contributing to the recalcitrance of infection.
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Mehaffy C, Ryan JM, Kruh-Garcia NA, Dobos KM. Extracellular Vesicles in Mycobacteria and Tuberculosis. Front Cell Infect Microbiol 2022; 12:912831. [PMID: 35719351 PMCID: PMC9204639 DOI: 10.3389/fcimb.2022.912831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) remains a public health issue causing millions of infections every year. Of these, about 15% ultimately result in death. Efforts to control TB include development of new and more effective vaccines, novel and more effective drug treatments, and new diagnostics that test for both latent TB Infection and TB disease. All of these areas of research benefit from a good understanding of the physiology of Mycobacterium tuberculosis (Mtb), the primary causative agent of TB. Mtb secreted protein antigens have been the focus of vaccine and diagnosis research for the past century. Recently, the discovery of extracellular vesicles (EVs) as an important source of secreted antigens in Mtb has gained attention. Similarly, the discovery that host EVs can carry Mtb products during in vitro and in vivo infection has spiked interest because of its potential use in blood-based diagnostics. Despite advances in understanding the content of Mtb and Mtb-infected host extracellular vesicles, our understanding on the biogenesis and role of Mtb and host extracellular vesicles during Mtb infection is still nascent. Here, we explore the current literature on extracellular vesicles regarding Mtb, discuss the host and Mtb extracellular vesicles as distinct entities, and discuss current gaps in the field.
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Urbaniec J, Xu Y, Hu Y, Hingley-Wilson S, McFadden J. Phenotypic heterogeneity in persisters: a novel 'hunker' theory of persistence. FEMS Microbiol Rev 2022; 46:fuab042. [PMID: 34355746 PMCID: PMC8767447 DOI: 10.1093/femsre/fuab042] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2021] [Indexed: 12/11/2022] Open
Abstract
Persistence has been linked to treatment failure since its discovery over 70 years ago and understanding formation, nature and survival of this key antibiotic refractory subpopulation is crucial to enhancing treatment success and combatting the threat of antimicrobial resistance (AMR). The term 'persistence' is often used interchangeably with other terms such as tolerance or dormancy. In this review we focus on 'antibiotic persistence' which we broadly define as a feature of a subpopulation of bacterial cells that possesses the non-heritable character of surviving exposure to one or more antibiotics; and persisters as cells that possess this characteristic. We discuss novel molecular mechanisms involved in persister cell formation, as well as environmental factors which can contribute to increased antibiotic persistence in vivo, highlighting recent developments advanced by single-cell studies. We also aim to provide a comprehensive model of persistence, the 'hunker' theory which is grounded in intrinsic heterogeneity of bacterial populations and a myriad of 'hunkering down' mechanisms which can contribute to antibiotic survival of the persister subpopulation. Finally, we discuss antibiotic persistence as a 'stepping-stone' to AMR and stress the urgent need to develop effective anti-persister treatment regimes to treat this highly clinically relevant bacterial sub-population.
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Affiliation(s)
- J Urbaniec
- Department of Microbial Sciences and University of Surrey, Guildford, Surrey, GU27XH, UK
| | - Ye Xu
- Department of Microbial Sciences and University of Surrey, Guildford, Surrey, GU27XH, UK
| | - Y Hu
- Farnborough Sensonic limited, Farnborough road, GU14 7NA, UK
| | - S Hingley-Wilson
- Department of Microbial Sciences and University of Surrey, Guildford, Surrey, GU27XH, UK
| | - J McFadden
- Department of Microbial Sciences and University of Surrey, Guildford, Surrey, GU27XH, UK
- Quantum biology doctoral training centre, University of Surrey, Guildford, Surrey, GU27XH, UK
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Nair RR, Sharan D, Srinivasan V, Mukkayyan N, Jakkala K, Ajitkumar P. The H2O2 inherently released by the mycobacterial minor subpopulation enhances the survival of the major kin subpopulation against rifampicin. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100148. [PMID: 35909613 PMCID: PMC9325904 DOI: 10.1016/j.crmicr.2022.100148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 06/04/2022] [Accepted: 06/15/2022] [Indexed: 11/30/2022] Open
Abstract
Stress survival of mycobacterial minor (SCs) and major (NCs) subpopulations. The SCs enhance survival of the NCs against rifampicin. H2O2 released by the SCs increased KatG levels in the NCs. Increased KatG levels neutralised the H2O2 formed during rifampicin exposure. The enhanced survival was not observed in the furA-katG/katG knockout mutants.
