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Mitchell JL, MacDougall L, Dobromylskyj MJ, Smith K, Stavinohova R, Gunn-Moore DA, Hope JC, Scurrell E. Ocular mycobacterial lesions in cats. Vet Pathol 2022; 59:792-805. [PMID: 35587045 PMCID: PMC9358306 DOI: 10.1177/03009858221098431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ocular mycobacterial infections are an under-recognized cause of morbidity in the
domestic cat. This study aimed to explore the distribution, histopathological
appearance, and severity of feline ocular mycobacterial lesions, and to
characterize the immune cell population with immunohistochemistry. Routine
histological staining with hematoxylin and eosin, and Masson’s trichrome, was
performed to identify ocular lesions and assign an inflammation score based on
the number of cells present. Acid-fast bacilli were detected with Ziehl-Neelsen,
and immunohistochemistry for ionized calcium-binding adaptor protein-1 (Iba1),
calprotectin, cluster of differentiation 3 (CD3), and Pax5 was undertaken on
formalin-fixed paraffin-embedded tissue samples from 24 cases of ocular
mycobacteriosis. Posterior or panuveitis with concurrent retinitis was
identified in 20/24 cases (83%), with retinal detachment in 16/20 (80%) of these
cases. Choroidal lesions had the highest median inflammation score.
Ziehl-Neelsen-positive organisms were detected in 20/24 cases (83%), with the
highest prevalence of acid-fast bacilli detected in choroidal lesions (16/20,
80%). Lesions were typically granulomatous to pyogranulomatous, characterized by
abundant numbers of Iba1-positive macrophages, followed by calprotectin-positive
granulocytes and monocytes, fewer T cells, and rarer B cells. However, where
iritis was identified, inflammation was typically lymphoplasmacytic (11/16
cases, 69%). Where diagnostic testing was performed, tuberculosis (ie, infection
with Mycobacterium bovis, Mycobacterium
microti, or a nonspeciated Mycobacterium
tuberculosis-complex pathogen) was diagnosed in 20/22 cats (91%),
with Mycobacterium lepraemurium infection identified in the
other 2/22 cats (9%). These results suggest the choroid is the primary site of
lesion development in most cases of feline ocular mycobacteriosis, and
inflammatory changes are associated with the presence of mycobacteria localized
to ocular tissues.
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Affiliation(s)
| | | | | | - Ken Smith
- Royal Veterinary College, Hatfield, UK
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2
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Mitchell JL, Ganis L, Blacklock BT, Petrushkin H, Hope JC, Gunn-Moore DA. Ocular Tuberculosis: More than 'Of Mice and Men'. Ocul Immunol Inflamm 2022; 30:34-38. [PMID: 32946291 DOI: 10.1080/09273948.2020.1797116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Tuberculosis (TB), caused by infection with members of the Mycobacterium tuberculosis-complex, is one of the oldest known infectious disease entities, resulting in the death of millions of humans each year. It also results in a substantial degree of morbidity and mortality in animal species. Extrapulmonary TB is well recognized in humans, and the eye is one site that can be affected. Studies seeking to understand ocular TB have often relied on animal models; however, these have their limitations and may not truly reflect what happens in humans. We wish to raise awareness among ophthalmologists and vision scientists of naturally occurring cases of ocular TB in animals, namely cattle and domestic cats, and the possibilities of gaining further understanding of this presentation of TB by adopting a collaborative approach. This will hopefully improve outcomes for both human and animal patients.
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Affiliation(s)
- Jordan L Mitchell
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Laura Ganis
- Barts Health NHS Trust, The Royal London Hospital, London, UK
| | - Benjamin T Blacklock
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Harry Petrushkin
- Moorfields Eye Hospital Foundation Trust, Uveitis and Scleritis Service, London, UK.,Rheumatology Department, Great Ormond Street Hospital, London, UK
| | - Jayne C Hope
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Danièlle A Gunn-Moore
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, The University of Edinburgh, Midlothian, UK
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3
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Harouna Hamidou Z, Mamadou S, Saad J. Molecular detection of Mycobacterium tuberculosis sensu stricto in the soil of Niger. New Microbes New Infect 2021; 44:100939. [PMID: 34621525 PMCID: PMC8479474 DOI: 10.1016/j.nmni.2021.100939] [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: 08/01/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/22/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) complex is comprising of pathogenic mycobacteria responsible for human and animal tuberculosis, a major public health problem in Niger. Although infected individuals are paramount sources of contamination, nevertheless alternative, neglected sources may play some role in minority forms of the infection. Accordingly, we investigated the presence of Mycobacterium tuberculosis complex in soil samples in Niger. A total of 103 soil samples were collected in six different areas in Niger in October and November 2018 and April and May 2020 from residential areas of tuberculosis patients. Screening PCR targeting M. tuberculosis complex CRISPR-Csm4 and Xpert MTB/RIF Ultra assay were applied to detect the M. tuberculosis complex. M. tuberculosis DNA was positively detected in five of 103 (5/103; 4.8%) soil samples (Dosso: one sample, Zinder: one sample and Niamey: three samples) using the CRISPR-Csm4 system. CRISPR-Csm4 gene sequence identified four M. tuberculosis sensu stricto (may be lineages 1, 3 or 4) and one M. tuberculosis L2 lineage (Beijing). Moreover, the five positive samples were confirmed by Xpert MTB/RIF Ultra assay as rifampicin-susceptible M. tuberculosis complex strains. However, culture remained negative after 42 days. In this study, we announced for the first time the presence of M. tuberculosis sensu stricto in the soil of Niger. Moreover, these detected lineages were identical to the dominant M. tuberculosis lineages in patients. The presence of common lineages of M. tuberculosis between the soil and human highlight the risk of transmission from the soil to human.
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Affiliation(s)
- Z Harouna Hamidou
- IHU Méditerranée Infection, Marseille, France
- Aix-Marseille-Université, IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - S Mamadou
- Laboratoire National de Référence des IST/VIH et de la Tuberculose, Niamey, Niger
| | - J Saad
- IHU Méditerranée Infection, Marseille, France
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4
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Tagliapietra V, Boniotti MB, Mangeli A, Karaman I, Alborali G, Chiari M, D’Incau M, Zanoni M, Rizzoli A, Pacciarini ML. Mycobacterium microti at the Environment and Wildlife Interface. Microorganisms 2021; 9:microorganisms9102084. [PMID: 34683407 PMCID: PMC8539169 DOI: 10.3390/microorganisms9102084] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
An unexpected high presence of Mycobacterium microti in wild boar in Northern Italy (Garda Lake) has been reported since 2003, but the factors contributing to the maintenance of this pathogen are still unclear. In this study, we investigated the presence of M. microti in wild rodents and in water and soil samples collected at wild boar aggregation areas, such as watering holes, with the aim of clarifying their role in M. microti transmission. In total, 8 out of 120 captured animals tested positive for the Mycobacterium tuberculosis complex (MTBC) as assessed by real-time PCR, and six samples were confirmed to be M. microti. A strain with a genetic profile similar to those previously isolated in wild boars in the same area was isolated from one sample. Of the 20 water and 19 mud samples, 3 and 1, respectively, tested positive for the presence of MTBC, and spacer oligotype SB0118 (vole type) was detected in one sample. Our study suggests that wild rodents, in particular Apodemus sylvaticus, Microtus sp. and Apodemus flavicollis, play roles in the maintenance of M. microti infections in wild boar through ingestion or by contact with either infected excreta or a contaminated environment, such as at animal aggregation sites.
