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 1,657 records · Page 92Linked to original sources
PubMed1996

Role of bronchoalveolar lavage in hospitalized pediatric patients.

Bronchoalveolar lavage (BAL) has been shown to be a rapid, relatively safe, and relatively noninvasive diagnostic procedure. Theoretically, BAL can be performed on all children hospitalized for pneumonia resistant to oral antibiotics, though practically and economically, this is not feasible. A 1-year retrospective review was conducted to define a cost-effective role for BAL in the management of hospitalized children with resistant pneumonia. The data revealed identification of at least one pathogen in 87% of sputum samples and in 95% of BAL specimens. Sputum samples provided the same information as the more invasive BAL technique in 60% of patients who had both sputum and BAL obtained for culture. Recommendations are made for the use of BAL as a diagnostic tool in the hospitalized child with resistant pneumonia.

Adolescent↗
PubMed2006

Study of Salmonella, Campylobacter, and Escherichia coli contamination in raw food available in factories, schools, and hospital canteens in Hanoi, Vietnam.

This study on the contamination rates of raw foods available in factory, school, and hospital canteens in Hanoi, Vietnam, with the bacteria of Salmonella, Campylobacter, and Escherichia coli (E. coli) was carried out between 2003 and 2004. A total of 177 raw food samples of vegetables, meat (beef and pork), fish, and poultry were examined to provide baseline data for evaluation of microbiological risks in general, and identification of potential vehicles for pathogenic cross-contamination in canteens. The study confirmed that unprocessed fish and poultry are likely to be contaminated with Salmonella and in the absence of proper kitchen hygiene and may contaminate processed foods. Raw poultry samples were highly contaminated with E. coli (45%), Campylobacter jejuni (C. jejuni) (28.3%), and Salmonella (8.3%) and classified as high-risk food. E. coli was also detected in raw meat, fish, and vegetables with the rate of 21.3%, 6.6%, and 18.5%, respectively. This article confirmed the importance of hygienic working practices when preparing food.

Animals↗
PubMed2001

Establishment of a new cross of the rice blast fungus derived from Japanese differential strain Ina168 and hermaphroditic rice pathogen Guy11.

Mating experiments between Magnaporthe grisea Japanese rice pathogens and Guy11, a hermaphroditic fertile rice pathogen, were done aimed at identification of avirulence genes. A cross named cross 2107 with thirty-six random progenies was obtained. Segregation analyses of genetic markers found that the cross was less suitable for genetic analysis. Backcrosses with cross 2107 progenies and Guy11 were done and another cross named cross 5307 with sixty-five progenies was obtained. A locus controlling kasugamycin resistance named Ksg1R was identified and used for a model case of genetic mapping. Bulked segregant analysis was done to find adjacent RAPD markers for mapping of the gene. Three adjacent markers to Ksg1R were obtained and a genetic map around the Ksg1R was made, but these markers were not located on a single chromosome. These results suggest that genetic analysis to identify a gene locus is available in cross 5307. Infection assay of parental strains of cross 5307 to Japanese differential rice cultivars suggested the possibility of genetic analysis of cultivar specificity toward four rice cultivars: Aichi-asahi, Kusabue, Tsuyuake, and K59.

Aminoglycosides↗
PubMed2005

The search for new antimicrobials: why we need new options.

The increasing identification of antibiotic-resistant pathogens that cause serious infections cannot be ignored. Although the future cannot be predicted with certainty, it is surely possible that an extensive epidemic of resistant bacterial infections could potentially harm millions of people. Given that it takes more than 10 years to establish the efficacy and safety of new compounds, there is an urgent need to restock the antibiotic pipeline. Only a few new antibacterial agents have received approval by the US Food and Drug Administration in the last 5 years, including linezolid in 2001, cefditoren, pivoxil and ertapenem in 2002, gemifloxacin and daptomycin in 2003, and telithromycin in 2004. Many of these agents are improved derivatives from established classes of antibiotics, and several are directed primarily at resistant Gram-positive bacteria (e.g., linezolid and daptomycin). One promising new addition is the recent approval of tigecycline (Tigacyl, Wyeth) in June 2005.

Animals↗
PubMed2005

Species concepts and biodiversity in Trichoderma and Hypocrea: from aggregate species to species clusters?

Trichoderma/Hypocrea is a genus of soil-borne or wood-decaying fungi containing members important to mankind as producers of industrial enzymes and biocontrol agents against plant pathogens, but also as opportunistic pathogens of immunocompromised humans. Species identification, while essential in view of the controversial properties of taxa of this genus, has been problematic by traditional methods. Here we will present a critical survey of the various identification methods in use. In addition, we will present an update on the taxonomy and phylogeny of the 88 taxa (which occur as 14 holomorphs, 49 teleomorphs and 25 anamorphs in nature) of Trichoderma/Hypocrea that have been confirmed by a combination of morphological, physiological and genetic approaches.

