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 1,045 records · Page 58Linked to original sources
PubMed1999

Diagnosis and prevention of equine infectious diseases: present status, potential, and challenges for the future.

The frequent transfers of horses, whether on a permanent or temporary basis, make strict control of infectious diseases essential. Such control needs a reliable and rapid means to accurately diagnose the relevant diseases. Indirect diagnosis based on antibody detection remains certainly the best method to secure the epidemiologic surveillance of the diseases at regional, national, or even world level, while direct diagnosis is the only way to diagnose a new outbreak. New diagnostic methods resulting from advances in biochemistry, molecular biology, and immunology are now available. As far as antibody detection is concerned, the new methods are mainly based on immunoassays, especially ELISAs. Regarding the identification of the pathogens, while isolation is still of importance, much progress has been made with immunocapture tests including capture ELISA based on monoclonal antibodies. DNA probes and amplification tests such as PCR or RT-PCR are representing a real breakthrough. Factors common to all of these tests are specificity, sensitivity, rapid implementation, and quick results. Such tests are, however, often still at the development stage. They absolutely need to be validated under multicentric evaluations prior to being used on a larger scale. At the same time there is an obvious need for the standardization of the reagents used. The technical and economic impact of a false (either positive or negative) diagnosis justifies such an harmonization which could effectively be achieved worldwide under the aegis of the Office International des Epizooties (OIE), which is itself the primary source of disease information. Vaccines are also essential for the control of equine infectious diseases. Most vaccines used in the prevention of viral or bacterial diseases are inactivated adjuvanted vaccines, which may cause unacceptable side effects. Also, their efficacy can sometimes be questioned. Subunit vaccines, when available, represent significant advances especially with regards to safety. Greater progress is expected from the use of new technologies taking advantage of recent developments in molecular biology (recombinant DNA technology) and in immunology (immunomodulators). Significant results have been obtained with subunit vaccines or with live vectored vaccines using recombinant DNA technology. Good results are on the way to be achieved with genetic (or naked-DNA) vaccines. It is therefore possible to expect the availability of a new generation of vaccines in the rather short term. Such vaccines will not only be safer and more efficacious, but they will also make it possible to differentiate vaccinated from infected animals, which will contribute to better control of the infection. Whatever the quality of the vaccines of the future may be, vaccination alone will never be sufficient to control infectious diseases. It is therefore essential to keep on making the animal owners and their veterinarians aware of the importance of the management and the hygiene in the diseases control and to organize them under "Common Codes of Practice."

Animals↗
PubMed2003

Eosinophils are derived from the neoplastic clone in patients with systemic mastocytosis and eosinophilia.

Twenty to thirty-three percent of systemic mast cell disease (SMCD) patients have some degree of peripheral blood and/or bone marrow eosinophilia. While the clonality of SMCD was established by identification of the pathogenic c-kit Asp816 to Val (D816V) mutation in sorted cells of different hematopoietic lineages, this mutation has not previously been demonstrated in eosinophils from SMCD patients. In the current study, we demonstrate the D816V mutation in purified eosinophils from two patients with aggressive, eosinophilia-associated SMCD, thus proving that the eosinophils are clonal and not reactive in nature. The clinical implications of this finding are discussed.

Aged↗
PubMed1999

The management of superficial candidiasis.

Superficial Candida infection includes several common conditions, most often related to some underlying local or systemic predisposition. Appropriate identification of the pathogen is important in the management of candidiasis as the result of differences in susceptibility among species and strains of Candida to different antifungal drugs. Treatment options are reviewed for oropharyngeal candidiasis, vaginal candidiasis, cutaneous candidiasis, paronychia and onychomycosis, and chronic mucocutaneous candidiasis. Because of the importance of predisposing conditions for candidiasis, adjunctive measures to abate these may be useful, although they are seldom effective in immunocompromised patients.

Antifungal Agents↗
PubMed1994

Molecular methods: applications for clinical infectious diseases.

