Detection of pathogenic fungi in human blood by the polymerase chain reaction

The ability of the polymerase chain reaction (PCR) to detect pathogenic fungi in human blood was investigated. A DNA fragment of about 300 bp from the 18S rDNA, highly conserved in all fungi, was amplified with target DNA from 18 different species of fungi commonly isolated from clinical samples. The presence of PCR products was confirmed by hybridization with a fluorescein-labelled internal probe (21-mer). The PCR assay described is sensitive enough to detect 125 fg of purified Candida albicans DNA and 10 to 100 yeast cells per millilitre of blood.     

Detection of the thermostable lipase gene (lipAH) in clinical isolates of Aeromonas hydrophila belonging to the major O serogroups O11, O16 and O34

On the basis of DNA hybridization data and phenotypes, most pathogenic strains of Aeromonas hydrophila are grouped into hybridization group 1 (HG1). These pathogenic strains secret the theromostable lipase, and it's gene (lipAH) has been cloned and sequenced. The present study was performed to identify the pathogenic strains of A. hydrophila by the polymerase chain reaction (PCR) technique to detect the lipAH. Synthetic oligonucleotide primers (lipAH-ns-1 and -na-1) were used in the PCR. The PCR identified 80% of lipAH-positive strains, consisting of seven of the 11 O11 strains (64%), 13 of the 15 O16 strains (87%) and 25 of the 30 O34 strains (83%) in clinical isolates of A. hydrophila used in this study.     

DNA probe hybridisation in microwells using a new bioluminescent system for the detection of PCR-amplified HIV-1 proviral DNA

A new bioluminescent detection system combined with a sandwich DNA hybridisation reaction in microwells has been developed for the detection of human immunodeficiency virus type 1 (HIV-1) provirus DNA amplified by the polymerase chain reaction (PCR). First, a fragment of the HIV-1 gag gene was amplified. The amplified DNA fragments were denatured and hybridised to a capture probe immobilised in microwells and to a biotinylated detection probe. A streptavidin-pyruvate kinase conjugate could then react on the biotinylated probe and the kinase activity detected by means of the luciferin-luciferase system, with production of a bioluminescent signal. This sandwich assay followed by a bioluminescent reaction detected as little as 7 amol of target DNA. The bioluminescent assay detected 5 HIV copies generated after one round of PCR, even if no band was seen on an agarose gel. The assay was applied to the detection of HIV-proviral DNA in peripheral blood mononuclear cells after one round of PCR and allowed to clearly identify a positive sample as compared to nested PCR.     

Haemolytic activity of Aeromonas species isolated in Libya

Twenty seven Aeromonas strains (5A. hydrophila, 8A. sobria and 14A. caviae) isolated from children with diarrhoea and 34 Aeromonas strains (9A. hydrophila, 7A. sobria an 18A. caviae) isolated from children without diarrhoea were tested from haemolysin production. The results obtained showed that haemolysin production using human, horse or sheep erythrocytes was significantly associated with A.hydrophila and A sobria but not with A.caviae, regardless of whether these strains were isolated from children with or without diarrhoea. Human or horse rather than sheep erythrocytes are recommended for use in the haemolysin assay.     

Variability of mitochondrial subgenomic molecules in the meristematic cells of higher plants

MtDNAs from BY-2 cells and rice root were analyzed by random amplified polymorphic DNA (RAPD) assay and Southern hybridization analysis. A number of differences were observed in the RAPD patterns amplified from mtDNAs sampled at different phases of the BY-2 cell culture. RAPD fragments also varied with the template DNAs derived from various areas of rice root tip. When a RAPD fragment was hybridized to restriction fragments of whole DNAs, isolated from the distal area of the apical meristem and differentiated elongation zone of a root, two distinct stoichiometric differences were observed in the hybridization signals. This suggests that the organization of mt-genome in prototypic cells in the root apical meristem differs from that found in the differentiated cells.     

