1
|
Scaltriti E, Iyad K, Boniotti MB, Menozzi I, Bolzoni L, Ippolito D, Ciarello FP, Loda D, D’Incau M, Zanoni M, Presti VDML, Mazzone P, Gavaudan S, Pacciarini ML. Inside Mycobacterium bovis SB0120 spoligotype circulating in Italy: analysis of the most frequent genotypes by whole genome sequencing. Front Microbiol 2024; 15:1416605. [PMID: 39132144 PMCID: PMC11310128 DOI: 10.3389/fmicb.2024.1416605] [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: 04/12/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Bovine tuberculosis (bTB) is a chronic inflammatory disease primarily caused by Mycobacterium bovis. The infection affects domestic animals and wildlife, posing a zoonotic risk to humans. To understand the dynamics of transmission and genetic diversity in Italy's M. bovis population, we conducted whole-genome sequencing (WGS) analysis on two prevalent genotypes, belonging to Spoligotype SB0120, identified in different geographical and temporal contexts. By comparing these genomes with international M. bovis isolates, we identified a distinct clade within the lineage La1.2, encompassing the Italian SB0120 isolates, indicating a genomic segregation of Italian M. bovis from other European isolates. Within Italy, a significant level of genetic variability emerged across regions, while isolates within epidemiologically linked outbreaks exhibited minimal genetic diversity. Additionally, isolates derived from cattle and wild boars within a tuberculosis hotspot in Central Italy and from cattle and black pigs in Sicily formed unified clonal clusters. This indicates the presence of persistent strains circulating in the examined regions. The genetic diversity within herds was limited, as specific clones endured over time within certain herds. This research enhances our comprehension of the epidemiology and transmission patterns of bTB in Italy, thereby aiding the development of precise control strategies and disease management. Using WGS and implementing standardized protocols and databases will be pivotal in combating bTB and promoting One-Health approaches to address this noteworthy public health concern.
Collapse
Affiliation(s)
- Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Karaman Iyad
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Maria Beatrice Boniotti
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Dorotea Ippolito
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Flavia Pruiti Ciarello
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Daniela Loda
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mario D’Incau
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mariagrazia Zanoni
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Vincenzo Di Marco Lo Presti
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Piera Mazzone
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Perugia, Italy
| | - Stefano Gavaudan
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Ancona, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| |
Collapse
|
2
|
Islam MR, Sharma MK, KhunKhun R, Shandro C, Sekirov I, Tyrrell GJ, Soualhine H. Whole genome sequencing-based identification of human tuberculosis caused by animal-lineage Mycobacterium orygis. J Clin Microbiol 2023; 61:e0026023. [PMID: 37877705 PMCID: PMC10662373 DOI: 10.1128/jcm.00260-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
A recently described member of the Mycobacterium tuberculosis complex (MTBC) is Mycobacterium orygis, which can cause disease primarily in animals but also in humans. Although M. orygis has been reported from different geographic regions around the world, due to a lack of proper identification techniques, the contribution of this emerging pathogen to the global burden of zoonotic tuberculosis is not fully understood. In the present work, we report single nucleotide polymorphism (SNP) analysis using whole genome sequencing (WGS) that can accurately identify M. orygis and differentiate it from other members of the MTBC species. WGS-based SNP analysis was performed for 61 isolates from different provinces in Canada that were identified as M. orygis. A total of 56 M. orygis sequences from the public databases were also included in the analysis. Several unique SNPs in the gyrB, PPE55, Rv2042c, leuS, mmpL6, and mmpS6 genes were used to determine their effectiveness as genetic markers for the identification of M. orygis. To the best of our knowledge, five of these SNPs, viz., gyrB 277 (A→G), gyrB 1478 (T→C), leuS 1064 (A→T), mmpL6 486 (T→C), and mmpS6 334 (C→G), are reported for the first time in this study. Our results also revealed several SNPs specific to other species within MTBC. The phylogenetic analysis shows that the studied genomes were genetically diverse and clustered with M. orygis sequences of human and animal origin reported from different geographic locations. Therefore, the present study provides a new insight into the high-confidence identification of M. orygis from MTBC species based on WGS data, which can be useful for reference and diagnostic laboratories.
Collapse
Affiliation(s)
- Md Rashedul Islam
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Meenu K. Sharma
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Rupinder KhunKhun
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Cary Shandro
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Inna Sekirov
- BC Center for Disease Control Public Health Laboratory, Vancouver, British Columbia, Canada
| | - Gregory J. Tyrrell
- Provincial Laboratory for Public Health, Alberta Precision Labs, Edmonton, Alberta, Canada
| | - Hafid Soualhine
- National Reference Centre for Mycobacteriology, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
| |
Collapse
|
3
|
Gonzalo X, Yrah S, Broda A, Laurenson I, Claxton P, Kostrzewa M, Drobniewski F, Larrouy-Maumus G. Performance of lipid fingerprint by routine matrix-assisted laser desorption/ionization time of flight for the diagnosis of Mycobacterium tuberculosis complex species. Clin Microbiol Infect 2023; 29:387.e1-387.e6. [PMID: 36270589 DOI: 10.1016/j.cmi.2022.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/21/2022] [Accepted: 10/13/2022] [Indexed: 11/19/2022]
Abstract
OBJECTIVES Rapid detection of bacterial pathogens at species and sub-species levels is crucial for appropriate treatment, infection control, and public health management. Currently, one of the challenges in clinical microbiology is the discrimination of mycobacterial sub-species within the M. tuberculosis complex (MTBC). Our objective was to evaluate the ability of a biosafe mycobacterial lipid-based approach to identify MTBC cultures and sub-species. METHODS A blinded study was conducted using 90 mycobacterial clinical isolate strains comprising MTBC strains sub-cultured in Middlebrook 7H11 medium supplemented with 10% oleic-acid, dextrose, catalase growth supplement and incubated for up to 6 weeks at 37°C and using the following seven reference strains (M. tuberculosis H37Rv, M canettii, M. africanum, M. pinnipedii, M. caprae, M. bovis, and M. bovis BCG) grown under the same conditions, to set the reference lipid database and test it against the 90 MTBC clinical isolates. Cultured mycobacteria were heat-inactivated and loaded onto the matrix-assisted laser desorption/ionization target followed by the addition of the matrix. Acquisition of the data was performed using the positive ion mode. RESULTS Based on the identification of clear and defined lipid signatures from the seven reference strains, the method that we developed was fast (<10 minutes) and produced interpretable profiles for all but four isolates, caused by poor ionization giving an n = 86 with interpretable spectra. The sensitivity and specificity of the matrix-assisted laser desorption/ionization time of flight were 94.4 (95% CI, 86.4-98.5) and 94.4 (95% CI, 72.7-99.9), respectively. CONCLUSIONS Mycobacterial lipid profiling provides a means of rapid, safe, and accurate discrimination of species within the MTBC.
Collapse
Affiliation(s)
- Ximena Gonzalo
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Shih Yrah
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Agnieszka Broda
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Ian Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | - Pauline Claxton
- Scottish Mycobacteria Reference Laboratory, Edinburgh, United Kingdom
| | | | - Francis Drobniewski
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom.
| |
Collapse
|
4
|
Vázquez-Chacón CA, de Jesús Rodríguez-Gaxiola F, Sánchez-Flores A, Montaño S, Bello-Rios C, Fonseca-Coronado S, López-Carrera CF, Martínez-Guarneros A, Parra-Unda R, García-Magallanes N, Arámbula-Meraz E, Escobar-Gutiérrez A, Cruz-Rivera M, López-Durán PA. Intra-host genetic population diversity: Role in emergence and persistence of drug resistance among Mycobacterium tuberculosis complex minor variants. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 101:105288. [PMID: 35489699 DOI: 10.1016/j.meegid.2022.105288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 04/02/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Drug resistant tuberculosis (DR-TB) is an important public health issue in different parts of the world. Mycobacterium tuberculosis complex variants (MTBC vars) preferentially infect certain hosts, limiting their distribution to different ecosystems. However, MTBC vars can infect other hosts beyond their preferred target potentially contributing to persistence of drug resistance (DR) in other niches. Here, we performed a comprehensive intra-host genetic analysis for the identification of DR-related mutations among all MTBC minor vars whole genome sequences (8,095 strains) publicly available worldwide. High confidence drug-resistance mutations in katG (isoniazid), rpsL (streptomycin), pncA (pyrazinamide), rpoB (rifampicin) and gyrA (fluoroquinolones) genes were identified among intrahost minor sub-populations in 197 different strains (2.43%) belonging to vars africanum, bovis, caprae, microti, orygis and pinnipedii. In addition, a three-dimensional structure modeling analysis to assess the role of novel mutations was also performed. Our findings highlight the importance of detecting discrete intra-host populations carrying DR mutations.
Collapse
Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, Mexico; Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, Mexico
| | | | - Alejandro Sánchez-Flores
- Unidad de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sarita Montaño
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Sinaloa, Mexico
| | - Ciresthel Bello-Rios
- Laboratorio de Biomedicina Molecular, Facultad de Ciencias Químico-Biológicas, Universidad Autonóma de Guerrero, Chilpancingo, Mexico
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, Mexico
| | | | | | - Ricardo Parra-Unda
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Sinaloa, Mexico
| | - Noemí García-Magallanes
- Laboratorio de Biomedicina y Biología Molecular, Universidad Politécnica de Sinaloa, Sinaloa, Mexico
| | - Eliakym Arámbula-Meraz
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Sinaloa, Mexico
| | | | - Mayra Cruz-Rivera
- Departamento de Microbiología y Parasitología. Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Paúl Alexis López-Durán
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico; Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, Mexico.
| |
Collapse
|
5
|
Conserving rhinoceros in the face of disease. Proc Natl Acad Sci U S A 2022; 119:e2206438119. [PMID: 35714286 DOI: 10.1073/pnas.2206438119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
6
|
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.
Collapse
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:
| |
Collapse
|
7
|
Kim TW, Jang YH, Jeong MK, Seo Y, Park CH, Kang S, Lee YJ, Choi JS, Yoon SS, Kim JM. Single-nucleotide polymorphism-based epidemiological analysis of Korean Mycobacterium bovis isolates. J Vet Sci 2021; 22:e24. [PMID: 33774940 PMCID: PMC8007439 DOI: 10.4142/jvs.2021.22.e24] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/03/2021] [Accepted: 01/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background Bovine tuberculosis (TB) is caused by Mycobacterium bovis, a well-known cause of zoonotic tuberculosis in cattle and deer, and has been investigated in many physiological and molecular studies. However, detailed genome-level studies of M. bovis have not been performed in Korea. Objectives To survey whole genome-wide single-nucleotide polymorphism (SNP) variants in Korean M. bovis field isolates and to define M. bovis groups in Korea by comparing SNP typing with spoligotyping and variable number tandem repeat typing. Methods A total of 46 M. bovis field isolates, isolated from laryngopharyngeal lymph nodes and lungs of Korean cattle, wild boar, and Korean water deer, were used to identify SNPs by performing whole-genome sequencing. SNP sites were confirmed via polymerase chain reaction using 87 primer pairs. Results We identified 34 SNP sites with different frequencies across M. bovis isolates, and performed SNP typing and epidemiological analysis, which divided the 46 field isolates into 16 subtypes. Conclusions Through SNP analysis, detailed differences in samples with identical spoligotypes could be detected. SNP analysis is, therefore, a useful epidemiological tracing tool that could enable better management of bovine TB, thus preventing further outbreaks and reducing the impact of this disease.