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Affiliation(s)
- Valentina Tagliapietra
- Departemt of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy;
- Correspondence:
| | - Maria Beatrice Boniotti
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Anna Mangeli
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Iyad Karaman
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Giovanni Alborali
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Mario Chiari
- Direzione Generale Welfare, U.O. Veterinaria, Regione Lombardia, Piazza Città di Lombardia 1, 20124 Milano, Italy;
| | - Mario D’Incau
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Mariagrazia Zanoni
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
| | - Annapaola Rizzoli
- Departemt of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, 38098 San Michele all’Adige, Italy;
| | - Maria Lodovica Pacciarini
- National Reference Centre of Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Via Bianchi 9, 25124 Brescia, Italy; (M.B.B.); (A.M.); (I.K.); (G.A.); (M.D.); (M.Z.); (M.L.P.)
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5
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Mitchell JL, Stanley P, McDonald K, Burr P, Rhodes SG, Gunn-Moore DA, Hope JC. Diagnostic accuracy of the interferon-gamma release assay (IGRA) for cases of feline mycobacteriosis. Prev Vet Med 2021; 193:105409. [PMID: 34126470 DOI: 10.1016/j.prevetmed.2021.105409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/22/2021] [Accepted: 06/06/2021] [Indexed: 10/21/2022]
Abstract
The aim of this study was to evaluate the sensitivity and specificity of the interferon-gamma release assay (IGRA) for diagnosing infections with members of the Mycobacterium (M.) tuberculosis-complex (MTBC) and non-tuberculous mycobacteria (NTM) in domestic cats, and to generate defined feline-specific cut-off values using receiver operating characteristic (ROC) curve analysis to improve test performance. Records of 594 cats that had been tested by IGRA were explored to identify individuals that had a culture and/or polymerase chain reaction (PCR)-confirmed case of mycobacterial disease, and those that had a final diagnosis of non-mycobacterial disease. A total of 117 cats - 80 with mycobacterial disease and 37 diagnosed with a condition other than mycobacteriosis - were identified for further detailed analysis. This population was used to estimate test sensitivity and specificity, as well as likelihood ratios for the IGRA to correctly identify a cat with or without mycobacterial disease. Agreement between IGRA results and culture/PCR using current and proposed new cut-off values was also determined. ROC analysis of defined confirmed infected and non-mycobacterial disease control cats allowed an adjustment of current test cut-offs that increased the overall test sensitivity for MTBC infections from 83.1 % (95 % confidence interval [CI]: 71.5-90.5 %) to 90.2 % (95 % CI: 80.2-95.4%), and M. bovis infection from 43 % (95 % CI: 28.2-60.7%) to 68 % (95 % CI: 51.4-82.1%) while maintaining high test specificity (100 % in both cases). Overall agreement between IGRA results and culture/PCR, while recognising that neither culture nor PCR tests have perfect sensitivity, improved from weak (κ = 0.57) to moderate (κ = 0.71) using new proposed IGRA test cut-off values. Application of these results, based upon the statistical analysis of accumulated test data, can improve the diagnostic performance of the feline IGRA, particularly for identifying infections with M. bovis, without compromising specificity.
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Affiliation(s)
- Jordan L Mitchell
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom.
| | - Paul Stanley
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Kieran McDonald
- Biobest Laboratories Ltd, 6 Charles Darwin House, Edinburgh Technopole, Milton Bridge, Near Penicuik, EH26 0PY, United Kingdom
| | - Paul Burr
- Biobest Laboratories Ltd, 6 Charles Darwin House, Edinburgh Technopole, Milton Bridge, Near Penicuik, EH26 0PY, United Kingdom
| | - Shelley G Rhodes
- Animal & Plant Health Agency, Woodham Lane, New Haw, Addlestone, Surrey, KT15 3NB, United Kingdom
| | - Danièlle A Gunn-Moore
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Jayne C Hope
- The Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, United Kingdom
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6
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Asare P, Asante-Poku A, Osei-Wusu S, Otchere ID, Yeboah-Manu D. The Relevance of Genomic Epidemiology for Control of Tuberculosis in West Africa. Front Public Health 2021; 9:706651. [PMID: 34368069 PMCID: PMC8342769 DOI: 10.3389/fpubh.2021.706651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), an airborne infectious disease caused by Mycobacterium tuberculosis complex (MTBC), remains a global health problem. West Africa has a unique epidemiology of TB that is characterized by medium- to high-prevalence. Moreover, the geographical restriction of M. africanum to the sub-region makes West Africa have an extra burden to deal with a two-in-one pathogen. The region is also burdened with low case detection, late reporting, poor treatment adherence leading to development of drug resistance and relapse. Sporadic studies conducted within the subregion report higher burden of drug resistant TB (DRTB) than previously thought. The need for more sensitive and robust tools for routine surveillance as well as to understand the mechanisms of DRTB and transmission dynamics for the design of effective control tools, cannot be overemphasized. The advancement in molecular biology tools including traditional fingerprinting and next generation sequencing (NGS) technologies offer reliable tools for genomic epidemiology. Genomic epidemiology provides in-depth insight of the nature of pathogens, circulating strains and their spread as well as prompt detection of the emergence of new strains. It also offers the opportunity to monitor treatment and evaluate interventions. Furthermore, genomic epidemiology can be used to understand potential emergence and spread of drug resistant strains and resistance mechanisms allowing the design of simple but rapid tools. In this review, we will describe the local epidemiology of MTBC, highlight past and current investigations toward understanding their biology and spread as well as discuss the relevance of genomic epidemiology studies to TB control in West Africa.
