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Hendrix J, Epperson LE, Durbin D, Honda JR, Strong M. Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates. Microb Genom 2021; 7:mgen000497. [PMID: 33355531 PMCID: PMC8115904 DOI: 10.1099/mgen.0.000497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 12/02/2020] [Indexed: 01/13/2023] Open
Abstract
Mycobacterium kubicae is 1 of nearly 200 species of nontuberculous mycobacteria (NTM), environmental micro-organisms that in some situations can infect humans and cause severe lung, skin and soft tissue infections. Although numerous studies have investigated the genetic variation among prevalent clinical NTM species, including Mycobacterium abscessus and Mycobacterium avium, many of the less common but clinically relevant NTM species, including M. kubicae, still lack complete genomes to serve as a comparative reference. Well-characterized representative genomes for each NTM species are important both for investigating the pathogenic potential of NTM, as well as for use in diagnostic methods, even for species that less frequently cause human disease. Here, we report the complete genomes of two M. kubicae strains, isolated from two unrelated patients. Hybrid short-read and long-read sequencing and assembly, using sequence reads from Illumina and Oxford Nanopore Technologies platforms, were utilized to resolve the chromosome and plasmid sequences of each isolate. The genome of NJH_MKUB1 had 5135 coding sequences (CDSs), a circular chromosome of length 5.3 Mb and two plasmids. The genome of NJH_MKUB2 had 5957 CDSs, a circular chromosome of 6.0 Mb and five plasmids. We compared our completed genomic assemblies to four recently released draft genomes of M. kubicae in order to better understand intraspecies genomic conservation and variability. We also identified genes implicated in drug resistance, virulence and persistence in the M. kubicae chromosome and plasmids. Virulence factors encoded in the genome and in the plasmids of M. kubicae provide a foundation for investigating how opportunistic environmental NTM may cause disease.
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Affiliation(s)
- Jo Hendrix
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - L. Elaine Epperson
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - David Durbin
- Advanced Diagnostics Laboratories, National Jewish Health, Denver, CO, USA
| | - Jennifer R. Honda
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Michael Strong
- Computational Bioscience, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 421] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Abstract
Four slowly growing mycobacteria isolates were isolated from the respiratory tract and soft tissue biopsies collected in four unrelated patients in Iran. Conventional phenotypic tests indicated that these four isolates were identical to Mycobacterium lentiflavum while 16S rRNA gene sequencing yielded a unique sequence separated from that of M. lentiflavum. One representative strain AFP-003T was characterized as comprising a 6,121,237-bp chromosome (66.24% guanosine-cytosine content) encoding for 5,758 protein-coding genes, 50 tRNA and one complete rRNA operon. A total of 2,876 proteins were found to be associated with the mobilome, including 195 phage proteins. A total of 1,235 proteins were found to be associated with virulence and 96 with toxin/antitoxin systems. The genome of AFP-003T has the genetic potential to produce secondary metabolites, with 39 genes found to be associated with polyketide synthases and non-ribosomal peptide syntases and 11 genes encoding for bacteriocins. Two regions encoding putative prophages and three OriC regions separated by the dnaA gene were predicted. Strain AFP-003T genome exhibits 86% average nucleotide identity with Mycobacterium genavense genome. Genetic and genomic data indicate that strain AFP-003T is representative of a novel Mycobacterium species that we named Mycobacterium ahvazicum, the nineteenth species of the expanding Mycobacterium simiae complex.
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Hernández-Toloza JE, Rincón-Serrano MDP, Celis-Bustos YA, Aguillón CI. [Identification of mycobacteria to the species level by molecular methods in the Public Health Laboratory of Bogotá, Colombia]. Enferm Infecc Microbiol Clin 2015; 34:17-22. [PMID: 25888362 DOI: 10.1016/j.eimc.2015.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 02/27/2015] [Accepted: 03/02/2015] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Global epidemiology of non-tuberculous mycobacteria (NTM) is unknown due to the fact that notification is not required in many countries, however the number of infection reports and outbreaks caused by NTM suggest a significant increase in the last years. Traditionally, mycobacteria identification is made through biochemical profiles which allow to differentiate M. tuberculosis from NTM, and in some cases the mycobacteria species. Nevertheless, these methods are technically cumbersome and time consuming. On the other hand, the introduction of methods based on molecular biology has improved the laboratory diagnosis of NTM. OBJECTIVE To establish the NTM frequency in positive cultures for acid-fast bacilli (AAFB) which were sent to Laboratorio de Salud Pública de Bogotá over a 12 month period. MATERIALS AND METHODS A total of 100 positive cultures for acid-fast bacilli from public and private hospitals from Bogotá were identified by both biochemical methods and the molecular methods PRA (PCR-restriction enzyme analysis) and multiplex-PCR. Furthermore, low prevalence mycobacteria species and non-interpretable results were confirmed by 16SrDNA sequentiation analysis. RESULTS Identification using the PRA method showed NMT occurrence in 11% of cultures. In addition, this molecular methodology allowed to detect the occurrence of more than one mycobacteria in 4% of the cultures. Interestingly, a new M. kubicae pattern of PCR-restriction analysis is reported in our study. CONCLUSION Using a mycobacteria identification algorithm, which includes the molecular method PRA, improves the diagnostic power of conventional methods and could help to advance both NTM epidemiology knowledge and mycobacteriosis control.
