Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria
Identifieur interne : 001079 ( Istex/Corpus ); précédent : 001078; suivant : 001080Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria
Auteurs : F. Pourahmad ; K D Thompson ; J B Taggart ; A. Adams ; R H RichardsSource :
- Journal of Fish Diseases [ 0140-7775 ] ; 2008-12.
English descriptors
- KwdEn :
Abstract
Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐Mycobacterium isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum–M. peregrinum probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.
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DOI: 10.1111/j.1365-2761.2008.00968.x
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ISTEX:2D5C2798410DFA20B562358AAACF5C085E18128ELe document en format XML
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Pourahmad</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation><affiliation><mods:affiliation> School of Veterinary Medicine, Ilam University, Ilam, Iran</mods:affiliation></affiliation></author><author><name sortKey="Thompson, K D" sort="Thompson, K D" uniqKey="Thompson K" first="K D" last="Thompson">K D Thompson</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Taggart, J B" sort="Taggart, J B" uniqKey="Taggart J" first="J B" last="Taggart">J B Taggart</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Adams, A" sort="Adams, A" uniqKey="Adams A" first="A" last="Adams">A. Adams</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Richards, R H" sort="Richards, R H" uniqKey="Richards R" first="R H" last="Richards">R H Richards</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:2D5C2798410DFA20B562358AAACF5C085E18128E</idno><date when="2008" year="2008">2008</date><idno type="doi">10.1111/j.1365-2761.2008.00968.x</idno><idno type="url">https://api.istex.fr/document/2D5C2798410DFA20B562358AAACF5C085E18128E/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">001079</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">001079</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria</title><author><name sortKey="Pourahmad, F" sort="Pourahmad, F" uniqKey="Pourahmad F" first="F" last="Pourahmad">F. Pourahmad</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation><affiliation><mods:affiliation> School of Veterinary Medicine, Ilam University, Ilam, Iran</mods:affiliation></affiliation></author><author><name sortKey="Thompson, K D" sort="Thompson, K D" uniqKey="Thompson K" first="K D" last="Thompson">K D Thompson</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Taggart, J B" sort="Taggart, J B" uniqKey="Taggart J" first="J B" last="Taggart">J B Taggart</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Adams, A" sort="Adams, A" uniqKey="Adams A" first="A" last="Adams">A. Adams</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author><author><name sortKey="Richards, R H" sort="Richards, R H" uniqKey="Richards R" first="R H" last="Richards">R H Richards</name><affiliation><mods:affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Fish Diseases</title><idno type="ISSN">0140-7775</idno><idno type="eISSN">1365-2761</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2008-12">2008-12</date><biblScope unit="volume">31</biblScope><biblScope unit="issue">12</biblScope><biblScope unit="page" from="931">931</biblScope><biblScope unit="page" to="940">940</biblScope></imprint><idno type="ISSN">0140-7775</idno></series><idno type="istex">2D5C2798410DFA20B562358AAACF5C085E18128E</idno><idno type="DOI">10.1111/j.1365-2761.2008.00968.x</idno><idno type="ArticleID">JFD968</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0140-7775</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>INNO‐LiPA mycobacteria V2 assay</term><term>ITS1 region sequencing</term><term>aquatic mycobacteria</term><term>identification</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐Mycobacterium isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum–M. peregrinum probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.