Collapse
Affiliation(s)
- Tae Woon Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yun Ho Jang
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Min Kyu Jeong
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yoonjeong Seo
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Chan Ho Park
- Gangwondo Livestock & Veterinary Service, Chuncheon 24203, Korea
| | - Sinseok Kang
- Chung Cheongbukdo Livestock & Veterinary Service, Jungbu-Branch, Chungju 27336, Korea
| | - Young Ju Lee
- College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Korea
| | - Jeong Soo Choi
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Soon Seek Yoon
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Jae Myung Kim
- Bacterial Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
| |
Collapse
|
8
|
Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
Collapse
Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| |
Collapse
|
9
|
Abstract
Mycobacterium tuberculosis complex (MTBC) species are classic examples of genetically monomorphic microorganisms due to their low genetic variability. Whole-genome sequencing made it possible to describe both the main species within the complex and M. tuberculosis lineages and sublineages. This differentiation is based on single nucleotide polymorphisms (SNPs) and large sequence polymorphisms in the so-called regions of difference (RDs). Although a number of studies have been performed to elucidate RD localizations, their distribution among MTBC species, and their role in the bacterial life cycle, there are some inconsistencies and ambiguities in the localization of RDs in different members of the complex. To address this issue, we conducted a thorough search for all possible deletions in the WGS data collection comprising 721 samples representing the full MTBC diversity. Discovered deletions were compared with a list of all previously described RDs. As with the SNP-based analysis, we confirmed the specificities of 79 regions at the species, lineage, or sublineage level, 17 of which are described for the first time. We also present RDscan (https://github.com/dbespiatykh/RDscan), an open-source workflow, which detects deletions from short-read sequencing data and correlates the results with high-specificity RDs, curated in this study. Testing of the workflow on a collection comprising ∼7,000 samples showed a high specificity of the found RDs. This study provides novel details that can contribute to a better understanding of the species differentiation within the MTBC and can help to determine how individual clusters evolve within various MTBC species. IMPORTANCE Reductive genome evolution is one of the most important and intriguing adaptation strategies of different living organisms to their environment. Mycobacterium offers several notorious examples of either naturally reduced (Mycobacterium leprae) or laboratory-reduced (Mycobacterium bovis BCG) genomes. Mycobacterium tuberculosis complex has its phylogeny unambiguously framed by large sequence polymorphisms that present unidirectional unique event changes. In the present study, we curated all known regions of difference and analyzed both Mycobacterium tuberculosis and animal-adapted MTBC species. For 79 loci, we have shown a relationship with phylogenetic units, which can serve as a marker for diagnosing or studying biological effects. Moreover, intersections were found for some loci, which may indicate the nonrandomness of these processes and the involvement of these regions in the adaptation of bacteria to external conditions.
Collapse
|
10
|
Analysis of Mycobacterium africanum in the last 17 years in Aragon identifies a specific location of IS6110 in Lineage 6. Sci Rep 2021; 11:10359. [PMID: 33990628 PMCID: PMC8121931 DOI: 10.1038/s41598-021-89511-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/23/2021] [Indexed: 11/12/2022] Open
Abstract
The purpose of this study was to increase our knowledge about Mycobacterium africanum and report the incidence and characteristics of tuberculosis (TB) due to their lineages in Aragon, Spain, over the period 2003–2019. The study includes all the cases in our region, where all the M. tuberculosis complex isolates are systematically characterised. We detected 31 cases of M. africanum among 2598 cases of TB in the period studied. TB caused by M. africanum is rare (1.19%) in our population, and it affects mainly men of economically productive age coming from West African countries. Among the isolates, Lineage (L) 6 was more frequent than L5. The genotyping of these strains identified five clusters and 13 strains with a unique pattern. The isolates’ characterisation identified a copy of IS6110 within the moaX gene, which turned out to be specific for L6. It will allow the differentiation of this lineage from the rest of MTBC with a simple PCR reaction. It remains to be established whether this polymorphism may limit M. africanum transmission. Furthermore, a mutation in the mutT2 promoter was found as specific for L6 strains, which could be related to the high variability found for L6 compared to L5.
Collapse
|
11
|
Vázquez-Chacón CA, Rodríguez-Gaxiola FDJ, López-Carrera CF, Cruz-Rivera M, Martínez-Guarneros A, Parra-Unda R, Arámbula-Meraz E, Fonseca-Coronado S, Vaughan G, López-Durán PA. Identification of drug resistance mutations among Mycobacterium bovis lineages in the Americas. PLoS Negl Trop Dis 2021; 15:e0009145. [PMID: 33591982 PMCID: PMC7886168 DOI: 10.1371/journal.pntd.0009145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/14/2021] [Indexed: 01/25/2023] Open
Abstract
Identifying the Mycobacterium tuberculosis resistance mutation patterns is of the utmost importance to assure proper patient's management and devising of control programs aimed to limit spread of disease. Zoonotic Mycobacterium bovis infection still represents a threat to human health, particularly in dairy production regions. Routinary, molecular characterization of M. bovis is performed primarily by spoligotyping and mycobacterial interspersed repetitive units (MIRU) while next generation sequencing (NGS) approaches are often performed by reference laboratories. However, spoligotyping and MIRU methodologies lack the resolution required for the fine characterization of tuberculosis isolates, particularly in outbreak settings. In conjunction with sophisticated bioinformatic algorithms, whole genome sequencing (WGS) analysis is becoming the method of choice for advanced genetic characterization of tuberculosis isolates. WGS provides valuable information on drug resistance and compensatory mutations that other technologies cannot assess. Here, we performed an analysis of the most frequently identified mutations associated with tuberculosis drug resistance and their genetic relationship among 2,074 Mycobacterium bovis WGS recovered primarily from non-human hosts. Full-length gene sequences harboring drug resistant associated mutations and their phylogenetic relationships were analyzed. The results showed that M. bovis isolates harbor mutations conferring resistance to both first- and second-line antibiotics. Mutations conferring resistance for isoniazid, fluoroquinolones, streptomycin, and aminoglycosides were identified among animal strains. Our findings highlight the importance of molecular surveillance to monitor the emergence of mutations associated with multi and extensive drug resistance in livestock and other non-human mammals.
Collapse
Affiliation(s)
- Carlos Arturo Vázquez-Chacón
- Facultad de Medicina y Cirugía, Universidad Autónoma Benito Juárez de Oaxaca, Oaxaca, México
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | | | | | - Mayra Cruz-Rivera
- Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Armando Martínez-Guarneros
- Laboratorio de Micobacterias, Instituto de Diagnóstico y Referencia Epidemiológicos, Ciudad de México, México
| | - Ricardo Parra-Unda
- Unidad de Investigaciones en Salud Pública, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Sinaloa, México
| | - Salvador Fonseca-Coronado
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
| | - Gilberto Vaughan
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
| | - Paúl Alexis López-Durán
- Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Estado de México, México
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
- Facultad de Ciencias de la Salud, Universidad Anáhuac, Campus Norte, Estado de México, México
- * E-mail:
| |
Collapse
|
12
|
Dorn-In S, Körner T, Büttner M, Hafner-Marx A, Müller M, Heurich M, Varadharajan A, Blum H, Gareis M, Schwaiger K. Shedding of Mycobacterium caprae by wild red deer (Cervus elaphus) in the Bavarian alpine regions, Germany. Transbound Emerg Dis 2019; 67:308-317. [PMID: 31512795 DOI: 10.1111/tbed.13353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/09/2019] [Accepted: 08/30/2019] [Indexed: 11/29/2022]
Abstract
The number of natural infections with Mycobacterium caprae in wildlife and in cattle in the Bavarian and Austrian alpine regions has increased over the last decade. Red deer (Cervus elaphus) have been recognized as maintenance reservoir; however, the transmission routes of M. caprae among and from naturally infected red deer are unknown. The unexpected high prevalence in some hot spot regions might suggest an effective indirect transmission of infection. Therefore, this study was undertaken to diagnose the occurrence of M. caprae in faeces and secretions of red deer in their natural habitat. A total of 2,806 red deer hunted in this region during 2014-2016 were included in this study. After pathological examination, organs (lymph nodes, lung, heart), excretions and secretions (faeces, urine, saliva and tonsil swabs) were further investigated by qPCR specific for Mycobacterium tuberculosis complex (MTC), M. bovis and M. caprae. Samples tested positive by qPCR were processed for culturing of mycobacteria. In total, 55 (2.0%) animals were confirmed positive for M. caprae by pathological examination, PCR and culturing of the affected organ material. With the exception of one sample, all of the secretion and excretion samples were negative for mycobacteria of the Mycobacterium tuberculosis complex (MTC). From one red deer, M. caprae could be isolated from the heart sac as well as from the faeces. Whole-genome sequencing confirmed that both strains were clonally related. This is the first confirmation that M. caprae can be shed with the faeces of a naturally infected red deer. However, further studies focusing on a higher number of infected animals, sample standardization and coordinated multiple sampling are necessary to improve the understanding of transmission routes under natural conditions.
