Genetic comparison ofNeospora caninum withToxoplasma andSarcocystis by random amplified polymorphic DNA-polymerase chain reaction

To determine the relationship ofNeospora caninum to protozoa classified in the family Sarcocystidae of the phylum Apicomplexa, the genomes ofN. caninum, threeToxoplasma gondii strains (RHa, CEP, TPR) and threeSarcocystis species (S. tenella, S. muris, S. gigantea) that were thought to be closely related coccidia were compared by the random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) technique. The genomic DNAs were amplified by the use of seven 10-mer arbitrary sequence primers to generate polymorphic DNA. Significant DNA polymorphisms were observed amongNeospora, Toxoplasma andSarcocystis. It appears that one primer tested may have value in a diagnostic RAPD-PCR to differentiateT. gondii from other closely related protozoa. The high level of genetic divergence ofN. caninum fromT. gondii strains and severalSarcocystis species observed in this study is consistent with the hypothesis thatN. caninum is indeed an independent species of protozoan parasite. As compared with theSarcocystis species tested, a closer genetic relationship ofN. caninum toT. gondii was not observed. By contrast, a closer genetic relationship ofS. muris toT. gondii was revealed in this study.     

Toxoplasma gondii virulence markers identified by random amplified polymorphic DNA polymerase chain reaction

Genomic DNAs from 35 Toxoplasma gondii strains were amplified by random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) using 18 arbitrary 10-mer primers. At least four primers were found to generate DNA fragments that discriminate the 35 T. gondii strains into a genotype of virulent strains and a genotype of avirulent strains. Primer B12 was found to generate a virulence-specific fragment and primers B5, C8, and C20 were found to generate avirulence-specific fragments, which in all cases clearly identified either the virulence phenotype or the avirulence phenotype, respectively. In addition, the DNA polymorphic bands detected were analyzed by parsimony and distance analysis. A similar genetic relationship among the T. gondii strains was determined by the two phylogenetic methods, which use completely different assumptions. Consistent with the division of the 35 strains into a genotype of virulent strains and a genotype of avirulent strains, both analyses revealed 2 clonal lineages directly correlated with murine virulence. These results strongly support the hypothesis that the genus Toxoplasma may actually contain two clonal lineages correlated with virulence, which have evolved independently following their initial separation. Received: 1 October 1996 / Accepted: 15 October 1996     

Genetic structure of Aedes albifasciatus (Diptera: Culicidae) populations in central Argentina determined by random amplified polymorphic DNA-polymerase chain reaction markers.

The floodwater mosquito, Aedes albifasciatus (Macquart), is the main vector of western equine encephalomyelitis virus in Argentina. Previous studies on the genetic structure of this species using allozymes showed low levels of polymorphism, absence of subpopulations at distinct habitats, and moderate differentiation among localities separated up to 500 km. To examine gene flow using other genetic methods, we analyzed random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) polymorphism in 28 presumptive loci of Ae. albifasciatus from 6 populations in central Argentina. Allele frequencies were estimated assuming that RAPD products segregate as dominants and that genotype frequencies at those loci are in Hardy-Weinberg equilibrium. Expected heterozygosity ranged between 0.19 and 0.31, approximately 3 times the value obtained on the basis of the 16 allozymic loci studied previously. Four of the populations formed a single panmictic unit. Allele frequencies in populations occupying different phytogeographic regions gave significant FST values at 5 loci. Effective migration rates among populations estimated from FST ranged from 2.3 to 9.0. The results support the existence of a north-south cline.     

