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Sequence‐Based Identification and Characterization of Mycobacteria. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mycobacterium tuberculosis complex mycobacteria as amoeba-resistant organisms. PLoS One 2011; 6:e20499. [PMID: 21673985 PMCID: PMC3108610 DOI: 10.1371/journal.pone.0020499] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/28/2011] [Indexed: 11/19/2022] Open
Abstract
Background Most environmental non-tuberculous mycobacteria have been demonstrated to invade amoebal trophozoites and cysts, but such relationships are largely unknown for members of the Mycobacterium tuberculosis complex. An environmental source has been proposed for the animal Mycobacterium bovis and the human Mycobacterium canettii. Methodology/Principal Findings Using optic and electron microscopy and co-culture methods, we observed that 89±0.6% of M. canettii, 12.4±0.3% of M. tuberculosis, 11.7±2% of M. bovis and 11.2±0.5% of Mycobacterium avium control organisms were phagocytized by Acanthamoeba polyphaga, a ratio significantly higher for M. canettii (P = 0.03), correlating with the significantly larger size of M. canetti organisms (P = 0.035). The percentage of intraamoebal mycobacteria surviving into cytoplasmic vacuoles was 32±2% for M. canettii, 26±1% for M. tuberculosis, 28±2% for M. bovis and 36±2% for M. avium (P = 0.57). M. tuberculosis, M. bovis and M. avium mycobacteria were further entrapped within the double wall of <1% amoebal cysts, but no M. canettii organisms were observed in amoebal cysts. The number of intracystic mycobacteria was significantly (P = 10−6) higher for M. avium than for the M. tuberculosis complex, and sub-culturing intracystic mycobacteria yielded significantly more (P = 0.02) M. avium organisms (34×104 CFU/mL) than M. tuberculosis (42×101 CFU/mL) and M. bovis (35×101 CFU/mL) in the presence of a washing fluid free of mycobacteria. Mycobacteria survived in the cysts for up to 18 days and cysts protected M. tuberculosis organisms against mycobactericidal 5 mg/mL streptomycin and 2.5% glutaraldehyde. Conclusions/Significance These data indicate that M. tuberculosis complex organisms are amoeba-resistant organisms, as previously demonstrated for non-tuberculous, environmental mycobacteria. Intercystic survival of tuberculous mycobacteria, except for M. canettii, protect them against biocides and could play a role in their life cycle.
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Rocha A, Elias AR, Sobral LF, Soares DF, Santos AC, Marsico AG, Hacker MA, Caldas PC, Parente LC, Silva MR, Fonseca L, Suffys P, Boéchat N. Genotyping did not evidence any contribution of Mycobacterium bovis to human tuberculosis in Brazil. Tuberculosis (Edinb) 2010; 91:14-21. [PMID: 21106441 DOI: 10.1016/j.tube.2010.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 09/06/2010] [Accepted: 10/19/2010] [Indexed: 12/14/2022]
Abstract
The contribution of Mycobacterium bovis to the global burden of tuberculosis (TB) in man is likely to be underestimated due to its dysgonic growth characteristics and because of the absence of pyruvate in most used media is disadvantageous for its primary isolation. In Brazil Mycobacterium culture, identification and susceptibility tests are performed only in TB reference centers, usually for selected cases. Moreover, solid, egg-based, glycerol-containing (without pyruvate supplementation) Löwenstein-Jensen (L-J) or Ogawa media are routinely used, unfavouring M. bovis isolation. To determine the importance of M. bovis as a public health threat in Brazil we investigated 3046 suspected TB patients inoculating their clinical samples onto routine L-J and L-J pyruvate enriched media. A total of 1796 specimens were culture positive for Mycobacterium spp. and 702 TB cases were confirmed. Surprisingly we did not detect one single case of M. bovis in the resulting collection of 1674 isolates recovered from M. bovis favourable medium analyzed by conventional and molecular speciation methods. Also, bacillary DNA present on 454 sputum smears from 223 TB patients were OxyR genotyped and none was recognized as M. bovis. Our data indicate that M. bovis importance on the burden of human TB in Brazil is marginal.
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Affiliation(s)
- Adalgiza Rocha
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
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Chen R, Bi Y, Yang G, Liu Z, Liu Z, Zeng B, Tong T. Development of a Fluorescent Microsphere-based Multiplex Assay for Simultaneous Rapid Detection of Mycobacterium tuberculosis Complex and Differentiation of M. tuberculosis and M. bovis in Clinical Samples. ACTA ACUST UNITED AC 2010; 19:172-9. [DOI: 10.1097/pdm.0b013e3181d8c241] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Etchechoury I, Valencia GE, Morcillo N, Sequeira MD, Imperiale B, López M, Caimi K, Zumárraga MJ, Cataldi A, Romano MI. Molecular Typing of Mycobacterium bovis Isolates in Argentina: First Description of a Person-to-Person Transmission Case. Zoonoses Public Health 2010; 57:375-81. [DOI: 10.1111/j.1863-2378.2009.01233.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Costa A, Silva N, Rocha V, Rosales Rodriguez C, Estrela-Lima A, Moreira E, Madruga C, Arruda S, Ferreira Neto J, Silva M, Oliveira EDD. TIPIFICAÇÃO GENÉTICA, ATRAVÉS DA TÉCNICA DE SPOLIGOTYPING, DE ISOLADOS DE MYCOBACTERIUM BOVIS EM ANIMAIS ABATIDOS NA REGIÃO METROPOLITANA DE SALVADOR, BAHIA, BRASIL. ARQUIVOS DO INSTITUTO BIOLÓGICO 2010. [DOI: 10.1590/1808-1657v77p2332010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
RESUMO A tuberculose é uma enfermidade infecciosa crônica, que afeta mamíferos e aves e constitui um sério problema de saúde pública e animal. Objetivando realizar um levantamento molecular da enfermidade em bovinos abatidos em matadouros frigoríficos no Estado da Bahia, Brasil, foram analisadas as lesões pulmonares e de linfonodos mediastínicos de 43 carcaças de animais abatidos em três matadouros-frigoríficos localizados na Região Metropolitana de Salvador, Bahia. Sete isolados de Mycobacterium bovis foram identificados, através da técnica do spolygotyping, e discriminados em três diferentes espoligotipos (SB1055, SB0120 e SB0268) descritos no Brasil e em diversas áreas do mundo. Os resultados indicam que o método de diagnóstico utilizado pode contribuir para a criação de uma base de dados para o estudo epidemiológico da tuberculose bovina no Estado da Bahia.
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Vasconcellos SEG, Huard RC, Niemann S, Kremer K, Santos AR, Suffys PN, Ho JL. Distinct genotypic profiles of the two major clades of Mycobacterium africanum. BMC Infect Dis 2010; 10:80. [PMID: 20350321 PMCID: PMC2859774 DOI: 10.1186/1471-2334-10-80] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 03/29/2010] [Indexed: 12/03/2022] Open
Abstract
Background Mycobacterium tuberculosis is the principal etiologic agent of human tuberculosis (TB) and a member of the M. tuberculosis complex (MTC). Additional MTC species that cause TB in humans and other mammals include Mycobacterium africanum and Mycobacterium bovis. One result of studies interrogating recently identified MTC phylogenetic markers has been the recognition of at least two distinct lineages of M. africanum, known as West African-1 and West African-2. Methods We screened a blinded non-random set of MTC strains isolated from TB patients in Ghana (n = 47) for known chromosomal region-of-difference (RD) loci and single nucleotide polymorphisms (SNPs). A MTC PCR-typing panel, single-target standard PCR, multi-primer PCR, PCR-restriction fragment analysis, and sequence analysis of amplified products were among the methods utilized for the comparative evaluation of targets and identification systems. The MTC distributions of novel SNPs were characterized in the both the Ghana collection and two other diverse collections of MTC strains (n = 175 in total). Results The utility of various polymorphisms as species-, lineage-, and sublineage-defining phylogenetic markers for M. africanum was determined. Novel SNPs were also identified and found to be specific to either M. africanum West African-1 (Rv1332523; n = 32) or M. africanum West African-2 (nat751; n = 27). In the final analysis, a strain identification approach that combined multi-primer PCR targeting of the RD loci RD9, RD10, and RD702 was the most simple, straight-forward, and definitive means of distinguishing the two clades of M. africanum from one another and from other MTC species. Conclusion With this study, we have organized a series of consistent phylogenetically-relevant markers for each of the distinct MTC lineages that share the M. africanum designation. A differential distribution of each M. africanum clade in Western Africa is described.
