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Journal of Clinical Microbiology, March 2005, p. 1142-1148, Vol. 43, No. 3
0095-1137/05/$08.00+0 doi:10.1128/JCM.43.3.1142-1148.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.
Department of Genetics and Ecology,1 Institute of Medical Microbiology and Immunology, University of Aarhus, Aarhus,6 Danish Centre for Experimental Parasitology, The Royal Veterinary and Agricultural University,2 Danish Bacon and Meat Council, Copenhagen,3 Department of Clinical Microbiology, Viborg-Kjellerup Hospital, Viborg, Denmark,5 Laboratory Sciences Division, International Centre for Diarrheal Diseases Research, Dhaka, Bangladesh4
Received 31 August 2004/ Returned for modification 19 October 2004/ Accepted 7 November 2004
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In recent years, several cases of child ascariasis with unexplained epidemiology were observed by the Department of Clinical Microbiology in Viborg County, Denmark (6). None of the children had been traveling, but we suspected that the cases were correlated with contact with pigs or pig manure (5).
A. lumbricoides and A. suum may constitute two different but closely related species or may represent host-associated subpopulations or races of the same species (12, 23). Ascaris populations obtained from humans and pigs both in Guatemala and in China were shown to represent sympatric populations (4, 28); i.e., there was no or very restricted gene flow between the Ascaris populations from the two different hosts living in the same areas. Furthermore, no cases of cross-infections were proven between humans and pigs living in close proximity in two Guatemalan villages (3). These observations suggest that the nematodes in the two hosts do constitute distinct taxa. On the other hand, Ascaris infections observed in humans living in areas considered to have a low prevalence of the human parasite indicated that pig Ascaris may cause zoonotic infections (10, 17, 22). Genetic analysis of worms indicated that some human Ascaris infections are zoonotic (2), and it has been shown that the parasites in the two hosts are able to cross-infect under experimental conditions (16, 35).
For the cases of ascariasis in Viborg County, it was not known for sure whether the infections were transmitted from other humans or from pigs. In order to reveal the source of the human Ascaris infections, we decided to compare Ascaris worms obtained from humans and from pigs in Denmark and in some developing countries. Our results confirm and extend Anderson's observation that pigs are the main source of human Ascaris infections in areas considered to have no or a low prevalence of the human form of this parasite (2).
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FIG. 1. Geographic origins and sources of the seven populations of collected Ascaris worms. Country: BD, Bangladesh; DK, Denmark; GT, Guatemala; NP, Nepal; PH, the Philippines. Hosts: H, humans; P, pigs. Numerals indicate the numbers of Ascaris worms obtained.
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TABLE 1. Ascaris worms collected from humans in Denmark
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DNA extraction. DNA was extracted from gonads by the cetyltrimethylammonium bromide (CTAB) method (14) with the following modification. The tissue was placed in 600 µl of CTAB buffer, digested with proteinase K (250 µg per ml) overnight at 56°C, and then treated with RNase A (0.2 mg) at 37°C for 15 min. Care was taken to avoid contamination of the samples with intestinal contents and the uterus in females, as this organ may contain stored sperm or fertilized eggs (1). DNA samples were stored at 20°C.
AFLP procedure. The amplified fragment length polymorphism (AFLP) procedure was carried out as described by Vos et al. (37) with some modifications. Briefly, 100 ng of genomic DNA was digested with both EcoRI and MseI, and adaptors (EcoRI, 5'-CTCGTAGACTGCGTACC and CATCTGACGCATGGTTAA-5'; and MseI, 5'-GACGATGAGTCCTGAG and TACTCAGGACTCAT-5') were ligated to the resulting fragments by use of T4 DNA ligase. The adaptors provide priming sites for selective PCR amplification of a subset of the restriction fragments by use of primers with various 3' nucleotide extensions. Digestion and ligation were performed in one step with a total volume of 20 µl. The process was initiated by digestion for 4 h at 37°C; the temperature was subsequently reduced by 0.1°C per s to 16°C, and ligation was continued at this temperature for another 2 h. Enzymes then were denatured by raising the temperature to 70°C for 10 min.
We used 0.5 µl of the treated DNA samples as templates for PCR preamplification and primers that had one selective nucleotide (underlined): EcoRI, GACTGCGTACCAATTCC (E+C), combined with MseI, GATGAGTCCTGAGTAAC (M+C); and EcoRI, GACTGCGTACCAATTCA (E+A), combined with MseI, GATGAGTCCTGAGTAAC (M+C). The following program was used: 20 cycles of 94°C for 30 s, 56°C for 1 min, and 72°C for 1 min.