Genetic differentiation of pathogenic and nonpathogenic strains ofEntamoeba histolytica by random amplified polymorphic DNA polymerase chain reaction

The random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) method was used to compare pathogenic and nonpathogenic strains ofEntamoeba histolytica. DNA polymorphisms were detected among the different strains and dendrograms were constructed by PHYLIP and PAUP analyses to study the relationship of the strains. Both analyses resulted in identical results, which indicated that pathogenic strains ofE. histolytica are closely related and clearly separated from the nonpathogenic strains. The results of this study agree with classification of the strains based on isoenzyme analyses. This suggests that RAPD-PCR is a valuable method in differentiating between strains of this parasite, and the results are consistent with the concept that pathogenic and nonpathogenicEntamoeba represent two different species.Abbreviations DNA Deoxyribonucleic acid - PAUP phylogenetic analysis using parsimony - RAPD random amplified polymorphic DNA - PCR polymerase chain reaction - PHYLIP phylogeny inference package - UPGMA unweighted pair-group method with arithmetic mean     

A preliminary assessment of genetic differentiation of Triatoma dimidiata (Hemiptera: Reduviidae) in Guatemala by random amplification of polymorphic DNA-polymerase chain reaction

The population genetics of Triatoma dimidiata (Latreille, 1811) from five different provinces in Guatemala, including three sylvan and three domestic populations, was investigated by random amplification of polymorphic DNA-polymerase chain reaction. There is a high degree of genetic variation in all of the T. dimidiata populations as evidenced by high levels of average expected heterozygosity and polymorphism. Domestic populations are more closely related to each other (D = 0.05-0.085, Nei's genetic distance) than are the sylvan (D = 0.121-0.189). Within the limited sample size of three populations, there was a correlation with geographic and genetic distance for the domestic populations, but not for the sylvan. Surprisingly, one of the sylvan populations was genetically very similar to the domestic populations. The FST demonstrated a high degree of differentiation at the country-wide level (FST = 0.175) and a moderate degree of differentiation within the sylvan (FST = 0.135) or domestic (FST = 0.097) populations. Although these results demonstrated that gene flow is limited between different provinces in Guatemala, hierarchical analysis showed that barriers between the Atlantic and Pacific drainage slopes were not biologically significant limiters of gene flow.     

Evidence of two genetic entities inBothriocephalus funiculus (Cestoda) detected by arbitrary-primer polymerase chain reaction random amplified polymorphic DNA fingerprinting

The genetic diversity of two samples of Cestoda (Bothriocephalus funiculus, Renaud and Gabrion, 1984) parasitizing two sympatric teleostean species was assessed using random amplified polymorphic DNA (RAPD). A total of 72Bothriocephalus were analyzed individually, and electrophoretic analysis of the amplification products of 65 primers among the 68 tested revealed monomorphic patterns, reflecting the close genetic relatedness within and between the parasites of the two samples. However, 3 primers showed polymorphic patterns at 6 RAPD sites. Analysis of the distribution of these genomic fragments, assuming random mating, showed strong linkage disequilibria (only 8 genetic combinations were observed among the 32 expected). Two genetic entities displaying a high degree of host specificity were evidence within our two samples ofB. funiculus. This powerful molecular technique can be used as a diagnostic tool in studies concerning the biodiversity of related genetic entities and could have broad applications in parasitology.     

Use of random amplified polymorphic DNA for identification of ruminant trichostrongylid nematodes

The aim of this work was to evaluate random amplified polymorphic DNA (RAPD) as a source of markers for species identification and phylogenetic analysis of ruminant trichostrongylid nematodes. As these nematodes are often polymorphic, species identification may be difficult. We tested eight species and several of their morphs:Haemonchus contortus (three vulvar morphotypes: flap, smooth, and knobbed),Teladorsagia circumcincta, Ashworthius gagarini, Spiculopteragia boehmi, Ostertagia leptospicularis (and its morphOstertagia kolchida), Cooperia oncophora (and its morphC. surnabada), Trichostrongylus colubriformis, andT. vitrinus. With five chosen 10-mer primers, genetic variations were assessed among individuals of each species or morphotype. In trichostrongylid nematodes, the identification of species is possible by means of RAPD on adult or larva DNA extracts, although the variability observed within species was very important for most species studied. The use of RAPD in phylogenetics studies is conversely questionable for this superfamily of parasitic nematodes. The interspecific distances were always larger than the intraspecific ones and did not vary much (between 0.8 and 0.9); they would not be of much use in the construction of a phylogenetic tree, at least for the species and the primers involved in this study.     

