Comparison of the levels of intra-specific genetic variation within Giardia muris and Giardia intestinalis

The extent of intra-specific genetic variation between isolates of Giardia muris was assessed by allozyme electrophoresis. Additionally, the levels of allozymic variation detected within G. muris were compared with those observed between members of the two major assemblages of the morphologically distinct species Giardia intestinalis. Four isolates of G. muris were analysed. Three (Ad-120, -150, -151) were isolated from mice in Australia, while the fourth (R-T) was isolated from a golden hamster in North America. The 11 isolates of G. intestinalis (Ad-1, -12, -2, -62, representing genetic Groups I and II of Assemblage A and BAH-12, BRIS/87/HEPU/694, Ad-19, -22, -28, -45, -52, representing genetic Groups III and IV of Assemblage B) were from humans in Australia. Intra-specific genetic variation was detected between G. muris isolates at four of the 23 enzyme loci examined. Similar levels of variation were found within the genetic groups that comprise Assemblages A and B of G. intestinalis. These levels of intra-specific variation are similar to those observed within other morphologically-distinct species of protozoan parasites. We suggest that the magnitude of the genetic differences detected within G. muris provides an indication of the range of genetic variation within other species of Giardia and that this can be used as a model to delineate morphologically similar but genetically distinct (cryptic) species within this genus.     

The Boston AIDS Survival Score (BASS): a multidimensional AIDS severity instrument

We report the results of molecular analysis of 39 isolates of Cryptosporidium parvum from human and bovine sources in nine human outbreaks and from bovine sources from a wide geographic distribution. All 39 isolates could be divided into either of two genotypes, on the basis of genetic polymorphism observed at the thrombospondin-related adhesion protein (TRAP-C2) locus. Genotype 1 was observed only in isolates from humans. Genotype 2, however, was seen in calf isolates and in isolates from a subset of human patients who reported direct exposure to infected cattle or consumed items thought to be contaminated with cattle faces. Furthermore, experimental infection studies showed that genotype 2 isolates were infective to mice or calves under routine laboratory conditions, whereas genotype 1 isolates were not. These results support the occurrence of two distinct transmission cycles of C. parvum in humans.     

Molecular microbiological investigation of an outbreak of hemolytic-uremic syndrome caused by dry fermented sausage contaminated with Shiga-like toxin-producing Escherichia coli

Shiga-like toxin-producing Escherichia coli (SLTEC) strains are a diverse group of organisms which are known to cause diarrhea and hemorrhagic colitis in humans. This can lead to potentially fatal systemic sequelae, such as hemolytic-uremic syndrome (HUS). Strains belonging to more than 100 different O:H serotypes have been associated with severe SLTEC disease in humans, of which only O157 strains (which are uncommon in Australia) have a distinguishable cultural characteristic (sorbitol negative). During an outbreak of HUS in Adelaide, South Australia, a sensitive PCR assay specific for Shiga-like toxin genes (slt) was used to test cultures of feces and suspected foods. This enabled rapid confirmation of infection and identified a locally produced dry fermented sausage (mettwurst) as the source of infection. Cultures of feces from 19 of 21 HUS patients and 7 of 8 mettwurst samples collected from their homes were PCR positive for slt-I and slt-II genes. SLTEC isolates belonging to serotype O111:H- was subsequently isolated from 16 patients and 4 mettwurst samples. Subsequent restriction fragment length polymorphism analysis of chromosomal DNA from these isolates with slt-specific probes indicated that at least three different O111:H- genotypes were associated with the outbreak. Pulsed-field gel electrophoresis of genomic DNA restricted with XbaI showed that two of these restriction fragment length polymorphism types were closely related, but the third was quite distinct. However, SLTEC strains of other serotypes, including O157:H-, were also isolated from some of the HUS patients.     

