1
|
Acosta F, Martínez-Lirola M, Sola-Campoy PJ, Sicilia J, Guerra-Galán T, Maus SR, Muñoz P, Pérez-Lago L, García de Viedma D. Insights into the Complexity of a Dormant Mycobacterium tuberculosis Cluster Once Transmission Is Resumed. Microbiol Spectr 2022; 10:e0138121. [PMID: 35044196 PMCID: PMC8768656 DOI: 10.1128/spectrum.01381-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022] Open
Abstract
Genotyping tools help identify the complexity in Mycobacterium tuberculosis transmission clusters. We carried out a thorough analysis of the epidemiological and bacteriological complexity of a cluster in Almería, Spain. The cluster, initially associated with Moroccan migrants and with no secondary cases identified in 4 years, then reappeared in Spanish-born individuals. In one case, two Mycobacterium tuberculosis clonal variants were identified. We reanalyzed the cluster, supported by the characterization of multiple cultured isolates and respiratory specimens, whole-genome sequencing, and epidemiological case interviews. Our findings showed that the cluster, which was initially thought to have restarted activity with just a single case harboring a small degree of within-host diversity, was in fact currently growing due to coincidental reactivation of past exposures, with clonal diversity transmitted throughout the cluster. In one case, within-host diversity was amplified, probably due to prolonged diagnostic delay. IMPORTANCE The precise study of the dynamics of tuberculosis transmission in socio-epidemiologically complex scenarios may require more thorough analysis than the standard molecular epidemiology strategies. Our study illustrates the epidemiological and bacteriological complexity present in a transmission cluster in a challenging epidemiological setting with a high proportion of migrant cases. The combination of whole-genome sequencing, refined and refocused epidemiological interviews, and in-depth analysis of the bacterial composition of sputa and cultured isolates was crucial in order to correctly reinterpret the true nature of this cluster. Our global approach allowed us to reinterpret correctly the unnoticed epidemiological and bacteriological complexity involved in the Mycobacterium tuberculosis transmission event under study, which had been overlooked by the usual molecular epidemiology approaches.
Collapse
Affiliation(s)
- Fermin Acosta
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Pedro J. Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Jon Sicilia
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Teresa Guerra-Galán
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra R. Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
- Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
| |
Collapse
|
2
|
Genestet C, Hodille E, Barbry A, Berland JL, Hoffmann J, Westeel E, Bastian F, Guichardant M, Venner S, Lina G, Ginevra C, Ader F, Goutelle S, Dumitrescu O. Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathog 2021; 17:e1009643. [PMID: 34166469 PMCID: PMC8224949 DOI: 10.1371/journal.ppat.1009643] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) genetic micro-diversity in clinical isolates may underline mycobacterial adaptation to tuberculosis (TB) infection and provide insights to anti-TB treatment response and emergence of resistance. Herein we followed within-host evolution of Mtb clinical isolates in two cohorts of TB patients, either with delayed Mtb culture conversion (> 2 months), or with fast culture conversion (< 2 months). We captured the genetic diversity of Mtb isolates obtained in each patient, by focusing on minor variants detected as unfixed single nucleotide polymorphisms (SNPs). To unmask antibiotic tolerant sub-populations, we exposed these isolates to rifampicin (RIF) prior to whole genome sequencing (WGS) analysis. Thanks to WGS, we detected at least 1 unfixed SNP within the Mtb isolates for 9/15 patients with delayed culture conversion, and non-synonymous (ns) SNPs for 8/15 patients. Furthermore, RIF exposure revealed 9 additional unfixed nsSNP from 6/15 isolates unlinked to drug resistance. By contrast, in the fast culture conversion cohort, RIF exposure only revealed 2 unfixed nsSNP from 2/20 patients. To better understand the dynamics of Mtb micro-diversity, we investigated the variant composition of a persistent Mtb clinical isolate before and after controlled stress experiments mimicking the course of TB disease. A minor variant, featuring a particular mycocerosates profile, became enriched during both RIF exposure and macrophage infection. The variant was associated with drug tolerance and intracellular persistence, consistent with the pharmacological modeling predicting increased risk of treatment failure. A thorough study of such