Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “pathogen identification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 865 records · Page 48Linked to original sources
PubMed2001

Activity of telithromycin, a new ketolide antibacterial, against atypical and intracellular respiratory tract pathogens.

Atypical respiratory pathogens such as Mycoplasma pneumoniae and intracellular pathogens such as Legionella spp. and Chlamydia spp. form a significant proportion of the aetiological agents underlying community-acquired pneumonia (CAP). The clinical signs or radiological features of atypical pneumonia are generally insufficient to predict accurately the pathogen involved; in addition, high costs and a considerable length of time are involved in the identification of atypical pathogens. Treatment is, therefore, most often empirical, and it is important that the activity of antibacterial agents available to treat CAP is sufficiently broad to eradicate infection with both common and atypical bacterial pathogens. Telithromycin (HMR 3647) is the first of a new family of antibacterials, the ketolides, and has been designed specifically for the treatment of community-acquired respiratory tract infections (RTIs). The excellent activity of telithromycin against the respiratory tract bacterial pathogens most commonly associated with community-acquired RTIs, including resistant strains, is well established. This review examines the considerable body of evidence showing that telithromycin also has a high level of activity against atypical and intracellular respiratory tract bacterial pathogens.

Anti-Bacterial Agents↗
PubMed2001

Identification of novel chemoattractant peptides for human leukocytes.

Superoxide is the most important armory on the primary defense line of monocytes against invading pathogens, and the identification of new stimuli and the characterization of the regulatory mechanism of superoxide generation are of paramount importance. In this study, we identified 3 novel peptides by screening a synthetic hexapeptide combinatorial library and modification of 1 of the peptides. The isolated peptides that can induce superoxide generation in human monocytes are His-Phe-Tyr-Leu-Pro-Met-CONH(2) (HFYLPM), Met-Phe-Tyr-Leu-Pro-Met-CONH(2) (MFYLPM), and His-Phe-Tyr-Leu-Pro-D-Met-CONH(2) (HFYLPm). All 3 peptides also caused intracellular calcium ([Ca(++)](i)) rise. We tested the specificities of the peptides on cells of different origin by looking at [Ca(++)](i) rise. All 3 peptides acted specifically on leukocytes and not on nonimmune cells. Among leukocytes, HL60 and Jurkat T cells were stimulated specifically by MFYLPM or HFYLPM, respectively. As a physiologic characteristic of the peptides, we observed that all 3 peptides induced chemotactic migration of monocytes. Studying receptor specificity, we concluded that the 3 peptides might act on some shared and some distinct receptor(s) on leukocytes. Studying intracellular signaling set in motion by the peptides revealed that HFYLPM, but not MFYLPM or HFYLPm, induced chemotaxis via phosphatidylinositol-3 kinase and protein kinase C. Because HFYLPM, MFYLPM, and HFYLPm not only exhibit different specificities depending on cell type and status of differentiation but also stimulate cells via distinct receptors and signaling, the 3 novel peptides might be useful tools to study leukocyte activation.

Chemotactic Factors↗
PubMed2003

Electrocatalytic detection of pathogenic DNA sequences and antibiotic resistance markers.

The detection of specific DNA sequences using electrochemical readout would permit the rapid and inexpensive detection and identification of bacterial pathogens. A new assay developed for this purpose is described that harnesses a sensitive electrocatalytic process to monitor DNA hybridization. Two sequences belonging to the pathogenic microbe Helicobacter pylori are used to demonstrate the versatility and specificity of the assay: one that codes for an unique H. pylori protein and one that represents a small portion of the 23S rRNA from this organism. Both sequences can be monitored into the nanomolar concentration range. Target sequences introduced to the electrode surface as synthetic oligonucleotides, PCR products, and RNA transcripts are all detected with high specificity. In addition to reporting the presence of pathogen-related sequences, this assay can accurately resolve single-base changes in target sequences. An A2143C substitution within the H. pylori rRNA that confers antibiotic resistance significantly attenuates hybridization to an immobilized probe corresponding to the WT sequence. The single-base mismatch introduced by this mutation slows the kinetics of hybridization and permits discrimination of the two sequences when short hybridization times are employed. The remarkable sensitivity of this label-free assay to small sequence changes may provide the basis of a new method for the detection and genotyping of infectious bacteria using electrochemical methods.

