{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T06:11:45Z","timestamp":1789625505965,"version":"build-2803163510"},"reference-count":46,"publisher":"Wiley","issue":"11","license":[{"start":{"date-parts":[[2018,7,27]],"date-time":"2018-07-27T00:00:00Z","timestamp":1532649600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/100000098","name":"NIH Clinical Center","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000098","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001807","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de S\u00e3o Paulo","doi-asserted-by":"publisher","award":["2013\/01280\u20107"],"award-info":[{"award-number":["2013\/01280\u20107"]}],"id":[{"id":"10.13039\/501100001807","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Mycoses"],"published-print":{"date-parts":[[2018,11]]},"abstract":"<jats:title>Summary<\/jats:title><jats:p><jats:italic>Pneumocystis jirovecii<\/jats:italic> can cause severe potentially life\u2010threatening pneumonia (<jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content>) in kidney transplant patients. Prophylaxis of patients against PCP in this setting is usually performed during 6\u00a0months after transplantation. The aim of this study is to describe the molecular epidemiology of a cluster of <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> in renal transplant recipients in Brazil. Renal transplant patients who developed <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> between May and December 2011 had their formalin\u2010fixed paraffin\u2010embedded (<jats:styled-content style=\"fixed-case\">FFPE<\/jats:styled-content>) lung biopsy samples analysed. <jats:italic>Pneumocystis jirovecii<\/jats:italic> 23S mitochondrial large subunit of ribosomal <jats:styled-content style=\"fixed-case\">RNA<\/jats:styled-content> (23S mt<jats:styled-content style=\"fixed-case\">LSU<\/jats:styled-content>\u2010<jats:styled-content style=\"fixed-case\">rRNA<\/jats:styled-content>), 26S <jats:styled-content style=\"fixed-case\">rRNA<\/jats:styled-content>, and dihydropteroate synthase (DHPS) genes were amplified by polymerase chain reaction (<jats:styled-content style=\"fixed-case\">PCR<\/jats:styled-content>), sequenced, and analysed for genetic variation. During the study period, 17 patients developed <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> (only four infections were documented within the first year after transplantation) and six (35.3%) died. Thirty <jats:styled-content style=\"fixed-case\">FFPE<\/jats:styled-content> samples from 11 patients, including one external control <jats:styled-content style=\"fixed-case\">HIV<\/jats:styled-content>\u2010infected patient, had fungal <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> successfully extracted for further amplification and sequencing for all three genes. A total of five genotypes were identified among the 10 infected patients. Of note, four patients were infected by more than one genotype and seven patients were infected by the same genotype. <jats:styled-content style=\"fixed-case\">DNA<\/jats:styled-content> extracted from <jats:styled-content style=\"fixed-case\">FFPE<\/jats:styled-content> samples can be used for genotyping; this approach allowed us to demonstrate that multiple <jats:italic>P.\u00a0jirovecii<\/jats:italic> strains were responsible for this cluster, and one genotype was found infecting seven patients. The knowledge of the causative agents of <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> may help to develop new initiatives for control and prevention of <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> among patients undergoing renal transplant and improve routine <jats:styled-content style=\"fixed-case\">PCP<\/jats:styled-content> prophylaxis.<\/jats:p>","DOI":"10.1111\/myc.12823","type":"journal-article","created":{"date-parts":[[2018,7,11]],"date-time":"2018-07-11T08:34:59Z","timestamp":1531298099000},"page":"845-852","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genetic diversity of <i>Pneumocystis jirovecii<\/i> from a cluster of cases of pneumonia in renal transplant patients: Cross\u2010sectional study"],"prefix":"10.1111","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4197-7905","authenticated-orcid":false,"given":"Giannina","family":"Ricci","sequence":"first","affiliation":[{"name":"Special Mycology Laboratory Division of Infectious Diseases Department of Medicine Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel Wagner","family":"Santos","sequence":"additional","affiliation":[{"name":"Special Mycology Laboratory Division of Infectious Diseases Department of Medicine Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"},{"name":"Hospital do Rim Funda\u00e7\u00e3o Oswaldo Ramos  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joseph A.","family":"Kovacs","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department NIH Clinical Center National Institutes of Health  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Angela Satie","family":"Nishikaku","sequence":"additional","affiliation":[{"name":"Special Mycology Laboratory Division of Infectious Diseases Department of Medicine Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taina Veras","family":"de Sandes\u2010Freitas","sequence":"additional","affiliation":[{"name":"Hospital do Rim Funda\u00e7\u00e3o Oswaldo Ramos  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anderson Messias","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Molecular Biology Division Department of Microbiology, Immunology and Parasitology (DMIP) Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geetha","family":"Kutty","sequence":"additional","affiliation":[{"name":"Critical Care Medicine Department NIH Clinical Center National Institutes of Health  Bethesda Maryland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Regina","family":"Affonso","sequence":"additional","affiliation":[{"name":"Biotechnology Center, Nuclear and Energy Research Institute (IPEN)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"H\u00e9lio Tedesco","family":"Silva","sequence":"additional","affiliation":[{"name":"Hospital do Rim Funda\u00e7\u00e3o Oswaldo Ramos  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 