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Catana-Botello N, Becerril-Montes P, Castro-Garza J, González-Salazar F, Almanza-Reyes H, Del Bosque-Moncayo MDLÁ, Morales-Vargas A, Velázquez-Moreno VM. Mycobacterium tuberculosis Beijing in the State of Nuevo Leon, Mexico. Rev Argent Microbiol 2024:S0325-7541(24)00046-4. [PMID: 38942679 DOI: 10.1016/j.ram.2023.12.007] [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: 05/05/2023] [Revised: 11/16/2023] [Accepted: 12/31/2023] [Indexed: 06/30/2024] Open
Abstract
Tuberculosis remains a serious threat to human health as an infectious disease in Mexico. Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in the State of Nuevo Leon, Mexico are scarce. We aimed to determine the genotypes of circulating MTB belonging to the Beijing lineage recovered from patients in the State of Nuevo Leon, Mexico. A total of 406 MTB isolates from this state were genotyped using the spoligotyping method and 18-locus MIRU-VNTR. Lineage classification and MTB transmission analysis were performed. Based on the spoligotyping analysis, we found 24 strains belonging to the Beijing genotype that were characterized phylogenetically. The MIRUs showed greater discriminatory power than the standard RFLP-IS6110 method; therefore, the greatest allelic diversity among the Beijing strains was observed with MIRU10, MIRU31, MIRU39, MRU40, and MIRU 26. MVLA analysis showed a profile variation between Beijing and non-Beijing strains. The minimum spanning tree (MST) showed that 79% (19) of the strains are related. All Beijing strains exhibited the deletion of region TbD1, which is a characteristic of modern strains. The application of spoligotyping and MIRU-VNTR-18 methods together proved to be more sensitive, discriminatory, and rapid than the standard method for the epidemiological analysis of Mycobacterium Beijing isolates. This study is one of the first to describe the genomic diversity of M. Beijing in the State of Nuevo Leon, Mexico.
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Affiliation(s)
- Nohemí Catana-Botello
- Faculty of Biological Sciences, Autonomous University of Nuevo León, Ave. Pedro de Alba S/N, Niños Héroes, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León 64260, Mexico
| | - Pola Becerril-Montes
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico.
| | - Jorge Castro-Garza
- Secretary of Health of the State of Nuevo León, C. Mariano Matamoros 520, Nuevo León 64000, Mexico
| | - Francisco González-Salazar
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico; Health Sciences, University of Monterrey, Av. Ignacio Morones Prieto 4500 poniente, Col. Jesús M. Garza, San Pedro Garza García, Nuevo León 66238, Mexico.
| | - Horacio Almanza-Reyes
- Faculty of Medicine and Psychology, Autonomous University of Baja California, Universidad 14418, UABC, Parque Internacional Industrial Tijuana, Tijuana Baja California 22390, Mexico.
| | | | - Alejandro Morales-Vargas
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
| | - Víctor Manuel Velázquez-Moreno
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
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Tzfadia O, Gijsbers A, Vujkovic A, Snobre J, Vargas R, Dewaele K, Meehan CJ, Farhat M, Hakke S, Peters PJ, de Jong BC, Siroy A, Ravelli RBG. Single nucleotide variation catalog from clinical isolates mapped on tertiary and quaternary structures of ESX-1-related proteins reveals critical regions as putative Mtb therapeutic targets. Microbiol Spectr 2024:e0381623. [PMID: 38874407 DOI: 10.1128/spectrum.03816-23] [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: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 06/15/2024] Open
Abstract
Proteins encoded by the ESX-1 genes of interest are essential for full virulence in all Mycobacterium tuberculosis complex (Mtbc) lineages, the pathogens causing the highest mortality worldwide. Identifying critical regions in these ESX-1-related proteins could provide preventive or therapeutic targets for Mtb infection, the game changer needed for tuberculosis control. We analyzed a compendium of whole genome sequences of clinical Mtb isolates from all lineages from >32,000 patients and identified single nucleotide polymorphisms. When mutations corresponding to all non-synonymous single nucleotide polymorphisms were mapped on structural models of the ESX-1 proteins, fully conserved regions emerged. Some could be assigned to known quaternary structures, whereas others could be predicted to be involved in yet-to-be-discovered interactions. Some mutants had clonally expanded (found in >1% of the isolates); these mutants were mostly located at the surface of globular domains, remote from known intra- and inter-molecular protein-protein interactions. Fully conserved intrinsically disordered regions of proteins were found, suggesting that these regions are crucial for the pathogenicity of the Mtbc. Altogether, our findings highlight fully conserved regions of proteins as attractive vaccine antigens and drug targets to control Mtb virulence. Extending this approach to the whole Mtb genome as well as other microorganisms will enhance vaccine development for various pathogens. IMPORTANCE We mapped all non-synonymous single nucleotide polymorphisms onto each of the experimental and predicted ESX-1 proteins' structural models and inspected their placement. Varying sizes of conserved regions were found. Next, we analyzed predicted intrinsically disordered regions within our set of proteins, finding two putative long stretches that are fully conserved, and discussed their potential essential role in immunological recognition. Combined, our findings highlight new targets for interfering with Mycobacterium tuberculosis complex virulence.
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Affiliation(s)
- Oren Tzfadia
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Abril Gijsbers
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alexandra Vujkovic
- Clinical Virology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- ADReM Data Lab, University of Antwerp, Antwerp, Belgium
| | - Jihad Snobre
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Klaas Dewaele
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biosciences, Nottingham Trent University, Nottingham, United Kingdom
| | - Maha Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sneha Hakke
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Axel Siroy
- Unité de soutien à l'Institut Européen de Chimie et Biologie (IECB), CNRS, INSERM, IECB, US1, Université de Bordeaux, Pessac, France
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht Multimodal Imaging Institute (M4i), Maastricht University, Maastricht, the Netherlands
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O'Halloran C, Barker EN, Hope JC, Gunn-Moore DA. Canine tuberculosis: A review of 18 new and 565 previously reported confirmed cases. Vet J 2024; 304:106089. [PMID: 38412886 DOI: 10.1016/j.tvjl.2024.106089] [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: 07/20/2023] [Revised: 01/30/2024] [Accepted: 02/23/2024] [Indexed: 02/29/2024]
Abstract
Cases of canine tuberculosis, a zoonotic infection of significant public health significance, are typically only sporadically reported in the literature. For this observational study, case details were collated both retrospectively and prospectively for dogs infected with Mycobacterium tuberculosis-complex (MTBC) organisms. A total of 18 previously unreported cases as well as 565 historically reported confirmed cases were reviewed. A variety of diagnostic techniques were used to make a confirmed diagnosis of tuberculosis (culture, interferon-gamma release assay [IGRA], and PCR). The reference standard for diagnosis is culture; however, this was negative or not attempted in some dogs. Where fully speciated, all cases were caused by infection with one of three MTBC organisms: M. tuberculosis, Mycobacterium bovis, or Mycobacterium microti. This study includes the first documented canine infections with M. microti in the UK. All cases were assigned to one of four clinical groups based on the presenting signs: 44.1% were primarily pulmonary, 14.5% were primarily abdominal, and the remainder were disseminated or miscellaneous. The development of adjunctive tests remains necessary to support early treatment decisions pending reporting of culture for MTBC organisms, which can take weeks to months. Definitive treatment, where attempted, was successful in most cases. Of the 13 dogs treated by the authors with triple combination antimicrobial therapy, a good clinical outcome was seen in 12 (92%) of them.
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Affiliation(s)
- Conor O'Halloran
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom.
| | - Emi N Barker
- Langford Vets, University of Bristol, Langford BS40 5DU, United Kingdom; Bristol Veterinary School, University of Bristol, Langford BS40 5DU, United Kingdom
| | - Jayne C Hope
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
| | - Danièlle A Gunn-Moore
- Royal (Dick) School of Veterinary Studies and The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG United Kingdom
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Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
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Ocampo JC, Alzate JF, Barrera LF, Baena A. Tuberculosis Severity Predictive Model Using Mtb Variants and Serum Biomarkers in a Colombian Cohort of APTB Patients. Biomedicines 2023; 11:3110. [PMID: 38137331 PMCID: PMC10740695 DOI: 10.3390/biomedicines11123110] [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: 09/11/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 12/24/2023] Open
Abstract
Currently, tuberculosis (TB) is a bacterial infection caused by Mycobacterium tuberculosis (Mtb) that primarily affects the lungs. The severity of active pulmonary TB (APTB) is an important determinant of transmission, morbidity, mortality, disease experience, and treatment outcomes. Several publications have shown a high prevalence of disabling complications in individuals who have had severe APTB. Furthermore, certain strains of Mtb were associated with more severe disease outcomes. The use of biomarkers to predict severe APTB patients who are candidates for host-directed therapies, due to the high risk of developing post-tuberculous lung disease (PTLD), has not yet been implemented in the management of TB patients. We followed 108 individuals with APTB for 6 months using clinical tools, flow cytometry, and whole-genome sequencing (WGS). The median age of the study population was 26.5 years, and the frequency of women was 53.7%. In this study, we aimed to identify biomarkers that could help us to recognize individuals with APTB and improve our understanding of the immunopathology in these individuals. In this study, we conducted a follow-up on the treatment progress of 121 cases of APTB. The follow-up process commenced at the time of diagnosis (T0), continued with a control visit at 2 months (T2), and culminated in an exit appointment at 6 months following the completion of medical treatment (T6). People classified with severe APTB showed significantly higher levels of IL-6 (14.7 pg/mL; p < 0.05) compared to those with mild APTB (7.7 pg/mL) at T0. The AUCs for the ROC curves and the Matthews correlation coefficient values (MCC) demonstrate correlations ranging from moderate to very strong. We conducted WGS on 88 clinical isolates of Mtb, and our analysis revealed a total of 325 genes with insertions and deletions (Indels) within their coding regions when compared to the Mtb H37Rv reference genome. The pattern of association was found between serum levels of CHIT1 and the presence of Indels in Mtb isolates from patients with severe APTB. A key finding in our study was the high levels of CHIT1 in severe APTB patients. We identified a biomarker profile (IL-6, IFN-γ, IL-33, and CHIT1) that allows us to identify individuals with severe APTB, as well as the identification of a panel of polymorphisms (125) in clinical isolates of Mtb from individuals with severe APTB. Integrating these findings into a predictive model of severity would show promise for the management of APTB patients in the future, to guide host-directed therapy and reduce the prevalence of PTLD.