Bacterial Proteins↗
PubMed2005

Genome-wide identification of Pseudomonas aeruginosa exported proteins using a consensus computational strategy combined with a laboratory-based PhoA fusion screen.

The Gram-negative pathogen Pseudomonas aeruginosa encodes multiple protein export systems, the substrates of which contain export signals such as N-terminal signal peptides. Here we report the first genome-wide computational and laboratory screen for N-terminal signal peptides in this important opportunistic pathogen. The computational identification of signal peptides was based on a consensus between multiple predictive tools and showed that 38% of the P. aeruginosa PAO1 proteome was predicted to encode exported proteins, most of which utilize cleavable type I signal peptides or uncleavable transmembrane helices. In addition, known and novel lipoproteins (type II), twin arginine transporter (TAT), and prepilin peptidase substrates (type IV) were also identified. A laboratory-based screen using the alkaline phosphatase (PhoA) fusion method was then used to test our predictions. In total, 310 nonredundant PhoA fusions were successfully identified, 296 of which possess a predicted export signal. Analysis of the PhoA fusion proteins lacking an export signal revealed that three proteins have alternate translation start sites that encode signal peptides, two proteins may use an unknown export signal, and the remaining nine proteins are likely cytoplasmic proteins and represent false positives associated with the PhoA screen. Our approach to identify exported proteins illustrates how computational and laboratory-based methods are complementary, where computational analyses provide a large number of accurate predictions while laboratory methods both confirm predictions and reveal unique cases meriting further analysis.

Alkaline Phosphatase↗
PubMed2004

Identification of P18, a surface protein produced by the fish pathogen Flavobacterium psychrophilum.

AIMS: This study was focused on the identification of associated outer membrane proteins which may play a role in the specific interactions between Flavobacterium psychrophilum (the aetiological agent of cold-water disease and rainbow trout fry syndrome in salmonid fish worldwide) and the fish tissues. METHODS AND RESULTS: The surface protein interactions with the outer membrane being mainly ionic, different methods were used for the detachment of proteins from the cell surface of Fl. psychrophilum involving detergent-free buffers or solutions known to perturb the ionic interactions. Such treatments led to the isolation of a surface protein, named P18 in accordance with its relative molecular mass. The expression of P18 was not related to the growth conditions (liquid or solid medium, temperature and aeration) or the strains of Fl. psychrophilum tested here. CONCLUSIONS: Preliminary characterization indicated that P18 is a surface antigen which is not sugar-modified and might be a subunit of a surface layer (i.e. S-layer), one of the most common surface structures on bacteria. SIGNIFICANCE AND IMPACT OF THE STUDY: Data reported here should be used as the basis for further works involving the purification and characterization of P18 to identify the specific roles of such a surface protein, especially the interaction between this protein and the host surface.

Animals↗
PubMed2004

Specificity and performance of PCR detection assays for microbial pathogens.

PCR has become a widely used tool for detection, identification and differentiation of pathogenic microorganisms in diagnosis of animal and human diseases. However, quite a number of currently used protocols can be further optimized to exclude nonspecific reactions. On the one hand, target sequences as defined by primer binding sites should be checked carefully for the absence of significant homologies to other organisms in order to insure high specificity of detection. A major part of PCR assays is still based on target sequences in the ribosomal RNA operon, but, as the differentiating potential of this region is limited, genes encoding cellular proteins, such as toxins, surface antigens or enzymes, have been shown to be a viable alternative in many instances. On the other hand, various approaches are available to improve the performance of the amplification reaction itself. The kinetics of amplification is known to be heavily dependent on primer-to-template ratio, efficiency of primer annealing and enzyme-to-template ratio. In the present paper, recently published PCR detection assays for microorganisms, particularly bacterial pathogens, are reviewed and optimization strategies are explained. The practical implications and epidemiological consequences of routine use of PCR in the diagnostic laboratory are also discussed.

Bacterial Typing Techniques↗
PubMed1992

Identification of uncultured microorganisms: expanding the spectrum of characterized microbial pathogens.

