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Okumu A, Orwa J, Sitati R, Omondi I, Odhiambo B, Ogoro J, Oballa G, Ochieng B, Wandiga S, Ouma C. Factors associated with tuberculosis drug resistance among presumptive multidrug resistance tuberculosis patients identified in a DRTB surveillance study in western Kenya. J Clin Tuberc Other Mycobact Dis 2024; 37:100466. [PMID: 39188352 PMCID: PMC11345928 DOI: 10.1016/j.jctube.2024.100466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is caused by M. tuberculosis (Mtb) with resistance to the first-line anti-TB medicines isoniazid (INH) and rifampicin (RIF). In Western Kenya, there is reported low prevalence of drug resistant strains among HIV tuberculosis patients, creating a need to determine factors associated with drug resistance patterns among presumptive MDR-TB patients. To determine factors associated with drug resistance patterns among presumptive MDR-TB patients in western Kenya. Three hundred and ninety (3 9 0) sputum sample isolates from among presumptive multidrug TB patients, were analyzed for TB drug resistance as per Ministry of Health (MoH) TB program diagnostic algorithm. Frequency and percentages were used to summarize categorical data while median and interquartile range (IQR) were used for continuous data. Multivariable logistic regression was carried out to identify factors associated with TB drug resistance. Out of 390 participants enrolled, 302/390 (77.4 %) were males, with a median age of 34 years. The HIV-infected were 118/390 (30.3 %). Samples included 322 (82.6 %) from presumptive patients, while 68/390 (17.4 %) were either lost to follow-up patients, failures to first-line treatment or newly diagnosed cases. A total of 64/390 (16.4 %) of the isolates had at least some form of drug resistance. Out of 390, 14/390 (3.6 %) had MDR, 12 (3.1 %) were RIF mono-resistance, 34 (8.7 %) had INH, while 4 (1 %) had ethambutol resistance. The category of previously treated patients (those who received or are currently on TB treatment) had a 70 % reduced likelihood of resistance (aOR: 0.30; 95 % CI: 0.13-0.70). In contrast, older age was associated with an increased likelihood of resistance to INH and RIF, with an adjusted odds ratio of 1.04 per year (95 % CI: 1.00-1.08). Prompt MDR-TB diagnosis is essential for appropriate patient care, management, and disease prevention and control. We recommend active surveillance on drug resistant TB in these regions to detect drug resistance patterns for rapid disease management.
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Affiliation(s)
- Albert Okumu
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
- Department of Biomedical Sciences and Technology, Maseno University, PO Box 333-40105, Maseno, Kenya
| | - James Orwa
- The Aga Khan University, Department of Population Health Science, University Center, PO BOX 30270- 00100, Nairobi, Kenya
| | - Ruth Sitati
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
| | - Isaiah Omondi
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
| | - Ben Odhiambo
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
| | - Jeremiah Ogoro
- Ministry of Health, National Leprosy and Tuberculosis Program, NLTP, Afya House Annex, Kenyatta National Hospital, Hospital Road, Nairobi P.O. Box, 30016-00100, Kenya
| | - George Oballa
- Ministry of Health, National Leprosy and Tuberculosis Program, NLTP, Afya House Annex, Kenyatta National Hospital, Hospital Road, Nairobi P.O. Box, 30016-00100, Kenya
| | - Benjamin Ochieng
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
| | - Steve Wandiga
- Kenya Medical Research Institute, Centre for Global Health Research, PO Box 1578 -40100, Kisumu, Kenya
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, Maseno University, PO Box 333-40105, Maseno, Kenya
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Moens C, Bogaerts B, Lorente-Leal V, Vanneste K, De Keersmaecker SCJ, Roosens NHC, Mostin L, Fretin D, Marché S. Genomic comparison between Mycobacterium bovis and Mycobacterium microti and in silico analysis of peptide-based biomarkers for serodiagnosis. Front Vet Sci 2024; 11:1446930. [PMID: 39372902 PMCID: PMC11449866 DOI: 10.3389/fvets.2024.1446930] [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: 06/10/2024] [Accepted: 08/28/2024] [Indexed: 10/08/2024] Open
Abstract
In recent years, there has been an increase in the number of reported cases of Mycobacterium microti infection in various animals, which can interfere with the ante-mortem diagnosis of animal tuberculosis caused by Mycobacterium bovis. In this study, whole genome sequencing (WGS) was used to search for protein-coding genes to distinguish M. microti from M. bovis. In addition, the population structure of the available M. microti genomic WGS datasets is described, including three novel Belgian isolates from infections in alpacas. Candidate genes were identified by examining the presence of the regions of difference and by a pan-genome analysis of the available WGS data. A total of 80 genes showed presence-absence variation between the two species, including genes encoding Proline-Glutamate (PE), Proline-Proline-Glutamate (PPE), and Polymorphic GC-Rich Sequence (PE-PGRS) proteins involved in virulence and host interaction. Filtering based on predicted subcellular localization, sequence homology and predicted antigenicity resulted in 28 proteins out of 80 that were predicted to be potential antigens. As synthetic peptides are less costly and variable than recombinant proteins, an in silico approach was performed to identify linear and discontinuous B-cell epitopes in the selected proteins. From the 28 proteins, 157 B-cell epitope-based peptides were identified that discriminated between M. bovis and M. microti species. Although confirmation by in vitro testing is still required, these candidate synthetic peptides containing B-cell epitopes could potentially be used in serological tests to differentiate cases of M. bovis from M. microti infection, thus reducing misdiagnosis in animal tuberculosis surveillance.
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Affiliation(s)
- Charlotte Moens
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
- Laboratory of Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Victor Lorente-Leal
- VISAVET Health Surveillance Centre, Complutense University of Madrid, Madrid, Spain
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Laurent Mostin
- Experimental Center Machelen, Sciensano, Machelen, Belgium
| | - David Fretin
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Sylvie Marché
- Laboratory of Veterinary Bacteriology, Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
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Soliman MS, Hansen CH, Hanafy M, Shawky S, Rashed H, Abdullah M, Soliman NS, Gad MA, Khairat S, El-Kholy A, Talaat AM. Drug resistance and genomic variations among Mycobacterium tuberculosis isolates from The Nile Delta, Egypt. Sci Rep 2024; 14:20401. [PMID: 39223176 PMCID: PMC11369133 DOI: 10.1038/s41598-024-70199-8] [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: 03/19/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024] Open
Abstract
Tuberculosis is a global public health concern. Earlier reports suggested the emergence of high rates of drug resistant tuberculosis in Egypt. This study included 102 isolates of Mycobacterium tuberculosis collected from two reference laboratories in Cairo and Alexandria. All clinical isolates were sub-cultured on Löwenstein-Jensen medium and analyzed using both BD BACTEC MGIT 960 SIRE Kit and standard diffusion disk assays to identify the antibiotic sensitivity profile. Extracted genomic DNA was subjected to whole genome sequencing (WGS) using Illumina platform. Isolates that belong to lineage 4 represented > 80%, while lineage 3 represented only 11% of the isolates. The percentage of drug resistance for the streptomycin, isoniazid, rifampicin and ethambutol were 31.0, 17.2, 19.5 and 20.7, respectively. Nearly 47.1% of the isolates were sensitive to the four anti-tuberculous drugs, while only one isolate was resistant to all four drugs. In addition, several new and known mutations were identified by WGS. High rates of drug resistance and new mutations were identified in our isolates. Tuberculosis control measures should focus on the spread of mono (S, I, R, E)- and double (S, E)-drug resistant strains present at higher rates throughout the whole Nile Delta, Egypt.
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Affiliation(s)
- May S Soliman
- Department of Clinical and Chemical Pathology, Kasr Al Aini, Faculty of Medicine, Cairo University, Giza, Egypt.
| | - Chungyi H Hansen
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, USA
| | - Mostafa Hanafy
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, USA
- Department of Microbiology and Immunology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Sherine Shawky
- Microbiology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Heba Rashed
- Clinical Pathology Department, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Mohamed Abdullah
- Central Public Health Laboratories, Ministry of Health and Population, Cairo, Egypt
| | - Noha Salah Soliman
- Department of Clinical and Chemical Pathology, Kasr Al Aini, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Maha A Gad
- Department of Clinical and Chemical Pathology, Kasr Al Aini, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Sahar Khairat
- Department of Clinical and Chemical Pathology, Kasr Al Aini, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Amani El-Kholy
- Department of Clinical and Chemical Pathology, Kasr Al Aini, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Adel M Talaat
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, USA
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Gröschel MI, Pérez-Llanos FJ, Diel R, Vargas R, Escuyer V, Musser K, Trieu L, Meissner JS, Knorr J, Klinkenberg D, Kouw P, Homolka S, Samek W, Mathema B, van Soolingen D, Niemann S, Ahuja SD, Farhat MR. Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nat Microbiol 2024:10.1038/s41564-024-01758-y. [PMID: 39090390 DOI: 10.1038/s41564-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/12/2024] [Indexed: 08/04/2024]
Abstract
Several human-adapted Mycobacterium tuberculosis complex (Mtbc) lineages exhibit a restricted geographical distribution globally. These lineages are hypothesized to transmit more effectively among sympatric hosts, that is, those that share the same geographical area, though this is yet to be confirmed while controlling for exposure, social networks and disease risk after exposure. Using pathogen genomic and contact tracing data from 2,279 tuberculosis cases linked to 12,749 contacts from three low-incidence cities, we show that geographically restricted Mtbc lineages were less transmissible than lineages that have a widespread global distribution. Allopatric host-pathogen exposure, in which the restricted pathogen and host are from non-overlapping areas, had a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure tenfold lower uptake of geographically restricted lineage 6 strains compared with widespread lineage 4 strains in allopatric macrophage infections. We conclude that Mtbc strain-human long-term coexistence has resulted in differential transmissibility of Mtbc lineages and that this differs by human population.
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Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Francy J Pérez-Llanos
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- West German Genome Center, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, The University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kimberlee Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Lisa Trieu
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | | | - Jillian Knorr
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Don Klinkenberg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Peter Kouw
- Department of Tuberculosis, Public Health Service, Amsterdam, The Netherlands
| | - Susanne Homolka
- Diagnostic Mycobacteriology, National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Wojciech Samek
- Department of Electrical Engineering and Computer Science, Technical University Berlin, Berlin, Germany
- Department of Artificial Intelligence, Fraunhofer Heinrich Hertz Institute, Berlin, Germany
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Dick van Soolingen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Shama Desai Ahuja
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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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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Esteves LS, Gomes LL, Brites D, Fandinho FCO, Bhering M, Pereira MADS, Conceição EC, Salvato R, da Costa BP, Medeiros RFDM, Caldas PCDS, Redner P, Dalcolmo MP, Eldholm V, Gagneux S, Rossetti ML, Kritski AL, Suffys PN. Genetic Characterization and Population Structure of Drug-Resistant Mycobacterium tuberculosis Isolated from Brazilian Patients Using Whole-Genome Sequencing. Antibiotics (Basel) 2024; 13:496. [PMID: 38927163 PMCID: PMC11200758 DOI: 10.3390/antibiotics13060496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
The present study aimed to determine the genetic diversity of isolates of Mycobacterium tuberculosis (Mtb) from presumed drug-resistant tuberculosis patients from several states of Brazil. The isolates had been submitted to conventional drug susceptibility testing for first- and second-line drugs. Multidrug-resistant (MDR-TB) (54.8%) was the most frequent phenotypic resistance profile, in addition to an important high frequency of pre-extensive resistance (p-XDR-TB) (9.2%). Using whole-genome sequencing (WGS), we characterized 298 Mtb isolates from Brazil. Besides the analysis of genotype distribution and possible correlations between molecular and clinical data, we determined the performance of an in-house WGS pipeline with other online pipelines for Mtb lineages and drug resistance profile definitions. Sub-lineage 4.3 (52%) was the most frequent genotype, and the genomic approach revealed a p-XDR-TB level of 22.5%. We detected twenty novel mutations in three resistance genes, and six of these were observed in eight phenotypically resistant isolates. A cluster analysis of 170 isolates showed that 43.5% of the TB patients belonged to 24 genomic clusters, suggesting considerable ongoing transmission of DR-TB, including two interstate transmissions. The in-house WGS pipeline showed the best overall performance in drug resistance prediction, presenting the best accuracy values for five of the nine drugs tested. Significant associations were observed between suffering from fatal disease and genotypic p-XDR-TB (p = 0.03) and either phenotypic (p = 0.006) or genotypic (p = 0.0007) ethambutol resistance. The use of WGS analysis improved our understanding of the population structure of MTBC in Brazil and the genetic and clinical data correlations and demonstrated its utility for surveillance efforts regarding the spread of DR-TB, hopefully helping to avoid the emergence of even more resistant strains and to reduce TB incidence and mortality rates.
