Previous Article | Next Article ![]()
Journal of Clinical Microbiology, March 2003, p. 967-975, Vol. 41, No. 3
0095-1137/03/$08.00+0 DOI: 10.1128/JCM.41.3.967-975.2003
Copyright © 2003, American Society for Microbiology. All Rights Reserved.
Department of Microbiology, Faculty of Science,1 Center for Biotechnology, Mahidol University,2 Department of Parasitology,3 Department of Microbiology, Phramongkutklao College of Medicine,5 Division of Research, Armed Forces Research Institute of Medical Sciences, Bangkok 10400, Thailand4
Received 23 September 2002/ Returned for modification 12 November 2002/ Accepted 16 December 2002
|
|
|---|
|
|
|---|
|
|
|---|
DNA extraction. Extraction of genomic DNA was performed by using the QIAamp DNA stool mini kit (Qiagen, Hilden, Germany), following the manufacturer's instructions. Genomic DNA of each sample was kept at -20°C until used.
PCR-RFLP analysis. Genotypic characterization of Blastocystis from humans and animals was determined by an RFLP analysis of partial ssu rDNA (4). Although a few different primer pairs were used for the PCR-RFLP analysis of this gene in recent reports (3, 7, 12, 19), we chose a primer pair specific to partial ssu rDNA of B. hominis (3) since mixed infection with intestinal protozoa might be found in some specimens. Genomic DNA and a primer pair (forward, 5'-GGAGGTAGTGACAATAAATC-3'; reverse, 5'-CGTTCATGATGAACAATT-3') were used in PCR with conditions as described by Böhm-Gloning et al. (3). PCR amplification was performed using a Perkin-Elmer 480 thermal cycler. After an initial 4-min denaturing step at 94°C, 35 PCR cycles were carried out, each consisting of a 30-s annealing at 54°C, 30-s extension at 72°C, 30-s denaturing at 94°C, and an additional cycle with a 5-min chain elongation at 72°C. The PCR products and molecular markers were electrophoresed in 2% agarose gel (FMC Bioproducts, Philadelphia, Pa.) with 1.5% Tris-borate-EDTA (TBE) buffer using a Mupid gel electrophoresis device (Cosmo Bio, Tokyo, Japan). Bands were visualized under UV light after being stained with ethidium bromide and documented on Polaroid film using a FoTo Prep (Fotodyne). Digestions of the PCR products were performed using three restriction enzymes, HinfI, RsaI, and AluI (Gibco-BRL, Gaithersburg, Md.), and separated by 2% agarose gel electrophoresis.
Amplification of ssu rDNA and sequencing. A partial sequence of ssu rDNA of Blastocystis isolated from a horse had been amplified by a pair of primers described by Böhm-Gloning et al. (3), but the complete ssu rDNA region of Blastocystis isolated from a human and a pig was amplified by a pair of primers described by Sogin (20). DNA sequencing was performed by an automated ABI PRISM 377 DNA sequencer at the Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand. Nucleotide sequences were determined with the Sequencer program (Gene Codes Corporation, Inc. [1995 release]).
Sequence and phylogenic analysis. There were two sets of partial ssu rDNA sequence alignments since total DNA of Blastocystis isolated from horse feces was not enough to reamplify for the complete region of ssu rDNA. The first set of partial ssu rDNA sequence alignment consists of 1,054 bp from nine taxa, including four taxa of B. hominis, four taxa of Blastocystis, and Caecitellus parvulus. The second set of ssu rDNA sequence alignment was 1,738 bp from four taxa of B. hominis, three taxa of Blastocystis, and C. parvulus. The details of these taxa are shown in Table 1.
|
View this table: [in a new window] |
TABLE 1. Selected Thai Blastocystis taxa for the ssu rDNA region sequenced and additional taxa from GenBank
|
The data were analyzed using the parsimony heuristic search, neighbor joining, and bootstrapping parsimony heuristic search of the Phylogeny Analysis Using Parsimony program (version 4.0b8). The stepwise addition option was used to find the most-parsimonious bootstrap trees. Bootstrapping by using the full heuristic search option of the Phylogeny Analysis Using Parsimony program was performed to calculate the robustness of each branch. The sequence of C. parvulus was considered to be an out-group. The analysis was set with the following parameters: 1,000 bootstrap replicates (10, 11), with gaps treated as missing data, tree bisection-reconnection branch swapping, and random sequence addition. All sites were weighted equally. The percentage of bootstrap replicates that confirmed each clade is indicated in Fig. 3 and 6. Hosts and geographical locations were also mapped onto a bootstrap single-most-parsimonious tree inferred from partial ssu rDNA.
