Genotyping and Coalescent Phylogenetic Analysis of Pneumocystis jiroveci from South Africa

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dc.contributor.authorRobberts F.J.L.
dc.contributor.authorLiebowitz L.D.
dc.contributor.authorChalkley L.J.
dc.date.accessioned2011-05-15T15:56:57Z
dc.date.available2011-05-15T15:56:57Z
dc.date.issued2004
dc.description.abstractSequence analysis of Pneumocystis jiroveci internal transcribed spacer (ITS) regions has become an important epidemiological tool. The objectives of the present study were to investigate sequence variations in the ITS1-5.8S ribosomal DNA (rDNA)-ITS2 regions; determine the P. jiroveci genotypes present in Cape Town, South Africa; and resolve the lineage evolution of the types by use of the coalescent theory. ITS regions were amplified from samples collected from 19 patients. PCR products were cloned, and four to five clones were sequenced from each specimen. Statistical parsimony was applied for coalescence-based network genotype analysis. The most prevalent type was Eg (14 of 19 patients, 33 of 83 clones), followed by Gg (4 of 19 patients, 7 of 83 clones), Eu (3 of 19 patients, 5 of 83 clones), and Gh (2 of 19 patients, 2 of 83 clones). Four new combinations (Eo, Je, Ge, and No), 11 new ITS1 sequences, and 13 new ITS2 sequences were identified. A new ITS2 type was detected in three patients and was designated type u. Coinfection appeared to be common, with 15 of 19 patients harboring more than one type and with up to six types per specimen. The resultant parsimony network identified Eg as the most probable ancestral haplotype and supported the occurrence of recombinational events within the population studied. Although the 5.8S rDNA region revealed only 13 clones containing one to two nucleotide polymorphisms, it may assist in defining types. Coalescent theory proposed that Eg is an ancestral type from which microevolutionary subtypes radiate.
dc.description.versionArticle
dc.identifier.citationJournal of Clinical Microbiology
dc.identifier.citation42
dc.identifier.citation4
dc.identifier.issn951137
dc.identifier.other10.1128/JCM.42.4.1505-1510.2004
dc.identifier.urihttp://hdl.handle.net/10019.1/10126
dc.subjectinternal transcribed spacer
dc.subjectribosome DNA
dc.subjectarticle
dc.subjectDNA extraction
dc.subjectevolution
dc.subjectgenotype
dc.subjecthaplotype
dc.subjectnonhuman
dc.subjectnucleotide sequence
dc.subjectparsimony analysis
dc.subjectphylogeny
dc.subjectPneumocystis
dc.subjectpneumocystis jiroveci
dc.subjectpolymerase chain reaction
dc.subjectpriority journal
dc.subjectsequence analysis
dc.subjectSouth Africa
dc.subjectAIDS-Related Opportunistic Infections
dc.subjectBase Sequence
dc.subjectDiseases in Twins
dc.subjectDNA, Ribosomal Spacer
dc.subjectEvolution, Molecular
dc.subjectGenotype
dc.subjectHIV Infections
dc.subjectHumans
dc.subjectMolecular Sequence Data
dc.subjectPhylogeny
dc.subjectPneumocystis
dc.subjectPneumonia, Pneumocystis
dc.subjectPolymerase Chain Reaction
dc.subjectRNA, Ribosomal, 5.8S
dc.subjectSequence Analysis, DNA
dc.subjectSouth Africa
dc.subjectTwins
dc.subjectPneumocystis
dc.subjectPneumocystis jirovecii
dc.subjectProtozoa
dc.titleGenotyping and Coalescent Phylogenetic Analysis of Pneumocystis jiroveci from South Africa
dc.typeArticle
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