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Getahun M, Beyene D, Mollalign H, Diriba G, Tesfaye E, Yenew B, Taddess M, Sinshaw W, Ameni G. Population structure and spatial distribution of Mycobacterium tuberculosis in Ethiopia. Sci Rep 2024; 14:10455. [PMID: 38714745 PMCID: PMC11076284 DOI: 10.1038/s41598-024-59435-3] [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: 12/21/2023] [Accepted: 04/10/2024] [Indexed: 05/10/2024] Open
Abstract
Ethiopia is one of the countries with a high tuberculosis (TB) burden, yet little is known about the spatial distribution of Mycobacterium tuberculosis (Mtb) lineages. This study identifies the spoligotyping of 1735 archived Mtb isolates from the National Drug Resistance Survey, collected between November 2011 and June 2013, to investigate Mtb population structure and spatial distribution. Spoligotype International Types (SITs) and lineages were retrieved from online databases. The distribution of lineages was evaluated using Fisher's exact test and logistic regression models. The Global Moran's Index and Getis-Ord Gi statistic were utilized to identify hotspot areas. Our results showed that spoligotypes could be interpreted and led to 4 lineages and 283 spoligotype patterns in 91% of the isolates, including 4% of those with multidrug/rifampicin resistance (MDR/RR) TB. The identified Mtb lineages were lineage 1 (1.8%), lineage 3 (25.9%), lineage 4 (70.6%) and lineage 7 (1.6%). The proportion of lineages 3 and 4 varied by regions, with lineage 3 being significantly greater than lineage 4 in reports from Gambella (AOR = 4.37, P < 0.001) and Tigray (AOR = 3.44, P = 0.001) and lineage 4 being significantly higher in Southern Nations Nationalities and Peoples Region (AOR = 1.97, P = 0.026) than lineage 3. Hotspots for lineage 1 were located in eastern Ethiopia, while a lineage 7 hotspot was identified in northern and western Ethiopia. The five prevalent spoligotypes, which were SIT149, SIT53, SIT25, SIT37 and SIT26 account for 42.8% of all isolates under investigation, while SIT149, SIT53 and SIT21 account for 52-57.8% of drug-resistant TB cases. TB and drug resistant TB are mainly caused by lineages 3 and 4, and significant proportions of the prevalent spoligotypes also influence drug-resistant TB and the total TB burden. Regional variations in lineages may result from both local and cross-border spread.
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Affiliation(s)
- Muluwork Getahun
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia.
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hilina Mollalign
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Getu Diriba
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Ephrem Tesfaye
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Mengistu Taddess
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
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2
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Folliero V, Ferravante C, Iovane V, Salvati A, Crescenzo L, Perna R, Corvino G, Della Rocca MT, Panetta V, Tranfa A, Greco G, Baldoni T, Pagnini U, Finamore E, Giurato G, Nassa G, Coppola M, Atripaldi L, Greco R, D'Argenio A, Foti MG, Abate R, Del Giudice A, Sarnelli B, Weisz A, Iovane G, Pinto R, Franci G, Galdiero M. Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region. Sci Data 2024; 11:220. [PMID: 38374088 PMCID: PMC10876956 DOI: 10.1038/s41597-024-03032-6] [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: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018-2021, obtained from the analysis of whole genome sequence. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB, 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB. This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of this disease.
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Affiliation(s)
- Veronica Folliero
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carlo Ferravante
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy
| | - Annamaria Salvati
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Laura Crescenzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Rossella Perna
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Giusy Corvino
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Maria T Della Rocca
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Vittorio Panetta
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Alessandro Tranfa
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Giuseppe Greco
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Teresa Baldoni
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Ugo Pagnini
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Emiliana Finamore
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Giovanni Nassa
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | | | - Luigi Atripaldi
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Rita Greco
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Annamaria D'Argenio
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Maria Grazia Foti
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Rosamaria Abate
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | | | - Bruno Sarnelli
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Renato Pinto
- UOD Prevenzione e Sanità Pubblica Veterinaria, Direzione Generale Tutela della Salute - Regione Campania, Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy.
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy.
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy.