The application of molecular biology to microbiology has led to a surge of new information about most infectious microorganisms, the pathogenesis of the infections they cause, and the specific microbial antigens involved in the immune response to these infections. The simultaneous application of the same techniques to diagnosis and epidemiology has also shown great promise, but these developments have not yet had a major effect on the routine practice of medicine. For some purposes, direct probe tests perform as well as other available methods. However, for most infections, these methods have not been proven sufficiently sensitive. The latest generation of highly sensitive diagnostics based on the polymerase chain reaction will overcome this technical obstacle and may revolutionize the management of many infections. Difficulties inherent in performing these tests will require special procedures and training in clinical laboratories to ensure that they are performed reliably. Nucleic acid-based methods for epidemiologic typing of microorganisms and for identification of noncultivatable pathogens are particularly useful for analysis of poorly cultivatable, dangerous, or otherwise untypeable microorganisms.

Base Sequence↗
PubMed1999

Pathophysiology of surgical site infection in total hip arthroplasty.

This article is a case report of a 69-year-old man who underwent a right total hip replacement procedure and developed a surgical site infection. Areas of concern in prevention and treatment of hip arthroplasty infection are presented, focusing on the pathophysiologic process involved. A review of the patient risk factors and the pathophysiologic action potentiating risk for infection include host immunity, nutritional status, diabetes, age, use of steroids or immunosuppressive drugs, rheumatoid arthritis, and urinary tract or other infections. The case report identifies the patient's age, multiple instrumentation of the bladder resulting in bacteriuria and the reinfusion of 400 cc of autologous shed blood via cell saver, a controversial risk subject, as the primary risk factors for surgical site infection in this patient. Readmission to the hospital on day 16 after the operation was completed on identification of 2 pathogenic organisms, methicillin-resistant Staphylococcus aureus and Acinetobacter calcoaceticus bio anitratus. The infection was successfully treated with oral ciprofloxacin and intravenous administration of tobramycin, preventing progression from superficial to deep infection and preserving the prosthesis.

Acinetobacter Infections↗
PubMed2003

High-quality mutant libraries of Xanthomonas oryzae pv. oryzae and X. campestris pv. campestris generated by an efficient transposon mutagenesis system.

A novel transposon mutagenesis system for the phytopathogenic bacteria Xanthomonas oryzae pv. oryzae (Xoo) and X. campestris pv. campestris (Xcc) was developed using a Tn5-based transposome. A highly efficient transformation up to 10(6) transformants per microg transposon DNA was obtained. Southern blot and thermal asymmetric interlaced polymerase chain reaction analyses of Tn5 insertion sites suggested a random mode of transposition. The transposition was stable in the transformants for 20 subcultures. Eighteen thousand and 17000 transformants for Xoo and Xcc, respectively, were generated, corresponding to 4X ORF coverage of the genomes. The libraries will facilitate the identification of pathogenicity-related genes as well as functional genomic analysis in Xoo and Xcc.

Blotting, Southern↗
PubMed2000

Identification of porcine intestinal spirochetes by PCR-restriction fragment length polymorphism analysis of ribosomal DNA encoding 23S rRNA.

The Brachyspira (formerly Serpulina) species rrl gene encoding 23S ribosomal RNA (rRNA) was used as a target for amplification of a 517bp DNA fragment by polymerase chain reaction (PCR). The primers for PCR amplification had sequences that were conserved among Brachyspira 23S rRNA gene and were designed from nucleotide sequences of Brachyspira hyodysenteriae, Serpulina intermedia, Brachyspira innocens and Brachyspira pilosicoli available from the GenBank database. Digestion of PCR-generated products from reference and field isolates of swine intestinal spirochetes with restriction enzymes Taq I and Alu I revealed five restriction fragment length polymorphism (RFLP) patterns. Each RFLP pattern corresponded to previously established genetic groups including B. hyodysenteriae (I), S. intermedia/B. innocens (II), Brachyspira murdochii (III), B. pilosicoli (IV) and B. alvinipulli (V). The 23S rRNA PCR/RFLP provided a relatively simple genotypic method for identification of porcine pathogenic B. hyodysenteriae and B. pilosicoli.

Animals↗
PubMed1999

Differentiation of Serpulina species by NADH oxidase gene (nox) sequence comparisons and nox-based polymerase chain reaction tests.

