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Briquet A, Vong R, Roseau JB, Javelle E, Cazes N, Rivière F, Aletti M, Otto MP, Ficko C, Duron S, Fabre M, Pourcel C, Simon F, Soler C. Clinical Features of Mycobacterium canettii Infection: A Retrospective Study of 20 Cases Among French Soldiers and Relatives. Clin Infect Dis 2020; 69:2003-2010. [PMID: 30753345 DOI: 10.1093/cid/ciz107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/31/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Mycobacterium canettii forms part of the Mycobacterium tuberculosis complex. Mycobacterium canettii infections are mainly described in the Horn of Africa. The permanent presence of French soldiers in Djibouti raises the question of the risk of being infected with M. canettii. Here, we describe M. canettii infections among French military and their families between 1998 and 2015. METHODS This retrospective study relied on 3 sources of data: the reference center for mycobacteria in the Biology Department at Percy Military Hospital in Paris, the French Military Center for Epidemiology and Public Health, and the scientific literature. After an exhaustive census of the strains, we studied the epidemiological data on 20 cases among French soldiers and their families. RESULTS Twenty cases of M. canettii infections are reported, including 5 unpublished cases. Adenitis predominates (n = 15), especially in the cervico facial area and among children; 1 case was observed 1 month after dental care in Djibouti. The pulmonary forms were less frequent (n = 6), and 3 atypical forms are described. All patients had stayed in Djibouti. CONCLUSIONS Cases of M. canettii infection among the French military consisted mainly of adenitis; disseminated forms were possible with immunodeficiency. Their evolution under specific treatments was comparable to that of tuberculosis. The presumed origin of the infection seemed to be environmental, possibly a water reservoir, and not due to human-to-human contagion.
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Affiliation(s)
- Anaïs Briquet
- Respiratory Department, Laveran Military Teaching Hospital, Marseille
| | - Rithy Vong
- Department of Biology, Percy Military Teaching Hospital, Clamart
| | | | - Emilie Javelle
- Department of Infectious Diseases, Laveran Military Teaching Hospital
| | - Nicolas Cazes
- Emergency Medical Department, Prehospital Emergency Medical Services of Marine Fire Battalion, Marseille
| | - Fréderic Rivière
- Respiratory Department, Percy Military Teaching Hospital, Clamart
| | - Marc Aletti
- Department of Infectious Diseases, Percy Military Teaching Hospital, Clamart
| | - Marie-Pierre Otto
- Department of Biology, Sainte-Anne Military Teaching Hospital, Toulon
| | - Cécile Ficko
- Department of Infectious Diseases, Bégin Military Teaching Hospital, Saint-Mandé l'Énergie Atomique, Centre National de la Recherche Scientifique, Univ. Paris Sud, Orsay, France
| | - Sandrine Duron
- French Military Center for Epidemiology and Public Health, Marseille
| | - Michel Fabre
- Department of Biology, Percy Military Teaching Hospital, Clamart
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), Commissariat á ľÉnergie Atomique, Centre National de la Recherche Scientifique, Univ. Paris Sud, Orsay, France
| | - Fabrice Simon
- Department of Infectious Diseases, Laveran Military Teaching Hospital
| | - Charles Soler
- Department of Biology, Percy Military Teaching Hospital, Clamart
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Havlicek J, Dachsel B, Slickers P, Andres S, Beckert P, Feuerriegel S, Niemann S, Merker M, Labugger I. Rapid microarray-based assay for detection of pyrazinamide resistant Mycobacterium tuberculosis. Diagn Microbiol Infect Dis 2018; 94:147-154. [PMID: 30733004 PMCID: PMC6531379 DOI: 10.1016/j.diagmicrobio.2018.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/17/2018] [Accepted: 12/24/2018] [Indexed: 01/25/2023]
Abstract
Pyrazinamide (PZA) is a key antibiotic for the treatment of drug susceptible tuberculosis. PZA-resistance is mainly mediated by mutations in the pncA gene; however the current gold standard is a phenotypic drug susceptibility test requiring a well-adjusted pH-value for reliable results. Our melting curve assay detects a non-wild type genotype in selected pncA regions in at least 3750 gene copies/mL within 2.5 hours. The prototype assay was further evaluated by analyzing 271 Mycobacterium tuberculosis complex isolates from Swaziland originating from a previously published drug resistance survey and including 118 isolates with pncA mutations. Sensitivity was 83% (95% CI 75-89%) and specificity was 100% (95% CI 98-100%). Under consideration of further improvements with regard to the target range our melting curve assay has the potential as a rapid rule-in test for PZA susceptibility (wild type pncA), however false resistant results (mutant pncA, but PZA susceptible) cannot be ruled out completely.