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Maiga M, Siddiqui S, Diallo S, Diarra B, Traoré B, Shea YR, Zelazny AM, Dembele BPP, Goita D, Kassambara H, Hammond AS, Polis MA, Tounkara A. Failure to recognize nontuberculous mycobacteria leads to misdiagnosis of chronic pulmonary tuberculosis. PLoS One 2012; 7:e36902. [PMID: 22615839 PMCID: PMC3353983 DOI: 10.1371/journal.pone.0036902] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 04/09/2012] [Indexed: 01/15/2023] Open
Abstract
Background Nontuberculous mycobacterial (NTM) infections cause morbidity worldwide. They are difficult to diagnose in resource-limited regions, and most patients receive empiric treatment for tuberculosis (TB). Our objective here is to evaluate the potential impact of NTM diseases among patients treated presumptively for tuberculosis in Mali. Methods We re-evaluated sputum specimens among patients newly diagnosed with TB (naïve) and those previously treated for TB disease (chronic cases). Sputum microscopy, culture and Mycobacterium tuberculosis drug susceptibility testing were performed. Identification of strains was performed using molecular probes or sequencing of secA1 and/or 16S rRNA genes. Results Of 142 patients enrolled, 61 (43%) were clinically classified as chronic cases and 17 (12%) were infected with NTM. Eleven of the 142 (8%) patients had NTM disease alone (8 M. avium, 2 M. simiae and 1 M. palustre). All these 11 were from the chronic TB group, comprising 11/61 (18%) of that group and all were identified as candidates for second line treatment. The remaining 6/17 (35.30%) NTM infected patients had coinfection with M. tuberculosis and all 6 were from the TB treatment naïve group. These 6 were candidates for the standard first line treatment regimen of TB. M. avium was identified in 11 of the 142 (8%) patients, only 3/11 (27.27%) of whom were HIV positive. Conclusions NTM infections should be considered a cause of morbidity in TB endemic environments especially when managing chronic TB cases to limit morbidity and provide appropriate treatment.
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Affiliation(s)
- Mamoudou Maiga
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Sophia Siddiqui
- CCRB, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
- * E-mail:
| | - Souleymane Diallo
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Bassirou Diarra
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Brehima Traoré
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Yvonne R. Shea
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Adrian M. Zelazny
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bindongo P. P. Dembele
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Drissa Goita
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Hamadoun Kassambara
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Abdulrahman S. Hammond
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
| | - Michael A. Polis
- CCRB, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Anatole Tounkara
- Project SEREFO-NIAID/University of Bamako Research Collaboration on HIV/TB, Bamako, Mali
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Choi SM, Kang HJ, Jeong YJ, Lim JH, Choe WS, Hwang SH, Park J, Hwangbo B, Lee HS. First Isolation of Segniliparus rugosusfrom a Patient with Radiologic Features Similar to Non-Tuberculous Mycobacteriosis. Tuberc Respir Dis (Seoul) 2012. [DOI: 10.4046/trd.2012.72.1.82] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Sun Mi Choi
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Jae Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Yun Jeong Jeong
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Joo Hyun Lim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Won Seok Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang-Hyun Hwang
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Jinkyeong Park
- Center for Lung Cancer, National Cancer Center, Goyang, Korea
| | - Bin Hwangbo
- Center for Lung Cancer, National Cancer Center, Goyang, Korea
| | - Hee Seok Lee
- Center for Lung Cancer, National Cancer Center, Goyang, Korea
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Tortoli E, Böttger EC, Fabio A, Falsen E, Gitti Z, Grottola A, Klenk HP, Mannino R, Mariottini A, Messinò M, Pecorari M, Rumpianesi F. Mycobacterium europaeum sp. nov., a scotochromogenic species related to the Mycobacterium simiae complex. Int J Syst Evol Microbiol 2010; 61:1606-1611. [PMID: 20693362 DOI: 10.1099/ijs.0.025601-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Four strains isolated in the last 15 years were revealed to be identical in their 16S rRNA gene sequences to MCRO19, the sequence of which was deposited in GenBank in 1995. In a polyphasic analysis including phenotypic and genotypic features, the five strains (including MCRO19), which had been isolated in four European countries, turned out to represent a unique taxonomic entity. They are scotochromogenic slow growers and are genetically related to the group that included Mycobacterium simiae and 15 other species. The novel species Mycobacterium europaeum sp. nov. is proposed to accommodate these five strains. Strain FI-95228(T) ( = DSM 45397(T) = CCUG 58464(T)) was chosen as the type strain. In addition, a thorough revision of the phenotypic and genotypic characters of the species related to M. simiae was conducted which leads us to suggest the denomination of the 'Mycobacterium simiae complex' for this group.