</div></front></TEI><istex><corpusName>wiley</corpusName><author><json:item><name>F Pourahmad</name><affiliations><json:string>Institute of Aquaculture, University of Stirling, Stirling, UK</json:string><json:string>School of Veterinary Medicine, Ilam University, Ilam, Iran</json:string></affiliations></json:item><json:item><name>K D Thompson</name><affiliations><json:string>Institute of Aquaculture, University of Stirling, Stirling, UK</json:string></affiliations></json:item><json:item><name>J B Taggart</name><affiliations><json:string>Institute of Aquaculture, University of Stirling, Stirling, UK</json:string></affiliations></json:item><json:item><name>A Adams</name><affiliations><json:string>Institute of Aquaculture, University of Stirling, Stirling, UK</json:string></affiliations></json:item><json:item><name>R H Richards</name><affiliations><json:string>Institute of Aquaculture, University of Stirling, Stirling, UK</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>aquatic mycobacteria</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>identification</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>INNO‐LiPA mycobacteria V2 assay</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>ITS1 region sequencing</value></json:item></subject><articleId><json:string>JFD968</json:string></articleId><language><json:string>eng</json:string></language><originalGenre><json:string>article</json:string></originalGenre><abstract>Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐Mycobacterium isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum–M. peregrinum probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. 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Journal compilation © 2008 Blackwell Publishing Ltd</p></availability><date>2008</date></publicationStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria</title><author xml:id="author-1"><persName><forename type="first">F</forename><surname>Pourahmad</surname></persName><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><affiliation> School of Veterinary Medicine, Ilam University, Ilam, Iran</affiliation></author><author xml:id="author-2"><persName><forename type="first">K D</forename><surname>Thompson</surname></persName><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation></author><author xml:id="author-3"><persName><forename type="first">J B</forename><surname>Taggart</surname></persName><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation></author><author xml:id="author-4"><persName><forename type="first">A</forename><surname>Adams</surname></persName><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation></author><author xml:id="author-5"><persName><forename type="first">R H</forename><surname>Richards</surname></persName><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation></author></analytic><monogr><title level="j">Journal of Fish Diseases</title><idno type="pISSN">0140-7775</idno><idno type="eISSN">1365-2761</idno><idno type="DOI">10.1111/(ISSN)1365-2761</idno><imprint><publisher>Blackwell Publishing Ltd</publisher><pubPlace>Oxford, UK</pubPlace><date type="published" when="2008-12"></date><biblScope unit="volume">31</biblScope><biblScope unit="issue">12</biblScope><biblScope unit="page" from="931">931</biblScope><biblScope unit="page" to="940">940</biblScope></imprint></monogr><idno type="istex">2D5C2798410DFA20B562358AAACF5C085E18128E</idno><idno type="DOI">10.1111/j.1365-2761.2008.00968.x</idno><idno type="ArticleID">JFD968</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2008</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐Mycobacterium isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum–M. peregrinum probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>keywords</head><item><term>aquatic mycobacteria</term></item><item><term>identification</term></item><item><term>INNO‐LiPA mycobacteria V2 assay</term></item><item><term>ITS1 region sequencing</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2008-12">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/document/2D5C2798410DFA20B562358AAACF5C085E18128E/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="Wiley, elements deleted: body"><istex:xmlDeclaration>version="1.0" encoding="UTF-8" standalone="yes"</istex:xmlDeclaration><istex:document><component version="2.0" type="serialArticle" xml:lang="en"><header><publicationMeta level="product"><publisherInfo><publisherName>Blackwell Publishing Ltd</publisherName><publisherLoc>Oxford, UK</publisherLoc></publisherInfo><doi origin="wiley" registered="yes">10.1111/(ISSN)1365-2761</doi><issn type="print">0140-7775</issn><issn type="electronic">1365-2761</issn><idGroup><id type="product" value="JFD"></id><id type="publisherDivision" value="ST"></id></idGroup><titleGroup><title type="main" sort="JOURNAL OF FISH DISEASES">Journal of Fish Diseases</title></titleGroup></publicationMeta><publicationMeta level="part" position="12012"><doi