Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)
1 Department of Microbiology, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul 110-799, Korea 2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea 3 Dep...
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| Veröffentlicht in: | International journal of systematic and evolutionary microbiology 2005-07, Vol.55 (4), p.1649-1656 |
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| creator | Kim, Hong Kim, Sun-Hyun Shim, Tae-Sun Kim, Mi-na Bai, Gill-Han Park, Young-Gil Lee, Sueng-Hyun Chae, Gue-Tae Cha, Chang-Yong Kook, Yoon-Hoh Kim, Bum-Joon |
| description | 1 Department of Microbiology, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul 110-799, Korea
2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
3 Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
4 The Korean Institute of Tuberculosis, The Korean National Tuberculosis Association, Seoul 137-140, Korea
5 Department of Microbiology, College of Medicine, Konkuk University, Chungju 380-230, Korea
6 Institute of Hansen's Disease, The Catholic University Medical College, Seoul 137-7014, Korea
Correspondence Bum-Joon Kim kbumjoon{at}snu.ac.kr
The nucleotide sequences (604 bp) of partial heat-shock protein genes ( hsp65 ) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an Xho I PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.
Abbreviations: NTM, non-tuberculous mycobacterium; PRA, PCR-restriction fragment analysis
The GenBank/EMBL/DDBJ accession numbers for the partial hsp65 sequences determined in this study are AF057449 AF057493.
Details of reference strains, including GenBank accession numbers, trees comparing the hsp65 and 16S rRNA genes of the same sample of reference strains and details of a protocol to distinguish M. tuberculosis complex and NTM isolates are available as supplementary material in IJSEM Online. |
| doi_str_mv | 10.1099/ijs.0.63553-0 |
| format | Article |
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2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
3 Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
4 The Korean Institute of Tuberculosis, The Korean National Tuberculosis Association, Seoul 137-140, Korea
5 Department of Microbiology, College of Medicine, Konkuk University, Chungju 380-230, Korea
6 Institute of Hansen's Disease, The Catholic University Medical College, Seoul 137-7014, Korea
Correspondence Bum-Joon Kim kbumjoon{at}snu.ac.kr
The nucleotide sequences (604 bp) of partial heat-shock protein genes ( hsp65 ) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an Xho I PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.
Abbreviations: NTM, non-tuberculous mycobacterium; PRA, PCR-restriction fragment analysis
The GenBank/EMBL/DDBJ accession numbers for the partial hsp65 sequences determined in this study are AF057449 AF057493.
Details of reference strains, including GenBank accession numbers, trees comparing the hsp65 and 16S rRNA genes of the same sample of reference strains and details of a protocol to distinguish M. tuberculosis complex and NTM isolates are available as supplementary material in IJSEM Online.</description><identifier>ISSN: 1466-5026</identifier><identifier>EISSN: 1466-5034</identifier><identifier>DOI: 10.1099/ijs.0.63553-0</identifier><identifier>PMID: 16014496</identifier><language>eng</language><publisher>Reading: Soc General Microbiol</publisher><subject>Bacterial Proteins - genetics ; Bacterial Typing Techniques ; Bacteriology ; Biological and medical sciences ; Chaperonin 60 ; Chaperonins - genetics ; Deoxyribonucleases, Type II Site-Specific - metabolism ; DNA, Bacterial - analysis ; DNA, Ribosomal - analysis ; Fundamental and applied biological sciences. Psychology ; Humans ; Microbiology ; Molecular Sequence Data ; Mycobacterium - classification ; Mycobacterium - genetics ; Mycobacterium tuberculosis ; Mycobacterium tuberculosis - classification ; Mycobacterium tuberculosis - genetics ; Phylogeny ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA ; Species Specificity ; Systematics</subject><ispartof>International journal of systematic and evolutionary microbiology, 2005-07, Vol.55 (4), p.1649-1656</ispartof><rights>2006 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c420t-eeb889d01fca95e018e5755f73f6ddaa629cf756d93934a2d0ce3939614ba32e3</citedby><cites>FETCH-LOGICAL-c420t-eeb889d01fca95e018e5755f73f6ddaa629cf756d93934a2d0ce3939614ba32e3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,3746,3747,27924,27925</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=16945255$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16014496$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, Hong</creatorcontrib><creatorcontrib>Kim, Sun-Hyun</creatorcontrib><creatorcontrib>Shim, Tae-Sun</creatorcontrib><creatorcontrib>Kim, Mi-na</creatorcontrib><creatorcontrib>Bai, Gill-Han</creatorcontrib><creatorcontrib>Park, Young-Gil</creatorcontrib><creatorcontrib>Lee, Sueng-Hyun</creatorcontrib><creatorcontrib>Chae, Gue-Tae</creatorcontrib><creatorcontrib>Cha, Chang-Yong</creatorcontrib><creatorcontrib>Kook, Yoon-Hoh</creatorcontrib><creatorcontrib>Kim, Bum-Joon</creatorcontrib><title>Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)</title><title>International journal of systematic and evolutionary microbiology</title><addtitle>Int J Syst Evol Microbiol</addtitle><description>1 Department of Microbiology, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul 110-799, Korea
2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
3 Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
4 The Korean Institute of Tuberculosis, The Korean National Tuberculosis Association, Seoul 137-140, Korea
5 Department of Microbiology, College of Medicine, Konkuk University, Chungju 380-230, Korea
6 Institute of Hansen's Disease, The Catholic University Medical College, Seoul 137-7014, Korea
Correspondence Bum-Joon Kim kbumjoon{at}snu.ac.kr
The nucleotide sequences (604 bp) of partial heat-shock protein genes ( hsp65 ) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an Xho I PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.