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Affiliation(s)
- Prince Asare
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Adwoa Asante-Poku
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorothy Yeboah-Manu
- College of Health Sciences, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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7
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Mitchell JL, Del Pozo J, Woolley CSC, Dheendsa R, Hope JC, Gunn-Moore DA. Histological and immunohistochemical features suggesting aetiological differences in lymph node and (muco)cutaneous feline tuberculosis lesions. J Small Anim Pract 2021; 63:174-187. [PMID: 34101189 DOI: 10.1111/jsap.13386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 04/20/2021] [Accepted: 05/16/2021] [Indexed: 12/01/2022]
Abstract
OBJECTIVES To identify and describe histological and immunohistochemical criteria that may differentiate between skin and lymph node lesions associated with Mycobacterium (M.) bovis and M. microti in a diagnostic pathology setting. MATERIALS AND METHODS Archived skin and lymph node biopsies of tuberculous lesions were stained with haematoxylin and eosin, Ziehl-Neelsen and Masson's Trichrome. Immunohistochemistry was performed to detect the expression of calprotectin, CD3 and Pax5. Samples were scored for histological parameters (i.e. granulomas with central necrosis versus small granulomas without central necrosis, percentage necrosis and/or multinucleated giant cells), number of acid-fast bacilli (bacterial index) and lesion percentage of fibrosis and positive immunohistochemical staining. RESULTS Twenty-two samples were examined (M. bovis n=11, M. microti n=11). When controlling for age, gender and tissue, feline M. bovis-associated lesions more often featured large multi-layered granulomas with central necrosis. Conversely, this presentation was infrequent in feline M. microti-associated lesions, where small granulomas without central necrosis predominated. The presence of an outer fibrous capsule was variable in both groups, as was the bacterial index. There were no differences in intralesional expression of immunohistochemical markers. CLINICAL SIGNIFICANCE Differences in the histological appearance of skin and lymph node lesions may help to infer feline infection with either M. bovis or M. microti at an earlier stage when investigating these cases, informing clinicians of the potential zoonotic risk. Importantly, cases of tuberculosis can present with numerous acid-fast bacilli. This implies that a high bacterial index does not infer infection with non-zoonotic non-tuberculous mycobacteria.
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Affiliation(s)
- J L Mitchell
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - J Del Pozo
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - C S C Woolley
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - R Dheendsa
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - J C Hope
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - D A Gunn-Moore
- *Royal (Dick) School of Veterinary Studies and The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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8
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Yamada H, Chikamatsu K, Aono A, Murata K, Miyazaki N, Kayama Y, Bhatt A, Fujiwara N, Maeda S, Mitarai S. Fundamental Cell Morphologies Examined With Cryo-TEM of the Species in the Novel Five Genera Robustly Correlate With New Classification in Family Mycobacteriaceae. Front Microbiol 2020; 11:562395. [PMID: 33304323 PMCID: PMC7701246 DOI: 10.3389/fmicb.2020.562395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 10/12/2020] [Indexed: 11/25/2022] Open
Abstract
A recent study proposed the novel classification of the family Mycobacteriaceae based on the genome analysis of core proteins in 150 Mycobacterium species. The results from these analyses supported the existence of five distinct monophyletic groups within the genus Mycobacterium. That is, Mycobacterium has been divided into two novel genera for rapid grower Mycobacteroides and Mycolicibacterium, and into three genera for slow grower Mycolicibacter, Mycolicibacillus, and an emended genus Mycobacterium, which include all the major human pathogens. Here, cryo-TEM examinations of 1,816 cells of 31 species (34 strains) belonging to the five novel genera were performed. The fundamental morphological properties of every single cell, such as cell diameter, cell length, cell perimeter, cell circularity, and aspect ratio were measured and compared between these genera. In 50 comparisons on the five parameters between any two genera, only five comparisons showed “non-significant” differences. That is, there are non-significant differences between slow grower genus Mycolicibacillus and genus Mycobacterium in average cell diameter (p = 0.15), between rapid grower genus Mycobacteroides and slow grower genus Mycobacterium in average cell length (p > 0.24), between genus Mycobacteroides and genus Mycobacterium (p > 0.68) and between genus Mycolicibacter and genus Mycolicibacillus (p > 0.11) in average cell perimeter, and between genus Mycolicibacterium and genus Mycobacterium in circularity (p > 0.73). The other 45 comparisons showed significant differences between the genera. Genus Mycobacteroides showed the longest average cell diameter, whereas the genus Mycolicibacter showed the shortest average diameter. Genus Mycolicibacterium showed the most extended average cell length, perimeter, and aspect ratio, whereas the genus Mycolicibacillus showed the shortest average cell length, perimeter, and aspect ratio. Genus Mycolicibacillus showed the highest average cell circularity, whereas genus Mycobacterium showed the lowest average cell circularity. These fundamental morphological data strongly support the new classification in the family Mycobacteriaceae, and this classification is rational and effective in the study of the members of the family Mycobacteriaceae. Because both the genus Mycolicibacterium and the genus Mycobacterium contain many species and showed larger significant standard deviations in every parameter, these genera may be divided into novel genera which show common genotype and phenotypes in morphology and pathogenicity.
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Affiliation(s)
- Hiroyuki Yamada
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kinuyo Chikamatsu
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Akio Aono
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Kazuyoshi Murata
- Supportive Center for Brain Research, National Institute for Physiological Science, Okazaki, Japan
| | - Naoyuki Miyazaki
- Supportive Center for Brain Research, National Institute for Physiological Science, Okazaki, Japan.,Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | | | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nagatoshi Fujiwara
- Department of Food and Nutrition, Faculty of Contemporary Human Life Science, Tezukayama University, Nara, Japan
| | - Shinji Maeda
- Department of Pharmacy, Faculty of Pharmaceutical Science, Hokkaido University of Science, Sapporo, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan.,Department of Basic Mycobacteriology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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9
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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.
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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
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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.
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Zumla A, Otchere ID, Mensah GI, Asante-Poku A, Gehre F, Maeurer M, Bates M, Mwaba P, Ntoumi F, Yeboah-Manu D. Learning from epidemiological, clinical, and immunological studies on Mycobacterium africanum for improving current understanding of host–pathogen interactions, and for the development and evaluation of diagnostics, host-directed therapies, and vaccines for tuberculosis. Int J Infect Dis 2017; 56:126-129. [DOI: 10.1016/j.ijid.2016.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 11/25/2022] Open
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Forst J, Brown TA. Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples. PLoS One 2016; 11:e0163031. [PMID: 27654468 PMCID: PMC5031403 DOI: 10.1371/journal.pone.0163031] [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] [Received: 04/27/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022] Open
Abstract
We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.