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Affiliation(s)
| | | | | | - Sönke Andres
- National Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Germany; German Center for Infection Research, Partner site Hamburg-Lübeck-, Borstel, -Riems, Germany.
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Bouzid F, Astier H, Osman DA, Javelle E, Hassan MO, Simon F, Garnotel E, Drancourt M. Extended spectrum of antibiotic susceptibility for tuberculosis, Djibouti. Int J Antimicrob Agents 2017; 51:235-238. [PMID: 28711677 DOI: 10.1016/j.ijantimicag.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/06/2017] [Accepted: 07/08/2017] [Indexed: 11/29/2022]
Abstract
In the Horn of Africa, there is a high prevalence of tuberculosis that is reported to be partly driven by multidrug-resistant (MDR) Mycobacterium tuberculosis strictu sensu strains. We conducted a prospective study to investigate M. tuberculosis complex species causing tuberculosis in Djibouti, and their in vitro susceptibility to standard anti-tuberculous antibiotics in addition to clofazimine, minocycline, chloramphenicol and sulfadiazine. Among the 118 mycobacteria isolates from 118 successive patients with suspected pulmonary tuberculosis, 111 strains of M. tuberculosis, five Mycobacterium canettii, one 'Mycobacterium simulans' and one Mycobacterium kansasii were identified. Drug-susceptibility tests performed on the first 78 isolates yielded nine MDR M. tuberculosis isolates. All isolates were fully susceptible to clofazimine, minocycline and chloramphenicol, and 75 of 78 isolates were susceptible to sulfadiazine. In the Horn of Africa, patients with confirmed pulmonary tuberculosis caused by an in vitro susceptible strain may benefit from anti-leprosy drugs, sulfamides and phenicol antibiotics.
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Affiliation(s)
- Fériel Bouzid
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille 13005, France; Aix-Marseille Univ, CNRS, EIPL, Marseille, France
| | - Hélène Astier
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Djaltou Aboubaker Osman
- Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Djibouti
| | - Emilie Javelle
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | | | - Fabrice Simon
- Pôle Formation-Recherche, Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Eric Garnotel
- Hôpital d'instruction des armées Alphonse Laveran, Marseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée Infection, Marseille 13005, France.
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Aboubaker Osman D, Bouzid F, Canaan S, Drancourt M. Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens. Front Public Health 2016; 3:283. [PMID: 26793699 PMCID: PMC4707939 DOI: 10.3389/fpubh.2015.00283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Smooth tubercle bacilli (STB) including “Mycobacterium canettii” are members of the Mycobacterium tuberculosis complex (MTBC), which cause non-contagious tuberculosis in human. This group comprises <100 isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa, and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes, which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Republic of Djibouti
| | - Feriel Bouzid
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille, France
| | - Stéphane Canaan
- Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université , Marseille , France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095 , Marseille , France
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Ueyama M, Chikamatsu K, Aono A, Murase Y, Kuse N, Morimoto K, Okumura M, Yoshiyama T, Ogata H, Yoshimori K, Kudoh S, Azuma A, Gemma A, Mitarai S. Sub-speciation of Mycobacterium tuberculosis complex from tuberculosis patients in Japan. Tuberculosis (Edinb) 2013; 94:15-9. [PMID: 24183617 DOI: 10.1016/j.tube.2013.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/27/2013] [Accepted: 09/27/2013] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis is the major causative agent of tuberculosis in humans. It is well known that Mycobacterium bovis and other species in the M. tuberculosis complex (MTC) can cause respiratory diseases as zoonosis. We analyzed the MTC isolates collected from tuberculosis patients from Japan in 2002 using a multiplex PCR system that detected cfp32, RD9 and RD12. A total of 970 MTC isolates that were representative of the tuberculosis cases throughout Japan, were examined using this method. As a result, 966 (99.6%) M. tuberculosis, two Mycobacterium africanum and two Mycobacterium canettii were identified using a multiplex PCR system, while no M. bovis was detected. Two isolates that lacked RD9 were initially considered to be M. canettii, but further analysis of the hsp65 sequence revealed them to be M. tuberculosis. Also two M. africanum were identified as M. tuberculosis using the -215 narG nucleotide polymorphism. Though PCR-linked methods have been used for a rapid differentiation of MTC and NTM, from our cases we suggest careful interpretation of RD based identification.