The combination of enzymatic nucleic acid amplification techniques with 16S rRNA-based molecular phylogeny has brought about a new approach to the identification of microbial pathogens that can not be cultivated in the laboratory. The applications of this experimental approach to bacillary angiomatosis and to Whipple's disease have revealed the presence of two previously uncharacterized organisms. These results suggest the existence of a far greater microbial diversity among human pathogens than has been so far appreciated with culture-dependent methods. PCR-based studies of aquatic environmental microbial communities have already reached similar conclusions. As a result, new and provocative questions are raised concerning the association of amplified 16S rRNA sequences with diseased tissue. The answers must await the results of further investigations and the expansion of sequence data bases.

Animals↗
PubMedDate not supplied

[Culture media for the detection and the identification of Streptococcus agalactiae].

Streptococcus agalactiae, a Group B streptococcus, is the main cause of bacterial perinatal infection and is also an important opportunistic pathogen. Detection and identification of S. agalactiae are straight forward with special culture media, where Group B streptococci show a specific, typical pink or red pigment. To quickly and easily detect the pigment, culture media should contain: (i) starch; (ii) an inhibitor of the folate pathway; (iii) animal serum; (iv) a pepsic proteic hydrolysate; and (v) glucose, together with a high-capacity buffer. When selective antibiotics are added to culture media designed in this way, it is possible to detect S. agalactiae directly from clinical samples by observation of its pigment after less than 12 hours of aerobic incubation.

Culture Media↗
PubMed2001

Ticks and tickborne bacterial diseases in humans: an emerging infectious threat.

Ticks are currently considered to be second only to mosquitoes as vectors of human infectious diseases in the world. Each tick species has preferred environmental conditions and biotopes that determine the geographic distribution of the ticks and, consequently, the risk areas for tickborne diseases. This is particularly the case when ticks are vectors and reservoirs of the pathogens. Since the identification of Borrelia burgdorferi as the agent of Lyme disease in 1982, 15 ixodid-borne bacterial pathogens have been described throughout the world, including 8 rickettsiae, 3 ehrlichiae, and 4 species of the Borrelia burgdorferi complex. This article reviews and illustrate various aspects of the biology of ticks and the tickborne bacterial diseases (rickettsioses, ehrlichioses, Lyme disease, relapsing fever borrelioses, tularemia, Q fever), particularly those regarded as emerging diseases. Methods are described for the detection and isolation of bacteria from ticks and advice is given on how tick bites may be prevented and how clinicians should deal with patients who have been bitten by ticks.

Animals↗
PubMed2003

[Virus infection in children after allogenic stem cell transplantation ].

Allogenic hematopoietic cell transplantation (alloHCT) is the treatment of choice for various pediatric malignancies and nonmalignant diseases. The most prominent complication of allotransplantation is graft vs host disease (GvHD). The treatment of GvHD influence negatively function of immune system and increase risk of bacterial, fungal and viral infections. Clinical symptoms of viral infection may mimic GvHD and lead to inappropriate treatment. Human cytomegalovirus (CMV, Herpesviridae) has been recognized as most important viral pathogen after alloHCT. Increasing number of procedures, especially from alternative donors, requiring more intensive immunosuppression, led to identification more viral pathogens causing transplant related mortality and morbidity. Among them are adenoviruses (ADV, Adenoviridae), BK and JC viruses (Papovaviridae) and human herpes virus 6 (HHV-6, Herpesviridae). Frequency of complications caused by those pathogens is higher in children then in adults.

Adult↗
PubMed2001

Pathogenic isolates in meningitis patients in Dar Es Salaam, Tanzania.