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Affiliation(s)
- Jannine Forst
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Terence A. Brown
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Yeboah-Manu D, Asare P, Asante-Poku A, Otchere ID, Osei-Wusu S, Danso E, Forson A, Koram KA, Gagneux S. Spatio-Temporal Distribution of Mycobacterium tuberculosis Complex Strains in Ghana. PLoS One 2016; 11:e0161892. [PMID: 27564240 PMCID: PMC5001706 DOI: 10.1371/journal.pone.0161892] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/12/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND There is a perception that genomic differences in the species/lineages of the nine species making the Mycobacterium tuberculosis complex (MTBC) may affect the efficacy of distinct control tools in certain geographical areas. We therefore analyzed the prevalence and spatial distribution of MTBC species and lineages among isolates from pulmonary TB cases over an 8-year period, 2007-2014. METHODOLOGY Mycobacterial species isolated by culture from consecutively recruited pulmonary tuberculosis patients presenting at selected district/sub-district health facilities were confirmed as MTBC by IS6110 and rpoß PCR and further assigned lineages and sub lineages by spoligotyping and large sequence polymorphism PCR (RDs 4, 9, 12, 702, 711) assays. Patient characteristics, residency, and risks were obtained with a structured questionnaire. We used SaTScan and ArcMap analyses to identify significantly clustered MTBC lineages within selected districts and spatial display, respectively. RESULTS Among 2,551 isolates, 2,019 (79.1%), 516 (20.2%) and 16 (0.6%) were identified as M. tuberculosis sensu stricto (MTBss), M. africanum (Maf), 15 M. bovis and 1 M. caprae, respectively. The proportions of MTBss and Maf were fairly constant within the study period. Maf spoligotypes were dominated by Spoligotype International Type (SIT) 331 (25.42%), SIT 326 (15.25%) and SIT 181 (14.12%). We found M. bovis to be significantly higher in Northern Ghana (1.9% of 212) than Southern Ghana (0.5% of 2339) (p = 0.020). Using the purely spatial and space-time analysis, seven significant MTBC lineage clusters (p< 0.05) were identified. Notable among the clusters were Ghana and Cameroon sub-lineages found to be associated with north and south, respectively. CONCLUSION This study demonstrated that overall, 79.1% of TB in Ghana is caused by MTBss and 20% by M. africanum. Unlike some West African Countries, we did not observe a decline of Maf prevalence in Ghana.
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Affiliation(s)
- Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
- * E-mail:
| | - P. Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - A. Asante-Poku
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - I. D. Otchere
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - S. Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - E. Danso
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - A. Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Korle-bu, Accra, Ghana
| | - K. A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Accra, Ghana
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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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.
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Wei J, Liang J, Shi Q, Yuan P, Meng R, Tang X, Yu L, Guo N. Genome-wide transcription analyses in Mycobacterium tuberculosis treated with lupulone. Braz J Microbiol 2014; 45:333-41. [PMID: 24948953 PMCID: PMC4059319 DOI: 10.1590/s1517-83822014005000032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 04/01/2013] [Indexed: 01/16/2023] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis), the causative agent of tuberculosis, still causes higher mortality than any other bacterial pathogen until now. With the emergence and spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR-TB) strains, it becomes more important to search for alternative targets to develop new antimycobacterial drugs. Lupulone is a compound extracted from Hops (Hurnulus lupulus), which exhibits a good antimicrobial activity against M. tuberculosis with minimal inhibitory concentration (MIC) value of 10 μg/mL, but the response mechanisms of lupulone against M. tuberculosis are still poorly understood. In this study, we used a commercial oligonucleotide microarray to determine the overall transcriptional response of M. tuberculosis H37Rv triggered by exposure to MIC of lupulone. A total of 540 genes were found to be differentially regulated by lupulone. Of these, 254 genes were upregulated, and 286 genes were downregulated. A number of important genes were significantly regulated which are involved in various pathways, such as surface-exposed lipids, cytochrome P450 enzymes, PE/PPE multigene families, ABC transporters, and protein synthesis. Real-time quantitative RT-PCR was performed for choosed genes to verified the microarray results. To our knowledge, this genome-wide transcriptomics approach has produced the first insights into the response of M. tuberculosis to a lupulone challenge.
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Affiliation(s)
- Jian Wei
- Life Science Department ChangChun Normal University Changchun P.R. China ; Bio-Reactor Center Jilin Agrichultural University Changchun P.R. China
| | - Junchao Liang
- Department of Food Quality and Safety Key Laboratory of Zoonosis Research Institute of Zoonosis Ministry of Education Changchun P. R. China
| | - Qiyun Shi
- Department of Food Quality and Safety Key Laboratory of Zoonosis Research Institute of Zoonosis Ministry of Education Changchun P. R. China
| | - Peng Yuan
- Department of Food Quality and Safety Key Laboratory of Zoonosis Research Institute of Zoonosis Ministry of Education Changchun P. R. China
| | - Rizeng Meng
- Jilin Enrty-Exit Inspection and Quarantine Bureau Changchun P.R. China
| | - Xudong Tang
- Key Lab for New Drug Research of TCM Research Institute of Tsinghua University in Shenzhen Shenzhen P.R. China
| | - Lu Yu
- Department of Food Quality and Safety Key Laboratory of Zoonosis Research Institute of Zoonosis Ministry of Education Changchun P. R. China
| | - Na Guo
- Department of Food Quality and Safety Key Laboratory of Zoonosis Research Institute of Zoonosis Ministry of Education Changchun P. R. China
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Ueyama M, Chikamatsu K, Aono A, Murase Y, Kuse N, Morimoto K, Okumura M, Yoshiyama T, Ogata H, Yoshimori K, Kudoh S, Azuma A, Gemma A, Mitarai S. Sub-speciation of Mycobacterium tuberculosis complex from tuberculosis patients in Japan. Tuberculosis (Edinb) 2013; 94:15-9. [PMID: 24183617 DOI: 10.1016/j.tube.2013.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/27/2013] [Accepted: 09/27/2013] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis is the major causative agent of tuberculosis in humans. It is well known that Mycobacterium bovis and other species in the M. tuberculosis complex (MTC) can cause respiratory diseases as zoonosis. We analyzed the MTC isolates collected from tuberculosis patients from Japan in 2002 using a multiplex PCR system that detected cfp32, RD9 and RD12. A total of 970 MTC isolates that were representative of the tuberculosis cases throughout Japan, were examined using this method. As a result, 966 (99.6%) M. tuberculosis, two Mycobacterium africanum and two Mycobacterium canettii were identified using a multiplex PCR system, while no M. bovis was detected. Two isolates that lacked RD9 were initially considered to be M. canettii, but further analysis of the hsp65 sequence revealed them to be M. tuberculosis. Also two M. africanum were identified as M. tuberculosis using the -215 narG nucleotide polymorphism. Though PCR-linked methods have been used for a rapid differentiation of MTC and NTM, from our cases we suggest careful interpretation of RD based identification.