Of the preamplification PCR products, samples of 0.4 µl were used as templates for the final selective PCR amplifications. The Eco primer was labeled with fluorescein Cy5 at the 5' end. Primers had three selective nucleotides (see below), and the following program was used: 94°C for 30 s, 65°C for 30 s, and 72°C for 1 min. The annealing temperature was subsequently reduced by 0.7°C per cycle for the next 12 cycles. This step was followed by 23 cycles of 94°C for 30 s, 56°C for 30 s, and 72°C for 1 min. PCRs were carried out under standard PCR conditions with a total volume of 20 µl.
All PCR products were examined by gel electrophoresis (1% agarose) to ensure that the amplifications were successful. Three microliters of the final PCR product was analyzed on an ALFexpress sequencer (Amersham Biosciences AB, Uppsala, Sweden). External (50- to 500-bp) and internal (300-bp) standards were included for accurate calculation of the sizes of the fragments. In addition, two previously examined DNA samples were included in each run in order to evaluate the size estimates from gel to gel. Based on the presence or absence of fragments, a binary matrix was generated by using the sequence analyzer software package AFLwin version 1.0 (Amersham Biosciences AB).
The following 14 primer combinations were tested: E+CAG in combination with M+CTG, M+CTC, M+CTT, M+CGA, M+CCG, and M+CAG; and E+ACT in combination with M+CTG, M+CTC, M+CTT, M+CGA, M+CCG, M+CAG, M+CTA, and M+CAC. E and M were the respective EcoRI and MseI adaptors, and the selective nucleotides were the extensions (37). Based on the number of polymorphic bands, reproducibility, and score ability, the following four combinations were chosen for use in the study: E+CAG/M+CAG, E+ACT/M+CTT, E+ACT/M+CTG, and E+ACT/M+CTC.
PCR-RFLP procedure. For the PCR-linked restricted fragment length polymorphism (PCR-RFLP) procedure, the forward and reverse primer sequences used for amplification of the internal transcribed spacer (ITS) region were 5'-TTGAACCGGGTAAAAGTCGT-3' and 5'-TTAGTTTCTTTTCCTCCGCT-3', respectively (2). PCR amplification was carried out with a total volume of 20 µl and 20 ng of DNA from each worm as a template. The following program was used for amplification of the ITS region: 94°C for 1 min; 40 cycles consisting of 94°C for 30 s, 55°C for 40 s, and 72°C for 1 min; and a final extension at 72°C for 7 min. Five-microliter samples of the PCR products were digested with restriction endonuclease HaeIII and analyzed by gel electrophoresis (2% agarose).
Data analysis. Interpopulational relationships of the collected Ascaris worms were analyzed by distance-based cluster analysis. Ascaris worms are diploid organisms; however, due to the dominant nature of the AFLP technique, heterozygotes could not be distinguished. The presence or absence of fragments was therefore treated as being effectively in the form of haplotypes (binary data).
A distance matrix based on the binary variables was calculated by using Excel spreadsheet software (Microsoft, Redmond, Wash.) as follows. Genetic similarity estimates between pairs of worms i and j were obtained by using the classical Jaccard coefficient gsij = a/(n d) (25). This coefficient rates the number of coincidences (a, bands present in both worms i and j) and the total number of bands (n, number of bands observed in all worms examined) without considering the negative cooccurrence (d, bands absent in both worms i and j). The latter were excluded because the absence of a band may be due to different genetic events and therefore does not necessarily imply identity. The similarities were transformed into genetic distances with the equation gdij = 1 gsij. This procedure was evaluated and was found to be appropriate for cluster analysis with dominant markers (25).
The resulting matrix was used to construct dendrograms according to the clustering procedures unweighted pair-group method using average linkages (UPGMA), minimum evolution (ME), and neighbor joining (NJ) by using the molecular evolutionary genetic analysis (MEGA) software package (version 3; Center for Evolutionary Functional Genomics, Arizona Biodesign Institute, Arizona State University, Tempe [http://www.megasoftware.net/mega3]) (21).
In a different approach, the results from the AFLP analysis were considered to be phenotypic data obtained from diploid dominant markers. Data were analyzed by using the tools for population genetic analysis (TFPGA) software package (version 1.3; Department of Forest, Range, and Wildlife, Utah State University, Logan [http://bioweb.usu.edu/mpmbio/tfpga.asp]). The presence of a band on the gel indicated the dominant genotype (homozygote or heterozygote), while the absence of this band (blank) represented the homozygote recessive genotype. Since it was not possible to read the allele frequencies directly from the phenotypic data (see above), it was assumed that the genotype frequencies of the subpopulations were in Hardy-Weinberg equilibrium and that the genetic markers were unlinked. In this scenario, the frequency of the recessive allele could be estimated either simply as the square root of the frequency of negative cooccurrence or by the Lynch-Milligan procedure (20) included in the TFPGA program. The distance matrix was calculated by using Nei's unbiased distance (26) in the TFPGA program. The matrix was transferred to the MEGA program, and a dendrogram was generated as described above.