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Affiliation(s)
- Sidra E Gonçalves Vasconcellos
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Avenida Brasil 4365, Rio de Janeiro, Brazil
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Kjeldsen MK, Bek D, Rasmussen EM, Priemé A, Thomsen VØ. Line probe assay for differentiation within Mycobacterium tuberculosis complex. Evaluation on clinical specimens and isolates including Mycobacterium pinnipedii. ACTA ACUST UNITED AC 2010; 41:635-41. [PMID: 20001279 DOI: 10.1080/00365540903127425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A line probe assay (GenoType MTBC) was evaluated for species differentiation within the Mycobacterium tuberculosis complex (MTBC). We included 387 MTBC isolates, 43 IS6110 low-copy MTBC isolates, 28 clinical specimens with varying microscopy grade, and 30 isolates of non-tuberculous mycobacteria. The assay was 100% specific and identified all 387 isolates and 98% of all IS6110 low-copy strains in concordance with the gold standard. The 2% discrepancy was caused by 1 isolate showing a faint restriction fragment length polymorphism (RFLP) pattern. The assay could provide specifies identification in 13 of 19 (68%) microscopy-positive specimens and 0 of 9 microscopy-negative specimens. To our surprise, the probe for M. africanum subtype I reacted with M. pinnipedii. This cross-reaction has not previously been reported. The assay was rapid, easy to perform and directly applicable in highly smear-positive specimens. We predict that the assay will enable enhanced surveillance of species-specific treatment outcome, which may change treatment regimens.
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Pavlin BI, Schloegel LM, Daszak P. Risk of importing zoonotic diseases through wildlife trade, United States. Emerg Infect Dis 2010. [PMID: 19891857 PMCID: PMC2857234 DOI: 10.3201/eid1511.090467] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The United States is the world's largest wildlife importer, and imported wild animals represent a potential source of zoonotic pathogens. Using data on mammals imported during 2000-2005, we assessed their potential to host 27 selected risk zoonoses and created a risk assessment that could inform policy making for wildlife importation and zoonotic disease surveillance. A total of 246,772 mammals in 190 genera (68 families) were imported. The most widespread agents of risk zoonoses were rabies virus (in 78 genera of mammals), Bacillus anthracis (57), Mycobacterium tuberculosis complex (48), Echinococcus spp. (41), and Leptospira spp. (35). Genera capable of harboring the greatest number of risk zoonoses were Canis and Felis (14 each), Rattus (13), Equus (11), and Macaca and Lepus (10 each). These findings demonstrate the myriad opportunities for zoonotic pathogens to be imported and suggest that, to ensure public safety, immediate proactive changes are needed at multiple levels.
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Affiliation(s)
- Boris I Pavlin
- World Health Organization, Communicable Disease Surveillance and Response, PO Box PS70, Department of Health and Social Affairs, Palikir, Pohnpei, FM 96941, Federated States of Micronesia.
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Immune responses in cattle inoculated with Mycobacterium bovis, Mycobacterium tuberculosis, or Mycobacterium kansasii. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2009; 17:247-52. [PMID: 20007361 DOI: 10.1128/cvi.00442-09] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cattle were inoculated with Mycobacterium bovis, Mycobacterium tuberculosis, or Mycobacterium kansasii to compare the antigen-specific immune responses to various patterns of mycobacterial disease. Disease expression ranged from colonization with associated pathology (M. bovis infection) and colonization without pathology (M. tuberculosis infection) to no colonization or pathology (M. kansasii infection). Delayed-type hypersensitivity and gamma interferon responses were elicited by each mycobacterial inoculation; however, the responses by the M. bovis- and M. tuberculosis-inoculated animals exceeded those of the M. kansasii-inoculated animals. Specific antibody responses were detected in all M. tuberculosis- and M. bovis-inoculated cattle 3 weeks after inoculation. From 6 to 16 weeks after M. tuberculosis inoculation, the antibody responses waned, whereas the responses persisted with M. bovis infection. With M. kansasii inoculation, initial early antibody responses waned by 10 weeks after inoculation and then increased 2 weeks after the injection of purified protein derivative for the skin test at 18 weeks after challenge. These findings indicate that antibody responses are associated with the antigen burden rather than the pathology, cellular immune responses to tuberculin correlate with infection but not necessarily with the pathology or bacterial burden, and exposure to mycobacterial antigens may elicit an antibody response in a presensitized animal.
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Herrera-León L, Pozuelo-Díaz R, Molina Moreno T, Valverde Cobacho A, Saiz Vega P, Jiménez Pajares MS. Aplicación de métodos moleculares para la identificación de las especies del complejo Mycobacterium tuberculosis. Enferm Infecc Microbiol Clin 2009; 27:496-502. [DOI: 10.1016/j.eimc.2009.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 12/01/2008] [Accepted: 01/07/2009] [Indexed: 11/30/2022]
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Aguilar León D, Zumárraga MJ, Jiménez Oropeza R, Gioffré AK, Bernardelli A, Orozco Estévez H, Cataldi AA, Hernández Pando R. Mycobacterium bovis with different genotypes and from different hosts induce dissimilar immunopathological lesions in a mouse model of tuberculosis. Clin Exp Immunol 2009; 157:139-47. [PMID: 19659779 DOI: 10.1111/j.1365-2249.2009.03923.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
With the hypothesis that genetic variability of Mycobacterium bovis could influence virulence and immunopathology, five M. bovis strains were selected from an epidemiological study in Argentina on the basis of their prevalence in cattle and occurrence in other species. We then determined the virulence and the immunopathology evoked by these strains in a well-characterized mouse model of progressive pulmonary tuberculosis. The reference strain AN5 was used as a control. BALB/c mice infected with this M. bovis reference strain showed 50% survival after 4 months of infection, with moderate bacillary counts in the lung. Two weeks after inoculation, it induced a strong inflammatory response with numerous granulomas and progressive pneumonia. In contrast, strain 04-303, isolated from a wild boar, was the most lethal and its most striking feature was sudden pneumonia with extensive necrosis. Strain 04-302, also isolated from wild boar but with a different spoligotype, induced similar pathology but to a lesser extent. In contrast, strains 534, V2 (both from cattle) and 02-2B (from human) were less virulent, permitting higher survival after 4 months of infection and limited tissue damage. Strain AN5 and the cattle and human isolates induced rapid, high and stable expression of interferon (IFN)-gamma and inducible nitric oxide synthase (iNOS). In contrast, the more virulent strains induced lower expression of IFN-gamma, tumour necrosis factor-alpha and iNOS. Interestingly, these more virulent strains induced very low expression of murine beta defensin 4 (mBD-4); whereas, the control strain AN5 induced progressive expression of this anti-microbial peptide, peaking at day 120. The less virulent strains induced high mBD-4 expression during early infection. Thus, as reported with clinical isolates of M. tuberculosis, M. bovis also showed variable virulence. This variability can be attributed to the induction of a different pattern of immune response.