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Affiliation(s)
- Juan C. Ocampo
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
| | - Juan F. Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
- Centro Nacional de Secuenciación Genómica (CNSG), Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Luis F. Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Instituto de Investigaciones Médicas, Universidad de Antioquia (UdeA), Medellín 050010, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Universidad de Antioquia (UdeA), Medellín 050010, Colombia; (J.C.O.); (L.F.B.)
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín 050010, Colombia;
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Yenew B, Ghodousi A, Diriba G, Tesfaye E, Cabibbe AM, Amare M, Moga S, Alemu A, Dagne B, Sinshaw W, Mollalign H, Meaza A, Tadesse M, Gamtesa DF, Abebaw Y, Seid G, Zerihun B, Getu M, Chiacchiaretta M, Gaudin C, Marceau M, Didelot X, Tolera G, Abdella S, Kebede A, Getahun M, Mehammed Z, Supply P, Cirillo DM. A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex. Nat Commun 2023; 14:7519. [PMID: 37980337 PMCID: PMC10657438 DOI: 10.1038/s41467-023-42755-9] [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: 11/02/2022] [Accepted: 10/18/2023] [Indexed: 11/20/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley.
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Affiliation(s)
- Bazezew Yenew
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Arash Ghodousi
- Vita-Salute San Raffaele University, Milan, Italy.
- IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Getu Diriba
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ephrem Tesfaye
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Misikir Amare
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Binyam Dagne
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Abyot Meaza
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | | | - Getachew Seid
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Melak Getu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Cyril Gaudin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Michael Marceau
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, CV4 7AL, Coventry, UK
| | | | - Saro Abdella
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | | | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France.
| | - Daniela Maria Cirillo
- Vita-Salute San Raffaele University, Milan, Italy.
- IRCCS San Raffaele Scientific Institute, Milan, Italy.
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Seid A, Kassa M, Girma Y, Dereb E, Nureddin S, Abebe A, Berhane N. Molecular characterization of genetic mutations with fitness loss in pulmonary tuberculosis patients associated with HIV co-infection in Northwest Amhara, Ethiopia. SAGE Open Med 2023; 11:20503121231208266. [PMID: 37933292 PMCID: PMC10625730 DOI: 10.1177/20503121231208266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/29/2023] [Indexed: 11/08/2023] Open
Abstract
Objectives Molecular approaches to identifying resistance-conferring mutations suggest a revolution in the field of tuberculosis. The aim of the study was to determine the association between resistance-conferring mutations with fitness loss in Mycobacterium tuberculosis clinical isolates and HIV co-infection in the Amhara region of Ethiopia. Methods A laboratory-based cross-sectional study was conducted between September 2022 and June 2023. A line probe assay was performed on 146 culture-positive clinical isolates. Logistic regression analysis was used to measure the strength of the association between the drug-resistance-conferring mutations with fitness loss in M. tuberculosis isolates and tuberculosis/HIV co-infection. A p-value ⩽ 0.05 was considered statistically significant. Results A total of 11 distinct mutations at four genetic loci among 19 resistant isolates were detected. The frequency of rifampicin, isoniazid, and fluoroquinolones resistance-conferring mutations was identified in 12 (8.2%), 17 (11.6%), and 2 (1.4%) of the isolates, respectively. The most prominent specific mutations were S450L (5/9, 55.6%), S315T (11/11, 100%), C-15T (4/4, 100%), and D94G (1/1, 100%). Double mutations were observed in 10 (52.6%) multidrug-resistant tuberculosis isolates; the most common were detected in both the rpoB and katG genes (8/10, 80.0%). The HIV-co-infected tuberculosis patients carried a higher proportion of low fitness of non-rpoB S450L variants than those tuberculosis patients without HIV (80.0% vs 14.3%) and showed a significant association (cOR = 0.042, 95% CI: 0.002-0.877, p = 0.041), but not with the low fitness of non-katG S315T variants (cOR = 3.00, 95% CI: 0.348-25.870, p = 0.318). Conclusion This study provides valuable information on the genetic variants with fitness loss associated with HIV co-infection, but requires further whole-genome-based mutation analysis.
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Affiliation(s)
- Aynias Seid
- Department of Biology, College of Natural and Computational Science, Debre-Tabor University, Debre-Tabor, Ethiopia
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Meseret Kassa
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Eseye Dereb
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Semira Nureddin
- Department of Biology, College of Natural and Computational Science, Woldia University, Woldia, Ethiopia
| | - Ayenesh Abebe
- TB Culture Laboratory, University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Nega Berhane
- Department of Medical Biotechnology, Institute of Biotechnology, University of Gondar, Gondar, Ethiopia
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Papa V, Galassi FM, Varotto E, Gori A, Vaccarezza M. The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review. Pathog Immun 2023; 8:93-116. [PMID: 37900966 PMCID: PMC10603826 DOI: 10.20411/pai.v8i1.597] [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: 05/31/2023] [Accepted: 08/21/2023] [Indexed: 10/31/2023] Open
Abstract
Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.
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Affiliation(s)
- Veronica Papa
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Department of Economics, Law, Cybersecurity, and Sports Sciences, University of Naples “Parthenope,” Naples, Italy
- School of Science, Engineering and Health, University of Naples “Parthenope,” Naples, Italy
| | - Francesco M. Galassi
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, 90-237, Lodz, Poland
| | - Elena Varotto
- Forensic Anthropology, Paleopathology and Bioarchaeology (FAPAB) Research Center, Avola, Italy
- Archaeology, College of Humanities, Arts and Social Sciences, Flinders University, Adelaide, SA, Australia
| | - Andrea Gori
- I Division of Infectious Diseases, “Luigi Sacco” Hospital, ASST Fatebenefratelli Sacco, Milan, Italy; Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Mauro Vaccarezza
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Perth, 6102 Western Australia, Australia
- Curtin Health Innovation Research Institute (CHIRI), Faculty of Health Sciences, Curtin University, Bentley, Perth, 6102 Western Australia, Australia
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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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10
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Brenner E, Sreevatsan S. Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae. Front Microbiol 2023; 14:1204838. [PMID: 37440893 PMCID: PMC10333696 DOI: 10.3389/fmicb.2023.1204838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial CRISPR/Cas systems target foreign genetic elements such as phages and regulate gene expression by some pathogens, even in the host. The system is a marker for evolutionary history and has been used for inferences in Mycobacterium tuberculosis for 30 years. However, knowledge about mycobacterial CRISPR/Cas systems remains limited. It is believed that Type III-A Cas systems are exclusive to Mycobacterium canettii and the M. tuberculosis complex (MTBC) of organisms and that very few of the >200 diverse species of non-tuberculous mycobacteria (NTM) possess any CRISPR/Cas system. This study sought unreported CRISPR/Cas loci across NTM to better understand mycobacterial evolution, particularly in species phylogenetically near the MTBC. An analysis of available mycobacterial genomes revealed that Cas systems are widespread across Mycobacteriaceae and that some species contain multiple types. The phylogeny of Cas loci shows scattered presence in many NTM, with variation even within species, suggesting gains/losses of these loci occur frequently. Cas Type III-A systems were identified in pathogenic Mycobacterium heckeshornense and the geological environmental isolate Mycobacterium SM1. In summary, mycobacterial CRISPR/Cas systems are numerous, Type III-A systems are unreliable as markers for MTBC evolution, and mycobacterial horizontal gene transfer appears to be a frequent source of genetic variation.
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Affiliation(s)
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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Negrete-Paz AM, Vázquez-Marrufo G, Gutiérrez-Moraga A, Vázquez-Garcidueñas MS. Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype. Microorganisms 2023; 11:1495. [PMID: 37374997 DOI: 10.3390/microorganisms11061495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/31/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene-phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene-phenotype associations in M. tuberculosis.