Exposure to antibiotics most often generates oxidative stress in bacteria. Oxidative stress survival mechanisms would facilitate the evolution of antibiotic resistance. As part of an effort to understand oxidative stress survival mechanisms in mycobacteria, here we show that the minor subpopulation (SCs; short-sized cells constituting 10% of the population) of Mycobacterium smegmatis significantly increased the survival of its major kin subpopulation (NCs; normal/long-sized cells constituting 90% of the population) in the mid-log-phase (MLP) cultures against the oxidative stress induced by rifampicin and exogenously added H2O2 (positive control). We had earlier shown that the SCs in the MLP cultures inherently and naturally release significantly high levels of H2O2 into the medium. Addition of the SCs’ culture supernatant, unlike the supernatant of the dimethylthiourea (H2O2 scavenger) exposed SCs, enhanced the survival of NCs. It indicated that NCs’ survival required the H2O2 present in the SCs’ supernatant. This H2O2 transcriptionally induced high levels of catalase-peroxidase (KatG) in the NCs. The naturally high KatG levels in the NCs significantly neutralised the endogenous H2O2 formed upon exposure to rifampicin or H2O2, thereby enhancing the survival of NCs against oxidative stress. The absence of such enhanced survival in the furA-katG and katG knockout (KO) mutants of NCs in the presence of wild-type SCs, confirmed the requirement of the H2O2 present in the SCs’ supernatant and NCs’ KatG for enhanced oxidative stress survival. The presence of SCs:NCs at 1:9 in the pulmonary tuberculosis patients’ sputum alludes to the clinical significance of the finding.
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Affiliation(s)
- Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Vijay Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbial Pathogenesis, University of Maryland, Baltimore 21201, Maryland, USA
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India
- Corresponding author.
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Pradhan A, Swaminath S, Jakkala K, Ajitkumar P. A method for the enrichment, isolation and validation of Mycobacterium smegmatis population surviving in the presence of bactericidal concentrations of rifampicin and moxifloxacin. FEMS Microbiol Lett 2021; 368:fnab090. [PMID: 34240144 DOI: 10.1093/femsle/fnab090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
The bacterial populations surviving in the presence of antibiotics contain cells that have gained genetic resistance, phenotypic resistance and tolerance to antibiotics. Isolation of live bacterial population, surviving against antibiotics, from the milieu of high proportions of dead/damaged cells will facilitate the study of the cellular/molecular processes used by them for survival. Here we present a Percoll gradient centrifugation based method for the isolation of enriched population of Mycobacterium smegmatis surviving in the presence of bactericidal concentrations of rifampicin and moxifloxacin. From the time of harvest, throughout the enrichment and isolation processes, and up to the lysis of the cells for total RNA preparation, we maintained the cells in the presence of the antibiotic to avoid changes in their metabolic status. The total RNA extracted from the enriched population of live antibiotic-surviving population showed structural integrity and purity. We analysed the transcriptome profile of the antibiotic-surviving population and compared it with the orthologue genes of Mycobacterium tuberculosis that conferred antibiotic tolerance on tubercle bacilli isolated from the tuberculosis patients under treatment with four antitubercular antibiotics. Statistically significant comparability between the gene expression profiles of the antibiotic tolerance associated genes of M. smegmatis and M. tuberculosis validated the reliability/utility of the method.