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Affiliation(s)
- Masako Ueyama
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
| | - Kinuyo Chikamatsu
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Akio Aono
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Yoshiro Murase
- Molecular Epidemiology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Naoyuki Kuse
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Kozo Morimoto
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masao Okumura
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Takashi Yoshiyama
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Hideo Ogata
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Kozo Yoshimori
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shoji Kudoh
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Arata Azuma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Akihiko Gemma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Satoshi Mitarai
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
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Kim Y, Choi Y, Jeon BY, Jin H, Cho SN, Lee H. A simple and efficient multiplex PCR assay for the identification of Mycobacterium genus and Mycobacterium tuberculosis complex to the species level. Yonsei Med J 2013; 54:1220-6. [PMID: 23918573 PMCID: PMC3743195 DOI: 10.3349/ymj.2013.54.5.1220] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE The Mycobacterium tuberculosis complex comprises M. tuberculosis, M. bovis, M. bovis bacillus Calmette-Guérin (BCG) and M. africanum, and causes tuberculosis in humans and animals. Identification of Mycobacterium spp. and M. tuberculosis complex to the species level is important for practical use in microbiological laboratories, in addition to optimal treatment and public health. MATERIALS AND METHODS A novel multiplex PCR assay targeting a conserved rpoB sequence in Mycobacteria spp., as well as regions of difference (RD) 1 and RD8, was developed and evaluated using 37 reference strains and 178 clinical isolates. RESULTS All mycobacterial strains produced a 518-bp product (rpoB), while other bacteria produced no product. Virulent M. tuberculosis complex strains, M. tuberculosis, M. bovis and M. africanum, produced a 254-bp product (RD1), while M. bovis BCG, M. microti and nontuberculous mycobacteria produced no RD1 region product. Additionally, M. tuberculosis and M. africanum produced a 150-bp product (RD8), while M. bovis and M. bovis BCG produced a 360-bp product (deleted form of RD8). M. microti and nontuberculous mycobacteria produced no RD8 region product. This assay identified all Mycobacterium spp. and all M. tuberculosis complex strains to the species level. CONCLUSION The multiplex PCR assay of the present study could be implemented as a routine test in microbiology laboratories, and may contribute to more effective treatment and surveillance of tuberculosis stemming from the M. tuberculosis complex.
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Affiliation(s)
- Yeun Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Yeonim Choi
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Bo-Young Jeon
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
| | - Hyunwoo Jin
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
- Department of Clinical Laboratory Science, College of Health Sciences, Catholic University of Pusan, Busan, Korea
| | - Sang-Nae Cho
- Department of Microbiology, Yonsei University College of Medicine, Seoul, Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, Korea
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Abstract
Recent years have witnessed an increased appreciation of the extent and relevance of strain-to-strain variation in Mycobacterium tuberculosis. This paradigm shift can largely be attributed to an improved understanding of the global population structure of this organism, and to the realisation that the various members of the M. tuberculosis complex (MTBC) harbour more genetic diversity than previously realised. Moreover, many studies using experimental models of infection have demonstrated that MTBC diversity translates into significant differences in immunogenecity and virulence . However, linking these experimental phenotypes to relevant clinical phenotypes has been difficult, and to date, largely unsuccessful. Nevertheless, emerging high-throughput technologies, in particular next-generation sequencing , offer new opportunities, and have already lead to important new insights. Given the complexity of the host-pathogen interaction in tuberculosis, systems approaches will be key to define the role of MTBC diversity in the fight against one of humankind's most important pathogens.
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Long-range transcriptional control of an operon necessary for virulence-critical ESX-1 secretion in Mycobacterium tuberculosis. J Bacteriol 2012; 194:2307-20. [PMID: 22389481 DOI: 10.1128/jb.00142-12] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The ESX-1 secretion system of Mycobacterium tuberculosis has to be precisely regulated since the secreted proteins, although required for a successful virulent infection, are highly antigenic and their continued secretion would alert the immune system to the infection. The transcription of a five-gene operon containing espACD-Rv3613c-Rv3612c, which is required for ESX-1 secretion and is essential for virulence, was shown to be positively regulated by the EspR transcription factor. Thus, transcription from the start site, found to be located 67 bp upstream of espA, was dependent upon EspR enhancer-like sequences far upstream (between 884 and 1,004 bp), which we term the espA activating region (EAR). The EAR contains one of the known binding sites for EspR, providing the first in vivo evidence that transcriptional activation at the espA promoter occurs by EspR binding to the EAR and looping out DNA between this site and the promoter. Regulation of transcription of this operon thus takes place over long regions of the chromosome. This regulation may differ in some members of the M. tuberculosis complex, including Mycobacterium bovis, since deletions of the intergenic region have removed the upstream sequence containing the EAR, resulting in lowered espA expression. Consequent differences in expression of ESX-1 in these bacteria may contribute to their various pathologies and host ranges. The virulence-critical nature of this operon means that transcription factors controlling its expression are possible drug targets.
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Djelouadji Z, Raoult D, Drancourt M. Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome. THE LANCET. INFECTIOUS DISEASES 2011; 11:641-50. [DOI: 10.1016/s1473-3099(11)70093-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Hong M, Zha L, Fu W, Zou M, Li W, Xu D. A modified visual loop-mediated isothermal amplification method for diagnosis and differentiation of main pathogens from Mycobacterium tuberculosis complex. World J Microbiol Biotechnol 2011; 28:523-31. [PMID: 22806847 DOI: 10.1007/s11274-011-0843-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 07/08/2011] [Indexed: 11/25/2022]
Abstract
This study was aimed to rapidly identify and differentiate two main pathogens of the Mycobacterium tuberculosis complex: Mycobacterium tuberculosis subsp. tuberculosis and Mycobacterium bovis by a modified loop-mediated isothermal amplification (LAMP) assay. The reaction results could be evaluated by naked eye with two optimized closed tube detection methods as follows: adding the modified fluorescence dye in advance into the reaction mix so as to observe the color changes or putting a tinfoil in the tube and adding the SYBR Green I dye on it, then making the dye drop into the bottom of the tube by centrifuge after reaction. The results showed that the two groups of primers used jointly in this assay could successfully identify and differentiate Mycobacterium tuberculosis subsp. tuberculosis and Mycobacterium tuberculosis bovis. Sensitivity test displayed that the modified LAMP assay with the closed tube system could determine the minimal template concentration of 1 copy/μl, which was more sensitive than that of routine PCR. The advantages of this LAMP method for detection of the Mycobacterium tuberculosis complex included high specificity, high sensitivity, simplicity, and superiority in avoidance of aerosol contamination. The modified LAMP assay would provide a potential for clinical diagnosis and therapy of tuberculosis in the developing countries and the resource-limited areas.
