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PubMed2001

Prevalence of virulent Rhodococcus equi in soil from five R. equi-endemic horse-breeding farms and restriction fragment length polymorphisms of virulence plasmids in isolates from soil and infected foals in Texas.

Rhodococcus equi isolates (462) obtained from 64 soil samples collected on 5 R. equi-endemic horse-breeding farms and isolates from 100 infected foals in Texas were examined to determine the prevalence and genotypic diversity of virulence-associated plasmids. Isolates were tested for the presence of 15-17-kDa virulence-associated protein antigens (VapA) by immunoblotting and virulence-associated plasmids by PCR. Plasmid DNAs were isolated and analyzed by digestion with restriction endonucleases for estimation of size and comparison of polymorphisims. Rhodococcus equi were isolated from soil of all 5 farms; however, virulent R. equi were only isolated from 3 of the 5 farms and represented 18.8% (87 of 462) of total isolates. Of the 87 virulent soil isolates, 56 (64.5%) contained an 85-kb type I plasmid, 23 (26.4%) an 87-kb type I plasmid, 7 (8%) a newly defined 85-kb type III plasmid (Tx 43), and 1 (1.1%) a newly defined 85-kb type IV plasmid (Tx 47). Of the 100 isolates from infected foals, 96 were virulent. Of the 96 virulent isolates, 51 (53.1%) contained an 85-kb type I plasmid, 39 (40.6%) an 87-kb type I plasmid, 4 (4.2%) an 85-kb type III plasmid (Tx 43), and 2 (2.1%) an 85-kb type IV plasmid (Tx 47). There are at least 4 different R. equi virulence-associated plasmids in Texas, 2 of which have not previously been described. Based upon virulence plasmid typing, there is geographic diversity among isolates of R. equi from clinical and environmental samples on horse-breeding farms in Texas. There is not a strong correlation between the presence of virulent R. equi in farm soils and the R. equi disease status of those farms.

Actinomycetales Infections↗
PubMed1996

Genetic diversity among Frankia strains nodulating members of the family Casuarinaceae in Australia revealed by PCR and restriction fragment length polymorphism analysis with crushed root nodules.

DNA extracted directly from nodules was used to assess the genetic diversity of Frankia strains symbiotically associated with two species of the genus Casuarina and two of the genus Allocasuarina naturally occurring in northeastern Australia. DNA from field-collected nodules or extracted from reference cultures of Casuarina-infective Frankia strains was used as the template in PCRs with primers targeting two DNA regions, one in the ribosomal operon and the other in the nif operon. PCR products were then analyzed by using a set of restriction endonucleases. Five distinct genetic groups were recognized on the basis of these restriction patterns. These groups were consistently associated with the host species from which the nodules originated. All isolated reference strains had similar patterns and were assigned to group 1 along with six of the eight unisolated Frankia strains from Casuarina equisetifolia in Australia. Group 2 consisted of two unisolated Frankia strains from C. equisetifolia, whereas groups 3 to 5 comprised all unisolated strains from Casuarina cunninghamiana, Allocasuarina torulosa, and Allocasuarina littoralis, respectively. These results demonstrate that, contrary to the results of previous molecular studies of isolated strains, there is genetic diversity among Frankia strains that infect members of the family Casuarinacaeae. The apparent high homogeneity of Frankia strains in these previous studies probably relates to the single host species from which the strains were obtained and the origin of these strains from areas outside the natural geographic range of members of the family Casuarinaceae, where genetic diversity could be lower than in Australia.

Actinomycetales↗
PubMed1986

Chromosome assignment and restriction fragment length polymorphism analysis of the anonymous DNA probe B79a at 7q22 (HMG8 assignment D7S13).

The anonymous DNA fragment B79a, which had previously been located to chromosome 7cen-7q22, has been more accurately assigned to 7q22 by dosage analysis in a patient hemizygous for a deletion of that region. By examination of a panel of genomic DNAs from unrelated individuals, digested with a number of different restriction enzymes, we have identified two frequent RFLPs detected by B79a. This probe will be important in the analysis of cystic fibrosis which has been mapped to the region around 7q22.