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Bermúdez-Hernández GA, Pérez-Martínez D, Ortiz-León MC, Muñiz-Salazar R, Licona-Cassani C, Zenteno-Cuevas R. Mutational Dynamics Related to Antibiotic Resistance in M. tuberculosis Isolates from Serial Samples of Patients with Tuberculosis and Type 2 Diabetes Mellitus. Microorganisms 2024; 12:324. [PMID: 38399727 PMCID: PMC10892438 DOI: 10.3390/microorganisms12020324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/05/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Genetic variation in tuberculosis is influenced by the host environment, patients with comorbidity, and tuberculosis-type 2 diabetes mellitus (TB-T2DM) and implies a higher risk of treatment failure and development of drug resistance. Considering the above, this study aimed to evaluate the influence of T2DM on the dynamic of polymorphisms related to antibiotic resistance in TB. Fifty individuals with TB-T2DM and TB were initially characterized, and serial isolates of 29 of these individuals were recovered on day 0 (diagnosis), 30, and 60. Genomes were sequenced, variants related to phylogeny and drug resistance analyzed, and mutation rates calculated and compared between groups. Lineage X was predominant. At day 0 (collection), almost all isolates from the TB group were sensitive, apart from four isolates from the TB-T2DM group showing the mutation katG S315T, from which one isolate had the mutations rpoB S450L, gyrA A90G, and gyrA D94G. This pattern was observed in a second isolate at day 30. The results provide a first overview of the dynamics of mutations in resistance genes from individuals with TB-T2DM, describing an early development of resistance to isoniazid and a rapid evolution of resistance to other drugs. Although preliminary, these results help to explain the increased risk of drug resistance in individuals with TB and T2DM.
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Affiliation(s)
- Gustavo A. Bermúdez-Hernández
- Biomedical Sciences Doctoral Program, Institute of Health Sciences, University of Veracruz, Xalapa 91190, Veracruz, Mexico;
| | - Damián Pérez-Martínez
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
| | - Maria Cristina Ortiz-León
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
| | - Raquel Muñiz-Salazar
- School of Health Sciences, Autonomous University of Baja California, Ensenada 22860, Baja California, Mexico;
| | - Cuauhtemoc Licona-Cassani
- Monterrey Institute of Technology, School of Engineering and Sciences, Monterrey 64700, Nuevo León, Mexico;
| | - Roberto Zenteno-Cuevas
- Institute of Public Health, University of Veracruz, Xalapa 91190, Veracruz, Mexico; (D.P.-M.); (M.C.O.-L.)
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Granados-Tristán AL, Hernández-Luna CE, González-Escalante LA, Camacho-Moll ME, Silva-Ramírez B, Bermúdez de León M, Peñuelas-Urquides K. ESX-3 secretion system in Mycobacterium: An overview. Biochimie 2024; 216:46-55. [PMID: 37879428 DOI: 10.1016/j.biochi.2023.10.013] [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: 04/17/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 10/27/2023]
Abstract
Mycobacteria are microorganisms distributed in the environment worldwide, and some of them, such as Mycobacterium tuberculosis or M. leprae, are pathogenic. The hydrophobic mycobacterial cell envelope has low permeation and bacteria need to export products across their structure. Mycobacteria possess specialized protein secretion systems, such as the Early Secretory Antigenic Target 6 secretion (ESX) system. Five ESX loci have been described in M. tuberculosis, called ESX-1 to ESX-5. The ESX-3 secretion system has been associated with mycobacterial metabolism and growth. The locus of this system is highly conserved across mycobacterial species. Metallo-proteins regulate negative ESX-3 transcription in high conditions of iron and zinc. Moreover, this secretion system is part of an antioxidant regulatory pathway linked to Zinc. EccA3, EccB3, EccC3, EccD3, and EccE3 are components of the ESX-3 secretion machinery, whereas EsxG-EsxH, PE5-PPE4, and PE15-PPE20 are proteins secreted by this system. In addition, EspG3 and MycP3 are complementary proteins involved in transport and proteolysis respectively. This system is associated to mycobacterial virulence by releasing the bacteria from the phagosome and inhibiting endomembrane damage response. Furthermore, components of this system inhibit the host immune response by reducing the recognition of M. tuberculosis-infected cells. The components of the ESX-3 secretion system play a role in drug resistance and cell wall integrity. Moreover, the expression data of this system indicated that external and internal factors affect ESX-3 locus expression. This review provides an overview of new findings on the ESX-3 secretion system, its regulation, expression, and functions.
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Affiliation(s)
- Ana Laura Granados-Tristán
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico; Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Carlos Eduardo Hernández-Luna
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, 66455, Nuevo León, Mexico.
| | - Laura Adiene González-Escalante
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey, 64720, Nuevo León, Mexico.