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Affiliation(s)
- Andrea Monserrat Negrete-Paz
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58020, Michoacán, Mexico
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro 58893, Michoacán, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro 58893, Michoacán, Mexico
| | - Ana Gutiérrez-Moraga
- Instituto de Ciencias Biomédicas, Vicerrectoría de Investigación y Doctorados, Universidad Autónoma de Chile, Santiago 7500912, Chile
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58020, Michoacán, Mexico
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Sierra A, Camelo D, Lota C, Arenas NE, Soto CY. Specific identification of Mycobacterium bovis by Loop-Mediated Isothermal Amplification (LAMP) targeting the Region of Difference 12 (RD12) of the M. tuberculosis complex. MethodsX 2023; 10:102223. [PMID: 37251650 PMCID: PMC10209011 DOI: 10.1016/j.mex.2023.102223] [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: 02/13/2023] [Accepted: 04/26/2023] [Indexed: 05/31/2023] Open
Abstract
Bovine tuberculosis is a prevalent zoonotic disease that causes high risks for production animals, dairy producers and consumers, together with significant economic losses. Thus, methods for easy, fast and specific detection of Mycobacterium bovis in small and medium-sized livestock under field conditions are very required. In this work, a Loop-Mediated Isothermal Amplification LAMP-PCR targeting the Region of Difference 12 (RD12) of M. bovis genome was designed for the purpose of identification. A set of six primers designed for the isothermal amplification of five different genomic fragments led to the specific identification of M. bovis from other mycobacterial species. A basic colorimetric reaction was clearly observed at first sight under natural light, indicating positive identification of M. bovis in a maximum of 30 min of isothermal amplification at 65 °C. The limit of detection was near 50 fg of M. bovis genomic DNA, corresponding approximately to 10 copies of the genome. •The proposed LAMP-PCR amplification of M. bovis genomic DNA might be performed by untrained laboratory personnel.•Specific identification of M. bovis LAMP is possible in 30 min at 65.. C using a simple water bath.•The basic colorimetric reaction for M. bovis identification could be observed with the naked eye under natural light.
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Affiliation(s)
- Alejandro Sierra
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30 N° 45-03, 111321, Bogotá, Colombia
| | - Danna Camelo
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30 N° 45-03, 111321, Bogotá, Colombia
| | - Camila Lota
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30 N° 45-03, 111321, Bogotá, Colombia
| | - Nelson Enrique Arenas
- Biology Department, Faculty of Sciences, Universidad Antonio Nariño. Carrera 1 Este #47a-15, Bogotá, Colombia
- Faculty of Agricultural Sciences, Universidad de Cundinamarca, Diagonal 18 No. 20-29, Fusagasugá, Colombia
| | - Carlos Y. Soto
- Chemistry Department, Faculty of Sciences, Universidad Nacional de Colombia, Ciudad Universitaria, Carrera 30 N° 45-03, 111321, Bogotá, Colombia
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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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Brown TS, Robinson DA, Buckee CO, Mathema B. Connecting the dots: understanding how human mobility shapes TB epidemics. Trends Microbiol 2022; 30:1036-1044. [PMID: 35597716 PMCID: PMC10068677 DOI: 10.1016/j.tim.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 01/13/2023]
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide. Reducing TB infections and TB-related deaths rests ultimately on stopping forward transmission from infectious to susceptible individuals. Critical to this effort is understanding how human host mobility shapes the transmission and dispersal of new or existing strains of Mycobacterium tuberculosis (Mtb). Important questions remain unanswered. What kinds of mobility, over what temporal and spatial scales, facilitate TB transmission? How do human mobility patterns influence the dispersal of novel Mtb strains, including emergent drug-resistant strains? This review summarizes the current state of knowledge on mobility and TB epidemic dynamics, using examples from three topic areas, including inference of genetic and spatial clustering of infections, delineating source-sink dynamics, and mapping the dispersal of novel TB strains, to examine scientific questions and methodological issues within this topic. We also review new data sources for measuring human mobility, including mobile phone-associated movement data, and discuss important limitations on their use in TB epidemiology.
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Affiliation(s)
- Tyler S Brown
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Infectious Diseases Division, Massachusetts General Hospital, Boston, MA, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
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15
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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16
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Katz H, Schelotto F, Bakker D, Castro-Ramos M, Gutiérrez-Expósito D, Panzera Y, Pérez R, Franco-Trecu V, Hernández E, Menéndez C, Meny P. Survey of selected pathogens in free-ranging pinnipeds in Uruguay. DISEASES OF AQUATIC ORGANISMS 2022; 150:69-83. [PMID: 35833546 DOI: 10.3354/dao03676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Marine mammals, regarded as sentinels of aquatic ecosystem health, are exposed to different pathogens and parasites under natural conditions. We surveyed live South American fur seals Arctocephalus australis and South American sea lions Otaria flavescens in Uruguay for Leptospira spp., canine distemper virus (CDV), Mycobacterium spp., Toxoplasma gondii, and Neospora caninum. Samples were collected from 2007 to 2013. The seroprevalence of Leptospira spp. was 37.6% positive, 50.9% negative, and 11.5% suspect for A. australis (n = 61) while for O. flavescens (n = 12) it was 67% positive, 25% negative, and 8% suspect. CDV RNA was not detected in any of the analyzed samples. Most animals tested seropositive to tuberculosis antigens by WiZo ELISA (A. australis: 29/30; O. flavescens: 20/20); reactivity varied with a novel ELISA test (antigens MPB70, MPB83, ESAT6 and MPB59). Seroprevalence against N. caninum and T. gondii was 6.7 and 13.3% positive for O. flavescens and 0 and 2.2% positive for A. australis respectively. To evaluate possible sources of infection for pinnipeds, wild rats Rattus rattus and semi-feral cats Felis catus were also tested for Leptospira spp. and T. gondii respectively. Water samples tested for Leptospira revealed saprofitic L. bioflexa. Pathogenic Leptospira were detected in the kidneys of 2 rats, and cats tested positive for T. gondii (100%). These results represent a substantial contribution to the study of the health status of wild pinnipeds in Uruguay.
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Affiliation(s)
- H Katz
- Facultad de Veterinaria, Universidad de la República (UdelaR), 11600 Montevideo, Uruguay
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Patil PG, Sharma J, Nanjundappa M, Singh NV, Bohra A, Gunnaiah R, Jamma SM, Vinayaka J, Sangnure VR, Marathe RA. Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate. 3 Biotech 2022; 12:153. [PMID: 35755801 DOI: 10.1007/s13205-022-03209-z] [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: 01/18/2022] [Accepted: 05/22/2022] [Indexed: 11/01/2022] Open
Abstract
This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodis pv. punicae strains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xap genomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xap isolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xap isolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xap isolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03209-z.
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Affiliation(s)
- Prakash G Patil
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Jyotsana Sharma
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Manjunatha Nanjundappa
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - N V Singh
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Abhishek Bohra
- State Agriculture Biotechnology, Centre, Centre for Crop & Food Innovation, Murdoch University, Perth, Western Australia
| | - Raghavendra Gunnaiah
- Department of Biotechnology and Crop Improvement, University of Horticultural Sciences (UHS), Bagalkot, 587104 India
| | - Shivani M Jamma
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Jeer Vinayaka
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - Vipul R Sangnure
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
| | - R A Marathe
- Biotechnology and Plant Pathology, ICAR-National Research Centre on Pomegranate (NRCP), Solapur, 413255 India
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Frequency of rpoB, katG, and inhA Gene Polymorphisms Associated with Multidrug-Resistant Mycobacterium tuberculosis Complex Isolates among Ethiopian TB Patients: A Systematic Review. Interdiscip Perspect Infect Dis 2022; 2022:1967675. [PMID: 35757683 PMCID: PMC9225881 DOI: 10.1155/2022/1967675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/05/2022] [Accepted: 05/26/2022] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) is one of the top 10 causes of mortality and the first killer among infectious diseases of poverty (IDoPs) worldwide. It disproportionately affects on-third of the world's low-income countries including Ethiopia. One of the factors driving the TB epidemic is the global rise of MDR/XDR-TB and their low detection affect the global TB control progress. Recently, the resistance-associated genetic mutations in MTBC known to confer drug resistance have been detected by rapid molecular diagnostic tests and sequencing methods. In this article, the published literature searched by PubMed database from 2010 to 2021 and English language were considered. The aim of this systematic review was to assess the prevalence of the most common rpoB, katG, and inhA gene mutations associated with multidrug resistance in MTBC clinical strains among TB patients in Ethiopia. Though 22 studies met our eligibility criteria, only 6 studies were included in the final analysis. Using the molecular GenoType MTBDRplus and MTBDRsl line probe assay and sequencing procedures, a total of 932 culture-positive MTBC isolates were examined to determine RIF, INH, and MDR-TB resistance patterns along with rpoB, katG, and inhA gene mutation analysis. As a result, among the genotypically tested MTBC isolates, 119 (12.77%), 83 (8.91%), and 73 (7.32%) isolates were INH, RIF, and MDR-TB resistant, respectively. In any RIF-resistant MTBC strains, the most common single point mutations were in codon 531 (S531L) followed by codon 526 (H526Y) of the rpoB gene. Besides, the most common mutations in any INH-resistant MTBC were strains observed at codon 315 (S315T) and WT probe in the katG gene and at codon C15T and WT1 probe in the inhA promoter region. Detection of resistance allele in rpoB, KatG, and inhA genes for RIF and INH could serve as a marker for MDR-TB strains. Tracking the most common S531L, S315T, and C15T mutations in rpoB, katG, and inhA genes among RIF- and INH-resistant isolates would be valuable in TB diagnostics and treatment regimens, and could reduce the development and risk of MDR/XDR-TB drug-resistance patterns.