Locomotion of neutrophil fragments occurs by graded radial extension

Neospora caninum is a protozoan parasite which causes neurological problems in dogs and abortion in cattle. As N. caninum is difficult to distinguish morphologically from Toxoplasma gondii, we developed a molecular tool capable of discriminating between the two parasites. Genomic DNA was isolated from in vitro cultured N. caninum tachyzoites and cloned into a plasmid vector. Resulting colonies were subsequently screened by differential hybridization using N. caninum and T. gondii DNA. Two clones were characterized in detail: one clone, termed pNc5, was found to be specific for N. caninum whereas the second clone, pNc1, hybridized with DNA from both parasites. The sequence of pNc5 was determined and different oligonucleotide primers were designed for use in the polymerase chain reaction (PCR). A 944 bp fragment was specifically amplified from N. caninum DNA, but not from DNA extracted from T. gondii or different Sarcocystis species. Positive signals in PCR were obtained with as little as 100 pg parasite template DNA. In addition, dual PCR with primer pairs specific for N. caninum and T. gondii allowed the detection of either parasite in mixed samples.     

Human cutaneous leishmaniasis caused by Leishmania (Viannia) braziliensis in Santiago del Estero, Argentina: identification of parasites by monoclonal antibodies and isoenzymes

Bacteroides forsythus is a fastidious anaerobic Gram-negative organism associated with active periodontal disease. The ability of random amplified polymorphic DNA (RAPD) fingerprinting to generate species-specific markers was exploited towards the construction of a polymerase chain reaction (PCR)-DNA probe assay specific for B. forsythus. The strategy included the four following steps: (1) construction of a first generation DNA probe based on a 507-bp RAPD species-specific marker; (2) cloning and sequencing the 507-bp RAPD marker; (3) design of the primer pair Bf 392-1/Bf 392-2 flanking a 392-bp specific internal sequence; and (4) synthesis of quantities of a 392-bp second generation DNA probe by PCR amplification. The PCR-DNA probe assay includes a PCR amplification of a 392-bp specific sequence in the genomic DNA of B. forsythus strains followed by hybridization with the 392-bp digoxigenin-labelled second generation probe. We observed strong, specific hybridization with the amplified DNAs from 11 stains of B. forsythus and no cross-hybridization with the PCR products from 22 foreign species. The PCR-DNA probe assay must be seen as a highly specific and sensitive method for the detection of B. forsythus in mixed infections.     

The development and evaluation of a probe hybridization method for subtyping HIV type 1 infection in Uganda

We developed a method for large-scale screening of HIV-1 genotypic variation based on DNA probe hybridization. Nested PCR amplifications were performed to generate fragments in the env C2-V3 region and also in the gp41 region, which encompasses the immunodominant domain. The proviral DNA sequences were derived from 68 samples and phylogenetically analyzed. For comparison, the C2-V3 fragment was used in DNA probe hybridization to rapidly determine the infecting HIV subtype. The hybridizing probes were designed on the basis of the two most prevalent subtypes in Uganda, A and D. The results were compared to evaluate the feasibility of using this hybridization method for large-scale genotypic screening. Sequence analysis of the 68 amplified PCR fragments showed that 39 were subtype A and 29 were subtype D. The results of DNA hybridization to the amplified products with A and D subtype-specific probes were more than 90% concordant with the subtypes determined by sequence analysis. Our findings suggest that probe hybridization with subtype-specific probes is effective for large-scale screening of HIV-infected populations. Application of this method will significantly reduce the time needed for large, population-based investigations.     

Cloning and nucleotide sequence of a specific DNA fragment from Paracoccidioides brasiliensis

We cloned and sequenced a species-specific 110-bp DNA fragment from Paracoccidioides brasiliensis. The DNA fragment was generated by PCR with primers complementary to the rat beta-actin gene under a low annealing temperature. Comparison of the nucleotide sequence, after excluding the primers, with those in the GenBank database identified approximately 60% homology with an exon of a major surface glycoprotein gene from Pneumocystis carinii and a fragment of unknown function in Saccharomyces cerevisiae chromosome VIII. By Southern hybridization analysis, the 32P-labelled fragment detected 1.0- and 1.9-kb restriction fragments within whole-cell genomic DNA of P. brasiliensis digested with HindIII and PstI, respectively, but failed to hybridize to genomic DNAs from Candida albicans, Blastomyces dermatitidis, Cryptococcus neoformans, Aspergillus fumigatus, Saccharomyces cerevisiae, Pneumocystis carinii, rat tissue, or humans under low-stringency hybridization conditions. Additionally, the specific DNA fragment from three different P. brasiliensis isolates (Pb18, RP18, RP17) was amplified by PCR with primers mostly complementary to nonactin sequences of the 110-bp DNA fragment. In contrast, there were no amplified products from other fungus genomic DNAs previously tested, including Histoplasma capsulatum. To date, this is the first species-specific DNA fragment cloned from P. brasiliensis which might be useful as a diagnostic marker for the identification and classification of different P. brasiliensis isolates.     

