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Numerous reports have presented puzzling discrepancies between diagnosis methods. We addressed this confusion using fluorescent <jats:italic>in situ<\/jats:italic> hybridization and immunofluorescence assays to evaluate 34 duodenal biopsies and 1 lymph node biopsy from Whipple\u2019s patients. We showed the presence of bacteria in both CK20<jats:sup>+<\/jats:sup> epithelial cells and CD68<jats:sup>+<\/jats:sup> macrophages. Bacteria are found embedded in a biofilm hindering the detection of <jats:italic>T. whipplei<\/jats:italic>. Only after treatment of biopsies by glycosidases, co-localization of <jats:italic>T. whipplei<\/jats:italic> RNA\/DNA with bacterial proteins was restored. Moreover, using 13 bronchoalveolar lavages and 7 duodenal biopsies, we found that hydrolysis of the biofilm weakened the bacteria, facilitated bacterial DNA extraction and improved the sensitivity of qPCR detection by up to 1000x opening new perspectives for diagnostic and scientific approaches.<\/jats:p>","DOI":"10.1038\/srep23883","type":"journal-article","created":{"date-parts":[[2016,3,30]],"date-time":"2016-03-30T09:17:13Z","timestamp":1459329433000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Deglycosylation of Tropheryma whipplei biofilm and discrepancies between diagnostic results during Whipple\u2019s disease progression"],"prefix":"10.1038","volume":"6","author":[{"given":"Gilles","family":"Audoly","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florence","family":"Fenollar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean-Christophe","family":"Lagier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hubert","family":"Lepidi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Didier","family":"Raoult","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,3,30]]},"reference":[{"key":"BFsrep23883_CR1","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1016\/S0140-6736(03)12274-X","volume":"361","author":"T Marth","year":"2003","unstructured":"Marth, T. & Raoult, D. 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