PCR-ribotyping of Xenorhabdus and Photorhabdus isolates from the Caribbean region in relation to the taxonomy and geographic distribution of their nematode hosts

The genetic diversity of symbiotic Xenorhabdus and Photorhabdus bacteria associated with entomopathogenic nematodes was examined by a restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes (rDNAs). A total of 117 strains were studied, most of which were isolated from the Caribbean basin after an exhaustive soil sampling. The collection consisted of 77 isolates recovered from entomopathogenic nematodes in 14 Caribbean islands and of 40 reference strains belonging to Xenorhabdus and Photorhabdus spp. collected at various localities worldwide. Thirty distinctive 16S rDNA genotypes were identified, and cluster analysis was used to distinguish the genus Xenorhabdus from the genus Photorhabdus. The genus Xenorhabdus appears more diverse than the genus Photorhabdus, and for both genera the bacterial genotype diversity is in congruence with the host-nematode taxonomy. The occurrence of symbiotic bacterial genotypes was related to the ecological distribution of host nematodes.     

Genotypic analysis of Toxoplasma gondii isolates from pigs

To determine the prevalence of the 3 primary clonal lineages of Toxoplasma gondii (strain types I, II, and III) in a potential food source of infection for humans, we analyzed 43 isolates of T. gondii that had been collected from pigs at an abattoir in Iowa. Parasites were harvested as in vitro-grown tachyzoites, and their genotypes were determined at the SAG1 and SAG2 loci. On the basis of the allele identified at the SAG2 locus, isolates were grouped into 1 of the 3 primary lineages. Type II strains were by far the most prevalent, accounting for 83.7% of the isolates. The type III genotype was identified in only 16.3% of the isolates. These prevalences differ significantly from a previous sampling of isolates from animals but are similar to the frequencies with which they occur in human disease cases. Similar to the previously characterized strain P89, strains P62 and P105 appeared to have recombinant genotypes. The type I genotype was not identified in the isolates from pigs although these strains have previously been shown to account for approximately 10-25% of toxoplasmosis cases in humans.     

Dideoxy fingerprinting: application to the genotyping of Echinococcus

Dideoxy fingerprinting is an efficient method for the detection of sequence variation in PCR-amplified DNA segments. It is a hybrid between single-strand conformation polymorphism and dideoxy sequencing, employing only one dideoxynucleotide in the sequencing reaction. Herein, we report the application of dideoxy fingerprinting to genetically type cestodes of the genus Echinococcus, utilising the mitochondrial cytochrome c oxidase subunit I as the gene sequence for analysis. All of the seven genotypes (G1, G4, G6, G8, O, V and M2) examined could be readily differentiated from one another by their characteristic and reproducible dideoxy fingerprinting profiles. Only subtle variation in profiles was detected among some of the eight isolates representing genotype G1, and no variation was detected between two samples of genotype G4 and of genotype M2. The capacity of dideoxy fingerprinting to detect all nucleotide variations over 150-250bp fragments indicates that it should be possible to distinguish among all of the genotypes of Echinococcus thus far described. Although employed herein to display sequence variation in the cytochrome c oxidase subunit I of Echinococcus, dideoxy fingerprinting could be used for the high-resolution analysis of nucleotide variations in other parasite genes, without the need for DNA sequencing. This has important implications for studying the genetic structure of parasite populations.     