Collapse
Affiliation(s)
- Samart Dorn-In
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Oberschleissheim, Germany
| | - Thomas Körner
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Oberschleissheim, Germany
| | - Mathias Büttner
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | | | - Matthias Müller
- Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Marco Heurich
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany
| | - Ashok Varadharajan
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Manfred Gareis
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Oberschleissheim, Germany
| | - Karin Schwaiger
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Oberschleissheim, Germany
| |
Collapse
|
13
|
Risco D, Martínez R, Bravo M, Fernández Llario P, Cerrato R, Garcia-Jiménez WL, Gonçalves P, García A, Barquero-Pérez Ó, Quesada A, Hermoso de Mendoza J. Nasal shedding of Mycobacterium tuberculosis in wild boar is related to generalised tuberculosis and concomitant infections. Vet Rec 2019; 185:629. [PMID: 31515441 DOI: 10.1136/vr.105511] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/09/2019] [Accepted: 08/28/2019] [Indexed: 11/04/2022]
Abstract
BACKGROUND Wild boar is an important reservoir of Mycobacterium tuberculosis variant bovis, the main causative agent of bovine tuberculosis (bTB). A proportion of tuberculosis (TB)-affected wild boars shed M tuberculosis by nasal route, favouring the maintenance of bTB in a multihost scenario. The aim of this work was to assess if M tuberculosis nasal excretion is influenced by factors commonly associated with high TB prevalence in wild boar. METHODS TB diagnosis and M tuberculosis isolation were carried out in 112 hunted wild boars from mid-western Spain. The association between the presence of M tuberculosis DNA in nasal secretions and explanatory factors was explored using partial least squares regression (PLSR) approaches. RESULTS DNA from M tuberculosis was detected in 40.8 per cent nasal secretions of the TB-affected animals. Explanatory factors provided a first significant PLSR X's component, explaining 25.70 per cent of the variability observed in M tuberculosis nasal shedding. The presence of M tuberculosis in nasal secretions is more probable in animals suffering from generalised TB and mainly coinfected with Metastrongylus species and porcine circovirus type 2, explaining nearly 90 per cent of the total variance of this model. CONCLUSION Measures aiming to control these factors could be useful to reduce M tuberculosis shedding in wild boar.
Collapse
Affiliation(s)
- David Risco
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain.,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Remigio Martínez
- Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain.,Instituto Universitario de Biotecnología Ganadera y Cinegética (INBIO G+C Research Institute), Universidad de Extremadura, Cáceres, Spain
| | - María Bravo
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain .,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Pedro Fernández Llario
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain.,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Rosario Cerrato
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain.,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Waldo Luis Garcia-Jiménez
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain.,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Pilar Gonçalves
- Innovación en Gestión y Conservación de Ungulados S.L, Cáceres, Spain.,Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Alfredo García
- Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain.,Centro de Investigaciones Científicas y Tecnológicas de Extremadura, Badajoz, Spain
| | - Óscar Barquero-Pérez
- Department of Signal Theory and Communications, Rey Juan Carlos University, Madrid, Spain
| | - Alberto Quesada
- Instituto Universitario de Biotecnología Ganadera y Cinegética (INBIO G+C Research Institute), Universidad de Extremadura, Cáceres, Spain.,Departamento de Bioquímica, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain
| | - Javier Hermoso de Mendoza
- Red de Grupos de Investigación en Recursos Faunísticos, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain.,Instituto Universitario de Biotecnología Ganadera y Cinegética (INBIO G+C Research Institute), Universidad de Extremadura, Cáceres, Spain
| |
Collapse
|
14
|
Landolt P, Stephan R, Stevens MJA, Scherrer S. Three-reaction high-resolution melting assay for rapid differentiation of Mycobacterium tuberculosis complex members. Microbiologyopen 2019; 8:e919. [PMID: 31448583 PMCID: PMC6925164 DOI: 10.1002/mbo3.919] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 02/02/2023] Open
Abstract
The possibility of introducing a reliable assay for a quick identification and differentiation of the main species of Mycobacterium tuberculosis complex (MTBC) supports the improvement of efficient tuberculosis combating strategies worldwide. Commercially available assays are often based on cultured samples; however, due to the long cultivation time of mycobacteria, results are delayed. Developed PCR approaches have been published previously, though, when testing intricate veterinary samples, the complex composition of multiplex qPCRs frequently leads to assay failure. In order to overcome those limits, a paradigm of a three-reaction high-resolution melting (HRM) assay for the simultaneous identification and differentiation of the main members of MTBC was established. The assay is based on single nucleotide polymorphisms within gyrB and gyrA, which have been used as target for the establishment of two highly specific HRM assays (HRM assays 1 and 2) discriminating M. tuberculosis/ Mycobacterium canetti, Mycobacterium bovis/M. bovis BCG, Mycobacterium caprae/rare M. caprae/M. bovis ecotypes, Mycobacterium africanum/Mycobacterium orygis/ Mycobacterium pinnipedii/Clade A1, Mycobacterium microti, and a rare subtype of M. canettii followed by a third HRM assay (HRM assay 3) allowing a further differentiation of M. bovis, M. bovis BCG, and a rare subtype of M. caprae/M. bovis, which is considered to be a novel ecotype. High-resolution melting assay 1 is described in a previously published report. High-resolution melting assay 2 showed 100% correlation of all 39 examined isolates with the results of a commercial identification kit. 96% of the clinical samples tested demonstrated concordant results. High-resolution melting assay 3 showed an accordance of 100% with the results of the commercially available identification kit of all 22 samples analyzed. The proposed strategy of the three-reaction HRM assay can be used for an accurate differentiation of up to seven groups of MTBC and potentially to identify a rare subtype of M. canettii either on isolates or on clinical samples.
Collapse
Affiliation(s)
- Patricia Landolt
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marc J A Stevens
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Simone Scherrer
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| |
Collapse
|
15
|
Retrospective Analysis of Archived Pyrazinamide Resistant Mycobacterium tuberculosis Complex Isolates from Uganda-Evidence of Interspecies Transmission. Microorganisms 2019; 7:microorganisms7080221. [PMID: 31362370 PMCID: PMC6723201 DOI: 10.3390/microorganisms7080221] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Accepted: 07/24/2019] [Indexed: 11/16/2022] Open
Abstract
The contribution of Mycobacterium bovis to the proportion of tuberculosis cases in humans is unknown. A retrospective study was undertaken on archived Mycobacterium tuberculosis complex (MTBC) isolates from a reference laboratory in Uganda to identify the prevalence of human M. bovis infection. A total of 5676 isolates maintained in this repository were queried and 136 isolates were identified as pyrazinamide resistant, a hallmark phenotype of M. bovis. Of these, 1.5% (n = 2) isolates were confirmed as M. bovis by using regions of difference PCR analysis. The overall size of whole genome sequences (WGSs) of these two M. bovis isolates were ~4.272 Mb (M. bovis Bz_31150 isolated from a captive chimpanzee) and 4.17 Mb (M. bovis B2_7505 from a human patient), respectively. Alignment of these genomes against 15 MTBC genome sequences revealed 7248 single nucleotide polumorphisms (SNPs). Theses SNPs were used for phylogenetic analysis that indicated a strong relationship between M. bovis and the chimpanzee isolate (Bz_31150) while the other M. bovis genome from the human patient (B2_7505) analyzed did not cluster with any M. bovis or M. tuberculosis strains. WGS analysis also revealed multidrug resistance genotypes; these genomes revealed pncA mutations at positions H57D in Bz_31150 and B2_7505. Phenotypically, B2_7505 was an extensively drug-resistant strain and this was confirmed by the presence of mutations in the major resistance-associated proteins for all anti-tuberculosis (TB) drugs, including isoniazid (KatG (S315T) and InhA (S94A)), fluoroquinolones (S95T), streptomycin (rrs (R309C)), and rifampin (D435Y, a rare but disputed mutation in rpoB). The presence of these mutations exclusively in the human M. bovis isolate suggested that these occurred after transmission from cattle. Genome analysis in this study identified M. bovis in humans and great apes, suggesting possible transmission from domesticated ruminants in the area due to a dynamic and changing interface, which has created opportunity for exposure and transmission.
Collapse
|
16
|
Dorn-In S, Gareis M, Schwaiger K. Differentiation of live and dead Mycobacterium tuberculosis complex in meat samples using PMA qPCR. Food Microbiol 2019; 84:103275. [PMID: 31421753 DOI: 10.1016/j.fm.2019.103275] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 01/28/2023]
Abstract
The causative agents of zoonotic bovine tuberculosis (bTB), Mycobacterium bovis and M. caprae, are members of the M. tuberculosis complex (MTC). Wildlife such as red deer infected with bTB are often without pathological findings, thus meat thereof may be classified as safe for human consumption. The culturing of MTC is time consuming and inappropriate to be applied with fresh meat and food. Therefore, a rapid method "PMA qPCR" to differentiate living and dead cells of MTC was developed in this study. By treating with 50 μM PMA™ dye, dead M. bovis BCG (≤104 cells/ml meat suspension) could be completely discriminated and was not detected by specific MTC PCR. The limit of detection of MTC without treatment with PMA™ dye was 10 cells/ml. All 50 venison samples obtained for field study purposes were negative for MTC. However, 40% were slightly PCR positive for non-TBC mycobacteria. By culturing using selective enrichment, one single colony of M. avium was isolated. This is the first report on the isolation of M. avium from venison. Considering the difficulties of diagnosing mycobacteria in various matrices, the developed PMA qPCR is applicable for the differentiation of dead and living cells of MTC in meat samples.
Collapse
Affiliation(s)
- Samart Dorn-In
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany.
| | - Manfred Gareis
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| | - Karin Schwaiger
- Chair of Food Safety, Faculty of Veterinary Medicine, LMU Munich, Schoenleutnerstr. 8, 85764, Oberschleissheim, Germany
| |
Collapse
|
17
|
Revised Interpretation of the Hain Lifescience GenoType MTBC To Differentiate Mycobacterium canettii and Members of the Mycobacterium tuberculosis Complex. Antimicrob Agents Chemother 2019; 63:AAC.00159-19. [PMID: 30962348 DOI: 10.1128/aac.00159-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/02/2019] [Indexed: 11/20/2022] Open
Abstract
Using 894 phylogenetically diverse genomes of the Mycobacterium tuberculosis complex (MTBC), we simulated in silico the ability of the Hain Lifescience GenoType MTBC assay to differentiate the causative agents of tuberculosis. Here, we propose a revised interpretation of this assay to reflect its strengths (e.g., it can distinguish some strains of Mycobacterium canettii and variants of Mycobacterium bovis that are not intrinsically resistant to pyrazinamide) and limitations (e.g., Mycobacterium orygis cannot be differentiated from Mycobacterium africanum).
Collapse
|
18
|
Hauer A, Michelet L, Cochard T, Branger M, Nunez J, Boschiroli ML, Biet F. Accurate Phylogenetic Relationships Among Mycobacterium bovis Strains Circulating in France Based on Whole Genome Sequencing and Single Nucleotide Polymorphism Analysis. Front Microbiol 2019; 10:955. [PMID: 31130937 PMCID: PMC6509552 DOI: 10.3389/fmicb.2019.00955] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 04/16/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years the diversity of the French Mycobacterium bovis population responsible for bovine tuberculosis (bTB) outbreaks since 1970 has been described in detail. To further understand bTB evolution in France, we used single nucleotide polymorphisms (SNPs) based on whole genome sequence versus classical genotyping methods in order to identify accurate phylogenetic relationships between M. bovis strains. Whole genome sequencing was carried out on a selection of 87 strains which reflect the French M. bovis population’s genetic diversity. Sequences were compared to the M. bovis reference genome AF2122/97. Comparison among the 87 genomes revealed 9,170 sites where at least one strain shows a SNP with respect to the reference genome; 1,172 are intergenic and 7,998 in coding sequences, of which 2,880 are synonymous and 5,118 non-synonymous. SNP-based phylogenetic analysis using these 9,170 SNP is congruent with the cluster defined by spoligotyping and multilocus variable number of tandem repeat analysis typing. In addition, some SNPs were identified as specific to genotypic groups. These findings suggest new SNP targets that can be used for the development of high-resolving methods for genotyping as well as for studying M. bovis evolution and transmission patterns. The detection of non-synonymous SNPs on virulence genes enabled us to distinguish different clusters. Our results seem to indicate that genetically differentiated clusters could also display distinctive phenotypic traits.