The NADH oxidase genes (nox) of 18 strains of intestinal spirochaetes were partially sequenced over 1246 bases. Strains examined included 17 representatives from six species of the genus Serpulina, and the type strain 513A(T) of the human intestinal spirochaete Brachyspira aalborgi. Sequences were aligned and used to investigate phylogenetic relationships between the organisms. Nox sequence identities between strains within the genus Serpulina were within the range 86.3-100%, whilst the nox gene of B. aalborgi shared between 78.8-83.0% sequence identity with the nox sequences of the various Serpulina strains. A phenogram produced based on sequence dissimilarities was in good agreement with the current classification of species in the genus Serpulina, although an atypical strongly beta-haemolytic porcine strain (P280/1), previously thought to be S. innocens, appeared distinct from other members of this species. Primer pairs were developed from the nox sequence alignments for use in polymerase chain reaction (PCR) identification of the pathogenic species S. hyodysenteriae (NOX1), S. intermedia (NOX2), and S. pilosicoli (NOX3), and for the combined non-pathogenic species S. innocens and S. murdochii (NOX4). The PCRs were optimised using 80 strains representing all currently described species in the genus Serpulina, as well as the type strain of B. aalborgi. Tests NOX1 and NOX4 specifically amplified DNA from all members of their respective target species, whilst tests NOX2 and NOX3 were less sensitive. NOX2 amplified DNA from all 10 strains of S. intermedia from pigs but from only 4 of 10 strains from chickens, whilst NOX3 amplified DNA from only 18 of 21 S. pilosicoli strains, even at low stringency. Tests NOX1 and NOX4 should prove useful in veterinary diagnostic laboratories, whilst NOX2 and NOX3 require further refinement.

Animals↗
PubMed2000

Rapid identification of clinical yeast isolates using the colorimetric AUXACOLOR system.

The AUXACOLOR colorimetric system (Sanofi Diagnostics Pasteur, Marnes-la-Coquette, France) for the identification of clinical yeast isolates, was compared in its identification of 100 yeast strains to conventional identification methods. Of the 94 correctly identified isolates, 47% (n = 44) were identified by 24 h, and 100% (n = 94) were identified by 48 h. AUXACOLOR is a simple, rapid and accurate method for the identification of yeast pathogens.

Antifungal Agents↗
PubMed2003

Temporomandibular joint involvement in malignant external otitis.

OBJECTIVE: The purpose of this study was to present 6 patients with malignant external otitis (MEO) that resulted in temporomandibular joint (TMJ) involvement and to discuss the incidence, clinical presentation, and treatment modalities. STUDY DESIGN: All patients diagnosed with MEO between 1994 and 2002 were reviewed for cases in which the TMJ was invaded by the infectious process. Only patients in whom TMJ involvement was documented radiographically and in whom the clinical course was well documented were included in this study. RESULTS: MEO was diagnosed in 42 patients over an 8-year period; TMJ involvement was recorded in 6 patients (14%). The medical history revealed controlled type 2 diabetes mellitus in 4 of the 6 patients. All patients reported early ear symptoms, mainly otalgia and otorrhea. Local signs included an ear canal filled with granulation material, edematous overlying skin, and sensitivity to palpation. Cultures taken from the external ear were positive for either Pseudomonas aeruginosa, Staphylococcus epidermidis, Aspergillus, or Proteus mirabilis. TMJ symptoms developed between 1 and 5 months after admission and included painful periauricular swelling and trismus. In 3 patients, healing was uneventful; 3 also died of the disease. CONCLUSIONS: TMJ involvement in MEO is associated with a resistant disease process, often with several recurrences. Prolonged administration of antibiotics is the treatment of choice. Surgical debridement of the TMJ is necessary for the positive identification of the pathogenic organism, in cases of abscess formation, or when osteomyelitic bone destruction of the condyle and glenoid fossa develop.

Aged↗
PubMed2002

Mass spectrometry and tandem mass spectrometry, alone or after liquid chromatography, for analysis of polymerase chain reaction products in the detection of genomic variation.