Flow cytometric analysis of microsporidia belonging to the genus Encephalitozoon

Flow cytometry was used in the identification of human microsporidia belonging to the genus Encephalitozoon. Microsporidian spores of Encephalitozoon hellem, E. cuniculi, and E. intestinalis were propagated in axenic cultures of monkey kidney E6 cells, purified with Percoll, and exposed to homologous and heterologous rabbit antiserum and monoclonal antibody prepared against E. hellem spores. After reaction to goat anti-rabbit immunoglobulin G (IgG) or goat anti-mouse IgG conjugated to fluorescein isothiocyanate, fluorescence histograms from gated data on light-scatter profiles showed that rabbit anti-E. hellem serum was reactive to E. hellem spores but also had cross-reactivity to spores of E. cuniculi and E. intestinalis. On the other hand, fluorescence histograms showed that rabbit anti-E. cuniculi and rabbit anti-E. intestinalis sera were reactive with homologous spores only. Monoclonal antibody prepared against E. hellem reacted only with spores of E. hellem. Neither the polyclonal antibodies nor the monoclonal antibodies reacted with Cryptosporidium parvum oocysts. Fluorescence histograms of spores treated with 10% formalin also showed reactivity, but the number of events in the most intense peaks of fluorescence was fewer (7 to 42%, depending on species) than the number of events in the most intense peaks of fluorescence for nontreated spores. By flow cytometry, formalin-treated and nontreated spores of Encephalitozoon were identified to the species level by using gated data on light-scatter profiles and analyzing the fluorescence histograms from the indirect immunofluorescence of the spores. Once a procedure is established for the isolation of Encephalitozoon spores from clinical specimens, identification of spores by flow cytometry may be useful not only for diagnosis but also for epidemiologic studies.     

Genotype-specific complementation of hepatitis delta virus RNA replication by hepatitis delta antigen

Characterizations of genetic variations among hepatitis delta virus (HDV) isolates have focused principally on phylogenetic analysis of sequences, which vary by 30 to 40% among three genotypes and about 10 to 15% among isolates of the same genotype. The significance of the sequence differences has been unclear but could be responsible for pathogenic variations associated with the different genotypes. Studies of the mechanisms of HDV replication have been limited to cDNA clones from HDV genotype I, which is the most common. To perform a comparative analysis of HDV RNA replication in genotypes I and III, we have obtained a full-length cDNA clone from an HDV genotype III isolate. In transfected Huh-7 cells, the functional roles of the two forms of the viral protein, hepatitis delta antigen (HDAg), in HDV RNA replication are similar for both genotypes I and III; the short form is required for RNA replication, while the long form inhibits replication. For both genotypes, HDAg was able to support replication of RNAs of the same genotype that were mutated so as to be defective for HDAg production. Surprisingly, however, neither genotype I nor genotype III HDAg was able to support replication of such mutated RNAs of the other genotype. The inability of genotype III HDAg to support replication of genotype I RNA could have been due to a weak interaction between the RNA and HDAg. The clear genotype-specific activity of HDAg in supporting HDV RNA replication confirms the original categorization of HDV sequences in three genotypes and further suggests that these should be referred to as types (i.e., HDV-I and HDV-III) rather than genotypes.     

Expression of growth factor mRNAs by human Tenon''s capsule fibroblasts

We determined the nucleotide sequences of Norwalk-like viruses in 10 PCR products from stool or oyster specimens obtained from four outbreaks of gastroenteritis in which shellfish was suspected as the cause in Shizuoka prefecture in Japan between 1987-94. The sequences were determined from nucleotide positions 4561-4852 (292 bp) in the polymerase region. Two types of sequences were detected. One (genotype 1) had 87% sequence homology with the prototype Norwalk virus, and the other (genotype 2) had 59% sequence homology. The sequences from isolates belonging to the same genotype were almost the same regardless of the year of isolation. Because sequences of 2 genotypes were detected in 2 of the 4 outbreaks, nested PCR was performed with genotype-specific primers to detect the presence of 2 genotypes in the same specimen. In 5 of 10 specimens, PCR bands were detected with both genotype-specific primers, indicating the coexistence of 2 genotypes in 1 specimen. We also detected two genotypes of Norwalk-like virus in an oyster from a sample implicated in one of the outbreaks which may provide direct evidence of oysters as the cause of the gastroenteritis.     