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Affiliation(s)
- Masako Ueyama
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
| | - Kinuyo Chikamatsu
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Akio Aono
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Yoshiro Murase
- Molecular Epidemiology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
| | - Naoyuki Kuse
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Kozo Morimoto
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masao Okumura
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Takashi Yoshiyama
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Hideo Ogata
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Kozo Yoshimori
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan; Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Shoji Kudoh
- Department of Respiratory Medicine, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Japan
| | - Arata Azuma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Akihiko Gemma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Satoshi Mitarai
- Bacteriology Division, Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Japan
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Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother 2012; 56:6080-7. [PMID: 23006760 DOI: 10.1128/aac.01641-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.
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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: 31] [Impact Index Per Article: 2.4] [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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Reddington K, O'Grady J, Dorai-Raj S, Maher M, van Soolingen D, Barry T. Novel multiplex real-time PCR diagnostic assay for identification and differentiation of Mycobacterium tuberculosis, Mycobacterium canettii, and Mycobacterium tuberculosis complex strains. J Clin Microbiol 2011; 49:651-7. [PMID: 21123525 PMCID: PMC3043491 DOI: 10.1128/jcm.01426-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/19/2010] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) in humans is caused by members of the Mycobacterium tuberculosis complex (MTC). Rapid detection of the MTC is necessary for the timely initiation of antibiotic treatment, while differentiation between members of the complex may be important to guide the appropriate antibiotic treatment and provide epidemiological information. In this study, a multiplex real-time PCR diagnostics assay using novel molecular targets was designed to identify the MTC while simultaneously differentiating between M. tuberculosis and M. canettii. The lepA gene was targeted for the detection of members of the MTC, the wbbl1 gene was used for the differentiation of M. tuberculosis and M. canettii from the remainder of the complex, and a unique region of the M. canettii genome, a possible novel region of difference (RD), was targeted for the specific identification of M. canettii. The multiplex real-time PCR assay was tested using 125 bacterial strains (64 MTC isolates, 44 nontuberculosis mycobacteria [NTM], and 17 other bacteria). The assay was determined to be 100% specific for the mycobacteria tested. Limits of detection of 2.2, 2.17, and 0.73 cell equivalents were determined for M. tuberculosis/M. canettii, the MTC, and M. canettii, respectively, using probit regression analysis. Further validation of this diagnostics assay, using clinical samples, should demonstrate its potential for the rapid, accurate, and sensitive diagnosis of TB caused by M. tuberculosis, M. canettii, and the other members of the MTC.
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Affiliation(s)
- Kate Reddington
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Justin O'Grady
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Siobhan Dorai-Raj
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Majella Maher
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Thomas Barry
- Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland
- Molecular Diagnostics Research Group, NCBES, National University of Ireland, Galway, Ireland
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Fabre M, Hauck Y, Soler C, Koeck JL, van Ingen J, van Soolingen D, Vergnaud G, Pourcel C. Molecular characteristics of "Mycobacterium canettii" the smooth Mycobacterium tuberculosis bacilli. INFECTION GENETICS AND EVOLUTION 2010; 10:1165-73. [PMID: 20692377 DOI: 10.1016/j.meegid.2010.07.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
Since the first discovery of the smooth tubercle (SmTB) bacilli "Mycobacterium canettii" less than 60 isolates have been reported, all but one originating from a limited geographical location, the Horn of Africa. In spite of its rarity, the SmTB lineage deserves special attention. Previous investigations suggested that SmTB isolates represent an ancestral lineage of the Mycobacterium tuberculosis complex (MTBC) and that consequently they might provide essential clues on the origin and evolution of the MTBC. There is evidence that unlike the rest of the MTBC, SmTB strains recombine chromosomal sequences with a yet unknown Mycobacterium species. This behavior contributes to the much larger genetic heterogeneity observed in the SmTB isolates compared to the other members of the MTBC. We have collected 59 SmTB isolates of which 14 were newly recovered since previous reports, and performed extensive phenotypical and genotypical characterization. We take advantage of these investigations to review the current knowledge of "M. canettii". Their characteristics and the apparent lack of human to human transmission are consistent with the previously proposed existence of non-human sources of infection. SmTB strains show remarkably common features together with secondary and taxonomically minor genetic differences such as the presence or absence of the CRISPR (Clustered Regularly Interspersed Palindromic Repeat) locus (usually called Direct Repeat or DR region) or number of IS sequences. Multiple Locus Variable number of tandem repeat Analysis (MLVA) and DR region analyses reveal one predominant clone, one minor clone and a number of more distantly related strains. This suggests that the two most frequent clones may represent successfully emerging lineages.
