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PubMed1978

The use of fluorescein-labelled lectins in the detection and identification of fungi pathogenic for man: a preliminary study.

Fluorescein-labelled lectins of known specificities for different sugars were used in an attempt to identify fungi in paraffin sections of surgical and post-mortem material. Aspergillus fumigatus, Blastomyces dermatitidis, Candida albicans, Cryptococcus neoformans, Paracoccidioides brasiliensis and Rhizopus oryzae have been studied with five fluorescein-labelled lectins and with basis of differences in their reactions with these stains. The results accord well with what is known of the chemistry of the organisms and the method offers promise to practising histopathologists.

Aspergillus fumigatus↗
PubMed2005

DNA identification of the pathogen of candidal aspiration pneumonia induced in the course of oral cancer therapy.

Aspiration of oropharyngeal bacteria and fungi is occasionally suspected in patients with pneumonia. A patient with oral carcinoma underwent chemoradioimmunotherapy and, about 4 weeks from the start of the therapy, the patient suffered from severe oral mucositis induced by chemoradiotherapy, and candidal pneumonia was subsequently induced. The candidal pneumonia was insufficiently improved by potent antifungal drugs, taking a lethal course. Randomly amplified polymorphic DNA analysis and DNA sequence examination of strains isolated from the oral cavity 1 week before the onset of pneumonia and autopsied lung revealed the identity of both strains as Candida albicans, and the DNA analysis supported aspiration of oral Candida. These results indicate that the pathogen of the pneumonia, C. albicans, was aspirated from the oral cavity and that oral Candida is easily aspirated and becomes the pathogen of pneumonia.

Aerosols↗
PubMed2005

Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species.

The release of the complete genome sequences of Neisseria meningitidis MC58 and Z2491 along with access to the sequences of N. meningitidis FAM18 and Neisseria gonorrhoeae FA1090 allowed the construction of a pan-Neisseria microarray, with every gene in all four genomes represented. The microarray was used to analyse a selection of strains including all N. meningitidis serogroups and commensal Neisseria species. For each strain, genes were defined as present, divergent or absent using gack analysis software. Comparison of the strains identified genes that were conserved within N. meningitidis serogroup B strains but absent from all commensal strains tested, consisting of mainly virulence-associated genes and transmissible elements. The microarray was able to distinguish between pilin genes, pilC orthologues and serogroup-specific capsule biosynthetic genes, and to identify dam and drg genotypes. Previously described N. meningitidis genes involved in iron response, adherence to epithelial cells, and pathogenicity were compared to the microarray analysis. The microarray data correlated with other genetic typing methods and were able to predict genotypes for uncharacterized strains and thus offer the potential for a rapid typing method. The subset of pathogen-specific genes identified represents potential drug or vaccine targets that would not eliminate commensal neisseriae and the associated naturally acquired immunity.

Antigens, Bacterial↗
PubMed2002

Identification of enteric pathogens by heat shock protein 60 kDa (HSP60) gene sequences.

A highly specific and reproducible approach for the simultaneous detection of enteric pathogenic bacteria was developed using bacterial hsp60 gene and molecular biological tools. A single pair of universal primers was derived from the highly conserved sequence of hsp60 genes encompassing a 600-bp hypervariable region. PCR amplification followed by either dot blot hybridization or restriction enzyme digestion performed on 38 enteric bacteria indicated that this approach could differentiate not only different genera such as Campylobacter, Yersinia and Vibrio, but also species that are closely related genetically, such as between C. jejuni and C. coli, or between Salmonella and Shigella or Escherichia coli.

Amino Acid Sequence↗
PubMed2005

Genetic variability of the heme uptake system among different strains of the fish pathogen Vibrio anguillarum: identification of a new heme receptor.

The ability to utilize heme compounds as iron sources was investigated in Vibrio anguillarum strains belonging to serotypes O1 to O10. All strains, regardless of their serotype or isolation origin could utilize hemin and hemoglobin as sole iron sources. Similarly, all of the isolates could bind hemin and Congo red, and this binding was mediated by cell envelope proteins. PCR and Southern hybridization were used to assay the occurrence of heme transport genes huvABCD, which have been previously described in serotype O1. Of 23 strains studied, two serotype O3 isolates proved negative for all huvABCD genes, whereas nine strains included in serotypes O2, O3, O4, O6, O7, and O10 tested negative for the outer membrane heme receptor gene huvA. A gene coding for a novel outer membrane heme receptor was cloned and characterized in a V. anguillarum serotype O3 strain lacking huvA. The new heme receptor, named HuvS, showed significant similarity to other outer membrane heme receptors described in Vibrionaceae, but little homology (39%) to HuvA. This heme receptor was present in 9 out of 11 of the V. anguillarum strains that tested negative for HuvA. Furthermore, complementation experiments demonstrated that HuvS could substitute for the HuvA function in Escherichia coli and V. anguillarum mutants. The huvS and huvA sequences alignment, as well as the analysis of their respective upstream and downstream DNA sequences, suggest that horizontal transfer and recombination might be responsible for generating this genetic diversity.