Characterization of serologically nontypeable Actinobacillus actinomycetemcomitans isolates

Our previous studies have shown that Actinobacillus actinomycetemcomitans isolates of a given arbitrarily primed PCR (AP-PCR) genotype belong to the same serotype (of serotypes a through e). In the present study we investigated whether the AP-PCR genotypes of nonserotypeable A. actinomycetemcomitans isolates match those of the serotypeable isolates. The isolates were additionally characterized by restriction analysis of the apaH PCR amplification products. The material included 75 nonserotypeable and 18 serotypeable A. actinomycetemcomitans isolates from 34 epidemiologically unrelated subjects. The serotypeable isolates were obtained from subjects who also harbored nonserotypeable isolates. Eight AP-PCR genotypes were distinguished among the isolates; six genotypes matched those detected in our previous studies, whereas two genotypes were new. Intraindividually, the A. actinomycetemcomitans isolates produced identical AP-PCR banding patterns, regardless of whether they were serotypeable or nonserotypeable, in 22 of 23 subjects participating with multiple isolates. AP-PCR genotype 3, corresponding to serotype c, was by far the most common among the nonserotypeable isolates (62% of subjects). Results obtained with the apaH restriction analysis confirmed the results obtained with AP-PCR for 31 of the 34 subjects. The results suggest that nonserotypeable A. actinomycetemcomitans isolates originate from serotypeable isolates, especially from serotype c isolates, and the likelihood of the existence of additional serotypes is small.     

Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans

Associations between known or putative virulence factors of Shiga toxin-producing Escherichia coli and disease in humans were investigated. Univariate analysis and multivariate logistic regression analysis of a set of 237 isolates from 118 serotypes showed significant associations between the presence of genes for intimin (eae) and Shiga toxin 2 (stx2) and isolates from serotypes reported in humans. Similar associations were found with isolates from serotypes reported in hemorrhagic colitis and hemolytic-uremic syndrome. The enterohemorrhagic E. coli (EHEC) hemolysin gene was significantly associated with isolates from serotypes found in severe diseases in univariate analysis but not in multivariate logistic regression models. A strong association between the intimin and EHEC-hemolysin genes may explain the lack of statistical significance of EHEC hemolysin in these multivariate models, but a true lack of biological significance of the hemolysin in humans or in disease cannot be excluded. This result warrants further investigations of this topic. Multivariate analysis revealed an interaction between the eae and stx2 genes, thus supporting the hypothesis of the synergism between the adhesin intimin and Shiga toxin 2. A strong statistical association was observed between the stx2 gene and severity of disease for a set of 112 human isolates from eight major serotypes. A comparison of 77 isolates of bovine origin and 91 human isolates belonging to six major serotypes showed significant associations of the genes for Shiga toxin 1 and EspP protease with bovine isolates and an increased adherence on HEp-2 cell cultures for human isolates, particularly from diarrheic patients and healthy persons.     

A new restriction fragment length polymorphism from Cryptosporidium parvum identifies genetically heterogeneous parasite populations and genotypic changes following transmission from bovine to human hosts

Length and restriction site polymorphism within a 2.8-kb threonine-rich open reading frame from Cryptosporidium parvum was identified and used to determine the genotypes of isolates from calves and humans. In agreement with observations of other genetic loci, all calf isolates were identical at this locus. In contrast, human isolates showed two profiles, one found exclusively in humans and one a superposition of both profiles, which were indicative of heterogeneous parasite populations. PCR fingerprints were consistent with a change in the genetic profile of C. parvum isolates following transmission from bovine to human hosts.     

The effect of number of days in culture and plasminogen activator inhibitor-1 (PAI-1) 4G/5G genotype on PAI-1 antigen release by cultured human umbilical vein endothelial cells