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Mvubu NE, Jacoby K. Mycobacterium tuberculosis complex molecular networks and their regulation: Implications of strain heterogeneity on epigenetic diversity and transcriptome regulation. Heliyon 2023; 9:e22611. [PMID: 38046135 PMCID: PMC10686871 DOI: 10.1016/j.heliyon.2023.e22611] [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: 01/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tuberculosis has been a public health crisis since the 1900, which has caused the highest mortalities due to a single bacterial infection worldwide, that was recently further complicated by the Coronavirus disease 2019 pandemic. The causative agent of Tuberculosis, Mycobacterium tuberculosis, belongs to a genetically well-characterized family of strains known as the Mycobacterium tuberculosis complex, which has complicated progress made towards eradicating Tuberculosis due to pathogen-specific phenotypic differences in the members of this complex. Mycobacterium tuberculosis complex strains are genetically diverse human- and animal-adapted pathogens belonging to 7 lineages (Indo-Oceanic, East-Asian, East-African Indian, Euro-American, M. africanum West Africa 1, M. africanum West Africa 2 and Ethopia), respectively and the recently identified Lineage 8 and M. africanum Lineage 9. Genomic studies have revealed that Mycobacterium tuberculosis complex members are ∼99 % similar, however, due to selective pressure and adaptation to human host, they are prone to mutations that have resulted in development of drug resistance and phenotypic heterogeneity that impact strain virulence. Furthermore, members of the Mycobacterium tuberculosis complex have preferred geographic locations and possess unique phenotypic characteristics that is linked to their pathogenicity. Due to the recent advances in development next generation sequencing platforms, several studies have revealed epigenetic changes in genomic regions combined with "unique" gene regulatory mechanisms through non-coding RNAs that are responsible for strain-specific behaviour on in vitro and in vivo infection models. The current review provides up to date epigenetic patterns, gene regulation through non-coding RNAs, together with implications of these mechanisms in down-stream proteome and metabolome, which may be responsible for "unique" responses to infection by members of the Mycobacterium tuberculosis complex. Understanding lineage-specific molecular mechanisms during infection may provide novel drug targets and disease control measures towards World Health organization END-TB strategy.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Kieran Jacoby
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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Kenarkoohi A, Abdoli A, Rostamzad A, Rashnavadi M, Naserifar R, Abdi J, Shams M, Bozorgomid A, Saeb S, Al-Fahad D, Khezri K, Falahi S. Presence of CRISPR CAS-Like Sequences as a Proposed Mechanism for Horizontal Genetic Exchanges between Trichomonas vaginalis and Its Associated Virus: A Comparative Genomic Analysis with the First Report of a Putative CRISPR CAS Structures in Eukaryotic Cells. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8069559. [PMID: 38058394 PMCID: PMC10696477 DOI: 10.1155/2023/8069559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/04/2023] [Accepted: 09/07/2023] [Indexed: 12/08/2023]
Abstract
Introduction Trichomonas vaginalis genome is among the largest genome size and coding capacities. Combinations of gene duplications, transposon, repeated sequences, and lateral gene transfers (LGTs) have contributed to the unexpected large genomic size and diversity. This study is aimed at investigating genomic exchange and seeking for presence of the CRISPR CAS system as one of the possible mechanisms for some level of genetic exchange. Material and Methods. In this comparative analysis, 398 publicly available Trichomonas vaginalis complete genomes were investigated for the presence of CRISPR CAS. Spacer sequences were also analyzed for their origin using BLAST. Results We identified a CRISPR CAS (Cas3). CRISPR spacers are highly similar to transposable genetic elements such as viruses of protozoan parasites, especially megavirals, some transposons, and, interestingly, papillomavirus and HIV-1 in a few cases. Discussion. There is a striking similarity between the prokaryotes/Archaean CRISPR and what we find as eukaryotic CRISPR. About 5-10% of the 398 T. vaginalis possess a CRISPR structure. Conclusion According to sequences and their organization, we assume that these repeated sequences and spacer, along with their mentioned features, could be the eukaryotic homolog of prokaryotes and Archaean CRISPR systems and may involve in a process similar to the CRISPR function.