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Affiliation(s)
- D Aguilar León
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, Salvador Zubirán, Mexico City, México
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Signal regulatory protein alpha (SIRPalpha) cells in the adaptive response to ESAT-6/CFP-10 protein of tuberculous mycobacteria. PLoS One 2009; 4:e6414. [PMID: 19641628 PMCID: PMC2714177 DOI: 10.1371/journal.pone.0006414] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 06/26/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Early secretory antigenic target-6 (ESAT-6) and culture filtrate protein-10 (CFP-10) are co-secreted proteins of Mycobacterium tuberculosis complex mycobacteria (includes M. bovis, the zoonotic agent of bovine tuberculosis) involved in phagolysosome escape of the bacillus and, potentially, in the efficient induction of granulomas. Upon tuberculosis infection, multi-nucleate giant cells are elicited, likely as a response aimed at containing mycobacteria. In tissue culture models, signal regulatory protein (SIRP)alpha (also referred to as macrophage fusion receptor or CD172a) is essential for multi-nucleate giant cell formation. METHODOLOGY/PRINCIPAL FINDINGS In the present study, ESAT-6/CFP-10 complex and SIRPalpha interactions were evaluated with samples obtained from calves experimentally infected with M. bovis. Peripheral blood CD172a(+) (SIRPalpha-expressing) cells from M. bovis-infected calves proliferated upon in vitro stimulation with ESAT-6/CFP-10 (either as a fusion protein or a peptide cocktail), but not with cells from animals receiving M. bovis strains lacking ESAT-6/CFP-10 (i.e, M. bovis BCG or M. bovis DeltaRD1). Sorted CD172a(+) cells from these cultures had a dendritic cell/macrophage morphology, bound fluorescently-tagged rESAT-6:CFP-10, bound and phagocytosed live M. bovis BCG, and co-expressed CD11c, DEC-205, CD44, MHC II, CD80/86 (a subset also co-expressed CD11b or CD8alpha). Intradermal administration of rESAT-6:CFP-10 into tuberculous calves elicited a delayed type hypersensitive response consisting of CD11c(+), CD172a(+), and CD3(+) cells, including CD172a-expressing multi-nucleated giant cells. CONCLUSIONS/SIGNIFICANCE These findings demonstrate the ability of ESAT-6/CFP-10 to specifically expand CD172a(+) cells, bind to CD172a(+) cells, and induce multi-nucleated giant cells expressing CD172a.
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Abstract
Mycobacterium microti is a member of the Mycobacterium tuberculosis complex of bacteria. This species was originally identified as a pathogen of small rodents and shrews and was associated with limited diversity and a much reduced spoligotype pattern. More recently, specific deletions of chromosomal DNA have been shown to define this group of organisms, which can be identified by the absence of chromosomal region RD1(mic). We describe here the molecular characteristics of 141 strains of the Mycobacterium tuberculosis complex isolated in Great Britain over a 14-year period. All strains have characteristic loss of some spoligotype spacers and characteristic alleles at the ETR-E and ETR-F variable-number tandem-repeat (VNTR) loci, and a sample of these strains was deleted for regions RD7, RD9, and RD1(mic) but intact for regions RD4 and RD12. We therefore identified these strains as M. microti and show that they have much more diverse spoligotype patterns and VNTR types than previously thought. The most common source of these strains was domestic cats, and we show that the molecular types of M. microti are geographically localized in the same way that molecular types of Mycobacterium bovis are geographically localized in cattle in the United Kingdom. We describe the pathology of M. microti infection in cats and suggest that the feline disease is a spillover from a disease maintained in an unknown wild mammal, probably field voles. The location of the cats with M. microti infection suggests that they do not overlap geographically with the strains of Mycobacterium bovis in Great Britain.
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Gordon SV, Bottai D, Simeone R, Stinear TP, Brosch R. Pathogenicity in the tubercle bacillus: molecular and evolutionary determinants. Bioessays 2009; 31:378-88. [DOI: 10.1002/bies.200800191] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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118
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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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"Mycobacterium canettii" isolated from a human immunodeficiency virus-positive patient: first case recognized in the United States. J Clin Microbiol 2008; 47:255-7. [PMID: 19020064 DOI: 10.1128/jcm.01268-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the first case of tuberculosis caused by "Mycobacterium canettii" recognized in the United States. The pathogen was isolated from the cerebrospinal fluid of a 30-year-old Sudanese refugee.
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Disseminated panniculitis in a bottlenose dolphin (Tursiops truncatus) due to Mycobacterium chelonae infection. J Zoo Wildl Med 2008; 39:412-20. [PMID: 18817005 DOI: 10.1638/2007-0135.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A 14-year-old female bottlenose dolphin was diagnosed with mycobacterial panniculitis based on punch biopsy specimens. The necropsy revealed numerous pyogranulomas in the blubber, as well as marked acute multifocal necrosuppurative pneumonia and lymphadenitis. In addition, the animal had marked scoliosis, which had first been noted clinically in the dolphin at about 1 mo of age. The animal had been treated with low-dose dexamethasone for approximately the last 19 mo to reduce perceived discomfort from spondyloarthritis and with the progestational agent altrogenest for approximately 8 yr to prevent pregnancy. Acid-fast positive bacilli were detected in the dermis but not in lung or lymph nodes. Mycobacterium chelonae was isolated from pooled skin, lung, and peripheral lymph-node tissue. Mycobacterial infection may be considered as a differential diagnosis in bottlenose dolphins with generalized cutaneous inflammation, particularly if chronic steroid and progesterone treatments were administered, both of which may have an immunomodulatory effect.
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Disseminated tuberculosis in hyrax (Procavia capensis) caused by Mycobacterium africanum. J Zoo Wildl Med 2008; 39:386-91. [PMID: 18817001 DOI: 10.1638/06-041.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tuberculosis due to Mycobacterium africanum was diagnosed in an adult female hyrax (Procavia capensis). Pathologic examination revealed disseminated tuberculous lesions. The same pathologic changes were also found in a male hyrax that died a year later. Both animals were imported from the United Arab Emirates and were held in captivity at the Zagreb Zoo in Croatia. The source of infection remains unknown. The acid-fast bacteria isolated from the lungs of the female hyrax were identifyed by polymerase chain reaction as Mycobacterium tuberculosis complex and Geno Type MTBC test confirmed the strain to be M. africanum I.