Collapse
Affiliation(s)
- Amandine Hauer
- University Paris-Est - ANSES, French Reference Laboratory for Tuberculosis, Maisons-Alfort, France.,ISP, INRA, UMR 1282, Université de Tours, Nouzilly, France
| | - Lorraine Michelet
- University Paris-Est - ANSES, French Reference Laboratory for Tuberculosis, Maisons-Alfort, France
| | | | - Maxime Branger
- ISP, INRA, UMR 1282, Université de Tours, Nouzilly, France
| | - Javier Nunez
- Animal and Plant Health Agency, Addlestone, United Kingdom
| | - Maria-Laura Boschiroli
- University Paris-Est - ANSES, French Reference Laboratory for Tuberculosis, Maisons-Alfort, France
| | - Franck Biet
- ISP, INRA, UMR 1282, Université de Tours, Nouzilly, France
| |
Collapse
|
19
|
Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening. Sci Rep 2019; 9:26. [PMID: 30631100 PMCID: PMC6328581 DOI: 10.1038/s41598-018-37176-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/03/2018] [Indexed: 01/08/2023] Open
Abstract
High-throughput screening facilities do not generally support biosafety level 3 organisms such as Mycobacterium tuberculosis. To discover not only antibacterials, but also virulence inhibitors with either bacterial or host cell targets, an assay monitoring lung fibroblast survival upon infection was developed and optimized for 384-plate format and robotic liquid handling. By using Mycobacterium marinum as surrogate organism, 28,000 compounds were screened at biosafety level 2 classification, resulting in 49 primary hits. Exclusion of substances with unfavourable properties and known antimicrobials resulted in 11 validated hits of which 7 had virulence inhibiting properties and one had bactericidal effect also in wild type Mycobacterium tuberculosis. This strategy to discover virulence inhibitors using a model organism in high-throughput screening can be a valuable tool for other researchers working on drug discovery against tuberculosis and other biosafety level 3 infectious agents.
Collapse
|
20
|
Brites D, Loiseau C, Menardo F, Borrell S, Boniotti MB, Warren R, Dippenaar A, Parsons SDC, Beisel C, Behr MA, Fyfe JA, Coscolla M, Gagneux S. A New Phylogenetic Framework for the Animal-Adapted Mycobacterium tuberculosis Complex. Front Microbiol 2018; 9:2820. [PMID: 30538680 PMCID: PMC6277475 DOI: 10.3389/fmicb.2018.02820] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/02/2018] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely related to the human-adapted Mycobacterium africanum Lineage 6 than to other animal-adapted strains. Furthermore, we identified four main animal-adapted MTBC clades that might correspond to four main host shifts; two of these clades are hypothesized to reflect independent cattle domestication events. Contrary to what would be expected from an obligate pathogen, MTBC nucleotide diversity was not positively correlated with host phylogenetic distances, suggesting that host tropism in the animal-adapted MTBC seems to be driven by contact rates and demographic aspects of the host population rather by than host relatedness. By combining phylogenomics with ecological data, we propose an evolutionary scenario in which the ancestor of Lineage 6 and all animal-adapted MTBC ecotypes was a generalist pathogen that subsequently adapted to different host species. This study provides a new phylogenetic framework to better understand the evolution of the different ecotypes of the MTBC and guide future work aimed at elucidating the molecular mechanisms underlying host range.
Collapse
Affiliation(s)
- Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Maria Beatrice Boniotti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna: Centro Nazionale di Referenza per la Tubercolosi Bovina, Brescia, Italy
| | - Robin Warren
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Anzaan Dippenaar
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Sven David Charles Parsons
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Marcel A Behr
- McGill International TB Centre, Infectious Diseases and Immunity in Global Health, McGill University Health Centre and Research Institute, Montréal, QC, Canada
| | - Janet A Fyfe
- Mycobacterium Reference Laboratory, Victoria Infectious Diseases Reference Laboratory, Peter Doherty Institute, Melbourne, VIC, Australia
| | - Mireia Coscolla
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| |
Collapse
|
21
|
DNA markers for tuberculosis diagnosis. Tuberculosis (Edinb) 2018; 113:139-152. [PMID: 30514496 DOI: 10.1016/j.tube.2018.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 09/23/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis complex (MTBC), is an infectious disease with more than 10.4 million cases and 1.7 million deaths reported worldwide in 2016. The classical methods for detection and differentiation of mycobacteria are: acid-fast microscopy (Ziehl-Neelsen staining), culture, and biochemical methods. However, the microbial phenotypic characterization is time-consuming and laborious. Thus, fast, easy, and sensitive nucleic acid amplification tests (NAATs) have been developed based on specific DNA markers, which are commercially available for TB diagnosis. Despite these developments, the disease remains uncontrollable. The identification and differentiation among MTBC members with the use of NAATs remains challenging due, among other factors, to the high degree of homology within the members and mutations, which hinders the identification of specific target sequences in the genome with potential impact in the diagnosis and treatment outcomes. In silico methods provide predictive identification of many new target genes/fragments/regions that can specifically be used to identify species/strains, which have not been fully explored. This review focused on DNA markers useful for MTBC detection, species identification and antibiotic resistance determination. The use of DNA targets with new technological approaches will help to develop NAATs applicable to all levels of the health system, mainly in low resource areas, which urgently need customized methods to their specific conditions.
Collapse
|
22
|
Ates LS, Dippenaar A, Sayes F, Pawlik A, Bouchier C, Ma L, Warren RM, Sougakoff W, Majlessi L, van Heijst JWJ, Brossier F, Brosch R. Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity. Genome Biol Evol 2018; 10:1858-1874. [PMID: 30010947 PMCID: PMC6071665 DOI: 10.1093/gbe/evy145] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium africanum consists of Lineages L5 and L6 of the Mycobacterium tuberculosis complex (MTBC) and causes human tuberculosis in specific regions of Western Africa, but is generally not transmitted in other parts of the world. Since M. africanum is evolutionarily closely placed between the globally dispersed Mycobacterium tuberculosis and animal-adapted MTBC-members, these lineages provide valuable insight into M. tuberculosis evolution. Here, we have collected 15 M. africanum L5 strains isolated in France over 4 decades. Illumina sequencing and phylogenomic analysis revealed a previously underappreciated diversity within L5, which consists of distinct sublineages. L5 strains caused relatively high levels of extrapulmonary tuberculosis and included multi- and extensively drug-resistant isolates, especially in the newly defined sublineage L5.2. The specific L5 sublineages also exhibit distinct phenotypic characteristics related to in vitro growth, protein secretion and in vivo immunogenicity. In particular, we identified a PE_PGRS and PPE-MPTR secretion defect specific for sublineage L5.2, which was independent of PPE38. Furthermore, L5 isolates were able to efficiently secrete and induce immune responses against ESX-1 substrates contrary to previous predictions. These phenotypes of Type VII protein secretion and immunogenicity provide valuable information to better link genome sequences to phenotypic traits and thereby understand the evolution of the MTBC.
Collapse
Affiliation(s)
- Louis S Ates
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anzaan Dippenaar
- DST-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
| | - Fadel Sayes
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Alexandre Pawlik
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Christiane Bouchier
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Laurence Ma
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Robin M Warren
- DST-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
| | - Wladimir Sougakoff
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Laleh Majlessi
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Florence Brossier
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Roland Brosch
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| |
Collapse
|
23
|
A Novel Oligonucleotide Pair for Genotyping Members of the Pseudomonas Genus by Single-Round PCR Amplification of the gyrB Gene. Methods Protoc 2018. [PMCID: PMC6481054 DOI: 10.3390/mps1030024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas is a phylogenetically diverse bacterial genus which is broadly distributed in different ecological niches, and whose taxonomy is continuously under revision. For that purpose, gyrB is one of the housekeeping genes routinely used for multilocus sequence analysis (MLSA). As we noticed that there was not a single primer pair available in the literature suitable for direct sequencing of this gene, we decided to design a unique oligonucleotide pair and to set up a polymerase chain reaction (PCR) protocol to obtain a single amplicon for the entire Pseudomonas genus. Based on the available gyrB sequence from 148 Pseudomonas species, we identified highly conserved regions to design oligonucleotides without fully degenerate positions. We then set up cycling conditions for achieving high specificity and yield of the PCR protocol. Then, we showed that the amplicons produced with this procedure were appropriate for direct sequencing with both primers, obtaining more than 95% of amplicons coverage. Finally, we demonstrated that a PCR-RFLP (restriction fragment length polymorphism) approach served to differentiate among Pseudomonas species, and even between members of the same species.
Collapse
|
24
|
Marcos LA, Spitzer ED, Mahapatra R, Ma Y, Halse TA, Shea J, Isabelle M, Lapierre P, Escuyer VE. Mycobacterium orygis Lymphadenitis in New York, USA. Emerg Infect Dis 2018; 23:1749-1751. [PMID: 28930016 PMCID: PMC5621560 DOI: 10.3201/eid2310.170490] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We report a case of lymphadenitis caused by Mycobacterium orygis in an immunocompetent person in Stony Brook, New York, USA. Initial real-time PCR assay failed to provide a final subspecies identification within the M. tuberculosis complex, but whole-genome sequencing characterized the isolate as M. orygis.