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi University Hospital, Florence, Italy
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Anna Fabio
- Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - Enevold Falsen
- Culture Collection University of Göteborg, Department of Clinical Bacteriology, Göteborg, Sweden
| | - Zoe Gitti
- Clinical Microbiology Laboratory, Mycobacteriology Department, University Hospital of Crete, Herakleon, Greece
| | - Antonella Grottola
- Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - Hans-Peter Klenk
- DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roberta Mannino
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi University Hospital, Florence, Italy
| | | | - Massimino Messinò
- Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - Monica Pecorari
- Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy
| | - Fabio Rumpianesi
- Laboratory of Microbiology and Virology, Modena University Hospital, Modena, Italy
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Mohamed AM, Abou El-Ella GA, Nasr EA. Phenotypic and molecular typing of tuberculous and nontuberculous Mycobacterium species from slaughtered pigs in Egypt. J Vet Diagn Invest 2009; 21:48-52. [PMID: 19139500 DOI: 10.1177/104063870902100107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A total of 745 slaughtered pigs were examined during routine meat inspection for suspected tuberculous lesions. Specimens from suspected lesions were collected for conventional mycobacteriologic examinations. Suspected mycobacterial colonies were subjected to molecular typing based on the Mycobacterium species-specific intergenic spacer (IGS) target. The study resulted in detection of suspected lesions in 110 (14.8%) carcasses, from which only 67 specimens produced suspected mycobacterial colonies. Conventional examination was only able to identify 56 isolates as Mycobacterium species, which was confirmed by polymerase chain reaction amplification of the IGS target. Interestingly, out of these, 18 and 12 isolates were Mycobacterium tuberculosis and Mycobacterium bovis, respectively. Sequence analysis of IGS resolved the identities of 10 of the 11 conventionally unidentified isolates as being 4 different nontuberculous Mycobacterium species. The last isolate was proposed as a non-Mycobacterium species and was confirmed by its identification as Rhodococcus equi based on the 16S ribosomal DNA sequence analysis. The study described the isolation of Mycobacterium tuberculosis from pigs and revealed high burden of infection with both tuberculous and nontuberculous mycobacterial species among pigs in Egypt. In addition, the study showed the usefulness of IGS sequence analysis as a reliable molecular tool that would be useful for further epidemiologic and public health studies.
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Affiliation(s)
- Amr M Mohamed
- Department of Animal Medicine, Faculty of Veterinary Medicine, Clinical Laboratory Diagnosis, Assiut University, Assiut, Egypt.
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Pourahmad F, Cervellione F, Thompson KD, Taggart JB, Adams A, Richards RH. Mycobacterium stomatepiae sp. nov., a slowly growing, non-chromogenic species isolated from fish. Int J Syst Evol Microbiol 2009; 58:2821-7. [PMID: 19060066 DOI: 10.1099/ijs.0.2008/001164-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Slowly growing, non-chromogenic mycobacteria were isolated from striped barombi mbo cichlids (Stomatepia mariae) maintained at the London Zoo Aquarium, UK. The isolates could be differentiated from other slowly growing, non-pigmented mycobacteria by a combination of phenotypic features including their inability to grow at 37 degrees C, positive tests for heat-stable catalase, tellurite reduction and arylsulfatase activity, and the absence of urease activity, Tween 80 hydrolysis, nitrate reductase, iron uptake and semiquantitative catalase. The almost full-length 16S rRNA gene sequence, together with partial sequences from the 65 kDa heat-shock protein (hsp65) and the beta-subunit of the bacterial RNA polymerase (rpoB) genes and the 16S-23S internal transcribed spacer 1 (ITS 1) region were identical for all three novel strains, but distinct from those of all known mycobacterial species. Phylogenetic analysis based on 16S rRNA gene sequences placed the novel isolates within the slowly growing mycobacteria group in close proximity to Mycobacterium florentinum. Based on genotypic and phenotypic findings, it is proposed that these isolates represent a novel species of the genus Mycobacterium, for which the name Mycobacterium stomatepiae sp. nov. is proposed with strain T11(T) (=DSM 45059(T)=CIP 109275(T)=NCIMB 14252(T)) as the type strain.
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Affiliation(s)
- Fazel Pourahmad
- Institute of Aquaculture, University of Stirling, Stirling, UK.
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Ruppitsch W, Stöger A, Indra A, Grif K, Schabereiter-Gurtner C, Hirschl A, Allerberger F. Suitability of partial 16S ribosomal RNA gene sequence analysis for the identification of dangerous bacterial pathogens. J Appl Microbiol 2007; 102:852-9. [DOI: 10.1111/j.1365-2672.2006.03107.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Iwen PC, Tarantolo SR, Mohamed AM, Hinrichs SH. First report of Mycobacterium nebraskense as a cause of human infection. Diagn Microbiol Infect Dis 2006; 56:451-3. [PMID: 16935454 DOI: 10.1016/j.diagmicrobio.2006.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2006] [Revised: 05/17/2006] [Accepted: 06/27/2006] [Indexed: 11/19/2022]
Abstract
Newly described nontuberculous Mycobacterium species have emerged as causes of opportunistic infection in compromised patients. This report describes the first case of Mycobacterium nebraskense isolated from a patient with a history of emphysema and details the need for adequate diagnostic capabilities to manage patients with infections caused by slow-growing pathogens.
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Affiliation(s)
- Peter C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA.