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Affiliation(s)
- Michel Fabre
- Laboratoire de biologie clinique, HIA Percy, Clamart, France
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Nakajima C, Rahim Z, Fukushima Y, Sugawara I, van der Zanden AGM, Tamaru A, Suzuki Y. Identification of Mycobacterium tuberculosis clinical isolates in Bangladesh by a species distinguishable multiplex PCR. BMC Infect Dis 2010; 10:118. [PMID: 20470432 PMCID: PMC2877677 DOI: 10.1186/1471-2334-10-118] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 05/15/2010] [Indexed: 11/21/2022] Open
Abstract
Background Species identification of isolates belonging to the Mycobacterium tuberculosis complex (MTC) seems to be important for the appropriate treatment of patients, since M. bovis is naturally resistant to a first line anti-tuberculosis (TB) drug, pyrazinamide, while most of the other MTC members are susceptible to this antimicrobial agent. A simple and low-cost differentiation method was needed in higher TB burden countries, such as Bangladesh, where the prevalence of M. bovis among people or cattle has not been investigated. Methods Genetic regions cfp32, RD9 and RD12 were chosen as targets for a species distinguishable multiplex PCR and the system was evaluated with twenty reference strains of mycobacterial species including non-tubercular mycobacteria (NTM). A total of 350 clinical MTC isolates obtained in Bangladesh were then analyzed with this multiplex PCR. Results All of the MTC reference strains gave expected banding patterns and no non-specific amplifications were observed in the NTM strains. Out of 350 clinical isolates examined by this method, 347 (99.1%) were positive for all of the cfp32, RD9 and RD12 and determined as M. tuberculosis. Two isolates lacked cfp32 PCR product and one lacked RD12, however, those three samples were further examined and identified as M. tuberculosis by the sequence analyses of hsp65 and gyrB. Conclusions The MTC-discrimination multiplex PCR (MTCD-MPCR) developed in this study showed high specificity and was thought to be very useful as a routine test because of its simplicity. In the current survey, all the 350 MTC isolates obtained from Bangladesh TB patients were determined as M. tuberculosis and no other MTC were detected. This result suggested the general TB treatment regimen including pyrazinamide to be the first choice in Bangladesh.
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Affiliation(s)
- Chie Nakajima
- Department of Global Epidemiology, Hokkaido University Research Center for Zoonosis Control, Kita-ku, Sapporo, Japan.
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11
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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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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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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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15
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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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16
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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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17
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Development of multiplex assay for rapid characterization of Mycobacterium tuberculosis. J Clin Microbiol 2007; 46:689-99. [PMID: 18077627 DOI: 10.1128/jcm.01821-07] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have developed a multiplex assay, based on multiplex ligation-dependent probe amplification (MLPA), that allows simultaneous detection of multiple drug resistance mutations and genotype-specific mutations at any location in the Mycobacterium tuberculosis genome. The assay was validated on a reference panel of well-characterized strains, and the results show that M. tuberculosis can be accurately characterized by our assay. Eighteen discriminatory markers identifying drug resistance (rpoB, katG, inhA, embB), members of the M. tuberculosis complex (16S rRNA, IS6110, TbD1), the principal genotypic group (katG, gyrA), and Haarlem and Beijing strains (ogt, mutT2, mutT4) were targeted. A sequence specificity of 100% was reached for 16 of the 18 selected genetic targets. In addition, a panel of 47 clinical M. tuberculosis isolates was tested by MLPA in order to determine the correlation between phenotypic drug resistance and MLPA and between spoligotyping and MLPA. Again, all mutations present in these isolates that were targeted by the 16 functional probes were identified. Resistance-associated mutations were detected by MLPA in 71% of the identified rifampin-resistant strains and in 80% of the phenotypically isoniazid-resistant strains. Furthermore, there was a perfect correlation between MLPA results and spoligotypes. When MLPA is used on confirmed M. tuberculosis clinical specimens, it can be a useful and informative instrument to aid in the detection of drug resistance, especially in laboratories where drug susceptibility testing is not common practice and where the rates of multidrug-resistant and extensively drug resistant tuberculosis are high. The flexibility and specificity of MLPA, along with the ability to simultaneously genotype and detect drug resistance mutations, make MLPA a promising tool for pathogen characterization.