origin="wiley">10.1111/jfd.2008.31.issue-12</doi><numberingGroup><numbering type="journalVolume" number="31">31</numbering><numbering type="journalIssue" number="12">12</numbering></numberingGroup><coverDate startDate="2008-12">December 2008</coverDate></publicationMeta><publicationMeta level="unit" type="article" position="6" status="forIssue"><doi origin="wiley">10.1111/j.1365-2761.2008.00968.x</doi><idGroup><id type="unit" value="JFD968"></id></idGroup><countGroup><count type="pageTotal" number="10"></count></countGroup><titleGroup><title type="tocHeading1">Original Articles</title></titleGroup><copyright>© 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd</copyright><eventGroup><event type="firstOnline" date="2008-10-16"></event><event type="publishedOnlineFinalForm" date="2008-11-07"></event><event type="xmlConverted" agent="Converter:BPG_TO_WML3G version:2.3.5 mode:FullText source:FullText result:FullText" date="2010-04-07"></event><event type="xmlConverted" agent="Converter:WILEY_ML3G_TO_WILEY_ML3GV2 version:3.8.8" date="2014-01-30"></event><event type="xmlConverted" agent="Converter:WML3G_To_WML3G version:4.1.7 mode:FullText,remove_FC" date="2014-10-30"></event></eventGroup><numberingGroup><numbering type="pageFirst" number="931">931</numbering><numbering type="pageLast" number="940">940</numbering></numberingGroup><correspondenceTo><i>F Pourahmad, Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
(e‐mail: </i><email>fp4@stir.ac.uk</email><i>)</i></correspondenceTo><linkGroup><link type="toTypesetVersion" href="file:JFD.JFD968.pdf"></link></linkGroup></publicationMeta><contentMeta><unparsedEditorialHistory>Recieved: 14 December 2007 Accepted: 5 May 2008</unparsedEditorialHistory><countGroup><count type="figureTotal" number="3"></count><count type="tableTotal" number="2"></count></countGroup><titleGroup><title type="main">Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria</title><title type="shortAuthors"><b>F Pourahmad et al.</b></title><title type="short"><i>Use of INNO‐LiPA v2 assay to identify mycobacteria</i></title></titleGroup><creators><creator creatorRole="author" xml:id="cr1" affiliationRef="#a1 #a2"><personName><givenNames>F</givenNames><familyName>Pourahmad</familyName></personName></creator><creator creatorRole="author" xml:id="cr2" affiliationRef="#a1"><personName><givenNames>K D</givenNames><familyName>Thompson</familyName></personName></creator><creator creatorRole="author" xml:id="cr3" affiliationRef="#a1"><personName><givenNames>J B</givenNames><familyName>Taggart</familyName></personName></creator><creator creatorRole="author" xml:id="cr4" affiliationRef="#a1"><personName><givenNames>A</givenNames><familyName>Adams</familyName></personName></creator><creator creatorRole="author" xml:id="cr5" affiliationRef="#a1"><personName><givenNames>R H</givenNames><familyName>Richards</familyName></personName></creator></creators><affiliationGroup><affiliation xml:id="a1" countryCode="GB"><unparsedAffiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</unparsedAffiliation></affiliation><affiliation xml:id="a2"><unparsedAffiliation> School of Veterinary Medicine, Ilam University, Ilam, Iran</unparsedAffiliation></affiliation></affiliationGroup><keywordGroup xml:lang="en"><keyword xml:id="k1">aquatic mycobacteria</keyword><keyword xml:id="k2">identification</keyword><keyword xml:id="k3">INNO‐LiPA mycobacteria V2 assay</keyword><keyword xml:id="k4">ITS1 region sequencing</keyword></keywordGroup><abstractGroup><abstract type="main" xml:lang="en"><title type="main">Abstract</title><p>Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐<i>Mycobacterium</i> isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the <i>Mycobacterium</i> genus probe on the LiPA strip. All <i>M. marinum</i>, <i>M. fortuitum</i> and <i>M. chelonae</i> reference and field strains and three out of the four <i>M. gordonae</i> isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. <i>M. chelonae</i> and <i>M. fortuitum.</i> A <i>Mycobacterium</i> isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of <i>M. shottsii</i> and <i>M. pseudoshottsii</i> with the kit because these isolates reacted with the <i>M. marinum</i>/<i>M. ulcerans</i> probe. Moreover, nine of the 13 field isolates presumed to be <i>M. fortuitum</i> from the results of the kit had closer ITS sequence homology with <i>M. conceptionense</i>, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the <i>M. fortuitum</i>–<i>M. peregrinum</i> probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.