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Affiliation(s)
- Azra Kenarkoohi
- Department of Laboratory Sciences, School of Allied Medical Sciences, Iran
- Department of Microbiology, Faculty of Medicine, Ilam University of Medical Sciences, Ilam, Iran
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Amir Abdoli
- Zoonoses Research Centre, Jahrom University of Medical Sciences, Jahrom, Iran
| | - Arman Rostamzad
- Department of Biology, Faculty of Sciences, Ilam University, Ilam, Iran
| | | | - Razi Naserifar
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Jahangir Abdi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Morteza Shams
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Arezoo Bozorgomid
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepideh Saeb
- Qaen School of Nursing and Midwifery, Birjand University of Medical Sciences, Birjand, Iran
| | - Dhurgham Al-Fahad
- Pharmaceutical Department, College of Pharmacy, University of Thi-Qar, Iraq
| | - Kosar Khezri
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Shahab Falahi
- Zoonotic Diseases Research Center, Ilam University of Medical Sciences, Ilam, Iran
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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8
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Zein-Eddine R, Refrégier G, Cervantes J, Yokobori NK. The future of CRISPR in Mycobacterium tuberculosis infection. J Biomed Sci 2023; 30:34. [PMID: 37245014 DOI: 10.1186/s12929-023-00932-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Clustered Regularly Interspaced Short Palindromic repeats (CRISPR)-Cas systems rapidly raised from a bacterial genetic curiosity to the most popular tool for genetic modifications which revolutionized the study of microbial physiology. Due to the highly conserved nature of the CRISPR locus in Mycobacterium tuberculosis, the etiological agent of one of the deadliest infectious diseases globally, initially, little attention was paid to its CRISPR locus, other than as a phylogenetic marker. Recent research shows that M. tuberculosis has a partially functional Type III CRISPR, which provides a defense mechanism against foreign genetic elements mediated by the ancillary RNAse Csm6. With the advent of CRISPR-Cas based gene edition technologies, our possibilities to explore the biology of M. tuberculosis and its interaction with the host immune system are boosted. CRISPR-based diagnostic methods can lower the detection threshold to femtomolar levels, which could contribute to the diagnosis of the still elusive paucibacillary and extrapulmonary tuberculosis cases. In addition, one-pot and point-of-care tests are under development, and future challenges are discussed. We present in this literature review the potential and actual impact of CRISPR-Cas research on human tuberculosis understanding and management. Altogether, the CRISPR-revolution will revitalize the fight against tuberculosis with more research and technological developments.
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Affiliation(s)
- Rima Zein-Eddine
- Laboratoire d'Optique et Biosciences (LOB), Ecole Polytechnique, Route de Saclay 91120, Palaiseau, France
| | - Guislaine Refrégier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique et Evolution, 91190, Gif-Sur-Yvette, France
| | - Jorge Cervantes
- Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX, 79905, USA
| | - Noemí Kaoru Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas (INEI)-ANLIS and CONICET, C1282AFF, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
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Conceição EC, da Conceição ML, Marcon DJ, Loubser J, Andrade GL, da Silva SP, Cruz ACR, Sharma A, Suffys P, Lima KVB. Genomic Diversity of the Rarely Observed Genotype of the Mycobacterium tuberculosis Central Asian (CAS) Lineage 3 from North Brazil. Microorganisms 2023; 11:microorganisms11010132. [PMID: 36677424 PMCID: PMC9862801 DOI: 10.3390/microorganisms11010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) Central Asian Strain (CAS) Lineage 3 (L3) genotype is predominantly found in East-Africa, Central-Asia, Western-Asia, and South-Asia; however, a new spoligotyping CAS/SIT2545 was found in northern regions of Brazil. We aimed to characterize and describe the genetic diversity and perform a phylogenetic assessment of this novel genotype. We performed 24-MIRU-VNTR loci and Whole-genome sequencing (WGS) of six Brazilian isolates previously spoligotyped. The libraries were prepared using a Nextera-XT kit and sequenced in a NextSeq 550 Illumina instrument. We performed lineage assignment and genomic characterization. From publicly available genomes of Mtb L3 and other lineages, we created a robust dataset to run the MTBSeq pipeline and perform a phylogenetic analysis. MIRU-VNTR and WGS confirmed CAS/SIT2545 belongs to L3. Out of 1691 genomes, 1350 (79.83%) passed in quality control (genomic coverage > 95%). Strain 431 differed in 52 single nucleotide variants (SNV), confirming it does not belong to the same transmission chain. The eight genomes from a global dataset clustered closer to Brazilian strains differed in >52 SNVs. We hypothesized L3 and L1 were introduced in Brazilian Northern in the same historical event; however, there is a need for additional studies exploring the genetic diversity of Mtb Brazilian Northern.