variants not necessarily linked to canonical drug-resistance, but which are prone to promote anti-TB drug tolerance, may be crucial to prevent the subsequent emergence of resistance. Taken together, the present findings support the further exploration of Mtb micro-diversity as a promising tool to detect patients at risk of poorly responding to anti-TB treatment, ultimately allowing improved and personalized TB management. Tuberculosis (TB) is caused by Mycobacterium tuberculosis (Mtb), bacteria that are able to persist inside the patient for many months or years, thus requiring long antibiotic treatments. Here we focused on TB patients with delayed response to treatment and we performed genetic characterization of Mtb isolates to search for sub-populations that may tolerate anti-TB drugs. We found that Mtb cultured from 9/15 patients contained different sub-populations, and in vitro drug exposure revealed Mtb sub-populations in 6/15 isolates, none related to known drug-resistance mechanisms. By contrast, drug exposure revealed Mtb sup-populations in 2/20 isolates in the control cohort of patients with fast culture conversion. Furthermore, we characterized a Mtb variant isolated from a sub-population growing in the presence of rifampicin (RIF), a major anti-TB drug. We found that this variant featured a modified lipidic envelope, and that it was able to develop in the presence of RIF and inside human macrophage cells. We performed pharmacological modelling and found that this kind of variant may be related to a poor response to treatment. In conclusion, searching for particular Mtb sub-populations may help to detect patients at risk of treatment failure and provide additional guidance for TB management.
Collapse
Affiliation(s)
- Charlotte Genestet
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- * E-mail:
| | - Elisabeth Hodille
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Alexia Barbry
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Jean-Luc Berland
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Jonathan Hoffmann
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Emilie Westeel
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Fondation Mérieux, Emerging Pathogens Laboratory, Lyon, France
| | - Fabiola Bastian
- Plateforme DTAMB, CNRS, Université Lyon 1, Villeurbanne, France
| | - Michel Guichardant
- CarMeN laboratory, INSA Lyon, INSERM U1060, INRA U1397, Université Lyon 1, Villeurbanne, France
| | - Samuel Venner
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
| | - Gérard Lina
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| | - Christophe Ginevra
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
| | - Florence Ader
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Service des Maladies infectieuses et tropicales, Lyon, France
| | - Sylvain Goutelle
- Laboratoire de Biométrie et Biologie Évolutive, CNRS UMR 5558, Université Lyon 1, Villeurbanne, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
- Hospices Civils de Lyon, Groupement Hospitalier Nord, Service pharmaceutique, Lyon, France
| | - Oana Dumitrescu
- CIRI—Centre International de Recherche en Infectiologie, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon-1, Inserm U1111, CNRS UMR5308, Lyon, France
- Hospices Civils de Lyon, Institut des Agents Infectieux, Laboratoire de bactériologie, Lyon, France
- Université Lyon 1, Facultés de Médecine et de Pharmacie de Lyon, Lyon, France
| |
Collapse
|
3
|
Survival of an epidemic MDR strain of Mycobacterium tuberculosis and its non-prosperous variant within activated macrophages. INFECTION GENETICS AND EVOLUTION 2019; 73:248-254. [PMID: 31077841 DOI: 10.1016/j.meegid.2019.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 11/20/2022]
Abstract
The fitness of a pathogen results from the interaction of multiple factors favoring either epidemiological success or failure. Herein, we studied the performance of the M strain, a highly successful multidrug resistant Mycobacterium tuberculosis genotype, and its non-prosperous variant, the 410 strain, in activated human monocyte-derived macrophages. Both strains showed comparable ability to induce necrotic cell death and to survive in apoptotic macrophages. Of the various macrophage activation conditions tested, none led to an enhanced control of the outbreak strain. The combination of 1,25(OH)2 vitaminD3 and IFN-γ favored significantly the control of the non-prosperous 410 strain. These observations indicate that the ability of the M strain to survive within the hostile intracellular milieu is conserved, and the overall fitness cost paid by this genotype would be low. Our results provide additional evidence on bacterial traits that may have contributed to the epidemiological success of the M strain.