Genetic relationships among Aedes aegypti (Diptera: Culicidae) populations from Argentina using random amplified polymorphic DNA polymerase chain reaction markers

Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) polymorphism was analyzed in five Aedes aegypti (L.) populations from Argentina and one from Puerto Rico to estimate levels of intraspecific polymorphism and genetic relatedness. Allele frequencies were estimated assuming that RAPD products segregate as dominants and that genotype frequencies at those loci are in Hardy-Weinberg equilibrium. Mean expected heterozygosity (He) was 0.350; F(ST) values were significant at all loci except one, supporting the usefulness of the fragments used here to discriminate among populations. Rogers' genetic similarity between samples ranged from 0.806 to 0.621. The population from Puerto Rico was the most different from the Argentina populations. Considering that Ae. aegypti eggs, larvae, and pupae can be transported easily, relationships among the Argentinian populations may reflect the routes and intensity of commercial transit.     

Comparative genetic analysis of tritrichomonadid protozoa by the random amplified polymorphic DNA technique

The taxonomic classification within the genus Tritrichomonas is a subject of controversy, and, potentially, separation of the tritrichomonads from cattle and swine on the species level is not valid. To tackle this hypothesis we comparatively assessed several isolates of protozoan parasites from the three Tritrichomonas species T. foetus, T. suis, and T. mobilensis by the RAPD (random amplified polymorphic DNA) technique. In this method with 20 different primers, all T. foetus and T. suis isolates resulted in identical genomic fingerprints, thus yielding additional evidence for the genetic identity of T. foetus and T. suis. In contrast, it turned out that the species T. mobilensis isolated from the squirrel monkey is genetically distinct and can clearly be discriminated from the other tritrichomonads. Consequently, the results obtained in this study support a possible future revision of the taxonomic classification of the genus Tritrichomonas. Received: 6 July 1997 / Accepted: 19 August 1997     

Molecular fingerprinting of fish-pathogenic Lactococcus garvieae strains by random amplified polymorphic DNA analysis

In this work, we used the random amplified polymorphic DNA (RAPD) technique to evaluate the genetic diversity in Lactococcus garvieae, an important pathogen for fish. Fifty-seven strains with different hosts and geographical origins, including Japan and several countries of the Mediterranean area such as Spain, Portugal, France, Italy, England, and Turkey, were analyzed. Two primers, oligonucleotides 5 and 6 (Pharmacia Biotech) were utilized; primer 5 was the most discriminative, since allowed us to differentiate 10 RAPD -types related to the origin of the strains. Regardless of the oligonucleotide primer employed, the 57 isolates of L. garvieae studied were separated into three genetic groups, composed of the Spanish, Portuguese, English, and Turkish strains (group A), the Italian and French strains (group B), and the Japanese strains (group C). The similarity of isolates within each group, estimated on the basis of the Dice coefficient, ranged from 75 to 100%. Our findings also indicate that RAPD profiling constitutes a useful tool for epidemiological studies of this fish pathogen.     

Rapid discrimination of Mycobacterium tuberculosis strains by random amplified polymorphic DNA analysis.

Investigations of the epidemiology of tuberculosis have been hampered by the lack of strain-specific markers that can be used to differentiate isolates of Mycobacterium tuberculosis. We report the development of a rapid protocol for random amplified polymorphic DNA analysis which included the use of a commercially available DNA extraction kit (GeneReleaser). This was applied to 14 strains of M. tuberculosis, including strains associated with temporal and geographical clusters of tuberculosis in the United Kingdom and those from India, Africa, and Saudi Arabia. Strains of M. tuberculosis could be discriminated in about 8 h by this method, which is therefore a rapid and simple alternative to restriction fragment length polymorphism analysis.     