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Affiliation(s)
- Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town P.O. Box 241, South Africa
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Correspondence:
| | | | - Davi Josué Marcon
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Centro de Genômica e Biologia de Sistemas, Universidade Federal do Pará, Belém 66075-110, PA, Brazil
| | - Johannes Loubser
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town P.O. Box 241, South Africa
| | - Gabrielly Leite Andrade
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Departamento de Medicina, Centro Universitário do Pará—CESUPA, Belém 66613-903, PA, Brazil
| | - Sandro Patroca da Silva
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
| | - Ana Cecília Ribeiro Cruz
- Seção de Arbovírus e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
| | - Abhinav Sharma
- Faculty of Engineering and Technology, Liverpool John Moores University (LJMU), Liverpool L35UX, UK
- Seqera Labs, 08005 Bacelona, Spain
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactéria, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, RJ, Brazil
| | - Karla Valéria Batista Lima
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua 67030-000, PA, Brazil
- Programa de Pós-graduação Biologia Parasitária na Amazônia, Universidade do Estado do Pará, Belém 66087-670, PA, Brazil
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10
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Thakur M, Muniyappa K. Macrophage activation highlight an important role for NER proteins in the survival, latency and multiplication of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2023; 138:102284. [PMID: 36459831 DOI: 10.1016/j.tube.2022.102284] [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: 08/15/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Nucleotide excision repair (NER) is one of the most extensively studied DNA repair processes in both prokaryotes and eukaryotes. The NER pathway is a highly conserved, ATP-dependent multi-step process involving several proteins/enzymes that function in a concerted manner to recognize and excise a wide spectrum of helix-distorting DNA lesions and bulky adducts by nuclease cleavage on either side of the damaged bases. As such, the NER pathway of Mycobacterium tuberculosis (Mtb) is essential for its survival within the hostile environment of macrophages and disease progression. This review focuses on present published knowledge about the crucial roles of Mtb NER proteins in the survival and multiplication of the pathogen within the macrophages and as potential targets for drug discovery.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
| | - K Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
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11
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Moopanar K, Nyide ANG, Senzani S, Mvubu NE. Clinical strains of Mycobacterium tuberculosis exhibit differential lipid metabolism-associated transcriptome changes in in vitro cholesterol and infection models. Pathog Dis 2022; 81:6889515. [PMID: 36509392 PMCID: PMC9936260 DOI: 10.1093/femspd/ftac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/30/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Many studies have identified host-derived lipids, characterised by the abundance of cholesterol, as a major source of carbon nutrition for Mycobacterium tuberculosis during infection. Members of the Mycobacterium tuberculosis complex are biologically different with regards to degree of disease, host range, pathogenicity and transmission. Therefore, the current study aimed at elucidating transcriptome changes during early infection of pulmonary epithelial cells and on an in vitro cholesterol-rich minimal media, in M. tuberculosis clinical strains F15/LAM4/KZN and Beijing, and the laboratory H37Rv strain. Infection of pulmonary epithelial cells elicited the upregulation of fadD28 and hsaC in both the F15/LAM4/KZN and Beijing strains and the downregulation of several other lipid-associated genes. Growth curve analysis revealed F15/LAM4/KZN and Beijing to be slow growers in 7H9 medium and cholesterol-supplemented media. RNA-seq analysis revealed strain-specific transcriptomic changes, thereby affecting different metabolic processes in an in vitro cholesterol model. The differential expression of these genes suggests that the genetically diverse M. tuberculosis clinical strains exhibit strain-specific behaviour that may influence their ability to metabolise lipids, specifically cholesterol, which may account for phenotypic differences observed during infection.
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Affiliation(s)
- Kynesha Moopanar
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Asanda Nomfundo Graduate Nyide
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Sibusiso Senzani
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st floor, Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - Nontobeko Eunice Mvubu
- Corresponding author. Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa.Tel: +27 31 260 7404; E-mail:
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12
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Berube BJ, Larsen SE, McNeil MB, Reese VA, Pecor T, Kaur S, Parish T, Baldwin SL, Coler RN. Characterizing in vivo loss of virulence of an HN878 Mycobacterium tuberculosis isolate from a genetic duplication event. Tuberculosis (Edinb) 2022; 137:102272. [PMID: 36375278 PMCID: PMC10019580 DOI: 10.1016/j.tube.2022.102272] [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: 07/15/2022] [Revised: 10/21/2022] [Accepted: 10/28/2022] [Indexed: 11/13/2022]
Abstract
The increase of global cases of drug resistant (DR) Mycobacterium tuberculosis (M.tb) is a serious problem for the tuberculosis research community and the goals to END TB by 2030. Due to the need for advancing and screening next generation therapeutics and vaccines, we aimed to design preclinical DR models of Beijing lineage M.tb HN878 strain in different mouse backgrounds. We found escalating sensitivities of morbidity due to low dose aerosol challenge (50-100 bacilli) in CB6F1, C57BL/6 and SWR mice, respectively. We also observed that pulmonary bacterial burden at morbidity endpoints correlated inversely with survival over time between mouse strains. Interestingly, with in vitro passaging and in the process of selecting individual DR mutant colonies, we observed a significant decrease in in vivo HN878 strain virulence, which correlated with the acquisition of a large genetic duplication. We confirmed that low passage infection stocks with no or low prevalence of the duplication, including stocks directly acquired from the BEI resources biorepository, retained virulence, measured by morbidity over time. These data help confirm previous reports and emphasize the importance of monitoring virulence and stock fidelity.