Collapse
|
4
|
Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
Collapse
|
5
|
Yokobori N, López B, Monteserin J, Paul R, Von Groll A, Martin A, Marquina-Castillo B, Palomino JC, Hernández-Pando R, Sasiain MDC, Ritacco V. Performance of a highly successful outbreak strain of Mycobacterium tuberculosis in a multifaceted approach to bacterial fitness assessment. Int J Med Microbiol 2018; 308:349-357. [DOI: 10.1016/j.ijmm.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/19/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022] Open
|
6
|
Navarro Y, Pérez-Lago L, Herranz M, Sierra O, Comas I, Sicilia J, Bouza E, García de Viedma D. In-Depth Characterization and Functional Analysis of Clonal Variants in a Mycobacterium tuberculosis Strain Prone to Microevolution. Front Microbiol 2017; 8:694. [PMID: 28484440 PMCID: PMC5403423 DOI: 10.3389/fmicb.2017.00694] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/04/2017] [Indexed: 11/16/2022] Open
Abstract
The role of clonal complexity has gradually been accepted in infection by Mycobacterium tuberculosis (MTB), although analyses of this issue are limited. We performed an in-depth study of a case of recurrent MTB infection by integrating genotyping, whole genome sequencing, analysis of gene expression and infectivity in in vitro and in vivo models. Four different clonal variants were identified from independent intrapatient evolutionary branches. One of the single-nucleotide polymorphisms in the variants mapped in mce3R, which encodes a repressor of an operon involved in virulence, and affected expression of the operon. Competitive in vivo and in vitro co-infection assays revealed higher infective efficiency for one of the clonal variants. A new clonal variant, which had not been observed in the clinical isolates, emerged in the infection assays and showed higher fitness than its parental strain. The analysis of other patients involved in the same transmission cluster revealed new clonal variants acquired through novel evolutionary routes, indicating a high tendency toward microevolution in some strains that is not host-dependent. Our study highlights the need for integration of various approaches to advance our knowledge of the role and significance of microevolution in tuberculosis.
Collapse
Affiliation(s)
- Yurena Navarro
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER Enfermedades Respiratorias, CIBERESMadrid, Spain.,CEI Campus Moncloa, UCM-UPMMadrid, Spain.,Centro de Vigilancia Sanitaria Veterinaria, Universidad Complutense MadridMadrid, Spain
| | - Laura Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER Enfermedades Respiratorias, CIBERESMadrid, Spain
| | - Marta Herranz
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER Enfermedades Respiratorias, CIBERESMadrid, Spain
| | - Olalla Sierra
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain
| | - Iñaki Comas
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de ValènciaValencia, Spain.,CIBER en Epidemiología y Salud PúblicaMadrid, Spain
| | - Javier Sicilia
- Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,Unidad de Medicina y Cirugía Experimental, Hospital General Universitario Gregorio MarañónMadrid, Spain
| | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER Enfermedades Respiratorias, CIBERESMadrid, Spain.,Departamento de Medicina, Facultad de Medicina, Universidad Complutense de MadridMadrid, Spain
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER Enfermedades Respiratorias, CIBERESMadrid, Spain.,CEI Campus Moncloa, UCM-UPMMadrid, Spain
| |
Collapse
|
7
|
Haas DJ, Dorneles EMS, Spier SJ, Carroll SP, Edman J, Azevedo VA, Heinemann MB, Lage AP. Molecular epidemiology of Corynebacterium pseudotuberculosis isolated from horses in California. INFECTION GENETICS AND EVOLUTION 2016; 49:186-194. [PMID: 27979735 DOI: 10.1016/j.meegid.2016.12.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/10/2016] [Accepted: 12/10/2016] [Indexed: 11/26/2022]
Abstract
Corynebacterium pseudotuberculosis biovar Equi is an important pathogen of horses. It is increasing in frequency in the United States, and is responsible for various clinical forms of infection, including external abscesses, internal abscesses of the abdominal or thoracic cavities, and ulcerative lymphangitis. The host/pathogen factors dictating the form or severity of infection are currently unknown. Our recent investigations have shown that genotyping C. pseudotuberculosis isolates using enterobacterial repetitive intergenic consensus (ERIC)-PCR is useful for understanding the evolutionary genetics of the species as well for molecular epidemiology studies. The aims of the present study were to assess (i) the genetic diversity of C. pseudotuberculosis strains isolated from horses in California, United States and (ii) the epidemiologic relationships among isolates. One hundred and seven C. pseudotuberculosis biovar Equi isolates from ninety-five horses, and two C. pseudotuberculosis biovar Ovis strains, C. pseudotuberculosis ATCC 19410T type strain and C. pseudotuberculosis 1002 vaccine strain, were fingerprinted using the ERIC 1+2-PCR. C. pseudotuberculosis isolated from horses showed a high genetic diversity, clustering in twenty-seven genotypes with a diversity index of 0.91. Minimal spanning tree showed four major clonal complexes with a pattern of temporal clustering. Strains isolated from the same horse showed identical ERIC 1+2-PCR genotype, with the exception of two strains isolated from the same animal that showed distinct genotypes, suggesting a co-infection. We found no strong genetic signals related to clinical form (including internal versus external infections). However, temporal clustering of genotypes was observed.
