Multilocus Sequence Typing of the Pathogenic Fungus
            <i>Aspergillus fumigatus</i>

Bain, Judith M.; Tavanti, Arianna; Davidson, Amanda Denise; Jacobsen, Martin; Shaw, Duncan; Gow, Neil A. R.; Odds, Frank C.

doi:10.1128/jcm.00064-07

Cited by 128 publications

(130 citation statements)

References 56 publications

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“…Thus, the ITS region lacks the resolution to resolve intraspecies phylogenetic patterns. To obtain this greater evolutionary clarity, additional studies are warranted, but they should focus on alternative targets, possibly adopting those typing methods used successfully for other pathogenic fungi, such as Candida albicans (4) and Aspergillus fumigatus (1).…”

Section: Discussionmentioning

confidence: 99%

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%

Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

et al. 2009

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“…It demonstrated poor levels of discrimination among C. dubliniensis isolates, identifying only 20 DSTs from 50 isolates. SNPs have been detected in 172 of these 2,883 nucleotides (6%) in C. albicans (5). To date, 1,391 isolates of C. albicans have been examined, identifying 1,005 DSTs (35).…”

Section: Discussionmentioning

confidence: 99%

Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans

et al. 2008

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The pathogenic yeast Candida dubliniensis is phylogenetically very closely related to Candida albicans, and both species share many phenotypic and genetic characteristics. DNA fingerprinting using the species-specific probe Cd25 and sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal gene cluster previously showed that C. dubliniensis is comprised of three major clades comprising four distinct ITS genotypes. Multilocus sequence typing (MLST) has been shown to be very useful for investigating the epidemiology and population biology of C. albicans and has identified many distinct major and minor clades. In the present study, we used MLST to investigate the population structure of C. dubliniensis for the first time. Combinations of 10 loci previously tested for MLST analysis of C. albicans were assessed for their discriminatory ability with 50 epidemiologically unrelated C. dubliniensis isolates from diverse geographic locations, including representative isolates from the previously identified three Cd25-defined major clades and the four ITS genotypes. Dendrograms created by using the unweighted pair group method with arithmetic averages that were generated using the data from all 10 loci revealed a population structure which supports that previously suggested by DNA fingerprinting and ITS genotyping. The MLST data revealed significantly less divergence within the C. dubliniensis population examined than within the C. albicans population. These findings show that MLST can be used as an informative alternative strategy for investigating the population structure of C. dubliniensis. On the basis of the highest number of genotypes per variable base, we recommend the following eight loci for MLST analysis of C. dubliniensis: CdAAT1b, CdACC1, CdADP1, CdMPIb, CdRPN2, CdSYA1, exCdVPS13, and exCdZWF1b, where "Cd" indicates C. dubliniensis and "ex" indicates extended sequence.Candida dubliniensis is a pathogenic yeast species that is phenotypically, genetically, and phylogenetically very closely related to Candida albicans, the yeast species most commonly associated with infection in humans (49, 51). Despite their close relationship, C. albicans is significantly more pathogenic (49, 50). C. dubliniensis is most commonly associated with oral carriage and infection in human immunodeficiency virus (HIV)-infected and diabetic patients, although it has been identified as a minor constituent of the commensal floras in the oral cavities of healthy individuals (40,49,50). Although C. dubliniensis has also been recovered from patients with systemic infections, its incidence is far lower than that of C. albicans. While the latter is responsible for 40 to 60% of cases of candidemia, C. dubliniensis has been identified in only 1 to 2% of blood culture yeast samples (11,15,27,(29)(30)(31). These epidemiological data are reflected in the results of animal infection model studies that demonstrated that C. albicans is significantly more pathogenic than C. dubliniensis (22,47,56). The reasons for the lower viru...

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“…It is important that the MLST schemes developed for the FIESC and FCSC in the present study, in contrast to those available via the Internet for some of the most important human pathogenic species (4,23), focused primarily on identifying species limits within these closely related species complexes. Nevertheless, the four-locus typing schemes for the FIESC and FCSC achieved indices of discrimination of 0.985 and 0.966, respectively, using Simpson's index of diversity (18).…”

Section: Vol 47 2009 Human Pathogenic Members Of the Fiesc And Fcscmentioning

confidence: 99%

Novel Multilocus Sequence Typing Scheme Reveals High Genetic Diversity of Human Pathogenic Members of theFusarium incarnatum-F.equisetiandF. chlamydosporumSpecies Complexes within the United States

et al. 2009

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Species limits within the clinically important Fusarium incarnatum-F. equiseti and F. chlamydosporum species complexes (FIESC and FCSC, respectively) were investigated using multilocus DNA sequence data. Maximumparsimony and maximum-likelihood analyses of aligned DNA sequences from four loci resolved 28 species within the FIESC, within which the species were evenly divided among two clades designated Incarnatum and Equiseti, and four species within the FCSC. Sequence data from a fifth locus, ␤-tubulin, was excluded from the study due to the presence of highly divergent paralogs or xenologs. The multilocus haplotype nomenclature adopted in a previous study

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Multilocus Sequence Typing of the Pathogenic Fungus Aspergillus fumigatus

Cited by 128 publications

References 56 publications

Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

Clinical Significance and Phylogenetic Relationship of Novel Australian Pneumocystis jirovecii Genotypes

Multilocus Sequence Typing Reveals that the Population Structure of Candida dubliniensis Is Significantly Less Divergent than That of Candida albicans

Novel Multilocus Sequence Typing Scheme Reveals High Genetic Diversity of Human Pathogenic Members of theFusarium incarnatum-F.equisetiandF. chlamydosporumSpecies Complexes within the United States

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