Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approa...
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| Veröffentlicht in: | Emerging infectious diseases 2017-08, Vol.23 (8), p.1237-1245 |
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| creator | Charpentier, Elena Garnaud, Cécile Wintenberger, Claire Bailly, Sébastien Murat, Jean-Benjamin Rendu, John Pavese, Patricia Drouet, Thibault Augier, Caroline Malvezzi, Paolo Thiébaut-Bertrand, Anne Mallaret, Marie-Reine Epaulard, Olivier Cornet, Muriel Larrat, Sylvie Maubon, Danièle |
| description | Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus. |
| doi_str_mv | 10.3201/eid2308.161295 |
| format | Article |
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Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. 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Garnaud, Cécile ; Wintenberger, Claire ; Bailly, Sébastien ; Murat, Jean-Benjamin ; Rendu, John ; Pavese, Patricia ; Drouet, Thibault ; Augier, Caroline ; Malvezzi, Paolo ; Thiébaut-Bertrand, Anne ; Mallaret, Marie-Reine ; Epaulard, Olivier ; Cornet, Muriel ; Larrat, Sylvie ; Maubon, Danièle</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c1741-1921345d24797a6e97bdfad0a52fe11890e7eddb958fc2572742ebfb09dd98ba3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Adolescent</topic><topic>Adult</topic><topic>Aged</topic><topic>Case-Control Studies</topic><topic>Child</topic><topic>Child, Preschool</topic><topic>Computational Biology - methods</topic><topic>Disease Outbreaks</topic><topic>Female</topic><topic>Genotype</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Humans</topic><topic>Infant</topic><topic>Life Sciences</topic><topic>Male</topic><topic>Microbiology and Parasitology</topic><topic>Middle Aged</topic><topic>Multilocus Sequence Typing</topic><topic>Mycology</topic><topic>Phylogeny</topic><topic>Pneumocystis carinii - classification</topic><topic>Pneumocystis carinii - genetics</topic><topic>Pneumonia, Pneumocystis - epidemiology</topic><topic>Pneumonia, Pneumocystis - microbiology</topic><topic>Pneumonia, Pneumocystis - transmission</topic><topic>Polymorphism, Genetic</topic><topic>Sensitivity and Specificity</topic><topic>Young Adult</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Charpentier, Elena</creatorcontrib><creatorcontrib>Garnaud, Cécile</creatorcontrib><creatorcontrib>Wintenberger, Claire</creatorcontrib><creatorcontrib>Bailly, Sébastien</creatorcontrib><creatorcontrib>Murat, Jean-Benjamin</creatorcontrib><creatorcontrib>Rendu, John</creatorcontrib><creatorcontrib>Pavese, Patricia</creatorcontrib><creatorcontrib>Drouet, Thibault</creatorcontrib><creatorcontrib>Augier, Caroline</creatorcontrib><creatorcontrib>Malvezzi, Paolo</creatorcontrib><creatorcontrib>Thiébaut-Bertrand, Anne</creatorcontrib><creatorcontrib>Mallaret, Marie-Reine</creatorcontrib><creatorcontrib>Epaulard, Olivier</creatorcontrib><creatorcontrib>Cornet, Muriel</creatorcontrib><creatorcontrib>Larrat, Sylvie</creatorcontrib><creatorcontrib>Maubon, Danièle</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><jtitle>Emerging infectious diseases</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Charpentier, Elena</au><au>Garnaud, Cécile</au><au>Wintenberger, Claire</au><au>Bailly, Sébastien</au><au>Murat, Jean-Benjamin</au><au>Rendu, John</au><au>Pavese, Patricia</au><au>Drouet, Thibault</au><au>Augier, Caroline</au><au>Malvezzi, Paolo</au><au>Thiébaut-Bertrand, Anne</au><au>Mallaret, Marie-Reine</au><au>Epaulard, Olivier</au><au>Cornet, Muriel</au><au>Larrat, Sylvie</au><au>Maubon, Danièle</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1</atitle><jtitle>Emerging infectious diseases</jtitle><addtitle>Emerg Infect Dis</addtitle><date>2017-08</date><risdate>2017</risdate><volume>23</volume><issue>8</issue><spage>1237</spage><epage>1245</epage><pages>1237-1245</pages><issn>1080-6040</issn><eissn>1080-6059</eissn><abstract>Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included. Among the 12 solid organ transplant patients, 5 shared a major and unique genotype that was also found as a minor strain in a sixth patient. A transmission map analysis strengthened the suspicion of nosocomial acquisition of this strain for the 6 patients. NGS-MLST enables accurate determination of subpopulation, which allowed excluding other patients from the transmission network. NGS-MLST genotyping approach was essential to deciphering this outbreak. This innovative approach brings new insights for future epidemiologic studies on this uncultivable opportunistic fungus.</abstract><cop>United States</cop><pub>Centers for Disease Control and Prevention</pub><pmid>28726611</pmid><doi>10.3201/eid2308.161295</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0002-0377-0807</orcidid><orcidid>https://orcid.org/0000-0002-9080-7638</orcidid><orcidid>https://orcid.org/0000-0002-2179-4650</orcidid></addata></record> |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; PubMed Central Open Access |
| subjects | Adolescent Adult Aged Case-Control Studies Child Child, Preschool Computational Biology - methods Disease Outbreaks Female Genotype High-Throughput Nucleotide Sequencing Humans Infant Life Sciences Male Microbiology and Parasitology Middle Aged Multilocus Sequence Typing Mycology Phylogeny Pneumocystis carinii - classification Pneumocystis carinii - genetics Pneumonia, Pneumocystis - epidemiology Pneumonia, Pneumocystis - microbiology Pneumonia, Pneumocystis - transmission Polymorphism, Genetic Sensitivity and Specificity Young Adult |
| title | Added Value of Next-Generation Sequencing for Multilocus Sequence Typing Analysis of a Pneumocystis jirovecii Pneumonia Outbreak1 |
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