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Krittanan P, Srimanote P, Thawornwan U, Chaiprasert A, Tapchaisri P, Tongtawe P. Spoligotype-based population structure and isoniazid-resistance gene mutation of Mycobacterium tuberculosis isolates from Thailand. J Glob Antimicrob Resist 2022; 30:319-325. [PMID: 35732265 DOI: 10.1016/j.jgar.2022.06.013] [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: 11/05/2019] [Revised: 05/20/2022] [Accepted: 06/14/2022] [Indexed: 10/17/2022] Open
Abstract
OBJECTIVES The present study aims to investigate the population structure of Thai Mycobacterium tuberculosis (MTB) isolates, the anti-tuberculosis (TB) drug resistance and to determine the most frequent genetic mutations conferring the isoniazid (INH) resistance. METHODS Genomic DNA from 287 MTB clinical isolates were extracted and used for: spoligotyping, amplification and sequencing analysis of region of different (RD) 105, and the INH-resistance (IR) associated genes, inhA, katG and oxyR-ahpC. RESULTS Eighty-one clinical isolates were resistant to at least one first-line drug, 53 of these were resistant to INH. All strains were classified into three lineages based on their spoligotypes: East-Asia (EA)/Beijing, Indo-Oceanic (IO) and Euro-American (EuA). EA and IO lineages revealed a strong association with anti-TB drug resistance (p=0.005 and 0.013, respectively). A total of 33 mutations were found among IR isolates, which for 28 (84.8%), 3 (9.1%) and 2 (6.1%) occurred in katG, inhA, and oxyR-ahpC genes, respectively. Moreover, the most commom mutations found were 54.7% of IR presented Ser315Thr at katG (54.7%) and C-15T at inhA (15.1%) presented. This result suggests the involvement of other genetic markers or other mechanisms of resistance. CONCLUSION This study provides information about strains diversity, drug resistance profiles and their possible association. EA and IO lineages were predominant in Thailand, and they were highly associated with anti-TB drug resistance. Testing two mutation including katGSer315Thr and inhA-15C→T could detect 68% of the IR strains.
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Affiliation(s)
- Peerapat Krittanan
- Graduate Programme in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, 99 Moo 18 Paholyothin Road, Klong-Luang, Pathumthani 12120, Thailand
| | - Potjanee Srimanote
- Graduate Programme in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, 99 Moo 18 Paholyothin Road, Klong-Luang, Pathumthani 12120, Thailand
| | - Unchana Thawornwan
- Microbiology Laboratory, Bamrasnaradura Infectious Diseases Institute, Tiwanan Road. Nonthaburi 11000, Thailand
| | - Angkana Chaiprasert
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pramaun Tapchaisri
- Graduate Programme in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, 99 Moo 18 Paholyothin Road, Klong-Luang, Pathumthani 12120, Thailand
| | - Pongsri Tongtawe
- Graduate Programme in Biomedical Sciences, Faculty of Allied Health Sciences, Thammasat University, 99 Moo 18 Paholyothin Road, Klong-Luang, Pathumthani 12120, Thailand.
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20
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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Mycobacterium tuberculosis Transcription Factor EmbR Regulates the Expression of Key Virulence Factors That Aid in Ex Vivo and In Vivo Survival. mBio 2022; 13:e0383621. [PMID: 35471080 PMCID: PMC9239209 DOI: 10.1128/mbio.03836-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis encodes ~200 transcription factors that modulate gene expression under different microenvironments in the host. Even though high-throughput chromatin immunoprecipitation sequencing and transcriptome sequencing (RNA-seq) studies have identified the regulatory network for ~80% of transcription factors, many transcription factors remain uncharacterized. EmbR is one such transcription factor whose in vivo regulon and biological function are yet to be elucidated. Previous in vitro studies suggested that phosphorylation of EmbR by PknH upregulates the embCAB operon. Using a gene replacement mutant of embR, we investigated its role in modulating cellular morphology, antibiotic resistance, and survival in the host. Contrary to the prevailing hypothesis, under normal growth conditions, EmbR is neither phosphorylated nor impacted by ethambutol resistance through the regulation of the embCAB operon. The embR deletion mutant displayed attenuated M. tuberculosis survival in vivo. RNA-seq analysis suggested that EmbR regulates operons involved in the secretion pathway, lipid metabolism, virulence, and hypoxia, including well-known hypoxia-inducible genes devS and hspX. Lipidome analysis revealed that EmbR modulates levels of all lysophospholipids, several phospholipids, and M. tuberculosis-specific lipids, which is more pronounced under hypoxic conditions. We found that the EmbR mutant is hypersusceptible to hypoxic stress, and RNA sequencing performed under hypoxic conditions indicated that EmbR majorly regulates genes involved in response to acidic pH, hypoxia, and fatty acid metabolism. We observed condition-specific phosphorylation of EmbR, which contributes to EmbR-mediated transcription of several essential genes, ensuring enhanced survival. Collectively, the study establishes EmbR as a key modulator of hypoxic response that facilitates mycobacterial survival in the host.
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https://doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https:/doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022; 13:genes13020263. [PMID: 35205308 PMCID: PMC8872330 DOI: 10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Affiliation(s)
- Shiv kumar Rashmi Mudliar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Umay Kulsum
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Syed Beenish Rufai
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada;
- McGill International TB Center, Montreal, QC H4A 3J1, Canada
| | - Mika Umpo
- Tomo Riba Institute of Health & Medical Sciences, Naharlagun 791110, Arunachal Pradesh, India;
| | - Moi Nyori
- State TB Cell, Naharlagun 791110, Arunachal Pradesh, India;
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
- Correspondence: ; Tel.: +91-9810813435
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Guyeux C, Senelle G, Refrégier G, Bretelle-Establet F, Cambau E, Sola C. Connection between two historical tuberculosis outbreak sites in Japan, Honshu, by a new ancestral Mycobacterium tuberculosis L2 sublineage. Epidemiol Infect 2022; 150:1-25. [PMID: 35042579 PMCID: PMC8931808 DOI: 10.1017/s0950268822000048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022] Open
Abstract
By gathering 680 publicly available Sequence Read Archives from isolates of Mycobacterium tuberculosis complex (MTBC) including 190 belonging to the lineage 2 Beijing , and using an in-house bioinformatical pipeline, the TB-Annotator , that analyses more than 50 000 characters, we describe herein a new L2 sublineage from 20 isolates found in the Tochigi province, (Japan), that we designate as asia ancestral 5 (AAnc5). These isolates harbour a number of specific criteria (42 SNPs) and their intra-cluster pairwise distance suggests historical and not epidemiological transmission. These isolates harbour a mutation in rpoC , and do not fulfil, any of the modern Beijing lineage criteria, nor any of the other ancestral Beijing lineages described so far. Asia ancestral 5 isolates do not possess mutT2 58 and ogt 12 characteristics of modern Beijing , but possess ancestral Beijing SNPs characteristics. By looking into the literature, we found a reference isolate ID381, described in Kobe and Osaka belonging to the ‘G3’ group, sharing 36 out of the 42 specific SNPs found in AAnc5. We also assessed the intermediate position of the asia ancestral 4 (AAnc4) sublineage recently described in Thailand and propose an improved classification of the L2 that now includes AAnc4 and AAnc5. By increasing the recruitment into TB-Annotator to around 3000 genomes (including 642 belonging to L2), we confirmed our results and discovered additional historical ancestral L2 branches that remain to be investigated in more detail. We also present, in addition, some anthropological and historical data from Chinese and Japan history of tuberculosis, as well as from Korea, that could support our results on L2 evolution. This study shows that the reconstruction of the early history of tuberculosis in Asia is likely to reveal complex patterns since its emergence.
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Affiliation(s)
- Christophe Guyeux
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Gaetan Senelle
- DISC Computer Science Department, FEMTO-ST Institute, UMR 6174 CNRS, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000Besançon, France
| | - Guislaine Refrégier
- Université Paris-Saclay, Saint-Aubin, France
- Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | | | - Emmanuelle Cambau
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
- AP-HP, GHU Nord, service de mycobactériologie spécialisée et de référence, Laboratoire associé du Centre National de Référence des mycobactéries et résistance des mycobactéries aux antituberculeux (CNR-MyRMA), Paris, France
| | - Christophe Sola
- Université Paris-Saclay, Saint-Aubin, France
- Université de Paris, IAME, UMR1137, INSERM, Paris, France
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Singh J, Singh N, Suresh G, Srivastava R, Aggarwal U, Behera D, Munisamy M, Malhotra AG, Singh S. A comparative analysis of molecular genotypes of Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative patients. Front Cell Infect Microbiol 2022; 12:953443. [PMID: 36310875 PMCID: PMC9597297 DOI: 10.3389/fcimb.2022.953443] [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: 05/26/2022] [Accepted: 08/30/2022] [Indexed: 02/05/2023] Open
Abstract
SETTING Tuberculosis Research Laboratory, Division of Clinical Microbiology and Molecular Medicine, Department of Laboratory Medicine, All India Institute of Medical Sciences, and the National Institute of Tuberculosis and Respiratory Diseases (NITRD), both situated in New Delhi. OBJECTIVES We aimed to identify the distribution of various genotypes of M. tuberculosis among HIV-positive and HIV-negative patients suspected of having Tuberculosis, seen at the National Institute of Tuberculosis and Respiratory Diseases, New Delhi, which is a tertiary care dedicated TB hospital. PATIENTS AND METHODS Genotyping by Spoligotyping and 24 loci MIRU-VNTR was performed and analyzed using SITVITWEB and MIRU-VNTRplus. Drug susceptibility patterns were also analyzed. RESULTS A total of 503 subjects who were PTB/EPTB suspected were recruited and 287 were culture positive. Among them, 276 had growth of Mycobacterium tuberculosis (MTB) and in 11 patients non-tuberculous mycobacteria (NTM) were grown. The isolation rate of NTM was predominantly from HIV positive [10 of 130 (7.6%)] patients. Of the total isolates of MTB, 156 (56.5%) were from HIV negative patients and 120 (43.5%) were from HIV positive patients. All 276 M. tuberculosis isolates were genotyped and tested for drug susceptibility patterns. The CAS genotype was most predominant [153 (55.4%)], followed by Beijing lineage [44 (15.9%)], East African India [25 (9.1%)] and others [54 (19.6%)]. Beijing genotype was significantly more common in HIV positive patients (22.5%) than in HIV negative patients (10.9%). In MIRU-VNTR analysis, clustering was found to be more frequent in CAS strains irrespective of HIV status. In the HIV positive group, spoligotyping could differentiate various genotypes in 90% of isolates and MIRU-VNTR analysis in 84.2% of isolates. The clustering of various MTB strains was more associated with drug resistance. CONCLUSION The Beijing lineage was predominant in HIV-TB coinfected cases, even though the Central Asian Strain (CAS) was overall more predominant in the region.
