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Oryan A, Yazdi HS, Alidadi S, Doostmohammadi S. Use of a gyrB PCR-RFLP method to diagnose tuberculosis and identify the causative Mycobacterium sp. in cattle and humans. Comp Immunol Microbiol Infect Dis 2022; 82:101767. [PMID: 35180476 DOI: 10.1016/j.cimid.2022.101767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 10/19/2022]
Abstract
GyrB PCR-restriction fragment length polymorphism (RFLP) could be applied to diagnose bovine and human tuberculosis and detect the causative agent. The lymph nodes and lungs from 50 cattle positive in tuberculin skin test were examined by histopathology and PCR-RFLP of a 1020-bp fragment of the gyrB gene. Swab smear samples from the nasal cavity, pleural, and abdominal cavities were also evaluated by cytological methods. Furthermore, the cultures of 50 sputum samples from the patients were assessed by PCR-RFLP using RsaI, TaqI, SacII enzymes. In histopathology, 39 cattle were positive and the acid-fast bacilli were seen in the Ziehl-Neelsen stained sections. Using gyrB PCR-RFLP, M. bovis was found as the etiological agent in 41 cattle. In terms of the human samples, the causative agent in 41 samples was M. tuberculosis, and M. bovis was isolated from two samples. It seems that gyrB PCR-RFLP could be applied as an accurate and reliable method for identifying the M. tuberculosis complex (MBTC) MBTC species. The isolation of M. bovis from the human specimens should be considered in the control strategies for tuberculosis.
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Affiliation(s)
- Ahmad Oryan
- Department of Pathology, School of Veterinary Medicine, Shiraz University, Shiraz, Iran.
| | - Hassan Sharifi Yazdi
- Department of Clinical Sciences, School of Veterinary Medicine, Shiraz University, Shiraz, Iran
| | - Soodeh Alidadi
- Department of Pathology, School of Veterinary Medicine, Ferdowsi University, Mashhad, Iran
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2
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Aboubaker Osman D, Garnotel E, Drancourt M. Dry-heat inactivation of "Mycobacterium canettii". BMC Res Notes 2017; 10:201. [PMID: 28599677 PMCID: PMC5466745 DOI: 10.1186/s13104-017-2522-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 05/31/2017] [Indexed: 12/27/2022] Open
Abstract
Objective “Mycobacterium canettii” is responsible for non-transmissible lymph node and pulmonary tuberculosis in persons exposed in the Horn of Africa. In the absence of direct human transmission, contaminated water and foodstuffs could be sources of contamination. We investigated the dry-heat inactivation of “M. canettii” alone and mixed into mock-infected foodstuffs by inoculating agar cylinders and milk with 104 colony-forming units of “M. canettii” CIPT140010059 and two “M. canettii” clinical strains with Mycobacterium tuberculosis H37Rv as a control. Results Exposed to 35 °C, M. tuberculosis H37Rv, “M canettii” CIPT140010059 and “M. canettii” 157 exhibited a survival rate of 108, 95 and 81%, which is significantly higher than that of “M. canettii” 173. However, all tested mycobacteria tolerated a 90-min exposure at 45 °C. In the foodstuff models set at 70 °C, no growing mycobacteria were visualized. This study supports the premise that “M. canettii” may survive up to 45 °C; and suggests that contaminated raw drinks and foodstuffs but not cooked ones may be sources of infection for populations.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. IHU Méditerranée Infection, 13005, Marseille, France.,Institut de Recherche Médicinale (IRM), Centre d'Études et de Recherche de Djibouti (CERD), Djibouti, Djibouti
| | - Eric Garnotel
- Hopital d'Instruction des Armées LAVERAN, 34 Boulevard Laveran, 13384, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095. IHU Méditerranée Infection, 13005, Marseille, France.