The availability of the sequences of entire bacterial and human genomes has opened up tremendous opportunities in biomedical research. The next stage in genomics will include utilizing this information to obtain a clearer understanding of molecular diversity among pathogens (helping improved identification and detection) and among normal and diseased people (e.g. aiding cancer diagnosis). To delineate such differences it may sometimes be necessary to sequence multiple representative genomes. However, often it may be adequate to delineate structural differences between genes among individuals. This may be readily achieved by high-throughput mass spectrometry analysis of polymerase chain reaction products.

Chromatography, High Pressure Liquid↗
PubMed2004

Influence of intramammary infection and non-infection factors on somatic cell counts in dairy goats.

A total of 1304 goat udder halves were sampled monthly during an entire lactation (6262 samples) with the aim of identifying factors affecting milk somatic cell count (SCC). Bacteriological analyses for identification of mastitis pathogens were carried out on all samples and SCC was also determined. All animals were examined for infection by caprine arthritis-encephalitis virus (CAEV) using a commercial ELISA test kit. Results obtained were arranged in two databases (whole-lactation average half-udder database and monthly half-udder database) and two mixed models were applied. Random effects of half udder nested into flock and fixed effects of flock, intramammary infection (IMI) status, number of kids born, length of lactation and interaction of parity with IMI status were significant for the first database. CAEV infection and its interaction with IMI status was not significant. Milk SCC was significantly increased for infected udder halves and milk from udder halves infected with minor pathogens had lower SCC than udder halves infected with major pathogens. For healthy udder halves, SCC was higher in older animals but this effect was not evident in halves with IMI. Multiple birth and short-duration lactation were factors associated with elevated milk SCC. The second mixed model considered repeated measures in time for consecutive samplings throughout lactation (stage of lactation) which was also a significant factor with increasing stage of lactation. The influence of all these factors should be taken into account in the establishment of more reliable diagnostic SCC thresholds for IMI.

Animals↗
PubMed1984

Complications of sinusitis caused by Streptococcus milleri.

Complications of sinusitis caused by 'viridans' streptococci, mainly Streptococcus milleri, are described. The identification, bacteriology and pathogenicity of the organism are discussed and an approach to antimicrobial therapy outlined.

Abscess↗
PubMed2005

Characterization of the surface enhanced raman scattering (SERS) of bacteria.

The surface enhanced Raman scattering (SERS) of a number of species and strains of bacteria obtained on novel gold nanoparticle (approximately 80 nm) covered SiO(2) substrates excited at 785 nm is reported. Raman cross-section enhancements of >10(4) per bacterium are found for both Gram-positive and Gram-negative bacteria on these SERS active substrates. The SERS spectra of bacteria are spectrally less congested and exhibit greater species differentiation than their corresponding non-SERS (bulk) Raman spectra at this excitation wavelength. Fluorescence observed in the bulk Raman emission of Bacillus species is not apparent in the corresponding SERS spectra. Despite the field enhancement effects arising from the nanostructured metal surface, this fluorescence component appears "quenched" due to an energy transfer process which does not diminish the Raman emission. The surface enhancement effect allows the observation of Raman spectra of single bacterial cells excited at low incident powers and short data acquisition times. SERS spectra of B. anthracis Sterne illustrate this single cell level capability. Comparison with previous SERS studies reveals how the SERS vibrational signatures are strongly dependent on the morphology and nature of the SERS active substrates. The potential of SERS for detection and identification of bacterial pathogens with species and strain specificity on these gold particle covered glassy substrates is demonstrated by these results.

Bacillus↗
PubMed2007

The neuropathic diabetic foot.

Diabetic foot problems are common throughout the world, and result in major medical, social and economic consequences for the patients, their families, and society. Foot ulcers are likely to be of neuropathic origin and, therefore, are eminently preventable. Individuals with the greatest risk of ulceration can easily be identified by careful clinical examination of their feet: education and frequent follow-up is indicated for these patients. When infection complicates a foot ulcer, the combination can be limb-threatening, or life-threatening. Infection is defined clinically, but wound cultures assist in identification of causative pathogens. Tissue specimens are strongly preferred to wound swabs for wound cultures. Antimicrobial therapy should be guided by culture results, and although such therapy may cure the infection, it does not heal the wound. Alleviation of the mechanical load on ulcers (offloading) should always be a part of treatment. Plantar neuropathic ulcers typically heal in 6 weeks with nonremovable casts, because pressure at the ulcer site is mitigated and compliance is enforced. The success of other approaches to offloading similarly depends on the patient's adherence to the strategy used for pressure relief.