</p></abstract></abstractGroup></contentMeta></header></component></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria</title></titleInfo><titleInfo type="abbreviated" lang="en"><title>Use of INNO‐LiPA v2 assay to identify mycobacteria</title></titleInfo><titleInfo type="alternative" contentType="CDATA" lang="en"><title>Evaluation of the INNO‐LiPA mycobacteria v2 assay for identification of aquatic mycobacteria</title></titleInfo><name type="personal"><namePart type="given">F</namePart><namePart type="family">Pourahmad</namePart><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><affiliation> School of Veterinary Medicine, Ilam University, Ilam, Iran</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">K D</namePart><namePart type="family">Thompson</namePart><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">J B</namePart><namePart type="family">Taggart</namePart><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A</namePart><namePart type="family">Adams</namePart><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">R H</namePart><namePart type="family">Richards</namePart><affiliation> Institute of Aquaculture, University of Stirling, Stirling, UK</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="article" displayLabel="article"></genre><originInfo><publisher>Blackwell Publishing Ltd</publisher><place><placeTerm type="text">Oxford, UK</placeTerm></place><dateIssued encoding="w3cdtf">2008-12</dateIssued><edition>Recieved: 14 December 2007 Accepted: 5 May 2008</edition><copyrightDate encoding="w3cdtf">2008</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType><extent unit="figures">3</extent><extent unit="tables">2</extent></physicalDescription><abstract lang="en">Fifty‐seven isolates of mycobacteria comprising 10 reference strains, 47 field isolates and one non‐Mycobacterium isolate were screened using commercial INNO‐LiPA v2 assay kits. All mycobacteria isolates tested hybridized with the Mycobacterium genus probe on the LiPA strip. All M. marinum, M. fortuitum and M. chelonae reference and field strains and three out of the four M. gordonae isolates hybridized to their corresponding species‐ or complex‐specific probes. Two cultures (a type strain and a field isolate) yielded mixed growth of two mycobacterial species, i.e. M. chelonae and M. fortuitum. A Mycobacterium isolate from one of these cultures was subsequently purified and correctly identified with the kit. However, sequence analysis of the 16S–23S rRNA internal transcribed spacer (ITS) region of various mycobacteria isolates revealed a misidentification of M. shottsii and M. pseudoshottsii with the kit because these isolates reacted with the M. marinum/M. ulcerans probe. Moreover, nine of the 13 field isolates presumed to be M. fortuitum from the results of the kit had closer ITS sequence homology with M. conceptionense, a species which, to our knowledge, has never been reported in fish. These findings highlight the need to redesign the M. fortuitum–M. peregrinum probe included in the INNO‐LiPA assay and to introduce additional complex‐specific probes into the kit. Nevertheless, the kit proved to be a rapid and reliable method for identifying mycobacteria in the aquatic environment and would be particularly useful in laboratories without sequencing facilities.</abstract><subject lang="en"><genre>keywords</genre><topic>aquatic mycobacteria</topic><topic>identification</topic><topic>INNO‐LiPA mycobacteria V2 assay</topic><topic>ITS1 region sequencing</topic></subject><relatedItem type="host"><titleInfo><title>Journal of Fish Diseases</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0140-7775</identifier><identifier type="eISSN">1365-2761</identifier><identifier type="DOI">10.1111/(ISSN)1365-2761</identifier><identifier type="PublisherID">JFD</identifier><part><date>2008</date><detail type="volume"><caption>vol.</caption><number>31</number></detail><detail type="issue"><caption>no.</caption><number>12</number></detail><extent unit="pages"><start>931</start><end>940</end><total>10</total></extent></part></relatedItem><identifier type="istex">2D5C2798410DFA20B562358AAACF5C085E18128E</identifier><identifier type="DOI">10.1111/j.1365-2761.2008.00968.x</identifier><identifier type="ArticleID">JFD968</identifier><accessCondition type="use and reproduction" contentType="copyright">© 2008 The Authors. 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