Abbreviations: NTM, non-tuberculous mycobacterium; PRA, PCR-restriction fragment analysis
The GenBank/EMBL/DDBJ accession numbers for the partial hsp65 sequences determined in this study are AF057449 AF057493.
Details of reference strains, including GenBank accession numbers, trees comparing the hsp65 and 16S rRNA genes of the same sample of reference strains and details of a protocol to distinguish M. tuberculosis complex and NTM isolates are available as supplementary material in IJSEM Online.</description><subject>Bacterial Proteins - genetics</subject><subject>Bacterial Typing Techniques</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>Chaperonin 60</subject><subject>Chaperonins - genetics</subject><subject>Deoxyribonucleases, Type II Site-Specific - metabolism</subject><subject>DNA, Bacterial - analysis</subject><subject>DNA, Ribosomal - analysis</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Humans</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Mycobacterium - classification</subject><subject>Mycobacterium - genetics</subject><subject>Mycobacterium tuberculosis</subject><subject>Mycobacterium tuberculosis - classification</subject><subject>Mycobacterium tuberculosis - genetics</subject><subject>Phylogeny</subject><subject>Polymerase Chain Reaction</subject><subject>Polymorphism, Restriction Fragment Length</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><subject>Species Specificity</subject><subject>Systematics</subject><issn>1466-5026</issn><issn>1466-5034</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqF0LuP1DAQBnALgbhjoaRFbkBHkWUcPxKX6HhKh2igxXKc8cVHHosnK7T_PV52BXRUHlk_fTP6GHsqYCvA2lfpjrawNVJrWcE9dimUMZUGqe7_mWtzwR4R3QGUD4CH7EKYMiprLtm3NylGzDivya9pmfkS-adDWDofVsxpP3HaYUhIvDtwP_vxQImOaB2QD-jXioYlfOe7vKyYZm40v8UZ-dVAO6NfPmYPoh8Jn5zfDfv67u2X6w_Vzef3H69f31RB1bBWiF3b2h5EDN5qBNGibrSOjYym7703tQ2x0aa30krl6x4ClskaoTova5Qb9uKUW-74sUda3ZQo4Dj6GZc9OdNC3QLU_4Wi0dA2YAqsTjDkhShjdLucJp8PToA7Nu9K8w7c7-YdFP_sHLzvJuz_6nPVBTw_A0_BjzH7OST6x1ml65K1YVcnN6Tb4WfK6EqhUypndGk5LtXaqcKVlb8AdCaZbg</recordid><startdate>20050701</startdate><enddate>20050701</enddate><creator>Kim, Hong</creator><creator>Kim, Sun-Hyun</creator><creator>Shim, Tae-Sun</creator><creator>Kim, Mi-na</creator><creator>Bai, Gill-Han</creator><creator>Park, Young-Gil</creator><creator>Lee, Sueng-Hyun</creator><creator>Chae, Gue-Tae</creator><creator>Cha, Chang-Yong</creator><creator>Kook, Yoon-Hoh</creator><creator>Kim, Bum-Joon</creator><general>Soc General Microbiol</general><general>Society for General Microbiology</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QL</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>20050701</creationdate><title>Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)</title><author>Kim, Hong ; Kim, Sun-Hyun ; Shim, Tae-Sun ; Kim, Mi-na ; Bai, Gill-Han ; Park, Young-Gil ; Lee, Sueng-Hyun ; Chae, Gue-Tae ; Cha, Chang-Yong ; Kook, Yoon-Hoh ; Kim, Bum-Joon</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c420t-eeb889d01fca95e018e5755f73f6ddaa629cf756d93934a2d0ce3939614ba32e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2005</creationdate><topic>Bacterial Proteins - genetics</topic><topic>Bacterial Typing Techniques</topic><topic>Bacteriology</topic><topic>Biological and medical sciences</topic><topic>Chaperonin 60</topic><topic>Chaperonins - genetics</topic><topic>Deoxyribonucleases, Type II Site-Specific - metabolism</topic><topic>DNA, Bacterial - analysis</topic><topic>DNA, Ribosomal - analysis</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Humans</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Mycobacterium - classification</topic><topic>Mycobacterium - genetics</topic><topic>Mycobacterium tuberculosis</topic><topic>Mycobacterium tuberculosis - classification</topic><topic>Mycobacterium tuberculosis - genetics</topic><topic>Phylogeny</topic><topic>Polymerase Chain Reaction</topic><topic>Polymorphism, Restriction Fragment Length</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><topic>Species Specificity</topic><topic>Systematics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Hong</creatorcontrib><creatorcontrib>Kim, Sun-Hyun</creatorcontrib><creatorcontrib>Shim, Tae-Sun</creatorcontrib><creatorcontrib>Kim, Mi-na</creatorcontrib><creatorcontrib>Bai, Gill-Han</creatorcontrib><creatorcontrib>Park, Young-Gil</creatorcontrib><creatorcontrib>Lee, Sueng-Hyun</creatorcontrib><creatorcontrib>Chae, Gue-Tae</creatorcontrib><creatorcontrib>Cha, Chang-Yong</creatorcontrib><creatorcontrib>Kook, Yoon-Hoh</creatorcontrib><creatorcontrib>Kim, Bum-Joon</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of systematic and evolutionary microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Hong</au><au>Kim, Sun-Hyun</au><au>Shim, Tae-Sun</au><au>Kim, Mi-na</au><au>Bai, Gill-Han</au><au>Park, Young-Gil</au><au>Lee, Sueng-Hyun</au><au>Chae, Gue-Tae</au><au>Cha, Chang-Yong</au><au>Kook, Yoon-Hoh</au><au>Kim, Bum-Joon</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65)</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2005-07-01</date><risdate>2005</risdate><volume>55</volume><issue>4</issue><spage>1649</spage><epage>1656</epage><pages>1649-1656</pages><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>1 Department of Microbiology, College of Medicine, Seoul National University, 28 Yongon-dong, Chongno-gu, Seoul 110-799, Korea
2 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
3 Department of Laboratory Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul 138-600, Korea
4 The Korean Institute of Tuberculosis, The Korean National Tuberculosis Association, Seoul 137-140, Korea
5 Department of Microbiology, College of Medicine, Konkuk University, Chungju 380-230, Korea
6 Institute of Hansen's Disease, The Catholic University Medical College, Seoul 137-7014, Korea
Correspondence Bum-Joon Kim kbumjoon{at}snu.ac.kr
The nucleotide sequences (604 bp) of partial heat-shock protein genes ( hsp65 ) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an Xho I PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.
Abbreviations: NTM, non-tuberculous mycobacterium; PRA, PCR-restriction fragment analysis
The GenBank/EMBL/DDBJ accession numbers for the partial hsp65 sequences determined in this study are AF057449 AF057493.
Details of reference strains, including GenBank accession numbers, trees comparing the hsp65 and 16S rRNA genes of the same sample of reference strains and details of a protocol to distinguish M. tuberculosis complex and NTM isolates are available as supplementary material in IJSEM Online.</abstract><cop>Reading</cop><pub>Soc General Microbiol</pub><pmid>16014496</pmid><doi>10.1099/ijs.0.63553-0</doi><tpages>8</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Microbiology Society; EZB-FREE-00999 freely available EZB journals; Alma/SFX Local Collection |
| subjects | Bacterial Proteins - genetics Bacterial Typing Techniques Bacteriology Biological and medical sciences Chaperonin 60 Chaperonins - genetics Deoxyribonucleases, Type II Site-Specific - metabolism DNA, Bacterial - analysis DNA, Ribosomal - analysis Fundamental and applied biological sciences. Psychology Humans Microbiology Molecular Sequence Data Mycobacterium - classification Mycobacterium - genetics Mycobacterium tuberculosis Mycobacterium tuberculosis - classification Mycobacterium tuberculosis - genetics Phylogeny Polymerase Chain Reaction Polymorphism, Restriction Fragment Length RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA Species Specificity Systematics |
| title | Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65) |
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