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Affiliation(s)
- Leonardo Souza Esteves
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Lia Lima Gomes
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
| | - Daniela Brites
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Fátima Cristina Onofre Fandinho
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Marcela Bhering
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Márcia Aparecida da Silva Pereira
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Emilyn Costa Conceição
- Department of Science and Innovation—National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa;
| | - Richard Salvato
- Centro de Desenvolvimento Científico e Tecnológico (CDCT), Secretaria Estadual de Saúde (SES-RS), Porto Alegre 90450-190, RS, Brazil;
| | - Bianca Porphirio da Costa
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Reginalda Ferreira de Melo Medeiros
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Paulo Redner
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Margareth Pretti Dalcolmo
- Centro de Referência Professor Hélio Fraga, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 22780-195, RJ, Brazil; (F.C.O.F.); (M.B.); (M.A.d.S.P.); (B.P.d.C.); (R.F.d.M.M.); (P.C.d.S.C.); (P.R.); (M.P.D.)
| | - Vegard Eldholm
- Norwegian Institute of Public Health, 0213 Oslo, Norway;
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute (Swiss TPH), CH-4123 Allschwil, Switzerland; (D.B.); (S.G.)
- University of Basel, CH-4001 Basel, Switzerland
| | - Maria Lucia Rossetti
- Laboratório de Biologia Molecular, Universidade Luterana do Brasil (ULBRA), Canoas 92425-020, RS, Brazil;
| | - Afrânio Lineu Kritski
- Programa Acadêmico de Tuberculose da Faculdade de Medicina, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-590, RJ, Brazil;
| | - Philip Noel Suffys
- Laboratório de Biologia Molecular Aplicado à Micobactérias, Fundação Oswaldo Cruz (FIOCRUZ), Instituto Oswaldo Cruz (IOC), Rio de Janeiro 21040-360, RJ, Brazil; (L.L.G.); (P.N.S.)
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7
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Getahun M, Beyene D, Mollalign H, Diriba G, Tesfaye E, Yenew B, Taddess M, Sinshaw W, Ameni G. Population structure and spatial distribution of Mycobacterium tuberculosis in Ethiopia. Sci Rep 2024; 14:10455. [PMID: 38714745 PMCID: PMC11076284 DOI: 10.1038/s41598-024-59435-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/10/2024] [Indexed: 05/10/2024] Open
Abstract
Ethiopia is one of the countries with a high tuberculosis (TB) burden, yet little is known about the spatial distribution of Mycobacterium tuberculosis (Mtb) lineages. This study identifies the spoligotyping of 1735 archived Mtb isolates from the National Drug Resistance Survey, collected between November 2011 and June 2013, to investigate Mtb population structure and spatial distribution. Spoligotype International Types (SITs) and lineages were retrieved from online databases. The distribution of lineages was evaluated using Fisher's exact test and logistic regression models. The Global Moran's Index and Getis-Ord Gi statistic were utilized to identify hotspot areas. Our results showed that spoligotypes could be interpreted and led to 4 lineages and 283 spoligotype patterns in 91% of the isolates, including 4% of those with multidrug/rifampicin resistance (MDR/RR) TB. The identified Mtb lineages were lineage 1 (1.8%), lineage 3 (25.9%), lineage 4 (70.6%) and lineage 7 (1.6%). The proportion of lineages 3 and 4 varied by regions, with lineage 3 being significantly greater than lineage 4 in reports from Gambella (AOR = 4.37, P < 0.001) and Tigray (AOR = 3.44, P = 0.001) and lineage 4 being significantly higher in Southern Nations Nationalities and Peoples Region (AOR = 1.97, P = 0.026) than lineage 3. Hotspots for lineage 1 were located in eastern Ethiopia, while a lineage 7 hotspot was identified in northern and western Ethiopia. The five prevalent spoligotypes, which were SIT149, SIT53, SIT25, SIT37 and SIT26 account for 42.8% of all isolates under investigation, while SIT149, SIT53 and SIT21 account for 52-57.8% of drug-resistant TB cases. TB and drug resistant TB are mainly caused by lineages 3 and 4, and significant proportions of the prevalent spoligotypes also influence drug-resistant TB and the total TB burden. Regional variations in lineages may result from both local and cross-border spread.
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Affiliation(s)
- Muluwork Getahun
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia.
| | - Dereje Beyene
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Hilina Mollalign
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Getu Diriba
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Ephrem Tesfaye
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Mengistu Taddess
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- Ethiopian Public Health Institute, P.O. Box 1242, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
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8
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Hiza H, Zwyer M, Hella J, Arbués A, Sasamalo M, Borrell S, Xu ZM, Ross A, Brites D, Fellay J, Reither K, Gagneux S, Portevin D. Bacterial diversity dominates variable macrophage responses of tuberculosis patients in Tanzania. Sci Rep 2024; 14:9287. [PMID: 38653771 DOI: 10.1038/s41598-024-60001-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/17/2024] [Indexed: 04/25/2024] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) comprises nine human-adapted lineages that differ in their geographical distribution. Local adaptation of specific MTBC genotypes to the respective human host population has been invoked in this context. We aimed to assess if bacterial genetics governs MTBC pathogenesis or if local co-adaptation translates into differential susceptibility of human macrophages to infection by different MTBC genotypes. We generated macrophages from cryopreserved blood mononuclear cells of Tanzanian tuberculosis patients, from which the infecting MTBC strains had previously been phylogenetically characterized. We infected these macrophages ex vivo with a phylogenetically similar MTBC strain ("matched infection") or with strains representative of other MTBC lineages ("mismatched infection"). We found that L1 infections resulted in a significantly lower bacterial burden and that the intra-cellular replication rate of L2 strains was significantly higher compared the other MTBC lineages, irrespective of the MTBC lineage originally infecting the patients. Moreover, L4-infected macrophages released significantly greater amounts of TNF-α, IL-6, IL-10, MIP-1β, and IL-1β compared to macrophages infected by all other strains. While our results revealed no measurable effect of local adaptation, they further highlight the strong impact of MTBC phylogenetic diversity on the variable outcome of the host-pathogen interaction in human tuberculosis.
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Affiliation(s)
- Hellen Hiza
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Michaela Zwyer
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jerry Hella
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Ainhoa Arbués
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mohamed Sasamalo
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Bagamoyo, Tanzania
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Zhi Ming Xu
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jacques Fellay
- School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Klaus Reither
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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9
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Kwon KW, Choi HG, Kim KS, Park SA, Kim HJ, Shin SJ. BCG-booster vaccination with HSP90-ESAT-6-HspX-RipA multivalent subunit vaccine confers durable protection against hypervirulent Mtb in mice. NPJ Vaccines 2024; 9:55. [PMID: 38459038 PMCID: PMC10923817 DOI: 10.1038/s41541-024-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024] Open
Abstract
The quest for effective and enhanced multiantigenic tuberculosis (TB) subunit vaccine necessitates the induction of a protective pathogen-specific immune response while circumventing detrimental inflammation within the lung milieu. In line with this goal, we engineered a modified iteration of the quadrivalent vaccine, namely HSP90-ESAT-6-HspX-RipA (HEHR), which was coupled with the TLR4 adjuvant, CIA09A. The ensuing formulation was subjected to comprehensive assessment to gauge its protective efficacy against the hypervirulent Mycobacterium tuberculosis (Mtb) Haarlem clinical strain M2, following a BCG-prime boost regimen. Regardless of vaccination route, both intramuscular and subcutaneous administration with the HEHR vaccine exhibited remarkable protective efficacy in significantly reducing the Mtb bacterial burden and pulmonary inflammation. This underscores its notably superior protective potential compared to the BCG vaccine alone or a former prototype, the HSP90-E6 subunit vaccine. In addition, this superior protective efficacy was confirmed when testing a tag-free version of the HEHR vaccine. Furthermore, the protective immune determinant, represented by durable antigen-specific CD4+IFN-γ+IL-17A+ T-cells expressing a CXCR3+KLRG1- cell surface phenotype in the lung, was robustly induced in HEHR-boosted mice at 12 weeks post-challenge. Collectively, our data suggest that the BCG-prime HEHR boost vaccine regimen conferred improved and long-term protection against hypervirulent Mtb strain with robust antigen-specific Th1/Th17 responses.
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Affiliation(s)
- Kee Woong Kwon
- Department of Microbiology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea
- Department of Microbiology, College of Medicine, Gyeongsang National University, Jinju, 52727, South Korea
| | - Han-Gyu Choi
- Department of Microbiology, and Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, South Korea
| | | | - Shin Ae Park
- R&D Center, EyeGene Inc., Goyang, 10551, South Korea
| | - Hwa-Jung Kim
- Department of Microbiology, and Medical Science, College of Medicine, Chungnam National University, Daejeon, 35015, South Korea.
| | - Sung Jae Shin
- Department of Microbiology, Graduate School of Medical Science, Brain Korea 21 Project, Yonsei University College of Medicine, Seoul, 03722, South Korea.
- Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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10
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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11
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Nysten J, Sofras D, Van Dijck P. One species, many faces: The underappreciated importance of strain diversity. PLoS Pathog 2024; 20:e1011931. [PMID: 38271302 PMCID: PMC10810500 DOI: 10.1371/journal.ppat.1011931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Affiliation(s)
- Jana Nysten
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Dimitrios Sofras
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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12
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Du DH, Geskus RB, Zhao Y, Codecasa LR, Cirillo DM, van Crevel R, Pascapurnama DN, Chaidir L, Niemann S, Diel R, Omar SV, Grandjean L, Rokadiya S, Ortitz AT, Lân NH, Hà ĐTM, Smith EG, Robinson E, Dedicoat M, Nhat LTH, Thwaites GE, Van LH, Thuong NTT, Walker TM. The effect of M. tuberculosis lineage on clinical phenotype. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001788. [PMID: 38117783 PMCID: PMC10732390 DOI: 10.1371/journal.pgph.0001788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Six lineages of Mycobacterium tuberculosis sensu stricto (which excludes M. africanum) are described. Single-country or small observational data suggest differences in clinical phenotype between lineages. We present strain lineage and clinical phenotype data from 12,246 patients from 3 low-incidence and 5 high-incidence countries. We used multivariable logistic regression to explore the effect of lineage on site of disease and on cavities on chest radiography, given pulmonary TB; multivariable multinomial logistic regression to investigate types of extra-pulmonary TB, given lineage; and accelerated failure time and Cox proportional-hazards models to explore the effect of lineage on time to smear and culture-conversion. Mediation analyses quantified the direct effects of lineage on outcomes. Pulmonary disease was more likely among patients with lineage(L) 2, L3 or L4, than L1 (adjusted odds ratio (aOR) 1.79, (95% confidence interval 1.49-2.15), p<0.001; aOR = 1.40(1.09-1.79), p = 0.007; aOR = 2.04(1.65-2.53), p<0.001, respectively). Among patients with pulmonary TB, those with L1 had greater risk of cavities on chest radiography versus those with L2 (aOR = 0.69(0.57-0.83), p<0.001) and L4 strains (aOR = 0.73(0.59-0.90), p = 0.002). L1 strains were more likely to cause osteomyelitis among patients with extra-pulmonary TB, versus L2-4 (p = 0.033, p = 0.008 and p = 0.049 respectively). Patients with L1 strains showed shorter time-to-sputum smear conversion than for L2. Causal mediation analysis showed the effect of lineage in each case was largely direct. The pattern of clinical phenotypes seen with L1 strains differed from modern lineages (L2-4). This has implications for clinical management and could influence clinical trial selection strategies.
