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We then analyzed 133 consecutive bronchoalveolar lavage (<jats:styled-content style=\"fixed-case\">BAL<\/jats:styled-content>) fluids tested positive for <jats:italic>P. jirovecii <\/jats:italic><jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> by quantitative real\u2010time <jats:styled-content style=\"fixed-case\">PCR<\/jats:styled-content>, obtained from two hospitals in different locations (Hospital 1 [<jats:italic>n\u00a0<\/jats:italic>=<jats:italic>\u00a0<\/jats:italic>95] and Hospital 2 [<jats:italic>n\u00a0<\/jats:italic>=<jats:italic>\u00a0<\/jats:italic>38]). We detected three different alleles, either singly (<jats:italic>mt85C<\/jats:italic>: 39.1%; <jats:italic>mt85T<\/jats:italic>: 24.1%; <jats:italic>mt85A<\/jats:italic>: 9.8%) or together (27%), and an association between <jats:italic>P. jirovecii mt85<\/jats:italic> genotype and the patient's place of hospitalization (<jats:italic>p\u00a0<\/jats:italic>=<jats:italic>\u00a0<\/jats:italic>0.011). The lowest fungal loads (median\u00a0=\u00a00.82\u00a0\u00d7\u00a010<jats:sup>3<\/jats:sup> copies\/\u03bcl; range: 15\u201311\u00a0\u00d7\u00a010<jats:sup>3<\/jats:sup>) were associated with <jats:italic>mt85<\/jats:italic>A and the highest (median\u00a0=\u00a01.4\u00a0\u00d7\u00a010<jats:sup>6<\/jats:sup> copies\/\u03bcl; range: 17\u00a0\u00d7\u00a010<jats:sup>3<\/jats:sup>\u20131.3\u00a0\u00d7\u00a010<jats:sup>7<\/jats:sup>) with <jats:italic>mt85<jats:styled-content style=\"fixed-case\">CTA<\/jats:styled-content><\/jats:italic> (<jats:italic>p\u00a0<\/jats:italic>=<jats:italic>\u00a0<\/jats:italic>0.010). The ratios of the various alleles differed between the 36 mixed\u2010genotype samples. In tests of serial <jats:styled-content style=\"fixed-case\">BAL<\/jats:styled-content>s (median: 20\u00a0d; range 4\u2013525) from six patients with mixed genotypes, allele ratio changes were observed five times and genotype replacement once. Therefore, allele ratio changes seem more frequent than genotype replacement when using a <jats:styled-content style=\"fixed-case\">SN<\/jats:styled-content>aPshot assay more sensitive for detecting minority alleles than Sanger sequencing. Moreover, because microscopy detects only high fungal loads, the selection of microscopy\u2010positive samples may miss genotypes associated with low loads.<\/jats:p>","DOI":"10.1111\/jeu.12222","type":"journal-article","created":{"date-parts":[[2015,5,4]],"date-time":"2015-05-04T07:35:01Z","timestamp":1430724901000},"page":"650-656","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Correlation Between <i>Pneumocystis jirovecii<\/i> Mitochondrial Genotypes and High and Low Fungal Loads Assessed by Single Nucleotide Primer Extension Assay and Quantitative Real\u2010Time <scp>PCR<\/scp>"],"prefix":"10.1111","volume":"62","author":[{"given":"Alexandre","family":"Alanio","sequence":"first","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie AP\u2010HP Groupe Hospitalier Saint\u2010Louis\u2010Lariboisi\u00e8re\u2010Fernand\u2010Widal Paris France"},{"name":"Universit\u00e9 Paris\u2010Diderot Sorbonne Cit\u00e9 Paris France"},{"name":"Institut Pasteur, Unit\u00e9 de Mycologie Mol\u00e9culaire Centre National de R\u00e9f\u00e9rence Mycologie et Antifongiques Paris France"},{"name":"CNRS URA3012 Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martine","family":"Olivi","sequence":"additional","affiliation":[{"name":"Laboratoire Cerba Cergy\u2010Pontoise Saint\u2010Ouen\u2010l'Aum\u00f4ne France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Odile","family":"Cabaret","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie AP\u2010HP Groupe hospitalier Chenevier\u2010Mondor Cr\u00e9teil France"},{"name":"Universit\u00e9 Paris\u2010Est\u2010Cr\u00e9teil Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fran\u00e7oise","family":"Foulet","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie AP\u2010HP Groupe hospitalier Chenevier\u2010Mondor Cr\u00e9teil France"},{"name":"Universit\u00e9 Paris\u2010Est\u2010Cr\u00e9teil Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anne\u2010Pauline","family":"Bellanger","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie Centre hospitalier universitaire Besan\u00e7on France"},{"name":"Laboratoire Chrono\u2010Environnement Universit\u00e9 Franche\u2010Comt\u00e9 UMR CNRS 6249 Besan\u00e7on France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurence","family":"Millon","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie Centre hospitalier universitaire Besan\u00e7on France"},{"name":"Laboratoire Chrono\u2010Environnement Universit\u00e9 Franche\u2010Comt\u00e9 UMR CNRS 6249 Besan\u00e7on France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Berceanu","sequence":"additional","affiliation":[{"name":"Service d'H\u00e9matologie Centre Hospitalier Universitaire Besan\u00e7on France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catherine","family":"Cordonnier","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris\u2010Est\u2010Cr\u00e9teil Cr\u00e9teil France"},{"name":"D\u00e9partement d'H\u00e9matologie APHP Groupe Hospitalier Albert Chenevier\u2010Henri Mondor Creteil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean\u2010Marc","family":"Costa","sequence":"additional","affiliation":[{"name":"Laboratoire Cerba Cergy\u2010Pontoise Saint\u2010Ouen\u2010l'Aum\u00f4ne France"},{"name":"Laboratoire de Parasitologie\u2010Mycologie AP\u2010HP Groupe hospitalier Chenevier\u2010Mondor Cr\u00e9teil France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phane","family":"Bretagne","sequence":"additional","affiliation":[{"name":"Laboratoire de Parasitologie\u2010Mycologie AP\u2010HP Groupe Hospitalier Saint\u2010Louis\u2010Lariboisi\u00e8re\u2010Fernand\u2010Widal Paris France"},{"name":"Universit\u00e9 Paris\u2010Diderot Sorbonne Cit\u00e9 Paris France"},{"name":"Institut Pasteur, Unit\u00e9 de Mycologie Mol\u00e9culaire Centre National de R\u00e9f\u00e9rence Mycologie et Antifongiques Paris France"},{"name":"CNRS URA3012 Paris France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2015,5,27]]},"reference":[{"key":"e_1_2_6_2_1","unstructured":"Alanio A. 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