Collapse
|
25
|
Genetic diversity of Mycobacterium tuberculosis isoniazid monoresistant and multidrug-resistant in Rio Grande do Sul, a tuberculosis high-burden state in Brazil. Tuberculosis (Edinb) 2018; 110:36-43. [DOI: 10.1016/j.tube.2018.02.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 02/09/2018] [Accepted: 02/26/2018] [Indexed: 11/19/2022]
|
26
|
Mycobacterium tuberculosis Complex Members Adapted to Wild and Domestic Animals. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1019:135-154. [PMID: 29116633 DOI: 10.1007/978-3-319-64371-7_7] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Mycobacterium tuberculosis complex (MTBC) is composed of several highly genetically related species that can be broadly classified into those that are human-host adapted and those that possess the ability to propagate and transmit in a variety of wild and domesticated animals. Since the initial description of the bovine tubercle bacillus, now known as Mycobacterium bovis, by Theobald Smith in the late 1800's, isolates originating from a wide range of animal hosts have been identified and characterized as M. microti, M. pinnipedii, the Dassie bacillus, M. mungi, M. caprae, M. orygis and M. suricattae. This chapter outlines the events resulting in the identification of each of these animal-adapted species, their close genetic relationships, and how genome-based phylogenetic analyses of species-specific variation amongst MTBC members is beginning to unravel the events that resulted in the evolution of the MTBC and the observed host tropism between the human- and animal-adapted member species.
Collapse
|
27
|
Abdallah AM, Behr MA. Evolution and Strain Variation in BCG. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1019:155-169. [PMID: 29116634 DOI: 10.1007/978-3-319-64371-7_8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BCG vaccines were derived by in vitro passage, during the years 1908-1921, at the Pasteur Institute of Lille. Following the distribution of stocks of BCG to vaccine production laboratories around the world, it was only a few decades before different BCG producers recognized that there were variants of BCG, likely due to different passaging conditions in the different laboratories. This ultimately led to the lyophilization of stable BCG products in the 1950s and 1960s, but not before considerable evolution of the different BCG strains had taken place. The application of contemporary research methodologies has now revealed genomic, transcriptomic and proteomic differences between BCG strains. These molecular differences in part account for phenotypic differences in vitro between BCG strains, such as their variable secretion of antigenic proteins. Yet, the relevance of BCG variability for immunization policy remains elusive. In this chapter we present an overview of what is known about BCG evolution and its resulting strain variability, and provide some speculation as to the potential relevance for a vaccine given to over 100 million newborns each year.
Collapse
Affiliation(s)
- Abdallah M Abdallah
- Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal, Jeddah, Kingdom of Saudi Arabia.
| | - Marcel A Behr
- Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
| |
Collapse
|
28
|
Chikamatsu K, Aono A, Hata H, Igarashi Y, Takaki A, Yamada H, Sakashita K, Mitarai S. Evaluation of PyroMark Q24 pyrosequencing as a method for the identification of mycobacteria. Diagn Microbiol Infect Dis 2017; 90:35-39. [PMID: 29107416 DOI: 10.1016/j.diagmicrobio.2017.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/07/2017] [Accepted: 09/07/2017] [Indexed: 11/16/2022]
Abstract
We evaluated PyroMark Q24 (QIAGEN) pyrosequencing as a method for the identification of mycobacteria, with potential application in clinical practice. Sequence data from the hypervariable region A of the 16S rRNA gene (43 and 35bp sequences) were obtained using PyroMark Q24, and a similarity search was performed automatically with PyroMark IdentiFire software. Of the 148 mycobacterial type strains tested, 138 (93.2%) were accurately identified to single or clade species level, including complex level. From the remaining 10 strains, 3 (Mycobacterium gilvum, Mycobacterium goodi, and Mycobacterium thermoresistible) showed poor sequencing quality of homopolymers. For 6 other strains (Mycobacterium cosmeticum, Mycobacterium flavescens, Mycobacterium pallens, Mycobacterium hodleri, Mycobacterium xenopi, and Mycobacterium crocinum), the sequences were unreadable from the middle, and Sanger sequencing indicated biallelic site. Finally, a 40bp sequence for Mycobacterium gordonae could not be obtained despite repeated attempts. PyroMark Q24 provided accurate identification of multiple mycobacterial strains isolated from common clinical settings, but additional gene sequencing is required to distinguish species identified as a group or complex.
Collapse
Affiliation(s)
- Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan.
| | - Akio Aono
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Hiroyuki Hata
- Kyokuto Pharmaceutical Industrial Co., Ltd., Tokyo, Japan
| | - Yuriko Igarashi
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Akiko Takaki
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan
| | - Kentaro Sakashita
- Basic Mycobacteriology, Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, the Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, Japan; Basic Mycobacteriology, Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
| |
Collapse
|
29
|
Michel AL, Lane EP, de Klerk-Lorist LM, Hofmeyr M, van der Heijden EMDL, Botha L, van Helden P, Miller M, Buss P. Experimental Mycobacterium bovis infection in three white rhinoceroses (Ceratotherium simum): Susceptibility, clinical and anatomical pathology. PLoS One 2017; 12:e0179943. [PMID: 28686714 PMCID: PMC5501512 DOI: 10.1371/journal.pone.0179943] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/09/2017] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis caused by Mycobacterium bovis is endemic in the African buffalo (Syncerus caffer) population in the Kruger National Park and other conservation areas in South Africa. The disease has been diagnosed in a total of 21 free ranging or semi-free ranging wildlife species in the country with highly variable presentations in terms of clinical signs as well as severity and distribution of tuberculous lesions. Most species are spillover or dead-end hosts without significant role in the epidemiology of the disease. White rhinoceroses (Ceratotherium simum) are translocated from the Kruger National Park in substantial numbers every year and a clear understanding of their risk to manifest overt tuberculosis disease and to serve as source of infection to other species is required. We report the findings of experimental infection of three white rhinoceroses with a moderately low dose of a virulent field isolate of Mycobacterium bovis. None of the animals developed clinical signs or disseminated disease. The susceptibility of the white rhinoceros to bovine tuberculosis was confirmed by successful experimental infection based on the ante mortem isolation of M. bovis from the respiratory tract of one rhinoceros, the presence of acid-fast organisms and necrotizing granulomatous lesions in the tracheobronchial lymph nodes and the detection of M. bovis genetic material by PCR in the lungs of two animals.
Collapse
Affiliation(s)
- Anita L. Michel
- Department of Veterinary Tropical Diseases, Bovine Tuberculosis and Brucellosis Research Programme, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- National Zoological Gardens of South Africa, Pretoria, South Africa
- * E-mail:
| | - Emily P. Lane
- Department of Research and Scientific Services, National Zoological Gardens of South Africa, Pretoria, South Africa
| | - Lin-Mari de Klerk-Lorist
- Department of Agriculture, Forestry and Fisheries, State Veterinary Office, Kruger National Park, Skukuza, South Africa
| | - Markus Hofmeyr
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa
| | - Elisabeth M. D. L. van der Heijden
- Department of Veterinary Tropical Diseases, Bovine Tuberculosis and Brucellosis Research Programme, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Louise Botha
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul van Helden
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michele Miller
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa
| |
Collapse
|
30
|
Viñuelas-Bayón J, Vitoria MA, Samper S. Rapid diagnosis of tuberculosis. Detection of drug resistance mechanisms. Enferm Infecc Microbiol Clin 2017; 35:520-528. [PMID: 28318570 DOI: 10.1016/j.eimc.2017.01.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 11/16/2022]
Abstract
Tuberculosis is still a serious public health problem, with 10.8 million new cases and 1.8 million deaths worldwide in 2015. The diversity among members of the Mycobacterium tuberculosis complex, the causal agent of tuberculosis, is conducive to the design of different methods for rapid diagnosis. Mutations in the genes involved in resistance mechanisms enable the bacteria to elude the treatment. We have reviewed the methods for the rapid diagnosis of M. tuberculosis complex and the detection of susceptibility to drugs, both of which are necessary to prevent the onset of new resistance and to establish early, appropriate treatment.
Collapse
Affiliation(s)
- Jesús Viñuelas-Bayón
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, España
| | - María Asunción Vitoria
- Servicio de Microbiología, Hospital Universitario Lozano Blesa, CIBERES, Zaragoza, España
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, IIS Aragón, CIBERES, Zaragoza, España.
| |
Collapse
|
31
|
Kalo D, Kant S, Srivastava K, Sharma AK. Assess drug resistance pattern and genetic profile of Mycobacterium tuberculosis clinical isolates by molecular typing methods using direct repeats and IS6110 in pulmonary tuberculosis cases. Lung India 2017; 34:155-159. [PMID: 28360464 PMCID: PMC5351358 DOI: 10.4103/0970-2113.201314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background: Tuberculosis (TB), a highly contagious disease that sees no gender, age, or race is mainly a disease of lungs. According to World Health Organization, a TB patient can be completely cured with 6–9 months of anti-TB treatment under directly observed treatment short course. Objectives: The aim of this study was to check the mono, multi- and triple-drug resistance to first line drugs (FLDs) among TB patients and to access their genetic profile using DR 3074, DR 0270, DR 0642, DR 2068, and DR 4110 using molecular techniques. Material and Methods: To gain a better understanding of drug resistant TB, we characterized 121 clinical isolates recovered from 159 drug resistant pulmonary tuberculosis patients by IS6110 genotyping. MTB isolates recovered from HIV- negative, and smear positive cases of both genders, age varied from 18 to 70 years with drug resistant-TB that was refractory to chemotherapy given for > 12 months. Of a total of 159 sputum smear positive patients sum number of male and female patients was 121 (76.10%) and 38 (23.89%), respectively. Among these patients, number of literate and illiterate patients were 123 (77.3%) and 36 (22.6%). 25 (15.7%) patients had farming as their occupation, 80 (50.3%) had nonagricultural occupation and 54 (33.9%) women were housewives. Results: Mono drug resistant, multi-drug resistant, and totally drug resistant (TDR) cases of TB were calculated as 113.83%, 125.1%, and 67.9%. Isoniazid showed the highest percentage of resistance among the patients. Conclusion: Any noncompliance to TB medications, lack of knowledge, and poor management in health centers, etc., results in the emergence of deadly direct repeat forms of TB, which are further complicated and complex to treat.
Collapse
Affiliation(s)
- Deepika Kalo
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Kanchan Srivastava
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Ajay K Sharma
- Department of Zoology, University of Lucknow, Lucknow, Uttar Pradesh, India
| |
Collapse
|
32
|
Rahim Z, Thapa J, Fukushima Y, van der Zanden AGM, Gordon SV, Suzuki Y, Nakajima C. Tuberculosis Caused by Mycobacterium orygis in Dairy Cattle and Captured Monkeys in Bangladesh: a New Scenario of Tuberculosis in South Asia. Transbound Emerg Dis 2016; 64:1965-1969. [PMID: 27888587 DOI: 10.1111/tbed.12596] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Mycobacterium orygis, commonly known as the oryx bacillus and a newly proposed Mycobacterium tuberculosis complex subspecies, was isolated from 18 cattle in a dairy farm and two captured rhesus monkeys in a zoo in Bangladesh. All the infected animals had tuberculosis lesions in their lungs, suggesting transmission and infection with M. orygis by an airborne route. The 20 isolates were analysed using a range of conventional and molecular typing methods, and RD-deletion typing and sequencing of selected genes confirmed the isolates as M. orygis. Multiple-locus variable-number tandem repeat analysis (MLVA) allowed the isolates to be divided into three clusters based on the relatedness of their MLVA profiles. The two monkey isolates shared the same MLVA pattern with 15 of the cattle isolates, whereas the remaining three cattle isolates had different patterns, even though the latter animals had been kept in the same dairy farm. The diversity observed among isolates may suggest the bacteria have been established in this area for a long period. This study along with other recent findings that report the detection of M. orygis from animals as well as humans originating from South Asia potentially indicate endemic distribution of M. orygis in South Asia.