![]() View larger version (21K): [in a new window] |
FIG. 3. Phylogenetic relationships of selected Blastocystis spp. inferred from partial ssu rDNA sequence (1,054 bp). A single most-parsimonious tree with tree length of 355, consistency index of 0.9352, and retention index of 0.8663 was found. Bootstrap replicates, 1,000. Bootstrap frequencies of more than 50 are indicated on each branch. GenBank accession numbers of sequences are in parentheses.
|
![]() View larger version (19K): [in a new window] |
FIG. 6. Phylogenetic relationships of selected Blastocystis spp. inferred from partial ssu rDNA sequence (1,738 bp). A single most-parsimonious tree with tree length of 520, consistency index of 0.9577, and retention index of 0. 9185 is shown. Bootstrap replicates, 1,000. Bootstrap frequencies of more than 50 are indicated on each branch. Nodes and clades are numbered in parentheses in the order in which they are described in the text. Bar, 10 substitutions. GenBank accession numbers of sequences are in parentheses.
|
|
|
|---|
|
View this table: [in a new window] |
TABLE 2. Distribution of Blastocystis subgroups among humans, pigs, and a horse using PCR-RFLP analysis of partial ssu rDNA (3)
|
![]() View larger version (65K): [in a new window] |
FIG. 1. Comparison of the representative PCR-RFLP analysis of partial ssu rDNA of Blastocystis isolates from a human (lanes 1 to 3), a pig (lanes 4 to 6), and a horse (lanes 7 to 9). These banding patterns were identified as subgroup III as previously described (3). The PCR product in lanes 1, 4, and 7 was digested by HinfI; the PCR product in lanes 2, 5, and 8 was digested by RsaI; and the PCR product in lane 3, 6, and 9 was digested with AluI. MW, molecular weight marker.
|
![]() View larger version (45K): [in a new window] |
FIG. 2. Banding patterns of subgroup I (A) and subgroup VI (B) using PCR-RFLP analysis of partial ssu rDNA of Blastocystis isolated from humans. The PCR product in lane 1 was digested by HinfI, the PCR product in lane 2 was digested by RsaI, and the PCR product in lane 3 was digested by AluI. MW, molecular weight marker.
|
For sequence analysis, the second data set consists of 1,738 alignable sites from seven taxa of Blastocystis mentioned previously, except Blastocystis sp. isolated from a horse (GenBank accession number AF538349, Thai isolate subgroup III; source, horse, Thailand). In 1,738 alignable sites, the 234 variable sites are parsimony uninformative, whereas the number of parsimony-informative sites equals 180. One thousand three hundred twenty-four base pairs are constant. Phylogenetic analysis of 1,738 bp of ssu rDNA resulted in parsimonious trees of 520 steps, with a consistency index of 0.9577 and a retention index of 0.9185. Comparison of the 1,738 bp of ssu rDNA showed 96% identity between two B. hominis isolates from humans (Thai isolate subgroup III AB023578 and GenBank accession number U51151) and a Blastocystis sp. isolated from a pig. In 4% (70 of 1,738) of base pair differences in ssu rDNA between B. hominis isolates from humans and a Blastocystis sp. isolate from a pig, transversion was about 2% (36 of 1,738 bp [9 A/C, 13 A/T, 3 G/C, and 11 G/T]) and transition was about 1% (17 of 1,738 bp [12 A/G and 5 C/T]), with 1% insertion-deletion events (17 of 1,738 bp). To facilitate discussion, we have defined these clades as groups 1 to 3 (Fig. 6). Group 1 was also divided into subgroups 1.1 to 1.3 (Fig. 6).
|
|
|---|
We also used this method to preliminarily compare Blastocystis isolates from humans and animals that lived in the same area. Banding patterns identical to subgroup III could be found in humans, pigs, and a horse, while other banding patterns were only found in human isolates. This suggests the existence of different host specificity among many different genotypes of Blastocystis. Snowden et al. found a common genotype in different animal hosts (19), which indicates that some genotypes of Blastocystis are not host specific. Moreover, cross infection of Blastocystis between humans and animals has been suggested by the observation of similar patterns of RFLP (7) and random amplified polymorphic DNA (25) analysis. Our data confirm these findings.