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Affiliation(s)
- Jitendra Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | - Niti Singh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Gayatri Suresh
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Rahul Srivastava
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Upasna Aggarwal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
| | - Digamber Behera
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases (NITRD), New Delhi, India
- Department of Pulmonary Medicine, PGIMER, Chandigarh, India
| | - Murali Munisamy
- Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal, India
| | | | - Sarman Singh
- Division of Clinical Microbiology and Molecular Medicine, All India Institute of Medical Sciences, New Delhi, India
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal, India
- Medical Science and Engineering Research Centre, Indian Institute of Science Education and Research, Bhopal, India
- *Correspondence: Sarman Singh, ;
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Bohr LL, Youngblom MA, Eldholm V, Pepperell CS. Genome reorganization during emergence of host-associated Mycobacterium abscessus. Microb Genom 2021; 7. [PMID: 34874249 PMCID: PMC8767326 DOI: 10.1099/mgen.0.000706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.
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Affiliation(s)
- Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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29
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Perez-Malagon CD, Barrera-Rodriguez R, Lopez-Gonzalez MA, Alva-Lopez LF. Diagnostic and Neurological Overview of Brain Tuberculomas: A Review of Literature. Cureus 2021; 13:e20133. [PMID: 34900500 PMCID: PMC8648135 DOI: 10.7759/cureus.20133] [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] [Accepted: 12/02/2021] [Indexed: 11/05/2022] Open
Abstract
Tuberculosis is a disease caused by a bacteria named Mycobacterium tuberculosis (M. tb). It is estimated by World Health Organization (WHO) that nearly a quarter of the world's population is infected. Tuberculoma of the brain is one of the most severe extrapulmonary forms that affects patients younger than 40 years of age. Brain parenchymal tuberculoma develops in nearly one of 300 non-treated cases of pulmonary tuberculosis cases. In endemic regions, tuberculomas account for as many as 50% of all intracranial masses. Tuberculoma results in a hematogenous spread of M. tb from an extracranial source. Tuberculomas can mimic a variety of diseases and can present themselves in a subacute or chronic course, from asymptomatic to severe intracranial hypertension. Diagnosis is based on computed tomography (CT) scan and magnetic resonance imaging (MRI) studies with a similar ring-enhancing lesion. Treatment is primarily medical, and the duration for brain tuberculoma can vary from six to 36 months. In certain cases, surgery is recommended.
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Affiliation(s)
| | - Raul Barrera-Rodriguez
- Immunopharmacology, Instituto Nacional de Enfermedades Respiratorias (INER), Mexico City, MEX
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30
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Freschi L, Vargas R, Husain A, Kamal SMM, Skrahina A, Tahseen S, Ismail N, Barbova A, Niemann S, Cirillo DM, Dean AS, Zignol M, Farhat MR. Population structure, biogeography and transmissibility of Mycobacterium tuberculosis. Nat Commun 2021; 12:6099. [PMID: 34671035 PMCID: PMC8528816 DOI: 10.1038/s41467-021-26248-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 09/06/2021] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium tuberculosis is a clonal pathogen proposed to have co-evolved with its human host for millennia, yet our understanding of its genomic diversity and biogeography remains incomplete. Here we use a combination of phylogenetics and dimensionality reduction to reevaluate the population structure of M. tuberculosis, providing an in-depth analysis of the ancient Indo-Oceanic Lineage 1 and the modern Central Asian Lineage 3, and expanding our understanding of Lineages 2 and 4. We assess sub-lineages using genomic sequences from 4939 pan-susceptible strains, and find 30 new genetically distinct clades that we validate in a dataset of 4645 independent isolates. We find a consistent geographically restricted or unrestricted pattern for 20 groups, including three groups of Lineage 1. The distribution of terminal branch lengths across the M. tuberculosis phylogeny supports the hypothesis of a higher transmissibility of Lineages 2 and 4, in comparison with Lineages 3 and 1, on a global scale. We define an expanded barcode of 95 single nucleotide substitutions that allows rapid identification of 69 M. tuberculosis sub-lineages and 26 additional internal groups. Our results paint a higher resolution picture of the M. tuberculosis phylogeny and biogeography.
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Affiliation(s)
- Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ashaque Husain
- Directorate General of Health Services, Ministry of Health and Family Welfare, Dhaka, Bangladesh
| | - S M Mostofa Kamal
- Department of Pathology and Microbiology, National Institute of Diseases of the Chest and Hospital, Dhaka, Bangladesh
| | - Alena Skrahina
- Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Sabira Tahseen
- National Reference Laboratory, National Tuberculosis Control Programme, Islamabad, Pakistan
| | - Nazir Ismail
- National Institute for Communicable Diseases, Sandringham, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anna Barbova
- Central Reference Laboratory on Tuberculosis Microbiological Diagnostics, Ministry of Health, Kiev, Ukraine
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Borstel Research Centre, Borstel, Germany
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna S Dean
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Matteo Zignol
- Global Tuberculosis Programme, World Health Organization, Geneva, Switzerland
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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31
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Mukundan S, Singh P, Shah A, Kumar R, O’Neill KC, Carter CL, Russell DG, Subbian S, Parekkadan B. In Vitro Miniaturized Tuberculosis Spheroid Model. Biomedicines 2021; 9:1209. [PMID: 34572395 PMCID: PMC8470281 DOI: 10.3390/biomedicines9091209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/01/2021] [Accepted: 09/06/2021] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) is a public health concern that impacts 10 million people around the world. Current in vitro models are low throughput and/or lack caseation, which impairs drug effectiveness in humans. Here, we report the generation of THP-1 human monocyte/macrophage spheroids housing mycobacteria (TB spheroids). These TB spheroids have a central core of dead cells co-localized with mycobacteria and are hypoxic. TB spheroids exhibit higher levels of pro-inflammatory factor TNFα and growth factors G-CSF and VEGF when compared to non-infected control. TB spheroids show high levels of lipid deposition, characterized by MALDI mass spectrometry imaging. TB spheroids infected with strains of differential virulence, Mycobacterium tuberculosis (Mtb) HN878 and CDC1551 vary in response to Isoniazid and Rifampicin. Finally, we adapt the spheroid model to form peripheral blood mononuclear cells (PBMCs) and lung fibroblasts (NHLF) 3D co-cultures. These results pave the way for the development of new strategies for disease modeling and therapeutic discovery.
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Affiliation(s)
- Shilpaa Mukundan
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Jersey City, NJ 08854, USA; (S.M.); (A.S.)
| | - Pooja Singh
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Jersey City, NJ 07103, USA; (P.S.); (R.K.); (S.S.)
| | - Aditi Shah
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Jersey City, NJ 08854, USA; (S.M.); (A.S.)
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Jersey City, NJ 07103, USA; (P.S.); (R.K.); (S.S.)
| | - Kelly C. O’Neill
- Department Center for Discovery and Innovation, Hackensack Meridian Health, Neptune, NJ 07110, USA; (K.C.O.); (C.L.C.)
| | - Claire L. Carter
- Department Center for Discovery and Innovation, Hackensack Meridian Health, Neptune, NJ 07110, USA; (K.C.O.); (C.L.C.)
| | - David G. Russell
- Department of Microbiology and Immunology, School of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA;
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Jersey City, NJ 07103, USA; (P.S.); (R.K.); (S.S.)
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Jersey City, NJ 08854, USA; (S.M.); (A.S.)
- Department of Medicine, Rutgers Biomedical Health Sciences, Rutgers, The State University of New Jersey, Jersey City, NJ 08854, USA
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Bosch B, DeJesus MA, Poulton NC, Zhang W, Engelhart CA, Zaveri A, Lavalette S, Ruecker N, Trujillo C, Wallach JB, Li S, Ehrt S, Chait BT, Schnappinger D, Rock JM. Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis. Cell 2021; 184:4579-4592.e24. [PMID: 34297925 PMCID: PMC8382161 DOI: 10.1016/j.cell.2021.06.033] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 06/29/2021] [Indexed: 01/09/2023]
Abstract
Antibacterial agents target the products of essential genes but rarely achieve complete target inhibition. Thus, the all-or-none definition of essentiality afforded by traditional genetic approaches fails to discern the most attractive bacterial targets: those whose incomplete inhibition results in major fitness costs. In contrast, gene "vulnerability" is a continuous, quantifiable trait that relates the magnitude of gene inhibition to the effect on bacterial fitness. We developed a CRISPR interference-based functional genomics method to systematically titrate gene expression in Mycobacterium tuberculosis (Mtb) and monitor fitness outcomes. We identified highly vulnerable genes in various processes, including novel targets unexplored for drug discovery. Equally important, we identified invulnerable essential genes, potentially explaining failed drug discovery efforts. Comparison of vulnerability between the reference and a hypervirulent Mtb isolate revealed incomplete conservation of vulnerability and that differential vulnerability can predict differential antibacterial susceptibility. Our results quantitatively redefine essential bacterial processes and identify high-value targets for drug development.
