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Mistretta M, Cimino M, Campagne P, Volant S, Kornobis E, Hebert O, Rochais C, Dallemagne P, Lecoutey C, Tisnerat C, Lepailleur A, Ayotte Y, LaPlante SR, Gangneux N, Záhorszká M, Korduláková J, Vichier-Guerre S, Bonhomme F, Pokorny L, Albert M, Tinevez JY, Manina G. Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy. Nat Commun 2024; 15:4175. [PMID: 38755132 PMCID: PMC11099131 DOI: 10.1038/s41467-024-48269-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Drug-recalcitrant infections are a leading global-health concern. Bacterial cells benefit from phenotypic variation, which can suggest effective antimicrobial strategies. However, probing phenotypic variation entails spatiotemporal analysis of individual cells that is technically challenging, and hard to integrate into drug discovery. In this work, we develop a multi-condition microfluidic platform suitable for imaging two-dimensional growth of bacterial cells during transitions between separate environmental conditions. With this platform, we implement a dynamic single-cell screening for pheno-tuning compounds, which induce a phenotypic change and decrease cell-to-cell variation, aiming to undermine the entire bacterial population and make it more vulnerable to other drugs. We apply this strategy to mycobacteria, as tuberculosis poses a major public-health threat. Our lead compound impairs Mycobacterium tuberculosis via a peculiar mode of action and enhances other anti-tubercular drugs. This work proves that harnessing phenotypic variation represents a successful approach to tackle pathogens that are increasingly difficult to treat.
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Affiliation(s)
- Maxime Mistretta
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Mena Cimino
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Pascal Campagne
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Etienne Kornobis
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Biomics Platform, 75015, Paris, France
| | | | | | | | | | | | | | - Yann Ayotte
- Institut National de la Recherche Scientifique-Armand-Frappier Santé Biotechnologie Research Centre, Laval, Quebec, H7V 1B7, Canada
| | - Steven R LaPlante
- Institut National de la Recherche Scientifique-Armand-Frappier Santé Biotechnologie Research Centre, Laval, Quebec, H7V 1B7, Canada
| | - Nicolas Gangneux
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Monika Záhorszká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Sophie Vichier-Guerre
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Epigenetic Chemical Biology Unit, 75015, Paris, France
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Epigenetic Chemical Biology Unit, 75015, Paris, France
| | - Laura Pokorny
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Marvin Albert
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015, Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015, Paris, France
| | - Giulia Manina
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France.
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2
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Park HE, Kim KM, Trinh MP, Yoo JW, Shin SJ, Shin MK. Bigger problems from smaller colonies: emergence of antibiotic-tolerant small colony variants of Mycobacterium avium complex in MAC-pulmonary disease patients. Ann Clin Microbiol Antimicrob 2024; 23:25. [PMID: 38500139 PMCID: PMC10949641 DOI: 10.1186/s12941-024-00683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Mycobacterium avium complex (MAC) is a group of slow-growing mycobacteria that includes Mycobacterium avium and Mycobacterium intracellulare. MAC pulmonary disease (MAC-PD) poses a threat to immunocompromised individuals and those with structural pulmonary diseases worldwide. The standard treatment regimen for MAC-PD includes a macrolide in combination with rifampicin and ethambutol. However, the treatment failure and disease recurrence rates after successful treatment remain high. RESULTS In the present study, we investigated the unique characteristics of small colony variants (SCVs) isolated from patients with MAC-PD. Furthermore, revertant (RVT) phenotype, emerged from the SCVs after prolonged incubation on 7H10 agar. We observed that SCVs exhibited slower growth rates than wild-type (WT) strains but had higher minimum inhibitory concentrations (MICs) against multiple antibiotics. However, some antibiotics showed low MICs for the WT, SCVs, and RVT phenotypes. Additionally, the genotypes were identical among SCVs, WT, and RVT. Based on the MIC data, we conducted time-kill kinetic experiments using various antibiotic combinations. The response to antibiotics varied among the phenotypes, with RVT being the most susceptible, WT showing intermediate susceptibility, and SCVs displaying the lowest susceptibility. CONCLUSIONS In conclusion, the emergence of the SCVs phenotype represents a survival strategy adopted by MAC to adapt to hostile environments and persist during infection within the host. Additionally, combining the current drugs in the treatment regimen with additional drugs that promote the conversion of SCVs to RVT may offer a promising strategy to improve the clinical outcomes of patients with refractory MAC-PD.