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12
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Mohamed AM, Kuyper DJ, Iwen PC, Ali HH, Bastola DR, Hinrichs SH. Computational approach involving use of the internal transcribed spacer 1 region for identification of Mycobacterium species. J Clin Microbiol 2005; 43:3811-7. [PMID: 16081916 PMCID: PMC1233978 DOI: 10.1128/jcm.43.8.3811-3817.2005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The rapid and reliable identification of clinically significant Mycobacterium species is a challenge for diagnostic laboratories. This study evaluates a unique sequence-dependent identification algorithm called MycoAlign for the differential identification of Mycobacterium species. The MycoAlign system uses pan-Mycobacterium-specific primer amplification in combination with a customized database and algorithm. The results of testing were compared with conventional phenotypic assays and GenBank sequence comparisons using the 16S rRNA target. Discrepant results were retested and evaluated using a third independent database. The custom database was generated using the hypervariable sequences of the internal transcribed spacer 1 (ITS-1) region of the rRNA gene complex from characterized Mycobacterium species. An automated sequence-validation process was used to control quality and specificity of evaluated sequence. A total of 181 Mycobacterium strains (22 reference strains and 159 phenotypically identified clinical isolates) and seven nonmycobacterial clinical isolates were evaluated in a comparative study to validate the accuracy of the MycoAlign algorithm. MycoAlign correctly identified all referenced strains and matched species in 94% of the phenotypically identified Mycobacterium clinical isolates. The ITS-1 sequence target showed a higher degree of specificity in terms of Mycobacterium identification than the 16S rRNA sequence by use of GenBank BLAST. This study showed the MycoAlign algorithm to be a reliable and rapid approach for the identification of Mycobacterium species and confirmed the superiority of the ITS-1 region sequence over the 16S rRNA gene sequence as a target for sequence-based species identification.
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Affiliation(s)
- Amr M. Mohamed
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
| | - Dan J. Kuyper
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
| | - Peter C. Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
- Corresponding author. Mailing address: Department of Pathology and Microbiology, University of Nebraska Medical Center, 986495 Nebraska Medical Center, Omaha, NE 68198-6495. Phone: (402) 559-7774. Fax: (402) 559-4077. E-mail:
| | - Hesham H. Ali
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
| | - Dhundy R. Bastola
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
| | - Steven H. Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-6495, Department of Computer Science, University of Nebraska at Omaha, Omaha, Nebraska 68182-0116
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13
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Butler WR, Floyd MM, Brown JM, Toney SR, Daneshvar MI, Cooksey RC, Carr J, Steigerwalt AG, Charles N. Novel mycolic acid-containing bacteria in the family Segniliparaceae fam. nov., including the genus Segniliparus gen. nov., with descriptions of Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov. Int J Syst Evol Microbiol 2005; 55:1615-1624. [PMID: 16014491 DOI: 10.1099/ijs.0.63465-0] [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: 11/18/2022] Open
Abstract
Four strains of novel, rapidly growing, acid–alcohol-fast-staining bacteria were characterized with a polyphasic approach. Isolates were received by the Centers for Disease Control and Prevention from domestic health department laboratories for reference testing as unidentifiable, clinical mycobacteria. Bacteria were rod-shaped and produced non-pigmented (white to beige), non-photochromogenic, smooth or wrinkled-rough colonies on Middlebrook 7H10 and 7H11 media at 33 °C. The smooth and wrinkled colony forms were representative of two species with 68·0 and 72·0 mol% DNA G+C content. The cell wall contained meso-diaminopimelic acid and mycolic acids. Species were characterized by cellular fatty acids of C10 : 0, C14 : 0, C16 : 1ω9t, C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0 (tuberculostearic acid). HPLC analysis of mycolic acids produced a novel late-emerging, genus-specific mycolate pattern. TLC analysis demonstrated a novel α
+-mycolate. Species were 98·9 % similar by comparison of 16S rRNA gene sequences; however, the DNA–DNA association was <28 %. Phylogenetic analysis of 16S rRNA gene sequences demonstrated an association with Rhodococcus equi, although a DNA–DNA relatedness value of 2 % did not support a close relationship. PCR analysis of a proposed, selected actinomycete-specific 439 bp fragment of the 65 kDa heat-shock protein was negative for three of the four isolates. The creation of Segniliparaceae fam. nov. is proposed to encompass the genus Segniliparus gen. nov., including two novel species, the type species Segniliparus rotundus sp. nov. and Segniliparus rugosus sp. nov., with the respective type strains CDC 1076T (=ATCC BAA-972T=CIP 108378T) and CDC 945T (=ATCC BAA-974T=CIP 108380T).
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Affiliation(s)
- W Ray Butler
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Margaret M Floyd
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - June M Brown
- Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sean R Toney
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maryam I Daneshvar
- Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert C Cooksey
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Janice Carr
- Division of Healthcare Quality Promotion, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Arnold G Steigerwalt
- Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nadege Charles
- Division of Tuberculosis Elimination, National Center for HIV, STD and Tuberculosis Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
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14
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Tortoli E, Rindi L, Goh KS, Katila ML, Mariottini A, Mattei R, Mazzarelli G, Suomalainen S, Torkko P, Rastogi N. Mycobacterium florentinum sp. nov., isolated from humans. Int J Syst Evol Microbiol 2005; 55:1101-1106. [PMID: 15879240 DOI: 10.1099/ijs.0.63485-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight mycobacterial strains isolated during an 11 year period from the sputum of independent patients with various pulmonary disorders and, in one case, from a lymph node of a young girl, were found to present identical features. Phenotypic and genotypic characteristics revealed that the most closely related species to these test isolates were Mycobacterium triplex and Mycobacterium lentiflavum. However, the lipids of the cell wall of the test isolates differed from those of the latter species by TLC and presented unique profiles by both GC and HPLC. Genotypic analysis showed that they had unique 16S rRNA gene and internal transcribed spacer (ITS) sequences, and could be differentiated from all other mycobacterial strains by PCR restriction analysis of hsp65. The strains presented high resistance to antimycobacterial drugs. The name Mycobacterium florentinum sp. nov. is proposed for this taxon, with strain FI-93171T (=DSM 44852T=CIP 108409T) as the type strain.