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Affiliation(s)
- Atul Pradhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Malleswaram, Bangalore 560012, Karnataka, India
| | - Sharmada Swaminath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Malleswaram, Bangalore 560012, Karnataka, India
| | - Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Malleswaram, Bangalore 560012, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Malleswaram, Bangalore 560012, Karnataka, India
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Kalsum S, Andersson B, Das J, Schön T, Lerm M. A high-throughput screening assay based on automated microscopy for monitoring antibiotic susceptibility of Mycobacterium tuberculosis phenotypes. BMC Microbiol 2021; 21:167. [PMID: 34090328 PMCID: PMC8178828 DOI: 10.1186/s12866-021-02212-3] [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: 12/21/2020] [Accepted: 04/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background Efficient high-throughput drug screening assays are necessary to enable the discovery of new anti-mycobacterial drugs. The purpose of our work was to develop and validate an assay based on live-cell imaging which can monitor the growth of two distinct phenotypes of Mycobacterium tuberculosis and to test their susceptibility to commonly used TB drugs. Results Both planktonic and cording phenotypes were successfully monitored as fluorescent objects using the live-cell imaging system IncuCyte S3, allowing collection of data describing distinct characteristics of aggregate size and growth. The quantification of changes in total area of aggregates was used to define IC50 and MIC values of selected TB drugs which revealed that the cording phenotype grew more rapidly and displayed a higher susceptibility to rifampicin. In checkerboard approach, testing pair-wise combinations of sub-inhibitory concentrations of drugs, rifampicin, linezolid and pretomanid demonstrated superior growth inhibition of cording phenotype. Conclusions Our results emphasize the efficiency of using automated live-cell imaging and its potential in high-throughput whole-cell screening to evaluate existing and search for novel antimycobacterial drugs. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02212-3.
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Affiliation(s)
- Sadaf Kalsum
- Division of Inflammation and Infection, Lab 1, floor 12, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-58185, Linköping, Sweden
| | - Blanka Andersson
- Division of Inflammation and Infection, Lab 1, floor 12, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-58185, Linköping, Sweden
| | - Jyotirmoy Das
- Division of Inflammation and Infection, Lab 1, floor 12, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-58185, Linköping, Sweden
| | - Thomas Schön
- Division of Clinical Microbiology, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-58185, Linköping, Sweden
| | - Maria Lerm
- Division of Inflammation and Infection, Lab 1, floor 12, Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, SE-58185, Linköping, Sweden.
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13
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Pradhan A, Mukkayyan N, Jakkala K, Ajitkumar P. Mycobacterial Populations Partly Change the Proportions of the Cells Undergoing Asymmetric/Symmetric Divisions in Response to Glycerol Levels in Growth Medium. Cells 2021; 10:1160. [PMID: 34064643 PMCID: PMC8151439 DOI: 10.3390/cells10051160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 12/25/2022] Open
Abstract
Twenty to thirty percent of the septating mycobacterial cells of the mid-log phase population showed highly deviated asymmetric constriction during division (ACD), while the remaining underwent symmetric constriction during division (SCD). The ACD produced short-sized cells (SCs) and normal/long-sized cells (NCs) as the sister-daughter cells, but with significant differential susceptibility to antibiotic/oxidative/nitrite stress. Here we report that, at 0.2% glycerol, formulated in the Middlebrook 7H9 medium, a significantly high proportion of the cells were divided by SCD. When the glycerol concentration decreased to 0.1% due to cell-growth/division, the ACD proportion gradually increased until the ACD:SCD ratio reached ~50:50. With further decrease in the glycerol levels, the SCD proportion increased with concomitant decrease in the ACD proportion. Maintenance of glycerol at 0.1%, through replenishment, held the ACD:SCD proportion at ~50:50. Transfer of the cells from one culture with a specific glycerol level to the supernatant from another culture, with a different glycerol level, made the cells change the ACD:SCD proportion to that of the culture from which the supernatant was taken. RT-qPCR data showed the possibility of diadenosine tetraphosphate phosphorylase (MSMEG_2932), phosphatidylinositol synthase (MSMEG_2933), and a Nudix family hydrolase (MSMEG_2936) involved in the ACD:SCD proportion-change in response to glycerol levels. We also discussed its physiological significance.
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Affiliation(s)
| | | | | | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, Karnataka, India; (A.P.); (N.M.); (K.J.)