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Affiliation(s)
- Hyun-Eui Park
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Minh Phuong Trinh
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, 52727, Republic of Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Diseases, Brain Korea 21 Program for Leading Universities and Students (PLUS) Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
| | - Min-Kyoung Shin
- Department of Microbiology and Convergence of Medical Science, College of Medicine, Gyeongsang National University, Jinju, 52727, Republic of Korea.
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3
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Sit B, Lamason RL. Pathogenic Rickettsia spp. as emerging models for bacterial biology. J Bacteriol 2024; 206:e0040423. [PMID: 38315013 PMCID: PMC10883807 DOI: 10.1128/jb.00404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Our understanding of free-living bacterial models like Escherichia coli far outpaces that of obligate intracellular bacteria, which cannot be cultured axenically. All obligate intracellular bacteria are host-associated, and many cause serious human diseases. Their constant exposure to the distinct biochemical niche of the host has driven the evolution of numerous specialized bacteriological and genetic adaptations, as well as innovative molecular mechanisms of infection. Here, we review the history and use of pathogenic Rickettsia species, which cause an array of vector-borne vascular illnesses, as model systems to probe microbial biology. Although many challenges remain in our studies of these organisms, the rich pathogenic and biological diversity of Rickettsia spp. constitutes a unique backdrop to investigate how microbes survive and thrive in host and vector cells. We take a bacterial-focused perspective and highlight emerging insights that relate to new host-pathogen interactions, bacterial physiology, and evolution. The transformation of Rickettsia spp. from pathogens to models demonstrates how recalcitrant microbes may be leveraged in the lab to tap unmined bacterial diversity for new discoveries. Rickettsia spp. hold great promise as model systems not only to understand other obligate intracellular pathogens but also to discover new biology across and beyond bacteria.
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Affiliation(s)
- Brandon Sit
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rebecca L. Lamason
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Huang X, Lowrie DB, Fan XY, Hu Z. Natural products in anti-tuberculosis host-directed therapy. Biomed Pharmacother 2024; 171:116087. [PMID: 38171242 DOI: 10.1016/j.biopha.2023.116087] [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: 10/25/2023] [Revised: 12/17/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Given that the disease progression of tuberculosis (TB) is primarily related to the host's immune status, it has been gradually realized that chemotherapy that targets the bacteria may never, on its own, wholly eradicate Mycobacterium tuberculosis, the causative agent of TB. The concept of host-directed therapy (HDT) with immune adjuvants has emerged. HDT could potentially interfere with infection and colonization by the pathogens, enhance the protective immune responses of hosts, suppress the overwhelming inflammatory responses, and help to attain a state of homeostasis that favors treatment efficacy. However, the HDT drugs currently being assessed in combination with anti-TB chemotherapy still face the dilemmas arising from side effects and high costs. Natural products are well suited to compensate for these shortcomings by having gentle modulatory effects on the host immune responses with less immunopathological damage at a lower cost. In this review, we first summarize the profiles of anti-TB immunology and the characteristics of HDT. Then, we focus on the rationale and challenges of developing and implementing natural products-based HDT. A succinct report of the medications currently being evaluated in clinical trials and preclinical studies is provided. This review aims to promote target-based screening and accelerate novel TB drug discovery.
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Affiliation(s)
- Xuejiao Huang
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China
| | - Douglas B Lowrie
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China
| | - Xiao-Yong Fan
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China.
| | - Zhidong Hu
- Shanghai Public Health Clinical Center & Shanghai Institute of Infectious Diseases and Biosecurity, Fudan University, Shanghai 201508, China.