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Affiliation(s)
- Duc Hong Du
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ronald B. Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Luigi Ruffo Codecasa
- Regional TB Reference Centre/ Istituto Villa Marelli- ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | | | - Reinout van Crevel
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Lidya Chaidir
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, Indonesia
| | - Stefan Niemann
- Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Lung Clinic Grosshansdorf, Airway Disease Center North (ARCN), German Center for Lung Research (DZL), Grosshansdorf, Germany
| | | | | | - Sakib Rokadiya
- University College London Hospital, London, United Kingdom
| | | | | | | | - E. Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Esther Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
| | - Martin Dedicoat
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, Birmingham, United Kingdom
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Le Hong Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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13
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Senelle G, Sahal MR, La K, Billard-Pomares T, Marin J, Mougari F, Bridier-Nahmias A, Carbonnelle E, Cambau E, Refrégier G, Guyeux C, Sola C. Towards the reconstruction of a global TB history using a new pipeline "TB-Annotator". Tuberculosis (Edinb) 2023; 143S:102376. [PMID: 38012933 DOI: 10.1016/j.tube.2023.102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 11/29/2023]
Abstract
Mycobacterium tuberculosis complex (MTBC) has a population structure consisting of 9 human and animal lineages. The genomic diversity within these lineages is a pathogenesis factor that affects virulence, transmissibility, host response, and antibiotic resistance. Hence it is important to develop improved information systems for tracking and understanding the spreading and evolution of genomes. We present results obtained thanks to a new informatics platform for computational biology of MTBC, that uses a convenience sample from public/private SRAs, designated as TB-Annotator. Version 1 was a first interactive graphic-based web tool based on 15,901 representative genomes. Version 2, still interactive, is a more sophisticated database, developed using the Snakemake Workflow Management System (WMS) that allows an unsupervised global and scalable analysis of the content of the USA National Center for Biotechnology Information Short Read Archives database. This platform analyzes nucleotide variants, the presence/absence of genes, known regions of difference and detect new deletions, the insertion sites of mobile genetic elements, and allows phylogenetic trees to be built, imported in a graphical interface and interactively analyzed between the data and the tree. The objective of TB-Annotator is triple: detect recent epidemiological links, reconstruct distant phylogeographical histories as well as perform more complex phenotypic/genotypic Genome-Wide Association Studies (GWAS). In this paper, we compare the various taxonomic SNPs-based labels and hierarchies previously described in recent reference papers for L1, and present a comparative analysis that allows identification of alias and thus provides the basis of a future unifying naming scheme for L1 sublineages. We present a global phylogenetic tree built with RAxML-NG, and one on L2; at the time of writing, we characterized about 200 sublineages, with many new ones; a detail tree for Modern L2 and a hierarchical scheme allowing to facilitate L2 lineage assignment are also presented.
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Affiliation(s)
- Gaetan Senelle
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Muhammed Rabiu Sahal
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France
| | - Kevin La
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Typhaine Billard-Pomares
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Julie Marin
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Faiza Mougari
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | | | - Etienne Carbonnelle
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Emmanuelle Cambau
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Guislaine Refrégier
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Christophe Sola
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France.
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14
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Schami A, Islam MN, Belisle JT, Torrelles JB. Drug-resistant strains of Mycobacterium tuberculosis: cell envelope profiles and interactions with the host. Front Cell Infect Microbiol 2023; 13:1274175. [PMID: 38029252 PMCID: PMC10664572 DOI: 10.3389/fcimb.2023.1274175] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
In the past few decades, drug-resistant (DR) strains of Mycobacterium tuberculosis (M.tb), the causative agent of tuberculosis (TB), have become increasingly prevalent and pose a threat to worldwide public health. These strains range from multi (MDR) to extensively (XDR) drug-resistant, making them very difficult to treat. Further, the current and future impact of the Coronavirus Disease 2019 (COVID-19) pandemic on the development of DR-TB is still unknown. Although exhaustive studies have been conducted depicting the uniqueness of the M.tb cell envelope, little is known about how its composition changes in relation to drug resistance acquisition. This knowledge is critical to understanding the capacity of DR-M.tb strains to resist anti-TB drugs, and to inform us on the future design of anti-TB drugs to combat these difficult-to-treat strains. In this review, we discuss the complexities of the M.tb cell envelope along with recent studies investigating how M.tb structurally and biochemically changes in relation to drug resistance. Further, we will describe what is currently known about the influence of M.tb drug resistance on infection outcomes, focusing on its impact on fitness, persister-bacteria, and subclinical TB.
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Affiliation(s)
- Alyssa Schami
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - M. Nurul Islam
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - John T. Belisle
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Jordi B. Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, United States
- International Center for the Advancement of Research & Education, International Center for the Advancement of Research & Education, Texas Biomedical Research Institute, San Antonio, TX, United States
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15
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Torrelles JB, Chatterjee D. Collected Thoughts on Mycobacterial Lipoarabinomannan, a Cell Envelope Lipoglycan. Pathogens 2023; 12:1281. [PMID: 38003746 PMCID: PMC10675199 DOI: 10.3390/pathogens12111281] [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: 08/30/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
The presence of lipoarabinomannan (LAM) in the Mycobacterium tuberculosis (Mtb) cell envelope was first reported close to 100 years ago. Since then, numerous studies have been dedicated to the isolation, purification, structural definition, and elucidation of the biological properties of Mtb LAM. In this review, we present a brief historical perspective on the discovery of Mtb LAM and the herculean efforts devoted to structurally characterizing the molecule because of its unique structural and biological features. The significance of LAM remains high to this date, mainly due to its distinct immunological properties in conjunction with its role as a biomarker for diagnostic tests due to its identification in urine, and thus can serve as a point-of-care diagnostic test for tuberculosis (TB). In recent decades, LAM has been thoroughly studied and massive amounts of information on this intriguing molecule are now available. In this review, we give the readers a historical perspective and an update on the current knowledge of LAM with information on the inherent carbohydrate composition, which is unique due to the often puzzling sugar residues that are specifically found on LAM. We then guide the readers through the complex and myriad immunological outcomes, which are strictly dependent on LAM's chemical structure. Furthermore, we present issues that remain unresolved and represent the immediate future of LAM research. Addressing the chemistry, functions, and roles of LAM will lead to innovative ways to manipulate the processes that involve this controversial and fascinating biomolecule.
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Affiliation(s)
- Jordi B. Torrelles
- International Center for the Advancement of Research and Education (I • Care), Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Delphi Chatterjee
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
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16
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Mekonnen D, Munshea A, Nibret E, Adnew B, Getachew H, Kebede A, Gebrewahid A, Herrera-Leon S, Aramendia AA, Benito A, Abascal E, Jacqueline C, Aseffa A, Herrera-Leon L. Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020-2022: In-silico Whole-Genome Sequence Analysis. Infect Drug Resist 2023; 16:6859-6870. [PMID: 37908783 PMCID: PMC10614653 DOI: 10.2147/idr.s429001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020-2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshea
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | | | | | - Amiro Kebede
- Amhara Public Health Institute, Bahir Dar, Ethiopia
| | | | - Silvia Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain
| | - Estefanía Abascal
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Jacqueline
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Laura Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
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Brenner EP, Sreevatsan S. Global-scale GWAS associates a subset of SNPs with animal-adapted variants in M. tuberculosis complex. BMC Med Genomics 2023; 16:260. [PMID: 37875894 PMCID: PMC10598944 DOI: 10.1186/s12920-023-01695-5] [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: 05/10/2023] [Accepted: 10/11/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND While Mycobacterium tuberculosis complex (MTBC) variants are clonal, variant tuberculosis is a human-adapted pathogen, and variant bovis infects many hosts. Despite nucleotide identity between MTBC variants exceeding 99.95%, it remains unclear what drives these differences. Markers of adaptation into variants were sought by bacterial genome-wide association study of single nucleotide polymorphisms extracted from 6,362 MTBC members from varied hosts and countries. RESULTS The search identified 120 genetic loci associated with MTBC variant classification and certain hosts. In many cases, these changes are uniformly fixed in certain variants while absent in others in this dataset, providing good discriminatory power in distinguishing variants by polymorphisms. Multiple changes were seen in genes for cholesterol and fatty acid metabolism, pathways previously proposed to be important for host adaptation, including Mce4F (part of the fundamental cholesterol intake Mce4 pathway), 4 FadD and FadE genes (playing roles in cholesterol and fatty acid utilization), and other targets like Rv3548c and PTPB, genes shown essential for growth on cholesterol by transposon studies. CONCLUSIONS These findings provide a robust set of genetic loci associated with the split of variant bovis and variant tuberculosis, and suggest that adaptation to new hosts could involve adjustments in uptake and catabolism of cholesterol and fatty acids, like the proposed specialization to different populations in MTB lineages by alterations to host lipid composition. Future studies are required to elucidate how the associations between cholesterol profiles and pathogen utilization differences between hosts and MTBC variants, as well as the investigation of uncharacterized genes discovered in this study. This information will likely provide an understanding on the diversification of MBO away from humans and specialization towards a broad host range.
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Affiliation(s)
- Evan P Brenner
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, 784 Wilson Road, East Lansing, MI, 48824, USA.
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18
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Klever AM, Alexander KA, Almeida D, Anderson MZ, Ball RL, Beamer G, Boggiatto P, Buikstra JE, Chandler B, Claeys TA, Concha AE, Converse PJ, Derbyshire KM, Dobos KM, Dupnik KM, Endsley JJ, Endsley MA, Fennelly K, Franco-Paredes C, Hagge DA, Hall-Stoodley L, Hayes D, Hirschfeld K, Hofman CA, Honda JR, Hull NM, Kramnik I, Lacourciere K, Lahiri R, Lamont EA, Larsen MH, Lemaire T, Lesellier S, Lee NR, Lowry CA, Mahfooz NS, McMichael TM, Merling MR, Miller MA, Nagajyothi JF, Nelson E, Nuermberger EL, Pena MT, Perea C, Podell BK, Pyle CJ, Quinn FD, Rajaram MVS, Mejia OR, Rothoff M, Sago SA, Salvador LCM, Simonson AW, Spencer JS, Sreevatsan S, Subbian S, Sunstrum J, Tobin DM, Vijayan KKV, Wright CTO, Robinson RT. The Many Hosts of Mycobacteria 9 (MHM9): A conference report. Tuberculosis (Edinb) 2023; 142:102377. [PMID: 37531864 PMCID: PMC10529179 DOI: 10.1016/j.tube.2023.102377] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 08/04/2023]
Abstract
The Many Hosts of Mycobacteria (MHM) meeting series brings together basic scientists, clinicians and veterinarians to promote robust discussion and dissemination of recent advances in our knowledge of numerous mycobacterial diseases, including human and bovine tuberculosis (TB), nontuberculous mycobacteria (NTM) infection, Hansen's disease (leprosy), Buruli ulcer and Johne's disease. The 9th MHM conference (MHM9) was held in July 2022 at The Ohio State University (OSU) and centered around the theme of "Confounders of Mycobacterial Disease." Confounders can and often do drive the transmission of mycobacterial diseases, as well as impact surveillance and treatment outcomes. Various confounders were presented and discussed at MHM9 including those that originate from the host (comorbidities and coinfections) as well as those arising from the environment (e.g., zoonotic exposures), economic inequality (e.g. healthcare disparities), stigma (a confounder of leprosy and TB for millennia), and historical neglect (a confounder in Native American Nations). This conference report summarizes select talks given at MHM9 highlighting recent research advances, as well as talks regarding the historic and ongoing impact of TB and other infectious diseases on Native American Nations, including those in Southwestern Alaska where the regional TB incidence rate is among the highest in the Western hemisphere.
