{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T23:20:23Z","timestamp":1790551223462,"version":"4.1.0"},"reference-count":53,"publisher":"American Society for Microbiology","issue":"8","license":[{"start":{"date-parts":[[2006,8,1]],"date-time":"2006-08-01T00:00:00Z","timestamp":1154390400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2006,8]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            In common with other diagnostic tests, detection of mycobacteria in tissue by microscopic examination is susceptible to spectrum bias. Since Crohn's disease is defined by the absence of detectable pathogenic organisms, the use of in situ techniques to search for\n            <jats:italic>Mycobacterium avium<\/jats:italic>\n            subsp.\n            <jats:italic>paratuberculosis<\/jats:italic>\n            in Crohn's disease samples requires validation of methods in a paucibacillary setting. To generate paucibacillary infection, C57BL\/6 mice were artificially infected with\n            <jats:italic>Mycobacterium avium<\/jats:italic>\n            subsp.\n            <jats:italic>paratuberculosis<\/jats:italic>\n            strain K10 and\n            <jats:italic>M. tuberculosis<\/jats:italic>\n            H37Rv, yielding tissues harboring fewer than one bacillus per oil immersion field. Serial sections of organs were then studied by cell wall-based staining techniques (Ziehl-Neelsen and auramine rhodamine) and nucleic acid-based staining techniques (in situ hybridization [ISH] and indirect in situ PCR [IS PCR]). Microscopic examination and measurement of morphometric parameters of bacilli revealed that for all methods,\n            <jats:italic>Mycobacterium avium<\/jats:italic>\n            subsp.\n            <jats:italic>paratuberculosis<\/jats:italic>\n            bacilli were observed to be shorter, smaller, and less rod shaped than\n            <jats:italic>M. tuberculosis<\/jats:italic>\n            bacilli. Ziehl-Neelsen, auramine rhodamine stains, ISH targeting rRNA, and IS-PCR targeting the IS\n            <jats:italic>900<\/jats:italic>\n            element afforded comparable sensitivities, but for all methods, visualization of individual bacterial forms required magnification \u00d71,000. Auramine rhodamine staining and IS-PCR generated positive signals in negative controls, indicating the nonspecificity of these assays. Together, our results indicate that detection of\n            <jats:italic>Mycobacterium avium<\/jats:italic>\n            subsp.\n            <jats:italic>paratuberculosis<\/jats:italic>\n            bacilli in tissue requires oil immersion microscopy, that rRNA-ISH provides sensitivity and specificity comparable to those of Ziehl-Neelsen staining, and that the microscopic detection limit for\n            <jats:italic>Mycobacterium avium<\/jats:italic>\n            subsp.\n            <jats:italic>paratuberculosis<\/jats:italic>\n            in tissue is governed more by bacterial burden than by staining method.\n          <\/jats:p>","DOI":"10.1128\/jcm.00585-06","type":"journal-article","created":{"date-parts":[[2006,8,5]],"date-time":"2006-08-05T01:54:18Z","timestamp":1154742858000},"page":"2942-2950","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":31,"title":["Evaluation of In Situ Methods Used To Detect\n            <i>Mycobacterium avium<\/i>\n            subsp.\n            <i>paratuberculosis<\/i>\n            in Samples from Patients with Crohn's Disease"],"prefix":"10.1128","volume":"44","author":[{"given":"Mangalakumari","family":"Jeyanathan","sequence":"first","affiliation":[{"name":"McGill University Health Centre, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Alexander","sequence":"additional","affiliation":[{"name":"McGill University Health Centre, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine Y.","family":"Turenne","sequence":"additional","affiliation":[{"name":"McGill University Health Centre, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christiane","family":"Girard","sequence":"additional","affiliation":[{"name":"Universite\u0301 de Montre\u0301al, Faculte\u0301 de Me\u0301decine Veterinaire, Ste.-Hyacinthe, Que\u0301bec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcel A.","family":"Behr","sequence":"additional","affiliation":[{"name":"McGill University Health Centre, Montreal, Quebec, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","first-page":"99","volume":"49","year":"1992","unstructured":"Allen, J. 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