Collapse
Affiliation(s)
- Z Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - J Thapa
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - Y Fukushima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan
| | - A G M van der Zanden
- Laboratory for Medical Microbiology and Public Health, Enschede, The Netherlands
| | - S V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Y Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - C Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Hokkaido, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| |
Collapse
|
33
|
da Silva PB, Campos DL, Ribeiro CM, da Silva IC, Pavan FR. New antimycobacterial agents in the pre-clinical phase or beyond: recent advances in patent literature (2001-2016). Expert Opin Ther Pat 2016; 27:269-282. [PMID: 27796146 DOI: 10.1080/13543776.2017.1253681] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Tuberculosis, an infectious disease, has caused more deaths worldwide than any other single infectious disease, killing more than 1.5 million people each year; equating to 4,100 deaths a day. In the past 60 years, no new drugs have been added to the first line regimen, in spite of the fact that thousands of papers have been published on drugs against tuberculosis and hundreds of drugs have received patents as new potential products. Thus, there is undoubtedly an urgent need for the deployment of new effective drugs against tuberculosis. Areas covered: This review brings to the reader the opportunity to understand the chemical and biological characteristics of all patented anti-tuberculosis drugs in North America, Europe, Japan, and Russia. The 116 patents discussed here concern new molecules in the early or advanced phase of development in the last 16 years. Expert opinion: Of all 116 patents, only one developed drug, bedaquiline, is used, and then, only in specific cases. Another three drugs are in clinical studies. However, many other compounds, for which there are in vitro and in vivo studies, seem to fulfil the requisite criteria to be a new anti-tuberculosis agent. However, why are they not in use? Why were so many studies interrupted? Why is there no more news for many of these drugs?
Collapse
Affiliation(s)
- Patricia Bento da Silva
- a Faculdade de Ciências Farmacêuticas , UNESP - Univ. Estadual Paulista, Campus Araraquara , Araraquara , São Paulo , Brazil
| | - Débora Leite Campos
- a Faculdade de Ciências Farmacêuticas , UNESP - Univ. Estadual Paulista, Campus Araraquara , Araraquara , São Paulo , Brazil
| | - Camila Maríngolo Ribeiro
- a Faculdade de Ciências Farmacêuticas , UNESP - Univ. Estadual Paulista, Campus Araraquara , Araraquara , São Paulo , Brazil
| | - Isabel Cristiane da Silva
- a Faculdade de Ciências Farmacêuticas , UNESP - Univ. Estadual Paulista, Campus Araraquara , Araraquara , São Paulo , Brazil
| | - Fernando Rogério Pavan
- a Faculdade de Ciências Farmacêuticas , UNESP - Univ. Estadual Paulista, Campus Araraquara , Araraquara , São Paulo , Brazil
| |
Collapse
|
34
|
DIAGNOSIS AND IMPLICATIONS OF MYCOBACTERIUM BOVIS INFECTION IN BANDED MONGOOSES (MUNGOS MUNGO) IN THE KRUGER NATIONAL PARK, SOUTH AFRICA. J Wildl Dis 2016; 53:19-29. [PMID: 27788055 DOI: 10.7589/2015-11-318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bovine tuberculosis (bTB) was first diagnosed in the Kruger National Park (KNP) in 1990. Research has since focused on the maintenance host, the African buffalo ( Syncerus caffer ) and clinically affected lion ( Panthera leo ). However, little is known about the role of small predators in tuberculosis epidemiology. During 2011-12, we screened banded mongooses ( Mungos mungo ) in the bTB high-prevalence zone of the KNP for Mycobacterium tuberculosis complex members. Fecal swabs, tracheal swabs, and tracheal lavages of 76 banded mongooses caught in cage traps within a 2-km radius of Skukuza Rest Camp were submitted for Mycobacterium culture, isolation, and species identification. Lesions and lymph node samples collected from 12 animals at postmortem examination were submitted for culture and histopathology. In lung and lymph nodes of two banded mongooses, well demarcated, irregularly margined, gray-yellow nodules of up to 5 mm diameter were identified with either central necrosis or calcification, characterized on histopathology as caseating necrosis with epithelioid macrophages or necrogranuloma with calcified centre. No acid fast bacteria were identified with Ziehl-Neelsen stain. We isolated Mycobacterium bovis from lung, lymph node, and liver samples, as well as from tracheal lavages and tracheal swab from the same two banded mongooses. Blood samples were positive by ElephantTB STAT-PAK® Assay for 12 and Enferplex™ TB Assay for five animals. Only the two banded mongooses positive on pathology and M. bovis culture were positive on both serologic assays. We provide evidence of bTB infection in banded mongooses in the KNP, demonstrate their ability to shed M. bovis , and propose a possible antemortem diagnostic algorithm. Our findings open the discussion around possible sources of infection and their significance at the human/wildlife interface in and around Skukuza.
Collapse
|
35
|
Multidrug-Resistant Mycobacterium tuberculosis of the Latin American Mediterranean Lineage, Wrongly Identified as Mycobacterium pinnipedii (Spoligotype International Type 863 [SIT863]), Causing Active Tuberculosis in South Brazil. J Clin Microbiol 2016; 53:3805-11. [PMID: 26400784 DOI: 10.1128/jcm.02012-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We recently detected the spoligotype patterns of strains of Mycobacterium pinnipedii, a species of the Mycobacterium tuberculosis complex, in sputum samples from nine cases with pulmonary tuberculosis residing in Porto Alegre, South Brazil. Because this species is rarely encountered in humans, we further characterized these nine isolates by additional genotyping techniques, including 24-locus mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing, verification of the loci TbD1, RD9, pks15/1, RD(Rio), and fbpC, the insertion of IS6110 at a site specific to the M. tuberculosis Latin American Mediterranean (LAM) lineage, and whole-genome sequencing. The combined analysis of these markers revealed that the isolates are in fact M. tuberculosis and more specifically belong to the LAM genotype. Most of these isolates (n8) were shown to be multidrug resistant (MDR), which prompted us to perform partial sequencing of the rpoA, rpoB, rpoC, katG, and inhA genes. Seven isolates (77.8%) carried the S315T mutation in katG, and one of these (11%) also presented the C((-17)T single-nucleotide polymorphism (SNP) in inhA. Interestingly, six of the MDR isolates also presented an undescribed insertion of 12 nucleotides (CCA GAA CAA CCC) in codon 516 of rpoB. No putative compensatory mutation was found in either rpoA or rpoC. This is the first report of an M. tuberculosis LAM family strain with a convergent M. pinnipedii spoligotype. These spoligotypes are observed in genotype databases at a modest frequency, highlighting that care must be taken when identifying isolates in the M. tuberculosis complex on the basis of single genetic markers.
Collapse
|
36
|
Quan Z, Haiming T, Xiaoyao C, Weifeng Y, Hong J, Hongfei Z. Development of one-tube multiplex polymerase chain reaction (PCR) for detecting Mycobacterium bovis. J Vet Med Sci 2016; 78:1873-1876. [PMID: 27534910 PMCID: PMC5240767 DOI: 10.1292/jvms.15-0216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A multiplex PCR (m-PCR) with primers targeting the 16S rRNA, Rv3873 and a 12.7-kb
fragment in the genomes of a Mycobacterium tuberculosis complex was
designed for the differential diagnosis of M. tuberculosis, M.
bovis, M. bovis BCG and non-tuberculosis
Mycobacterium (NTM). The specificity of this assay was 100%, and the
detection limit was 15 pg of genomic DNA. Of the 206 blinded clinical
samples, the detection rate of M. bovis infection by m-PCR was lower than
that of the interferon gamma (IFN-γ) release assay; however, the false-positive rate by
the tuberculin skin test and false-negative samples in the IFN-γ release assay were
reduced. Our findings indicated that our m-PCR method is a useful tool for complementation
to differentiate M. bovis from M. tuberculosis and NTM
species.
Collapse
Affiliation(s)
- Zhang Quan
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, Jiangsu, China
| | | | | | | | | | | |
Collapse
|
37
|
Clegg SR, Carter SD, Birtles RJ, Brown JM, Hart CA, Evans NJ. Multilocus Sequence Typing of Pathogenic Treponemes Isolated from Cloven-Hoofed Animals and Comparison to Treponemes Isolated from Humans. Appl Environ Microbiol 2016; 82:4523-4536. [PMID: 27208135 PMCID: PMC4984274 DOI: 10.1128/aem.00025-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/11/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Treponema species are implicated in many diseases of humans and animals. Digital dermatitis (DD) treponemes are reported to cause severe lesions in cattle, sheep, pigs, goats, and wild elk, causing substantial global animal welfare issues and economic losses. The fastidiousness of these spirochetes has previously precluded studies investigating within-phylogroup genetic diversity. An archive of treponemes that we isolated enabled multilocus sequence typing to quantify the diversity and population structure of DD treponemes. Isolates (n = 121) were obtained from different animal hosts in nine countries on three continents. The analyses herein of currently isolated DD treponemes at seven housekeeping gene loci confirm the classification of the three previously designated phylogroups: the Treponema medium, Treponema phagedenis, and Treponema pedis phylogroups. Sequence analysis of seven DD treponeme housekeeping genes revealed a generally low level of diversity among the strains within each phylogroup, removing the need for the previously used "-like" suffix. Surprisingly, all isolates within each phylogroup clustered together, regardless of host or geographic origin, suggesting that the same sequence types (STs) can infect different animals. Some STs were derived from multiple animals from the same farm, highlighting probable within-farm transmissions. Several STs infected multiple hosts from similar geographic regions, identifying probable frequent between-host transmissions. Interestingly, T. pedis appears to be evolving more quickly than the T. medium or T. phagedenis DD treponeme phylogroup, by forming two unique ST complexes. The lack of phylogenetic discrimination between treponemes isolated from different hosts or geographic regions substantially contrasts with the data for other clinically relevant spirochetes. IMPORTANCE The recent expansion of the host range of digital dermatitis (DD) treponemes from cattle to sheep, goats, pigs, and wild elk, coupled with the high level of 16S rRNA gene sequence similarity across hosts and with human treponemes, suggests that the same bacterial species can cause disease in multiple different hosts. This multilocus sequence typing (MLST) study further demonstrates that these bacteria isolated from different hosts are indeed very similar, raising the potential for cross-species transmission. The study also shows that infection spread occurs frequently, both locally and globally, suggesting transmission by routes other than animal-animal transmission alone. These results indicate that on-farm biosecurity is important for controlling disease spread in domesticated species. Continued surveillance and vigilance are important for ascertaining the evolution and tracking any further host range expansion of these important pathogens.