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Affiliation(s)
- Abigail Marie Klever
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Kathleen A Alexander
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, VA, USA; CARACAL/Chobe Research Institute Kasane, Botswana
| | - Deepak Almeida
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Matthew Z Anderson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA; Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | | | - Gillian Beamer
- Host Pathogen Interactions and Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Paola Boggiatto
- Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA
| | - Jane E Buikstra
- Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Bruce Chandler
- Division of Public Health, Alaska Department of Health, AK, USA
| | - Tiffany A Claeys
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Aislinn E Concha
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Paul J Converse
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Keith M Derbyshire
- Division of Genetics, The Wadsworth Center, New York State Department of Health, Albany, NY, USA; Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Karen M Dobos
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Kathryn M Dupnik
- Center for Global Health, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Janice J Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark A Endsley
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kevin Fennelly
- Pulmonary Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Carlos Franco-Paredes
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA; Hospital Infantil de México Federico Gómez, México, USA
| | | | - Luanne Hall-Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Don Hayes
- Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Courtney A Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK, USA
| | - Jennifer R Honda
- Department of Cellular and Molecular Biology, University of Texas Health Science Center at Tyler, Tyler, TX, USA
| | - Natalie M Hull
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, OH, USA
| | - Igor Kramnik
- Pulmonary Center, The Department of Medicine, Boston University Chobanian & Aveedisian School of Medicine, National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Karen Lacourciere
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Ramanuj Lahiri
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Elise A Lamont
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Michelle H Larsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Sandrine Lesellier
- French Agency for Food, Environmental & Occupational Health & Safety (ANSES), Laboratory for Rabies and Wildlife,Nancy, France
| | - Naomi R Lee
- Department of Chemistry and Biochemistry, Northern Arizona University, Flagstaff, AZ, USA
| | - Christopher A Lowry
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Najmus S Mahfooz
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Temet M McMichael
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Marlena R Merling
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Michele A Miller
- DSI-NRF 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, Cape Town, South Africa
| | - Jyothi F Nagajyothi
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Elizabeth Nelson
- Microbial Paleogenomics Unit, Dept of Genomes and Genetics, Institut Pasteur, Paris, France
| | - Eric L Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University, Baltimore, MD, USA
| | - Maria T Pena
- United States Department of Health and Human Services, Health Resources and Services Administration, Health Systems Bureau, National Hansen's Disease Program, Baton Rouge, LA, USA
| | - Claudia Perea
- Animal & Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Brendan K Podell
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Charlie J Pyle
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Fred D Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Murugesan V S Rajaram
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | - Oscar Rosas Mejia
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA
| | | | - Saydie A Sago
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Andrew W Simonson
- Department of Microbiology and Molecular Genetics and the Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John S Spencer
- Department of Microbiology, Immunology, and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, USA
| | - Srinand Sreevatsan
- Pathobiology & Diagnostic Investigation Department, College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Selvakumar Subbian
- Public Health Research Institute (PHRI), New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | | | - David M Tobin
- Department of Molecular Genetics & Microbiology, Duke University School of Medicine, Durham, NC, USA; Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - K K Vidya Vijayan
- Department of Microbiology and Immunology, Center for AIDS Research, and Children's Research Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Caelan T O Wright
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA
| | - Richard T Robinson
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA; Infectious Diseases Institute, The Ohio State University, OH, USA.
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Shitikov E, Bespiatykh D. A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates. mSphere 2023; 8:e0016923. [PMID: 37314207 PMCID: PMC10449489 DOI: 10.1128/msphere.00169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/28/2023] [Indexed: 06/15/2023] Open
Abstract
The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the Mycobacterium tuberculosis complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of M. tuberculosis/M. africanum and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread. IMPORTANCE Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.
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Affiliation(s)
- Egor Shitikov
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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Osei-Wusu S, Tetteh JKA, Musah AB, Ntiamoah DO, Arthur N, Adjei A, Arbues A, Ofori EA, Mensah KA, Galevo SEA, Frempong AF, Asare P, Asante-Poku A, Otchere ID, Kusi KA, Lenz TL, Gagneux S, Portevin D, Yeboah-Manu D. Macrophage susceptibility to infection by Ghanaian Mycobacterium tuberculosis complex lineages 4 and 5 varies with self-reported ethnicity. Front Cell Infect Microbiol 2023; 13:1163993. [PMID: 37645380 PMCID: PMC10461633 DOI: 10.3389/fcimb.2023.1163993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023] Open
Abstract
Background The epidemiology of Mycobacterium tuberculosis complex (MTBC) lineage 5 (L5) infections in Ghana revealed a significantly increased prevalence in Ewes compared to other self-reported ethnic groups. In that context, we sought to investigate the early phase of tuberculosis (TB) infection using ex vivo infection of macrophages derived from the blood of Ewe and Akan ethnic group volunteers with MTBC L4 and L5 strains. Methods The study participants consisted of 16 controls, among which self-reported Akan and Ewe ethnicity was equally represented, as well as 20 cured TB cases consisting of 11 Akans and 9 Ewes. Peripheral blood mononuclear cells were isolated from both healthy controls and cured TB cases. CD14+ monocytes were isolated and differentiated into monocyte-derived macrophages (MDMs) before infection with L4 or L5 endemic strains. The bacterial load was assessed after 2 hours (uptake) as well as 3 and 7 days post-infection. Results We observed a higher capacity of MDMs from Ewes to phagocytose L4 strains (p < 0.001), translating into a higher bacillary load on day 7 (p < 0.001) compared to L5, despite the higher replication rate of L5 in Ewe MDMs (fold change: 1.4 vs. 1.2, p = 0.03) among the controls. On the contrary, within macrophages from Akans, we observed a significantly higher phagocytic uptake of L5 (p < 0.001) compared to L4, also translating into a higher load on day 7 (p = 0.04). However, the replication rate of L4 in Akan MDMs was higher than that of L5 (fold change: L4 = 1.2, L4 = 1.1, p = 0.04). Although there was no significant difference in the uptake of L4 and L5 among cured TB cases, there was a higher bacterial load of both L4 (p = 0.02) and L5 (p = 0.02) on day 7 in Ewe MDMs. Conclusion Our results suggest that host ethnicity (driven by host genetic diversity), MTBC genetic diversity, and individual TB infection history are all acting together to modulate the outcome of macrophage infections by MTBC.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Legon, Ghana
| | - John K. A. Tetteh
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Nelly Arthur
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Abraham Adjei
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Ainhoa Arbues
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Ebenezer Addo Ofori
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Akyea Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Abena Frema Frempong
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Asamoah Kusi
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Tobias L. Lenz
- Research Group for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Damien Portevin
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [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: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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22
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Yu J, Liu M, Mijiti X, Liu H, Wang Q, Yin C, Anwaierjiang A, Xu M, Li M, Deng L, Xiao H, Zhao X, Wan K, Li G, Yuan X. Association of Single-Nucleotide Polymorphisms in the VDR Gene with Tuberculosis and Infection of Beijing Genotype Mycobacterium tuberculosis. Infect Drug Resist 2023; 16:3157-3169. [PMID: 37235072 PMCID: PMC10208660 DOI: 10.2147/idr.s407595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Background The aim of the present study was to investigate the association between vitamin D receptor (VDR) gene polymorphism and tuberculosis susceptibility, as well as the potential interaction of host genetic factors with the heterogeneity of Mycobacterium tuberculosis in the population from Xinjiang, China. Methods From January 2019 to January 2020, we enrolled 221 tuberculosis patients as the case group and 363 staff with no clinical symptoms as the control group from four designated tuberculosis hospitals in southern Xinjiang, China. The polymorphisms of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in the VDR were detected by sequencing. M. tuberculosis isolates were collected from the case group and identified as Beijing or non-Beijing lineage by multiplex PCR. Propensity score (PS), univariate analysis and multivariable logistic regression models were used to perform the analysis. Results Our results showed that the allele and genotype frequencies of Fok I, Taq I, Apa I, Bsm I, rs3847987 and rs739837 in VDR were not correlated with tuberculosis susceptibility or lineages of M. tuberculosis. Two out of six loci of the VDR gene formed one haplotype block, and none of the haplotypes was found to correlate with tuberculosis susceptibility or lineages of M. tuberculosis infected. Conclusion Polymorphisms in the VDR gene may not indicate susceptibility to tuberculosis. There was also no evidence on the interaction between the VDR gene of host and the lineages of M. tuberculosis in the population from Xinjiang, China. Further studies are nonetheless required to prove our conclusions.
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Affiliation(s)
- Jinjie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Mengwen Liu
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Chunjie Yin
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | | | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830049, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Lele Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xiao
- School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang, 830011, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
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23
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Hailu E, Cantillon D, Madrazo C, Rose G, Wheeler PR, Golby P, Adnew B, Gagneux S, Aseffa A, Gordon SV, Comas I, Young DB, Waddell SJ, Larrouy-Maumus G, Berg S. Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex. Microb Genom 2023; 9:mgen001011. [PMID: 37171244 PMCID: PMC10272862 DOI: 10.1099/mgen.0.001011] [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: 09/26/2022] [Accepted: 03/07/2023] [Indexed: 05/13/2023] Open
Abstract
Lineage 7 (L7) emerged in the phylogeny of the Mycobacterium tuberculosis complex (MTBC) subsequent to the branching of 'ancient' lineage 1 and prior to the Eurasian dispersal of 'modern' lineages 2, 3 and 4. In contrast to the major MTBC lineages, the current epidemiology suggests that prevalence of L7 is highly confined to the Ethiopian population, or when identified outside of Ethiopia, it has mainly been in patients of Ethiopian origin. To search for microbiological factors that may contribute to its restricted distribution, we compared the genome of L7 to the genomes of globally dispersed MTBC lineages. The frequency of predicted functional mutations in L7 was similar to that documented in other lineages. These include mutations characteristic of modern lineages - such as constitutive expression of nitrate reductase - as well as mutations in the VirS locus that are commonly found in ancient lineages. We also identified and characterized multiple lineage-specific mutations in L7 in biosynthesis pathways of cell wall lipids, including confirmed deficiency of methoxy-mycolic acids due to a stop-gain mutation in the mmaA3 gene that encodes a methoxy-mycolic acid synthase. We show that the abolished biosynthesis of methoxy-mycolates of L7 alters the cell structure and colony morphology on selected growth media and impacts biofilm formation. The loss of these mycolic acid moieties may change the host-pathogen dynamic for L7 isolates, explaining the limited geographical distribution of L7 and contributing to further understanding the spread of MTBC lineages across the globe.
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Affiliation(s)
- Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Daire Cantillon
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
- Present address: Department of Tropical Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Carlos Madrazo
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Graham Rose
- Francis Crick Institute, London, UK
- Present address: North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK
| | | | - Paul Golby
- Animal and Plant Health Agency, Weybridge, UK
| | | | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Iñaki Comas
- Biomedicine Institute of Valencia, Spanish Research Council (IBV-CSIC), Valencia, Spain
| | - Douglas B. Young
- Francis Crick Institute, London, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Simon J. Waddell
- Brighton and Sussex Centre for Global Health Research, Department of Global Health and Infection, Brighton and Sussex Medical School, University of Sussex, Falmer, UK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
| | - Stefan Berg
- Animal and Plant Health Agency, Weybridge, UK
- Present address: Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
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24
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Domínguez J, Boeree MJ, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat MR, Gagneux S, Grobusch MP, Gröschel MI, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas AM, Maurer FP, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh CR, Lange C. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. THE LANCET. INFECTIOUS DISEASES 2023; 23:e122-e137. [PMID: 36868253 DOI: 10.1016/s1473-3099(22)00875-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 03/05/2023]
Abstract
Drug-resistant tuberculosis is a substantial health-care concern worldwide. Despite culture-based methods being considered the gold standard for drug susceptibility testing, molecular methods provide rapid information about the Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs. This consensus document was developed on the basis of a comprehensive literature search, by the TBnet and RESIST-TB networks, about reporting standards for the clinical use of molecular drug susceptibility testing. Review and the search for evidence included hand-searching journals and searching electronic databases. The panel identified studies that linked mutations in genomic regions of M tuberculosis with treatment outcome data. Implementation of molecular testing for the prediction of drug resistance in M tuberculosis is key. Detection of mutations in clinical isolates has implications for the clinical management of patients with multidrug-resistant or rifampicin-resistant tuberculosis, especially in situations when phenotypic drug susceptibility testing is not available. A multidisciplinary team including clinicians, microbiologists, and laboratory scientists reached a consensus on key questions relevant to molecular prediction of drug susceptibility or resistance to M tuberculosis, and their implications for clinical practice. This consensus document should help clinicians in the management of patients with tuberculosis, providing guidance for the design of treatment regimens and optimising outcomes.
