1dfd7d85f6d85842a4e618526a780a21 pmc_33143112.pdf 39033d052d7919da191152eafbadbc0eae0378eb pmc_33143112.pdf 1bb5241e646eb3e27d47f07f39bdfcc2be60d07a2f2b2e1d5a3f275144570477 pmc_33143112.pdf Title: Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii Subject: Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, -TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: -TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen. Keywords: P. jirovecii; consensus MLST scheme; -TUB; CYB; mt26S and SOD Author: Lana Pasic, Lidia Goterris, Mercedes Guerrero-Murillo, Laszlo Irinyi, Alex Kan, Carolina A. Ponce, Sergio L. Vargas, M. Teresa Martin-Gomez and Wieland Meyer Creator: LaTeX with hyperref package Producer: pdfTeX-1.40.18 CreationDate: Fri Oct 30 11:00:09 2020 CET ModDate: Fri Oct 30 11:42:29 2020 CET Custom Metadata: no Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 20 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 2407454 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- CDJWEZ+Pxsy Type 1 Builtin yes yes no 10 0 MWHIBA+VnURWPalladioL Type 1 Custom yes yes no 14 0 OTGAEV+URWPalladioL-Ital Type 1 Custom yes yes no 19 0 SXQODV+URWPalladioL-Bold Type 1 Custom yes yes no 24 0 LOYRGX+URWPalladioL-BoldItal Type 1 Custom yes yes no 28 0 JZKNOS+URWPalladioL-Roma Type 1 Custom yes yes no 32 0 OFLXAT+Rpxr Type 1 Builtin yes yes no 36 0 YNURIB+Rpxmi Type 1 Builtin yes yes no 40 0 QTLELQ+Pxbsy Type 1 Builtin yes yes no 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IJRJYD+PalatinoLinotype-Italic TrueType WinAnsi yes yes yes 537 0 IJRJYD+PalatinoLinotype-Bold TrueType WinAnsi yes yes yes 541 0 OKQTER+PalatinoLinotype-Roman TrueType WinAnsi yes yes yes 545 0 TimesNewRomanPSMT TrueType WinAnsi no no no 549 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2024-10-02 04:00:51 CEST RepresentationInformation: pmc_33143112.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2023-03-31 11:47:35 CEST Size: 2407454 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 911 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: section.1 Item: Title: Investigated Loci and Typing Schemes Destination: section.2 Children: Item: Title: Nuclear rRNA Gene Cluster Destination: subsection.2.1 Item: Title: Mitochondrial Genes Destination: subsection.2.2 Item: Title: Nuclear Genes Destination: subsection.2.3 Item: Title: Amplification Rate and Variation of Target Loci Destination: section.3 Item: Title: Case Study: Assessing the Ability to Discriminate between Clinical Isolates Destination: section.4 Item: Title: Discussion Destination: section.5 Item: Title: Conclusions Destination: section.6 Item: Title: References Destination: section.6 Info: Title: Consensus Multilocus Sequence Typing Scheme for Pneumocystis jirovecii Author: Lana Pasic, Lidia Goterris, Mercedes Guerrero-Murillo, Laszlo Irinyi, Alex Kan, Carolina A. Ponce, Sergio L. Vargas, M. Teresa Martin-Gomez and Wieland Meyer Subject: Pneumocystis jirovecii is an opportunistic human pathogenic fungus causing severe pneumonia mainly in immunocompromised hosts. Multilocus sequence typing (MLST) remains the gold standard for genotyping of this unculturable fungus. However, the lack of a consensus scheme impedes a global comparison, large scale population studies and the development of a global MLST database. To overcome this problem this study compared all genetic regions (19 loci) currently used in 31 different published Pneumocystis MLST schemes. The most diverse/commonly used eight loci, -TUB, CYB, DHPS, ITS1, ITS1/2, mt26S and SOD, were further assess for their ability to be successfully amplified and sequenced, and for their discriminatory power. The most successful loci were tested to identify genetically related and unrelated cases. A new consensus MLST scheme consisting of four genetically independent loci: -TUB, CYB, mt26S and SOD, is herein proposed for standardised P. jirovecii typing, successfully amplifying low and high fungal burden specimens, showing adequate discriminatory power, and correctly identifying suspected related and unrelated isolates. The new consensus MLST scheme, if accepted, will for the first time provide a powerful tool to investigate outbreak settings and undertake global epidemiological studies shedding light on the spread of this important human fungal pathogen. 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