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Calvet-Seral J, Crespo-Yuste E, Mathys V, Rodriguez-Villalobos H, Ceyssens PJ, Martin A, Gonzalo-Asensio J. Targeted Chromosomal Barcoding Establishes Direct Genotype-Phenotype Associations for Antibiotic Resistance in Mycobacterium abscessus. Microbiol Spectr 2023; 11:e0534422. [PMID: 36988496 PMCID: PMC10269753 DOI: 10.1128/spectrum.05344-22] [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: 12/28/2022] [Accepted: 03/04/2023] [Indexed: 03/30/2023] Open
Abstract
A bedaquiline-resistant Mycobacterium abscessus isolate was sequenced, and a candidate mutation in the atpE gene was identified as responsible for the antibiotic resistance phenotype. To establish a direct genotype-phenotype relationship of this mutation which results in a Asp-to-Ala change at position 29 (D29A), we developed a recombineering-based method consisting of the specific replacement of the desired mutation in the bacterial chromosome. As surrogate bacteria, we used two M. abscessus bedaquiline-susceptible strains: ATCC 19977 and the SL541 clinical isolate. The allelic exchange substrates used in recombineering carried either the sole D29A mutation or a genetic barcode of silent mutations in codons flanking the D29A mutation. After selection of bedaquiline-resistant M. abscessus colonies transformed with both substrates, we obtained equivalent numbers of recombinants. These resistant colonies were analyzed by allele-specific PCR and Sanger sequencing, and we demonstrated that the presence of the genetic barcode was linked to the targeted incorporation of the desired mutation in its chromosomal location. All recombinants displayed the same MIC to bedaquiline as the original isolate, from which the D29A mutation was identified. Finally, to demonstrate the broad applicability of this method, we confirmed the association of bedaquiline resistance with the atpE A64P mutation in analysis performed in independent M. abscessus strains and by independent researchers. IMPORTANCE Antimicrobial resistance (AMR) threatens the effective prevention and treatment of an ever-increasing range of infections caused by microorganisms. On the other hand, infections caused by Mycobacterium abscessus affect people with chronic lung diseases, and their incidence has grown alarmingly in recent years. Further, these bacteria are known to easily develop AMR to the few therapeutic options available, making their treatment long-lasting and challenging. The recent introduction of new antibiotics against M. abscessus, such as bedaquiline, makes us anticipate a future when a plethora of antibiotic-resistant strains will be isolated and sequenced. However, in the era of whole-genome sequencing, one of the challenges is to unequivocally assign a biological function to each identified polymorphism. Thus, in this study, we developed a fast, robust, and reliable method to assign genotype-phenotype associations for putative antibiotic-resistant polymorphisms in M. abscessus.
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Affiliation(s)
- Juan Calvet-Seral
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Estefanía Crespo-Yuste
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Vanessa Mathys
- Unit of Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Hector Rodriguez-Villalobos
- Cliniques Universitaires Saint-Luc, Microbiology Department, Université Catholique de Louvain, Brussels, Belgium
| | | | - Anandi Martin
- Institute of Experimental and Clinical Research, Université Catholique de Louvain, Woluwe-Saint-Lambert, Belgium
- Syngulon, Seraing, Belgium
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad de Zaragoza IIS-Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Zaragoza, Spain
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Armianinova DK, Karpov DS, Kotliarova MS, Goncharenko AV. Genetic Engineering in Mycobacteria. Mol Biol 2022. [DOI: 10.1134/s0026893322060036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Abstract
Genetic tools for targeted modification of the mycobacterial genome contribute to the understanding of the physiology and virulence mechanisms of mycobacteria. Human and animal pathogens, such as the Mycobacterium tuberculosis complex, which causes tuberculosis, and M. leprae, which causes leprosy, are of particular importance. Genetic research opens up novel opportunities to identify and validate new targets for antibacterial drugs and to develop improved vaccines. Although mycobacteria are difficult to work with due to their slow growth rate and a limited possibility to transfer genetic information, significant progress has been made in developing genetic engineering methods for mycobacteria. The review considers the main approaches to changing the mycobacterial genome in a targeted manner, including homologous and site-specific recombination and use of the CRISPR/Cas system.