Isolation of a specific chromosomic DNA sequence of Bacillus anthracis and its possible use in diagnosis

A 277-bp long DNA fragment, Ba813, was isolated from an avirulent Bacillus anthracis strain 7700 genomic library. Two oligonucleotides derived from the Ba813 sequence were used as primers in polymerase chain reaction tests on genomic DNA from 28 Bacillus anthracis and from 33 heterologous bacteria strains. A specific, 152-bp long DNA fragment was amplified only when Bacillus anthracis DNA was used as the target. The amplified product was analysed by non-radioactive sandwich hybridisation in microtiter plates using two oligonucleotides. The capture oligonucleotide C1 was covalently linked onto aminated wells of microtiter plates. The detection oligonucleotide D3 was labelled with biotine. The hybrid molecules were detected by avidine conjugated with alkaline phosphatase and chromogenic substrate. Amplification of Ba813 sequence may provide the basis for rapid and reliable assay for the detection and identification of Bacillus anthracis.     

Doctor''s future

In this paper it is described the detection enteroxigenic Escherichia coli LT (+). This method is based on the amplification of a DNA fragment of 400 pairs of bases by polymerase chain reaction (PRC). The oligonucleotides were designed by the authors and the characteristic patterns were observed when the samples were submitted to an electrophoresis in an Agarose gel at 2%. The PCR had positive results with the strains of Escherichia coli 0:149 K; 88 (LT+) collection and with 20 strains isolated from patients with acute diarrhea. Negative results were found in Escherichia coli 0:101 K:99 NM (ST+), Vibrio cholerae 01 and Aeromonas hydrophila.     

Chloroquine treatment for uncomplicated childhood malaria in an area with drug resistance: early treatment failure aggravates anaemia

Using the polymerase chain reaction (PCR) and two primers for conserved regions of the small subunit ribosomal RNA (SSU-rRNA) of Microsporidia, a DNA segment about 1,195 base pairs long was amplified from a DNA template prepared from purified spores of the microsporidian species Pleistophora anguillarum. These spores had been isolated from adult eels (Anguilla japonica) with "Beko Disease." A comparison of sequence data from other microsporidian species showed P. anguillarum SSU-rRNA to be most similar to Vavraia oncoperae. When juvenile eels were artificially infected with P. anguillarum, enzyme-linked immunosorbent assay could detect a positive infection only 12 days post-infection. However, when suitable PCR primers were used, a DNA fragment of about 0.8 kb was detected from these juvenile eels after only 3 days post infection. No PCR product was obtained with templates prepared from clinically healthy control animals.     

Detection and characterization of the fimA gene of Escherichia coli O157:H7

An expected 850-bp DNA fragment containing fimA, the structural gene for type 1 fimbriae, and flanking sequences was amplified from 39 (of 46) pathogenic and commensal strains of Escherichia coli using the polymerase chain reaction (PCR). Restriction fragment length polymorphism (RFLP) analysis of the amplified products showed 13 HinP1 and four Sau961 restriction profiles among these 39 E. coli strains, revealing the polymorphic nature of this allele. A unique RFLP pattern was shared by E. coli O157:H7, O157:H- and a few O55 serotype strains. DNA sequence analysis of the fimA region demonstrated that E. coli O157:H7 strain 933 and O157:H- strain E32511 contained identical DNA sequences that were distinct from other E. coli strains, especially a 16-bp sequence 5' to fimA that was conspicuously absent only in E. coli O157 strains. Exploiting these differences, a PCR assay was developed that amplifies a 936-bp fragment from all E. coli O157:H7 strains examined to date. This PCR assay offers a simple, rapid, and reliable means to detect E. coli strains of the O157:H7 serotype.     