Ascaris worms were placed into groups based on the known origins and by assigning arbitrary cutoff points on the dendrograms. Medians and 25th to 75th percentiles for the overall pairwise genetic distances of worms belonging to the same groups (genetic distances within groups) and of worms belonging to different groups (genetic distances between groups) were calculated by using the Excel program.
The Structure computer program (version 2.1; Department of Human Genetics, University of Chicago, Chicago, Ill. [http://pritch.bsd.uchicago.edu/software.html]) (29) was used to infer population structures by a model-based method for cluster analysis. The AFLP primary data were treated as being haploid, and the model of no admixture was assumed. The program probabilistically assigns the individual worms to subpopulations without prior information about the origins of the specimens. Series of independent runs for models simulating different numbers (K) of subpopulations were performed (K values, 1 to 10; program parameters: burn-in period and collect data iterations 5 x 104). The posterior probability [Pr(K)] for each model was calculated according to the manual for the Structure program.
Analyses of molecular variance (AMOVA) were used to estimate the partitioning of AFLP genotypic variations between and within groups. Distance matrices were constructed for the groups as described above, and calculations were performed by using the Arlequin program (version 2; Genetics and Biometry Laboratory, Department of Anthropology, University of Geneva, Geneva, Switzerland [http://cmpg.unibe.ch/arlequin]).
The distributions of the ITS genotypes among worms collected from the different hosts and sources were compared, and probabilities were calculated by the chi-square test with the SigmaStat for Windows program (version 1.1; Jandel Coporation, San Rafael, Calif.). Hardy-Weinberg equilibrium was tested by using the TFPGA program.
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AFLP analysis. A total of 135 Ascaris worms were analyzed from five different countries worldwide (Fig. 1). Of these, 71 worms were of human origins and 64 were obtained from pigs. The 32 worms obtained from 29 Danish patients are listed in Table 1; of these, 27 were examined by AFLP.
The four primer combinations used in the AFLP analysis amplified variable numbers of bands (35 to 61). A total of 193 bands were detected, 151 (78%) of which were polymorphic. The proportions of polymorphic bands for the four primer sets varied from 60 to 89% (Table 2). Monomorphic bands were excluded from the cluster analysis. Each worm possessed a unique AFLP band pattern. Several tests of DNA prepared from the same specimens yielded identical patterns, demonstrating the reproducibility of data obtained by AFLP analysis.
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TABLE 2. Primer combinations, number of bands, and degree of polymorphisms found in the three major Ascaris populations
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FIG. 2. Dendrogram constructed for examined Ascaris worms by using the Jaccard coefficient and ME clustering. Each label refers to a single specimen. The first letter indicates the host: H, human; P, pig. Numerals indicate the designations of specimens (Table 1). The next two (uppercase) letters indicate the geographic origins (Fig. 1). The final (lowercase) letter indicates the local area in Denmark: j, Jutland; s, Zealand; f, Funen. The Danish worms are randomly distributed in the upper cluster independent of their sources and geographic origins.
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TABLE 3. Genetic distances within and between groups of Ascaris worms
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TABLE 4. Proportion of membership of each predefined Ascaris population in each of the four inferred clustersa
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TABLE 5. AMOVA for 130 Ascaris worms assigned to seven populations in three groupsa
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TABLE 6. AMOVA for Danish Ascaris worms obtained from 27 humans and from 55 pigsa
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2 = 88.0, P < 0.001). Pairwise chi-square tests showed that the distribution of band patterns in Danish human Ascaris worms did not differ from the distribution in worms obtained from Danish pigs (
2 = 1.53, P = 0.46). These results support the assumption that all Danish worms, irrespective of host origin, were drawn from the same population. |
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TABLE 7. Fragment types (band patterns) generated for human and pig Ascaris worms by digestion of the ITS region with restriction enzyme HaeIII
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2 = 37.3, P < 0.0001), indicating that population subdivisions existed for these worms. In contrast, the genotype frequencies in the total population of worms obtained from Danish pigs and humans did not differ significantly from the expected frequencies at Hardy-Weinberg equilibrium (
2 = 3.56, P = 0.06), indicating that worms obtained from both humans and pigs belonged to a random mating population in Denmark. |
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The Ascaris worms were compared by AFLP analysis, a technique that detects DNA polymorphisms at multiple specific restriction sites simultaneously. AFLP analysis has been successfully used to reveal a high degree of genetic information from other nematode species (15, 24, 34). The number of polymorphic loci is more important than the allelic diversity at each locus for the statistical power of analysis used for population assignment (7). At present, AFLP analysis seems to have the highest potential for screening a maximum number of loci and is therefore useful for analysis of population diversity; however, due to the dominant nature of the AFLP data, analysis of the results was not straightforward. The results obtained from the AFLP analysis of the Ascaris worms were therefore analyzed by several different clustering methods.