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Trubitsyn IV, Belousova EV, Tutukina MN, Merkel AY, Dubinina GA, Grabovich MY. Expansion of ability of denitrification within the filamentous colorless sulfur bacteria of the genusThiothrix. FEMS Microbiol Lett 2014; 358:72-80. [DOI: 10.1111/1574-6968.12548] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 11/28/2022] Open
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Rodriguez-Campos S, Smith NH, Boniotti MB, Aranaz A. Overview and phylogeny of Mycobacterium tuberculosis complex organisms: implications for diagnostics and legislation of bovine tuberculosis. Res Vet Sci 2014; 97 Suppl:S5-S19. [PMID: 24630673 DOI: 10.1016/j.rvsc.2014.02.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/04/2014] [Accepted: 02/15/2014] [Indexed: 10/25/2022]
Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) cause a serious disease with similar pathology, tuberculosis; in this review, bovine tuberculosis will be considered as disease caused by any member of the MTBC in bovids. Bovine tuberculosis is responsible for significant economic loss due to costly eradication programs and trade limitations and poses a threat to both endangered and protected species as well as to public health. We here give an overview on all members of the MTBC, focusing on their isolation from different animal hosts. We also review the recent advances made in elucidating the evolutionary and phylogenetic relationships of members of the MTBC. Because the nomenclature of the MTBC is controversial, its members have been considered species, subspecies or ecotypes, this review discusses the possible implications for diagnostics and the legal consequences of naming of new species.
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Affiliation(s)
- Sabrina Rodriguez-Campos
- Institute of Veterinary Bacteriology, Veterinary Faculty, University of Bern, Laenggassstrasse 122, 3012 Bern, Switzerland.
| | - Noel H Smith
- Animal Health and Veterinary Laboratories Agency, Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK
| | - Maria B Boniotti
- Centro Nazionale di Referenza per la Tubercolosi Bovina, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, via Bianchi 9, 25124 Brescia, Italy
| | - Alicia Aranaz
- Departamento de Sanidad Animal, Veterinary Faculty, Universidad Complutense de Madrid, Avda. Puerta de Hiero s/n, 28040 Madrid, Spain
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Coscolla M, Lewin A, Metzger S, Maetz-Rennsing K, Calvignac-Spencer S, Nitsche A, Dabrowski PW, Radonic A, Niemann S, Parkhill J, Couacy-Hymann E, Feldman J, Comas I, Boesch C, Gagneux S, Leendertz FH. Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee. Emerg Infect Dis 2013; 19:969-76. [PMID: 23735084 PMCID: PMC3713819 DOI: 10.3201/eid1906.121012] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) is caused by gram-positive bacteria known as the Mycobacterium tuberculosis complex (MTBC). MTBC include several human-associated lineages and several variants adapted to domestic and, more rarely, wild animal species. We report an M. tuberculosis strain isolated from a wild chimpanzee in Côte d’Ivoire that was shown by comparative genomic and phylogenomic analyses to belong to a new lineage of MTBC, closer to the human-associated lineage 6 (also known as M. africanum West Africa 2) than to the other classical animal-associated MTBC strains. These results show that the general view of the genetic diversity of MTBC is limited and support the possibility that other MTBC variants exist, particularly in wild mammals in Africa. Exploring this diversity is crucial to the understanding of the biology and evolutionary history of this widespread infectious disease.
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Affiliation(s)
- Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland
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Almeida LA, Araujo R. Highlights on molecular identification of closely related species. INFECTION GENETICS AND EVOLUTION 2012; 13:67-75. [PMID: 22982158 DOI: 10.1016/j.meegid.2012.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 10/27/2022]
Abstract
The term "complex" emerged in the literature at the beginning of the genomic era associated to taxonomy and grouping organisms that belong to different species but exhibited similar patterns according to their morphological, physiological and/or other phenotypic features. DNA-DNA hybridization values ~70% and high identity on 16S rRNA gene sequences were recommended for species delineation. Electrophoretic methods showed in some cases to be useful for species identification and population structure but the reproducibility was questionable. Later, the implementation of polyphasic approaches involving phenotypic and molecular methods brought new insights into the analysis of population structure and phylogeny of several "species complexes", allowing the identification of new closely related species. Likewise, the introduction of multilocus sequence typing and sequencing analysis of several genes offered an evolutionary perspective to the term "species complex". Several centres worldwide have recently released increasing genetic information on distinct microbial species. A brief review will be presented to highlight the definition of "species complex" for selected microorganisms, mainly the prokaryotic Acinetobacter calcoaceticus -Acinetobacter baumannii, Borrelia burgdorferi sensu lato, Burkholderia cepacia, Mycobacterium tuberculosis and Nocardia asteroides complexes, and the eukaryotic Aspergillus fumigatus, Leishmania donovani and Saccharomyces sensu stricto complexes. The members of these complexes may show distinct epidemiology, pathogenicity and susceptibility, turning critical their correct identification. Dynamics of prokaryotic and eukaryotic genomes can be very distinct and the term "species complex" should be carefully extended.