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Gwin CM, Gupta KR, Lu Y, Shao L, Rego EH. Spatial segregation and aging of metabolic processes underlie phenotypic heterogeneity in mycobacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569614. [PMID: 38076906 PMCID: PMC10705497 DOI: 10.1101/2023.12.01.569614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Individual cells within clonal populations of mycobacteria vary in size, growth rate, and antibiotic susceptibility. Heterogeneity is, in part, determined by LamA, a protein found exclusively in mycobacteria. LamA localizes to sites of new cell wall synthesis where it recruits proteins important for polar growth and establishing asymmetry. Here, we report that in addition to this function, LamA interacts with complexes involved in oxidative phosphorylation (OXPHOS) at a subcellular location distinct from cell wall synthesis. Importantly, heterogeneity depends on a unique extension of the mycobacterial ATP synthase, and LamA mediates the coupling between ATP production and cell growth in single cells. Strikingly, as single cells age, concentrations of proteins important for oxidative phosphorylation become less abundant, and older cells rely less on oxidative phosphorylation for growth. Together, our data reveal that central metabolism is spatially organized within a single mycobacterium and varies within a genetically identical population of mycobacteria. Designing therapeutic regimens to account for this heterogeneity may help to treat mycobacterial infections faster and more completely.
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Affiliation(s)
- Celena M. Gwin
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Kuldeepkumar R. Gupta
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Yao Lu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Lin Shao
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - E. Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
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Zachariou M, Arandjelović O, Dombay E, Sabiiti W, Mtafya B, Ntinginya NE, Sloan DJ. Localization and phenotyping of tuberculosis bacteria using a combination of deep learning and SVMs. Comput Biol Med 2023; 167:107573. [PMID: 37913616 DOI: 10.1016/j.compbiomed.2023.107573] [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: 06/07/2023] [Revised: 09/09/2023] [Accepted: 10/11/2023] [Indexed: 11/03/2023]
Abstract
Successful treatment of pulmonary tuberculosis (TB) depends on early diagnosis and careful monitoring of treatment response. Identification of acid-fast bacilli by fluorescence microscopy of sputum smears is a common tool for both tasks. Microscopy-based analysis of the intracellular lipid content and dimensions of individual Mycobacterium tuberculosis (Mtb) cells also describe phenotypic changes which may improve our biological understanding of antibiotic therapy for TB. However, fluorescence microscopy is a challenging, time-consuming and subjective procedure. In this work, we automate examination of fields of view (FOVs) from microscopy images to determine the lipid content and dimensions (length and width) of Mtb cells. We introduce an adapted variation of the UNet model to efficiently localising bacteria within FOVs stained by two fluorescence dyes; auramine O to identify Mtb and LipidTox Red to identify intracellular lipids. Thereafter, we propose a feature extractor in conjunction with feature descriptors to extract a representation into a support vector multi-regressor and estimate the length and width of each bacterium. Using a real-world data corpus from Tanzania, the proposed method i) outperformed previous methods for bacterial detection with a 8% improvement (Dice coefficient) and ii) estimated the cell length and width with a root mean square error of less than 0.01%. Our network can be used to examine phenotypic characteristics of Mtb cells visualised by fluorescence microscopy, improving consistency and time efficiency of this procedure compared to manual methods.
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Affiliation(s)
- Marios Zachariou
- School of Computer Science, University of St Andrews, St Andrews, KY16 9SX, United Kingdom.