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Djelouadji Z, Raoult D, Daffé M, Drancourt M. A single-step sequencing method for the identification of Mycobacterium tuberculosis complex species. PLoS Negl Trop Dis 2008; 2:e253. [PMID: 18618024 PMCID: PMC2453075 DOI: 10.1371/journal.pntd.0000253] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Accepted: 05/20/2008] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The Mycobacterium tuberculosis complex (MTC) comprises closely related species responsible for strictly human and zoonotic tuberculosis. Accurate species determination is useful for the identification of outbreaks and epidemiological links. Mycobacterium africanum and Mycobacterium canettii are typically restricted to Africa and M. bovis is a re-emerging pathogen. Identification of these species is difficult and expensive. METHODOLOGY/PRINCIPAL FINDINGS The Exact Tandem Repeat D (ETR-D; alias Mycobacterial Interspersed Repetitive Unit 4) was sequenced in MTC species type strains and 110 clinical isolates, in parallel to reference polyphasic identification based on phenotype profiling and sequencing of pncA, oxyR, hsp65, gyrB genes and the major polymorphism tandem repeat. Inclusion of M. tuberculosis isolates in the expanding, antibiotic-resistant Beijing clone was determined by Rv0927c gene sequencing. The ETR-D (780-bp) sequence unambiguously identified MTC species type strain except M. pinnipedii and M. microti thanks to six single nucleotide polymorphisms, variable numbers (1-7 copies) of the tandem repeat and two deletions/insertions. The ETR-D sequencing agreed with phenotypic identification in 107/110 clinical isolates and with reference polyphasic molecular identification in all isolates, comprising 98 M. tuberculosis, 5 M. bovis BCG type, 5 M. canettii, and 2 M. africanum. For M. tuberculosis isolates, the ETR-D sequence was not significantly associated with the Beijing clone. CONCLUSIONS/SIGNIFICANCE ETR-D sequencing allowed accurate, single-step identification of the MTC at the species level. It circumvented the current expensive, time-consuming polyphasic approach. It could be used to depict epidemiology of zoonotic and human tuberculosis, especially in African countries where several MTC species are emerging.
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Affiliation(s)
- Zoheira Djelouadji
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Didier Raoult
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
| | - Mamadou Daffé
- Département de Mécanismes Moléculaires des Infections Mycobactériennes, Institut de Pharmacologie et Biologie structurale, Toulouse, France
| | - Michel Drancourt
- Unité des Rickettsies CNRS UMR6020, IFR 48, Faculté de Médecine, Université de la Méditerranée, Marseille, France
- * E-mail:
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Osinga N, ‘t Hart P, Morick D. By-catch and drowning in harbour porpoises (Phocoena phocoena) stranded on the northern Dutch coast. EUR J WILDLIFE RES 2008. [DOI: 10.1007/s10344-008-0193-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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124
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Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol 2008; 6:387-94. [PMID: 18392032 DOI: 10.1038/nrmicro1889] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The increasing availability of DNA-sequence information for multiple pathogenic and non-pathogenic variants of individual bacterial species has indicated that both DNA acquisition and genome reduction have important roles in genome evolution. Such genomic fluidity, which is found in human pathogens such as Escherichia coli, Helicobacter pylori and Mycobacterium tuberculosis, has important consequences for the clinical management of the diseases that are caused by these pathogens and for the development of diagnostics and new molecular epidemiological methods.
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125
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Direct comparison of the genotype MTBC and genomic deletion assays in terms of ability to distinguish between members of the Mycobacterium tuberculosis complex in clinical isolates and in clinical specimens. J Clin Microbiol 2008; 46:1854-7. [PMID: 18353933 DOI: 10.1128/jcm.00105-07] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The automated GenoType MTBC assay was evaluated for the ability to detect and identify members of the Mycobacterium tuberculosis complex. In addition to 35 reference strains and 157 clinical isolates, performance of this assay was tested directly on 79 smear-positive clinical specimens. The assay proved as accurate as the reference deletion analysis for all 192 isolates and detected and identified M. tuberculosis complex members in 93.2% of the specimens containing the M. tuberculosis complex.
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Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK, Tyagi AK, Hasnain SE. Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution. PLoS One 2007; 2:e968. [PMID: 17912347 PMCID: PMC1989137 DOI: 10.1371/journal.pone.0000968] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2007] [Accepted: 09/10/2007] [Indexed: 11/18/2022] Open
Abstract
Background Evolutionary dynamics plays a central role in facilitating the mechanisms of species divergence among pathogenic and saprophytic mycobacteria. The ability of mycobacteria to colonize hosts, to proliferate and to cause diseases has evolved due to its predisposition to various evolutionary forces acting over a period of time. Mycobacterium indicus pranii (MIP), a taxonomically unknown ‘generalist’ mycobacterium, acts as an immunotherapeutic against leprosy and is approved for use as a vaccine against it. The large-scale field trials of this MIP based leprosy vaccine coupled with its demonstrated immunomodulatory and adjuvant property has led to human clinical evaluations of MIP in interventions against HIV-AIDS, psoriasis and bladder cancer. MIP, commercially available as ‘Immuvac’, is currently the focus of advanced phase III clinical trials for its antituberculosis efficacy. Thus a comprehensive analysis of MIP vis-à-vis evolutionary path, underpinning its immanent immunomodulating properties is of the highest desiderata. Principal Findings Genome wide comparisons together with molecular phylogenetic analyses by fluorescent amplified fragment length polymorphism (FAFLP), enterobacterial repetitive intergenic consensus (ERIC) based genotyping and candidate orthologues sequencing revealed that MIP has been the predecessor of highly pathogenic Mycobacterium avium intracellulare complex (MAIC) that did not resort to parasitic adaptation by reductional gene evolution and therefore, preferred a free living life-style. Further analysis suggested a shared aquatic phase of MAIC bacilli with the early pathogenic forms of Mycobacterium, well before the latter diverged as ‘specialists’. Conclusions/Significance This evolutionary paradigm possibly affirms to marshal our understanding about the acquisition and optimization of virulence in mycobacteria and determinants of boundaries therein.
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Affiliation(s)
- Niyaz Ahmed
- Pathogen Evolution Laboratory, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Vikram Saini
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Saurabh Raghuvanshi
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Jitendra P. Khurana
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Akhilesh K. Tyagi
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Anil K. Tyagi
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Seyed E. Hasnain
- University of Hyderabad, Hyderabad, India
- Institute of Life Sciences, University of Hyderabad, Hyderabad, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
- * To whom correspondence should be addressed. E-mail:
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Pate M, Svara T, Gombac M, Paller T, Zolnir-Dovc M, Emersic I, Prodinger WM, Bartos M, Zdovc I, Krt B, Pavlik I, Cvetnić Z, Pogacnik M, Ocepek M. Outbreak of tuberculosis caused by Mycobacterium caprae in a zoological garden. ACTA ACUST UNITED AC 2007; 53:387-92. [PMID: 17010043 DOI: 10.1111/j.1439-0450.2006.01000.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the autumn of 2004, tuberculosis caused by Mycobacterium caprae occurred in a zoo in Slovenia. A dromedary camel (Camelus dromedarius) was killed after a history of progressive emaciation. Necropsy findings indicated disseminated tuberculosis, which was confirmed by cultivation of M. caprae. Consequently, a tuberculin skin test was performed in all epidemiologically linked animals and another dromedary camel and six bison (Bison bison) were positive and killed. Mycobacterium caprae was isolated from two bison while M. scrofulaceum and Mycobacterium spp. were found in two other bison, respectively. The second dromedary camel was found to be negative for mycobacteria under both microscopic and culture tests. The isolates were investigated with commercial identification kits, IS6110 PCR, IS6110 restriction fragment length polymorphism analysis, spoligotyping and mycobacterial interspersed repetitive units typing. Genotyping results revealed that the dromedary camel and the two bison were infected by the same M. caprae.
