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The present work was conducted to investigate the presence of <jats:italic>Legionella<\/jats:italic> spp. and its common species in hospital water supplies. Considering the limitations of culture method, polymerase chain reaction (PCR) assays were developed to detect the gene 16S rRNA irrespective of the bacterial serotype. Four well-established DNA extraction protocols (freeze &amp; thaw and phenol-chloroform as two manual protocols and two commercial kits) were tested and evaluated to release DNA from bacterial cells. A total of 45 samples were collected from seven distinct hospitals\u2019 sites during a period of 10\u00a0months. The PCR assay was used to amplify a 654-bp fragment of the 16S rRNA gene. <jats:italic>Legionella<\/jats:italic> were detected in 13 samples (28.9%) by all of the methods applied for DNA extraction. Significant differences were noted in the yield of extracted nucleic acids. <jats:italic>Legionella<\/jats:italic> were not detected in any of the samples when DNA extraction by freeze &amp; thaw was used. Excluding this method and comparing manual protocol with commercial kits, Kappa coefficient was calculated as 0.619 with <jats:italic>p<\/jats:italic>\u2009&lt;\u20090.05. Although no meaningful differences were found between the kits, DNA extraction with Bioneer kit exhibited a higher sensitivity than classical Qiagen. Showerheads and cold-water taps were the most and least contaminated sources with 55.5 and 9 percent positive samples, respectively. Moreover two positive samples were identified for species by DNA sequencing and submitted to the Gene Bank database with accession Nos. FJ480932 and FJ480933. The results obtained showed that despite the advantages of molecular assays in <jats:italic>Legionella<\/jats:italic> tracing in environmental sources, the use of optimised DNA extraction methods is critical.<\/jats:p>","DOI":"10.1186\/2052-336x-12-83","type":"journal-article","created":{"date-parts":[[2014,5,9]],"date-time":"2014-05-09T13:04:18Z","timestamp":1399640658000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Detection and identification of Legionella species in hospital water supplies through Polymerase Chain Reaction (16S rRNA)"],"prefix":"10.1186","volume":"12","author":[{"given":"Mohammad","family":"Rafiee","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mahsa","family":"Jahangiri-rad","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Homa","family":"Hajjaran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alireza","family":"Mesdaghinia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammad","family":"Hajaghazadeh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2014,5,9]]},"reference":[{"issue":"3\u20134","key":"5099_CR1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/j.ijheh.2007.06.002","volume":"211","author":"F Morio","year":"2008","unstructured":"Morio F, Corvec S, Caroff N, Legallou F, Drugeon H, Reynaud A: Real-time PCR assay for the detection and quantification of Legionella pneumophila in environmental water samples: utility for daily practice. 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