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Affiliation(s)
- José Domínguez
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain.
| | - Martin J Boeree
- Department of Lung Diseases, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Emmanuelle Cambau
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France, APHP-Hôpital Bichat, Mycobacteriology Laboratory, INSERM, University Paris Cite, IAME UMR1137, Paris, France
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemițanu State University of Medicine and Pharmacy, Chisinau, Moldova; Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Francesca Conradie
- Department of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Vivian Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrii Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergy, National Pirogov Memorial Medical University, Vinnytsia, Ukraine; Public Health Center, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Martin P Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Berit Lange
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research, TI BBD, Braunschweig, Germany
| | - Frank van Leth
- Department of Health Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Christian Lienhardt
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; UMI 233 IRD-U1175 INSERM - Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Anna M Mandalakas
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Merker
- Division of Evolution of the Resistome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Molina-Moya
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain
| | - Florence Morel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Stefan Niemann
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia
| | - Nicolas Veziris
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charles R Horsburgh
- Departments of Epidemiology, Biostatistics, Global Health and Medicine, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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25
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Du DH, Geskus RB, Zhao Y, Codecasa LR, Cirillo DM, van Crevel R, Pascapurnama DN, Chaidir L, Niemann S, Diel R, Omar SV, Grandjean L, Rokadiya S, Ortitz AT, Lân NH, Hà ÐTM, Smith EG, Robinson E, Dedicoat M, Nhat LTH, Thwaites GE, Van LH, Thuong NTT, Walker TM. The effect of M. tuberculosis lineage on clinical phenotype. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.14.23287284. [PMID: 36993190 PMCID: PMC10055556 DOI: 10.1101/2023.03.14.23287284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Eight lineages of Mycobacterium tuberculosis sensu stricto are described. Single-country or small observational data suggest differences in clinical phenotype between lineages. We present strain lineage and clinical phenotype data from 12,246 patients from 3 low-incidence and 5 high-incidence countries. We used multivariable logistic regression to explore the effect of lineage on site of disease and on cavities on chest radiography, given pulmonary TB; multivariable multinomial logistic regression to investigate types of extra-pulmonary TB, given lineage; and accelerated failure time and Cox proportional-hazards models to explore the effect of lineage on time to smear and culture-conversion. Mediation analyses quantified the direct effects of lineage on outcomes. Pulmonary disease was more likely among patients with lineage(L) 2, L3 or L4, than L1 (adjusted odds ratio (aOR) 1.79, (95% confidence interval 1.49-2.15), p<0.001; aOR=1.40(1.09-1.79), p=0.007; aOR=2.04(1.65-2.53), p<0.001, respectively). Among patients with pulmonary TB, those with L1 had greater risk of cavities on chest radiography versus those with L2 (aOR=0.69(0.57-0.83), p<0.001) and L4 strains (aOR=0.73(0.59-0.90), p=0.002). L1 strains were more likely to cause osteomyelitis among patients with extra-pulmonary TB, versus L2-4 (p=0.033, p=0.008 and p=0.049 respectively). Patients with L1 strains showed shorter time-to-sputum smear conversion than for L2. Causal mediation analysis showed the effect of lineage in each case was largely direct. The pattern of clinical phenotypes seen with L1 strains differed from modern lineages (L2-4). This has implications for clinical management and could influence clinical trial selection strategies.
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Affiliation(s)
- Duc Hong Du
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Ronald B Geskus
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Luigi Ruffo Codecasa
- Regional TB Reference Centre/Istituto Villa Marelli- ASST Grande Ospedale Metropolitano Niguarda, Milano, Italy
| | | | - Reinout van Crevel
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Lidya Chaidir
- Division of Microbiology, Department of Biomedical Science, Faculty of Medicine, Padjadjaran University, Bandung, West Java, Indonesia
| | - Stefan Niemann
- Research Center Borstel, Germany
- German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Roland Diel
- University Hospital Schleswig-Holstein, Campus Kiel, Germany
- Lung Clinic Grosshansdorf, Germany, Airway Disease Center North (ARCN), German Center for Lung Research (DZL)
| | | | | | | | | | | | | | - E Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Esther Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Martin Dedicoat
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
- University Hospitals Birmingham NHS Foundation Trust, UK
| | | | - Guy E Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Le Hong Van
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy M Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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26
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Ordaz-Vázquez A, Torres-González P, Ferreyra-Reyes L, Canizales-Quintero S, Delgado-Sánchez G, García-García L, Ponce-De-León A, Sifuentes-Osornio J, Bobadilla-Del-Valle M. Mycobacterium tuberculosis lineage 4 associated with cavitations and treatment failure. BMC Infect Dis 2023; 23:154. [PMID: 36918814 PMCID: PMC10012486 DOI: 10.1186/s12879-023-08055-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/06/2023] [Indexed: 03/16/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis genotyping has been crucial to determining the distribution and impact of different families on disease clinical presentation. The aim of the study was to evaluate the associations among sociodemographic and clinical characteristics and M. tuberculosis lineages from patients with pulmonary tuberculosis in Orizaba, Veracruz, Mexico. METHODS We analyzed data from 755 patients whose isolates were typified by 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR). The associations among patient characteristics and sublineages found were evaluated using logistic regression analysis. RESULTS Among M. tuberculosis isolates, 730/755 (96.6%) were assigned to eight sublineages of lineage 4 (Euro-American). Alcohol consumption (adjusted odds ratio [aOR] 1.528, 95% confidence interval (CI) 1.041-2.243; p = 0.030), diabetes mellitus type 2 (aOR 1.625, 95% CI 1.130-2.337; p = 0.009), sputum smear positivity grade (3+) (aOR 2.198, 95% CI 1.524-3.168; p < 0.001) and LAM sublineage isolates (aOR 1.023, 95% CI 1.023-2.333; p = 0.039) were associated with the presence of cavitations. Resistance to at least one drug (aOR 25.763, 95% CI 7.096-93.543; p < 0.001) and having isolates other than Haarlem and LAM sublineages (aOR 6.740, 95% CI 1.704-26.661; p = 0.007) were associated with treatment failure. In a second model, multidrug resistance was associated with treatment failure (aOR 31.497, 95% CI 5.119-193.815; p < 0.001). Having more than 6 years of formal education was not associated with treatment failure. CONCLUSIONS Knowing M. tuberculosis genetic diversity plays an essential role in disease development and outcomes, and could have important implications for guiding treatment and improving tuberculosis control.
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Affiliation(s)
- Anabel Ordaz-Vázquez
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Pedro Torres-González
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Leticia Ferreyra-Reyes
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Sergio Canizales-Quintero
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Lourdes García-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - Alfredo Ponce-De-León
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - José Sifuentes-Osornio
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Mexico City, Mexico
| | - Miriam Bobadilla-Del-Valle
- Departamento de Infectología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Sección XVI, Tlalpan, 14080, Mexico City, Mexico.
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27
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Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains. Tuberculosis (Edinb) 2023; 139:102324. [PMID: 36848710 DOI: 10.1016/j.tube.2023.102324] [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: 10/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/15/2023]
Abstract
Whole-genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a rapidly growing tool to obtain results regarding the resistance and phylogeny of the strains. We evaluated the performances of two bioinformatics tools for the analysis of whole-genome sequences of MTBC strains. Two hundred and twenty-seven MTBC strains were isolated and whole-genome sequenced at the laboratory of Avicenne Hospital between 2015 and 2021. We investigated the resistance and susceptibility status of strains using two online tools, Mykrobe and PhyResSE. We compared the genotypic and phenotypic resistance results obtained by drug susceptibility testing. Unlike with the Mykrobe tool, sequencing quality data were obtained using PhyResSE: average coverage of 98% and average depth of 119X. We found a similar concordance between phenotypic and genotypic results when determining susceptibility to first-line anti-tuberculosis drugs (95%) with both tools. The sensitivity and specificity of each tool compared to the phenotypic method were respectively 72% [52-87] and 98% [96-99] for Mykrobe and 76% [57-90] and 97% [94-99] for PhyResSE. Mykrobe and PhyResSE were easy to use and efficient. These platforms are accessible to people not trained in bioinformatics and constitute a complementary approach to phenotypic methods for the study of MTBC strains.
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Naz S, Paritosh K, Sanyal P, Khan S, Singh Y, Varshney U, Nandicoori VK. GWAS and functional studies suggest a role for altered DNA repair in the evolution of drug resistance in Mycobacterium tuberculosis. eLife 2023; 12:75860. [PMID: 36695572 PMCID: PMC9876569 DOI: 10.7554/elife.75860] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
The emergence of drug resistance in Mycobacterium tuberculosis (Mtb) is alarming and demands in-depth knowledge for timely diagnosis. We performed genome-wide association analysis using 2237 clinical strains of Mtb to identify novel genetic factors that evoke drug resistance. In addition to the known direct targets, we identified for the first time, a strong association between mutations in DNA repair genes and the multidrug-resistant phenotype. To evaluate the impact of variants identified in the clinical samples in the evolution of drug resistance, we utilized knockouts and complemented strains in Mycobacterium smegmatis and Mtb. Results show that variant mutations compromised the functions of MutY and UvrB. MutY variant showed enhanced survival compared with wild-type (Rv) when the Mtb strains were subjected to multiple rounds of ex vivo antibiotic stress. In an in vivo guinea pig infection model, the MutY variant outcompeted the wild-type strain. We show that novel variant mutations in the DNA repair genes collectively compromise their functions and contribute to better survival under antibiotic/host stress conditions.
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Affiliation(s)
- Saba Naz
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
- Department of Zoology, University of DelhiDelhiIndia
| | - Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South CampusNew DelhiIndia
| | | | - Sidra Khan
- National Institute of ImmunologyNew DelhiIndia
| | | | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science BangaloreBangaloreIndia
| | - Vinay Kumar Nandicoori
- National Institute of ImmunologyNew DelhiIndia
- Centre for Cellular and Molecular BiologyHyderabadIndia
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Skhairia MA, Dekhil N, Mardassi H. Evolutionary history and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage, Tunisia. Tuberculosis (Edinb) 2023; 138:102297. [PMID: 36584485 DOI: 10.1016/j.tube.2022.102297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND To infer the origin and spread of the Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in a Mediterranean country, Tunisia, where it predominates. METHODS We combined Bayesian (STRUCTURE) and maximum likelihood (MIGRAINE) estimation approaches based on a global 24-loci mycobacterial interspersed repetitive units-variable numbers of tandem repeats (MIRU-VNTR24) genotyping dataset consisting of 1573 L4.3/LAM clinical strains from four continents, including 252 isolates originating from Tunisia. RESULTS Phylogenetic analyses coupled with Bayesian estimations suggested that the most predominant L4.3/LAM subpopulation in Tunisia (65.07%), which is dominated by a single clonal complex, TUN4.3_CC1 (94.51%), has evolved from an ancestral pool that is restricted to Europe and Africa, contrasting with the remaining L4.3/LAM subpopulations whose ancestry was traced all over the word. Maximum likelihood analysis revealed that TUN4.3_CC1 has been undergoing a demographic expansion since 131 years ago (CI95%: 90.7-205), thus explaining its preponderance relative to the second most predominant CC, TUN4.3_CC2, whose population was found under contraction. CONCLUSIONS The preponderance of L4.3/LAM in Tunisia stems from a 130-year expansion process of a locally evolved clone.
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Affiliation(s)
- Mohamed Amine Skhairia
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.
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Moopanar K, Nyide ANG, Senzani S, Mvubu NE. Clinical strains of Mycobacterium tuberculosis exhibit differential lipid metabolism-associated transcriptome changes in in vitro cholesterol and infection models. Pathog Dis 2022; 81:6889515. [PMID: 36509392 PMCID: PMC9936260 DOI: 10.1093/femspd/ftac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/30/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Many studies have identified host-derived lipids, characterised by the abundance of cholesterol, as a major source of carbon nutrition for Mycobacterium tuberculosis during infection. Members of the Mycobacterium tuberculosis complex are biologically different with regards to degree of disease, host range, pathogenicity and transmission. Therefore, the current study aimed at elucidating transcriptome changes during early infection of pulmonary epithelial cells and on an in vitro cholesterol-rich minimal media, in M. tuberculosis clinical strains F15/LAM4/KZN and Beijing, and the laboratory H37Rv strain. Infection of pulmonary epithelial cells elicited the upregulation of fadD28 and hsaC in both the F15/LAM4/KZN and Beijing strains and the downregulation of several other lipid-associated genes. Growth curve analysis revealed F15/LAM4/KZN and Beijing to be slow growers in 7H9 medium and cholesterol-supplemented media. RNA-seq analysis revealed strain-specific transcriptomic changes, thereby affecting different metabolic processes in an in vitro cholesterol model. The differential expression of these genes suggests that the genetically diverse M. tuberculosis clinical strains exhibit strain-specific behaviour that may influence their ability to metabolise lipids, specifically cholesterol, which may account for phenotypic differences observed during infection.