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Affiliation(s)
- M Pate
- Institute of Microbiology and Parasitology, Vetinary Faculty, Gerbiceva, Ljubljana, Slovenia
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Javed MT, Aranaz A, de Juan L, Bezos J, Romero B, Alvarez J, Lozano C, Mateos A, Domínguez L. Improvement of spoligotyping with additional spacer sequences for characterization of Mycobacterium bovis and M. caprae isolates from Spain. Tuberculosis (Edinb) 2007; 87:437-45. [PMID: 17569586 DOI: 10.1016/j.tube.2007.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2006] [Revised: 04/19/2007] [Accepted: 04/21/2007] [Indexed: 11/24/2022]
Abstract
Spoligotyping is a typing tool used worldwide for epidemiological studies on Mycobacterium tuberculosis complex organisms; however it has received little attention regarding improvement of its discriminatory power (DP). In this study, we have evaluated a spoligotyping membrane prepared with 25 novel spacer sequences selected from a previous study [van der Zanden AG, Kremer K, Schouls LM. Improvement of differentiation and interpretability of spoligotyping for Mycobacterium tuberculosis complex isolates by introduction of new spacer oligonucleotides. J Clin Microbiol 2002;40:4628-39] on 308 M. bovis and 88 M. caprae Spanish isolates in comparison with the traditional spoligotyping membrane. The results obtained by combining the two membranes together revealed an improvement of 45 patterns instead of 31. The spacers used in the second membrane were able to distinguish 8 out of the 16 M. bovis types that had more than one isolate. Seven of these types were differentiated into two subtypes with the second-generation membrane, while spb-7, the most prevalent in Spain, was further differentiated into eight subtypes. This second-generation membrane also differentiates M. bovis from M. caprae. A set of 39 spacers (1, 2, 4-8, 10-15, 17-21, 23, 26-32, 37, 44-49, 51-54, 56 and 57) contain all the DP for both M. bovis and M. caprae isolates; and a set of 35 spacers (1, 2, 4-8, 10-15, 17-21, 26-32, 37, 44-48, 52-54 and 57) had all the DP for the M. bovis isolates. Our results show that the research on new spacers and the design of a new membrane may be useful for epidemiological studies of M. bovis and M. caprae isolates.
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Affiliation(s)
- M Tariq Javed
- Grupo de Vigilancia Sanitaria Veterinaria, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
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129
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Taylor GM, Worth DR, Palmer S, Jahans K, Hewinson RG. Rapid detection of Mycobacterium bovis DNA in cattle lymph nodes with visible lesions using PCR. BMC Vet Res 2007; 3:12. [PMID: 17567891 PMCID: PMC1904440 DOI: 10.1186/1746-6148-3-12] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 06/13/2007] [Indexed: 11/10/2022] Open
Abstract
Background We have evaluated a sensitive screening assay for Mycobacterium tuberculosis (MTB) complex organisms and a specific assay for detecting Mycobacterium bovis DNA in lymph nodes taken from cattle with evidence of bovine tuberculosis. Underlying these series of experiments was the need for a versatile DNA extraction protocol which could handle tissue samples and with the potential for automation. The target for the screening assay was the multi-copy insertion element IS1081, present in 6 copies in the MTB complex. For confirmation of M. bovis we used primers flanking a specific deletion in the genome of M. bovis known as region of difference 4 (RD4). The sensitivity and specificity of these PCRs has been tested on genomic DNA from MTB complex reference strains, mycobacteria other than tuberculosis (MOTT), spiked samples and on clinical material. Results The minimum detection limits of the IS1081 method was < I genome copy and for the RD4 PCR was 5 genome copies. Both methods can be readily adapted for quantitative PCR with the use of SYBR Green intercalating dye on the RotorGene 3000 platform (Corbett Research). Initial testing of field samples of bovine lymph nodes with visible lesions (VL, n = 109) highlighted two shortfalls of the molecular approach. Firstly, comparison of IS1081 PCR with the "gold standard" of culture showed a sensitivity of approximately 70%. The sensitivity of the RD4 PCR method was 50%. Secondly, the success rate of spoligotyping applied directly to clinical material was 51% compared with cultures. A series of further experiments indicated that the discrepancy between sensitivity of detection found with purified mycobacterial DNA and direct testing of field samples was due to limited mycobacterial DNA recovery from tissue homogenates rather than PCR inhibition. The resilient mycobacterial cell wall, the presence of tissue debris and the paucibacillary nature of some cattle VL tissue may all contribute to this observation. Any of these factors may restrict application of other more discriminant typing methods. A simple means of increasing the efficiency of mycobacterial DNA recovery was assessed using a further pool of 95 cattle VL. Following modification of the extraction protocol, detection rate with the IS1081 and RD4 methods increased to 91% and 59% respectively. Conclusion The IS1081 PCR is a realistic screening method for rapid identification of positive cases but the sensitivity of single copy methods, like RD4 and also of spoligotyping will need to be improved to make these applicable for direct testing of tissue extracts.
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Affiliation(s)
- G Michael Taylor
- Centre for Microbiology and Infectious Diseases, Flowers Building, Imperial College, Armstrong Road, London SW7 4AZ, UK
| | - Danny R Worth
- TB Diagnostic Section, Veterinary Laboratory Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Si Palmer
- TB Diagnostic Section, Veterinary Laboratory Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Keith Jahans
- TB Diagnostic Section, Veterinary Laboratory Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - R Glyn Hewinson
- TB Diagnostic Section, Veterinary Laboratory Agency, Woodham Lane, New Haw, Addlestone, Surrey KT15 3NB, UK
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130
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Neonakis IK, Gitti Z, Petinaki E, Maraki S, Spandidos DA. Evaluation of the GenoType MTBC assay for differentiating 120 clinical Mycobacterium tuberculosis complex isolates. Eur J Clin Microbiol Infect Dis 2007; 26:151-2. [PMID: 17256112 DOI: 10.1007/s10096-007-0255-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- I K Neonakis
- Department of Clinical Bacteriology, Parasitology, Zoonoses and Geographical Medicine, Mycobacteriology Laboratory, University Hospital of Heraklion, Heraklion, Crete, 71201, Greece
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Abstract
The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.
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Affiliation(s)
- Christine Y Turenne
- McGill University Health Centre, A5.156, 1650 Cedar Avenue, Montreal H3G 1A4, Canada
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132
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Gómez MPR, Herrera-León L, Jiménez MS, Rodríguez JG. Comparison of GenoType MTBC with RFLP-PCR and multiplex PCR to identify Mycobacterium tuberculosis complex species. Eur J Clin Microbiol Infect Dis 2007; 26:63-6. [PMID: 17146674 DOI: 10.1007/s10096-006-0231-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The aims of the work presented here were to evaluate a commercial system based on DNA hybridization technology on nitrocellulose strips (GenoType MTBC; Hain Diagnostika, Nehren, Germany) for identifying Mycobacterium tuberculosis complex isolates to the species level and to compare the results with those obtained using the RFLP-PCR and multiplex PCR molecular techniques, biochemical tests and susceptibility testing. The commercial system correctly identified 102 of 103 (99.03%) strains studied, indicating it is capable of discriminating among the tuberculosis complex species.