Collapse
Affiliation(s)
- Dionei J Haas
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elaine M S Dorneles
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Departamento de Medicina Veterinária, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - Sharon J Spier
- Department of Medicine and Epidemiology, University of California, Davis, California, USA
| | - Scott P Carroll
- Department of Medicine and Epidemiology, University of California, Davis, California, USA
| | - Judy Edman
- Department of Medicine and Epidemiology, University of California, Davis, California, USA
| | - Vasco A Azevedo
- Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcos B Heinemann
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Andrey P Lage
- Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| |
Collapse
|
8
|
Pérez-Lago L, Rodríguez Borlado AI, Comas I, Herranz M, Ruiz-Serrano MJ, Bouza E, García-de-Viedma D. Subtle genotypic changes can be observed soon after diagnosis in Mycobacterium tuberculosis infection. Int J Med Microbiol 2016; 306:401-5. [DOI: 10.1016/j.ijmm.2016.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 04/15/2016] [Accepted: 05/09/2016] [Indexed: 11/30/2022] Open
|
9
|
Ssengooba W, de Jong BC, Joloba ML, Cobelens FG, Meehan CJ. Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients. BMC Infect Dis 2016; 16:371. [PMID: 27495002 PMCID: PMC4974755 DOI: 10.1186/s12879-016-1737-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 07/28/2016] [Indexed: 03/14/2023] Open
Abstract
Background In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments. Methods From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis. Results Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16–101)/mm3 and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical. Conclusions Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1737-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda. .,Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
| | - Bouke C de Jong
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases, New York University, New York, NY, USA
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| |
Collapse
|
10
|
Streit E, Millet J, Rastogi N. Mycobacterium tuberculosis polyclonal infections and microevolution identified by MIRU-VNTRs in an epidemiological study. Int J Mycobacteriol 2015; 4:222-7. [DOI: 10.1016/j.ijmyco.2015.05.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022] Open
|
11
|
Navarro Y, Romero B, Copano MF, Bouza E, Domínguez L, de Juan L, García-de-Viedma D. Multiple sampling and discriminatory fingerprinting reveals clonally complex and compartmentalized infections by M. bovis in cattle. Vet Microbiol 2014; 175:99-104. [PMID: 25439651 DOI: 10.1016/j.vetmic.2014.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 10/27/2014] [Accepted: 11/02/2014] [Indexed: 10/24/2022]
Abstract
The combination of new genotyping tools and a more exhaustive sampling policy in the analysis of infection by Mycobacterium tuberculosis has shown that infection by this pathogen is more complex than initially expected. Mixed infections, coexistence of clonal variants from a parental strain, and compartmentalized infections are all different modalities of this clonal complexity. Until recently, genotyping of Mycobacterium bovis in animal populations was based on spoligotyping and analysis of a single isolate per infection; therefore, clonal complexity is probably underdetected. We used multiple sampling combined with highly discriminatory MIRU-VNTR to study compartmentalized infections by M. bovis in a low-tuberculosis prevalence setting. We spoligotyped the M. bovis isolates from two or more anatomic locations sampled from 55 animals on 39 independent farms. Compartmentalized infections, with two different strains infecting independent lymph nodes in the same animal, were found in six cases (10.9%). MIRU-VNTR analysis confirmed that the compartmentalization was strict and that only one strain was present in each infected node. MIRU-VNTR analysis of additional infected animals on one of the farms confirmed that the compartmentalized infection was a consequence of superinfection, since the two strains were independently infecting other animals. This same analysis revealed the emergence of a microevolved clonal variant in one of the lymph nodes of the compartmentalized animal. Clonal complexity must also be taken into consideration in M. bovis infection, even in low-prevalence settings, and analyses must be adapted to detect it and increase the accuracy of molecular epidemiology studies.