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MESH Headings
- Adult
- Aged
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Cell Wall/chemistry
- Chaperonin 60
- Chaperonins/genetics
- Child
- Chromatography, Gas
- Chromatography, High Pressure Liquid
- Chromatography, Thin Layer
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer
- Drug Resistance, Bacterial
- Feces/microbiology
- Female
- Genes, rRNA
- Humans
- Lipids/analysis
- Lipids/isolation & purification
- Lymph Nodes/microbiology
- Male
- Molecular Sequence Data
- Mycobacterium/classification
- Mycobacterium/cytology
- Mycobacterium/isolation & purification
- Mycobacterium/physiology
- Phylogeny
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sputum/microbiology
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Laura Rindi
- Department of Experimental Pathology, Medical Biotechnologies, Infectivology and Epidemiology, University of Pisa, 56127 Pisa, Italy
| | - Khye S Goh
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, 97165 Pointe-à-Pitre, Guadeloupe, France
| | - Marja L Katila
- Department of Clinical Microbiology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Alessandro Mariottini
- Genetics and Cytogenetics Unit, Careggi Hospital, 50134 Florence, Italy
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Romano Mattei
- Clinical Laboratory, Campo di Marte Hospital, 55100 Lucca, Italy
| | - Gianna Mazzarelli
- Microbiological and Virological Serum-immunology Laboratory, Careggi Hospital, 50134 Florence, Italy
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Sini Suomalainen
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Pirjo Torkko
- Laboratory of Environmental Microbiology, National Public Health Institute, 70211 Kuopio, Finland
- Department of Clinical Microbiology, Kuopio University Hospital, 70211 Kuopio, Finland
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, 97165 Pointe-à-Pitre, Guadeloupe, France
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15
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Fanti F, Tortoli E, Hall L, Roberts GD, Kroppenstedt RM, Dodi I, Conti S, Polonelli L, Chezzi C. Mycobacterium parmense sp. nov. Int J Syst Evol Microbiol 2005; 54:1123-1127. [PMID: 15280280 DOI: 10.1099/ijs.0.02760-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The isolation and identification of a novel, slow-growing, scotochromogenic, mycobacterial species is reported. A strain, designated MUP 1182T, was isolated from a cervical lymph node of a 3-year-old child. MUP 1182T is alcohol- and acid-fast, with a lipid pattern that is consistent with those of species that belong to the genus Mycobacterium. It grows slowly at 25-37 degrees C, but does not grow at 42 degrees C. The isolate was revealed to be biochemically distinct from previously described mycobacterial species: it has urease and Tween hydrolysis activities and lacks nitrate reductase, 3-day arylsulfatase and beta-glucosidase activities. Comparative 16S rDNA sequencing showed that isolate MUP 1182T represents a novel, slow-growing species that is related closely to Mycobacterium lentiflavum and Mycobacterium simiae. On the basis of these findings, the name Mycobacterium parmense sp. nov. is proposed, with MUP 1182T (=CIP 107385T=DSM 44553T) as the type strain.
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Affiliation(s)
- Franco Fanti
- Sezione di Microbiologia, Dipartimento di Patologia e Medicina di Laboratorio, Università degli Studi di Parma, 43100 Parma, Italy
| | - Enrico Tortoli
- Laboratorio di Microbiologia e Virologia, Ospedale di Careggi, 50139 Florence, Italy
| | - Leslie Hall
- Mayo Clinic and Mayo Foundation, Division of Clinical Microbiology, Rochester, MN 55905, USA
| | - Glenn D Roberts
- Mayo Clinic and Mayo Foundation, Division of Clinical Microbiology, Rochester, MN 55905, USA
| | - Reiner M Kroppenstedt
- Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany
| | - Icilio Dodi
- Dipartimento Materno-Infantile, Reparto di Pediatria e Oncoematologia, Azienda Ospedaliera di Parma, 43100 Parma, Italy
| | - Stefania Conti
- Sezione di Microbiologia, Dipartimento di Patologia e Medicina di Laboratorio, Università degli Studi di Parma, 43100 Parma, Italy
| | - Luciano Polonelli
- Sezione di Microbiologia, Dipartimento di Patologia e Medicina di Laboratorio, Università degli Studi di Parma, 43100 Parma, Italy
| | - Carlo Chezzi
- Sezione di Microbiologia, Dipartimento di Patologia e Medicina di Laboratorio, Università degli Studi di Parma, 43100 Parma, Italy
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16
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Mohamed AM, Iwen PC, Tarantolo S, Hinrichs SH. Mycobacterium nebraskense sp. nov., a novel slowly growing scotochromogenic species. Int J Syst Evol Microbiol 2004; 54:2057-2060. [PMID: 15545434 DOI: 10.1099/ijs.0.63126-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The characterization of a novel slowly growing, scotochromogenic Mycobacterium species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus Mycobacterium. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30–35 °C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to Mycobacterium malmoense, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium scrofulaceum. These data support the conclusion that the related five described organisms represent a novel Mycobacterium species, for which the name Mycobacterium nebraskense sp. nov. is proposed, with the type strain UNMC-MY1349T (=ATCC BAA-837T=DSM 44803T).