Chromosome Mapping↗
PubMed2003

Factor V Leiden detection by polymerase chain reaction-restriction fragment length polymorphism with mutagenic primers in a multiplex reaction with Pro G20210A--a novel technique.

Factor V Leiden (FVL) R506Q and Prothrombin G20210A are clinically important genetic mutations associated with increased susceptibility to venous thrombosis. The objective of our study was to design a polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) reaction that allows simultaneous detection of these two mutations. The reaction can be used in routine diagnostic settings. We have analysed 4504 alleles for each mutation with a mutagenic primer-based PCR system with a low failure rate. The system eliminates the false positive FVL G1691A results associated with other PCR/RFLP caused by rare confounding mutations adjacent to restriction endonuclease recognition sites. This multiplex PCR/RFLP reaction is rapid, robust and dependable.

3' Untranslated Regions↗
PubMed1995

Restriction fragment length polymorphism analysis of PCR-amplified 16S ribosomal DNA of human Capnocytophaga.

The confusion in the taxonomic status of the genus Capnocytophaga has made identification of strains and studies on the role of this genus in infectious diseases equivocal. In this study 33 strains of Capnocytophaga including reference strains and various clinical isolates, were studied using RFLP analysis of 16S ribosomal RNA genes. The 16S ribosomal RNA (rRNA) gene sequences from whole cell suspensions and isolated genomic DNA samples were amplified by the polymerase chain reaction (PCR) using eubacterial specific primers. PCR products were purified and characterized by single digestions with 12 restriction endonucleases. Five of these, BanI, CfoI, HaeIII, HphI and RsaII were found to discriminate reproducibly between strains, and restriction patterns (ribotypes) produced by these were analysed to clarify the classification of Capnocytophaga strains. Dendrograms inferring similarities were derived from these data by the UPGMA method. This analysis produced three major clusters of strains, each of which was associated with a previously proposed species type strain: C. gingivalis, C. sputigena and C. ochracea. The results support the division of Capnocytophaga into three species and demonstrate that, despite the heterogeneity of this genus, the modified ribotyping method provides a simple, rapid and reproducible way to identify Capnocytophaga strains.

Bacterial Typing Techniques↗
PubMed1989

Human IGHC locus restriction fragment length polymorphisms in IgG4 deficiency: evidence for a structural IGHC defect.

In man, IgG4 is the least abundant of the four IgG subclasses, and its serum levels vary considerably from one subject to another. Its deficiency has been thought to lead to recurrent infections; nevertheless, it is also commonly found in healthy individuals (1/400 in the Italian population). In 39 subjects with IgG4 serum levels less than 1 microgram/ml, we used 4 different probes (described in the accompanying study, Bottaro et al., Eur. J. Immunol. 1989. 19: 2151) to examine 13 loci within the IGHC region and analyzed the RFLP for 7 of them. No aberrant restriction patterns were identified in any of the subjects, showing the absence of major IGHC structural alterations. The allele frequency of some loci, however, was significantly different from that of a control group of 95 random subjects. This variation was shown to depend on a selective increase in the number of homozygotes for the associated alleles, that reached significant levels for the IGHGP, G2, PG2, PG4 and SG4 loci, but not for SG1 and A2T. The highest value was reached for alleles in the PG4 region, just 5' of SG4. These data indicate that a minor structural IGHC defect is probably the cause of a significant fraction of IgG4 deficiencies. Moreover, the different association levels of the PG4 and SG4 regions suggest that this defect is likely to lie in an upstream regulatory region rather than in the structural G4 gene.

Gene Frequency↗
PubMedDate not supplied

Species identification of Streptococcus porcinus by restriction fragment length polymorphism analysis of 16S ribosomal DNA.