Collapse
Affiliation(s)
- Simon R Clegg
- Department of Infection Biology, Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Stuart D Carter
- Department of Infection Biology, Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - Richard J Birtles
- School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Jennifer M Brown
- Department of Infection Biology, Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| | - C Anthony Hart
- Department of Medical Microbiology, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas J Evans
- Department of Infection Biology, Institute of Infection and Global Health, School of Veterinary Science, University of Liverpool, Liverpool, United Kingdom
| |
Collapse
|
38
|
Tuberculosis Caused by Mycobacterium bovis in a Capybara (Hydrochoerus hydrochaeris). J Comp Pathol 2016; 155:254-258. [PMID: 27363904 DOI: 10.1016/j.jcpa.2016.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/22/2016] [Accepted: 05/29/2016] [Indexed: 10/21/2022]
Abstract
Tuberculosis, associated with Mycobacterium bovis, was diagnosed post mortem in an adult female capybara (Hydrochoerus hydrochaeris), kept at the Pampulha Ecological Park, Belo Horizonte, Brazil, in a large metropolitan area. On post-mortem examination, there were numerous firm white nodules scattered throughout all lobes of both lungs. Tissue samples were collected for histological and microbiological examination. Microscopically, the pulmonary nodules were multifocal to coalescing granulomas and intralesional acid-fast bacilli were evident in Ziehl-Neelsen-stained sections of the lung and spleen. Colonies with morphological features of Mycobacterium spp. were isolated from lung samples and conventional polymerase chain reaction (PCR) with genomic DNA from the isolates was positive for M. bovis; sequencing indicated 100% identity with the region of difference 4 (RD4) of M. bovis. In addition, M. bovis DNA was detected in the lung by quantitative PCR. The finding of M. bovis in a capybara indicates a potential public health risk in a zoological collection.
Collapse
|
39
|
Emerging Tuberculosis Pathogen Hijacks Social Communication Behavior in the Group-Living Banded Mongoose (Mungos mungo). mBio 2016; 7:mBio.00281-16. [PMID: 27165798 PMCID: PMC4895101 DOI: 10.1128/mbio.00281-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
An emerging Mycobacterium tuberculosis complex (MTC) pathogen, M. mungi, infects wild banded mongooses (Mungos mungo) in Northern Botswana, causing significant mortality. This MTC pathogen did not appear to be transmitted through a primary aerosol or oral route. We utilized histopathology, spoligotyping, mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR), quantitative PCR (qPCR), and molecular markers (regions of difference [RDs] from various MTC members, including region of difference 1 [RD1] from M. bovis BCG [RD1BCG], M. microti [RD1mic], and M. pinnipedii [RD1seal], genes Rv1510 [RD4], Rv1970 [RD7], Rv3877/8 [RD1], and Rv3120 [RD12], insertion element IS1561, the 16S RNA gene, and gene Rv0577 [cfp32]), including the newly characterized mongoose-specific deletion in RD1 (RD1mon), in order to demonstrate the presence of M. mungi DNA in infected mongooses and investigate pathogen invasion and exposure mechanisms. M. mungi DNA was identified in 29% of nasal planum samples (n = 52), 56% of nasal rinses and swabs (n = 9), 53% of oral swabs (n = 19), 22% of urine samples (n = 23), 33% of anal gland tissue (n = 18), and 39% of anal gland secretions (n = 44). The occurrence of extremely low cycle threshold values obtained with qPCR in anal gland and nasal planum samples indicates that high levels of M. mungi can be found in these tissue types. Histological data were consistent with these results, suggesting that pathogen invasion occurs through breaks in the nasal planum and/or skin of the mongoose host, which are in frequent contact with anal gland secretions and urine during olfactory communication behavior. Lesions in the lung, when present, occurred only with disseminated disease. No environmental sources of M. mungi DNA could be found. We report primary environmental transmission of an MTC pathogen that occurs in association with social communication behavior. Organisms causing infectious disease evolve modes of transmission that exploit environmental and host conditions favoring pathogen spread and persistence. We report a novel mode of environmental infectious disease transmission that occurs in association with olfactory secretions (e.g., urine and anal gland secretions), allowing pathogen exposure to occur within and between social groups through intricate social communication behaviors of the banded mongoose host. The presence of M. mungi in these environmentally deposited secretions would effectively circumvent natural social barriers (e.g., territoriality), facilitating between-group pathogen transmission in the absence of direct physical contact, a rare occurrence in this highly territorial species. This work identifies an important potential mechanism of pathogen transmission of epidemiological significance in social species. We also provide evidence of a novel mechanism of pathogen transmission for the MTC complex, where pathogen movement in the environment and host exposure dynamics are driven by social behavior.
Collapse
|
40
|
Clarke C, Van Helden P, Miller M, Parsons S. Animal-adapted members of the Mycobacterium tuberculosis complex endemic to the southern African subregion. J S Afr Vet Assoc 2016; 87:1322. [PMID: 27246904 PMCID: PMC6138107 DOI: 10.4102/jsava.v87i1.1322] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/30/2015] [Accepted: 12/02/2015] [Indexed: 11/15/2022] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTC) cause tuberculosis (TB) in both animals and humans. In this article, three animal-adapted MTC strains that are endemic to the southern African subregion – that is, Mycobacterium suricattae, Mycobacterium mungi, and the dassie bacillus – are reviewed with a focus on clinical and pathological presentations, geographic distribution, genotyping methods, diagnostic tools and evolution. Moreover, factors influencing the transmission and establishment of TB pathogens in novel host populations, including ecological, immunological and genetic factors of both the host and pathogen, are discussed. The risks associated with these infections are currently unknown and further studies will be required for greater understanding of this disease in the context of the southern African ecosystem.
Collapse
Affiliation(s)
| | | | | | - Sven Parsons
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University.
| |
Collapse
|
41
|
Barbier E, Boschiroli ML, Gueneau E, Rochelet M, Payne A, de Cruz K, Blieux AL, Fossot C, Hartmann A. First molecular detection of Mycobacterium bovis in environmental samples from a French region with endemic bovine tuberculosis. J Appl Microbiol 2016; 120:1193-207. [PMID: 26855378 DOI: 10.1111/jam.13090] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 01/11/2016] [Accepted: 02/03/2016] [Indexed: 11/24/2022]
Abstract
AIMS The aim of the study was to determine the prevalence of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in environmental matrices within a French region (Côte d'Or) affected by this zoonotic disease. METHODS AND RESULTS We report here the development and the use of molecular detection assays based on qPCR (double fluorescent dye-labelled probe) to monitor the occurrence of Mycobacterium tuberculosis complex (MTBC) or Myco. bovis in environmental samples collected in pastures where infected cattle and wildlife had been reported. Three qPCR assays targeting members of the MTBC (IS1561' and Rv3866 loci) or Myco. bovis (RD4 locus) were developed or refined from existing assays. These tools were validated using Myco. bovis spiked soil, water and faeces samples. Environmental samples were detected positive for the presence of MTBC strains and Myco. bovis in the environment of bTB-infected farms in the Côte d'Or region. CONCLUSIONS The development of molecular assays permitted testing of several types of environmental samples including spring water, sediment samples and soils from badger setts entrance located in the vicinity of these farms, which were repeatedly contaminated with Myco. bovis (up to 8·7 × 10(3) gene copies per gram of badger sett soil). For the first time, direct spoligotyping of soil DNA enabled identification of Myco. bovis genotypes from environmental matrices. SIGNIFICANCE AND IMPACT OF THE STUDY All together, these results suggest that Myco. bovis occurs at low levels in environmental matrices in Côte d'Or within the bTB-infected area. Drinking contaminated water or inhaling contaminated bioaerosols might explain cattle infection in some cases.
Collapse
Affiliation(s)
- E Barbier
- UMR 1347 Agroécologie, INRA, Dijon Cedex, France.,UMR 1347 Agroécologie, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - M L Boschiroli
- Unité de Zoonoses Bactériennes, Laboratoire National de Référence de la Tuberculose, Laboratoire de Santé Animale, ANSES, Université Paris-Est, Maisons-Alfort Cedex, France
| | - E Gueneau
- Laboratoire Départemental de la Côte d'Or, Dijon Cedex, France
| | - M Rochelet
- UMR 1347 Agroécologie, Université de Bourgogne Franche Comté, Dijon Cedex, France
| | - A Payne
- UMR 1347 Agroécologie, INRA, Dijon Cedex, France
| | - K de Cruz
- Unité de Zoonoses Bactériennes, Laboratoire National de Référence de la Tuberculose, Laboratoire de Santé Animale, ANSES, Université Paris-Est, Maisons-Alfort Cedex, France
| | - A L Blieux
- Welience, AgrOnov, SATT Grand-Est, Bretenière Cedex, France
| | - C Fossot
- Phytocontrol Paris, Rungis Cedex, France
| | - A Hartmann
- UMR 1347 Agroécologie, INRA, Dijon Cedex, France
| |
Collapse
|
42
|
El-Sayed A, El-Shannat S, Kamel M, Castañeda-Vazquez MA, Castañeda-Vazquez H. Molecular Epidemiology of Mycobacterium bovis in Humans and Cattle. Zoonoses Public Health 2015; 63:251-64. [PMID: 26684712 DOI: 10.1111/zph.12242] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), is a serious re-emerging disease in both animals and humans. The evolution of the Multi- and Extensively drug-resistant M. bovis strains (MDR-TB and XDR-TB) represents a global threat to public health. Worldwide, the disease is responsible for great economic losses in the veterinary field, serious threat to the ecosystem, and about 3.1% of human TB cases, up to 16% in Tanzania. Only thorough investigation to understand the pathogen's epidemiology can help in controlling the disease and minimizing its threat. For this purpose, various tools have been developed for use in advanced molecular epidemiological studies of bTB, either alone or in combination with standard conventional epidemiological approaches. These techniques enable the analysis of the intra- and inter-species transmission dynamics of bTB. The delivered data can reveal detailed insights into the source of infection, correlations among human and bovine isolates, strain diversity and evolution, spread, geographical localization, host preference, tracing of certain virulence factors such as antibiotic resistance genes, and finally the risk factors for the maintenance and spread of M. bovis. They also allow for the determination of epidemic and endemic strains. This, in turn, has a significant diagnostic impact and helps in vaccine development for bTB eradication programs. The present review discusses many topics including the aetiology, epidemiology and importance of M. bovis, the prevalence of bTB in humans and animals in various countries, the molecular epidemiology of M. bovis, and finally applied molecular epidemiological techniques.