OBJECTIVES: To determine, from laboratory records, the spectrum of bacterial and fungal pathogens isolated from cerebrospinal fluids (CSF) of in-patients with meningitis at Muhimbili Medical Centre (MMC) in Dar es Salaam and to ascertain the laboratory results (based on microscopy and culture) using the latex agglutination technique. DESIGN: A retrospective study based on laboratory records of CSF samples investigated between November 1999 and June 2000 and a cross-sectional study involving investigation of 60 freshly collected CSF samples by conventional (microscopy and culture) and antigen detection by latex agglutination technique (LAT). SETTING: Muhimbili Medical Centre in Dar es Salaam, Tanzania. INVESTIGATIONS: Information from laboratory records, bacteriological examination of CSF by microscopy, culture and agglutination techniques. RESULTS: According to records, a total of 1144 CSF samples were investigated between November 1999 and June 2000, of which two hundred and twenty two specimens (19.4%) had a positive bacterial or fungal culture. Fifty five of the isolates were from children (aged less than 15 years) and were; 20 (36.4%) were Streptococcus pneumoniae, 12(21.8%) were Cryptococcus neoformans, and nine (16.4%) were Haemophilus influenzae type b. The remaining 14 (25%) isolates included three group B streptococci, three Klebsiella spp, two E. coli, two Staphylococcus aureus, two Pseudomonas spp, one Moraxella and one Salmonella group B. For adults a total of 167 positive cultures were reported and 163 (97.6%) of the isolates were Cryptococcus neoformans, two (1.2%) were Pseudomonas spp. and two were S. aureus. There was good agreement between conventional microscopy and culture with the latex agglutination technique in the identification of CSF pathogens. CONCLUSION: In children, S. pneumonia, and bacteria in general constituted the majority of isolates. Adult cases of meningitis were almost exclusively due to C. neoformans. Overall, C. neoformans appears to be the most common isolate among meningitis cases. Based on LAT results, our routine diagnostic methods seem to be adequate in the identification of the common CSF pathogens.

Adolescent↗
PubMed2006

Rapid nested PCR-based detection of Ramularia collo-cygni direct from barley.

Ramularia collo-cygni is a barley pathogen of increasing importance in Northern and Central Europe, New Zealand and South America. Accurate visual and microscopic identification of the pathogen from diseased tissue is difficult. A nested PCR-based diagnostic test has been developed as part of an initiative to map the distribution of the pathogen in Scotland. The entire nuclear ribosomal internal transcribed spacer and 5.8S rRNA gene regions from 14 isolates of diverse global origin exhibited complete homology following sequence characterization. Two pairs of species-specific primers, based on inter-specific sequence divergence with closely related species, were designed and empirically evaluated for diagnostic nested PCR. Nested primers Rcc3 and Rcc4 consistently amplified a single product of 256 bp from DNA of 24 R. collo-cygni isolates of diverse global provenance, but not from other Ramularia species, or other fungi commonly encountered in cereal pathosystems, as well as Hordeum or Secale DNA preparations. Using this approach, R. collo-cygni was successfully identified from naturally infected barley leaf, awn and grain samples of diverse geographical provenance, in particular from symptoms that lacked the presence of characteristic conidiophores. It is envisaged that this assay will become established as an important tool in continuing studies into the ecology, aetiology and epidemiology of this poorly understood yet economically damaging plant pathogen.

Ascomycota↗
PubMed2003

[Analysis of RAPD fingerprinting in Exserohilum monoceras strains].

Exserohilium monoseras is a potential agent for barnyardgrass (Echinochlao crus-galli) control. This study was to evaluate the genetic diversity of this fungus with 17 strains isolated from different rice growing regions of China by the random amplified polymorphic DNA (RAPD). Among 25 arbitrary primers, 20 primers could get enough amplified bands for all the strains. A total 239 products were amplified. Polymorphic bands were 95.8% of the total products. The 17 strains could be identified based on RAPD fingerprinting established in this study. Genetic distance calculation and cluster analysis resulted in great genetic variation among the strains. The genetic similarity was related with the morphology and the pathogenicity of the strains. The results showed that RAPD maker could be applied in the utilization and the identification of weed pathogen resources.

Ascomycota↗
PubMed1987

Specific and rapid identification of medically important fungi by exoantigen detection.

