Genetic Diversity of
            <i>Pneumocystis carinii</i>
            f. sp.
            <i>hominis</i>
            Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Nimri, Laila; Moura, Iaci N. S.; Huang, Laurence; Rı́o, Carlos del; Rimland, David; Duchin, Jeffrey S.; Dotson, Ellen M.; Beard, Charles B.

doi:10.1128/jcm.40.4.1146-1151.2002

Cited by 38 publications

(28 citation statements)

References 24 publications

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“…The most prevalent haplotype worldwide, including Australia, is Eg, accounting for 23% of all published combinations (10,13,24,26,27,30). Unlike previous studies, a novel genotype (Isyd2) was found to be the second most common Australian haplotype, occurring in 18% of our samples.…”

Section: Discussionmentioning

confidence: 99%

“…Sequence gaps (caused by insertions and deletions in the alignment) are considered missing data, thereby greatly reducing the probability of incorrect and inaccurate phylogenies in the tree and hence faulty interpretations of global haplotype relationships. In addition, several ITS1 (n ϭ 12) and ITS2 (n ϭ 18) types were not included in this analysis, as the haplotypes formed by these ITS genotypes have not been detailed to allow inclusion (24,29).…”

Section: Methodsmentioning

confidence: 99%

“…P. jirovecii ITS genotypes were aligned with previously published and unpublished genotypes (GenBank accession no. AF013806 to AF013834, AF374238 to AF374265, AF498265, AF135711 to AF135712, AY328043 to AY328066, AY550105 to AY550109, and AF013835 to AF013840) (13,23,24,26,27,29,31). The mt LSU rRNA genotypes were characterized based on the polymorphic sites at codons 85 and 248: genotypes 1 (85:C/248:C), 2 (85:A/248:C), 3 (85:T/248:C), and 4 (85:C/248:T) (12).…”

Section: Methodsmentioning

confidence: 99%

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Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

et al. 2009

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Pneumocystis jirovecii is an important opportunistic pathogen in immunocompromised patients. Molecular typing is employed to study this pathogen, as no culture system exists. No Australian P. jirovecii strains have been previously studied. Direct sequencing, targeting the internal transcribed spacer (ITS) regions of the nuclear rRNA operon, the mitochondrial large-subunit rRNA (mt LSU rRNA), and the dihydropteroate synthase (DHPS) gene, was performed on 68 Australian samples, collected between 2001 and 2007. Seven novel Australian ITS haplotypes (a composite of the ITS1 and ITS2 regions) were identified (SYD1m, SYD1g, Isyd2, Esyd3, Osyd4, Ag, and Hc). A dendrogram of published ITS haplotypes revealed that of the seven novel haplotypes, three (SYD1m, SYD1g, and Osyd4) are closely related to the haplotype Eg. Applying statistical parsimony, an Australian haplotype network was constructed which identified Eg as the ancestral haplotype, with two unresolved loops encountered. This suggests that the ITS lacks the resolution required for evolutionary analysis. Only two mt LSU rRNA genotypes were detected, with genotype 1 predominating. Mutant DHPS genotypes were present in 13% (8/60) of the samples. The novel haplotype Isyd2 was associated with less severe disease than the other Australian haplotypes. In contrast, patients with mutant DHPS genotypes were more likely to have severe disease, require invasive ventilation, and have a poor outcome than patients with wild-type DHPS genotypes. In conclusion, genetic clinical correlates continue to be found for Pneumocystis pneumonia; however, they remain controversial and warrant further study.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

et al. 2009

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“…However, because of the high level of polymorphism in the composition of the ITSrDNA locus, several molecular epidemiological studies have been conducted by using this tool. Analysis of the ITS regions of the nuclear rRNA operon for different parasites has demonstrated the utility of this marker in detect genetic diversity and the association of this with several epidemiological aspects (9,26) The present study also indicates that most of the genotypes are specific to some geographic areas (e.g., genotype B1 contains isolates from one geographic location, in Espírito Santo, that were collected over a distinct period of time [between 1982 and 1995]), showing the importance of clonal dissemination versus sexual reproduction for this organism in nature, at least occurring in some regions. The stability of this genotype adapting to some environmental modifications through years in the same area is a clear proof of the aforementioned statement.…”

Section: Discussionmentioning

confidence: 99%

Genetic Polymorphism and Molecular Epidemiology ofLeishmania(Viannia)braziliensisfrom Different Hosts and Geographic Areas in Brazil