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Affiliation(s)
- Ming Hong
- Department of Genome Engineering, Beijing Institute of Basic Medical Sciences, Taiping Road 27, Beijing, 100850, China
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Zanolari P, Robert N, Lyashchenko K, Pfyffer G, Greenwald R, Esfandiari J, Meylan M. Tuberculosis Caused byMycobacterium microtiin South American Camelids. J Vet Intern Med 2009; 23:1266-72. [DOI: 10.1111/j.1939-1676.2009.0377.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Frank W, Reisinger EC, Brandt-Hamerla W, Schwede I, Handrick W. Mycobacterium microti--pulmonary tuberculosis in an immunocompetent patient. Wien Klin Wochenschr 2009; 121:282-6. [PMID: 19562286 DOI: 10.1007/s00508-009-1164-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Accepted: 02/23/2009] [Indexed: 11/27/2022]
Abstract
Human tuberculosis is caused by members of the Mycobacterium tuberculosis complex, which includes M. tuberculosis, M. bovis, M. africanum and M. bovis BCG. However there are increasing reports of rarely occurring genetic variants such as M. canettii, M. microti and M. pinipedii. The natural reservoir, mode of transmission and potential modification of host interaction of these species is not yet fully elucidated. We report a rare case of extensive cavitary smear-positive tuberculosis of the left lung caused by M. microti in an immunocompetent tuberculin-negative 68-year-old man. Transmission by a raccoon dog or raccoon as a novel M. microti reservoir was suspected. Spoligotyping of the isolate revealed the llama subtype. The strain exhibited no detectable drug resistance. Response to standard tuberculosis treatment, initially comprising isoniacid, rifampicin, pyrazinamide and ethambutol, was excellent. Delayed growth on solid media, specific phenotypic features and contact with animals should raise suspicion for this rare mycobacterial infection.
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Chang HJ, Huang MY, Yeh CS, Chen CC, Yang MJ, Sun CS, Lee CK, Lin SR. Rapid diagnosis of tuberculosis directly from clinical specimens using a gene chip. Clin Microbiol Infect 2009; 16:1090-6. [PMID: 19732084 DOI: 10.1111/j.1469-0691.2009.03045.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aim of this study was to explore a gene chip capable of detecting the presence of Mycobacterium tuberculosis isolates directly in clinical sputum specimens and to compare it with current molecular detection techniques. At first, we selected 13 M. tuberculosis-specific target genes to construct a gene chip for rapid diagnosis. Using the membrane array method, we diagnosed M. tuberculosis by gene chip directly from 246 sputum specimens from patients suspected of having tuberculosis. Among 80 M. tuberculosis complex (MTBC) culture-positive sputum specimens, the MTBC detection rate was 62.5% (50/80) by PCR-restriction fragment length polymorphism (RFLP), 70% (56/80) by acid-fast staining, and 85% (68/80) by the membrane array method. Furthermore, subspecies showed different gene expression patterns in the membrane array. In conclusion, MTBC could be detected directly in sputum by the membrane array method. The rapidity of detection and the capability of differentiating subspecies could make this method useful in the control and prevention of tuberculosis.
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Affiliation(s)
- H J Chang
- Biomedical Technology Developmental Centre, Fooyin University, Ta-Liao Hsiang, Kaohsiung Hsien, Taiwan
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Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2009; 6:e311. [PMID: 19090620 PMCID: PMC2602723 DOI: 10.1371/journal.pbio.0060311] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/31/2008] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis. Tuberculosis remains a worldwide public health emergency. The emergence of drug-resistant forms of tuberculosis in many parts of the world is threatening to make this important human disease incurable. Even though many resources are being invested into the development of new tuberculosis control tools, we still do not know the extent of genetic diversity in tuberculosis bacteria, nor do we understand the evolutionary forces that shape this diversity. To address these questions, we studied a large collection of human tuberculosis strains using DNA sequencing. We found that strains originating in different parts of the world are more genetically diverse than previously recognized. Our results also suggest that much of this diversity has functional consequences and could affect the efficacy of new tuberculosis diagnostics, drugs, and vaccines. Furthermore, we found that the global diversity in tuberculosis strains can be linked to the ancient human migrations out of Africa, as well as to more recent movements that followed the increases of human populations in Europe, India, and China during the past few hundred years. Taken together, our findings suggest that the evolutionary characteristics of tuberculosis bacteria could synergize with the effects of increasing globalization and human travel to enhance the global spread of drug-resistant tuberculosis. DNA sequence analysis of a global collection ofM. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.
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Affiliation(s)
- Ruth Hershberg
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Mikhail Lipatov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Peter M Small
- Institute for Systems Biology, Seattle, Washington, United States of America
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Hadar Sheffer
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Stefan Niemann
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Susanne Homolka
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Jared C Roach
- Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
| | - Kristin Kremer
- Mycobacteria Reference Unit (CIb-LIS), National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sebastien Gagneux
- Institute for Systems Biology, Seattle, Washington, United States of America
- MRC National Institute for Medical Research, London, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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Species of environmental mycobacteria differ in their abilities to grow in human, mouse, and carp macrophages and with regard to the presence of mycobacterial virulence genes, as observed by DNA microarray hybridization. Appl Environ Microbiol 2007; 74:275-85. [PMID: 17981953 DOI: 10.1128/aem.01480-07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
There are many species of environmental mycobacteria (EM) that infect animals that are important to the economy and research and that also have zoonotic potential. The genomes of very few of these bacterial species have been sequenced, and little is known about the molecular mechanisms by which most of these opportunistic pathogens cause disease. In this study, 18 isolates of EM isolated from fish and humans (including strains of Mycobacterium avium, Mycobacterium peregrinum, Mycobacterium chelonae, and Mycobacterium salmoniphilum) were examined for their abilities to grow in macrophage lines from humans, mice, and carp. Genomic DNA from 14 of these isolates was then hybridized against DNA from an M. avium reference strain, with a custom microarray containing virulence genes of mycobacteria and a selection of representative genes from metabolic pathways. The strains of EM had different abilities to grow within the three types of cell lines, which grouped largely according to the host from which they were isolated. Genes identified as being putatively absent in some of the strains included those with response regulatory functions, cell wall compositions, and fatty acid metabolisms as well as a recently identified pathogenicity island important to macrophage uptake. Further understanding of the role these genes play in host specificity and pathogenicity will be important to gain insight into the zoonotic potential of certain EM as well as their mechanisms of virulence.