An insertion/deletion (4G/5G) polymorphism in what has been shown to be an enhancer/repressor binding site in the promoter region of the PAI-1 gene has been related to plasma PAI-1 activity. Transfection studies demonstrated increased interleukin-1 stimulated PAI-1 synthesis in cells containing the 4G sequence. To study this response in endothelial cells, first passage HUVEC from 26 umbilical cords were stimulated with interleukin-1 and tumor necrosis factor-alpha. PAI-1 antigen was measured in 24-hour conditioned medium and allele-specific PCR utilized to determine genotype at the 4G/5G locus. Analysis of covariance was used to determine whether the effect of a variable time in culture was masking a difference between genotypes. A trend towards higher PAI-1 levels with increasing time in culture was observed. The geometric mean (95% confidence interval) of the basal rate of PAI-1 release was, 4G/4G 9.7 (7.0, 13.5) ng/24 hours (n=11), 4G/5G 9.5 (6.5, 13.9) ng/24 hours (n=9), and 5G/5G 10.9 (7.8, 15.1) ng/24 hours (n=6). In cells of the same cultures, the interleukin-1 stimulated levels were 25.9 (23.1, 29.1), 27.2 (23.6, 31.3), and 23.1 (19.5, 27.3) ng/24 hours, respectively, corresponding to ratios of stimulated to basal levels of 2.68, 2.87, and 2.12. After adjustment for time in culture the basal PAI-1 release was 4G/4G 10.7, 4G/5G 9.1, and 5G/5G 9.7 ng/24 hours. For interleukin-1 stimulated release the adjusted levels were 26.3, 27.0, and 22.7 ng/24 hours, respectively. Adjusted levels in 4G/4G genotype cells were non-significantly greater than those in cells of 5G/5G genotype by a factor of 1.16 (0.95, 4.08). This study did not demonstrate a significant difference in basal or cytokine stimulated PAI-1 release from cells of different PAI-1 promoter (4G/5G) genotypes but does not exclude increased interleukin-1 stimulated PAI-1 release in the 4G/4G compared with the 5G/5G genotype.     

Genetic polymorphism at the beta-tubulin locus among human and animal isolates of Cryptosporidium parvum

Sequence analysis of a fragment of the beta-tubulin gene was performed on 13 isolates of the parasite Cryptosporidium parvum, eight from humans and five from animals. A total of 12 synonymous substitutions and a deletion of two bases within the intron sequence were found. This genetic variation defined two alleles at the beta-tubulin locus, which can be identified by a simple polymerase chain reaction-restriction fragment length polymorphism assay. A total of 20 isolates were also tested using four available molecular markers. These analyses showed congruently that the C. parvum isolates segregate into two groups, one found exclusively in humans and the other found in both humans and animals. Since no recombinant genotypes were observed, the results are consistent with the hypothesis of a substantially clonal reproduction in this parasite.     

Genotypic and phenotypic characterization of Cryptosporidium parvum isolates from people with AIDS

Genotypic analysis of Cryptosporidium parvum has demonstrated the presence of two subgroups within the species, whereas biochemical and antigenic characterization have shown more heterogeneity. The clinical relevance of these observations is unknown. C. parvum isolates from people with AIDS were studied with respect to parasite genotypes and virulence in cell monolayers and laboratory animals. Ten of 13 oocyst samples had a characteristic human-associated (H) genotype; 3 had a genotype typical of calf-excreted oocysts (C). Virulence in cell culture was mildly or markedly lower in the 5 isolates tested (4 H and 1 C) compared with the GCH1 reference isolate. H isolates did not infect newborn ICR mice, whereas 1 of the 2 C isolates tested did. These findings reinforce the concept of C. parvum genetic subgroupings that correlate to some extent with infectivity and suggest that additional heterogeneity is present within the subgroups.     

Evidence of genomic instability in Campylobacter jejuni isolated from poultry

Poultry isolates of Campylobacter jejuni derived from a survey of meat processing batches were genotyped by pulsed-field gel electrophoresis (PFGE) of chromosomal DNA to establish the clonal relationships between single-colony isolates. In the majority of batches studied, one or two genotype patterns predominated. However, in one batch (batch A), 21 single-colony isolates gave 14 different PFGE genotypes. The banding patterns obtained with SmaI were sufficiently different to distinguish between genotypes, although the patterns also produced many common bands. The question of whether these isolates represented different clones or had a common clonal ancestry was addressed by additional genotypic and phenotypic methods. Restriction length polymorphism of PCR products obtained from the flagellin genes showed an identical flagellin genotype for all of these isolates. In contrast, unrelated control isolates resulted in different flagellin genotypes. Moreover, all 14 different PFGE genotypes of batch A had identical Penner serotypes and identical or similar biotypes and phage types. It was concluded that the isolates were of clonal origin and that the diversity in the PFGE banding patterns had most likely originated from genomic rearrangements. However, the PFGE genotypes were shown to be stable upon subculturing in vitro and after in vivo passage in chickens, and natural transformation between isogenic mutants carrying antibiotic markers did not occur in vivo in a chick colonization model. The possible mechanisms for the hypothesized genomic recombinations and the conditions that allow, induce, or select for such events are discussed.     