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Affiliation(s)
- M P Romero Gómez
- Department of Microbiology and Parasitology, La Paz University Hospital, Madrid, Spain
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133
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Meikle V, Schneider M, Azenzo G, Zumárraga M, Magnano G, Cataldi A. Individual Animals of a Cattle Herd Infected with the Same Mycobacterium bovis Genotype Shows Important Variations in Bacteriological, Histopathological and Immune Response Parameters. Zoonoses Public Health 2007; 54:86-93. [PMID: 17348912 DOI: 10.1111/j.1863-2378.2007.01027.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cattle are the host and main reservoir of the etiologic agent of bovine tuberculosis, Mycobacterium bovis; although other mammalian species, including humans, are susceptible. The tuberculin test and/or slaughterhouse surveillance is the diagnostic method used by control programs all around the world to control and eradicate the disease. In order to compare different tuberculosis diagnostic tests and to reach disease confirmation, a study was performed in a group of 14 steers of Friesian breed, reacting positively to tuberculin test. Three ante-mortem assays were performed according to the type of sample: the gamma interferon (IFN-gamma) test (which quantifies the release of this cytokine by sensitized lymphocytes in whole blood in response to purified protein derivative (PPD) and recombinant ESAT-6 and CFP10 proteins); PCR and bacteriologic culture from nasal swab and intradermal tuberculin test. These assays were taken at different times to assess the evolution of clinical parameters. Post-mortem examination showed macroscopic and microscopic tuberculosis lesions with acid-fast bacillus and positive cultures. By spoligotyping, we observed that all the isolates showed the same pattern. The positive results based on comparison to lesions observed ranged from 58% to 75% for the IFN-gamma assays, to 72% for cultures, and ranged from 50% to 90% for PCR in nasal swabs. In conclusion, in a herd infected by the same strain, ante-mortem direct and immune-diagnostic parameters change, suggesting that several tests are needed for a faster control of infection at herd level.
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Affiliation(s)
- V Meikle
- Instituto de Biotecnología. CNIA-INTA, Castelar, Argentina
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134
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Abstract
The continuous evolution of mycobacterial taxonomy may represent a source of confusion for laboratories and clinicians. Apart from the obvious pathogenic strains of the Mycobacterium tuberculosis complex, Mycobacterium leprae and Mycobacterium ulcerans, the role of other mycobacteria may be associated with varying conditions ranging from contamination to specific disease processes. Of the more than 120 mycobacterial species recognized currently, very few have not been reported as pathogenic in humans or animals. Although the attempt to keep pace with the steadily increasing number of mycobacterial species seems hopeless, a careful review of the recent literature relevant to the newly described species may be advantageous. The aim of this present update is to provide epidemiological and clinical information along with major phenotypic and genotypic characteristics of the species described in the last 3 years.
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Centre for Mycobacteria, Careggi Hospital, Florence, Italy.
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135
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Somoskovi A, Dormandy J, Parsons LM, Kaswa M, Goh KS, Rastogi N, Salfinger M. Sequencing of the pncA gene in members of the Mycobacterium tuberculosis complex has important diagnostic applications: Identification of a species-specific pncA mutation in "Mycobacterium canettii" and the reliable and rapid predictor of pyrazinamide resistance. J Clin Microbiol 2006; 45:595-9. [PMID: 17135430 PMCID: PMC1829052 DOI: 10.1128/jcm.01454-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Testing for susceptibility to pyrazinamide (PZA) and analysis of the pncA gene sequences of 423 Mycobacterium tuberculosis complex isolates have revealed a unique silent nucleotide substitution that enables the rapid identification of "M. canettii" (proposed name). Moreover, the lack of a defined mutation within the pncA gene strongly suggests that an alternative mechanism is responsible for PZA resistance. Our results indicate that DNA sequencing of the pncA gene has the potential to shorten the turnaround time and increase the accuracy of PZA susceptibility testing of the M. tuberculosis complex.
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Affiliation(s)
- Akos Somoskovi
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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Saïd-Salim B, Mostowy S, Kristof AS, Behr MA. Mutations in Mycobacterium tuberculosis Rv0444c, the gene encoding anti-SigK, explain high level expression of MPB70 and MPB83 in Mycobacterium bovis. Mol Microbiol 2006; 62:1251-63. [PMID: 17064366 DOI: 10.1111/j.1365-2958.2006.05455.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has recently been advanced that Mycobacterium tuberculosis sigma factor K (SigK) positively regulates expression of the antigenic proteins MPB70 and MPB83. As expression of these proteins differs between M. tuberculosis (low) and Mycobacterium bovis (high), this study set out to determine whether M. bovis lacks a functional SigK repressor (anti-SigK). By comparing genes near sigK in M. tuberculosis H37Rv and M. bovis AF2122/97, we observed that Rv0444c, annotated as unknown function, had variable sequence in M. bovis. Analysis of in vitro mpt70/mpt83 expression and Rv0444c sequencing across M. tuberculosis complex (MTC) members revealed that high-level expression was associated with a mutated Rv0444c. Complementation of M. bovis bacillus Calmette-Guerin Russia, a high producer of MPB70/MPB83, with wild-type Rv0444c resulted in a significant decrease in mpb70/mpb83 expression. Conversely, a M. tuberculosis H37Rv mutant which expressed sigK but not Rv0444c manifested the M. bovis phenotype of high-level MPB70/MPB83 expression. Further support that Rv0444c encodes the anti-SigK was obtained by yeast two-hybrid studies, where the N-terminal region of Rv0444c-encoded protein interacted with SigK. Together these findings indicate that Rv0444c encodes the regulator of SigK (RskA) and mutations in this gene explain high-level MPT70/MPT83 expression by certain MTC members.
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137
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Sintchenko V, Jelfs P, Dally M, Crighton T, Gilbert GL. A case of urinary tuberculosis due to Mycobacterium bovis subspecies caprae. Pathology 2006; 38:376-8. [PMID: 16916737 DOI: 10.1080/00313020600821391] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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138
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Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006; 19:658-85. [PMID: 17041139 PMCID: PMC1592690 DOI: 10.1128/cmr.00061-05] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.
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Affiliation(s)
- Barun Mathema
- Tuberculosis Center, Public Health Research Institute, Newark, NJ 07103, USA.
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139
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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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140
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Goh KS, Fabre M, Huard RC, Schmid S, Sola C, Rastogi N. Study of the gyrB gene polymorphism as a tool to differentiate among Mycobacterium tuberculosis complex subspecies further underlines the older evolutionary age of ‘Mycobacterium canettii’. Mol Cell Probes 2006; 20:182-90. [PMID: 16517119 DOI: 10.1016/j.mcp.2005.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2005] [Accepted: 11/21/2005] [Indexed: 11/30/2022]
Abstract
The present investigation evaluated the PCR-restriction fragment length polymorphism (RFLP) analysis of hsp65 and gyrB targets for differentiation of the species within the Mycobacterium tuberculosis complex (MTC) both by including new restriction enzymes and previously unstudied species. The hsp65 restriction analysis using HhaI resulted in a characteristic 'Mycobacterium canettii' pattern. A study of the gyrB gene polymorphism using TaqIalpha and HinfI allowed the initial division of MTC into two major groups, one consisting of M. tuberculosis and 'M. canettii' as opposed to another single group with other species. Three different patterns were observed with RsaI, the first characteristic of Mycobacterium microti, the second with Mycobacterium bovis, M. bovis BCG and Mycobacterium caprae (M. caprae was easily separated from M. bovis, and M. bovis BCG by SacII digestion), and the third with M. tuberculosis, 'M. canettii', Mycobacterium africanum, Mycobacterium pinnipedii, and the dassie bacillus. Although further discrimination within the last group was not obtained using additional restriction enzymes, the HaeIII and RsaI digestions highlighted an important gyrB polymorphism among 'M. canettii' strains. A study of the single nucleotide polymorphisms (SNP) within the gyrB by sequence analysis not only confirmed the results of the restriction analysis, but showed further differences among 'M. canettii' isolates that were not picked up using the existing battery of restriction enzymes. As many as 11 different SNPs were identified in the collection of eight 'M. canettii' isolates studied. Considering that gyrB variability among MTC member species other than 'M. canettii' is as restricted as hsp65 variability among MTC, our data corroborate a recent proposition that the 'M. canettii' group is evolutionary much older than the other MTC members. In conclusion, gyrB PCR-RFLP is a simple and rapid low-cost method that combined with phenotypic characteristics, may be helpful to differentiate most of the subspecies within the MTC.