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27
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Käser M, Rondini S, Naegeli M, Stinear T, Portaels F, Certa U, Pluschke G. Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans. BMC Evol Biol 2007; 7:177. [PMID: 17900363 PMCID: PMC2098775 DOI: 10.1186/1471-2148-7-177] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2007] [Accepted: 09/27/2007] [Indexed: 11/30/2022] Open
Abstract
Background Comparative genomics has greatly improved our understanding of the evolution of pathogenic mycobacteria such as Mycobacterium tuberculosis. Here we have used data from a genome microarray analysis to explore insertion-deletion (InDel) polymorphism among a diverse strain collection of Mycobacterium ulcerans, the causative agent of the devastating skin disease, Buruli ulcer. Detailed analysis of large sequence polymorphisms in twelve regions of difference (RDs), comprising irreversible genetic markers, enabled us to refine the phylogenetic succession within M. ulcerans, to define features of a hypothetical M. ulcerans most recent common ancestor and to confirm its origin from Mycobacterium marinum. Results M. ulcerans has evolved into five InDel haplotypes that separate into two distinct lineages: (i) the "classical" lineage including the most pathogenic genotypes – those that come from Africa, Australia and South East Asia; and (ii) an "ancestral" M. ulcerans lineage comprising strains from Asia (China/Japan), South America and Mexico. The ancestral lineage is genetically closer to the progenitor M. marinum in both RD composition and DNA sequence identity, whereas the classical lineage has undergone major genomic rearrangements. Conclusion Results of the InDel analysis are in complete accord with recent multi-locus sequence analysis and indicate that M. ulcerans has passed through at least two major evolutionary bottlenecks since divergence from M. marinum. The classical lineage shows more pronounced reductive evolution than the ancestral lineage, suggesting that there may be differences in the ecology between the two lineages. These findings improve the understanding of the adaptive evolution and virulence of M. ulcerans and pathogenic mycobacteria in general and will facilitate the development of new tools for improved diagnostics and molecular epidemiology.
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Affiliation(s)
- Michael Käser
- Swiss Tropical Institute, Socinstr. 57, 4002 Basel, Switzerland
| | - Simona Rondini
- Swiss Tropical Institute, Socinstr. 57, 4002 Basel, Switzerland
| | - Martin Naegeli
- Swiss Tropical Institute, Socinstr. 57, 4002 Basel, Switzerland
| | - Tim Stinear
- Department of Microbiology, Monash University, Wellington Rd, Clayton 3800, Australia
| | | | - Ulrich Certa
- F. Hoffmann-La Roche Ltd., 4070 Basel, Switzerland
| | - Gerd Pluschke
- Swiss Tropical Institute, Socinstr. 57, 4002 Basel, Switzerland
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Menéndez MC, Buxton RS, Evans JT, Gascoyne-Binzi D, Barlow RE, Hinds J, Hawkey PM, Colston MJ. Genome analysis shows a common evolutionary origin for the dominant strains of Mycobacterium tuberculosis in a UK South Asian community. Tuberculosis (Edinb) 2007; 87:426-36. [PMID: 17719277 PMCID: PMC2963927 DOI: 10.1016/j.tube.2007.05.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Revised: 04/27/2007] [Accepted: 05/03/2007] [Indexed: 01/23/2023]
Abstract
We have investigated the Mycobacterium tuberculosis strain types present in the South Asian population of the UK, in which tuberculosis is particularly prevalent. In contrast to the widespread Beijing strains which have the variable number tandem repeats (VNTR) profile 42435, isolates with the VNTR profile 42235, jointly with 02335 or 42234 profiles, appear more frequently in tuberculosis patients of South Asian ethnic origin (SA-strains) in the UK than in any other ethnic group. Using microarray-based comparative genomics to distinguish total or partially deleted genes, we found that three of the common deleted regions in the SA-strains were identical to some deleted genes in the strain CH, which caused an outbreak among South Asian patients in Leicester in 2001 but were different from genomic deletions found in Beijing/W strains. Analysis of some of the deleted regions revealed differences in comparison to the strain CH including the polymorphism in some of the PE/PPE and Esat-6 genes, which may be responsible for the diversity of antigenic variation or differences in the activation of the host immune response. Interrupted genes or the replacement by insertion elements was confirmed in some of the deleted genomic regions. Our results are consistent with the hypothesis that the SA-strains may present common features, implying a common origin for this group of strains.
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Affiliation(s)
- M. Carmen Menéndez
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Roger S. Buxton
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
- Corresponding author. Tel.: +44 20 8816 2225; fax: +44 20 8906 4477. (R.S. Buxton)
| | - Jason T. Evans
- Division of Immunity and Infection, University of Birmingham, The Medical School, Edgbaston, Birmingham B15 2TT, UK
- Health Protection Agency – West Midlands Laboratory, Birmingham, Heartlands Hospital, Birmingham B9 5SS, UK
| | | | | | - Jason Hinds
- Bacterial Microarray Group, Division of Cellular and Molecular Medicine, St. George's, University of London, Crammer Terrace, London SW17 0RE, UK
| | - Peter M. Hawkey
- Division of Immunity and Infection, University of Birmingham, The Medical School, Edgbaston, Birmingham B15 2TT, UK
- Health Protection Agency – West Midlands Laboratory, Birmingham, Heartlands Hospital, Birmingham B9 5SS, UK
| | - M. Joseph Colston
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Huard RC, Fabre M, de Haas P, Lazzarini LCO, van Soolingen D, Cousins D, Ho JL. Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol 2006; 188:4271-87. [PMID: 16740934 PMCID: PMC1482959 DOI: 10.1128/jb.01783-05] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for "Mycobacterium canettii," Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.
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Affiliation(s)
- Richard C Huard
- Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, Room A-421, 525 East 68th St., New York, NY 10021, USA
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30
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Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol 2006; 8:620-6. [PMID: 16125441 PMCID: PMC7108221 DOI: 10.1016/j.mib.2005.08.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/15/2005] [Indexed: 10/31/2022]
Abstract
DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria, highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens, the levels of diversity and plasticity in the genome of a species, as well as the differences in virulence amongst pathogenic bacteria.
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31
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Smith NH, Kremer K, Inwald J, Dale J, Driscoll JR, Gordon SV, van Soolingen D, Hewinson RG, Smith JM. Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol 2005; 239:220-5. [PMID: 16242724 DOI: 10.1016/j.jtbi.2005.08.036] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Revised: 04/26/2005] [Accepted: 07/23/2005] [Indexed: 10/25/2022]
Abstract
A phylogeny of the Mycobacterium tuberculosis complex has recently shown that the animal-adapted strains are found in a single lineage marked by the deletion of chromosomal region 9 (RD9) [Brosch et al., 2002. A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc. Natl Acad. Sci. USA 99 (6), 3684-3689]. We have obtained the spoligotype patterns of the RD9 deleted strains used to generate this new evolutionary scenario and we show that the presence of spoligotype spacers 3, 9, 16, 39, and 40-43 is phylogenetically informative in this lineage. We have used the phylogenetically informative spoligotype spacers to screen a database of spoligotype patterns and have identified further members of a group of strains apparently host-adapted to antelopes. The presence of the spoligotype spacers is congruent with the phylogeny generated by chromosomal deletions, suggesting that recombination is rare or absent between strains of this lineage. The phylogenetically informative spacers, in concert with the previously identified single nucleotide mutations and chromosomal deletions, can be used to identify a series of clades in the RD9 deleted lineage each with a separate host preference. Finally, we discuss the application of the ecotype concept to this series of clades and suggest that the M. tuberculosis complex may best be described as a series of host-adapted ecotypes.