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Affiliation(s)
- Bryan J Berube
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Sasha E Larsen
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Matthew B McNeil
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA
| | - Valerie A Reese
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tiffany Pecor
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Suhavi Kaur
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Tanya Parish
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Susan L Baldwin
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA
| | - Rhea N Coler
- Seattle Children's Research Institute, Center for Global Infectious Disease Research, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA.
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13
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Heyckendorf J, Georghiou SB, Frahm N, Heinrich N, Kontsevaya I, Reimann M, Holtzman D, Imperial M, Cirillo DM, Gillespie SH, Ruhwald M. Tuberculosis Treatment Monitoring and Outcome Measures: New Interest and New Strategies. Clin Microbiol Rev 2022; 35:e0022721. [PMID: 35311552 PMCID: PMC9491169 DOI: 10.1128/cmr.00227-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Despite the advent of new diagnostics, drugs and regimens, tuberculosis (TB) remains a global public health threat. A significant challenge for TB control efforts has been the monitoring of TB therapy and determination of TB treatment success. Current recommendations for TB treatment monitoring rely on sputum and culture conversion, which have low sensitivity and long turnaround times, present biohazard risk, and are prone to contamination, undermining their usefulness as clinical treatment monitoring tools and for drug development. We review the pipeline of molecular technologies and assays that serve as suitable substitutes for current culture-based readouts for treatment response and outcome with the potential to change TB therapy monitoring and accelerate drug development.
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Affiliation(s)
- Jan Heyckendorf
- Department of Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | | | - Nicole Frahm
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, USA
| | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, Medical Centre of the University of Munich (LMU), Munich, Germany
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Maja Reimann
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), Braunschweig, Germany
- International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - David Holtzman
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
| | - Marjorie Imperial
- University of California San Francisco, San Francisco, California, USA, United States
| | - Daniela M. Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stephen H. Gillespie
- School of Medicine, University of St Andrewsgrid.11914.3c, St Andrews, Fife, Scotland
| | - Morten Ruhwald
- FIND, the Global Alliance for Diagnostics, Geneva, Switzerland
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14
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
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15
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Thakur M, Parulekar RS, Barale SS, Sonawane KD, Muniyappa K. Interrogating the substrate specificity landscape of UvrC reveals novel insights into its non-canonical function. Biophys J 2022; 121:3103-3125. [PMID: 35810330 PMCID: PMC9463653 DOI: 10.1016/j.bpj.2022.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/23/2022] [Accepted: 07/07/2022] [Indexed: 11/29/2022] Open
Abstract
Although it is relatively unexplored, accumulating data highlight the importance of tripartite crosstalk between nucleotide excision repair (NER), DNA replication, and recombination in the maintenance of genome stability; however, elucidating the underlying mechanisms remains challenging. While Escherichia coli uvrA and uvrB can fully complement polAΔ cells in DNA replication, uvrC attenuates this alternative DNA replication pathway, but the exact mechanism by which uvrC suppresses DNA replication is unknown. Furthermore, the identity of bona fide canonical and non-canonical substrates for UvrCs are undefined. Here, we reveal that Mycobacterium tuberculosis UvrC (MtUvrC) strongly binds to, and robustly cleaves, key intermediates of DNA replication/recombination as compared with the model NER substrates. Notably, inactivation of MtUvrC ATPase activity significantly attenuated its endonuclease activity, thus suggesting a causal link between these two functions. We built an in silico model of the interaction of MtUvrC with the Holliday junction (HJ), using a combination of homology modeling, molecular docking, and molecular dynamic simulations. The model predicted residues that were potentially involved in HJ binding. Six of these residues were mutated either singly or in pairs, and the resulting MtUvrC variants were purified and characterized. Among them, residues Glu595 and Arg597 in the helix-hairpin-helix motif were found to be crucial for the interaction between MtUvrC and HJ; consequently, mutations in these residues, or inhibition of ATP hydrolysis, strongly abrogated its DNA-binding and endonuclease activities. Viewed together, these findings expand the substrate specificity landscape of UvrCs and provide crucial mechanistic insights into the interplay between NER and DNA replication/recombination.