| | - Ognjen Arandjelović
- School of Computer Science, University of St Andrews, St Andrews, KY16 9SX, United Kingdom
| | - Evelin Dombay
- School of Medicine, University of St Andrews, St Andrews, KY16 9AJ, United Kingdom
| | - Wilber Sabiiti
- School of Medicine, University of St Andrews, St Andrews, KY16 9AJ, United Kingdom
| | | | | | - Derek J Sloan
- School of Medicine, University of St Andrews, St Andrews, KY16 9AJ, United Kingdom
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Hu Z, Zeng D, Yang Y, Liu H, Wang A, Li D, Liu M, Feng Y. Pathomorphological characteristics of tuberculous placenta and its clinical implication. Diagn Pathol 2023; 18:128. [PMID: 38031157 PMCID: PMC10685481 DOI: 10.1186/s13000-023-01419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 11/17/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The study of pathologic diagnosis of placental TB is rare. The aim of this study is analyzing the pathomorphological characteristics of tuberculosis (TB) placenta during pregnancy and its clinical significance. METHODS Nineteen cases of placental tissue specimens during pregnancy were collected from June 2015 to February 2022 at Shanghai Public Health Clinical Center, the only inpatient center for pregnant women with TB in Shanghai, China. Hematoxylin-eosin staining, acid-fast staining, and molecular testing were applied to analyze them comprehensively in combination with clinical information. RESULTS Among the 19 cases, 7 cases caused intrauterine stillbirth, 3 cases received artificial abortion required by the pregnant woman, the other 9 cases received standard delivery and the infants survived, however, 3 of them were low-weight preterm infants, and another 1 case suffered mild intrauterine asphyxia. The 9 surviving infants were followed-up, of which 3 cases got congenital TB. For pathological characteristics of placental tissues under light microscopy, there were 3 cases of epithelioid granuloma formation, 13 cases of acute fetal membranitis, 4 cases of caseous necrosis, 7 cases of inflammatory necrosis, 10 cases of coagulative necrosis, and 6 cases with small focal calcifications. All placental tissues were positive for acid-fast staining and polymerase chain reaction (PCR). Molecular pathological diagnosis showed that 18 cases were positive for Mycobacterium tuberculosis, with 1 case not having received examination. CONCLUSIONS Combining acid-fast staining and molecular pathological testing is helpful for accurately diagnosing placental TB.
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Affiliation(s)
- Zhidong Hu
- Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Dong Zeng
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yuexiang Yang
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Huijun Liu
- Department of Pathology, The Fifth People's Hospital of Puyang, Puyang, Henan Province, China
| | - Ao Wang
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Duoduo Li
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Min Liu
- Department of Obstetrics and Gynecology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Yanling Feng
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
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8
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Gouzy A. Use of single-cell technology to improve our understanding of the role of TLR2 in macrophage- Mycobacterium tuberculosis interaction. mSystems 2023; 8:e0073023. [PMID: 37787569 PMCID: PMC10654086 DOI: 10.1128/msystems.00730-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
The interaction between Mycobacterium tuberculosis, the agent of tuberculosis (TB), and its host cell, the macrophage, is multifaceted, dynamic, and involves multiple molecular partners. A better understanding of this interaction could help researchers manipulate the immune system in order to design host-targeted immunotherapies and/or develop a novel vaccine protecting better adults against TB. Jani and coworkers studied the role of the macrophage receptor TLR2 in the response to M. tuberculosis using single-cell technologies (C. Jani, S. L. Solomon, J. M. Peters, and S. C. Pringle, et al., mSystems, https://doi.org/10.1128/msystems.00052-23, 2023). This work addresses the multiple challenges associated with such studies and shows how informative single-cell analysis can be for the study of heterogeneous and complex host-pathogen interactions.
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Affiliation(s)
- Alexandre Gouzy
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
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9
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Lanni A, Iacobino A, Fattorini L, Giannoni F. Eradication of Drug-Tolerant Mycobacterium tuberculosis 2022: Where We Stand. Microorganisms 2023; 11:1511. [PMID: 37375013 DOI: 10.3390/microorganisms11061511] [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: 04/28/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
The lungs of tuberculosis (TB) patients contain a spectrum of granulomatous lesions, ranging from solid and well-vascularized cellular granulomas to avascular caseous granulomas. In solid granulomas, current therapy kills actively replicating (AR) intracellular bacilli, while in low-vascularized caseous granulomas the low-oxygen tension stimulates aerobic and microaerophilic AR bacilli to transit into non-replicating (NR), drug-tolerant and extracellular stages. These stages, which do not have genetic mutations and are often referred to as persisters, are difficult to eradicate due to low drug penetration inside the caseum and mycobacterial cell walls. The sputum of TB patients also contains viable bacilli called differentially detectable (DD) cells that, unlike persisters, grow in liquid, but not in solid media. This review provides a comprehensive update on drug combinations killing in vitro AR and drug-tolerant bacilli (persisters and DD cells), and sterilizing Mycobacterium tuberculosis-infected BALB/c and caseum-forming C3HeB/FeJ mice. These observations have been important for testing new drug combinations in noninferiority clinical trials, in order to shorten the duration of current regimens against TB. In 2022, the World Health Organization, following the results of one of these trials, supported the use of a 4-month regimen for the treatment of drug-susceptible TB as a possible alternative to the current 6-month regimen.