Amino Acid Sequence↗
PubMed1968

Lysozyme production as an aid for identification of potentially pathogenic strains of staphylococci.

Lysozyme production is a frequent property of potentially pathogenic staphylococci. In the present study, 1,186 strains of human origin, 85 strains of animal origin, and 156 strains of Staphylococcus albus (epidermidis) were tested. Of 1,114 coagulase-positive strains of human and animal origin, 1,098 were lysozyme-positive (98.5%). On the other hand, of 157 coagulase-negative strains which, based on further investigations, belong to the potentially pathogenic staphylococci, all were lysozyme-positive. All of the 156 strains (100%) belonging to the species S. albus (epidermidis) were lysozyme-negative. We conclude that lysozyme production is a better index of potentially pathogenic staphylococci than the measurement of free coagulase, especially in cases of strains of animal origin. It is possible that lysozyme production allows a differentiation between pathogenic and nonpathogenic coagulase-negative staphylococci.

Animal Population Groups↗
PubMed1990

Identification of a pathogenic isolate-specific 30,000-Mr antigen of Entamoeba histolytica by using a monoclonal antibody.

A monoclonal antibody (MAb) produced against trophozoites of Entamoeba histolytica strain HM-1:IMSS, reacted with all of 42 isolates and 4 clones showing pathogenic zymodeme (Z) patterns, i.e., Z-II, Z-II alpha-, Z-II (glucose phosphate isomerase: gamma +), Z-VII, Z-VII (glucose phosphate isomerase: alpha lack, gamma +), Z-XI, Z-XIV, and Z-XIX, regardless of culture conditions, geographical origins, or host symptoms in an indirect fluorescence antibody test. In contrast, the MAb failed to react with 14 isolates possessing nonpathogenic zymodemes Z-I and Z-VIII and did not react with other enteric protozoan parasites, such as E. histolytica-like Laredo, Entamoeba hartmanni, Entamoeba coli, Endolimax nana, Dientamoeba fragilis, Trichomonas hominis, and Giardia lamblia. Western immunoblotting analysis showed that the molecular weight of the antigenic component recognized by the MAb was exclusively 30,000 in pathogenic isolates of different zymodemes. These results suggest that the 30,000-molecular-weight antigen is a marker of pathogenic isolates and that the indirect fluorescent-antibody test with the MAb is useful for the accurate discrimination of pathogenic amebae.

Animals↗
PubMed2006

High-throughput identification of clinical pathogenic fungi by hybridization to an oligonucleotide microarray.

Here we report the development of an oligonucleotide microarray method that can identify fungal pathogens in a single reaction. Specific oligonucleotide probes targeted to internal transcribed spacer 2 were designed and synthesized. Fungal DNA was amplified by universal primers, and the PCR product was hybridized with the oligonucleotide microarray. A series of specific hybridization profiles corresponding to species were obtained. The 122 strains of fungal pathogens, including standard and clinically isolated strains, used to test the specificity, stability, and sensitivity of the microarray system belonged to 20 species representing 8 genera. We found that the microarray system can successfully discriminate among the fungal pathogens to the species level, with high specificity and stability. The sensitivity was 15 pg/ml of DNA. This oligonucleotide microarray system represents a rapid, simple, and reliable alternative to conventional methods of identifying common clinical fungal isolates.

DNA, Fungal↗
PubMed1975

Motility-indole-lysine medium for presumptive identification of enteric pathogens of Enterobacteriaceae.

Detection of lysine decarboxylase activity is a useful supplement to reactions on triple sugar-iron (TSI) and urea agars in the initial examination of suspected pathogenic isolates from fecal cultures. Owing to the added value of motility and indole production in the differentiation of enteric pathogens, we prepared and evaluated a motility-indole-lysine (MIL) medium. The following 890 organisms were tested: 264 Shigella, 2 Edwardsiella, 182 Salmonella enteritidis, 235 S. typhi, 3 Arizona, 32 Yersinia enterocolitica, and 172 other members of the family Enterobacteriaceae. With few exceptions the MIL medium gave the same results as the standard motility, indole, and lysine decarboxylase (Moeller) test media. All discrepancies were with the indole reaction, which was weak in 2 of 67 strains of Escherichia coli and falsely negative in 6 of 32 strains of Y. enterocolitica. When both TSI agar and lysine-iron agar (LIA) slants are used in the evaluation isolates from fecal cultures, detection of H2S is duplicated. Both LIA and MIL medium detect lysine decarboxylase and deaminase activity equally well. Because of its ability to detect motility and indole production, the MIL medium is more useful than LIA when used with TSI agar. The combination of TSI agar, MIL medium, and urea agar enables reliable initial recognition of enteric pathogens of the Enterobacteriaceae.