Collapse
Affiliation(s)
- A El-Sayed
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - S El-Shannat
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - M Kamel
- Laboratory of Molecular Epidemiology, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt.,Faculty of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - M A Castañeda-Vazquez
- Laboratory of Mastitis and Molecular Diagnostic, Department of Veterinary Medicine, Division of Veterinary Sciences, University of Guadalajara, Guadalajara, Mexico
| | - H Castañeda-Vazquez
- Laboratory of Mastitis and Molecular Diagnostic, Department of Veterinary Medicine, Division of Veterinary Sciences, University of Guadalajara, Guadalajara, Mexico
| |
Collapse
|
43
|
Dippenaar A, Parsons SDC, Sampson SL, van der Merwe RG, Drewe JA, Abdallah AM, Siame KK, Gey van Pittius NC, van Helden PD, Pain A, Warren RM. Whole genome sequence analysis of Mycobacterium suricattae. Tuberculosis (Edinb) 2015; 95:682-688. [DOI: 10.1016/j.tube.2015.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/29/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
|
44
|
Genomic expression catalogue of a global collection of BCG vaccine strains show evidence for highly diverged metabolic and cell-wall adaptations. Sci Rep 2015; 5:15443. [PMID: 26487098 PMCID: PMC4614345 DOI: 10.1038/srep15443] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/22/2015] [Indexed: 11/09/2022] Open
Abstract
Although Bacillus Calmette-Guérin (BCG) vaccines against tuberculosis have been available for more than 90 years, their effectiveness has been hindered by variable protective efficacy and a lack of lasting memory responses. One factor contributing to this variability may be the diversity of the BCG strains that are used around the world, in part from genomic changes accumulated during vaccine production and their resulting differences in gene expression. We have compared the genomes and transcriptomes of a global collection of fourteen of the most widely used BCG strains at single base-pair resolution. We have also used quantitative proteomics to identify key differences in expression of proteins across five representative BCG strains of the four tandem duplication (DU) groups. We provide a comprehensive map of single nucleotide polymorphisms (SNPs), copy number variation and insertions and deletions (indels) across fourteen BCG strains. Genome-wide SNP characterization allowed the construction of a new and robust phylogenic genealogy of BCG strains. Transcriptional and proteomic profiling revealed a metabolic remodeling in BCG strains that may be reflected by altered immunogenicity and possibly vaccine efficacy. Together, these integrated-omic data represent the most comprehensive catalogue of genetic variation across a global collection of BCG strains.
Collapse
|
45
|
Mycobacterium bovis Bacillus Calmette-Guérin Vertebral Osteomyelitis After Intravesical Bacillus Calmette-Guérin Used for Bladder Cancer. INFECTIOUS DISEASES IN CLINICAL PRACTICE 2015. [DOI: 10.1097/ipc.0000000000000255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
46
|
Correlates between models of virulence for Mycobacterium tuberculosis among isolates of the Central Asian lineage: a case for lysozyme resistance testing? Infect Immun 2015; 83:2213-23. [PMID: 25776753 DOI: 10.1128/iai.03080-14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/09/2015] [Indexed: 12/30/2022] Open
Abstract
Virulence factors (VFs) contribute to the emergence of new human Mycobacterium tuberculosis strains, are lineage dependent, and are relevant to the development of M. tuberculosis drugs/vaccines. VFs were sought within M. tuberculosis lineage 3, which has the Central Asian (CAS) spoligotype. Three isolates were selected from clusters previously identified as dominant in London, United Kingdom. Strain-associated virulence was studied in guinea pig, monocyte-derived macrophage, and lysozyme resistance assays. Whole-genome sequencing, single nucleotide polymorphism (SNP) analysis, and a literature review contributed to the identification of SNPs of interest. The animal model revealed borderline differences in strain-associated pathogenicity. Ex vivo, isolate C72 exhibited statistically significant differences in intracellular growth relative to C6 and C14. SNP candidates inducing lower fitness levels included 123 unique nonsynonymous SNPs, including three located in genes (lysX, caeA, and ponA2) previously identified as VFs in the laboratory-adapted reference strain H37Rv and shown to confer lysozyme resistance. C72 growth was most affected by lysozyme in vitro. A BLAST search revealed that all three SNPs of interest (C35F, P76Q, and P780R) also occurred in Tiruvallur, India, and in Uganda. Unlike C72, however, no single isolate identified through BLAST carried all three SNPs simultaneously. CAS isolates representative of three medium-sized human clusters demonstrated differential outcomes in models commonly used to estimate strain-associated virulence, supporting the idea that virulence varies within, not just across, M. tuberculosis lineages. Three VF SNPs of interest were identified in two additional locations worldwide, which suggested independent selection and supported a role for these SNPs in virulence. The relevance of lysozyme resistance to strain virulence remains to be established.
Collapse
|
47
|
Antemortem diagnosis of Mycobacterium bovis infection in free-ranging African lions (Panthera leo) and implications for transmission. J Wildl Dis 2015; 51:493-7. [PMID: 25647595 DOI: 10.7589/2014-07-170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Diagnosis of tuberculosis in wildlife often relies on postmortem samples because of logistical challenges and lack of field-friendly techniques for live animal testing. Confirmation of infection through detection of infectious organisms is essential for studying the pathogenesis and epidemiology of disease. We describe the application of a technique to obtain respiratory samples from free-ranging living lions to facilitate detection of viable Mycobacterium bovis under field conditions. We identified M. bovis by mycobacterial culture and PCR in tracheobronchial lavage samples from 8/134 (6.0%) lions tested in Kruger National Park, South Africa. This confirms the respiratory shedding of viable M. bovis in living lions. The implications of these results are that infected lions have the potential to transmit this disease and serve as maintenance hosts.
Collapse
|
48
|
Costa P, Couto I, Viveiros M, Inácio J. Nested and multiplex real-time PCR using dual-labeled probes: detecting and discriminating Mycobacterium tuberculosis complex members in cultures and animal tissues. Methods Mol Biol 2015; 1247:133-43. [PMID: 25399092 DOI: 10.1007/978-1-4939-2004-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Members of the Mycobacterium tuberculosis complex (MTC) are causative agents of tuberculosis (TB) in both humans and animals. In the last two decades, the accumulating knowledge of the nucleotide sequences of several genes, and of the whole genomes, of MTC members has allowed the development of novel molecular assays able to detect and discriminate between these species. However, despite the significant advances in the development of molecular assays for detecting MTC members in human samples, only a few assays have been described for detecting these agents in animal tissues. In this chapter we describe the use of two TaqMan (®)-based real-time PCR approaches, highly sensitive and specific and easy to perform, to detect and identify veterinary-relevant MTC species in both animal tissue samples and cultures.
Collapse
Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IP, Lisbon, Portugal
| | | | | | | |
Collapse
|
49
|
Costa P, Botelho A, Couto I, Viveiros M, Inácio J. Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members. Front Mol Biosci 2014; 1:16. [PMID: 25988157 PMCID: PMC4428369 DOI: 10.3389/fmolb.2014.00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.
Collapse
Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - Ana Botelho
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Recursos Microbiológicos (CREM), Universidade Nova de LisboaCaparica, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - João Inácio
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
| |
Collapse
|
50
|
Vasconcellos SEG, Acosta CC, Gomes LL, Conceição EC, Lima KV, de Araujo MI, Leite MDL, Tannure F, Caldas PCDS, Gomes HM, Santos AR, Gomgnimbou MK, Sola C, Couvin D, Rastogi N, Boechat N, Suffys PN. Strain classification of Mycobacterium tuberculosis isolates in Brazil based on genotypes obtained by spoligotyping, mycobacterial interspersed repetitive unit typing and the presence of large sequence and single nucleotide polymorphism. PLoS One 2014; 9:e107747. [PMID: 25314118 PMCID: PMC4196770 DOI: 10.1371/journal.pone.0107747] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Accepted: 08/21/2014] [Indexed: 11/26/2022] Open
Abstract
Rio de Janeiro is endemic for tuberculosis (TB) and presents the second largest prevalence of the disease in Brazil. Here, we present the bacterial population structure of 218 isolates of Mycobacterium tuberculosis, derived from 186 patients that were diagnosed between January 2008 and December 2009. Genotypes were generated by means of spoligotyping, 24 MIRU-VNTR typing and presence of fbpC103, RDRio and RD174. The results confirmed earlier data that predominant genotypes in Rio de Janeiro are those of the Euro American Lineages (99%). However, we observed differences between the classification by spoligotyping when comparing to that of 24 MIRU-VNTR typing, being respectively 43.6% vs. 62.4% of LAM, 34.9% vs. 9.6% of T and 18.3% vs. 21.5% of Haarlem. Among isolates classified as LAM by MIRU typing, 28.0% did not present the characteristic spoligotype profile with absence of spacers 21 to 24 and 32 to 36 and we designated these conveniently as “LAM-like”, 79.3% of these presenting the LAM-specific SNP fbpC103. The frequency of RDRio and RD174 in the LAM strains, as defined both by spoligotyping and 24 MIRU-VNTR loci, were respectively 11% and 15.4%, demonstrating that RD174 is not always a marker for LAM/RDRio strains. We conclude that, although spoligotyping alone is a tool for classification of strains of the Euro-American lineage, when combined with MIRU-VNTRs, SNPs and RD typing, it leads to a much better understanding of the bacterial population structure and phylogenetic relationships among strains of M. tuberculosis in regions with high incidence of TB.
Collapse
Affiliation(s)
- Sidra E. G. Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chyntia Carolina Acosta
- Laboratory of Cellular Microbiology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lia Lima Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Karla Valéria Lima
- Instituto Evandro Chagas, Section of Bacteriology and Mycology, Belém, Pará, Brazil
| | - Marcelo Ivens de Araujo
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria de Lourdes Leite
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flávio Tannure
- Hospital Municipal Rafael de Paula Souza, Municipal Secretary of Health, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Cesar de Souza Caldas
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Publica Sergio Arouca, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adalberto Rezende Santos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michel K. Gomgnimbou
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - Christophe Sola
- CNRS–Université Paris–Sud, Institut de Génétique et Microbiologie–Infection Genetics Emerging Pathogens Evolution Team, Orsay, France
| | - David Couvin
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe, France
| | - Neio Boechat
- Multidisciplinary Research Laboratory, University Hospital Clementino Fraga Filho – HUCFF, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Graduate Program in Clinical Medicine, Faculty of Medicine, University Hospital Clementino Fraga Filho, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Philip Noel Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail:
| |
Collapse
|