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Affiliation(s)
- Khye Seng Goh
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Morne Jolivière, BP484, F97183 Abymes, Cedex, Guadeloupe
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141
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Filliol I, Motiwala AS, Cavatore M, Qi W, Hazbón MH, Bobadilla del Valle M, Fyfe J, García-García L, Rastogi N, Sola C, Zozio T, Guerrero MI, León CI, Crabtree J, Angiuoli S, Eisenach KD, Durmaz R, Joloba ML, Rendón A, Sifuentes-Osornio J, Ponce de León A, Cave MD, Fleischmann R, Whittam TS, Alland D. Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set. J Bacteriol 2006; 188:759-72. [PMID: 16385065 PMCID: PMC1347298 DOI: 10.1128/jb.188.2.759-772.2006] [Citation(s) in RCA: 340] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis.
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Affiliation(s)
- Ingrid Filliol
- Division of Infectious Disease, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave., MSB A920C, Newark, NJ 07103.
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142
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Abstract
Mycobacterium bovis and closely associated acid-fast bacilli cause disease in humans. Epidemiologic investigations reveal that the organism may be ingested or inhaled. Extra pulmonary lesions may occur associated to the consumption of infected milk, even though with the practice of boiling milk, and the growth of milk pasteurization plants all over the world, the digestive route of infection became less important. On the other hand, airborne infection continues to occur among meat industry and slaughterhouse workers, in regions where the infection is still prevalent in cattle. Evidence of person to person transmission is rare. Main causes of concern related to M. bovis in industrialized countries are: epizootics in domesticated and wild mammals and latent infection in immigrants. Although multidrug-resistant (MDR) strains of M. bovis have been identified, case reports reveal that anti-tuberculosis drugs routinely used to treat Mycobacterium tuberculosis-infected patients are effective when properly administered.
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Affiliation(s)
- Charles Thoen
- Department of Veterinary Microbiology and Preventative Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, USA.
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143
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Kassama Y, Shemko M, Shetty N, Fang Z, Macintire G, Gant V, Zumla A, Goodacre R. An improved fluorescent amplified fragment length polymorphism method for typing Mycobacterium tuberculosis. J Clin Microbiol 2006; 44:288-9. [PMID: 16390994 PMCID: PMC1351977 DOI: 10.1128/jcm.44.1.288-289.2006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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144
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Prodinger WM, Brandstätter A, Naumann L, Pacciarini M, Kubica T, Boschiroli ML, Aranaz A, Nagy G, Cvetnic Z, Ocepek M, Skrypnyk A, Erler W, Niemann S, Pavlik I, Moser I. Characterization of Mycobacterium caprae isolates from Europe by mycobacterial interspersed repetitive unit genotyping. J Clin Microbiol 2005; 43:4984-92. [PMID: 16207952 PMCID: PMC1248478 DOI: 10.1128/jcm.43.10.4984-4992.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium caprae, a recently defined member of the Mycobacterium tuberculosis complex, causes tuberculosis among animals and, to a limited extent, in humans in several European countries. To characterize M. caprae in comparison with other Mycobacterium tuberculosis complex members and to evaluate genotyping methods for this species, we analyzed 232 M. caprae isolates by mycobacterial interspersed repetitive unit (MIRU) genotyping and by spoligotyping. The isolates originated from 128 distinct epidemiological settings in 10 countries, spanning a period of 25 years. We found 78 different MIRU patterns (53 unique types and 25 clusters with group sizes from 2 to 9) but only 17 spoligotypes, giving Hunter-Gaston discriminatory indices of 0.941 (MIRU typing) and 0.665 (spoligotyping). For a subset of 103 M. caprae isolates derived from outbreaks or endemic foci, MIRU genotyping and IS 6110 restriction fragment length polymorphism were compared and shown to provide similar results. MIRU loci 4, 26, and 31 were most discriminant in M. caprae, followed by loci 10 and 16, a combination which is different than those reported to discriminate M. bovis best. M. caprae MIRU patterns together with published data were used for phylogenetic inference analysis employing the neighbor-joining method. M. caprae isolates were grouped together, closely related to the branches of classical M. bovis, M. pinnipedii, M. microti, and ancestral M. tuberculosis, but apart from modern M. tuberculosis. The analysis did not reflect geographic patterns indicative of origin or spread of M. caprae. Altogether, our data confirm M. caprae as a distinct phylogenetic lineage within the Mycobacterium tuberculosis complex.
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Affiliation(s)
- Wolfgang M Prodinger
- Department of Hygiene, Microbiology, and Social Medicine, Innsbruck Medical University, Fritz Pregl-Strasse 3, A-6020 Innsbruck, Austria.
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145
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Mostowy S, Inwald J, Gordon S, Martin C, Warren R, Kremer K, Cousins D, Behr MA. Revisiting the evolution of Mycobacterium bovis. J Bacteriol 2005; 187:6386-95. [PMID: 16159772 PMCID: PMC1236643 DOI: 10.1128/jb.187.18.6386-6395.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Though careful consideration has been placed towards genetic characterization of tubercle bacillus isolates causing disease in humans, those causing disease predominantly among wild and domesticated mammals have received less attention. In contrast to Mycobacterium tuberculosis, whose host range is largely specific to humans, M. bovis and "M bovis-like" organisms infect a broad range of animal species beyond their most prominent host in cattle. To determine whether strains of variable genomic content are associated with distinct distributions of disease, the DNA contents of M. bovis or M. bovis-like isolates from a variety of hosts were investigated via Affymetrix GeneChip. Consistent with previous genomic analysis of the M. tuberculosis complex (MTC), large sequence polymorphisms of putative diagnostic and biological consequence were able to unambiguously distinguish interrogated isolates. The distribution of deleted regions indicates organisms genomically removed from M. bovis and also points to structured genomic variability within M. bovis. Certain genomic profiles spanned a variety of hosts but were clustered by geography, while others associated primarily with host type. In contrast to the prevailing assumption that M. bovis has broad host capacity, genomic profiles suggest that distinct MTC lineages differentially infect a variety of mammals. From this, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC.
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Affiliation(s)
- Serge Mostowy
- McGill University Health Centre, Montreal, Quebec, Canada
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146
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Dupont C, Thompson K, Heuer C, Gicquel B, Murray A. Identification and characterization of an immunogenic 22 kDa exported protein of Mycobacterium avium subspecies paratuberculosis. J Med Microbiol 2005; 54:1083-1092. [PMID: 16192441 DOI: 10.1099/jmm.0.46163-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An exported 22 kDa putative lipoprotein was identified in an alkaline phosphatase gene fusion library ofMycobacterium aviumsubsp.paratuberculosisand expressed inMycobacterium smegmatis. The full nucleic acid sequence of the gene encoding P22 was determined and the ORF was cloned into a mycobacterial expression vector, enabling full-length P22 to be produced as a C-terminal polyhistidine-tagged protein inM. smegmatis. N-terminal sequencing of the recombinant protein confirmed cleavage of a signal sequence. Native P22 was detected in culture supernatants and cell sonicates ofM. aviumsubsp.paratuberculosisstrain 316F using rabbit antibody raised to recombinant P22. Investigation of the presence of similar genes in other mycobacterial species revealed that the gene was present inMycobacterium aviumsubsp.aviumand similar genes existed inMycobacterium intracellulareandMycobacterium scrofulaceum. Database searches showed that P22 belonged to the LppX/LprAFG family of mycobacterial lipoproteins also found inMycobacterium lepraeand in members of theMycobacterium tuberculosiscomplex. P22 shared less than 75 % identity to these proteins. Recombinant P22 was able to elicit interferon-gamma secretion in blood from eight of a group of nine sheep vaccinated with a live attenuated strain ofM. aviumsubsp.paratuberculosis(strain 316F) compared to none from a group of five unvaccinated sheep. Antibody to P22 was detected by Western blot analysis in 10 out of 11 vaccinated sheep, in two out of two clinically affected cows and in 11 out of 13 subclinically infected cows.