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Affiliation(s)
- Barbara Bosch
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Nicholas C Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Curtis A Engelhart
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Anisha Zaveri
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sophie Lavalette
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Nadine Ruecker
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Carolina Trujillo
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Joshua B Wallach
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Shuqi Li
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10065, USA.
| | - Jeremy M Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY 10065, USA.
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Comas I, Cancino-Muñoz I, Mariner-Llicer C, Goig GA, Ruiz-Hueso P, Francés-Cuesta C, García-González N, González-Candelas F. Use of next generation sequencing technologies for the diagnosis and epidemiology of infectious diseases. Enferm Infecc Microbiol Clin 2021; 38 Suppl 1:32-38. [PMID: 32111363 DOI: 10.1016/j.eimc.2020.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the first time, next generation sequencing technologies provide access to genomic information at a price and scale that allow their implementation in routine clinical practice and epidemiology. While there are still many obstacles to their implementation, there are also multiple examples of their major advantages compared with previous methods. Their main advantage is that a single determination allows epidemiological information on the causative microorganism to be obtained simultaneously, as well as its resistance profile, although these advantages vary according to the pathogen under study. This review discusses several examples of the clinical and epidemiological use of next generation sequencing applied to complete genomes and microbiomes and reflects on its future in clinical practice.
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Affiliation(s)
- Iñaki Comas
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España; CIBER en Epidemiología y Salud Pública, Valencia, España.
| | | | | | - Galo A Goig
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia, España
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Carlos Francés-Cuesta
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Neris García-González
- Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
| | - Fernando González-Candelas
- CIBER en Epidemiología y Salud Pública, Valencia, España; Unidad Mixta "Infección y Salud Pública" FISABIO-Universitat de València, Instituto de Biología Integrativa de Sistemas, I2SysBio (CSIC-UV), Valencia, España
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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Abstract
Mycobacterium tuberculosis complex (MTBC) species are classic examples of genetically monomorphic microorganisms due to their low genetic variability. Whole-genome sequencing made it possible to describe both the main species within the complex and M. tuberculosis lineages and sublineages. This differentiation is based on single nucleotide polymorphisms (SNPs) and large sequence polymorphisms in the so-called regions of difference (RDs). Although a number of studies have been performed to elucidate RD localizations, their distribution among MTBC species, and their role in the bacterial life cycle, there are some inconsistencies and ambiguities in the localization of RDs in different members of the complex. To address this issue, we conducted a thorough search for all possible deletions in the WGS data collection comprising 721 samples representing the full MTBC diversity. Discovered deletions were compared with a list of all previously described RDs. As with the SNP-based analysis, we confirmed the specificities of 79 regions at the species, lineage, or sublineage level, 17 of which are described for the first time. We also present RDscan (https://github.com/dbespiatykh/RDscan), an open-source workflow, which detects deletions from short-read sequencing data and correlates the results with high-specificity RDs, curated in this study. Testing of the workflow on a collection comprising ∼7,000 samples showed a high specificity of the found RDs. This study provides novel details that can contribute to a better understanding of the species differentiation within the MTBC and can help to determine how individual clusters evolve within various MTBC species. IMPORTANCE Reductive genome evolution is one of the most important and intriguing adaptation strategies of different living organisms to their environment. Mycobacterium offers several notorious examples of either naturally reduced (Mycobacterium leprae) or laboratory-reduced (Mycobacterium bovis BCG) genomes. Mycobacterium tuberculosis complex has its phylogeny unambiguously framed by large sequence polymorphisms that present unidirectional unique event changes. In the present study, we curated all known regions of difference and analyzed both Mycobacterium tuberculosis and animal-adapted MTBC species. For 79 loci, we have shown a relationship with phylogenetic units, which can serve as a marker for diagnosing or studying biological effects. Moreover, intersections were found for some loci, which may indicate the nonrandomness of these processes and the involvement of these regions in the adaptation of bacteria to external conditions.
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36
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Bose D, Mukhopadhyay S. The hunt for a yet unknown: Common molecular signature in some genetically monomorphic enterobacteria. J Basic Microbiol 2021; 61:524-546. [PMID: 33991346 DOI: 10.1002/jobm.202000630] [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: 11/24/2020] [Revised: 04/04/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Mark Achtman introduced the term "genetically monomorphic bacteria" (GM bacteria) for some human and plant pathogens. They displayed a great uniformity in terms of their "genetic" properties. This "uniformity" poses a challenge to microbiologists. To address these problems, we used CodonW and IslandViewer 3 as analytical tools and took Escherichia coli, Salmonella, and Shigella strains as a model organisms. We hypothesized that GM bacterium contains a common molecular signature among them. We have found a significant correlation regarding the number of protein-coding genes, predicted highly expressed genes, and the highest length of gene in this regard. On the other hand, the correspondence analysis of pathogenicity-related genes identified by IslandViewer 3 displayed a somewhat unique pattern in GM bacteria. The probable pathogenic genes are clustered into two separate groups, which is a hallmark of some pattern. Similar genes of non-monomorphic pathogenic strain clustered almost similarly, but the clusters are joined together, they are not completely separated. These features, in our considered view, may be considered as codon usages signatures of these bacteria, and E. coli in particular.
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Affiliation(s)
- Debadin Bose
- Department of Botany, Kabi Nazrul College, Murarai, West Bengal, India
| | - Subhasis Mukhopadhyay
- Distributed Information Centre for Bioinformatics, Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Calcutta, West Bengal, India
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37
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Momen G, Aainouss A, Lamaammal A, Chettioui F, Blaghen M, Messoudi M, Belghmi K, Mouslim J, El Mzibri M, El Messaoudi MD, Khyatti M, Chaoui I. Molecular characterization of mutations associated with resistance to second line drugs in Mycobacterium tuberculosis patients from Casablanca, Morocco. Rev Inst Med Trop Sao Paulo 2021; 63:e19. [PMID: 33787739 PMCID: PMC7997671 DOI: 10.1590/s1678-9946202163019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/22/2021] [Indexed: 12/02/2022] Open
Abstract
The emergence and spread of extensively drug-resistant tuberculosis (XDR-TB) is a
serious threat to global health. Therefore, its rapid diagnosis is crucial. The
present study aimed to characterize mutations conferring resistance to second
line drugs (SLDs) within multidrug Mycobacterium tuberculosis
(MDR-MTB) isolates and to estimate the occurrence of XDR-TB in Casablanca,
Morocco. A panel of 200 MDR-TB isolates was collected at the Pasteur Institute
between 2015-2018. Samples were subjected to drug susceptibility testing to
Ofloxacin (OFX), Kanamycin (KAN) and Amikacin (AMK). The mutational status of
gyrA, gyrB, rrs,
tlyA and eis was assessed by sequencing
these target genes. Drug susceptibility testing for SLDs showed that among the
200 MDR strains, 20% were resistant to OFX, 2.5% to KAN and 1.5% to AMK.
Overall, 14.5% of MDR strains harbored mutations in gyrA,
gyrB, rrs and tlyA genes.
From the 40 OFXR isolates, 67.5% had mutations in QRDR of
gyrA and gyrB genes, the most frequent one
being Ala90Val in gyrA gene. Of note, none of the isolates
harbored simultaneously mutations in gyrA and
gyrB genes. In eight out of the 200 MDR-TB isolates
resistant either to KAN or AMK, only 25% had A1401G or Lys89Glu change in
rrs and tlyA genes respectively. This
study is very informative and provides data on the alarming rate of
fluoroquinolone resistance which warrants the need to implement appropriate drug
regimens to prevent the emergence and spread of more severe forms of
Mycobacterium tuberculosis drug resistance.
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Affiliation(s)
- Ghizlane Momen
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco.,Faculté des Sciences, Laboratoire de Microbiologie, Pharmacologie, Biotechnologie et Environnement, Casablanca, Morocco
| | - Achraf Aainouss
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco.,Faculté des Sciences Ben M'Sik, Laboratoire d'Ecologie et Environment, Casablanca, Morocco
| | | | - Fouad Chettioui
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Mohamed Blaghen
- Faculté des Sciences, Laboratoire de Microbiologie, Pharmacologie, Biotechnologie et Environnement, Casablanca, Morocco
| | - Malika Messoudi
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Khalid Belghmi
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Jamal Mouslim
- Faculté des Sciences Ben M'Sik, Laboratoire d'Ecologie et Environment, Casablanca, Morocco
| | - Mohammed El Mzibri
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Département des Sciences du Vivant, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
| | | | - Meriem Khyatti
- Institut Pasteur du Maroc, Laboratoire des Mycobactéries, Casablanca, Morocco
| | - Imane Chaoui
- Centre National de l'Energie, des Sciences et Techniques Nucléaires, Département des Sciences du Vivant, Unité de Recherches Médicales et Biologiques, Rabat, Morocco
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Hakim JMC, Yang Z. Predicted Structural Variability of Mycobacterium tuberculosis PPE18 Protein With Immunological Implications Among Clinical Strains. Front Microbiol 2021; 11:595312. [PMID: 33488541 PMCID: PMC7819968 DOI: 10.3389/fmicb.2020.595312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
Recent advancements in vaccinology have led to the development of the M72/AS01E subunit vaccine, of which the major component is the Mycobacterium tuberculosis (MTB) PPE18 protein. Previous studies have demonstrated the genetic variability of the gene encoding PPE18 protein and the resulting peptide changes in diverse clinical strains of MTB; however, none have modeled the structural changes resulting from these peptide changes and their immunological implications. In this study, we investigated the structural predictions of 29 variant PPE18 proteins previously reported. We found evidence that PPE18 is at least a two-domain protein, with a highly conserved first domain and a largely variable second domain that has different coevolutionary clusters. Further, we investigated putative epitope sites in the clinical variants of PPE18 using prediction software. We found a negative relationship between T-cell epitope number and residue variability, while B-cell epitope likelihood was positively correlated with residue variability. Moreover, we found far more residues in the second domain predicted to be B-cell epitopes compared with the first domain. These results suggest an important functional role of the first domain and a role in immune evasion for the second, which extends our knowledge base of the basic biology of the PPE18 protein and indicates the need for further study into non-traditional immunological responses to TB.