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14
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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15
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Weeks JW, Segars K, Guha S. The Research Gap in Non-tuberculous Mycobacterium (NTM) and Reusable Medical Devices. Front Public Health 2020; 8:399. [PMID: 32974254 PMCID: PMC7468515 DOI: 10.3389/fpubh.2020.00399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/07/2020] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jon W Weeks
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
| | - Katharine Segars
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
| | - Suvajyoti Guha
- Center for Devices and Radiological Health, U. S. Food and Drug Administration, Silver Spring, MD, United States
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16
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Boldrin F, Provvedi R, Cioetto Mazzabò L, Segafreddo G, Manganelli R. Tolerance and Persistence to Drugs: A Main Challenge in the Fight Against Mycobacterium tuberculosis. Front Microbiol 2020; 11:1924. [PMID: 32983003 PMCID: PMC7479264 DOI: 10.3389/fmicb.2020.01924] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
The treatment of tuberculosis is extremely long. One of the reasons why Mycobacterium tuberculosis elimination from the organism takes so long is that in particular environmental conditions it can become tolerant to drugs and/or develop persisters able to survive killing even from very high drug concentrations. Tolerance develops in response to a harsh environment exposure encountered by bacteria during infection, mainly due to the action of the immune system, whereas persistence results from the presence of heterogeneous bacterial populations with different degrees of drug sensitivity, and can be induced by exposure to stress conditions. Here, we review the actual knowledge on the stress response mechanisms enacted by M. tuberculosis during infection, which leads to increased drug tolerance or development of a highly drug-resistant subpopulation.
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Affiliation(s)
- Francesca Boldrin
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | | | - Greta Segafreddo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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17
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Jakkala K, Ajitkumar P. Hypoxic Non-replicating Persistent Mycobacterium tuberculosis Develops Thickened Outer Layer That Helps in Restricting Rifampicin Entry. Front Microbiol 2019; 10:2339. [PMID: 31681204 PMCID: PMC6797554 DOI: 10.3389/fmicb.2019.02339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 09/25/2019] [Indexed: 01/25/2023] Open
Abstract
Bacteria undergo adaptive morphological changes to survive under stress conditions. The present work documents the morphological changes in Mycobacterium tuberculosis (Mtb) cells cultured under hypoxic condition using Wayne’s in vitro hypoxia model involving non-replicating persistence stages 1 and 2 (NRP stage 1 and NRP stage 2) and reveals their physiological significance. Transmission electron microscopy of the NRP stage 2 cells showed uneven but thick outer layer (TOL), unlike the evenly thin outer layer of the actively growing mid-log phase (MLP) cells. On the contrary, the saprophytic Mycobacterium smegmatis NRP stage 2 cells lacked TOL. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) of the Mtb NRP stage 2 cells confirmed the rough uneven surface unlike the smooth surface of the MLP cells. Zeta potential measurements showed high negative charge on the surface of NRP stage 2 cells and polysaccharide specific calcofluor white (CFW) staining of the cells revealed high content of polysaccharide in the TOL. This observation was supported by the real-time PCR data showing high levels of expression of the genes involved in the synthesis of sugars, such as trehalose, mannose and others, which are implicated in polysaccharide synthesis. Experiments to understand the physiological significance of the TOL revealed restricted entry of the biologically low-active 5-carboxyfluorescein-rifampicin (5-FAM-RIF), at concentrations equivalent to microbicidal concentrations of the unconjugated biologically active rifampicin, into the NRP stage 2 cells, unlike in the MLP cells. Further, as expected, mechanical removal of the TOL by mild bead beating or release of the NRP stage 2 cells from hypoxia into normoxia in fresh growth medium also significantly increased 5-FAM-RIF permeability into the NRP stage 2 cells to an extent comparable to that into the MLP cells. Taken together, these observations revealed that Mtb cells under hypoxia develop TOL that helps in restricting rifampicin entry, thereby conferring rifampicin tolerance.