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Affiliation(s)
- Lígia A Almeida
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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Castellanos E, Juan LD, Domínguez L, Aranaz A. Progress in molecular typing of Mycobacterium avium subspecies paratuberculosis. Res Vet Sci 2012; 92:169-79. [DOI: 10.1016/j.rvsc.2011.05.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Revised: 05/08/2011] [Accepted: 05/21/2011] [Indexed: 10/18/2022]
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Matrix-assisted laser desorption ionization-time of flight mass spectrometry-based single nucleotide polymorphism genotyping assay using iPLEX gold technology for identification of Mycobacterium tuberculosis complex species and lineages. J Clin Microbiol 2011; 49:3292-9. [PMID: 21734028 DOI: 10.1128/jcm.00744-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major goal of the present study was to investigate the potential use of a novel single nucleotide polymorphism (SNP) genotyping technology, called iPLEX Gold (Sequenom), for the simultaneous analysis of 16 SNPs that have been previously validated as useful for identification of Mycobacterium tuberculosis complex (MTBC) species and classification of MTBC isolates into distinct genetic lineages, known as principal genetic groups (PGGs) and SNP cluster groups (SCGs). In this context, we developed a 16-plex iPLEX assay based on an allele-specific-primer single-base-extension reaction using the iPLEX Gold kit (Sequenom), followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis on the commercially available Sequenom MassARRAY platform. This assay was tested on a panel of 55 well-characterized MTBC strains that were also genotyped for the same loci using the previously reported SNaPshot assay, as well as 10 non-MTBC mycobacteria and 4 bacteria not belonging to the genus Mycobacterium. All MTBC samples were successfully analyzed with the iPLEX assay, which yielded clear allelic data for 99.9% of the SNPs (879 out of 880). No false-positive results were obtained with the negative controls. Compared to the SNaPshot assay, the newly developed 16-plex iPLEX assay produced fully concordant results that allowed reliable differentiation of MTBC species and recognition of lineages, thus demonstrating its potential value in diagnostic, epidemiological, and evolutionary applications. Compared to the SNaPshot approach, the implementation of the iPLEX technology could offer a higher throughput and could be a more flexible and cost-effective option for microbiology laboratories.
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Marianelli C, Cifani N, Capucchio MT, Fiasconaro M, Russo M, La Mancusa F, Pasquali P, Di Marco V. A case of generalized bovine tuberculosis in a sheep. J Vet Diagn Invest 2010; 22:445-8. [PMID: 20453224 DOI: 10.1177/104063871002200319] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The present report describes a rare case of generalized bovine-type tuberculosis in a slaughtered 4-year-old ewe discovered during routine surveillance at an abattoir. A postmortem examination revealed lesions in the ewe's thoracic and abdominal cavities, ranging from encapsulated, mineralized foci to extensive, soft, caseous tissue. Lesions in the lungs, liver, and lymph nodes were consistent with mycobacterial infection. A histopathological examination detected granulomatous lesions in all tissue samples. The presence of Mycobacterium tuberculosis complex genome was confirmed through a polymerase chain reaction (PCR) analysis of tissues, using IS6110 primers, followed by a nucleotide sequence analysis of PCR products. Acid-fast bacteria, characterized as Mycobacterium bovis, were isolated from lesions following 38 days of incubation.
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Affiliation(s)
- Cinzia Marianelli
- Department of Food Safety and Veterinary Public Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.