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Affiliation(s)
- Kynesha Moopanar
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Asanda Nomfundo Graduate Nyide
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa
| | - Sibusiso Senzani
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st floor, Doris Duke Medical Research Institute, Congella, Private Bag 7, Durban, 4013, South Africa
| | - Nontobeko Eunice Mvubu
- Corresponding author. Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville Campus, Private Bag X54001, Durban, 4000, South Africa.Tel: +27 31 260 7404; E-mail:
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van Doren TP. Biocultural perspectives of infectious diseases and demographic evolution: Tuberculosis and its comorbidities through history. Evol Anthropol 2022; 32:100-117. [PMID: 36436141 DOI: 10.1002/evan.21970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/09/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
Anthropologists recognize the importance of conceptualizing health in the context of the mutually evolving nature of biology and culture through the biocultural approach, but biocultural anthropological perspectives of infectious diseases and their impacts on humans (and vice versa) through time are relatively underrepresented. Tuberculosis (TB) has been a constant companion of humans for thousands of years and has heavily influenced population health in almost every phase of cultural and demographic evolution. TB in human populations has been dramatically influenced by behavior, demographic and epidemiological shifts, and other comorbidities through history. This paper critically discusses TB and some of its major comorbidities through history within a biocultural framework to show how transitions in human demography and culture affected the disease-scape of TB. In doing so, I address the potential synthesis of biocultural and epidemiological transition theory to better comprehend the mutual evolution of infectious diseases and humans.
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Analysis of the twenty-six largest outbreaks of tuberculosis in Aragon using whole-genome sequencing for surveillance purposes. Sci Rep 2022; 12:18766. [PMID: 36335223 PMCID: PMC9637126 DOI: 10.1038/s41598-022-23343-1] [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: 06/29/2022] [Accepted: 10/30/2022] [Indexed: 11/08/2022] Open
Abstract
The incidence of tuberculosis in Aragon, Spain, is around ten cases per 100,000 inhabitants. Since 2004, a molecular surveillance protocol has been carried out; therefore, all M. tuberculosis strains are genotyped. Recently, whole-genome sequencing has been implemented for relevant isolates. The aim of this work is to characterise at the molecular level the causative strains of the 26 largest outbreaks of the community (including ten or more cases), genotyped by IS6110-RFLP and causing 26% of tuberculosis cases. To achieve this objective, two or three isolates of each IS6110-cluster belonging to different years were selected for sequencing. We found that strains of lineages L4.8, L4.3 and L4.1.2 were the most frequent. The threshold of 12 SNPs as the maximum distance for confirming the belonging to an outbreak was met for 18 of the 26 IS6110-clusters. Four pairs of isolates with more than 90 SNPs were identified as not belonging to the same strain, and four other pairs were kept in doubt as the number of SNPs was close to 12, between 14 and 35. The study of Regions of Difference revealed that they are lineage conserved. Moreover, we could analyse the IS6110 locations for all genome-sequenced isolates, finding some frequent locations in isolates belonging to the same lineage and certain IS6110 movements between the paired isolates. In the vast majority, these movements were not captured by the IS6110-RFLP pattern. After classifying the genes containing SNP by their functional category, we could confirm that the number of SNPs detected in genes considered as virulence factors and the number of cases the strain produced were not related, suggesting that a particular SNP is more relevant than the number. The characteristics found in the most successful strains in our community could be useful for other researchers in epidemiology, virulence and pathogenesis.
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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Lin X, Jia W, Feng G, Su Y, Kang Y, Zhang C, Liu W, Lu Z, Xue D. The role of APTX4870 peptide in reducing cellular inflammatory responses by inhibiting Mycobacterium tuberculosis-derived mycolic acid-induced cytotoxicity. Front Microbiol 2022; 13:993897. [DOI: 10.3389/fmicb.2022.993897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/07/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis is a serious zoonotic disease caused by Mycobacterium tuberculosis (M.tb) and the M.tb complex. Mycolic acid is an extracellular carbohydrate polymer produced, secreted, and accumulated outside the cells of various Mycobacterium tuberculosis strains. Mycolic acid produced by Mycobacterium plays an important role in infection. However, there have been few reports on drugs that inhibit mycolic acid-induced cytotoxicity. The purpose of this study was to investigate the role of the panned peptide in Mycobacterium-derived mycolic acid (M.tb-MA)-induced cell injury. The heptapeptide (APTX4870) was isolated from various phage libraries using phage display (Ph.D-7, Ph.D-12, and Ph.D-C7C). The efficacy of APTX4870 against mycolic acid was demonstrated by evaluating clinical samples and conducting in vitro and Vivo. APTX4870 inhibited apoptosis, increased autophagy to decrease inflammation, and reduced M.tb-MA-induced lung damage. These findings suggest that this heptapeptide, which selectively targets M.tb-MA, might be exploited as a potential novel M.tb therapeutic treatment.
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Abd El-Hack ME, El-Saadony MT, Ellakany HF, Elbestawy AR, Abaza SS, Geneedy AM, Khafaga AF, Salem HM, Abd El-Aziz AH, Selim S, Babalghith AO, AbuQamar SF, El-Tarabily KA. Inhibition of microbial pathogens in farmed fish. MARINE POLLUTION BULLETIN 2022; 183:114003. [PMID: 36030638 DOI: 10.1016/j.marpolbul.2022.114003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/18/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Aquaculture, also known as aqua farming, is defined as farming fish, crustaceans, mollusks, aquatic plants, algae, and other marine organisms. It includes cultivating fresh- and saltwater populations under controlled conditions compared to commercial fishing or wild fish harvesting. Worldwide, carp, salmon, tilapia, and catfish are the most common fish species used in fish farming in descending order. Disinfectants prevent and/or treat different infections in aquatic animals. The current review indicates the uses of different disinfectants against some important pathogens in aquaculture, with particular reference to tilapia (Oreochromis niloticus) farming. A single review cannot cover all aspects of disinfection throughout aquaculture, so the procedures and principles of disinfection in tilapia farming/aquaculture have been chosen for illustration purposes.
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Affiliation(s)
- Mohamed E Abd El-Hack
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Mohamed T El-Saadony
- Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt
| | - Hany F Ellakany
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Ahmed R Elbestawy
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Samar S Abaza
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Amr M Geneedy
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Asmaa F Khafaga
- Department of Pathology, Faculty of Veterinary Medicine, Alexandria University, Edfina 22758, Egypt
| | - Heba M Salem
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt
| | - Ayman H Abd El-Aziz
- Animal Husbandry and Animal Wealth Development Department, Faculty of Veterinary Medicine, Damanhour University, Damanhour 22511, Egypt
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Ahmad O Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates.
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates; Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain 15551, United Arab Emirates; Harry Butler Institute, Murdoch University, Murdoch 6150, Western Australia, Australia.
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36
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Ncube P, Bagheri B, Goosen WJ, Miller MA, Sampson SL. Evidence, Challenges, and Knowledge Gaps Regarding Latent Tuberculosis in Animals. Microorganisms 2022; 10:1845. [PMID: 36144447 PMCID: PMC9503773 DOI: 10.3390/microorganisms10091845] [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: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 01/30/2023] Open
Abstract
Mycobacterium bovis and other Mycobacterium tuberculosis complex (MTBC) pathogens that cause domestic animal and wildlife tuberculosis have received considerably less attention than M. tuberculosis, the primary cause of human tuberculosis (TB). Human TB studies have shown that different stages of infection can exist, driven by host-pathogen interactions. This results in the emergence of heterogeneous subpopulations of mycobacteria in different phenotypic states, which range from actively replicating (AR) cells to viable but slowly or non-replicating (VBNR), viable but non-culturable (VBNC), and dormant mycobacteria. The VBNR, VBNC, and dormant subpopulations are believed to underlie latent tuberculosis (LTB) in humans; however, it is unclear if a similar phenomenon could be happening in animals. This review discusses the evidence, challenges, and knowledge gaps regarding LTB in animals, and possible host-pathogen differences in the MTBC strains M. tuberculosis and M. bovis during infection. We further consider models that might be adapted from human TB research to investigate how the different phenotypic states of bacteria could influence TB stages in animals. In addition, we explore potential host biomarkers and mycobacterial changes in the DosR regulon, transcriptional sigma factors, and resuscitation-promoting factors that may influence the development of LTB.
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Affiliation(s)
| | | | | | | | - Samantha Leigh Sampson
- DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Department of Biomedical Sciences, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Francie Van Zijl Dr, Parow, Cape Town 7505, South Africa
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Acquah SEK, Asare P, Danso EK, Tetteh P, Tetteh AY, Boateng D, Osei-Wusu S, Afum T, Ayamdooh YI, Akugre EA, Samad OA, Quaye L, Obiri-Danso K, Kock R, Asante-Poku A, Yeboah-Manu D. Molecular epidemiology of bovine tuberculosis in Northern Ghana identifies several uncharacterized bovine spoligotypes and suggests possible zoonotic transmission. PLoS Negl Trop Dis 2022; 16:e0010649. [PMID: 35951638 PMCID: PMC9398027 DOI: 10.1371/journal.pntd.0010649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 08/23/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Objective
We conducted an abattoir-based cross-sectional study in the five administrative regions of Northern Ghana to determine the distribution of bovine tuberculosis (BTB) among slaughtered carcasses and identify the possibility of zoonotic transmission.
Methods
Direct smear microscopy was done on 438 tuberculosis-like lesions from selected cattle organs and cultured on Lowenstein-Jensen media. Acid-fast bacilli (AFB) isolates were confirmed as members of the Mycobacterium tuberculosis complex (MTBC) by PCR amplification of IS6110 and rpoß. Characterization and assignment into MTBC lineage and sub-lineage were done by spoligotyping, with the aid of the SITVIT2, miruvntrplus and mbovis.org databases. Spoligotype data was compared to that of clinical M. bovis isolates from the same regions to identify similarities.
Results
A total of 319/438 (72.8%) lesion homogenates were smear positive out of which, 84.6% (270/319) had microscopic grade of at least 1+ for AFB. Two hundred and sixty-five samples (265/438; 60.5%) were culture positive, of which 212 (80.0%) were MTBC. Approximately 16.7% (34/203) of the isolates with correctly defined spoligotypes were negative for IS6110 PCR but were confirmed by rpoß. Spoligotyping characterized 203 isolates as M. bovis (198, 97.5%), M. caprae (3, 1.5%), M. tuberculosis (Mtbss) lineage (L) 4 Cameroon sub-lineage, (1, 0.5%), and M. africanum (Maf) L6 (1, 0.5%). A total of 53 unique spoligotype patterns were identified across the five administrative regions (33 and 28 were identified as orphan respectively by the SITVIT2 and mbovis.org databases), with the most dominant spoligotype being SIT1037/ SB0944 (77/203, 37.93%). Analysis of the bovine and human M. bovis isolates showed 75% (3/4) human M. bovis isolates sharing the same spoligotype pattern with the bovine isolates.
Conclusion
Our study identified that approximately 29% of M. bovis strains causing BTB in Northern Ghana are caused by uncharacterized spoligotypes. Our findings suggest possible zoonotic transmission and highlight the need for BTB disease control in Northern Ghana.