Application of random amplified polymorphic DNA analysis to differentiate strains of Salmonella enteritidis.

A random amplified polymorphic DNA (RAPD) fingerprinting method has been developed to differentiate Salmonella enteritidis isolates. A total of 65 arbitrary primers were screened with S. enteritidis isolates of different phage types. This allowed selection of a panel of primers capable of detecting DNA polymorphisms among S. enteritidis isolates. This panel was used to examine a panel of 29 isolates of S. enteritidis which had been previously characterized by other subtyping methods, including phage typing (PT) (n = 7), ribotyping (RT) (n = 13), and pulsed-field gel electrophoresis (PFGE). Applied collectively, these three methods resolved the collection into 20 different subtypes. However, by the RAPD fingerprinting method alone, 14 RAPD subtypes were revealed. Eight isolates of S. enteritidis phage type 8 that failed to be discriminated by other typing methods (PT, RT, and PFGE) were resolved into three different subtypes by RAPD analysis. In contrast, isolates that were derived from the same sources were not differentiated by any of the subtyping methods employed, including PT, RT, PFGE, and RAPD analysis. This RAPD approach to S. enteritidis subtyping provided more discriminatory power than did any of several other subtyping methods applied individually. Once the challenging step of primer identification was accomplished, determinations of the appropriate concentrations of arbitrary primer, DNA template, and MG2+ ion were also necessary for optimal discriminatory power. The bacterial DNA used in this RAPD protocol was obtained by boiling the bacterial sample. This simple procedure yielded DNA that produced fingerprint patterns as consistent as those obtained from phenol-chloroform-extracted DNA. Clearly, when appropriately constituted primer sets are identified and employed, RAPD analysis provides a simple, rapid, and powerful subtyping method for S. enteritidis.     

Analysis of isolates within species of anuran trypanosomes using random amplified polymorphic DNA

 A total of 20 decamer primers were used to generate random applied polymorphic DNA (RAPD) markers from 5 isolates of Trypanosoma fallisi, 3 isolates of T. ranarum, 2 isolates of T. rotatorium, and 2 isolates of T. rotatorium-like trypanosomes in addition to 2 species from the American Type Culture Collection, T. chattoni (ATCC 50294) and Trypanosoma sp. (ATCC 50295). A slight polymorphism was observed among the four isolates of T. fallisi obtained from American toads, Bufo americanus, collected in Algonquin Park, Ontario, Canada, and an isolate obtained from the same species of host collected in Marquette, Michigan, United States, and produced similarity coefficients ranging from 80.7% to 96.9%. Pronounced polymorphism was recorded among the three isolates of T. ranarum from bullfrogs, Rana catesbeiana, collected in Ontario, Canada, and in Maryland, United States, and from a Northern leopard frog, R. pipiens, collected in Minnesota (USA). The similarity coefficients ranged from 54.7% to 59.5%, suggesting that alleles of these isolates were conserved over a wide geographic range. The high degree of polymorphism observed in two isolates of T. rotatorium from a bullfrog collected in Ontario and two isolates of a T. rotatorium-like parasite from the green frog R. clamitans, collected in Louisiana (USA) suggests that they are different species. These results reflect the high similarity among isolates from the same geographic location and the pronounced polymorphism apparent among isolates from distant geographic locations. Received: 9 February 1995 / Accepted: 24 May 1995     

Analysis of isolates within species of anuran trypanosomes using random amplified polymorphic DNA