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Goh KS, Rastogi N. Simple and rapid method for detection of nitrate reductase activity of Mycobacterium tuberculosis and Mycobacterium canettii grown in the Bactec MGIT960 system. J Microbiol Methods 2010; 81:208-10. [PMID: 20298726 DOI: 10.1016/j.mimet.2010.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 02/23/2010] [Accepted: 03/04/2010] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis reduces nitrate very strongly as compared to Mycobacterium bovis and M. bovis BCG. Nitrate reductase, in conjunction with niacin accumulation, constitutes one of the major biochemical tests used in clinical microbiology laboratories to differentiate M. tuberculosis from other members of the M. tuberculosis complex, as well as nontuberculous Mycobacteria. Determination of nitrate reductase activity is currently performed using cultures grown on solid media with a slow detection time and the need for large quantities of bacilli, as otherwise the test is not reliable. Hereby, we propose a nitrate reduction test coupled to Bactec MGIT960 system as a simple, rapid and economic method with a total gain of time of about 3 to 4weeks over the conventional solid medium. In our study, almost all the M. tuberculosis and Mycobacterium canettii strains gave a strongly positive nitrate reductase result within 1day of positive detection by the MGIT960 system. In contrast, M. bovis, M. bovis BCG and M. africanum strains remained negative even after 14days of incubation. The possibility to detect nitrate reductase within 1 to 3days of a positive culture using MGIT960 opens new perspectives with the possibility of confirming M. tuberculosis - starting directly from pathological specimens.
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Affiliation(s)
- Khye Seng Goh
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Abymes, Guadeloupe
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Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-based assay. J Clin Microbiol 2010; 48:1758-66. [PMID: 20220173 DOI: 10.1128/jcm.02255-09] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The aim of the present study was to investigate the use of the SNaPshot minisequencing method for the identification of Mycobacterium tuberculosis complex (MTBC) isolates to the species level and for further genotyping of M. tuberculosis isolates. We developed an innovative strategy based on two multiplex allele-specific minisequencing assays that allowed detection of eight species-specific and eight lineage-specific single nucleotide polymorphisms (SNPs). Each assay consisted of an eightplex PCR amplification, followed by an eightplex minisequencing reaction with the SNaPshot multiplex kit (Applied Biosystems) and, finally, analysis of the extension products by capillary electrophoresis. The whole strategy was developed with a panel of 56 MTBC strains and 15 negative controls. All MTBC strains tested except one M. africanum clinical isolate were accurately identified to the species level, and all M. tuberculosis isolates were successfully further genotyped. This two-step strategy based on SNaPshot minisequencing allows the simultaneous differentiation of closely related members of the MTBC, the distinction between principal genetic groups, and the characterization of M. tuberculosis isolates into one of the seven prominent SNP cluster groups (SCGs) and could be a useful tool for diagnostic and epidemiological purposes.
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Palomino JC. Molecular detection, identification and drug resistance detection inMycobacterium tuberculosis: Table 1. ACTA ACUST UNITED AC 2009; 56:103-11. [DOI: 10.1111/j.1574-695x.2009.00555.x] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Insights into the evolutionary history of tubercle bacilli as disclosed by genetic rearrangements within a PE_PGRS duplicated gene pair. BMC Evol Biol 2006; 6:107. [PMID: 17163995 PMCID: PMC1762029 DOI: 10.1186/1471-2148-6-107] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 12/12/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The highly homologous PE_PGRS (Proline-glutamic acid_polymorphic GC-rich repetitive sequence) genes are members of the PE multigene family which is found only in mycobacteria. PE genes are particularly abundant within the genomes of pathogenic mycobacteria where they seem to have expanded as a result of gene duplication events. PE_PGRS genes are characterized by their high GC content and extensive repetitive sequences, making them prone to recombination events and genetic variability. RESULTS Comparative sequence analysis of Mycobacterium tuberculosis genes PE_PGRS17 (Rv0978c) and PE_PGRS18 (Rv0980c) revealed a striking genetic variation associated with this typical tandem duplicate. In comparison to the M. tuberculosis reference strain H37Rv, the variation (named the 12/40 polymorphism) consists of an in-frame 12-bp insertion invariably accompanied by a set of 40 single nucleotide polymorphisms (SNPs) that occurs either in PE_PGRS17 or in both genes. Sequence analysis of the paralogous genes in a representative set of worldwide distributed tubercle bacilli isolates revealed data which supported previously proposed evolutionary scenarios for the M. tuberculosis complex (MTBC) and confirmed the very ancient origin of "M. canettii" and other smooth tubercle bacilli. Strikingly, the identified polymorphism appears to be coincident with the emergence of the post-bottleneck successful clone from which the MTBC expanded. Furthermore, the findings provide direct and clear evidence for the natural occurrence of gene conversion in mycobacteria, which appears to be restricted to modern M. tuberculosis strains. CONCLUSION This study provides a new perspective to explore the molecular events that accompanied the evolution, clonal expansion, and recent diversification of tubercle bacilli.
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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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