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Affiliation(s)
- Kishor Jakkala
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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18
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Watching DNA Replication Inhibitors in Action: Exploiting Time-Lapse Microfluidic Microscopy as a Tool for Target-Drug Interaction Studies in Mycobacterium. Antimicrob Agents Chemother 2019; 63:AAC.00739-19. [PMID: 31383667 PMCID: PMC6761567 DOI: 10.1128/aac.00739-19] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/26/2019] [Indexed: 01/08/2023] Open
Abstract
Spreading resistance to antibiotics and the emergence of multidrug-resistant strains have become frequent in many bacterial species, including mycobacteria, which are the causative agents of severe diseases and which have profound impacts on global health. Here, we used a system of microfluidics, fluorescence microscopy, and target-tagged fluorescent reporter strains of Mycobacterium smegmatis to perform real-time monitoring of replisome and chromosome dynamics following the addition of replication-altering drugs (novobiocin, nalidixic acid, and griselimycin) at the single-cell level. We found that novobiocin stalled replication forks and caused relaxation of the nucleoid and that nalidixic acid triggered rapid replisome collapse and compaction of the nucleoid, while griselimycin caused replisome instability, with the subsequent overinitiation of chromosome replication and overrelaxation of the nucleoid. In addition to study target-drug interactions, our system also enabled us to observe how the tested antibiotics affected the physiology of mycobacterial cells (i.e., growth, chromosome segregation, etc.).
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19
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Nair RR, Sharan D, Ajitkumar P. A Minor Subpopulation of Mycobacteria Inherently Produces High Levels of Reactive Oxygen Species That Generate Antibiotic Resisters at High Frequency From Itself and Enhance Resister Generation From Its Major Kin Subpopulation. Front Microbiol 2019; 10:1842. [PMID: 31456773 PMCID: PMC6700507 DOI: 10.3389/fmicb.2019.01842] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022] Open
Abstract
Antibiotic-exposed bacteria produce elevated levels of reactive oxygen species (ROS), to which either they succumb or get mutated genome-wide to generate antibiotic resisters. We recently showed that mycobacterial cultures contained two subpopulations, short-sized cells (SCs; ∼10%) and normal/long-sized cells (NCs; ∼90%). The SCs were significantly more antibiotic-susceptible than the NCs. It implied that the SCs might naturally be predisposed to generate significantly higher levels of ROS than the NCs. This in turn could make the SCs more susceptible to antibiotics or generate more resisters as compared to the NCs. Investigation into this possibility showed that the SCs in the actively growing mid-log phase culture naturally generated significantly high levels of superoxide, as compared to the equivalent NCs, due to the naturally high expression of a specific NADH oxidase in the SCs. This caused labile Fe2+ leaching from 4Fe-4S proteins and elevated H2O2 formation through superoxide dismutation. Thus, the SCs of both Mycobacterium smegmatis and Mycobacterium tuberculosis inherently contained significantly higher levels of H2O2 and labile Fe2+ than the NCs. This in turn produced significantly higher levels of hydroxyl radical through Fenton reaction, promoting enhanced antibiotic resister generation from the SCs than from the NCs. The SCs, when mixed back with the NCs, at their natural proportion in the actively growing mid-log phase culture, enhanced antibiotic resister generation from the NCs, to a level equivalent to that from the unfractionated whole culture. The enhanced antibiotic resister generation from the NCs in the reconstituted SCs-NCs natural mixture was found to be due to the high levels of H2O2 secreted by the SCs. Thus, the present work unveils and documents the metabolic designs of two mycobacterial subpopulations where one subpopulation produces high ROS levels, despite higher susceptibility, to generate significantly higher number of antibiotic resisters from itself and to enhance resister generation from its kin subpopulation. These findings show the existence of an inherent natural mechanism in both the non-pathogenic and pathogenic mycobacteria to generate antibiotic resisters. The presence of the SCs and the NCs in the pulmonary tuberculosis patients’ sputum, reported by us earlier, alludes to the clinical significance of the study.