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MESH Headings
- Animals
- Antibodies, Bacterial/blood
- Antigens, Bacterial/chemistry
- Antigens, Bacterial/immunology
- Antigens, Bacterial/isolation & purification
- Bacterial Proteins/chemistry
- Bacterial Proteins/immunology
- Bacterial Proteins/isolation & purification
- Blotting, Western
- Cattle
- Cloning, Molecular
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- Interferon-gamma/blood
- Lipoproteins/chemistry
- Lipoproteins/immunology
- Lipoproteins/isolation & purification
- Models, Animal
- Molecular Sequence Data
- Molecular Weight
- Mycobacterium avium/genetics
- Mycobacterium avium Complex/genetics
- Mycobacterium avium subsp. paratuberculosis/genetics
- Mycobacterium avium subsp. paratuberculosis/immunology
- Mycobacterium leprae/genetics
- Mycobacterium scrofulaceum/genetics
- Mycobacterium smegmatis/genetics
- Mycobacterium tuberculosis/genetics
- Open Reading Frames
- Protein Sorting Signals
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/genetics
- Sequence Analysis, DNA
- Sequence Analysis, Protein
- Sequence Homology, Amino Acid
- Sheep
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Affiliation(s)
- Chris Dupont
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North, Private Bag 11 222, New Zealand 2Unite de Genetique Mycobacterienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Keith Thompson
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North, Private Bag 11 222, New Zealand 2Unite de Genetique Mycobacterienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Cord Heuer
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North, Private Bag 11 222, New Zealand 2Unite de Genetique Mycobacterienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Brigitte Gicquel
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North, Private Bag 11 222, New Zealand 2Unite de Genetique Mycobacterienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Alan Murray
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North, Private Bag 11 222, New Zealand 2Unite de Genetique Mycobacterienne, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
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147
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Kremer K, Arnold C, Cataldi A, Gutiérrez MC, Haas WH, Panaiotov S, Skuce RA, Supply P, van der Zanden AGM, van Soolingen D. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains. J Clin Microbiol 2005; 43:5628-38. [PMID: 16272496 PMCID: PMC1287774 DOI: 10.1128/jcm.43.11.5628-5638.2005] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2005] [Revised: 04/18/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.
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Affiliation(s)
- Kristin Kremer
- Mycobacteria Reference Unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, P.O. Box 1, 3720 BA Bilthoven, The Netherlands.
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148
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Cobos-Marín L, Montes-Vargas J, Zumarraga M, Cataldi A, Romano MI, Estrada-Garcia I, Gonzalez-y-Merchand JA. Spoligotype analysis ofMycobacterium bovisisolates from Northern México. Can J Microbiol 2005; 51:996-1000. [PMID: 16333340 DOI: 10.1139/w05-083] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Bovine tuberculosis is still rife in Latin America, producing huge economic losses. There are very few studies of the way this disease is spread through this geographical region, particularly in countries that border those that are almost free of Mycobacterium bovis. In this work, we have analyzed the spacer oligonucleotide typing (spoligotype) patterns of M. bovis isolates from cattle at Ciudad Juárez, a Mexican city close to El Paso, Texas. Fifty-eight M. bovis isolates collected from a herd in Northern Mexico were studied by spoligotyping. Nine spoligotype patterns were observed in total. Two were predominant (SB0121 and SB0140) and accounted for 50% and 14% of the isolates, respectively. Six patterns were found to be already described in an international M. bovis spoligotype database, while the other three (SB0985, SB0986, and SB0987) were novel. Interestingly, none of the isolates corresponded to any other Mexican pattern previously reported. This is the first spoligotype analysis of M. bovis strains from a border city between Mexico and the United States. The necessity for further studies to formulate a better identification of M. bovis strains within, and its dissemination between, the two countries is discussed.Key words: Mycobacterium bovis, spoligotyping, bovine tuberculosis.
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Affiliation(s)
- Laura Cobos-Marín
- Department of Immunology, Escuela Nacional de Ciencias Biologicas, IPN. Prolongacion Carpio y Plan de Ayala s/n, Colonia Santo Tomas, Mexico, DF 11340, Mexico
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149
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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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150
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Goh KS, Rastogi N, Berchel M, Huard RC, Sola C. Molecular evolutionary history of tubercle bacilli assessed by study of the polymorphic nucleotide within the nitrate reductase (narGHJI) operon promoter. J Clin Microbiol 2005; 43:4010-4. [PMID: 16081943 PMCID: PMC1233921 DOI: 10.1128/jcm.43.8.4010-4014.2005] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A well-characterized collection of Mycobacterium tuberculosis complex (MTC) isolates, representing all known subspecies as well as some relevant genotypic families of M. tuberculosis, was analyzed for the newly discovered narGHJI -215 C-to-T promoter single-nucleotide polymorphism (SNP). This point mutation has been shown in earlier studies to be responsible for the differential nitrate reductase activity of M. tuberculosis versus M. bovis. As previously defined by the presence or the absence of the TbD1 genetic locus, the group included both the "modern" W-Beijing, Haarlem, and Central-Asian1 (CAS1) families as well as the "ancestral" East-African-Indian (EAI) clade. Interestingly, among "modern" M. tuberculosis isolates, those previously classified as Principal Genetic Group 1 (PGG1) organisms by katG463-gyrA95 polymorphism analysis did not present the two-banded narGHJI restriction fragment length polymorphism analysis of PCR products pattern common to the other PGG1 MTC members, including the "ancestral" M. tuberculosis isolates. Instead, they showed a one-banded pattern, aligning them with other evolutionarily recent M. tuberculosis isolates of the PGG2 and PGG3 groups, such as Haarlem, Latin-American and Mediterranean (LAM), and X families. The presence of a nitrate reductase producer phenotype in "Mycobacterium canettii" and some "ancestral" M. tuberculosis isolates, despite a two-band -215C genotype, argues in favor of an alternate mechanism to explain the differential nitrate reductase activity of certain PGG1 subspecies of the MTC. Overall, these findings may help to establish the precise evolutionary history of important genotype families such as W-Beijing and suggest that the -215T genotype may have contributed the virulence, spread, and evolutionary success of "modern" M. tuberculosis strains compared to the remaining MTC organisms.
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Affiliation(s)
- Khye Seng Goh
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York
- Corresponding authors. Mailing address: Institut Pasteur de Guadeloupe, Morne Jolivière, BP484, F97165-Pointe-à-Pitre, Guadeloupe. Phone: 590-590-893881. Fax: 590-590-893880. E-mail for N. Rastogi: . E-mail for C. Sola:
| | - Mylène Berchel
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York
| | - Richard C. Huard
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Pointe-à-Pitre, Guadeloupe, Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York
- Corresponding authors. Mailing address: Institut Pasteur de Guadeloupe, Morne Jolivière, BP484, F97165-Pointe-à-Pitre, Guadeloupe. Phone: 590-590-893881. Fax: 590-590-893880. E-mail for N. Rastogi: . E-mail for C. Sola:
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