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Affiliation(s)
- Alessio Lanni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Angelo Iacobino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Lanfranco Fattorini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
| | - Federico Giannoni
- Department of Infectious Diseases, Istituto Superiore di Sanità, Via Regina Elena 299, 00161 Rome, Italy
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10
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Chung ES, Kar P, Kamkaew M, Amir A, Aldridge BB. Mycobacterium tuberculosis grows linearly at the single-cell level with larger variability than model organisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.17.541183. [PMID: 37292927 PMCID: PMC10245742 DOI: 10.1101/2023.05.17.541183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The ability of bacterial pathogens to regulate growth is crucial to control homeostasis, virulence, and drug response. Yet, we do not understand the growth and cell cycle behaviors of Mycobacterium tuberculosis (Mtb), a slow-growing pathogen, at the single-cell level. Here, we use time-lapse imaging and mathematical modeling to characterize these fundamental properties of Mtb. Whereas most organisms grow exponentially at the single-cell level, we find that Mtb exhibits a unique linear growth mode. Mtb growth characteristics are highly variable from cell-to-cell, notably in their growth speeds, cell cycle timing, and cell sizes. Together, our study demonstrates that growth behavior of Mtb diverges from what we have learned from model bacteria. Instead, Mtb generates a heterogeneous population while growing slowly and linearly. Our study provides a new level of detail into how Mtb grows and creates heterogeneity, and motivates more studies of growth behaviors in bacterial pathogens.
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11
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Schrader SM, Botella H, Vaubourgeix J. Reframing antimicrobial resistance as a continuous spectrum of manifestations. Curr Opin Microbiol 2023; 72:102259. [PMID: 36608373 DOI: 10.1016/j.mib.2022.102259] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
To fight antimicrobial resistance (AMR), we must recognize and target all its manifestations. In this review, we briefly summarize the history that led to recognition of the various manifestations of AMR in bacterial pathogens and the ways in which they interrelate. We emphasize the importance of distinguishing between AMR arising from genetic alterations versus induction of endogenous machinery in response to environmental triggers, including - paradoxically - stresses from host immunity and antimicrobial therapy. We present an integrated view of AMR by reframing it as a spectrum of phenotypes within a continuous three-dimensional space defined by the growth rate, prevalence, and kill rate of cells displaying AMR. Finally, we reflect on strategies that may help stem the emergence of AMR.
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Affiliation(s)
- Sarah M Schrader
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, USA
| | - Hélène Botella
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julien Vaubourgeix
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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12
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Bonnett S, Jee JA, Chettiar S, Ovechkina Y, Korkegian A, Greve E, Odingo J, Parish T. Identification of 2-Amino Benzothiazoles with Bactericidal Activity against Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0497422. [PMID: 36688635 PMCID: PMC9927457 DOI: 10.1128/spectrum.04974-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/24/2023] Open
Abstract
We identified an amino-benzothiazole scaffold from a whole-cell screen against recombinant Mycobacterium tuberculosis under expressing the essential signal peptidase LepB. The seed molecule had 2-fold higher activity against the LepB hypomorph. Through a combination of purchase and chemical synthesis, we explored the structure-activity relationship for this series; 34 analogs were tested for antitubercular activity and for cytotoxicity against eukaryotic cells. We identified molecules with improved potency and reduced cytotoxicity. However, molecules did not appear to target LepB directly and did not inhibit protein secretion. Key compounds showed good permeability, low protein binding, and lack of CYP inhibition, but metabolic stability was poor with short half-lives. The seed molecule showed good bactericidal activity against both replicating and nonreplicating bacteria, as well as potency against intracellular M. tuberculosis in murine macrophages. Overall, the microbiological properties of the series are attractive if metabolic stability can be improved, and identification of the target could assist in the development of this series. IMPORTANCE Mycobacterium tuberculosis, the causative agent of tuberculosis, is a serious global health problem requiring the development of new therapeutics. We previously ran a high-throughput screen and identified a series of compounds with antitubercular activity. In this paper, we test analogs of our hit molecules for activity against M. tuberculosis, as well as for activity against eukaryotic cells. We identified molecules with improved selectivity. Our molecules killed both replicating and nonreplicating bacteria but did not work by targeting protein secretion.