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Affiliation(s)
- Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
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20
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Nair RR, Sharan D, Sebastian J, Swaminath S, Ajitkumar P. Heterogeneity of ROS levels in antibiotic-exposed mycobacterial subpopulations confers differential susceptibility. MICROBIOLOGY-SGM 2019; 165:668-682. [PMID: 31091187 DOI: 10.1099/mic.0.000797] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypically heterogeneous but genetically identical mycobacterial subpopulations exist in in vitro cultures, in vitro-infected macrophages, infected animal models and tuberculosis patients. In this regard, we recently reported the presence of two subpopulations of cells, which are phenotypically different in length and buoyant density, in mycobacterial cultures. These are the low-buoyant-density short-sized cells (SCs), which constitute ~10-20 % of the population, and the high-buoyant-density normal/long-sized cells (NCs), which form ~80-90 % of the population. The SCs were found to be significantly more susceptible to rifampicin (RIF), isoniazid (INH), H2O2 and acidified nitrite than the NCs. Here we report that the RIF-/INH-/H2O2-exposed SCs showed significantly higher levels of oxidative stress and therefore higher susceptibility than the equivalent number of exposed NCs. Significantly higher levels of hydroxyl radical and superoxide were found in the antibiotic-exposed SCs than in the equivalently exposed NCs. Different proportions of the subpopulation of SCs were found to have different levels of reactive oxygen species (ROS). The hydroxyl radical quencher, thiourea, and the superoxide dismutase mimic, TEMPOL, significantly reduced hydroxyl radical and superoxide levels, respectively, in the antibiotic-exposed SCs and NCs and thereby decreased their differential susceptibility to antibiotics. Thus, the present study shows that the heterogeneity of the reactive oxygen species (ROS) levels in these mycobacterial subpopulations confers differential susceptibility to antibiotics. We have discussed the possible mechanisms that can generate differential ROS levels in the antibiotic-exposed SCs and NCs. The present study advances our current understanding of the molecular mechanisms underlying antibiotic tolerance in mycobacteria.
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Affiliation(s)
- Rashmi Ravindran Nair
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Jees Sebastian
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Sharmada Swaminath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, Karnataka, India
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21
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Vij R, Cordero RJB, Casadevall A. The Buoyancy of Cryptococcus neoformans Is Affected by Capsule Size. mSphere 2018; 3:e00534-18. [PMID: 30404928 PMCID: PMC6222054 DOI: 10.1128/msphere.00534-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/17/2018] [Indexed: 12/16/2022] Open
Abstract
Cryptococcus neoformans is an environmental pathogenic fungus with a worldwide geographical distribution that is responsible for hundreds of thousands of human cryptococcosis cases each year. During infection, the yeast undergoes a morphological transformation involving capsular enlargement that increases microbial volume. To understand the factors that play a role in environmental dispersal of C. neoformans and C. gattii, we evaluated the cell density of Cryptococcus using Percoll isopycnic gradients. We found differences in the cell densities of strains belonging to C. neoformans and C. gattii species complexes. The buoyancy of C. neoformans strains varied depending on growth medium. In minimal medium, the cryptococcal capsule made a major contribution to the cell density such that cells with larger capsules had lower density than those with smaller capsules. Removing the capsule, by chemical or mechanical methods, increased the C. neoformans cell density and reduced buoyancy. Melanization of the C. neoformans cell wall, which also contributes to virulence, produced a small but consistent increase in cell density. Encapsulated C. neoformans sedimented much more slowly in seawater as its density approached the density of water. Our results suggest a new function for the capsule whereby it can function as a flotation device to facilitate transport and dispersion in aqueous fluids.IMPORTANCE The buoyancy of a microbial cell is an important physical characteristic that may affect its transportability in fluids and interactions with tissues during infection. The polysaccharide capsule surrounding C. neoformans is required for infection and dissemination in the host. Our results indicate that the capsule has a significant effect on reducing cryptococcal cell density, altering its sedimentation in seawater. Modulation of microbial cell density via encapsulation may facilitate dispersal for other important encapsulated pathogens.