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Affiliation(s)
- Samuel Ekuban Kobina Acquah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- Department of Clinical Microbiology, School of Medicine and Health Sciences, University for Development Studies, Tamale, Ghana
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
| | - Emelia Konadu Danso
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Phillip Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Amanda Yaa Tetteh
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniel Boateng
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Theophilus Afum
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - Eric Agongo Akugre
- Veterinary Services Directorate, Ministry of Food and Agriculture, Bolgatanga, Ghana
| | - Omar Abdul Samad
- Veterinary Services Directorate, Ministry of Food and Agriculture, Wa, Ghana
| | - Lawrence Quaye
- Department of Biomedical Laboratory Sciences, School of Allied Health Sciences, University for Development Studies, Tamale, Ghana
| | - Kwasi Obiri-Danso
- Department of Theoretical and Applied Biology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richard Kock
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
- * E-mail: (PA); (DYM)
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Use of Whole-Genome Sequencing to Explore Mycobacterium tuberculosis Complex Circulating in a Hotspot Department in France. Microorganisms 2022; 10:microorganisms10081586. [PMID: 36014004 PMCID: PMC9414808 DOI: 10.3390/microorganisms10081586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
The Seine-Saint-Denis is the French metropolitan department with the highest incidence of tuberculosis (TB). Our aim was to explore epidemiological and phylogenetic characteristics of TB strains in this hotspot department. We performed WGS on 227 strains of Mycobacterium tuberculosis complex isolated from patients at the Avicenne Hospital from 2016 to 2021 and randomly selected to represent the clinical diversity of French TB localization. Clinical and demographic data were recorded for each TB patient. The mean age of patients was 36 years old. They came from Africa (44%), Asia (27%), Europe (26%) and America (3%). Strains isolated from extrapulmonary samples were associated with Asian patients, whereas strains isolated from pulmonary samples were associated with European patients. We observed a high level of lineage diversity in line with the known worldwide diversity. Interestingly, lineage 3 was associated with lymph node TB. Additionally, the sensitivity of WGS for predicting resistance was 100% for rifampicin, isoniazid and ethambutol and 66.7% for pyrazinamide. The global concordance with drug-susceptibility testing using the phenotypic approach was 97%. In microbiology laboratories, WGS turns out to be an essential tool for better understanding local TB epidemiology, with direct access to circulating lineage identification and to drug susceptibilities to first- and second-line anti-TB drugs.
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39
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Wang J, Li Y, Yang Z, Sun T, Yu X, Zhao Y, Tang X, Xiao H. Sex plays a role in the construction of epiphytic bacterial communities on the algal bodies and receptacles of Sargassum thunbergii. Front Microbiol 2022; 13:935222. [PMID: 35958132 PMCID: PMC9360977 DOI: 10.3389/fmicb.2022.935222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/01/2022] [Indexed: 11/21/2022] Open
Abstract
The community structures of epiphytic bacteria on the surface of macroalgae are closely related to their host algae, but there is a lack of research on the differences between the epiphytic bacterial communities of male and female algae and their reproductive tissues. In this study, high-throughput sequencing was used to compare epiphytic bacterial community structures on the intertidal macroalgae Sargassum thunbergii and their receptacles between male and female samples. The epiphytic bacteria on the male and female algal bodies and receptacles had similar community structures with a large number of shared bacteria, but the samples clearly clustered separately, and the abundances of dominant taxa, specific bacteria, and indicator species differed, indicating that epiphytic bacterial communities differed significantly between the male and female S. thunbergii and their receptacles. In addition, the abundance of many predicted functional genes was significantly different between epiphytic bacteria on male and female algal bodies and receptacles, especially metabolism-related genes, and the abundances of predicted functional genes of epiphytic bacteria were significantly higher on both types of male samples than on female samples. Our study confirmed that the sex of the host algae influenced the epiphytic bacterial community structures on algae and algal reproductive tissues, and this role was mainly related to the host metabolism. The results reveal the role of host plant sex in the formation of epiphytic bacterial communities. These findings are helpful for obtaining an in-depth understanding of the construction mechanism of algae-associated bacteria.
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Affiliation(s)
- Jing Wang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yang Li
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhibo Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Tao Sun
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xinlong Yu
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Yayun Zhao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xuexi Tang
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- *Correspondence: Xuexi Tang,
| | - Hui Xiao
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Hui Xiao,
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40
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Mascarell P, de la Rica A, Padilla S, Ruiz-García M, López-Escudero J, García-Abellán J, Botella Á, Masiá M, Gutiérrez F. Pericarditis caused by Mycobacterium africanum: case report. BMC Infect Dis 2022; 22:628. [PMID: 35850703 PMCID: PMC9290226 DOI: 10.1186/s12879-022-07540-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 06/15/2022] [Indexed: 11/26/2022] Open
Abstract
Background Mycobacterium africanum is a member of the Mycobacterium tuberculosis complex (MTBC) and is endemic in West Africa, where it causes up to half of all cases of pulmonary tuberculosis. Here, we report the first isolation of Mycobacterium africanum from the pericardial effusion culture of a patient with tuberculous pericarditis. Case presentation A 31-year-old man, native from Senegal, came to the emergency room with massive pericardial effusion and cardiac tamponade requiring pericardiocentesis. M. africanum subtype II was identified in the pericardial fluid. The patient completed 10 months of standard treatment, with a favorable outcome. Conclusions We report the first case of tuberculous pericarditis caused by Mycobacterium africanum, which provide evidence that this microorganism can cause pericardial disease and must be considered in patients from endemic areas presenting with pericardial effusion.
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Affiliation(s)
- Paula Mascarell
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain.
| | - Alba de la Rica
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Sergio Padilla
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | | | - José López-Escudero
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | | | - Ángela Botella
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Mar Masiá
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Félix Gutiérrez
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
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41
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Saavedra Cervera B, López MG, Chiner-Oms Á, García AM, Cancino-Muñoz I, Torres-Puente M, Villamayor L, Madrazo-Moya C, Mambuque E, Sequera GV, Respeito D, Blanco S, Augusto O, López-Varela E, García-Basteiro AL, Comas I. Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area. Microb Genom 2022; 8. [PMID: 35787782 PMCID: PMC9455694 DOI: 10.1099/mgen.0.000844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genomic studies of the Mycobacterium tuberculosis complex (MTBC) might shed light on the dynamics of its transmission, especially in high-burden settings, where recent outbreaks are embedded in the complex natural history of the disease. To this end, we conducted a 1 year prospective surveillance-based study in Mozambique. We applied whole-genome sequencing (WGS) to 295 positive cultures. We fully characterized MTBC isolates by phylogenetics and dating evaluation, and carried out a molecular epidemiology analysis to investigate further associations with pre-defined transmission risk factors. The majority of strains (49.5%, 136/275) belonged to lineage (L) 4; 57.8 % of them (159/275) were in genomic transmission clusters (cut-off 5 SNPs), and a strikingly high proportion (45.5%) shared an identical genotype (0 SNP pairwise distance). We found two ‘likely endemic’ clades, comprising 67 strains, belonging to L1.2, which dated back to the late 19th century and were associated with recent spread among people living with human immunodeficiency virus (PLHIV). We describe for the first time the population structure of MTBC in our region, a high tuberculosis (TB)/HIV burden area. Clustering analysis revealed an unforeseen pattern of spread and high rates of progression to active TB, suggesting weaknesses in TB control activities. The long-term presence of local strains in Mozambique, which were responsible for large transmission among HIV/TB-coinfected patients, calls into question the role of HIV in TB transmission.
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Affiliation(s)
- Belén Saavedra Cervera
- PhD Programin Medicine and Translational Research, Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Mariana G López
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | | | - Ana María García
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain.,Universidad de Valencia, Valencia, Spain
| | | | | | | | | | - Edson Mambuque
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | | | - Durval Respeito
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Silvia Blanco
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Orvalho Augusto
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique
| | - Elisa López-Varela
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Alberto L García-Basteiro
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique.,ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain.,CIBER in Epidemiology and Public Health, Madrid, Spain
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42
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Silva ML, Cá B, Osório NS, Rodrigues PNS, Maceiras AR, Saraiva M. Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns. PLoS Pathog 2022; 18:e1010490. [PMID: 35617217 PMCID: PMC9135246 DOI: 10.1371/journal.ppat.1010490] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB), one of the deadliest threats to human health, is mainly caused by 2 highly related and human-adapted bacteria broadly known as Mycobacterium tuberculosis and Mycobacterium africanum. Whereas M. tuberculosis is widely spread, M. africanum is restricted to West Africa, where it remains a significant cause of tuberculosis. Although several differences have been identified between these 2 pathogens, M. africanum remains a lot less studied than M. tuberculosis. Here, we discuss the genetic, phenotypic, and clinical similarities and differences between strains of M. tuberculosis and M. africanum. We also discuss our current knowledge on the immune response to M. africanum and how it possibly articulates with distinct disease progression and with the geographical restriction attributed to this pathogen. Understanding the functional impact of the diversity existing in TB-causing bacteria, as well as incorporating this diversity in TB research, will contribute to the development of better, more specific approaches to tackle TB.
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Affiliation(s)
- Marta L. Silva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- Doctoral Program in Molecular and Cell Biology, ICBAS - Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto, Portugal
| | - Baltazar Cá
- INASA - Instituto Nacional de Saúde Pública da Guiné-Bissau, Bissau, Guinea-Bissau
- Bandim Health Project, Indepth Network, Bissau, Guinea-Bissau
| | - Nuno S. Osório
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Pedro N. S. Rodrigues
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Ana Raquel Maceiras
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
| | - Margarida Saraiva
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- IBMC - Instituto de Biologia Molecular e Celular, University of Porto, Porto, Portugal
- * E-mail:
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43
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Harouna Hamidou Z, Morsli M, Mamadou S, Drancourt M, Saad J. Emergence of multi-drug-resistant Mycobacterium tuberculosis in Niger: A snapshot based on whole-genome sequencing. PLoS Negl Trop Dis 2022; 16:e0010443. [PMID: 35613072 PMCID: PMC9132302 DOI: 10.1371/journal.pntd.0010443] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/22/2022] [Indexed: 11/27/2022] Open
Abstract
Background Among other West African countries experiencing the high endemicity of deadly tuberculosis, the situation in Niger is poorly evidenced by microbiological investigations. Methodology/Principal findings The study of 42 isolates of Mycobacterium tuberculosis from Niger by whole genome sequencing using Illumina iSeq technology yielded four M. tuberculosis lineages: Indo-Oceanic L1 (n = 1) (2.3%), East-Asian (n = 1) (2.3%), East-African Indian L3 (n = 2) (4.7%) and Euro-American L4 (n = 38) (90.4%). The sub-lineage L4.1.3 comprising 18 isolates (47.3%) was predominant, followed by the L4.6.2.2 sub-lineage (Cameroon genotype, n = 13 isolates) (34.2%). Investigating drug resistance profile for 12 antibiotics found 8/42 (19%) pan-susceptible isolates and 34/42 (81%) resistant isolates; with 40/42 (95.2%) isolates being susceptible to clofazimine-bedaquiline. Conclusions/Significance These unprecedented data from Niger highlight the dynamics of tuberculosis transmission and drug resistance in Niger and may assist tuberculosis control in this country which continues to support a high burden of tuberculosis. Tuberculosis is a major public health problem in Niger, in West Africa. Niger has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from the regions in Niger. In this study, most isolates of M. tuberculosis from this dataset belonged to the L4.6.2.2 sub-lineage and L4.1.3 sub-lineage within the Euro-American lineage. Thirty-four out of 42 (81%) isolates were detected as resistant isolates. Our study highlights the need for epidemiological surveillance and more concerted efforts to ensure that patients are put through treatment.