Cloning and characterization of two immunophilin-like genes, ilpA and fkpA, on a single 3.9-kilobase fragment of Aeromonas hydrophila genomic DNA

Antiserum to Aeromonas hydrophila A6 cell envelopes was shown in a previous study (C. Y. F. Wong, G. Mayrhofer, M. W. Heuzenroeder, H. M. Atkinson, D. M. Quinn, and R. L. P. Flower, FEMS Immunol. Med. Microbiol. 15:233-241, 1996) to protect mice against lethal infection by this organism. In this study, colony blot analysis of an A. hydrophila genomic library using antiserum to A. hydrophila A6 cell envelopes revealed a cosmid clone expressing a 30-kDa protein which has not been described previously in aeromonads. The nucleotide sequence of a 3.9-kb fragment derived from this cosmid which expressed the 30-kDa protein revealed two potential open reading frames (ORFs) with homology to known immunophilin proteins. ORF1 encoded a 212-amino-acid protein (molecular mass, 22.4 kDa) with 56% identity to the immunophilin SlyD protein of Escherichia coli. ORF1 was subsequently designated ilpA (immunophilin-like protein). ORF3 encoded a potential gene product of 268 amino acids with a typical signal sequence and a predicted molecular size of 28.7 kDa. The inferred amino acid sequence showed 46% identity with the sequence of the FkpA protein of E. coli and 40% identity with the sequence of the macrophage infectivity potentiator (Mip) protein of Legionella pneumophila. ORF3 was designated fkpA (FK506 binding protein) by analogy with the E. coli FkpA protein. Expression of the FkpA protein was confirmed by Western blot (immunoblot) analysis, which detected a 30-kDa protein, with antiserum to the Mip protein of Legionella longbeachae and a specific antiserum to anA. hydrophila 30-kDa membrane protein. PCR and Southern analysis showed that a DNA sequence encoding FkpA was found in all 178 aeromonads of diverse origins tested. A nonpolar insertion mutation in the fkpA gene did not attenuate virulence in a suckling mouse model nor did it affect the expression of hemolysins or DNase. This suggests that either the fkpA gene is not essential in the virulence of A. hydrophila under these conditions or there are other genes in A. hydrophila coding for proteins with similar functions.     

First melanoma metastases after 10 years and more of remission

The aim of this study was to combine immunomagnetic capture and a polymerase chain reaction (PCR) followed by hybridization with a DNA probe for the detection of Bacteroides forsythus. Magnetic beads were coated with the immunoglobulin G fraction of an antiserum specific for B. forsynthus. Aliquots were incubated with various concentrations of a suspension of B. forsythus or with a suspension containing 16 bacterial species, at a concentration of 10(10) cells/ml, spiked with dilutions of B. forsythus. Beads with bound bacteria were boiled, and the target DNA in the supernatant was amplified to generate a 392-bp PCR fragment specific for B. forsythus. The amplified product was detected by dot-blot hybridization with a digoxigenin-labeled 392-bp probe. The detection limit was determined to be 10 cells/ml using immunocapture on a suspension of B. forsythus and 100 on spiked bacterial suspensions. Subgingival plaque samples were obtained from 39 Bolivian individuals with poor oral hygiene. Each sample was analyzed by the above procedure and by immunofluorescence. The overall prevalence of individuals harboring B. forsythus was 62% by immunofluorescence and 82% by PCR-DNA probe assay. The immunocapture, PCR. DNA-probe procedure should be useful for the detection of B. forsythus, particularly in false-negative samples obtained by less sensitive techniques.     

Group specific PCR-detection of potential trichothecene-producing Fusarium-species in pure cultures and cereal samples

A PCR based assay (Tox5 PCR) which analyses Fusarium species potentially producing trichothecenes was developed using a pair of primers derived from the DNA-sequence of the trichodiene synthase gene (tri5). The primer pair was tested using DNA isolated from a variety of strains representing 64 species and varieties of Fusarium as well as from other fungi, bacteria and cereals. A 658 bp PCR fragment was specifically amplified with DNA isolated from strains of species belonging to the Fusarium sections Discolor, Sporotrichiella, Arthrosporiella, Gibbosum, and "Dlaminia". PCR products obtained were sequenced. Alignment to tri5 sequences given in the literature revealed a high degree of homology. Results of the PCR developed correlated well with literature data on the trichothecene producing capabilities of the respective species. Potential trichothecene producing fusaria were detected in contaminated cereals and malts using the Tox5 PCR assay. Intensity of the signals produced were well correlated with the concentration of deoxynivalenol (DON) in samples of wheat.     