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Affiliation(s)
- Raghav Vij
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Radames J B Cordero
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Arturo Casadevall
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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22
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Gupta S, Rodriguez GM. Mycobacterial extracellular vesicles and host pathogen interactions. Pathog Dis 2018; 76:4963744. [PMID: 29722822 PMCID: PMC5930244 DOI: 10.1093/femspd/fty031] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/05/2018] [Indexed: 12/11/2022] Open
Abstract
Mycobacteria, like other bacteria, archaea and eukaryotic cells, naturally release extracellular vesicles (EVs) to interact with their environment. EVs produced by pathogenic bacteria are involved in many activities including cell-cell communication, immunomodulation, virulence and cell survival. Although EVs released by thick cell wall microorganisms like mycobacteria were recognized only recently, studies of Mycobacterium tuberculosis EVs already point to their important roles in host pathogen interactions, opening exciting new areas of investigation. This minireview will summarize the current understanding of mycobacterial EV biology and roles in pathogenesis and will discuss their potential therapeutic applications.
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Affiliation(s)
- Shamba Gupta
- Public Health Research Institute Center and New Jersey Medical School-Rutgers, The State University of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
| | - G Marcela Rodriguez
- Public Health Research Institute Center and New Jersey Medical School-Rutgers, The State University of New Jersey, 225 Warren Street, Newark, NJ 07103, USA
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Hage-Hülsmann J, Grünberger A, Thies S, Santiago-Schübel B, Klein AS, Pietruszka J, Binder D, Hilgers F, Domröse A, Drepper T, Kohlheyer D, Jaeger KE, Loeschcke A. Natural biocide cocktails: Combinatorial antibiotic effects of prodigiosin and biosurfactants. PLoS One 2018; 13:e0200940. [PMID: 30024935 PMCID: PMC6053208 DOI: 10.1371/journal.pone.0200940] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/05/2018] [Indexed: 11/18/2022] Open
Abstract
Bacterial secondary metabolites are naturally produced to prevail amongst competitors in a shared habitat and thus represent a valuable source for antibiotic discovery. The transformation of newly discovered antibiotic compounds into effective drugs often requires additional surfactant components for drug formulation. Nature may also provide blueprints in this respect: A cocktail of two compounds consisting of the antibacterial red pigment prodigiosin and the biosurfactant serrawettin W1 is naturally produced by the bacterium Serratia marcescens, which occurs in highly competitive habitats including soil. We show here a combinatorial antibacterial effect of these compounds, but also of prodigiosin mixed with other (bio)surfactants, against the soil-dwelling bacterium Corynebacterium glutamicum taken as a model target bacterium. Prodigiosin exerted a combinatorial inhibitory effect with all tested surfactants in a disk diffusion assay which was especially pronounced in combination with N-myristoyltyrosine. Minimal inhibitory and bactericidal concentrations (MIC and MBC) of the individual compounds were 2.56 μg/mL prodigiosin and 32 μg/mL N-myristoyltyrosine, and the MIC of prodigiosin was decreased by 3 orders of magnitude to 0.005 μg/mL in the presence of 16 μg/mL N-myristoyltyrosine, indicative of synergistic interaction. Investigation of bacterial survival revealed similar combinatorial effects; moreover, antagonistic effects were observed at higher compound concentrations. Finally, the investigation of microcolony formation under combined application of concentrations just below the MBC revealed heterogeneity of responses with cell death or delayed growth. In summary, this study describes the combinatorial antibacterial effects of microbial biomolecules, which may have ecological relevance by inhibiting cohabiting species, but shall furthermore inspire drug development in the combat of infectious disease.