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Affiliation(s)
- Jill M C Hakim
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Zhenhua Yang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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40
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Váradi OA, Rakk D, Spekker O, Terhes G, Urbán E, Berthon W, Pap I, Szikossy I, Maixner F, Zink A, Vágvölgyi C, Donoghue HD, Minnikin DE, Szekeres A, Pálfi G. Verification of tuberculosis infection among Vác mummies (18th century CE, Hungary) based on lipid biomarker profiling with a new HPLC-HESI-MS approach. Tuberculosis (Edinb) 2020; 126:102037. [PMID: 33338873 DOI: 10.1016/j.tube.2020.102037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 11/19/2022]
Abstract
Tuberculosis (TB) was a large burden of infections that peaked during the 19th century in Europe. Mummies from the 18th century CE, discovered in the crypt of a church at Vác, Hungary, had high TB prevalence, as revealed by amplification of key fragments of TB DNA and genome-wide TB analysis. Complementary methods are needed to confirm these diagnoses and one approach uses the identification of specific lipid biomarkers, such as TB mycocerosic acids (MCs). Previously, MC derivatives were profiled by specialised gas chromatography-mass spectrometry (GC-MS), so an alternative more direct approach has been developed. Underivatized MCs are extracted and analysed by high-performance liquid chromatography linked to a mass spectrometer, in heated electrospray ionisation mode (HPLC-HESI-MS). The method was validated using representatives of the Mycobacterium tuberculosis complex and other mycobacteria and tested on six Vác mummy cases, previously considered positive for TB infection. Analysing both rib and soft tissue samples, four out of six cases gave profiles of main C32 and major C29 and C39 mycocerosates correlating well with those of M. tuberculosis. Multidisciplinary methods are needed in the diagnosis of ancient tuberculosis; this new protocol accesses important confirmatory evidence, as demonstrated by the confirmation of TB in the Vác mummies.
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Affiliation(s)
- Orsolya Anna Váradi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary; Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Dávid Rakk
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Olga Spekker
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Gabriella Terhes
- Institute of Clinical Microbiology, Faculty of Medicine, University of Szeged, Hungary. Postal address: P.O.B. 427, H-6701, Szeged, Hungary.
| | - Edit Urbán
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Hungary. Postal address: Szigeti út 12, H-7624 Pécs, Hungary; Institute of Translational Medicine, Medical School, University of Pécs, Hungary. Postal address: Szigeti út 12, H-7624, Pécs, Hungary.
| | - William Berthon
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Hungary. Postal address: Ludovika tér 2-6, H-1083, Budapest, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Hungary. Postal address: Ludovika tér 2-6, H-1083, Budapest, Hungary.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Postal address: Viale Druso, 1, I-39100, Bolzano, Italy.
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, Bolzano, Italy. Postal address: Viale Druso, 1, I-39100, Bolzano, Italy.
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - Helen D Donoghue
- Centre for Clinical Microbiology, University College London, London, UK. Postal address: Gower Street, London, WC1E 6BT, UK.
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, UK. Postal Address: B15 2TT Birmingham, UK.
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, Hungary. Postal address: Közép fasor 52, H-6726, Szeged, Hungary.
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41
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Hu Y, Liu J, Shen J, Feng X, Liu W, Zhu D, Zheng H, Hu D. Genotyping and Molecular Characterization of Fluoroquinolone's Resistance Among Multidrug-Resistant Mycobacterium tuberculosis in Southwest of China. Microb Drug Resist 2020; 27:865-870. [PMID: 33305990 DOI: 10.1089/mdr.2019.0339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although fluoroquinolones (FQs) are the backbone drugs for the treatment of multidrug-resistant tuberculosis (MDR-TB), the knowledge about the resistance pattern and molecular characterization of new-generation FQs in Chongqing is limited. This study aimed to investigate the resistance rate and mutation types of later-generation FQs against MDR-TB in Chongqing, and further to explore the relationship between different genotypes and phenotypes. A total of 967 clinical strains were characterized using multilocus sequence typing and drug susceptibility testing, followed by analysis of genotype/phenotype association. The 229 (23.7%, 229/967) isolates were identified as MDR-TB. The most effective agent against MDR-TB was gatifloxacin (GFX) (20.1%, 46/229), and the highest resistant rate was observed in ofloxacin (OFX) (41.0%, 94/229). Of the 190 strains (83.0%) identified as Beijing genotype, 111 isolates were modern Beijing genotype (58.4%) and 79 isolates were ancient Beijing genotype (41.6%). By analyzing 94 OFX-resistant isolates, 13 isolates were clustered with the cumulative clustering rate of 13.8% (13/94). Of the 91 isolates (39.7%, 91/229) with a mutation in gyrA gene, mutation in codon 94 was the most prevalent. Only 15 isolates (6.6%, 15/229) harbored a mutation in gyrB gene. There was no significant difference in the mutation rate of gyrA gene between Beijing and non-Beijing genotype, clustered isolates, and nonclustered isolates (p > 0.05).
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Affiliation(s)
- Yan Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jie Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Jing Shen
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Xin Feng
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Wenguo Liu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Damian Zhu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
| | - Huiwen Zheng
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Daiyu Hu
- Tuberculosis Reference Laboratory, Chongqing Tuberculosis Control Institute, Chongqing, China
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Subbian S, Singh P, Kolloli A, Nemes E, Scriba T, Hanekom WA, Kaplan G. BCG Vaccination of Infants Confers Mycobacterium tuberculosis Strain-Specific Immune Responses by Leukocytes. ACS Infect Dis 2020; 6:3141-3146. [PMID: 33226778 DOI: 10.1021/acsinfecdis.0c00696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The efficacy of bacille Calmette-Guerin (BCG) vaccination against tuberculosis is highly variable, and protective immunity elicited by BCG is poorly understood. We compared the cytokine/chemokine profiles of peripheral blood mononuclear cells (PBMC) obtained from infants BCG-vaccinated at birth to those of PBMC obtained from infants before (delayed) BCG vaccination. The PBMC from 10-week-old BCG-vaccinated infants released higher levels of pro-inflammatory molecules than PBMCs from the nonvaccinated counterpart. In vitro exposure of PBMCs from BCG-vaccinated infants, but not nonvaccinated infants, to two different Mycobacterium tuberculosis strains showed distinct pro- and anti-inflammatory cytokine/chemokine patterns. Thus, BCG-induced infant immune responses and their potential protective capacity may be shaped by the nature of the infecting Mtb strain.
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Affiliation(s)
- Selvakumar Subbian
- The Public Health Research Institute at New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, United States
| | - Pooja Singh
- The Public Health Research Institute at New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, United States
- Department of Pulmonary, Allergy, and Critical Care Medicine, The University of Alabama at Birmingham, Birmingham, Alabama 35294, United States
| | - Afsal Kolloli
- The Public Health Research Institute at New Jersey Medical School, Rutgers University, Newark, New Jersey 07103, United States
| | - Elisa Nemes
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Thomas Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town 7925, South Africa
| | - Willem A. Hanekom
- Africa Health Research Institute, KwaZulu-Natal Durban 4013, South Africa
| | - Gilla Kaplan
- Department of Medicine, University of Cape Town, Cape Town 7925, South Africa
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43
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- 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 7505, South Africa; ,
| | - Anzaan Dippenaar
- 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 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- 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 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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Sabin S, Herbig A, Vågene ÅJ, Ahlström T, Bozovic G, Arcini C, Kühnert D, Bos KI. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol 2020; 21:201. [PMID: 32778135 PMCID: PMC7418204 DOI: 10.1186/s13059-020-02112-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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Affiliation(s)
- Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Torbjörn Ahlström
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Gracijela Bozovic
- Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00 Lund, Sweden
| | - Caroline Arcini
- Arkeologerna, National Historical Museum, 226 60 Lund, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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Ghosh A, N S, Saha S. Survey of drug resistance associated gene mutations in Mycobacterium tuberculosis, ESKAPE and other bacterial species. Sci Rep 2020; 10:8957. [PMID: 32488120 PMCID: PMC7265455 DOI: 10.1038/s41598-020-65766-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/09/2020] [Indexed: 02/08/2023] Open
Abstract
Tuberculosis treatment includes broad-spectrum antibiotics such as rifampicin, streptomycin and fluoroquinolones, which are also used against other pathogenic bacteria. We developed Drug Resistance Associated Genes database (DRAGdb), a manually curated repository of mutational data of drug resistance associated genes (DRAGs) across ESKAPE (i.e. Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens, and other bacteria with a special focus on Mycobacterium tuberculosis (MTB). Analysis of mutations in drug-resistant genes listed in DRAGdb suggested both homoplasy and pleiotropy to be associated with resistance. Homoplasy was observed in six genes namely gidB, gyrA, gyrB, rpoB, rpsL and rrs. For these genes, drug resistance-associated mutations at codon level were conserved in MTB, ESKAPE and many other bacteria. Pleiotropy was exemplified by a single nucleotide mutation that was associated with resistance to amikacin, gentamycin, rifampicin and vancomycin in Staphylococcus aureus. DRAGdb data also revealed that mutations in some genes such as pncA, inhA, katG and embA,B,C were specific to Mycobacterium species. For inhA and pncA, the mutations in the promoter region along with those in coding regions were associated with resistance to isoniazid and pyrazinamide respectively. In summary, the DRAGdb database is a compilation of all the major MTB drug resistance genes across bacterial species, which allows identification of homoplasy and pleiotropy phenomena of DRAGs.