Detection and identification of Actinobacillus pleuropneumoniae serotype 5 by multiplex PCR

Serotyping of Actinobacillus pleuropneumoniae is based on detection of the serotype-specific capsular antigen. However, not all isolates can be serotyped, and some may cross-react with multiple serotyping reagents. To improve sensitivity and specificity of serotyping and for early detection, a multiplex PCR assay was developed for detection of A. pleuropneumoniae and identification of serotype 5 isolates. DNA sequences specific to the conserved export and serotype-specific biosynthesis regions of the capsular polysaccharide of A. pleuropneumoniae serotype 5 were used as primers to amplify 0.7- and 1.1-kb DNA fragments, respectively. The 0.7-kb fragment was amplified from all strains of A. pleuropneumoniae tested with the exception of serotype 4. The 0.7-kb fragment was not amplified from any heterologous species that are also common pathogens or commensals of swine. In contrast, the 1.1-kb fragment was amplified from all serotype 5 strains only. The assay was capable of amplifying DNA from less than 10(2) CFU. The A. pleuropneumoniae serotype 5 capsular DNA products were readily amplified from lung tissues obtained from infected swine, although the 1.1-kb product was not amplified from some tissues stored frozen for 6 years. The multiplex PCR assay enabled us to detect A. pleuropneumoniae rapidly and to distinguish serotype 5 strains from other serotypes. The use of primers specific to the biosynthesis regions of other A. pleuropneumoniae serotypes would expand the diagnostic and epidemiologic capabilities of this assay.     

Sex determination of forensic samples: co-amplification and simultaneous detection of a Y-specific and an X-specific DNA sequence

The detection of restriction fragment length polymorphisms (RFLP) (1) in DNA extracted from forensic samples remains impossible in a significant number of cases due to deterioration and contamination of the biological material and the extremely low quantities of DNA isolated. The polymerase chain reaction (PCR) is a recent and particularly convenient method for analysing and typing very small amounts (10-20 ng) of degraded human DNA. DNA analysis at the level of a few cells present in forensic samples such as bloodstains, semen stains, vaginal swabs and head hair bulbs now appears possible using DNA amplification. A PCR protocol was adapted to simultaneously amplify a Y-specific DNA repeat sequence from the DYZ1 locus and an X-specific DNA repeat sequence from the DXS424 locus. The co-amplified Y-specific DNA fragment (102 bp) and X-specific DNA fragments (181-199 bp) were visualized on an ethidium bromide-stained 4% agarose gel. The male or female type of the amplified DNA extracted from blood samples, bloodstains, semen stains, vaginal swabs, brain tissue and 1, 2, 5, or 10 head hair bulbs was determined.     

Comprehensive mutational scanning of the p53 coding region by two-dimensional gene scanning

A comprehensive mutational scanning test for the p53 coding region based on multiplex PCR and two-dimensional DNA electrophoresis was designed and evaluated. In a 2-step multiplex PCR, the p53 coding region (exons 2-11) was amplified as a single 8646-bp fragment by long-distance PCR in step one. This fragment served as a template for the subsequent co-amplification of the individual exons in two multiplex groups in step two. The multiplex products were then separated, first on the basis of size in non-denaturant polyacrylamide gels and then on the basis of sequence by denaturing gradient gel electrophoresis (DGGE). Primers for optimal PCR, melting behavior and 2-D gel distribution were designed using a recently developed computer program. The resulting two-dimensional gene scanning (TDGS) test was evaluated by screening, in a blinded fashion, 29 coded DNA samples from Li-Fraumeni syndrome patients with previously identified germline mutations. All mutations were correctly detected. This assay provides an accurate, cost-effective and non-radioactive method for simultaneous mutational scanning of all p53 coding exons.