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Affiliation(s)
- Noel H Smith
- TB Research Group, Veterinary Laboratories Agency, VLA, Addlestone, Surrey KT15 3NB, UK.
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32
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Abstract
Every 10 seconds, one person in the world dies of tuberculosis (TB). It is estimated that one third of the world's population is latently infected with Mycobacterium tuberculosis. The proportion of multidrug-resistant strains of M. tuberculosis is increasing at an alarming rate in some parts of the world linked in part with the human immunodeficiency virus epidemic. For these reasons, TB remains a major public health problem, both in less-developed countries and in many industrialized countries, with 8-10 million new cases and 2 million deaths yearly in the world. Clinical, radiological and histological signs are not specific for tuberculosis or for other mycobacterial infections and allow only a presumptive diagnosis. In the same way, the tuberculin skin test is useful if the reaction is strong or phlyctenular because this test depends on various factors as previous BCG vaccination, contact or primary infection and host immune responses. The diagnosis of mycobacterial infection is proved only when bacilli are present in biological samples. Nevertheless, only 50% of cases in adults and 30% in infants have a positive bacteriological result. It seems necessary to develop new methods for a rapid and efficient diagnosis to optimize the therapy and the control of the epidemic. Laboratory testing in the mycobacterium field is experiencing more changes today than ever before. Determining what assays will be most useful to the clinician is a challenge, and acceptance of the new technology is under discussion. Progress in future will be linked probably to the progress of the genomic area. However the incidence rate is higher in less-developed countries, it is also important to develop now techniques possible to use in these countries. This review focuses on the current state-of-the-art resources useful for accurate and rapid laboratory diagnosis of mycobacterial infections.
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Affiliation(s)
- V Martinez
- Unité de génétique des mycobactéries, Institut Pasteur, 75015 Paris, France.
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33
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Curry JM, Whalan R, Hunt DM, Gohil K, Strom M, Rickman L, Colston MJ, Smerdon SJ, Buxton RS. An ABC transporter containing a forkhead-associated domain interacts with a serine-threonine protein kinase and is required for growth of Mycobacterium tuberculosis in mice. Infect Immun 2005; 73:4471-7. [PMID: 16040957 PMCID: PMC1201257 DOI: 10.1128/iai.73.8.4471-4477.2005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Forkhead-associated (FHA) domains are modular phosphopeptide recognition motifs with a striking preference for phosphothreonine-containing epitopes. FHA domains have been best characterized in eukaryotic signaling pathways but have been identified in six proteins in Mycobacterium tuberculosis, the causative organism of tuberculosis. One of these, coded by gene Rv1747, is an ABC transporter and the only one to contain two such modules. A deletion mutant of Rv1747 is attenuated in a mouse intravenous injection model of tuberculosis where the bacterial load of the mutant is 10-fold lower than that of the wild type in both lungs and spleen. In addition, growth of the mutant in mouse bone marrow-derived macrophages and dendritic cells is significantly impaired. In contrast, growth of this mutant in vitro was indistinguishable from that of the wild type. The mutant phenotype was lost when the mutation was complemented by the wild-type allele, confirming that it was due to mutation of Rv1747. Using yeast two-hybrid analysis, we have shown that the Rv1747 protein interacts with the serine-threonine protein kinase PknF. This interaction appears to be phospho-dependent since it is abrogated in a kinase-dead mutant and by mutations in the presumed activation loop of PknF and in the first FHA domain of Rv1747. These results demonstrate that the protein coded by Rv1747 is required for normal virulent infection by M. tuberculosis in mice and, since it interacts with a serine-threonine protein kinase in a kinase-dependent manner, indicate that it forms part of an important phospho-dependent signaling pathway.
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Affiliation(s)
- Juliet M Curry
- Division of Mycobacterial Research, National Institute for Medical Research, Mill Hill, London, NW7 1AA, United Kingdom
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Collins DM, Skou B, White S, Bassett S, Collins L, For R, Hurr K, Hotter G, de Lisle GW. Generation of attenuated Mycobacterium bovis strains by signature-tagged mutagenesis for discovery of novel vaccine candidates. Infect Immun 2005; 73:2379-86. [PMID: 15784584 PMCID: PMC1087418 DOI: 10.1128/iai.73.4.2379-2386.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium bovis, a member of the Mycobacterium tuberculosis complex, has a particularly wide host range and causes tuberculosis in most mammals, including humans. A signature tag mutagenesis approach, which employed illegitimate recombination and infection of guinea pigs, was applied to M. bovis to discover genes important for virulence and to find potential vaccine candidates. Fifteen attenuated mutants were identified, four of which produced no lesions when inoculated separately into guinea pigs. One of these four mutants had nine deleted genes including mmpL4 and sigK and, in guinea pigs with aerosol challenge, provided protection against tuberculosis at least equal to that of M. bovis BCG. Seven mutants had mutations near the esxA (esat-6) locus, and immunoblot analysis of these confirmed the essential role of other genes at this locus in the secretion of EsxA (ESAT-6) and EsxB (CFP10). Mutations in the eight other attenuated mutants were widely spread through the chromosome and included pks1, which is naturally inactivated in clinical strains of M. tuberculosis. Many genes identified were different from those found by signature tag mutagenesis of M. tuberculosis by use of a mouse infection model and illustrate how the use of different approaches enables identification of a wider range of attenuating mutants.
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Affiliation(s)
- Desmond M Collins
- AgResearch, Wallaceville Animal Research Centre, P.O. Box 40063, Upper Hutt, New Zealand.
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35
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Kendall SL, Rison SCG, Movahedzadeh F, Frita R, Stoker NG. What do microarrays really tell us about M. tuberculosis? Trends Microbiol 2004; 12:537-44. [PMID: 15539113 DOI: 10.1016/j.tim.2004.10.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bacterial pathogens adapt to their host environments to a large extent through switching on complex transcriptional programmes, and whole-genome microarray experiments promise to reveal this complexity. There has been a recent burst of articles reporting transcriptome analyses of Mycobacterium tuberculosis, including for the first time studies in macrophages and mice. We review gene expression reports, and compare them with each other and with microarray-based gene essentiality studies, revealing at times a startling lack of correlation. Additionally, we suggest a standardization format for the submission of processed data for publication, to facilitate cross-experiment analyses.
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Affiliation(s)
- Sharon L Kendall
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London NW1 0TU, UK
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