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Gonzalo-Asensio J, Pérez I, Aguiló N, Uranga S, Picó A, Lampreave C, Cebollada A, Otal I, Samper S, Martín C. New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages. PLoS Genet 2018; 14:e1007282. [PMID: 29649213 PMCID: PMC5896891 DOI: 10.1371/journal.pgen.1007282] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/28/2018] [Indexed: 11/19/2022] Open
Abstract
The insertion Sequence IS6110, only present in the pathogens of the Mycobacterium tuberculosis Complex (MTBC), has been the gold-standard epidemiological marker for TB for more than 25 years, but biological implications of IS6110 transposition during MTBC adaptation to humans remain elusive. By studying 2,236 clinical isolates typed by IS6110-RFLP and covering the MTBC, we remarked a lineage-specific content of IS6110 being higher in modern globally distributed strains. Once observed the IS6110 distribution in the MTBC, we selected representative isolates and found a correlation between the normalized expression of IS6110 and its abundance in MTBC chromosomes. We also studied the molecular regulation of IS6110 transposition and we found a synergistic action of two post-transcriptional mechanisms: a -1 ribosomal frameshift and a RNA pseudoknot which interferes translation. The construction of a transcriptionally active transposase resulted in 20-fold increase of the transposition frequency. Finally, we examined transposition in M. bovis and M. tuberculosis during laboratory starvation and in a mouse infection model of TB. Our results shown a higher transposition in M. tuberculosis, that preferably happens during TB infection in mice and after one year of laboratory culture, suggesting that IS6110 transposition is dynamically adapted to the host and to adverse growth conditions. Since the pioneering discovery of transposition by Barbara McClintock in eukaryotes and later in prokaryotes by Robert W. Hedges and Alan E. Jacob, it has become clear the key role of mobile genetics elements in chromosome remodelling, microbial evolution and host adaptation. The insertion sequence IS6110 is widely recognized for its utility in TB diagnosis and epidemiology because it is only present in the M. tuberculosis Complex (MTBC) and its transposition provides an excellent chromosomal polymorphic variability allowing the study of recent TB transmission. This inherent feature of IS6110 leads us to hypothesize that IS6110 plays a crucial role during the TB infectious cycle. However, the biological significance of IS6110 has been hindered by its almost exclusive use as an epidemiological marker. Here, we study the regulatory mechanisms and the distribution of IS6110 in the different MTBC lineages. We discuss the potential biological implications of IS6110, that is much more than an excellent TB epidemiological tool. Since IS6110 could play an important role in the adaptation of MTBC to the host, this study opens new avenues to decipher the biological roles of IS6110 in TB pathogenesis.
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Affiliation(s)
- Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Zaragoza, Spain
- * E-mail: (JGA); (CM)
| | - Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Picó
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Lampreave
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Cebollada
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Otal
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Unidad de Investigación Translacional, Hospital Universitario Miguel Servet, Instituto de Investigación Sanitaria Aragón. Zaragoza, Spain
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
- * E-mail: (JGA); (CM)
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Clark TG, Mallard K, Coll F, Preston M, Assefa S, Harris D, Ogwang S, Mumbowa F, Kirenga B, O’Sullivan DM, Okwera A, Eisenach KD, Joloba M, Bentley SD, Ellner JJ, Parkhill J, Jones-López EC, McNerney R. Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing. PLoS One 2013; 8:e83012. [PMID: 24349420 PMCID: PMC3859632 DOI: 10.1371/journal.pone.0083012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Understanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years. METHODS AND FINDINGS We used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort. CONCLUSIONS Whole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.
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Affiliation(s)
- Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Mark Preston
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Samuel Assefa
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David Harris
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sam Ogwang
- Joint Clinical Research Centre, Kampala, Uganda
| | - Francis Mumbowa
- Joint Clinical Research Centre, Kampala, Uganda
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bruce Kirenga
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Denise M. O’Sullivan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alphonse Okwera
- Mulago Hospital Tuberculosis Clinic, Mulago Hospital, Kampala, Uganda
| | - Kathleen D. Eisenach
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- Uganda-Case Western Reserve University Research Collaboration, Kampala, Uganda
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Muwonge A, Kankya C, Olea-Popelka F, Biffa D, Ssengooba W, Berit D, Skjerve E, Johansen TB. Molecular investigation of multiple strain infections in patients with tuberculosis in Mubende district, Uganda. INFECTION GENETICS AND EVOLUTION 2013; 17:16-22. [PMID: 23548804 DOI: 10.1016/j.meegid.2013.03.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/18/2013] [Accepted: 03/19/2013] [Indexed: 02/07/2023]
Abstract
Multiple strain tuberculosis (TB) infections are now an acceptable facet of tuberculosis epidemiology. Identification of patients infected with more than one strain gives an insight in disease dynamics at individual and population level. This study therefore aimed at identifying multiple strain infections among TB infected patients. Furthermore, to determine factors associated with multiple strain infections in Mubende district of Uganda. A total of 72 Mycobacterium tuberculosis isolates from patients at Mubende regional referral hospital were characterized using 15 loci MIRU-VNTR, Spoligotyping and deletion analysis. Genotypic and epidemiological data were analyzed using MIRU-VNTR plus, Bionumerics software version 6.1 and an exact logistic regression model respectively. Eight (11.1%) of the 72 patients had mixed TB infections. Five were exclusively pulmonary mixed infections while three had both pulmonary and extra-pulmonary infections (Compartmentalized TB infections). Unlike previous studies that have linked this phenomenon to Beijing strains, multiple strains in this study belonged to T2-Uganda, X2 and T1 lineages. Two of the pulmonary mixed infections were resistant to rifampicin or isoniazid. All except one were HIV positive, newly diagnosed cases and urban residents of Mubende district. The study revealed that one in nine urban dwelling, HIV/TB co-infected patient were infected with more than one M. tuberculosis strains. The molecular findings give indications of a vital component of the disease dynamics that is most likely under looked at clinical level.
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Affiliation(s)
- Adrian Muwonge
- Department of Food Safety and Infection Biology, Centre for Epidemiology and Biostatistics, Norwegian School of Veterinary Science, PO Box 8146 Dep, 0033 Oslo, Norway.
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Pérez-Lago L, Navarro Y, Herranz M, Bouza E, García-de-Viedma D. Genetic features shared by Mycobacterium tuberculosis strains involved in microevolution events. INFECTION GENETICS AND EVOLUTION 2013; 16:326-9. [PMID: 23499710 DOI: 10.1016/j.meegid.2013.02.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Revised: 02/18/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
Microevolved Mycobacterium tuberculosis (MTB) clonal variants from a parental strain can emerge within a single patient infection and during transmission events. Genotypic rearrangements may involve functional changes conferring advantages to favor strain adaptation to the host. In the present study, we analyzed in depth some genotypic characteristics of a strain with a high tendency to microevolve that generated 6 clonal variants during transmission of sequential hosts. In order to identify genetic features potentially associated to microevolution in MTB, we analyzed 56 3R genes and the IS6110 insertion sites from this strain and identified an SNP in alkA and an IS6110 copy located upstream of a transposase (Rv0755A). These markers could be involved in mechanisms leading to genotypic variation. Both features were shared by strains from our collection that were also involved in microevolution, suggesting their putative association with these events.
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Affiliation(s)
- Laura Pérez-Lago
- Servicio de Microbiología y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
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