Collapse
Affiliation(s)
- Yurena Navarro
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Beatriz Romero
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain
| | | | - Emilio Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Lucas Domínguez
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Lucía de Juan
- CEI Campus Moncloa, UCM-UPM, Madrid, Spain; Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense Madrid, 28040 Madrid, Spain; Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense Madrid, 28040 Madrid, Spain
| | - Darío García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
| |
Collapse
|
12
|
Pérez-Lago L, Palacios JJ, Herranz M, Ruiz Serrano MJ, Bouza E, García-de-Viedma D. Revealing hidden clonal complexity in Mycobacterium tuberculosis infection by qualitative and quantitative improvement of sampling. Clin Microbiol Infect 2014; 21:147.e1-7. [PMID: 25658553 DOI: 10.1016/j.cmi.2014.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/22/2014] [Accepted: 09/26/2014] [Indexed: 11/30/2022]
Abstract
The analysis of microevolution events, its functional relevance and impact on molecular epidemiology strategies, constitutes one of the most challenging aspects of the study of clonal complexity in infection by Mycobacterium tuberculosis. In this study, we retrospectively evaluated whether two improved sampling schemes could provide access to the clonal complexity that is undetected by the current standards (analysis of one isolate from one sputum). We evaluated in 48 patients the analysis by mycobacterial interspersed repetitive unit-variable number tandem repeat of M. tuberculosis isolates cultured from bronchial aspirate (BAS) or bronchoalveolar lavage (BAL) and, in another 16 cases, the analysis of a higher number of isolates from independent sputum samples. Analysis of the isolates from BAS/BAL specimens revealed clonal complexity in a very high proportion of cases (5/48); in most of these cases, complexity was not detected when the isolates from sputum samples were analysed. Systematic analysis of isolates from multiple sputum samples also improved the detection of clonal complexity. We found coexisting clonal variants in two of 16 cases that would have gone undetected in the analysis of the isolate from a single sputum specimen. Our results suggest that analysis of isolates from BAS/BAL specimens is highly efficient for recording the true clonal composition of M. tuberculosis in the lungs. When these samples are not available, we recommend increasing the number of isolates from independent sputum specimens, because they might not harbour the same pool of bacteria. Our data suggest that the degree of clonal complexity in tuberculosis has been underestimated because of the deficiencies inherent in a simplified procedure.
Collapse
Affiliation(s)
- L Pérez-Lago
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain
| | - J J Palacios
- Unidad de Referencia Regional de Micobacterias, Servicio de Microbiología, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - M Herranz
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain
| | - M J Ruiz Serrano
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain
| | - E Bouza
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain; Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - D García-de-Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain; CIBER Enfermedades respiratorias, CIBERES, Spain; CEI Campus Moncloa, UCM-UPM, Madrid, Spain.
| |
Collapse
|