Streptococcus porcinus reference strains and routine isolates belonging to Lancefield's serogroup E, P, U and V and to various serotypes of serogroup E were examined for their 16S ribosomal DNA fingerprint pattern. Oligonucleotide primers complementary to 16S rRNA genes were used to amplify gene fragments by polymerase chain reaction from genomic DNA. The amplified 1450 bp fragment was subsequently digested with the restriction enzyme BpiI resulting in two fragments with a size of approximately 1250 bp and 200 bp. All 45 S porcinus investigated in the present study could be identified on the basis of this characteristic 16S rDNA fingerprint pattern and clearly differentiated from 16 control strains of various species and serogroups of genus Streptococcus. The present results demonstrate the potential application of 16S rDNA analysis for identification of S porcinus, a species which might express various group- and type-specific antigens.

Animals↗
PubMed1996

Pseudomonas (Burkholderia) cepacia in children with cystic fibrosis: epidemiological investigation by analysis or restriction fragment length polymorphism.

Since 1987, Pseudomonas cepacia has been isolated with an increasing frequency in the expectorants of children with cystic fibrosis followed at the Hôpital d'enfants Armand Trousseau (Paris, France). Colonization by P. cepacia may be responsible for serious secondary infections and rapid deterioration in respiratory function in these patients. Among the 130 children attending our centre, 14 (8 girls and 6 boys) aged 3 to 18, exhibited chronic colonization. 132 isolates, originating from sputum obtained between 1992 and 1994 were studied. Nine biochemical patterns and 6 antibiotic susceptibility patterns at least were defined, therefore exhibiting great polymorphism. Chromosome restriction patterns with Xba I after pulsed field gel electrophoresis enabled 4 pulsotypes to be identified: A, B, C and D. Thirteen patients harboured pulsotypes A, C and D, and 1 patient pulsotype B, the last being quite distinct from the first three. Pulsotypes A, C and D were almost similar, suggesting that closely related strains, probably the same strain, was harboured by 13 of the 14 patients. The origin could be contamination from a single source, or stem from patient-to-patient crossed transmission.

Adolescent↗
PubMed1995

Prevalence of Vibrio cholerae with heat-stable enterotoxin (NAG-ST) and cholera toxin genes; restriction fragment length polymorphisms of NAG-ST genes among V. cholerae O serogroups from a major shrimp production area in Thailand.

A total of 148 Vibrio cholerae isolates from a major shrimp production area in Southern Thailand were examined by colony hybridisation for genes encoding heat-stable enterotoxin (NAG-ST) and cholera toxin (CT). Only non-O1 V. cholerae strains were found to harbour NAG-ST (14 of 146) whereas no strains hybridised with the CT probe. NAG-ST-positive V. cholerae non-O1 strains were isolated from shrimp farms situated close to urban areas. Five different O serogroups were found among NAG-ST positive non-O1 strains. Southern blot and restriction endonuclease analysis of NAG-ST-positive strains revealed a high degree of genetic divergence. A total of seven classes of enterotoxin gene patterns were found with HindIII and EcoRI restriction endonucleases. Enterotoxin gene patterns correlated with O-antigen expression in 84% of isolates tested. In combination with other molecular techniques Southern blot analysis with an NAG-ST oligonucleotide probe could be useful for studying the molecular epidemiology of V. cholerae non-O1 strains.

Animals↗
PubMed1993

Heterogeneity of Porphyromonas gingivalis strains on fimbrillin gene locus by restriction fragment length polymorphism analysis.

The adherence of Porphyromonas gingivalis (P. gingivalis) to the periodontal tissue may be an initial step in the pathogenesis of periodontal disease, and fimbriae is believed to play an important role in such processes. However, the heterogeneity of the size, sequence and antigenic reactivity of the fimbriae have been reported. The aim of the present study was to investigate the heterogeneity of P. gingivalis strains on the fimbrillin gene locus by RFLPs analysis. Fourty-seven P. gingivalis strains including 5 reference strains were used in this study. The plasmid (pUC13Bg 12.1) with the insert of fimA381 was modified with bisulfite and used as the probe. The genomic DNAs from P. gingivalis were digested with the restriction endonuclease SacI and PstI, electrophoresed, transferred and hybridized with the DNA probe. All Sac I digests generated one major band and the band size was almost the same (ca 2.5-kb), except strain W50. The Pst I digests showed one or two major bands and could be divided into 9 groups based on the band patterns. Moreover, isolates from one patient showed different band patterns. By RFLPs analysis, genetic heterogeneity seems to exist within the fimbrillin gene locus of P. gingivalis strains. Such genetic heterogeneity may reflect the previously reported difference of P. gingivalis fimbriae and moreover a single patient could be infected with more than one genotype of P. gingivalis.

