16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory
Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phen...
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| Veröffentlicht in: | Journal of Clinical Microbiology 2006-04, Vol.44 (4), p.1359-1366 |
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| container_title | Journal of Clinical Microbiology |
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| creator | Bosshard, P. P Zbinden, R Abels, S Böddinghaus, B Altwegg, M Böttger, E. C |
| description | Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phenotypic with molecular identification. Results of molecular analyses were compared with two commercially available identification systems (API 20 NE, VITEK 2 fluorescent card; bioMérieux, Marcy l'Etoile, France). By 16S rRNA gene sequence analyses, 92% of the isolates were assigned to species level and 8% to genus level. Using API 20 NE, 54% of the isolates were assigned to species and 7% to genus level, and 39% of the isolates could not be discriminated at any taxonomic level. The respective numbers for VITEK 2 were 53%, 1%, and 46%, respectively. Fifteen percent and 43% of the isolates corresponded to species not included in the API 20 NE and VITEK 2 databases, respectively. We conclude that 16S rRNA gene sequencing is an effective means for the identification of clinically relevant nonfermenting gram-negative bacilli. Based on our experience, we propose an algorithm for proper identification of nonfermenting gram-negative bacilli in the diagnostic laboratory. |
| doi_str_mv | 10.1128/jcm.44.4.1359-1366.2006 |
| format | Article |
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P ; Zbinden, R ; Abels, S ; Böddinghaus, B ; Altwegg, M ; Böttger, E. C</creator><creatorcontrib>Bosshard, P. P ; Zbinden, R ; Abels, S ; Böddinghaus, B ; Altwegg, M ; Böttger, E. C</creatorcontrib><description>Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phenotypic with molecular identification. Results of molecular analyses were compared with two commercially available identification systems (API 20 NE, VITEK 2 fluorescent card; bioMérieux, Marcy l'Etoile, France). By 16S rRNA gene sequence analyses, 92% of the isolates were assigned to species level and 8% to genus level. Using API 20 NE, 54% of the isolates were assigned to species and 7% to genus level, and 39% of the isolates could not be discriminated at any taxonomic level. The respective numbers for VITEK 2 were 53%, 1%, and 46%, respectively. Fifteen percent and 43% of the isolates corresponded to species not included in the API 20 NE and VITEK 2 databases, respectively. We conclude that 16S rRNA gene sequencing is an effective means for the identification of clinically relevant nonfermenting gram-negative bacilli. Based on our experience, we propose an algorithm for proper identification of nonfermenting gram-negative bacilli in the diagnostic laboratory.</description><identifier>ISSN: 0095-1137</identifier><identifier>EISSN: 1098-660X</identifier><identifier>EISSN: 1098-5530</identifier><identifier>DOI: 10.1128/jcm.44.4.1359-1366.2006</identifier><identifier>PMID: 16597863</identifier><identifier>CODEN: JCMIDW</identifier><language>eng</language><publisher>Washington, DC: American Society for Microbiology</publisher><subject>Bacterial Typing Techniques - instrumentation ; Bacterial Typing Techniques - methods ; Bacterial Typing Techniques - standards ; Bacteriology ; Biological and medical sciences ; DNA, Bacterial - genetics ; Fermentation ; Fundamental and applied biological sciences. Psychology ; Gram-Negative Bacteria - genetics ; Gram-Negative Bacteria - isolation & purification ; Gram-Negative Bacterial Infections - diagnosis ; Gram-Negative Bacterial Infections - microbiology ; Humans ; Infectious diseases ; Laboratories ; Medical sciences ; Microbiology ; Prospective Studies ; Reagent Kits, Diagnostic ; RNA, Ribosomal, 16S - analysis ; RNA, Ribosomal, 16S - genetics</subject><ispartof>Journal of Clinical Microbiology, 2006-04, Vol.44 (4), p.1359-1366</ispartof><rights>2006 INIST-CNRS</rights><rights>Copyright © 2006, American Society for Microbiology 2006</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c592t-88da7a4112e391e9547ee95cf93c67695950a8da88f6daa59a3f313b802f08c73</citedby><cites>FETCH-LOGICAL-c592t-88da7a4112e391e9547ee95cf93c67695950a8da88f6daa59a3f313b802f08c73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448638/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC1448638/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,315,728,781,785,886,3189,3190,27925,27926,53792,53794</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=17700862$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16597863$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bosshard, P. P</creatorcontrib><creatorcontrib>Zbinden, R</creatorcontrib><creatorcontrib>Abels, S</creatorcontrib><creatorcontrib>Böddinghaus, B</creatorcontrib><creatorcontrib>Altwegg, M</creatorcontrib><creatorcontrib>Böttger, E. C</creatorcontrib><title>16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory</title><title>Journal