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Rominski A, Selchow P, Becker K, Brülle JK, Dal Molin M, Sander P. Elucidation of Mycobacterium abscessus aminoglycoside and capreomycin resistance by targeted deletion of three putative resistance genes. J Antimicrob Chemother 2018; 72:2191-2200. [PMID: 28486671 DOI: 10.1093/jac/dkx125] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/03/2017] [Indexed: 12/20/2022] Open
Abstract
Objectives Mycobacterium abscessus is innately resistant to a variety of drugs thereby limiting therapeutic options. Bacterial resistance to aminoglycosides (AGs) is conferred mainly by AG-modifying enzymes, which often have overlapping activities. Several putative AG-modifying enzymes are encoded in the genome of M. abscessus . The aim of this study was to investigate the molecular basis underlying AG resistance in M. abscessus . Methods M. abscessus deletion mutants deficient in one of three genes potentially involved in AG resistance, aac(2 ' ) , eis1 and eis2 , were generated by targeted gene inactivation, as were combinatorial double and triple deletion mutants. MICs were determined to study susceptibility to a variety of AG drugs and to capreomycin. Results Deletion of aac(2 ' ) increased susceptibility of M. abscessus to kanamycin B, tobramycin, dibekacin and gentamicin C. Deletion of eis2 increased susceptibility to capreomycin, hygromycin B, amikacin and kanamycin B. Deletion of eis1 did not affect drug susceptibility. Equally low MICs of apramycin, arbekacin, isepamicin and kanamycin A for WT and mutant strains indicate that these drugs are not inactivated by either AAC(2 ' ) or Eis enzymes. Conclusions M. abscessus expresses two distinct AG resistance determinants, AAC(2 ' ) and Eis2, which confer clinically relevant drug resistance.
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Affiliation(s)
- Anna Rominski
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Petra Selchow
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Katja Becker
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Juliane K Brülle
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Michael Dal Molin
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Peter Sander
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland.,Nationales Zentrum für Mykobakterien, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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Liu QY, Han F, Pan LP, Jia HY, Li Q, Zhang ZD. Inflammation responses in patients with pulmonary tuberculosis in an intensive care unit. Exp Ther Med 2018; 15:2719-2726. [PMID: 29456674 PMCID: PMC5795479 DOI: 10.3892/etm.2018.5775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 08/18/2017] [Indexed: 01/05/2023] Open
Abstract
Pulmonary tuberculosis caused by Mycobacterium tuberculosis remains a global problem. Inflammatory responses are the primary characteristics of patients with pulmonary tuberculosis in intensive care units (ICU). The aim of the present study was to investigate the clinical importance of inflammatory cells and factors for patients with pulmonary tuberculosis in ICU. A total of 124 patients with pulmonary tuberculosis in ICU were recruited for the present study. The inflammatory responses in patients with pulmonary tuberculosis in ICU were examined by changes in inflammatory cells and factors in the serum. The results indicated that serum levels of lymphocytes, plasma cells, granulocytes and monocytes were increased in patients with pulmonary tuberculosis in ICU compared with healthy controls. The serum levels of inflammatory factors interleukin (IL)-1, IL-6, IL-10, IL-12, and IL-4 were upregulated in patients with pulmonary tuberculosis in ICU. Lower plasma concentrations of IL-2, IL-15 and interferon-γ were detected in patients with pulmonary tuberculosis compared with healthy controls. It was demonstrated that high mobility group box-1 protein expression levels were higher in the serum of patients with pulmonary tuberculosis compared with healthy controls. Notably, an imbalance of T-helper cell (Th)1/Th2 cytokines was observed in patients with pulmonary tuberculosis. Pulmonary tuberculosis caused by M. tuberculosis also upregulated expression of matrix metalloproteinase (MMP)-1 and MMP-9 in hPMCs. In conclusion, these outcomes demonstrated that inflammatory responses and inflammatory factors are associated with the progression of pulmonary tuberculosis, suggesting that inhibition of inflammatory responses and inflammatory factors may be beneficial for the treatment of patients with pulmonary tuberculosis in ICU.
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Affiliation(s)
- Qiu-Yue Liu
- Department of Tuberculosis, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
| | - Fen Han
- Intensive Care Unit, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
| | - Li-Ping Pan
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
| | - Hong-Yan Jia
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
| | - Qi Li
- Department of Tuberculosis, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
| | - Zong-De Zhang
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing 101149, P.R. China
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Malikanti R, Vadija R, Veeravarapu H, Mustyala KK, Malkhed V, Vuruputuri U. Identification of small molecular ligands as potent inhibitors of fatty acid metabolism in Mycobacterium tuberculosis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.08.090] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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van Elsland DM, Bos E, de Boer W, Overkleeft HS, Koster AJ, van Kasteren SI. Detection of bioorthogonal groups by correlative light and electron microscopy allows imaging of degraded bacteria in phagocytes. Chem Sci 2016; 7:752-758. [PMID: 28791116 PMCID: PMC5529995 DOI: 10.1039/c5sc02905h] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/21/2015] [Indexed: 01/07/2023] Open
Abstract
The interaction between parasites and phagocytic immune cells is a key inter-species interaction in biology. Normally, phagocytosis results in the killing of invaders, but obligate intracellular parasites hijack the pathway to ensure their survival and replication. The in situ study of these parasites in the phagocytic pathway is very difficult, as genetic modification is often complicated and, if successful, only allows the tracking of pathogen phagocytosis up until the degradation of the engineered reporter constructs. Here we combine bioorthogonal chemistry with correlative light-electron microscopy (CLEM) to follow bacterial processing in the phagolysosomal system. Labelled bacteria are produced using bioorthogonal non-canonical amino tagging (BONCAT), precluding the need for any genetic modification. The bacterial proteome - even during degradation - was then visualised using a novel CLEM-based approach. This allowed us to obtain high resolution information about the subcellular location of the degrading bacteria, even after the proteolytic degradation of reporter constructs. To further explore the potential of CLEM-based imaging of bioorthogonal functionalities, azide-labelled glycans were imaged by this same approach, as well as active-subpopulations of enzymes using a 2-step activity-based protein profiling strategy.