The ME dendrogram shown in Fig. 2 depicts the results. All the of human Ascaris worms collected in the three developing countries, Bangladesh, Guatemala, and Nepal, were found in two clusters containing no worms from pigs. These two clusters may represent evolutionary lines of the human form of the parasite (i.e., A. lumbricoides). Worms obtained from pigs in both of the two developing countries, Guatemala and the Philippines, and from Denmark were located in a single mixed cluster. This cluster may represents the pig parasite A. suum. All worms obtained from Danes were assigned to this cluster of pig Ascaris worms without any subdivisions. The close relationship between worms obtained from Danish humans and pigs was confirmed by structure analysis (Table 4) and by AMOVA (Tables 5 and 6).
This is the first time that AFLP analysis has been used for the examination of Ascaris; thus, it was impossible to compare the results with published observations. Therefore, the worms were also examined by scoring of HaeIII restriction sites in the ITS region of the rRNA gene by PCR-RFLP analysis, a technique previously used by others (2, 28, 38). One or two HaeIII restriction sites are present in the ITS region of Ascaris; hence, two or three fragment patterns will be generated after digestion of the ITS region PCR product by this enzyme. The differences are due to a transversional change (C to G) that results in the loss of an HaeIII restriction site. The rRNA gene of which ITS is a part exists in multiple copies and, in general, only a single repeat type is found within an individual genome (38). Unequal crossing over and gene conversion are believed to cause this homogenization of the rRNA gene repeats (13). However, in Ascaris, the two types can be found together in one individual (2, 28). Samples from these "heterozygous" individuals therefore produce a four-band pattern on the gel. The occurrence of the three different band patterns in worms from the inferred clusters (Table 7) was in agreement with the results of an analysis of Ascaris worms collected in China (28), except that the distribution of the band patterns in the Ascaris worms obtained from Danish patients matched the distribution in the Ascaris worms obtained from pigs. We also found some instances of the two fragment types in worms obtained from Danish pigs. Anderson (2) found that most worms obtained from people living in North America had ITS regions characteristic of worms obtained from pigs; from a comparison with human and pig parasites obtained worldwide, it was concluded that the ITS region similarity to A. suum was not due to regional genetic variations in an A. lumbricoides population. The fragment pattern for the ITS region provided further evidence for the pig origin of Danish human Ascaris worms; however, the presence of the two-band type in worms obtained from Danish pigs demonstrated that, unfortunately, the number of bands cannot be used for distinguishing between A. suum and A. lumbricoides (38).
By using the two independent techniques, we demonstrated that all 27 worms obtained from Danish patients in the present study belonged to the same population as the worms obtained from pigs, and more than 80% of the patients had known contact with pigs or pig manure. The above results suggest that cross-infections from pigs are a common transmission route for human ascariasis in Denmark. An epidemiological study showed that 8% of Dutch primary schoolchildren and 7% of Swedish adults had antibodies to Ascaris (36), but ascariasis was seldom reported. It was shown that humans developed a smaller number of adult worms in the intestine when experimentally infected with eggs from pig Ascaris versus eggs from human Ascaris (35), and often no large worms were established at all (8, 18). These data, together with small inocula, may explain why more than 80% of our patients and the North American patients of Anderson (2) carried only a single worm. In Denmark, there is no registration system for ascariasis; therefore, it is normally a "hidden" disease. Only a few cases with multiple worms may be recorded. In Scotland, 53 cases were reported within a 5-year period (11); of these, 66% were considered not to be travel related and 79% were among adults. Ten out of 12 cases (83%) of ascariasis reported in Finland occurred in patients younger than 10 years old (30), and children under this age accounted for 76% of the cases in our survey. During our 9-month survey, approximately 0.3% of the children younger than 5 years old and living in rural areas in Viborg County were reported to be expelling Ascaris (5).
Our results demonstrate that all of the cases of ascariasis in Danish patients examined in this study can be ascribed to cross-infections with Ascaris from pigs. This conclusion is supported by the fact that none of the patients had a traveling history. Thus, human ascariasis is a zoonosis in Denmark. We cannot exclude the possibility that some cases of A. lumbricoides infections are imported to Denmark; however, we observed the human form of the parasite only among worms collected in developing countries and not among worms collected in Denmark. Zoonotic ascariasis may also be a problem in other industrialized countries having high hygienic standards for human waste (2), and precautions to control this parasitic disease deserve renewed attention.
This work was funded by the National Research Foundation under the auspices of The Danish Centre for Experimental Parasitology, The Royal Veterinary and Agricultural University, and the Viborg County Research Fund for Health Science.
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. 1997. Taxonomic deliberations on human and pigs ascarids. Helminthologia 34:167-171.
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