et al. 2003

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Numerical zymotaxonomy and variability of the internal transcribed spacers (ITS) between the small and large subunits of the rRNA genes were used to examine strain variation and relationships in natural populations of Leishmania (Viannia) braziliensis. A total of 101 strains from distinct hosts and Brazilian geographic regions were assigned to 15 zymodemes clustered in two major genetic groups. The great number of isolates (48.5%) placed in zymodeme IOC/Z-27 were collected on the Atlantic coast. The high molecular diversity found in populations in the Amazon Basin was related to the great number of sandfly vector(s) in that region. The results of the restriction fragment length polymorphism analysis of the ITS depicted considerable intraspecific variation. Genotypic groups A, B, and C contained 39, 40, and 22 isolates, which were divided into 16, 10, and 15 genotypes, respectively. The genetic polymorphism observed demonstrates the degree of diversity of L. Infections with the parasitic protozoan Leishmania (Viannia) braziliensis Vianna 1911 (Kinetoplastida: Trypanosomatidae) or strain variants are recognized as causing human illness in many areas of (sub)tropical America (at least 15 countries), where it constitutes a significant public health problem. Many of these parasites seem to have a unique life cycle, with different phlebotomine sandfly (Diptera: Psychodidae) vectors and/or animal reservoirs and a different geographic distribution (13). This pathogen is capable of producing a variety of clinical manifestations, such as (i) cutaneous leishmaniasis (CL), which may heal spontaneously; (ii) mucosal leishmaniasis (ML), a hyperergic invasive ulcerative form that progresses in the absence of any apparent cellular defect (15); and (iii) disseminated CL (4).Most of the environmental factors affecting the epidemiology of the various leishmaniases are still poorly understood. Wild mammals serve as reservoirs for most of the New World Leishmania spp. (21), but there is increasing evidence that some of the human pathogenic Leishmania strains can be maintained in both sylvan and urban cycles. In the case of L. (V.) braziliensis, the principal vertebrate hosts in the sylvan cycle have not been identified, but there is evidence that dogs, horses, and donkeys may serve as reservoir hosts of this parasite (15). The existence of an urban cycle involving peridomestic sandfly species for L. (V.) braziliensis reflects the ability of these parasites and their vectors to adapt to changes in their original forested habitats with important public health implications. Studies using molecular techniques to characterize L. (V.) braziliensis populations from different regions have shown a relationship between level of similarity among the parasite populations (12, 24) and their geographic range, but recent data have also indicated that the considerable variability detected among these parasites is more probably related to the sandfly vector(s) and/or animal reservoir(s) involved in the transmission cycles (18).Pathogens that produce...

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“…To date, more than 30 ITS1 genotypes and 40 ITS2 genotypes with more than 90 haplotypes (combinations of ITS1 and ITS2 types) have been described worldwide, based on two different but similar typing systems (8,26). Some ITS haplotypes are globally more common, and coinfections with multiple types of P. jirovecii often occur (4,8,11,15,17,25,26). Although these typing systems have been useful, questions have been raised about the extensive polymorphism and stability of the ITS locus and its use for the genotyping of P. jirovecii.…”

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confidence: 99%

Frequent In Vitro Recombination in Internal Transcribed Spacers 1 and 2 during Genotyping of Pneumocystis jirovecii

2007

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Pneumocystis jirovecii is the causative agent of Pneumocystis pneumonia (PCP) in immunocompromised persons. Knowledge of the transmission and epidemiology of PCP is still incipient, and investigations on these subjects are based exclusively on applications of molecular typing techniques. The polymorphic internal transcribed spacers ITS1 and ITS2 in the ribosomal DNA operon, which in the P. jirovecii genome exist as single-copy DNA, are commonly used as target loci for isolate typing. In the course of genotyping P. jirovecii in respiratory specimens from PCP patients by amplification and cloning of a large number of ITS sequences, we found mixed infections (two or more types) in 50% of the samples. In a majority of the specimens with mixed infections, we detected many ITS haplotypes (combinations of ITS1 and ITS2 types) that appeared to be products of recombination between globally common ITS haplotypes present in the same sample. Here we present results of a series of experiments showing that essentially all ITS recombinants are chimeras formed during the genotyping process. Under standard conditions, as many as 37% of the amplified sequences could be hybrid DNA artifacts. We show that by modifying PCR amplification conditions, ITS chimera formation could be largely abolished and the erroneous establishment of artifactual haplotypes avoided. The accurate assessment of genetic diversity is fundamental for a better understanding of the epidemiology and biology of P. jirovecii infections.The infectious fungus Pneumocystis jirovecii is the etiological agent of Pneumocystis pneumonia (PCP) in immunocompromised individuals. Since P. jirovecii cannot be cultivated in vitro, investigations of the transmission and epidemiology of this organism have been based on applications of molecular typing techniques (1). For P. jirovecii, sequence analysis of the internal transcribed spacer (ITS) regions in the nuclear ribosomal DNA (rDNA) gene complex, which in this fungus exists as a single-copy locus (2, 24), is the most informative epidemiological tool available at present. ITS1 is located between the coding regions of the 18S and 5.8S rRNA genes, and ITS2 is located between the 5.8S and 26S rRNA genes. The sequence diversity of ITS1 and ITS2 among different strains of P. jirovecii and the fact that these segments are removed during ribosomal biogenesis and should not be subjected to selective pressure make them suitable targets for genotyping (10). To date, more than 30 ITS1 genotypes and 40 ITS2 genotypes with more than 90 haplotypes (combinations of ITS1 and ITS2 types) have been described worldwide, based on two different but similar typing systems (8, 26). Some ITS haplotypes are globally more common, and coinfections with multiple types of P. jirovecii often occur (4,8,11,15,17,25,26). Although these typing systems have been useful, questions have been raised about the extensive polymorphism and stability of the ITS locus and its use for the genotyping of P. jirovecii.During the genotyping of specimens from patients with ...

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Genetic Diversity of Pneumocystis carinii f. sp. hominis Based on Variations in Nucleotide Sequences of Internal Transcribed Spacers of rRNA Genes

Cited by 38 publications

References 24 publications

Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

Genetic Polymorphism and Molecular Epidemiology ofLeishmania(Viannia)braziliensisfrom Different Hosts and Geographic Areas in Brazil

Frequent In Vitro Recombination in Internal Transcribed Spacers 1 and 2 during Genotyping of Pneumocystis jirovecii

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