Adult↗
PubMedDate not supplied

Genetic relationships of Corynebacterium diphtheriae strains isolated from a diphtheria case and carriers by restriction fragment length polymorphism of rRNA genes.

In the present study we report the results of an analysis, based on ribotyping of Corynebacterium diphtheriae intermedius strains isolated from a 9 years old child with clinical diphtheria and his 5 contacts. Quantitative analysis of RFLPs of rRNA was used to determine relatedness of these 7 C.diphtheriae strains providing support data in the diphtheria epidemiology. We have also tested those strains for toxigenicity in vitro by using the Elek's gel diffusion method and in vivo by using cell culture method on cultured monkey kidney cell (VERO cells). The hybridization results revealed that the 5 C.diphtheriae strains isolated from contacts and one isolated from the clinical case (nose case strain) had identical RFLP patterns with all 4 restriction endonucleases used, ribotype B. The genetic distance from this ribotype and ribotype A (throat case strain), that we initially assumed to be responsible for the illness of the patient, was of 0.450 showing poor genetic correlation among these two ribotypes. We found no significant differences concerned to the toxin production by using the cell culture method. In conclusion, the use of RFLPs of rRNA gene was successful in detecting minor differences in closely related toxigenic C.diphtheriae intermedius strains and providing information about genetic relationships among them.

Adult↗
PubMed2000

Identification of acetic acid bacteria by restriction fragment length polymorphism analysis of a PCR-amplified fragment of the gene coding for 16S rRNA.

Acetic acid bacteria (AAB) irreversibly spoil wines and represent a serious problem. Limited studies on the ecology of AAB during winemaking have been done due to the lack of rapid and precise techniques for their identification. RFLP analysis of PCR-amplified fragment of 16S rDNA was performed on AAB reference strains. The amplified rDNAs were approximately 870-bp long for all AAB species while no amplicons were detected for lactic acid bacteria and yeasts. Out of the four restriction enzymes tested, TaqI was the most efficient one and divided the studied AAB into six groups. However, complete differentiation among collection strains of Acetobacter pasteurianus and Gluconoacetobacter hansenii was not possible.

Acetic Acid↗
PubMed1987

Restriction-fragment-length polymorphisms of 5'-flanking region of insulin I gene in BB and other rat strains. Absence of association with IDDM.

Because the 5'-flanking hypervariable region of the human insulin gene may be associated with insulin-dependent diabetes mellitus (IDDM), we examined the spontaneously diabetic BB rat and other rat strains for polymorphisms of the two rat insulin genes, the localization of such polymorphisms, and their possible association with IDDM. By use of restriction-fragment-length polymorphism analysis, we found that the transcribed portion of the insulin I gene, its 3'-flanking region, and the insulin II gene were not polymorphic. However, four alleles of the insulin I gene were identified, two of which (IA and IB) were found in BB rats. Alleles IA and IB varied in their 5'-flanking regions, yet neither was associated with IDDM in the BB rat.

Alleles↗
PubMed1990

Restriction fragment length polymorphism (RFLP) at the DNF15S2 locus in three ethnic groups of Singapore.

Three different ethnic groups from Singapore comprising 79 Chinese, 34 Malays and 23 Indians of Dravidian origin, were investigated for the HindIII RFLP at the DNF15S2 locus. The three populations had very similar allele frequencies and the frequency of rarer(S) allele was significantly (p less than 0.01) lower (0.21) in these ethnic groups compared to that in Caucasians (0.41). The phenotypic distributions were at Hardy-Weinberg equilibrium.

China↗