We then analyzed the partial ssu rDNA sequences of Blastocystis isolates from a human, a pig, and a horse that exhibited similar banding patterns of RFLP. There are two lines of evidence suggesting that the Blastocystis isolates from a pig and a horse are very closely related to B. hominis isolates from humans. First, phylogenetic analysis based on ssu rDNA sequences depicted that the Blastocystis isolates from pigs and horses always form a sister clade to B. hominis isolates from humans. Second, the 92 to 94% (
6% divergence) identity of partial ssu rDNA sequences is found among B. hominis isolates from humans and Blastocystis isolates from a pig and a horse. Furthermore, this result is consistent with reports done by Kukoschke and Müller (13) and Boreham et al. (5). The results of sequence analysis of ssu rDNA here perhaps reveal host nonspecificity of Blastocystis species.
The results of comparison of 1,054 bp of ssu rDNA sequences of Blastocystis species also imply that the level of similarity of partial ssu rDNA is quite correlated with hosts from which Blastocystis species were isolated. High similarity (97 to 99%) of partial ssu rDNA sequences is found among B. hominis strains isolated from the same host, while low identity (79 to 89%) of partial ssu rDNA sequences is noticeable among Blastocystis species isolated from different hosts, except that 92% homology was found between partial ssu rDNA sequences from a pig and a horse. For example, a comparison of ssu rDNA sequences of B. hominis (Thai isolate subgroup III) and B. hominis (GenBank accession number U51151; strain Nand) showed 99% homology (Fig. 3). There was 97% homology of the ssu rDNA region among B. hominis (Thai isolate subgroup III), B. hominis (GenBank accession number AB023578; strain HE87, Japan), and B. hominis (GenBank accession number AB023499; strain HE87, Japan), while there was 89% homology of the ssu rDNA region among B. hominis (Thai isolate subgroup III), Blastocystis sp. (GenBank accession number U26177; source, unidentified guinea pig; isolate U26177) and Blastocystis sp. (GenBank accession number U51152; source, unidentified guinea pig; strain NIH:1295:1) (Fig. 3). There was 80% identity of partial ssu rDNA between B. hominis and C. parvulus.
However, the dendrogram from the bootstrapping analysis (Fig. 3) suggested that 1,054 alignable sites are not divergent enough to distinguish between four taxa of B. hominis (GenBank accession number AF439782; Thai isolate subgroup III), Blastocystis sp. (GenBank accession number AF538348, Thai isolate subgroup III; source, pig, Thailand), Blastocystis sp. (GenBank accession number AF538349; Thai isolate subgroup III; source, horse, Thailand), and B. hominis (GenBank accession number U51151; strain Nand). This clade was only supported by 59% bootstrap values and unresolved topologies of four taxa of Blastocystis derived from the bootstrap analysis. Thus, the 1,738 bp of ssu rDNA sequence analysis of the second data set from seven taxa of Blastocystis was constructed.
Phylogenetic analysis based on ssu rDNA sequences from the second data set indicated that B. hominis isolated from humans and Blastocystis isolated from a pig form a monophyletic clade separately from Blastocystis isolates from guinea pigs. This result was strongly supported by 100% bootstrap values and identical topologies of all dendrograms derived from the bootstrap analysis, neighbor joining analysis, and heuristic search (data not shown). The other evidence is the 98 to 99% similarity of ssu rDNA sequences between B. hominis isolates from Japan, Thailand, and the United States and the 93 to 95% identity between B. hominis and Blastocystis isolates from a pig. In contrast, there is 88 to 89% nucleotide similarity between B. hominis isolates from humans, Blastocystis isolates from a pig, and Blastocystis isolates from guinea pigs. In the meantime, we regard the overall topology in Fig. 6 as a working hypothesis of evolutionary relationships that requires further testing. The remaining discussion focuses on the taxonomically evolutionary relationships of groups 1 to 3.