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Affiliation(s)
- Shilah Bonnett
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Jo-Ann Jee
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Somsundaram Chettiar
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Yulia Ovechkina
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Aaron Korkegian
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Eric Greve
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joshua Odingo
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, USA
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
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13
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Immune cell interactions in tuberculosis. Cell 2022; 185:4682-4702. [PMID: 36493751 DOI: 10.1016/j.cell.2022.10.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/26/2022] [Indexed: 12/13/2022]
Abstract
Despite having been identified as the organism that causes tuberculosis in 1882, Mycobacterium tuberculosis has managed to still evade our understanding of the protective immune response against it, defying the development of an effective vaccine. Technology and novel experimental models have revealed much new knowledge, particularly with respect to the heterogeneity of the bacillus and the host response. This review focuses on certain immunological elements that have recently yielded exciting data and highlights the importance of taking a holistic approach to understanding the interaction of M. tuberculosis with the many host cells that contribute to the development of protective immunity.
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14
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Abstract
Tuberculosis (TB) is an infectious disease bedeviled by complexity. This poses myriad challenges for a research ecosystem organized around specialist host- and/or pathogen-focused thrusts. Here, we highlight the key challenges and their implications for developing new tools to control TB.
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Affiliation(s)
- Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ryan Dinkele
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Digby F. Warner
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa
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15
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Jones RM, Adams KN, Eldesouky HE, Sherman DR. The evolving biology of Mycobacterium tuberculosis drug resistance. Front Cell Infect Microbiol 2022; 12:1027394. [PMID: 36275024 PMCID: PMC9579286 DOI: 10.3389/fcimb.2022.1027394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/20/2022] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb) is an ancient disease that has remained a leading cause of infectious death. Mtb has evolved drug resistance to every antibiotic regimen ever introduced, greatly complicating treatment, lowering rates of cure and menacing TB control in parts of the world. As technology has advanced, our understanding of antimicrobial resistance has improved, and our models of the phenomenon have evolved. In this review, we focus on recent research progress that supports an updated model for the evolution of drug resistance in Mtb. We highlight the contribution of drug tolerance on the path to resistance, and the influence of heterogeneity on tolerance. Resistance is likely to remain an issue for as long as drugs are needed to treat TB. However, with technology driving new insights and careful management of newly developed resources, antimicrobial resistance need not continue to threaten global progress against TB, as it has done for decades.
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Affiliation(s)
| | | | | | - David R. Sherman
- Department of Microbiology, University of Washington, Seattle, WA, United States
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16
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Tomasi FG, Rubin EJ. Failing upwards: Genetics-based strategies to improve antibiotic discovery and efficacy in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:932556. [PMID: 36189351 PMCID: PMC9519881 DOI: 10.3389/fcimb.2022.932556] [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: 04/29/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
Therapeutic advances in the 20th century significantly reduced tuberculosis (TB) mortality. Nonetheless, TB still poses a massive global health challenge with significant annual morbidity and mortality that has been amplified during the COVID-19 pandemic. Unlike most common bacterial infectious diseases, successful TB treatment requires months-long regimens, which complicates the ability to treat all cases quickly and effectively. Improving TB chemotherapy by reducing treatment duration and optimizing combinations of drugs is an important step to reducing relapse. In this review, we outline the limitations of current multidrug regimens against TB and have reviewed the genetic tools available to improve the identification of drug targets. The rational design of regimens that sterilize diverse phenotypic subpopulations will maximize bacterial killing while minimizing both treatment duration and infection relapse. Importantly, the TB field currently has all the necessary genetic and analytical tools to screen for and prioritize drug targets in vitro based on the vulnerability of essential and non-essential genes in the Mtb genome and to translate these findings in in vivo models. Combining genetic methods with chemical screens offers a formidable strategy to redefine the preclinical design of TB therapy by identifying powerful new targets altogether, as well as targets that lend new efficacy to existing drugs.
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