Osmar","family":"Medina\u2010Pestana","sequence":"additional","affiliation":[{"name":"Hospital do Rim Funda\u00e7\u00e3o Oswaldo Ramos  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcello Fabiano","family":"de Franco","sequence":"additional","affiliation":[{"name":"Pathology Department Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arnaldo Lopes","family":"Colombo","sequence":"additional","affiliation":[{"name":"Special Mycology Laboratory Division of Infectious Diseases Department of Medicine Universidade Federal de S\u00e3o Paulo (UNIFESP)  S\u00e3o Paulo SP Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,7,27]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2009.880"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro1621"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1086\/513198"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cir996"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis217"},{"key":"e_1_2_7_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cir329"},{"key":"e_1_2_7_8_1","doi-asserted-by":"publisher","DOI":"10.1038\/ki.2013.212"},{"issue":"7","key":"e_1_2_7_9_1","first-page":"673","article-title":"Outbreaks and clustering of Pneumocystis pneumonia in kidney transplant recipients: a systematic review","volume":"49","author":"Boer MG","year":"2011","journal-title":"Med Mycol"},{"key":"e_1_2_7_10_1","doi-asserted-by":"publisher","DOI":"10.1097\/TP.0b013e3182a1618c"},{"key":"e_1_2_7_11_1","doi-asserted-by":"publisher","DOI":"10.1097\/TP.0b013e3181aed389"},{"key":"e_1_2_7_12_1","doi-asserted-by":"publisher","DOI":"10.1093\/ndt\/gfq689"},{"key":"e_1_2_7_13_1","doi-asserted-by":"publisher","DOI":"10.1111\/ajt.12119"},{"key":"e_1_2_7_14_1","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.057794-0"},{"key":"e_1_2_7_15_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1399-3062.2009.00447.x"},{"key":"e_1_2_7_16_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1399-3062.2011.00691.x"},{"key":"e_1_2_7_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/cis810"},{"key":"e_1_2_7_18_1","doi-asserted-by":"publisher","DOI":"10.1086\/644643"},{"key":"e_1_2_7_19_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.38.8.2940-2942.2000"},{"key":"e_1_2_7_20_1","doi-asserted-by":"publisher","DOI":"10.1093\/occmed\/50.7.508"},{"key":"e_1_2_7_21_1","first-page":"315","volume-title":"PCR Protocols: A Guide to Methods and Applications","author":"White TJ","year":"1990"},{"key":"e_1_2_7_22_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsim.2005.06.006"},{"key":"e_1_2_7_23_1","doi-asserted-by":"publisher","DOI":"10.1080\/00365540510038505"},{"issue":"12","key":"e_1_2_7_24_1","doi-asserted-by":"crossref","first-page":"3086","DOI":"10.1128\/jcm.35.12.3086-3091.1997","article-title":"Typing of Pneumocystis carinii f. sp. hominis by single\u2010strand conformation polymorphism of four genomic regions","volume":"35","author":"Hauser PM","year":"1997","journal-title":"J Clin Microbiol"},{"key":"e_1_2_7_25_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-015-0793-3"},{"key":"e_1_2_7_26_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.186"},{"key":"e_1_2_7_27_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.175"},{"key":"e_1_2_7_28_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.8.3.195"},{"key":"e_1_2_7_29_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/mst010"},{"key":"e_1_2_7_30_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp187"},{"key":"e_1_2_7_31_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1365-294X.2006.02908.x"},{"key":"e_1_2_7_32_1","doi-asserted-by":"publisher","DOI":"10.1093\/oxfordjournals.molbev.a026036"},{"key":"e_1_2_7_33_1","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msw054"},{"key":"e_1_2_7_34_1","doi-asserted-by":"publisher","DOI":"10.1109\/TAC.1974.1100705"},{"issue":"4","key":"e_1_2_7_35_1","first-page":"678","article-title":"Estimation of the number of nucleotide substitutions when there are strong transition\u2010transversion and G+C\u2010content biases","volume":"9","author":"Tamura K","year":"1992","journal-title":"Mol Biol Evol"},{"issue":"4","key":"e_1_2_7_36_1","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2408678","article-title":"Confidence limits on phylogenies: an approach using the bootstrap","volume":"39","author":"Felsenstein J","year":"1974","journal-title":"Evolution"},{"key":"e_1_2_7_37_1","doi-asserted-by":"publisher","DOI":"10.1086\/345721"},{"key":"e_1_2_7_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2011.03.007"},{"key":"e_1_2_7_39_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.39.10.3789-3792.2001"},{"key":"e_1_2_7_40_1","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.10.75"},{"key":"e_1_2_7_41_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.2006.00104.x"},{"key":"e_1_2_7_42_1","doi-asserted-by":"publisher","DOI":"10.3109\/13693786.2011.593051"},{"key":"e_1_2_7_43_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-015-0847-6"},{"key":"e_1_2_7_44_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajic.2015.11.012"},{"key":"e_1_2_7_45_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.transproceed.2016.05.017"},{"key":"e_1_2_7_46_1","doi-asserted-by":"publisher","DOI":"10.4103\/0971-4065.132987"},{"key":"e_1_2_7_47_1","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00043-16"}],"container-title":["Mycoses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1111%2Fmyc.12823","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/myc.12823","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,15]],"date-time":"2023-09-15T11:16:21Z","timestamp":1694776581000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/myc.12823"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,7,27]]},"references-count":46,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,11]]}},"alternative-id":["10.1111\/myc.12823"],"URL":"https:\/\/doi.org\/10.1111\/myc.12823","archive":["Portico"],"relation":{},"ISSN":["0933-7407","1439-0507"],"issn-type":[{"value":"0933-7407","type":"print"},{"value":"1439-0507","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,7,27]]},"assertion":[{"value":"2018-01-16","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-07-01","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2018-07-27","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}