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MESH Headings
- Catalase/analysis
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/isolation & purification
- Enzyme Stability
- Genes, rRNA
- Humans
- Molecular Sequence Data
- Mycobacterium/chemistry
- Mycobacterium/classification
- Mycobacterium/isolation & purification
- Mycobacterium/physiology
- Mycobacterium Infections/microbiology
- Mycobacterium avium/genetics
- Mycobacterium kansasii/genetics
- Mycobacterium scrofulaceum/genetics
- Mycolic Acids/analysis
- Mycolic Acids/isolation & purification
- Phylogeny
- Pigments, Biological/biosynthesis
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Sputum/microbiology
- Temperature
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Affiliation(s)
- Amr M Mohamed
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Peter C Iwen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Stefano Tarantolo
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
| | - Steven H Hinrichs
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
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17
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Herdman AV, Steele JCH. The new mycobacterial species—emerging or newly distinguished pathogens. Clin Lab Med 2004; 24:651-90, vi. [PMID: 15325060 DOI: 10.1016/j.cll.2004.05.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Diseases due to nontuberculous mycobacteria are increasing in frequency, especially in patients with compromised immunity. A number of "new" mycobacterial species have been described in the last decade, largely as the result of the use of new tools to identify previously unrecognized mycobacteria found in the environment and in clinical specimens. This article reviews many of these potentially pathogenic organisms, summarizing what is known regarding their phenotypic and genotypic characterization, antimicrobial susceptibility, and clinical significance.
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Affiliation(s)
- Anne V Herdman
- Department of Pathology, Medical College of Georgia, 1120 15th Street, Augusta, GA 30912, USA
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18
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Tortoli E. Clinical features of infections caused by new nontuberculous mycobacteria, part I. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.clinmicnews.2004.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Harmsen D, Dostal S, Roth A, Niemann S, Rothgänger J, Sammeth M, Albert J, Frosch M, Richter E. RIDOM: comprehensive and public sequence database for identification of Mycobacterium species. BMC Infect Dis 2003; 3:26. [PMID: 14611664 PMCID: PMC280682 DOI: 10.1186/1471-2334-3-26] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2003] [Accepted: 11/11/2003] [Indexed: 11/27/2022] Open
Abstract
Background Molecular identification of Mycobacterium species has two primary advantages when compared to phenotypic identification: rapid turn-around time and improved accuracy. The information content of the 5' end of the 16S ribosomal RNA gene (16S rDNA) is sufficient for identification of most bacterial species. However, reliable sequence-based identification is hampered by many faulty and some missing sequence entries in publicly accessible databases. Methods In order to establish an improved 16S rDNA sequence database for the identification of clinical and environmental isolates, we sequenced both strands of the 5' end of 16S rDNA (Escherichia coli positions 54 to 510) from 199 mycobacterial culture collection isolates. All validly described species (n = 89; up to March 21, 2000) and nearly all published sequevar variants were included. If the 16S rDNA sequences were not discriminatory, the internal transcribed spacer (ITS) region sequences (n = 84) were also determined. Results Using 5'-16S rDNA sequencing a total of 64 different mycobacterial species (71.9%) could be identified. With the additional input of the ITS sequence, a further 16 species or subspecies could be differentiated. Only Mycobacterium tuberculosis complex species, M. marinum / M. ulcerans and the M. avium subspecies could not be differentiated using 5'-16S rDNA or ITS sequencing. A total of 77 culture collection strain sequences, exhibiting an overlap of at least 80% and identical by strain number to the isolates used in this study, were found in the GenBank. Comparing these with our sequences revealed that an average of 4.31 nucleotide differences (SD ± 0.57) were present. Conclusions The data from this analysis show that it is possible to differentiate most mycobacterial species by sequence analysis of partial 16S rDNA. The high-quality sequences reported here, together with ancillary information (e.g., taxonomic, medical), are available in a public database, which is currently being expanded in the RIDOM project ), for similarity searches.
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Affiliation(s)
- Dag Harmsen
- Institut für Hygiene, Universität Münster, Münster, Germany
| | - Stefan Dostal
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Würzburg, Germany
| | - Andreas Roth
- Institut für Mikrobiologie und Immunologie, Lungenklinik Heckeshorn, Berlin, Germany
| | - Stefan Niemann
- Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel, Germany
| | | | - Michael Sammeth
- Lehrstuhl für Informatik II, Universität Würzburg, Würzburg, Germany
| | - Jürgen Albert
- Lehrstuhl für Informatik II, Universität Würzburg, Würzburg, Germany
| | - Matthias Frosch
- Institut für Hygiene und Mikrobiologie, Universität Würzburg, Würzburg, Germany
| | - Elvira Richter
- Nationales Referenzzentrum für Mykobakterien, Forschungszentrum Borstel, Borstel, Germany
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20
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Casal M. [What terms can be applied to mycobacteria other than M. tuberculosis and M. leprae]. Enferm Infecc Microbiol Clin 2003; 21:296-8. [PMID: 12809584 DOI: 10.1016/s0213-005x(03)72944-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A review of the terms used to name mycobacteria other than M. tuberculosis and M. leprae was performed. A system using binomial nomenclature is defended. The author comments on the various names applied to mycobacteria over the history of medicine, from 1899 to the present, and the reasons why terms such as environmental mycobacteria or nontuberculous mycobacteria are incorrect and should not be used. In the case that a general name must be chosen for these mycobacteria, the term atypical mycobacteria is advocated.