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18
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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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19
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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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20
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Marsh IB, Whittington RJ. Genomic diversity in Mycobacterium avium: single nucleotide polymorphisms between the S and C strains of M. avium subsp. paratuberculosis and with M. a. avium. Mol Cell Probes 2006; 21:66-75. [PMID: 17049206 DOI: 10.1016/j.mcp.2006.08.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Revised: 07/26/2006] [Accepted: 08/03/2006] [Indexed: 11/29/2022]
Abstract
Following identification of large genomic polymorphisms in a previous study, a polymerase chain reaction and sequencing strategy was used to identify single nucleotide polymorphisms (SNPs) in 25 genes in the sheep (S) and cattle (C) strains of Mycobacterium avium subsp. paratuberculosis (M. a. paratuberculosis) and between M. a. paratuberculosis and M. a. avium. From 12,117 bp of sequence representing 26 loci across 25 genes, 11 SNPs were identified between the S and C strains in eight genes: hsp65, sodA, dnaA, dnaN, recF, gyrB, inhA, and pks8. An in silico comparison of these M. a. paratuberculosis sequences and the M. a. avium 104 genome revealed 86 SNPs, which corresponded well with similar studies of SNPs in the M. avium complex.
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Affiliation(s)
- I B Marsh
- Faculty of Veterinary Science, University of Sydney, Private Bag 3, Camden NSW 2570, Australia.
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21
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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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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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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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Arnold C, Westland L, Mowat G, Underwood A, Magee J, Gharbia S. Single-nucleotide polymorphism-based differentiation and drug resistance detection in Mycobacterium tuberculosis from isolates or directly from sputum. Clin Microbiol Infect 2005; 11:122-30. [PMID: 15679486 DOI: 10.1111/j.1469-0691.2004.01034.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The rapid technique of pyrosequencing was used to examine 123 samples (in the form of DNA extracts and inactivated sputum) of Mycobacterium spp. Of 99 Mycobacterium tuberculosis samples investigated for single-nucleotide polymorphisms (SNPs), 68% of isoniazid-resistant isolates analysed had an AGC --> ACC mutation in katG at codon 315, resulting in the Ser --> Thr substitution associated previously with isoniazid resistance. Of the rifampicin-resistant isolates, 92% showed SNPs in rpoB at codons 516, 531 or 526. Inactivated sputum samples and DNA extracts could both be analysed by pyrosequencing, and the method was able to differentiate rapidly between the closely related species of the M. tuberculosis complex (M. tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium canetti and Mycobacterium microti), except between M. tuberculosis, M. canetti and one of two M. africanum strains. This low-cost, high-throughput technique could be used as a rapid screen for drug resistance and as a replacement for some of the time-consuming tests used currently for species identification.
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Affiliation(s)
- C Arnold
- Genomics, Proteomics and Bioinformatics Unit, Centre for Infections, Health Protection Agency, London, UK.
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Shamputa IC, Rigouts And L, Portaels F. Molecular genetic methods for diagnosis and antibiotic resistance detection of mycobacteria from clinical specimens. APMIS 2004; 112:728-52. [PMID: 15638836 DOI: 10.1111/j.1600-0463.2004.apm11211-1203.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mycobacteria comprise a diverse group of bacteria that are widespread in nature, some of which cause significant disease in humans. Members of the Mycobacterium tuberculosis complex (MTBC) are the most important human pathogens of the genus Mycobacterium. Traditional methods for detection and identification of mycobacteria include microscopy, culture and phenotypic tests. These methods either lack sensitivity, specificity, or are time consuming. Advances in the field of molecular biology have provided rapid diagnostic tools that have reduced the turnaround times for detecting MTBC and drug resistance in cultures and directly in clinical specimens from weeks to days. This review discusses the molecular genetic techniques for detecting and identifying MTBC as well as drug resistance of mycobacteria in clinical specimens.