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Affiliation(s)
- Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Saran N
- Division of Bioinformatics, Bose Institute, Kolkata, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata, India.
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Van Rie A, Meehan C. The devil is in the diversity: Exploring within-person evolution of Mycobacterium tuberculosis. EBioMedicine 2020; 55:102758. [PMID: 32339938 PMCID: PMC7184153 DOI: 10.1016/j.ebiom.2020.102758] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 11/17/2022] Open
Affiliation(s)
- Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of medicine and health sciences, University of Antwerp, Antwerp, Belgium.
| | - Conor Meehan
- School of Chemistry and Biosciences, University of Bradford, UK
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47
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Nachappa SA, Neelambike SM, Sarikhani A, Ramachandra NB. Simultaneous Detection of Drug-resistant Mutations in Mycobacterium tuberculosis and Determining their Role through In Silico Docking. Infect Disord Drug Targets 2020; 21:134-141. [PMID: 32188396 DOI: 10.2174/1871526520666200318111140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 02/12/2020] [Accepted: 02/15/2020] [Indexed: 11/22/2022]
Abstract
A molecular method for diagnosis of drug-resistant Tuberculosis is Multiplex allele-specific PCR (MAS-PCR), which is more time-efficient, and its accuracy is studied using DNA sequencing. Also, understanding the role of mutations, when translated to protein, in causing resistance helps in better drug designing. AIM To study MAS-PCR in the detection of drug resistance in comparison to DNA sequencing in Mycobacterium tuberculosis, and understand the mechanism of interaction of drugs with mutant proteins. METHODS MAS-PCR was used for the detection of drug-resistant mutations and validation was done through DNA sequencing. MAS-PCR targeted four genes, iniA for the drug Ethambutol, rpsL and rrs for Streptomycin, and gyrA for Fluoroquinolone resistance, respectively. Further, the sequence data was analysed and modeled for in silico docking to study the effect on the interaction of the anti-TB drug molecule with the target protein. RESULTS We identified drug-resistant mutations in four out of 95 isolates with one of them carrying a mutation at codon iniA501, two at gyrA94, and one for both iniA501 and gyrA94 using MASPCR. DNA sequencing confirmed drug-resistant mutations in only two isolates, whereas two others had mutation adjacent to the target allele. Drug-protein docking showed Estimated Free Energy of Binding to be higher for Fluoroquinolone binding with GyrA D94V mutant. Both wild and mutant IniA interact with EMB but had no significant effect on binding energy. CONCLUSION DNA sequencing-based drug resistance detection of TB is more accurate than MASPCR. Understanding the role of mutations in influencing the drug-protein interaction will help in designing effective drug alternatives.
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Affiliation(s)
- Somanna Ajjamada Nachappa
- Department of Studies in Genetics and Genomics, Genetics and Genomics Lab, University of Mysore, Mysuru, Karnataka, India
| | - Sumana M Neelambike
- Department of Microbiology, JSS Medical College and Hospital, Mysuru, Karnataka, India
| | - Ahmad Sarikhani
- Department of Studies in Genetics and Genomics, Genetics and Genomics Lab, University of Mysore, Mysuru, Karnataka, India
| | - Nallur B Ramachandra
- Department of Studies in Genetics and Genomics, Genetics and Genomics Lab, University of Mysore, Mysuru, Karnataka, India
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Tudó G, Lopez-Gavin A, Portell-Buj E, Freixes J, Vila J, Roman A, Monté MR, Gonzalez-Martin J. In Vitro Activity of a Novel Quinolone, UB-8902, Against Ofloxacin-Resistant Mycobacterium tuberculosis Isolates. Microb Drug Resist 2020; 26:1019-1022. [PMID: 32159449 DOI: 10.1089/mdr.2019.0367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The main objective of this study was to compare in vitro activities of a novel fluoroquinolone (FQ), UB-8902, with ofloxacin (OFX), levofloxacin (LFX), and moxifloxacin (MOX) against Mycobacterium tuberculosis isolates. Eleven OFX-resistant and 11 drug-susceptible clinical isolates were studied. Individual minimum inhibitory concentrations of OFX, LFX, MOX, and UB-8902 were determined using Middlebrook 7H11 agar. The concentrations studied ranged from 0.125 to 128 μg/mL in twofold dilutions. UB-8902 was more active than LFX and similar to MOX for OFX-resistant M. tuberculosis isolates. In addition, UB-8902 and MOX showed equal activity against drug-susceptible isolates, both being more active than OFX and LFX. In conclusion, the new FQ, UB-8902, showed good activity against OFX-resistant isolates. Moreover, it showed better activity than OFX and LFX and was equivalent to MOX against FQ-susceptible clinical isolates. UB-8902 can be considered as a drug with potential antituberculous activity, similar to MOX.
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Affiliation(s)
- Griselda Tudó
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Alexandre Lopez-Gavin
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Elena Portell-Buj
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Joan Freixes
- Cenavisa Plc Laboratories, Reus, Tarragona, Spain
| | - Jordi Vila
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Angely Roman
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Maria Rosa Monté
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Julian Gonzalez-Martin
- Microbiology Department, CDB, Hospital Clinic-Barcelona Institute of Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
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Perdigão J, Gomes P, Miranda A, Maltez F, Machado D, Silva C, Phelan JE, Brum L, Campino S, Couto I, Viveiros M, Clark TG, Portugal I. Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. Sci Rep 2020; 10:2600. [PMID: 32054988 PMCID: PMC7018963 DOI: 10.1038/s41598-020-59558-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/13/2019] [Indexed: 01/12/2023] Open
Abstract
Portugal is a low incidence country for tuberculosis (TB) disease. Now figuring among TB low incidence countries, it has since the 1990s reported multidrug resistant and extensively drug resistant (XDR) TB cases, driven predominantly by two strain-types: Lisboa3 and Q1. This study describes the largest characterization of the evolutionary trajectory of M/XDR-TB strains in Portugal, spanning a time-period of two decades. By combining whole-genome sequencing and phenotypic susceptibility data for 207 isolates, we report the geospatial patterns of drug resistant TB, particularly the dispersion of Lisboa3 and Q1 clades, which underly 64.2% and 94.0% of all MDR-TB and XDR-TB isolates, respectively. Genomic-based similarity and a phylogenetic analysis revealed multiple clusters (n = 16) reflecting ongoing and uncontrolled recent transmission of M/XDR-TB, predominantly associated with the Lisboa3 and Q1 clades. These clades are now thought to be evolving in a polycentric mode across multiple geographical districts. The inferred evolutionary history is compatible with MDR- and XDR-TB originating in Portugal in the 70's and 80's, respectively, but with subsequent multiple emergence events of MDR and XDR-TB particularly involving the Lisboa3 clade. A SNP barcode was defined for Lisboa3 and Q1 and comparison with a phylogeny of global strain-types (n = 28 385) revealed the presence of Lisboa3 and Q1 strains in Europe, South America and Africa. In summary, Portugal displays an unusual and unique epidemiological setting shaped by >40 years of uncontrolled circulation of two main phylogenetic clades, leading to a sympatric evolutionary trajectory towards XDR-TB with the potential for global reach.
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Affiliation(s)
- João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
| | - Pedro Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Anabela Miranda
- Departamento de Doenças Infeciosas, Instituto Nacional de Saúde Dr. Ricardo Jorge, Porto, Portugal
| | - Fernando Maltez
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Serviço de Doenças Infecciosas, Hospital de Curry Cabral, Lisboa, Portugal
| | - Diana Machado
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Carla Silva
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody E Phelan
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | | | - Susana Campino
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Couto
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Miguel Viveiros
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Taane G Clark
- Unidade de Microbiologia Médica, Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, United Kingdom
| | - Isabel Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal.
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50
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An ancestral genomic locus in Mycobacterium tuberculosis clinical isolates from India hints the genetic link with Mycobacterium canettii. Int Microbiol 2020; 23:397-404. [PMID: 31898033 DOI: 10.1007/s10123-019-00113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Tuberculosis remains a worldwide public health emergency. To better understand M. tuberculosis and to identify genomic variations characteristic to the Indian clinical isolates by a low-cost method, a genomic subtractive hybridization between M. tuberculosis H37Rv and a clinical isolate from South India was performed. RESULTS This revealed a novel 0.4-kb subtractive fragment which was used as a handle to pull out a 4.5-kb genomic region characteristic to the clinical isolate and was absent in H37Rv. On further studies, this 4.5-kb region was found to be present in 91% of the M. tuberculosis clinical isolates screened from Kerala, a state in South India. Interestingly, this novel region has 99% identity (with 100% query coverage) with genomic regions of M. canettii. DISCUSSION The present study hypothesizes that this locus was present in the recent common environmental ancestor of mycobacteria, retained to the maximum extent in M. canettii and ancestral isolates of M. tuberculosis, and later deleted in other modern lineages of M. tuberculosis. Thus, this region may serve as one of the links between the pathogenic mycobacteria and the environmental species. We also propose that the Indian isolates of M. tuberculosis might be closely related to the putative progenitor M. prototuberculosis with respect to this locus. More studies on other genomic loci from different strains of M. tuberculosis are required to establish more links in this direction.
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