Algorithms↗
PubMed2006

Quantifying viable virus-specific T cells without a priori knowledge of fine epitope specificity.

Identification of pathogen-specific T cells has been greatly facilitated by the advent of synthetic peptide-major histocompatibility complex (MHC) tetramers. In many cases, however, specific epitopes have not been defined, necessitating detection methods that function independently of exact peptide-MHC specificity. Lymphocytes acquire surface proteins from antigen-presenting cells (APCs), and we have exploited this phenomenon to develop the T-cell recognition of APCs by protein transfer (TRAP) assay. This method is based on biotinylation and streptavidin-fluorochrome labeling of APCs, followed by subsequent acquisition of this label by antigen-specific T cells. The TRAP procedure detects MHC class I-restricted T cells regardless of their cytokine profiles or peptide-MHC affinities, and provides a versatile tool for monitoring the phenomenon of APC membrane acquisition by antigen-specific T cells.

Animals↗
PubMed2006

Associations between aortic calcification and components of body composition in elderly men.

OBJECTIVE: To investigate associations among body composition, cardiovascular risk factors, and atherosclerosis in middle-aged and elderly men for the identification of potential pathogenic links. RESEARCH METHODS AND PROCEDURES: The study included 168 white men 44 to 86 years old. Severity of aortic calcification (AC) was graded on lateral radiographs, and body fat and lean mass were measured by DXA. Information on demographic and lifestyle characteristics also was gathered. RESULTS: A strong and independent inverse association was found between AC and peripheral lean mass (PLM), even after adjusting for age and BMI (p < 0.05). Independently of the influence of PLM, AC was directly correlated with truncal fat mass (p < 0.05). Furthermore, AC was inversely associated with tertiles of the free androgen index (p < 0.05). In a multiple regression model, age and serum cholesterol (p < 0.01) contributed directly, and truncal fat mass tended also to contribute directly (p = 0.09), whereas PLM contributed borderline inversely (p = 0.06) to the variation of AC (R = 0.635, p < 0.0001). DISCUSSION: Severity of AC is strongly dependent on age and further modulated by an array of traditional cardiovascular risk factors. Sarcopenia and truncal fat mass are reciprocal correlates of atherosclerosis of borderline statistical significance in multivariate models. To clarify whether sarcopenia is an atherogenic risk factor or rather a parallel consequence of low-grade inflammation also promoting atherogenic trends, further longitudinal studies in larger sample sizes of men and women are needed.

Absorptiometry, Photon↗
PubMed2025

Creating an atlas of variant effects to resolve variants of uncertain significance and guide cardiovascular medicine.

Cardiovascular diseases are leading global causes of death and disability, often presenting as interrelated phenotypes of atherosclerotic vascular disease, heart failure and arrhythmias. Cardiovascular diseases arise from interactions between environmental factors and predisposing genotypes and include common Mendelian lipid disorders, cardiomyopathies and arrhythmia syndromes. The identification of a pathogenic variant through genetic testing can inform disease diagnosis, risk prediction, treatment and family screening. However, a major roadblock in genomic medicine is that for many variants, especially missense variants, we lack sufficient evidence to enable a definitive classification, and therefore these variants are deemed as 'variants of uncertain significance'. In this Review, we describe how multiplexed assays of variant effects can enable the functional assessment of nearly all coding variants in a target sequence, potentially offering a proactive approach to identifying the functional significance of gene variants that are observed later in a patient. We discuss validation, including the role of in silico variant effect predictors, and how multiplexed experimental methods are informing cardiovascular disease biology and ultimately resolving the problem of variants of uncertain significance at scale.

Humans↗