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Affiliation(s)
- Manoj Thakur
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
| | | | - Sagar S Barale
- Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kailas D Sonawane
- Department of Microbiology, Shivaji University, Kolhapur, India; Structural Bioinformatics Unit, Shivaji University, Kolhapur, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India.
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16
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Welekidan LN, Yimer SA, Skjerve E, Dejene TA, Homberset H, Tønjum T, Brynildsrud O. Whole Genome Sequencing of Drug Resistant and Drug Susceptible Mycobacterium tuberculosis Isolates From Tigray Region, Ethiopia. Front Microbiol 2021; 12:743198. [PMID: 34938276 PMCID: PMC8685502 DOI: 10.3389/fmicb.2021.743198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Tuberculosis, mainly caused by Mycobacterium tuberculosis (Mtb), is an ancient human disease that gravely affects millions of people annually. We wanted to explore the genetic diversity and lineage-specific association of Mtb with drug resistance among pulmonary tuberculosis patients. Methods: Sputum samples were collected from pulmonary tuberculosis patients at six different healthcare institutions in Tigray, Ethiopia, between July 2018 and August 2019. DNA was extracted from 74 Mtb complex isolates for whole-genome sequencing (WGS). All genomes were typed and screened for mutations with known associations with antimicrobial resistance using in silico methods, and results were cross-verified with wet lab methods. Results: Lineage (L) 4 (55.8%) was predominant, followed by L3 (41.2%); L1 (1.5%) and L2 (1.5%) occurred rarely. The most frequently detected sublineage was CAS (38.2%), followed by Ural (29.4%), and Haarlem (11.8%). The recent transmission index (RTI) was relatively low. L4 and Ural strains were more resistant than the other strains to any anti-TB drug (P < 0.05). The most frequent mutations to RIF, INH, EMB, SM, PZA, ETH, FLQs, and 2nd-line injectable drugs occurred at rpoB S450L, katG S315T, embB M306I/V, rpsL K43R, pncA V139A, ethA M1R, gyrA D94G, and rrs A1401G, respectively. Disputed rpoB mutations were also shown in four (16%) of RIF-resistant isolates. Conclusion: Our WGS analysis revealed the presence of diverse Mtb genotypes. The presence of a significant proportion of disputed rpoB mutations highlighted the need to establish a WGS facility at the regional level to monitor drug-resistant mutations. This will help control the transmission of DR-TB and ultimately contribute to the attainment of 100% DST coverage for TB patients as per the End TB strategy.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Solomon Abebe Yimer
- Coalition for Epidemic Preparedness Innovations, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Division of Biomedical Sciences, Department of Medical Microbiology and Immunology, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Håvard Homberset
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Unit for Genome Dynamics, Department of Microbiology, University of Oslo, Oslo, Norway.,Unit for Genome Dynamics, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Ola Brynildsrud
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway.,Norwegian Institute of Public Health, Oslo, Norway
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17
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Shi A, Broach JR. Microbial adaptive evolution. J Ind Microbiol Biotechnol 2021; 49:6407523. [PMID: 34673973 PMCID: PMC9118994 DOI: 10.1093/jimb/kuab076] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/27/2021] [Indexed: 01/08/2023]
Abstract
Bacterial species can adapt to significant changes in their environment by mutation followed by selection, a phenomenon known as “adaptive evolution.” With the development of bioinformatics and genetic engineering, research on adaptive evolution has progressed rapidly, as have applications of the process. In this review, we summarize various mechanisms of bacterial adaptive evolution, the technologies used for studying it, and successful applications of the method in research and industry. We particularly highlight the contributions of Dr. L. O. Ingram. Microbial adaptive evolution has significant impact on our society not only from its industrial applications, but also in the evolution, emergence, and control of various pathogens.
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Affiliation(s)
- Aiqin Shi
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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18
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Khoshnood S, Taki E, Sadeghifard N, Kaviar VH, Haddadi MH, Farshadzadeh Z, Kouhsari E, Goudarzi M, Heidary M. Mechanism of Action, Resistance, Synergism, and Clinical Implications of Delamanid Against Multidrug-Resistant Mycobacterium tuberculosis. Front Microbiol 2021; 12:717045. [PMID: 34690963 PMCID: PMC8529252 DOI: 10.3389/fmicb.2021.717045] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
Multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis (MTB) remain a primary global threat to the end of tuberculosis (TB) era. Delamanid (DLM) is a nitro-dihydro-imidazooxazole derivative utilized to treat MDR-TB. DLM has distinct mechanism of action, inhibiting methoxy- and keto-mycolic acid (MA) synthesis through the F420 coenzyme mycobacteria system and generating nitrous oxide. While DLM resistance among MTB strains is uncommon, there are increasing reports in Asia and Europe, and such resistance will prolong the treatment courses of patients infected with MDR-TB. In this review, we address the antimycobacterial properties of DLM, report the global prevalence of DLM resistance, discuss the synergism of DLM with other anti-TB drugs, and evaluate the documented clinical trials to provide new insights into the clinical use of this antibiotic.