Carboxy-Lyases↗
PubMed2000

Development of a PCR-based line probe assay for identification of fungal pathogens.

We report on a reverse-hybridization line probe assay (LiPA) which when combined with PCR amplification detects and identifies clinically significant fungal pathogens including Candida, Aspergillus, and Cryptococcus species. DNA probes have been designed from the internal transcribed-spacer (ITS) regions of Candida albicans, Candida parapsilosis, Candida glabrata, Candida tropicalis, Candida krusei, Candida dubliniensis, Cryptococcus neoformans, Aspergillus fumigatus, Aspergillus versicolor, Aspergillus nidulans and Aspergillus flavus. The probes were incorporated into a LiPA for detection of biotinylated ITS PCR products, and the specificity of the probes was evaluated. We established LiPA detection limits for ITS 1 and for full ITS amplicons for genomic DNA from C. albicans, A. fumigatus, and C. neoformans. Further evaluation of the LiPA was carried out on clinical fungal isolates. One hundred twenty-seven isolates consisting of dimorphic yeasts and dermatophytic and filamentous fungi were tested by the LiPA, which correctly identified 77 dimorphic yeasts and 23 of the filamentous isolates; the remaining 27 isolates represented species of fungi for which probes were not included in the LiPA. The fungal-PCR-LiPA technology was applied to blood samples inoculated with Candida cells which were pretreated by minibead beating to mechanically disrupt the cells, with the DNA extracted by either a previously described guanidium thiocyanate-silica method or the commercially available QIAmp tissue kit. PCR amplification of the extracted DNA and subsequent DNA probe hybridization in the LiPA assay yielded detection limits of 2 to 10 cells/ml. An internal standard control was included in the PCR amplification to monitor for PCR inhibition. This fungal PCR-LiPA assay is robust and sensitive and can easily be integrated into a clinical-testing laboratory with the potential for same-day diagnosis of fungal infection.

DNA Primers↗
PubMed2001

Development of a rapid and sensitive test for identification of major pathogens in bovine mastitis by PCR.

Bovine mastitis is the most important source of loss for the dairy industry. A rapid and specific test for the detection of the main pathogens of bovine mastitis is not actually available. Molecular probes reacting in PCR with bacterial DNA from bovine milk, providing direct and rapid detection of Escherichia coli, Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus parauberis, and Streptococcus uberis, have been developed. Two sets of specific primers were designed for each of these microorganisms and appeared to discriminate close phylogenic bacterial species (e.g., S. agalactiae and S. dysgalactiae). In addition, two sets of universal primers were designed to react as positive controls with all major pathogens of bovine mastitis. The sensitivities of the test using S. aureus DNA extracted from milk with and without a pre-PCR enzymatic lysis step of bacterial cells were compared. The detection limit of the assay was 3.125 x 10(2) CFU/ml of milk when S. aureus DNA was extracted with the pre-PCR enzymatic step compared to 5 x 10(3) CFU/ml of milk in the absence of the pre-PCR enzymatic step. This latter threshold of sensitivity is still compatible with its use as an efficient tool of diagnosis in bovine mastitis, allowing the elimination of expensive reagents. The two PCR tests avoid cumbersome and lengthy cultivation steps, can be performed within hours, and are sensitive, specific, and reliable for the direct detection in milk of the six most prevalent bacteria causing bovine mastitis.

Animals↗
PubMed1985

Rapid identification of periodontal pathogens in subgingival plaque: comparison of indirect immunofluorescence microscopy with bacterial culture for detection of Actinobacillus actinomycetemcomitans.

The sensitivity of indirect immunofluorescence microscopy using specific polyclonal or monoclonal serodiagnostic reagents for Actinobacillus actinomycetemcomitans in subgingival dental plaque ranged from 82-100% as compared with culture on selective or non-selective media. This bacterium was found in 100% of the periodontally diseased sites examined in localized juvenile periodontitis patients and was statistically related to clinical indices of periodontal disease including the Gingival Index, Plaque Index, and Pocket Depth. Indirect immunofluorescence microscopy is a useful technique for the rapid and reliable determination of A. actinomycetemcomitans in human subgingival dental plaque which may be applied to the clinical diagnosis, treatment, and monitoring of periodontitis associated with A. actinomycetemcomitans.

Actinobacillus↗
PubMed2000

Identification of periodontal pathogens in atheromatous plaques.