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Affiliation(s)
- Daphne M van Elsland
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Erik Bos
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Wouter de Boer
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Herman S Overkleeft
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
| | - Abraham J Koster
- Department of Molecular Cell Biology , Section Electron Microscopy , Leiden University Medical Center , Leiden , The Netherlands .
| | - Sander I van Kasteren
- Division of Bio-organic Synthesis , Leiden Institute of Chemistry , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands .
- Institute for Chemical Immunology , Gorlaeus Laboratories , Leiden University , Leiden , The Netherlands
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Gopinath K, Warner DF, Mizrahi V. Targeted gene knockout and essentiality testing by homologous recombination. Methods Mol Biol 2015; 1285:131-149. [PMID: 25779314 DOI: 10.1007/978-1-4939-2450-9_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
This chapter provides an updated experimental protocol for generating allelic exchange mutants of mycobacteria by two-step selection using the p2NIL/pGOAL system. The types of mutants that can be generated using this approach are targeted gene knockouts marked with a drug resistance gene, unmarked deletion mutants, or strains in which a point mutation/s has been introduced into the target gene. A method for assessing the essentiality of a gene for mycobacterial growth by means of allelic exchange is also described. This method, which utilizes a merodiploid strain carrying a second copy of the gene of interest on an integration vector, allows the exploration by means of complement switching of structure-function relationships in proteins that are essential for mycobacterial growth.
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Affiliation(s)
- Krishnamoorthy Gopinath
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit and DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Hyper-attenuated MTBVAC erp mutant protects against tuberculosis in mice. Vaccine 2014; 32:5192-7. [PMID: 25066740 DOI: 10.1016/j.vaccine.2014.07.047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/23/2014] [Accepted: 07/15/2014] [Indexed: 11/23/2022]
Abstract
Safety of individuals at risk of immune suppression is an important concern for live vaccines. The new-generation tuberculosis vaccine candidate MTBVAC, a genetically engineered doubly attenuated Mycobacterium tuberculosis mutant with deletions in phoP and fadD26 virulence genes has demonstrated comparable safety in different relevant animal models and superior protection in mice as compared to the only currently licensed tuberculosis vaccine Mycobacterium bovis BCG. Here we describe the construction of a highly attenuated MTBVAC-based live vaccine by an additional gene inactivation generated in erp of MTBVAC. The gene product of erp is an exported repeated protein (Erp), a virulence factor described to be involved in intracellular replication of M. tuberculosis. The resultant strain, MTBVAC erp(-), was tested in severe combined immunodeficiency (SCID) mouse model showing to be severely attenuated when compared to BCG and MTBVAC. Experiments conducted in immunocompetent mice revealed that the hyper-attenuated profile observed with MTBVAC erp(-) strain did not compromise its protective efficacy profile in comparison with BCG. These results postulate MTBVAC erp(-) as a potential tuberculosis vaccine candidate for use in high-risk populations of immune suppression (e.g., due to HIV infection), where the use of BCG is not recommended.
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Mustyala KK, Malkhed V, Potlapally SR, Chittireddy VR, Vuruputuri U. Macromolecular structure and interaction studies of SigF and Usfx inMycobacterium tuberculosis. J Recept Signal Transduct Res 2014; 34:162-73. [DOI: 10.3109/10799893.2013.868903] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Stucki D, Gagneux S. Single nucleotide polymorphisms in Mycobacterium tuberculosis and the need for a curated database. Tuberculosis (Edinb) 2012; 93:30-9. [PMID: 23266261 DOI: 10.1016/j.tube.2012.11.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 11/25/2012] [Indexed: 12/12/2022]
Abstract
Recent advances in DNA sequencing have led to the discovery of thousands of single nucleotide polymorphisms (SNPs) in clinical isolates of Mycobacterium tuberculosis complex (MTBC). This genetic variation has changed our understanding of the differences and phylogenetic relationships between strains. Many of these mutations can serve as phylogenetic markers for strain classification, while others cause drug resistance. Moreover, SNPs can affect the bacterial phenotype in various ways, which may have an impact on the outcome of tuberculosis (TB) infection and disease. Despite the importance of SNPs for our understanding of the diversity of MTBC populations, the research community currently lacks a comprehensive, well-curated and user-friendly database dedicated to SNP data. First attempts to catalogue and annotate SNPs in MTBC have been made, but more work is needed. In this review, we discuss the biological and epidemiological relevance of SNPs in MTBC. We then review some of the analytical challenges involved in processing SNP data, and end with a list of features, which should be included in a new SNP database for MTBC.
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Affiliation(s)
- David Stucki
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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