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Affiliation(s)
- I C Shamputa
- Mycobacteriology Unit, Department of Microbiology, Institute of Tropical Medicine, Antwerp, Belgium
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Fabre M, Koeck JL, Le Flèche P, Simon F, Hervé V, Vergnaud G, Pourcel C. High genetic diversity revealed by variable-number tandem repeat genotyping and analysis of hsp65 gene polymorphism in a large collection of "Mycobacterium canettii" strains indicates that the M. tuberculosis complex is a recently emerged clone of "M. canettii". J Clin Microbiol 2004; 42:3248-55. [PMID: 15243089 PMCID: PMC446256 DOI: 10.1128/jcm.42.7.3248-3255.2004] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have analyzed, using complementary molecular methods, the diversity of 43 strains of "Mycobacterium canettii" originating from the Republic of Djibouti, on the Horn of Africa, from 1998 to 2003. Genotyping by multiple-locus variable-number tandem repeat analysis shows that all the strains belong to a single but very distant group when compared to strains of the Mycobacterium tuberculosis complex (MTBC). Thirty-one strains cluster into one large group with little variability and five strains form another group, whereas the other seven are more diverged. In total, 14 genotypes are observed. The DR locus analysis reveals additional variability, some strains being devoid of a direct repeat locus and others having unique spacers. The hsp65 gene polymorphism was investigated by restriction enzyme analysis and sequencing of PCR amplicons. Four new single nucleotide polymorphisms were discovered. One strain was characterized by three nucleotide changes in 441 bp, creating new restriction enzyme polymorphisms. As no sequence variability was found for hsp65 in the whole MTBC, and as a single point mutation separates M. tuberculosis from the closest "M. canettii" strains, this diversity within "M. canettii" subspecies strongly suggests that it is the most probable source species of the MTBC rather than just another branch of the MTBC.
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Affiliation(s)
- Michel Fabre
- Laboratoire de Mycobactériologie, HIA Percy, HIA Val de Grâce, France
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Hugard L, Dubrous P, Massoure PL, Renoux E, Désèmerie F. Mycobacterium canettii chez un tuberculeux ayant séjourné en Afrique. Med Mal Infect 2004; 34:142-3. [PMID: 15617357 DOI: 10.1016/j.medmal.2003.12.005] [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: 10/26/2022]
Affiliation(s)
- L Hugard
- Laboratoire de biologie médicale, hôpital d'instruction des armées Robert-Picqué, BP 28, 33998 Bordeaux armées, France.
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Huard RC, Lazzarini LCDO, Butler WR, van Soolingen D, Ho JL. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 2003; 41:1637-50. [PMID: 12682155 PMCID: PMC153936 DOI: 10.1128/jcm.41.4.1637-1650.2003] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The classical Mycobacterium tuberculosis complex (MtbC) subspecies include Mycobacterium tuberculosis, Mycobacterium africanum (subtypes I and II), Mycobacterium bovis (along with the attenuated M. bovis bacillus Calmette-Guérin [BCG]), and Mycobacterium microti; increasingly recognized MtbC groupings include Mycobacterium bovis subsp. caprae and "Mycobacterium tuberculosis subsp. canettii." Previous investigations have documented each MtbC subspecies as a source of animal and/or human tuberculosis. However, study of these organisms is hindered by the lack of a single protocol that quickly and easily differentiates all of the MtbC groupings. Towards this end we have developed a rapid, simple, and reliable PCR-based MtbC typing method that makes use of MtbC chromosomal region-of-difference deletion loci. Here, seven primer pairs (which amplify within the loci 16S rRNA, Rv0577, IS1561', Rv1510, Rv1970, Rv3877/8, and Rv3120) were run in separate but simultaneous reactions. Each primer pair either specifically amplified a DNA fragment of a unique size or failed, depending upon the source mycobacterial DNA. The pattern of amplification products from all of the reactions, visualized by agarose gel electrophoresis, allowed immediate identification either as MtbC composed of M. tuberculosis (or M. africanum subtype II), M. africanum subtype I, M. bovis, M. bovis BCG, M. caprae, M. microti, or "M. canettii" or as a Mycobacterium other than MtbC (MOTT). This MtbC PCR typing panel provides an advanced approach to determine the subspecies of MtbC isolates and to differentiate them from clinically important MOTT species. It has proven beneficial in the management of Mycobacterium collections and may be applied for practical clinical and epidemiological use.
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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, New York, New York 10021, USA
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Tortoli E. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 2003; 16:319-54. [PMID: 12692101 PMCID: PMC153139 DOI: 10.1128/cmr.16.2.319-354.2003] [Citation(s) in RCA: 343] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Center for Mycobacteria, Microbiological and Virological Laboratory, Careggi Hospital, 50134 Florence, Italy.
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