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Affiliation(s)
- Manuel Casal
- Centro de Referencia de Micobacterias. Facultad de Medicina. Universidad de Córdoba. España.
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21
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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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22
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Hall L, Doerr KA, Wohlfiel SL, Roberts GD. Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J Clin Microbiol 2003; 41:1447-53. [PMID: 12682128 PMCID: PMC153882 DOI: 10.1128/jcm.41.4.1447-1453.2003] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
An evaluation of the MicroSeq 500 microbial identification system by nucleic acid sequencing and the Mayo Clinic experience with its integration into a routine clinical laboratory setting are described. Evaluation of the MicroSeq 500 microbial identification system was accomplished with 59 American Type Culture Collection (ATCC) strains and 328 clinical isolates of mycobacteria identified by conventional and 16S ribosomal DNA sequencing by using the MicroSeq 500 microbial identification system. Nucleic acid sequencing identified 58 of 59 (98.3%) ATCC strains to the species level or to the correct group or complex level. The identification results for 219 of 243 clinical isolates (90.1%) with a distance score of <1% were concordant with the identifications made by phenotypic methods. The remaining 85 isolates had distance scores of >1%; 35 (41.1%) were identified to the appropriate species level or group or complex level; 13 (15.3%) were identified to the species level. All 85 isolates were determined to be mycobacterial species, either novel species or species that exhibited significant genotypic divergence from an organism in the database with the closest match. Integration of nucleic acid sequencing into the routine mycobacteriology laboratory and use of the MicroSeq 500 microbial identification system and Mayo Clinic databases containing additional genotypes of common species and added species significantly reduced the number of organisms that could not be identified by phenotypic methods. The turnaround time was shortened to 24 h, and results were reported much earlier. A limited number of species could not be differentiated from one another by 16S ribosomal DNA sequencing; however, the method provides for the identification of unusual species and more accurate identifications and offers the promise of being the most accurate method available.
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Affiliation(s)
- Leslie Hall
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota 55905, USA
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23
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Han XY, Pham AS, Tarrand JJ, Sood PK, Luthra R. Rapid and accurate identification of mycobacteria by sequencing hypervariable regions of the 16S ribosomal RNA gene. Am J Clin Pathol 2002; 118:796-801. [PMID: 12428802 DOI: 10.1309/hn44-xqym-jmaq-2edl] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
We developed a method to identify mycobacteria by sequencing hypervariable regions of the polymerase chain reaction-amplified 16S ribosomal RNA gene. This method is nearly specific for mycobacteria and uses positive culture from liquid or solid medium without the needfor lengthy subculture. It shortens identification time to 3 days, which is much faster than the conventional biochemical method (mean, 8 weeks). It applies to all mycobacteria (approximately 100 species), unlike current nucleic acid hybridization methods, which probe only 4 species. The identifications are the same or are species specific for the well-characterized mycobacteria (59/68 [87%]) or more accurate for recently proposed species (9/68 [13%]). The method requires a single sequencing reaction, which is efficient and cost-effective. Therefore, this method is clinically and academically useful.
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Affiliation(s)
- Xiang Y Han
- Division of Pathology and Laboratory Medicine, University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
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24
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Brown-Elliott BA, Griffith DE, Wallace RJ. Newly described or emerging human species of nontuberculous mycobacteria. Infect Dis Clin North Am 2002; 16:187-220. [PMID: 11917813 DOI: 10.1016/s0891-5520(03)00052-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The advent of molecular testing in the laboratory has brought about the recognition of multiple newly characterized mycobacterial species not previously recognizable with most standard techniques. Some of the species are nonpathogenic, but the majority may cause clinical disease. Each is likely to have its own biology, drug susceptibility pattern, and response to drug/surgical therapy. Thus, it is important to try to recognize these new species in the laboratory. A study of the phenotypic and genotypic characteristics of these new species also may help to elucidate the epidemiology and pathogenesis of these organisms. In addition, there are multiple emerging species of nontuberculous mycobacteria including M. ulcerans, M. haemophilum, M. xenopi, and M. malmoense. [table: see text] These species are being recognized increasingly as a cause of human disease and recovered within the laboratory. The clinician must learn about these new pathogens to recognize them clinically and assist the laboratory in their recovery.
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Affiliation(s)
- Barbara A Brown-Elliott
- Mycobacteria/Nocardia Laboratory, Department of Microbiology, University of Texas Health Center, Tyler, Texas, USA.