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Affiliation(s)
- Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Alexander Grünberger
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Beatrix Santiago-Schübel
- Central Division of Analytical Chemistry ZEA-3: Analytik/Biospec, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andreas Sebastian Klein
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Jörg Pietruszka
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Dietrich Kohlheyer
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Aachener Verfahrenstechnik (AVT.MSB), RWTH Aachen University, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
- * E-mail:
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24
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Mukkayyan N, Sharan D, Ajitkumar P. A Symmetric Molecule Produced by Mycobacteria Generates Cell-Length Asymmetry during Cell-Division and Thereby Cell-Length Heterogeneity. ACS Chem Biol 2018; 13:1447-1454. [PMID: 29757604 DOI: 10.1021/acschembio.8b00080] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Diadenosine polyphosphates, Ap(2-7)A, which contain two adenosines in a 5',5' linkage through phosphodiester bonds involving 2-7 phosphates, regulate diverse cellular functions in all organisms, from bacteria to humans, under normal and stress conditions. We had earlier reported consistent occurrence of asymmetric constriction during division (ACD) in 20-30% of dividing mycobacterial cells in culture, irrespective of different growth media, implying exogenous action of some factor of mycobacterial origin. Consistent with this premise, concentrated culture supernatant (CCS), but not the equivalent volume-wise concentrated unused medium, dramatically enhanced the ACD proportion to 70-90%. Mass spectrometry and biochemical analyses of the bioactive fraction from CCS revealed the ACD-effecting factor to be Ap6A. Synthetic Ap6A showed a mass spectrometry profile, biochemical characteristics, and bioactivity identical to native Ap6A in the CCS. Thus, the present work reveals a novel role for Ap6A in generating cell-length asymmetry during mycobacterial cell-division and thereby cell-length heterogeneity in the population.
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Affiliation(s)
- Nagaraja Mukkayyan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Deepti Sharan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Parthasarathi Ajitkumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, Karnataka, India
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25
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Vijay S, Vinh DN, Hai HT, Ha VTN, Dung VTM, Dinh TD, Nhung HN, Tram TTB, Aldridge BB, Hanh NT, Thu DDA, Phu NH, Thwaites GE, Thuong NTT. Influence of Stress and Antibiotic Resistance on Cell-Length Distribution in Mycobacterium tuberculosis Clinical Isolates. Front Microbiol 2017; 8:2296. [PMID: 29209302 PMCID: PMC5702322 DOI: 10.3389/fmicb.2017.02296] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/07/2017] [Indexed: 11/25/2022] Open
Abstract
Mycobacterial cellular variations in growth and division increase heterogeneity in cell length, possibly contributing to cell-to-cell variation in host and antibiotic stress tolerance. This may be one of the factors influencing Mycobacterium tuberculosis persistence to antibiotics. Tuberculosis (TB) is a major public health problem in developing countries, antibiotic persistence, and emergence of antibiotic resistance further complicates this problem. We wanted to investigate the factors influencing cell-length distribution in clinical M. tuberculosis strains. In parallel we examined M. tuberculosis cell-length distribution in a large set of clinical strains (n = 158) from ex vivo sputum samples, in vitro macrophage models, and in vitro cultures. Our aim was to understand the influence of clinically relevant factors such as host stresses, M. tuberculosis lineages, antibiotic resistance, antibiotic concentrations, and disease severity on the cell size distribution in clinical M. tuberculosis strains. Increased cell size and cell-to-cell variation in cell length were associated with bacteria in sputum and infected macrophages rather than liquid culture. Multidrug-resistant (MDR) strains displayed increased cell length heterogeneity compared to sensitive strains in infected macrophages and also during growth under rifampicin (RIF) treatment. Importantly, increased cell length was also associated with pulmonary TB disease severity. Supporting these findings, individual host stresses, such as oxidative stress and iron deficiency, increased cell-length heterogeneity of M. tuberculosis strains. In addition we also observed synergism between host stress and RIF treatment in increasing cell length in MDR-TB strains. This study has identified some clinical factors contributing to cell-length heterogeneity in clinical M. tuberculosis strains. The role of these cellular adaptations to host and antibiotic tolerance needs further investigation.
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Affiliation(s)
- Srinivasan Vijay
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Dao N Vinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hoang T Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu T N Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu T M Dung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tran D Dinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hoang N Nhung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Trinh T B Tram
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States.,Department of Biomedical Engineering, Tufts University School of Engineering, Medford, MA, United States
| | - Nguyen T Hanh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Do D A Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen H Phu
- Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nguyen T T Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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