Within a decade of its introduction, the exoantigen technique has won general acceptance for accurate and rapid identification of fungal pathogens. This acceptance is emphasized by the fact that positive exoantigen results obtained with the dimorphic pathogenic fungi B. dermatitidis, C. immitis, H. capsulatum varieties capsulatum, duboisii, and farciminosum, and P. brasiliensis are no longer considered presumptive evidence but are considered definitive data for species identification. Technical problems associated with poor sensitivity and false-positives in some of the early tests have been resolved. The test expands the diagnostic capabilities of the laboratory. We encourage the establishment of libraries of antisera for species identification and, where appropriate, for serotyping. Since the test is simple and reagents for many of the pathogens are commercially available, the test can be performed in most laboratories. As highly defined antigens are produced, more standardized and specific tests will be developed. Hybridoma technology may provide the means for producing specific antibodies without the need for highly purified antigens, which have been difficult to produce. The identification of numerous fungi could be facilitated by application of exoantigen techniques. Specific antisera should be developed to achieve this goal and to obtain antigenic data useful for elucidating taxonomic relationships. Some fungi cannot be classified on the basis of morphologic and biochemical qualities alone. Supplementary data obtained with exoantigen analyses could undoubtedly aid in resolving such problems.

Antigens, Fungal↗
PubMed2006

Using capillary electrophoresis-selective tandem mass spectrometry to identify pathogens in clinical samples.

Analysis of microbial mixtures in complex systems, such as clinical samples, using mass spectrometry can be challenging because the specimens may contain mixtures of several pathogens or both pathogens and nonpathogens. We have successfully applied capillary electrophoresis-selective MS/MS of unique peptide marker ions to the identification of common pathogens in clinical diagnosis. We searched the CE-MS/MS spectra acquired from the proteolytic digests of pure bacterial cell extracts against protein databases. The identified peptides that matched a protein associated with a particular pathogen were selected as marker ions to identify that bacterium in clinical specimens. Thirty-four clinical specimens, obtained from pus, wound, sputum, and urine samples, were analyzed using both biochemical and selective MS/MS methods. The bacteria in these clinical samples were cultivated directly, without prior isolation of a pure colony, before performing the selective MS/MS analyses. The bacteria analyzed included both Gram-positive and -negative strains. The match with respect to the pathogens identified was good between the biochemical and the selective MS/MS methods; the matching rate was 91%. The rate was as high as 97% when not considering two specimens for which the bacteria were not grown successfully. Two of the specimens that we identified using the biochemical method as containing two bacterial species were confirmed also through selective tandem MS analysis.

Electrophoresis, Capillary↗
PubMed2003

Screening for urinary tract infection with the Mastascan Elite.

Mastascan Elite urine screen (MUS) is compared to a conventional method to determine significant growth of urinary pathogens and determine identification and susceptibility. MUS can detect at least 10(3) colony-forming units (cfu)/mL of commonly isolated pathogens and in this study identified 161 true positive bacterial growths (15.2%), 840 true negatives (79.2%), 54 false positives (5.1%) and six false negatives (0.6%). Overall performance in determining susceptibility to nine antibiotics directly from urine was 10.5% true resistance, 82.4% true susceptibility, 5.3% false resistance and 1.8% false susceptibility. Using limited tests, the system correctly identified 80.7% of isolates, 11.8% could not be identified at all and 7.5% were incorrectly identified. In this study, MUS provided 94.7% of results in 24 h, compared to 78.4% produced by the conventional method. Thus, MUS proved an effective and efficient method for processing urines, saving significant time, materials and human resources.

Bacteria↗
PubMed1993

Entamoeba histolytica: an explanation for the reported conversion of "nonpathogenic" amebae to the "pathogenic" form.

The reported conversion of "nonpathogenic" Entamoeba histolytica isolates to the "pathogenic" form during attempted axenization of the amebae is highly controversial. After failing to obtain conversions ourselves we concluded that the simplest explanation for the published observations would be contamination of nonpathogenic cultures with pathogenic amebae. To address this possibility we used a method based on analysis of stable DNA polymorphisms that allows the positive identification of individual pathogenic isolates. The DNA patterns obtained using the "converted" amebae proved to be identical to those of reference isolates present in the laboratories at the time of conversion. We also found that very few cells need be transferred for a pathogenic contaminant to become established in a nonpathogenic culture. Cross-contamination fully explains the conversion phenomenon and thus recognition of nonpathogenic and pathogenic amebae as the distinct species Entamoeba dispar Brumpt 1925 and E. histolytica Schaudinn 1903 (Emend. Walker 1911), respectively, is upheld.

Animals↗