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25
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De Baere T, de Mendonça R, Claeys G, Verschraegen G, Mijs W, Verhelst R, Rottiers S, Van Simaey L, De Ganck C, Vaneechoutte M. Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of cultured mycobacteria in a diagnostic laboratory. BMC Microbiol 2002; 2:4. [PMID: 11945178 PMCID: PMC101405 DOI: 10.1186/1471-2180-2-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2001] [Accepted: 03/01/2002] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The development of DNA amplification for the direct detection of M. tuberculosis from clinical samples has been a major goal of clinical microbiology during the last ten years. However, the limited sensitivity of most DNA amplification techniques restricts their use to smear positive samples. On the other hand, the development of automated liquid culture has increased the speed and sensitivity of cultivation of mycobacteria. We have opted to combine automated culture with rapid genotypic identification (ARDRA: amplified rDNA restriction analysis) for the detection resp. identification of all mycobacterial species at once, instead of attempting direct PCR based detection from clinical samples of M. tuberculosis only. RESULTS During 1998-2000 a total of approx. 3500 clinical samples was screened for the presence of M. tuberculosis. Of the 151 culture positive samples, 61 were M. tuberculosis culture positive. Of the 30 smear positive samples, 26 were M. tuberculosis positive. All but three of these 151 mycobacterial isolates could be identified with ARDRA within on average 36 hours. The three isolates that could not be identified belonged to rare species not yet included in our ARDRA fingerprint library or were isolates with an aberrant pattern. CONCLUSIONS In our hands, automated culture in combination with ARDRA provides with accurate, practically applicable, wide range identification of mycobacterial species. The existing identification library covers most species, and can be easily updated when new species are studied or described. The drawback is that ARDRA is culture-dependent, since automated culture of M. tuberculosis takes on average 16.7 days (range 6 to 29 days). However, culture is needed after all to assess the antibiotic susceptibility of the strains.
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Affiliation(s)
- Thierry De Baere
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Ricardo de Mendonça
- Université Libre de Bruxelles, Hôpital Erasme, Service de Microbiologie, Route de Lennik 808,1070 Bruxelles, Belgium
| | - Geert Claeys
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Gerda Verschraegen
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Wouter Mijs
- Innogenetics, Industriepark 7, Box 5, 9052 Zwijnaarde, Belgium
| | - Rita Verhelst
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Sylvianne Rottiers
- Université Libre de Bruxelles, Hôpital Erasme, Service de Microbiologie, Route de Lennik 808,1070 Bruxelles, Belgium
| | - Leen Van Simaey
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Catharine De Ganck
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
| | - Mario Vaneechoutte
- Department Clinical Chemistry, Microbiology & Immunology, Ghent University Hospital, Ghent, Belgium
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26
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Cloud JL, Neal H, Rosenberry R, Turenne CY, Jama M, Hillyard DR, Carroll KC. Identification of Mycobacterium spp. by using a commercial 16S ribosomal DNA sequencing kit and additional sequencing libraries. J Clin Microbiol 2002; 40:400-6. [PMID: 11825949 PMCID: PMC153382 DOI: 10.1128/jcm.40.2.400-406.2002] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Current methods for identification of Mycobacterium spp. rely upon time-consuming phenotypic tests, mycolic acid analysis, and narrow-spectrum nucleic acid probes. Newer approaches include PCR and sequencing technologies. We evaluated the MicroSeq 500 16S ribosomal DNA (rDNA) bacterial sequencing kit (Applied Biosystems, Foster City, Calif.) for its ability to identify Mycobacterium isolates. The kit is based on PCR and sequencing of the first 500 bp of the bacterial rRNA gene. One hundred nineteen mycobacterial isolates (94 clinical isolates and 25 reference strains) were identified using traditional phenotypic methods and the MicroSeq system in conjunction with separate databases. The sequencing system gave 87% (104 of 119) concordant results when compared with traditional phenotypic methods. An independent laboratory using a separate database analyzed the sequences of the 15 discordant samples and confirmed the results. The use of 16S rDNA sequencing technology for identification of Mycobacterium spp. provides more rapid and more accurate characterization than do phenotypic methods. The MicroSeq 500 system simplifies the sequencing process but, in its present form, requires use of additional databases such as the Ribosomal Differentiation of Medical Microorganisms (RIDOM) to precisely identify subtypes of type strains and species not currently in the MicroSeq library.
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Affiliation(s)
- J L Cloud
- Associated Regional and University Pathologists (ARUP), Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
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Hale YM, Pfyffer GE, Salfinger M. Laboratory diagnosis of mycobacterial infections: new tools and lessons learned. Clin Infect Dis 2001; 33:834-46. [PMID: 11512089 DOI: 10.1086/322607] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2000] [Revised: 03/14/2001] [Indexed: 11/04/2022] Open
Abstract
Even in the 21st century, tuberculosis continues to be a problem. Although the number of cases continues gradually to decrease in the United States, cases get more difficult to treat, specifically those that are multiple-drug resistant. Infection of one-third of the world's population ensures that tuberculosis will not disappear in the near future. In light of this, it will be useful to know the goals for the health care system and how these goals may be accomplished. Laboratory testing in the mycobacteriology field is experiencing more changes today than ever before. Determining what assays will be most useful to the clinician is a challenge, and acceptance of the new technology by the medical community an even greater one. Clinicians must use the best available resources to determine the most appropriate care for their patients and work together with the laboratory to ensure that the communication channels are open. This review focuses on current state-of-the-art resources useful for accurate and rapid laboratory diagnosis of mycobacterial infections.
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Affiliation(s)
- Y M Hale
- Bureau of Laboratories, Florida Department of Health, Jacksonville, FL, USA
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