Suitability of internal transcribed spacers (ITS) as markers for the population genetic structure of Blastocystis spp

• Published in: Parasites & vectors Vol. 7; no. 1; p. 461
• Main Authors: Villalobos, Guiehdani, Orozco-Mosqueda, Guadalupe Erendira, Lopez-Perez, Merle, Lopez-Escamilla, Eduardo, Córdoba-Aguilar, Alex, Rangel-Gamboa, Lucia, Olivo-Diaz, Angelica, Romero-Valdovinos, Mirza, Maravilla, Pablo, Martinez-Hernandez, Fernando
• Format: Journal Article
• Language: English
• Published: England Springer-Verlag 03.10.2014; BioMed Central Ltd; BioMed Central; BMC
• Subjects: Adolescent; Base Sequence; Biological diversity; Blastocystis; Blastocystis - genetics; Blastocystis - isolation & purification; Blastocystis Infections - parasitology; Blastocystis spp; Blastocystis subtypes; Child; Child, Preschool; children; Cluster Analysis; Deoxyribonucleic acid; DNA; DNA, Ribosomal Spacer - chemistry; DNA, Ribosomal Spacer - genetics; Evolution; feces; Feces - parasitology; Female; gastrointestinal system; Gene Flow; Genes; Genetic aspects; Genetic diversity; Genetic markers; Genetic Markers - genetics; Genetic Variation; Genetics, Population; Haplotypes; Humans; Infant; Internal transcribed spacers; Male; Mexico; Molecular Sequence Data; Parasites; phylogeny; polymerase chain reaction; ribosomal DNA; Sequence Analysis, DNA; Short Report; Software; Values; Libya; Mexico
• ISSN: 1756-3305; 1756-3305
• DOI: 10.1186/s13071-014-0461-2

BACKGROUND: The purpose of this study was to assess the genetic variation and differentiation of Blastocystis subtypes (STs) recovered from symptomatic children by analysing partial sequences of the small subunit rDNA gene region (SSUrDNA) and internal transcribed spacers (1 and 2) plus the 5.8S region (ITS, ITS1 + 5.8S + ITS2) and comparing with isolates from other countries. FINDINGS: Faecal samples from 47 Blastocystis-infected children with gastrointestinal symptoms and negative for pathogenic enterobacteria were analysed. PCR was performed on DNA from all the samples to identify Blastocystis STs, amplifying a fragment of SSUrDNA and the ITS region. The amplicons were purified and sequenced, and consensus sequences were submitted to GenBank; afterwards, SSUrDNA sequences were analysed for genetic diversity according to geographic area. Regarding the Blastocystis STs found, 51% were ST1, 23% ST2, 19% ST3 and 2% ST7. For ITS, a haplotype network tree and Bayesian inference revealed the presence of two novel variants of ST1, clustering some sequences into ST1A and ST1B. The values of nucleotide diversity (π) and haplotype polymorphism (θ) for ST1, ST2 and ST3 ranged from 0 to 1, whereas the ratio of genetic differentiation (FST)/migration index (Nm) showed the highest differentiation between Libya and Thailand-Philippines for ST2 (0.282/0.63). In contrast, a high flow gene was observed between Czech Republic-Denmark-Holland-Spain and USA-Mexico-Colombia for ST1 (0.003/84). CONCLUSION: Our data on genetic differentiation and gene flow might explain the differences for the prevalence of Blastocystis STs. Moreover, the ITS region could be used as a genetic marker to assess genetic variation in this parasite.