Group 1 represents taxa including B. hominis GenBank accession number AB023578; B. hominis GenBank accession number AB023499; B. hominis Thai isolate, subgroup III, GenBank accession number AF439782; B. hominis GenBank accession number U51151; and Blastocystis sp. subgroup III, isolated from a pig. This branch was supported with a 100% confident bootstrap value (Fig. 6). Four different B. hominis isolates from humans in this clade have shown 1 to 2% variation of ssu rDNA sequence alignment. Group 1 was divided into three subgroups, which are 1.1, 1.2, and 1.3. Subgroup 1.1 is composed of B. hominis Thai isolate subgroup III, B. hominis GenBank accession number AB023578 and AB023499, and B. hominis GenBank accession number U51151, with 100% bootstrapping and 99% identity of partial ssu rDNA sequences. Subgroup 1.2 includes B. hominis GenBank accession number U51151 and B. hominis GenBank accession number AB023578 and AB023499 (97% bootstrapping). B. hominis GenBank accession numbers AB023578 and AB023499 in group 1.3 were strains isolated from Japan with 100% bootstrapping and 99% identity of partial ssu rDNA sequences. The phylogenic tree of ssu rDNA sequences showed that Blastocystis sp. subgroup III, isolated from a pig, is part of a sister group with B. hominis isolates from humans, with a 100% confident bootstrap value, and that the sequences of B. hominis, isolated from humans, have been diverged recently. This result is consistent with 93 to 96% similarity of ssu rDNA between B. hominis isolates from humans and Blastocystis sp. isolates from a pig. In 1,738 bp, the homology of ssu rDNA between B. hominis isolates from humans in Japan and Blastocystis sp. isolates from a pig are 93 to 94%. There is about 96% identity of 1,738 bp of ssu rDNA between two B. hominis isolates from humans (Thai isolate subgroup III AB023578 and GenBank accession number U51151) and a Blastocystis sp. isolated from pig.
In group 2, both Blastocystis species were isolated from guinea pigs (GenBank accession numbers U51152 and U26177), with the strong robustness of a 100% bootstrap value. The homologies of ssu rDNA sequences of Blastocystis sp. isolates from guinea pigs and those from humans and a pig are 88 and 89%, respectively.
In conclusion, phylogeny analyses of partial ssu rDNA sequences of selected isolates of Blastocystis with the same pattern of restriction site analysis of amplified ssu rDNA suggests that B. hominis isolates are monophyletic, forming a sister group to Blastocystis species isolated from a pig and a horse. These results perhaps imply that B. hominis has evolved from Blastocystis sp. isolates from domestic animals closely linked with humans, such as pigs and horses. There is no correlation between host and geographical origin for clades of the inferred trees. The high values of the consistency index and retention index suggest that there is no homoplasy in these tested sequences. Using PCR-RFLP and phylogeny analyses of partial ssu rDNA, our data might be evidence of the zoonotic potential of Blastocystis. Nonetheless, interpretation of the phylogenetic results is restricted to selected species in Blastocystis; more samples from pigs, horses, and humans from different geographic locations (examined by RFLP analysis of ssu rDNA) and complete sequences of ssu rDNA should be examined for further biodiversity studies of Blastocystis. Since one molecular phylogeny of one gene cannot explain all evolutionary relationships among organisms, other genes, such as complete internal transcribed spacers 1 and 2 and 5.8S rDNA, from many species of Blastocystis as well as epidemiological data may imply more evolutionary relationships between Blastocystis isolates from different hosts, the origin of the pathogenic Blastocystis, and the correlation between species of Blastocystis and geographic locations.
![]() View larger version (20K): [in a new window] |
FIG. 4. Maximum analysis of ssu rDNA sequences of 1,054 bp for selected genera in Blastocystis and Caecitellus parvulus as a reference taxon. GenBank accession numbers and hosts of each taxon are in parentheses.
|
![]() View larger version (20K): [in a new window] |
FIG. 5. Neighbor-joining based on ssu rDNA analysis containing 9 taxa of selected genera in Blastocystis. The designated outgroup is Caecitellus parvulus. GenBank accession numbers and hosts of each taxon are in parentheses.
|
This work was financially supported by Thailand-Tropical Diseases Research Programme (T2) (ID 00-1-HEL-24-011).
|
|
|---|
This article has been cited by other articles:
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Copyright © 2009 by the American Society for Microbiology. For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»