Abstract
BackgroundGenetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.MethodsWe selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C® system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.ResultsAmong 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C® profiles, ITS sequencing identified one C. lusitaniae strain, three C. intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.ConclusionsMolecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-015-0793-3) contains supplementary material, which is available to authorized users.
Highlights
Genetic variation in the ribosomal DNA internal transcribed spacer (ITS) region has been studied among fungi
Growth tests in hypertonic broth and at 42°C allowed for the presumptive identification of 14 C. dubliniensis and 76 C. albicans isolates, and ITS sequencing confirmed the identification of these two species, indicating 100% concordance (Additional file 2: Table S2)
Among 69 isolates phenotypically identified as C. parapsilosis, ITS sequencing distinguished 34 C. parapsilosis, 31 C. orthopsilosis and three C. metapsilosis isolates and one Lodderomyces elongisporus isolate
Summary
Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. The numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. In resource-limited settings, commercial biochemical tests still represent the cornerstone for the identification of human yeast pathogens [4]. These methods are usually time-consuming and have potential limitations with respect to the accurate identification of rare pathogens and of cryptic species of Candida [6]. Other important issues include the quality of reference nucleotide sequences derived from well-characterized yeast collections deposited in public genomic databases and the limited number of fungal species, especially those related to human infections, for which data are present in sequence databases [10,11]. There is a need to expand public nucleotide databases to include sequences of emerging fungal pathogens [10,11]
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