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Affiliation(s)
- Zelika Harouna Hamidou
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - Madjid Morsli
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Saidou Mamadou
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
- Université Abdou Moumouni, Niamey, Niger
| | - Michel Drancourt
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jamal Saad
- Aix-Marseille-Univ, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- * E-mail:
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44
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Multiplexed Strain Phenotyping Defines Consequences of Genetic Diversity in Mycobacterium tuberculosis for Infection and Vaccination Outcomes. mSystems 2022; 7:e0011022. [PMID: 35430871 PMCID: PMC9239107 DOI: 10.1128/msystems.00110-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There is growing evidence that genetic diversity in Mycobacterium tuberculosis, the causative agent of tuberculosis, contributes to the outcomes of infection and public health interventions, such as vaccination. Epidemiological studies suggest that among the phylogeographic lineages of M. tuberculosis, strains belonging to a sublineage of Lineage 2 (mL2) are associated with concerning clinical features, including hypervirulence, treatment failure, and vaccine escape. The global expansion and increasing prevalence of this sublineage has been attributed to the selective advantage conferred by these characteristics, yet confounding host and environmental factors make it difficult to identify the bacterial determinants driving these associations in human studies. Here, we developed a molecular barcoding strategy to facilitate high-throughput, experimental phenotyping of M. tuberculosis clinical isolates. This approach allowed us to characterize growth dynamics for a panel of genetically diverse M. tuberculosis strains during infection and after vaccination in the mouse model. We found that mL2 strains exhibit distinct growth dynamics in vivo and are resistant to the immune protection conferred by Bacillus Calmette-Guerin (BCG) vaccination. The latter finding corroborates epidemiological observations and demonstrates that mycobacterial features contribute to vaccine efficacy. To investigate the genetic and biological basis of mL2 strains’ distinctive phenotypes, we performed variant analysis, transcriptional studies, and genome-wide transposon sequencing. We identified functional genetic changes across multiple stress and host response pathways in a representative mL2 strain that are associated with variants in regulatory genes. These adaptive changes may underlie the distinct clinical characteristics and epidemiological success of this lineage. IMPORTANCE Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, is a remarkably heterogeneous disease, a feature that complicates clinical care and public health interventions. The contributions of pathogen genetic diversity to this heterogeneity are uncertain, in part due to the challenges of experimentally manipulating M. tuberculosis, a slow-growing, biosafety level 3 organism. To overcome these challenges, we applied a molecular barcoding strategy to a panel of M. tuberculosis clinical isolates. This novel application of barcoding permitted the high-throughput characterization of M. tuberculosis strain growth dynamics and vaccine resistance in the mouse model of infection. Integrating these results with genomic analyses, we uncover bacterial pathways that contribute to infection outcomes, suggesting targets for improved therapeutics and vaccines.
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45
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Balamurugan M, Banerjee R, Kasibhatla SM, Achalere A, Joshi R. Understanding the Genetic Diversity of Mycobacterium africanum Using Phylogenetics and Population Genomics Approaches. Front Genet 2022; 13:800083. [PMID: 35495132 PMCID: PMC9043288 DOI: 10.3389/fgene.2022.800083] [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: 11/13/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
A total of two lineages of Mycobacterium tuberculosis var. africanum (Maf), L5 and L6, which are members of the Mycobacterium tuberculosis complex (MTBC), are responsible for causing tuberculosis in West Africa. Regions of difference (RDs) are usually used for delineation of MTBC. With increased data availability, single nucleotide polymorphisms (SNPs) promise to provide better resolution. Publicly available 380 Maf samples were analyzed for identification of “core-cluster-specific-SNPs,” while additional 270 samples were used for validation. RD-based methods were used for lineage-assignment, wherein 31 samples remained unidentified. The genetic diversity of Maf was estimated based on genome-wide SNPs using phylogeny and population genomics approaches. Lineage-based clustering (L5 and L6) was observed in the whole genome phylogeny with distinct sub-clusters. Population stratification using both model-based and de novo approaches supported the same observations. L6 was further delineated into three sub-lineages (L6.1–L6.3), whereas L5 was grouped as L5.1 and L5.2 based on the occurrence of RD711. L5.1 and L5.2 were further divided into two (L5.1.1 and L5.1.2) and four (L5.2.1–L5.2.4) sub-clusters, respectively. Unassigned samples could be assigned to definite lineages/sub-lineages based on clustering observed in phylogeny along with high-confidence posterior membership scores obtained during population stratification. Based on the (sub)-clusters delineated, “core-cluster-specific-SNPs” were derived. Synonymous SNPs (137 in L5 and 128 in L6) were identified as biomarkers and used for validation. Few of the cluster-specific missense variants in L5 and L6 belong to the central carbohydrate metabolism pathway which include His6Tyr (Rv0946c), Glu255Ala (Rv1131), Ala309Gly (Rv2454c), Val425Ala and Ser112Ala (Rv1127c), Gly198Ala (Rv3293) and Ile137Val (Rv0363c), Thr421Ala (Rv0896), Arg442His (Rv1248c), Thr218Ile (Rv1122), and Ser381Leu (Rv1449c), hinting at the differential growth attenuation. Genes harboring multiple (sub)-lineage-specific “core-cluster” SNPs such as Lys117Asn, Val447Met, and Ala455Val (Rv0066c; icd2) present across L6, L6.1, and L5, respectively, hinting at the association of these SNPs with selective advantage or host-adaptation. Cluster-specific SNPs serve as additional markers along with RD-regions for Maf delineation. The identified SNPs have the potential to provide insights into the genotype–phenotype correlation and clues for endemicity of Maf in the African population.
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46
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Country-wide genotyping of Mycobacterium tuberculosis complex in Singapore, 2011–2017. Tuberculosis (Edinb) 2022; 134:102204. [DOI: 10.1016/j.tube.2022.102204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022]
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47
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Asante-Poku A, Morgan P, Osei-Wusu S, Aboagye SY, Asare P, Otchere ID, Adadey SM, Mnika K, Esoh K, Mawuta KH, Arthur N, Forson A, Mazandu GK, Wonkam A, Yeboah-Manu D. Genetic Analysis of TB Susceptibility Variants in Ghana Reveals Candidate Protective Loci in SORBS2 and SCL11A1 Genes. Front Genet 2022; 12:729737. [PMID: 35242163 PMCID: PMC8886735 DOI: 10.3389/fgene.2021.729737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/08/2021] [Indexed: 12/31/2022] Open
Abstract
Despite advancements made toward diagnostics, tuberculosis caused by Mycobacterium africanum (Maf) and Mycobacterium tuberculosis sensu stricto (Mtbss) remains a major public health issue. Human host factors are key players in tuberculosis (TB) outcomes and treatment. Research is required to probe the interplay between host and bacterial genomes. Here, we explored the association between selected human/host genomic variants and TB disease in Ghana. Paired host genotype datum and infecting bacterial isolate information were analyzed for associations using a multinomial logistic regression. Mycobacterium tuberculosis complex (MTBC) isolates were obtained from 191 TB patients and genotyped into different phylogenetic lineages by standard methods. Two hundred and thirty-five (235) nondisease participants were used as healthy controls. A selection of 29 SNPs from TB disease-associated genes with high frequency among African populations was assayed using a TaqMan® SNP Genotyping Assay and iPLEX Gold Sequenom Mass Genotyping Array. Using 26 high-quality SNPs across 326 case-control samples in an association analysis, we found a protective variant, rs955263, in the SORBS2 gene against both Maf and Mtb infections (PBH = 0.05; OR = 0.33; 95% CI = 0.32–0.34). A relatively uncommon variant, rs17235409 in the SLC11A1 gene was observed with an even stronger protective effect against Mtb infection (MAF = 0.06; PBH = 0.04; OR = 0.05; 95% CI = 0.04–0.05). These findings suggest SLC11A1 and SORBS2 as a potential protective gene of substantial interest for TB, which is an important pathogen in West Africa, and highlight the need for in-depth host-pathogen studies in West Africa.
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Affiliation(s)
- Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
- *Correspondence: Adwoa Asante-Poku,
| | - Portia Morgan
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Samuel Yaw Aboagye
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
| | - Samuel Mawuli Adadey
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Khuthala Mnika
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kevin Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kenneth Hayibor Mawuta
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Nelly Arthur
- Department of Chest Diseases, Korle-Bu Teaching Hospital Korle-Bu, Accra, Ghana
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital Korle-Bu, Accra, Ghana
| | - Gaston Kuzamunu Mazandu
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Biochemistry, Cell, and Molecular Biology, University of Ghana, Accra, Ghana
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48
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Smith CM, Baker RE, Proulx MK, Mishra BB, Long JE, Park SW, Lee HN, Kiritsy MC, Bellerose MM, Olive AJ, Murphy KC, Papavinasasundaram K, Boehm FJ, Reames CJ, Meade RK, Hampton BK, Linnertz CL, Shaw GD, Hock P, Bell TA, Ehrt S, Schnappinger D, Pardo-Manuel de Villena F, Ferris MT, Ioerger TR, Sassetti CM. Host-pathogen genetic interactions underlie tuberculosis susceptibility in genetically diverse mice. eLife 2022; 11:74419. [PMID: 35112666 PMCID: PMC8846590 DOI: 10.7554/elife.74419] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/27/2022] [Indexed: 11/21/2022] Open
Abstract
The outcome of an encounter with Mycobacterium tuberculosis (Mtb) depends on the pathogen’s ability to adapt to the variable immune pressures exerted by the host. Understanding this interplay has proven difficult, largely because experimentally tractable animal models do not recapitulate the heterogeneity of tuberculosis disease. We leveraged the genetically diverse Collaborative Cross (CC) mouse panel in conjunction with a library of Mtb mutants to create a resource for associating bacterial genetic requirements with host genetics and immunity. We report that CC strains vary dramatically in their susceptibility to infection and produce qualitatively distinct immune states. Global analysis of Mtb transposon mutant fitness (TnSeq) across the CC panel revealed that many virulence pathways are only required in specific host microenvironments, identifying a large fraction of the pathogen’s genome that has been maintained to ensure fitness in a diverse population. Both immunological and bacterial traits can be associated with genetic variants distributed across the mouse genome, making the CC a unique population for identifying specific host-pathogen genetic interactions that influence pathogenesis.
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Affiliation(s)
- Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Megan K Proulx
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Bibhuti B Mishra
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Jarukit E Long
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Ha-Na Lee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Michael C Kiritsy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Michelle M Bellerose
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Andrew J Olive
- Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Frederick J Boehm
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Charlotte J Reames
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
| | - Rachel K Meade
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Morrisville, United States
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Timothy A Bell
- Department of Genetics,, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | - Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, United States
| | | | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, United States
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, United States
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Mtetwa HN, Amoah ID, Kumari S, Bux F, Reddy P. Molecular surveillance of tuberculosis-causing mycobacteria in wastewater. Heliyon 2022; 8:e08910. [PMID: 35198775 PMCID: PMC8842018 DOI: 10.1016/j.heliyon.2022.e08910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 11/24/2022] Open
Abstract
The surveillance of tuberculosis infections has largely depended on clinical diagnostics and hospitalization data. The advancement in molecular methods creates an opportunity for the adoption of alternative surveillance systems, such as wastewater-based epidemiology. This study presents the use of conventional and advanced polymerase chain reaction techniques (droplet digital PCR) to determine the occurrence and concentration of total mycobacteria and members of the Mycobacterium tuberculosis complex (MTBC) in treated and untreated wastewater. Wastewater samples were taken from three wastewater treatment plants (WWTPs) in the city of Durban, South Africa, known for a high burden of TB/MDR-TB due to HIV infections. All untreated wastewater samples contained total mycobacteria and MTBC at varying percentages per WWTP studied. Other members of the MTBC related to tuberculosis infection in animals, M. bovis and M. caprae were also detected. The highest median concentration detected in untreated wastewater was up to 4.9 (±0.2) Log10 copies/ml for total mycobacteria, 4.0 (±0.85) Log10 copies/ml for MTBC, 3.9 (±0.54) Log10 copies/ml for M. tuberculosis, 2.7 (±0.42) Log10 copies/ml for M. africanum, 4.0 (±0.29) Log10 copies/ml for M. bovis and 4.5 (±0.52) Log10 copies/ml for M. caprae. Lower concentrations were detected in the treated wastewater, with a statistically significant difference (P-value ≤ 0.05) in concentrations observed. The log reduction achieved for these bacteria in the respective WWTPs was not statistically different, indicating that the treatment configuration did not have an impact on their removal. The detection of M. africanum in wastewater from South Africa shows that it is possible that some of the TB infections in the community could be caused by this mycobacterium. This study, therefore, highlights the potential of wastewater-based epidemiology for monitoring tuberculosis infections.
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Affiliation(s)
- Hlengiwe N. Mtetwa
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Isaac D. Amoah
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology (IWWT), Durban University of Technology, PO Box 1334, Durban, 4000, South Africa
| | - Poovendhree Reddy
- Department of Community Health Studies, Faculty of Health Sciences, Durban University of Technology, PO Box 1334, Durban, 4000, 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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