A total of 20 decamer primers were used to generate random applied polymorphic DNA (RAPD) markers from 5 isolates of Trypanosoma fallisi, 3 isolates of T. ranarum, 2 isolates of T. rotatorium, and 2 isolates of T. rotatorium-like trypanosomes in addition to 2 species from the American Type Culture Collection, T. chattoni (ATCC 50294) and Trypanosoma sp. (ATCC 50295). A slight polymorphism was observed among the four isolates of T. fallisi obtained from American toads, Bufo americanus, collected in Algonquin Park, Ontario, Canada, and an isolate obtained from the same species of host collected in Marquette, Michigan, United States, and produced similarity coefficients ranging from 80.7% to 96.9%. Pronounced polymorphism was recorded among the three isolates of T. ranarum from bullfrogs, Rana catesbeiana, collected in Ontario, Canada, and in Maryland, United States, and from a Northern leopard frog, R. pipiens, collected in Minnesota (USA). The similarity coefficients ranged from 54.7% to 59.5%, suggesting that alleles of these isolates were conserved over a wide geographic range. The high degree of polymorphism observed in two isolates of T. rotatorium from a bullfrog collected in Ontario and two isolates of a T. rotatorium-like parasite from the green frog R. clamitans, collected in Louisiana (USA) suggests that they are different species. These results reflect the high similarity among isolates from the same geographic location and the pronounced polymorphism apparent among isolates from distant geographic locations.     

Use of cleaved amplified polymorphic sequences to distinguish strains of Staphylococcus epidermidis.

We examined the utility of a PCR-based method termed cleaved amplified polymorphic sequences (CAPS) to type 35 well-characterized isolates of Staphylococcus epidermidis. The results were compared with detailed epidemiologic information and typing obtained by using pulsed-field gel electrophoresis (PFGE). To identify CAPS markers for this study, eight pairs of oligonucleotide primers corresponding to five previously sequenced S. epidermidis genes were synthesized and then used to amplify DNA sequences from the S. epidermidis strains by using PCR. Amplified products were reproducibly obtained for seven of eight primer pairs from chromosomal DNA of 33 of the 35 isolates. Seven restriction site polymorphisms were found in five of the amplified products when they were subjected to digestion with a panel of restriction endonucleases. Each fragment-enzyme combination that was polymorphic demonstrated only two alleles in the 33 S. epidermidis isolates analyzed, corresponding to the presence or absence of a single restriction site. Overall, five distinct combinations of alleles were detected and were designated CAPS types A through E. There was a close correlation between the CAPS grouping, the epidemiologic information for the strains, and grouping by PFGE following SmaI digestion of chromosomal DNA. Although PFGE analysis was more discriminatory than typing based on the limited number of CAPS markers used in this study (isolates from the same CAPS group were sometimes distributed into more than one PFGE group), no isolates from the same PFGE group were found in more than one CAPS group. The CAPS procedure was highly reproducible, in contrast to published experience with arbitrarily primed PCR. These preliminary data suggest that CAPS represents a PCR-based technique for strain typing that is highly reproducible, rapid, utilizes widely available technologies, and provides results that are relatively easy to interpret and express.     

Intraspecific variation in two species of Rhizomucor assessed by random amplified polymorphic DNA analysis

Twenty-three Rhizomucor isolates were characterized by random amplified polymorphic DNA-PCR (RAPD-PCR) with 10-bp oligonucleotide primers. These data were used for numerical analyses to obtain information on the intraspecific genetic polymorphism of Rhizomucor species. The genetic variability in Rhizomucor pusillus and Rhizomucor miehei isolates was found to differ; the latter revealed less intraspecific polymorphism. The different levels of genotypic diversity suggest a correlation with the different forms of mating behaviour of these species. Rhizomucor tauricus displayed amplification patterns similar to those of the investigated R. pusillus strains, reinforcing the assumption that R. tauricus does not represent a separate species. Characteristic RAPD markers allowing PCR-based species identification of Rhizomucor isolates were determined.     

Use of random amplified polymorphic DNA analysis to compareBabesia bovis andB. bigemina isolates

Random amplified polymorphic DNA analysis provides characteristic fingerprints forBabesia bovis andB. bigemina. This genetic profile reflects similarities and minor differences between closely related regional isolates and the greater diversity representative of species from distant geographic locations.