BACKGROUND: Recent studies suggest that chronic infections including those associated with periodontitis increase the risk for coronary vascular disease (CVD) and stroke. We hypothesize that oral microorganisms including periodontal bacterial pathogens enter the blood stream during transient bacteremias where they may play a role in the development and progression of atherosclerosis leading to CVD. METHODS: To test this hypothesis, 50 human specimens obtained during carotid endarterectomy were examined for the presence of Chlamydia pneumoniae, human cytomegalovirus, and bacterial 16S ribosomal RNA using specific oligonucleotide primers in polymerase chain reaction (PCR) assays. Approximately 100 ng of chromosomal DNA was extracted from each specimen and then amplified using standard conditions (30 cycles of 30 seconds at 95 degrees C, 30 seconds at 55 degrees C, and 30 seconds at 72 degrees C). Bacterial 16S rDNA was amplified using 2 synthetic oligonucleotide primers specific for eubacteria. The PCR product generated with the eubacterial primers was transferred to a charged nylon membrane and probed with digoxigenin-labeled synthetic oligonucleotides specific for Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Porphyromonas gingivalis, and Prevotella intermedia. RESULTS: Eighty percent of the 50 endarterectomy specimens were positive in 1 or more of the PCR assays. Thirty-eight percent were positive for HCMV and 18% percent were positive for C. pneumoniae. PCR assays for bacterial 16S rDNA also indicated the presence of bacteria in 72% of the surgical specimens. Subsequent hybridization of the bacterial 16S rDNA positive specimens with species-specific oligonucleotide probes revealed that 44% of the 50 atheromas were positive for at least one of the target periodontal pathogens. Thirty percent of the surgical specimens were positive for B. forsythus, 26% were positive for P. gingivalis, 18% were positive for A. actinomycetemcomitans, and 14% were positive for P. intermedia. In the surgical specimens positive for periodontal pathogens, more than 1 species was most often detected. Thirteen (59%) of the 22 periodontal pathogen-positive surgical specimens were positive for 2 or more of the target species. CONCLUSIONS: Periodontal pathogens are present in atherosclerotic plaques where, like other infectious microorganisms such as C. pneumoniae, they may play a role in the development and progression of atherosclerosis leading to coronary vascular disease and other clinical sequelae.

Aged↗
PubMed2005

Identification of periodontal pathogens in atherosclerotic vessels.

BACKGROUND: Epidemiological studies have shown that periodontitis may be associated with presence of atherosclerosis. DNA from periodontal pathogens has been detected in atherosclerotic lesions, but viable oral bacteria have not yet been isolated from atherosclerotic plaques. The purpose of the present study was to determine if viable oral bacteria could be isolated from atherosclerotic lesions and if DNA from periodontal pathogens could be detected by use of polymerase chain reaction (PCR) techniques. METHODS: Seventy-nine specimens of atherosclerotic plaque removed from carotid or femoral arteries during surgery were immediately transferred to reduced transport fluid and brought to the laboratory. The calcified tissue was meticulously cut into fine pieces and used for cultivation of Porphyromonas gingivalis, Prevotella intermedia, P. nigrescens, Campylobacter rectus, Actinobacillus actinomycetemcomitans, Tannerella forsythensis, and oral streptococci. The material from 24 of the specimens was homogenized, DNA was extracted, and PCR amplification of 16S rDNA with universal and specific primers was carried out. Finally, the PCR products were sequenced. RESULTS: None of the samples yielded growth of the oral bacteria under investigation. In all the 24 specimens bacterial DNA was detected and likewise DNA of P. intermedia was found in the samples. P. nigrescens and P. gingivalis were found sporadically. CONCLUSIONS: Viable oral bacteria could not be isolated from the atheromas, but the data confirm that DNA of periodontal pathogens can be detected in atherosclerotic plaques. However, the finding that DNA from P. intermedia constantly occured in the examined samples was new. Further studies may focus on the simultaneous occurrence of identical clones of this species in subgingival plaque and atherosclerotic plaques.

Aged↗
PubMed2005

Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays.

AIM: To detect the common intestinal pathogenic bacteria quickly and accurately. METHODS: A rapid (<3 h) experimental procedure was set up based upon the gene chip technology. Target genes were amplified and hybridized by oligonucleotide microarrays. RESULTS: One hundred and seventy strains of bacteria in pure culture belonging to 11 genera were successfully discriminated under comparatively same conditions, and a series of specific hybridization maps corresponding to each kind of bacteria were obtained. When this method was applied to 26 divided cultures, 25 (96.2%) were identified. CONCLUSION: Salmonella sp., Escherichia coli, Shigella sp., Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, Proteus sp., Bacillus cereus, Vibrio cholerae, Enterococcus faecalis, Yersinia enterocolitica, and Campylobacter jejuni can be detected and identified by our microarrays. The accuracy, range, and discrimination power of this assay can be continually improved by adding further oligonucleotides to the arrays without any significant increase of complexity or cost.

Bacteria↗