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Affiliation(s)
- Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Elahe Taki
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Zahra Farshadzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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19
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Epidemiology of Mycobacterium tuberculosis lineages and strain clustering within urban and peri-urban settings in Ethiopia. PLoS One 2021; 16:e0253480. [PMID: 34252107 PMCID: PMC8274931 DOI: 10.1371/journal.pone.0253480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 06/06/2021] [Indexed: 11/25/2022] Open
Abstract
Background Previous work has shown differential predominance of certain Mycobacterium tuberculosis (M. tb) lineages and sub-lineages among different human populations in diverse geographic regions of Ethiopia. Nevertheless, how strain diversity is evolving under the ongoing rapid socio-economic and environmental changes is poorly understood. The present study investigated factors associated with M. tb lineage predominance and rate of strain clustering within urban and peri-urban settings in Ethiopia. Methods Pulmonary Tuberculosis (PTB) and Cervical tuberculous lymphadenitis (TBLN) patients who visited selected health facilities were recruited in the years of 2016 and 2017. A total of 258 M. tb isolates identified from 163 sputa and 95 fine-needle aspirates (FNA) were characterized by spoligotyping and compared with international M.tb spoligotyping patterns registered at the SITVIT2 databases. The molecular data were linked with clinical and demographic data of the patients for further statistical analysis. Results From a total of 258 M. tb isolates, 84 distinct spoligotype patterns that included 58 known Shared International Type (SIT) patterns and 26 new or orphan patterns were identified. The majority of strains belonged to two major M. tb lineages, L3 (35.7%) and L4 (61.6%). The observed high percentage of isolates with shared patterns (n = 200/258) suggested a substantial rate of overall clustering (77.5%). After adjusting for the effect of geographical variations, clustering rate was significantly lower among individuals co-infected with HIV and other concomitant chronic disease. Compared to L4, the adjusted odds ratio and 95% confidence interval (AOR; 95% CI) indicated that infections with L3 M. tb strains were more likely to be associated with TBLN [3.47 (1.45, 8.29)] and TB-HIV co-infection [2.84 (1.61, 5.55)]. Conclusion Despite the observed difference in strain diversity and geographical distribution of M. tb lineages, compared to earlier studies in Ethiopia, the overall rate of strain clustering suggests higher transmission and warrant more detailed investigations into the molecular epidemiology of TB and related factors.
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Nicholson KR, Mousseau CB, Champion MM, Champion PA. The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens. PLoS Pathog 2021; 17:e1009124. [PMID: 33411813 PMCID: PMC7790235 DOI: 10.1371/journal.ppat.1009124] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mycobacterial pathogens pose a sustained threat to human health. There is a critical need for new diagnostics, therapeutics, and vaccines targeting both tuberculous and nontuberculous mycobacterial species. Understanding the basic mechanisms used by diverse mycobacterial species to cause disease will facilitate efforts to design new approaches toward detection, treatment, and prevention of mycobacterial disease. Molecular, genetic, and biochemical approaches have been widely employed to define fundamental aspects of mycobacterial physiology and virulence. The recent expansion of genetic tools in mycobacteria has further increased the accessibility of forward genetic approaches. Proteomics has also emerged as a powerful approach to further our understanding of diverse mycobacterial species. Detection of large numbers of proteins and their modifications from complex mixtures of mycobacterial proteins is now routine, with efforts of quantification of these datasets becoming more robust. In this review, we discuss the “genetic proteome,” how the power of genetics, molecular biology, and biochemistry informs and amplifies the quality of subsequent analytical approaches and maximizes the potential of hypothesis-driven mycobacterial research. Published proteomics datasets can be used for hypothesis generation and effective post hoc supplementation to experimental data. Overall, we highlight how the integration of proteomics, genetic, molecular, and biochemical approaches can be employed successfully to define fundamental aspects of mycobacterial pathobiology.
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Affiliation(s)
- Kathleen R. Nicholson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - C. Bruce Mousseau
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
| | - Patricia A. Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame Indiana, United States of America
- * E-mail: (MMC); (PAC)
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