Validation of an electronic, population-based prescription database

BACKGROUND: Helicobacter pylori vacuolating cytotoxin encoded by vacA plays an essential role in H. pylori-related pathogenesis. Specific vacA alleles are believed to be associated with increased virulence. Association among vacA polymorphism, vacA middle genotypes, and various H. pylori-related diseases was thus investigated. METHODS: Eighty-nine isolates from patients with various gastrointestinal diseases were examined for restriction fragment length polymorphism (RFLP) of the 2.0-kb polymerase chain reaction-amplified vacA middle region. Further genetic heterogeneity was assessed with ureA-ureB RFLP. RESULTS: Twenty-eight distinct vacA RFLPs were seen among 89 isolates. Each pattern was associated with one specific vacA middle genotype. The association of specific RFLPs with certain clinical manifestations was noted among six common groups. Further RFLP analysis of the 2.4-kb ureA-ureB segment from isolates in four popular vacA RFLPs showed high genetic variation. CONCLUSIONS: The vacA genetic polymorphism may be associated with different gastrointestinal diseases.     

Evaluation of urinary level of NMP22 as a diagnostic marker for stage pTa-pT1 bladder cancer: comparison with urinary cytology and BTA test

The protein profile and the antigenic cross-reactivity of 18 axenic isolates of Blastocystis hominis obtained from symptomatic patients with chronic diarrhea (14 isolates) showing no evidence of parasitic etiology and from patients with acute diarrhea attributable in 2 cases to Salmonella spp. were analyzed. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of soluble proteins showed the existence of a common profile composed of 31 bands, with molecular weights ranging between 24 and >200 kDa, and minor differences in the proteins of 149, 118, 106, 50, 48, 47, and 30 kDa. These differences allowed us to classify the strains into three related patterns (I-III). In an indirect immunofluorescence assay, all strains were serologically identical, but two related antigenic groups (1 and 2) were found in double-immunodiffusion and Western-blot studies. The isolates of protein patterns I and II belonging to antigenic group 1 were isolated from patients with chronic diarrhea, whereas the four isolates from patients with acute diarrhea were clustered in protein pattern III and in antigenic group 2. These results confirm the protein and antigenic heterogeneity of B. hominis and the existence of demes with different pathogenic roles.     

Coronary stent implantation without preliminary dilatation]

The development of a polymerase chain reaction (PCR) based fingerprinting method for the characterization of Giardia duodenalis isolates is described. The method uses three different PCRs; one is specific for the A ("Polish") major group of G. duodenalis isolates, another is specific for the B ("Belgian") group of isolates; and one amplifies a fragment of the glutamate dehydrogenase gene present in all G. duodenalis isolates. The PCRs perform highly sensitively on DNA from cultured trophozoites. Isolates were further characterized by restriction-fragment-length polymorphism (RFLP) analysis of the PCR products. In this way, representative isolates from the A and B groups could be grouped together into a number of subgroups. The stability of the genotypes with time and the reproducibility of the two methods were tested on cloned and subcloned lines from a number of isolates and proved to be highly satisfactory. The PCR/RFLP method was evaluated on cysts derived from a number of human patients. It is concluded that the PCR fingerprinting method described in this paper provides a reliable characterization method for Giardia isolates and has the potential to be used as a direct method of typing G. duodenalis cysts from feces.