of Clinical Microbiology</title><addtitle>J Clin Microbiol</addtitle><description>Over a period of 26 months, we have evaluated in a prospective fashion the use of 16S rRNA gene sequencing as a means of identifying clinically relevant isolates of nonfermenting gram-negative bacilli (non-Pseudomonas aeruginosa) in the microbiology laboratory. The study was designed to compare phenotypic with molecular identification. Results of molecular analyses were compared with two commercially available identification systems (API 20 NE, VITEK 2 fluorescent card; bioMérieux, Marcy l'Etoile, France). By 16S rRNA gene sequence analyses, 92% of the isolates were assigned to species level and 8% to genus level. Using API 20 NE, 54% of the isolates were assigned to species and 7% to genus level, and 39% of the isolates could not be discriminated at any taxonomic level. The respective numbers for VITEK 2 were 53%, 1%, and 46%, respectively. Fifteen percent and 43% of the isolates corresponded to species not included in the API 20 NE and VITEK 2 databases, respectively. We conclude that 16S rRNA gene sequencing is an effective means for the identification of clinically relevant nonfermenting gram-negative bacilli. Based on our experience, we propose an algorithm for proper identification of nonfermenting gram-negative bacilli in the diagnostic laboratory.</description><subject>Bacterial Typing Techniques - instrumentation</subject><subject>Bacterial Typing Techniques - methods</subject><subject>Bacterial Typing Techniques - standards</subject><subject>Bacteriology</subject><subject>Biological and medical sciences</subject><subject>DNA, Bacterial - genetics</subject><subject>Fermentation</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gram-Negative Bacteria - genetics</subject><subject>Gram-Negative Bacteria - isolation & purification</subject><subject>Gram-Negative Bacterial Infections - diagnosis</subject><subject>Gram-Negative Bacterial Infections - microbiology</subject><subject>Humans</subject><subject>Infectious diseases</subject><subject>Laboratories</subject><subject>Medical sciences</subject><subject>Microbiology</subject><subject>Prospective Studies</subject><subject>Reagent Kits, Diagnostic</subject><subject>RNA, Ribosomal, 16S - analysis</subject><subject>RNA, Ribosomal, 16S - genetics</subject><issn>0095-1137</issn><issn>1098-660X</issn><issn>1098-5530</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2006</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFktGOEyEUhidG466rr-Dihd5NhYEB5sakW2ut1mrsrvGOnM5Ay2YGVpjW9IV8Tum2sXrlDSSc7_wcfv4suyR4QEghX9_W3YCxARsQWlY5oZwPCoz5g-yc4ErmnOPvD7NzjKsyJ4SKs-xJjLcYE8bK8nF2RnhZCcnpefaL8AUKX-dDNNFOo4X-sdGutm6FtjrETUT9WqPhlykqMJqP0WIXe90hcM194dv0evwRFWj6Np_Mr9AIQoOMD2jaaNdbY2vorXfIGzT3zujQ7Y-T9iRAl8_1KpW3Gl1B3etgAVl3rzpqrUutLZrB0gfofdg9zR4ZaKN-dtwvspt34-vR-3z2eTIdDWd5XVZFn0vZgACWLNK0IroqmdBprU1Fay54VVYlhsRIaXgDUFZADSV0KXFhsKwFvcjeHHTvNstON3WaN0Cr7oLtIOyUB6v-rTi7Viu_VcnZ5KdMAq-OAsEnK2OvOhtr3bbgtN9ExYVkWJL_g0SQgjBMEygOYB18jEGbP9MQrPZhUB9GnxRjiql9GNQ-DGofhtT5_O_HnPqOv5-Al0cAYvLbBEhfH0-cEBhLXiTuxYFb29X6pw1aQexUyuDp2sRcHhgDXsEqJJ2bRYEJxQRzwTCjvwFEL9Fg</recordid><startdate>20060401</startdate><enddate>20060401</enddate><creator>Bosshard, P. 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Psychology</topic><topic>Gram-Negative Bacteria - genetics</topic><topic>Gram-Negative Bacteria - isolation & purification</topic><topic>Gram-Negative Bacterial Infections - diagnosis</topic><topic>Gram-Negative Bacterial Infections - microbiology</topic><topic>Humans</topic><topic>Infectious diseases</topic><topic>Laboratories</topic><topic>Medical sciences</topic><topic>Microbiology</topic><topic>Prospective Studies</topic><topic>Reagent Kits, Diagnostic</topic><topic>RNA, Ribosomal, 16S - analysis</topic><topic>RNA, Ribosomal, 16S - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bosshard, P. P</creatorcontrib><creatorcontrib>Zbinden, R</creatorcontrib><creatorcontrib>Abels, S</creatorcontrib><creatorcontrib>Böddinghaus, B</creatorcontrib><creatorcontrib>Altwegg, M</creatorcontrib><creatorcontrib>Böttger, E. 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| subjects | Bacterial Typing Techniques - instrumentation Bacterial Typing Techniques - methods Bacterial Typing Techniques - standards Bacteriology Biological and medical sciences DNA, Bacterial - genetics Fermentation Fundamental and applied biological sciences. Psychology Gram-Negative Bacteria - genetics Gram-Negative Bacteria - isolation & purification Gram-Negative Bacterial Infections - diagnosis Gram-Negative Bacterial Infections - microbiology Humans Infectious diseases Laboratories Medical sciences Microbiology Prospective Studies Reagent Kits, Diagnostic RNA, Ribosomal, 16S - analysis RNA, Ribosomal, 16S - genetics |
| title | 16S rRNA Gene Sequencing versus the API 20 NE System and the VITEK 2 ID-GNB Card for Identification of Nonfermenting Gram-Negative Bacteria in the Clinical Laboratory |
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