Chromosome Mapping↗
PubMed1990

Laboratory identification and sensitivity testing of yeast isolates.

Methods used for identification and sensitivity testing of yeasts are presented. Identification depends on both morphologic features and biochemical characteristics. The germ tube test is a simple test for the identification of the commonest yeast pathogen, Candida albicans. Species not identified by this method can be identified by means of several other tests, the most important being the carbohydrate assimilation test. Several kits are commercially available and most appear to be satisfactory. Antifungal susceptibility tests are not standardized, and results are often subject to considerable variation. Until improved methods are developed, it might be advisable that smaller laboratories only do a preliminary screening test for flucytosine susceptibility and, if indicated, also for amphotericin B susceptibility. Important isolates should be sent to laboratories with a special interest in antifungal susceptibility testing for more extensive testing.

Antifungal Agents↗
PubMed2001

A novel approach of direct ex vivo epitope mapping identifies dominant and subdominant CD4 and CD8 T cell epitopes from Listeria monocytogenes.

We used a novel approach for the direct ex vivo identification and characterization of T cell epitopes based on the screening of peptide spot libraries with freshly isolated splenocytes in a sensitive enzyme-linked immunospot (ELISPOT) assay. This technique was applied for the analysis of splenocytes from Listeria monocytogenes-infected BALB/c and C57BL/6 mice. The screening of peptide spot libraries covering the whole listeriolysin O and p60 of L. monocytogenes confirmed all known CD4 and CD8 T cell epitopes of these proteins and additionally revealed six new H-2(d) and six new H-2(b)-restricted T cell epitopes. New epitopes were categorized into CD4 and CD8 T cell epitopes by ex vivo ELISPOT analysis with separated T cell populations. The quantitative analysis of cells reactive with these CD4 and CD8 T cell epitopes revealed the existence of dominant and subdominant CD4 and CD8 T cell populations during L. monocytogenes infection. As a consequence of these data we suggest that ELISPOT-based screening of peptide spot libraries could be a general approach for the rapid identification and characterization of pathogen-specific T cell populations during various infectious diseases.

Animals↗
PubMed2000

Prophylactic antibiotics in surgery and surgical wound infections.

Wound infection remains a considerable cause of morbidity and mortality among surgical patients, despite the relative success of prophylactic antibiotics. In modern efforts to control healthcare costs while improving the quality of patient care, we must not overlook the basic principles of wound infections and their appropriate treatment. Predisposing factors for the development of surgical wound infection include the creation of a surgical wound, the presence of bacteria, and a susceptible host. The selection of an appropriate antimicrobial drug depends on the identification of the most likely pathogens associated with a given procedure, as well as the expected antibiotic susceptibility of those pathogens. Ideally, a prophylactic antibiotic should achieve high peak tissue concentration at the site of the wound before the first incision and should be maintained until the time of closure. Currently, the administration of prophylactic antibiotics is indicated for contaminated and clean-contaminated wounds. Despite the proven effectiveness of antibiotic prophylaxis, many researchers would argue that contemporary dosing regimens should be reevaluated. The debates concerning the dosage and timing of ideal prophylactic administration are likely to continue.

Antibiotic Prophylaxis↗
PubMed2001

Acid-fast bodies in faecal smears stained by the modified Ziehl-Neelsen technique.

The modified Ziehl-Neelsen (ZN) stain has proved useful in the laboratory diagnosis of cryptosporidiosis and, more recently, for the laboratory diagnosis of cyclospora. Apart from cryptosporidia and cyclospora, many other organisms and artefacts are present in faeces, and may be seen in faecal smears stained by the modified ZN method. Described here is the presence of such organisms and artefacts in faecal samples submitted to the routine microbiology laboratory of a district general hospital. Over 6000 faecal smears were examined using the modified ZN method, with an incidence of cyclospora and cryptosporidium of approximately 0.1% and 1%, respectively. Other organisms and artefacts were observed, with an incidence ranging from 0.1% to 1%. It is emphasised that the identification of known gastrointestinal tract pathogens should not rely solely on the results of their staining reactions. It is essential that criteria such as morphology and size be taken into account to differentiate organisms with similar staining reactions.

Animals↗
PubMed2001

Evaluation of sexually transmitted disease control practices for male patients with urethritis at a large group practice affiliated with a managed care organization--Massachusetts, 1995-1997.

Effective management for sexually transmitted diseases (STDs) depends on appropriate testing, treatment, partner management, and complete and timely reporting of positive STD tests (1). Testing can ensure appropriate treatment of initial or recurrent infections and identification of drug-resistant pathogens, appropriate treatment can reduce risk for complications and development of drug resistance, and complete and timely reporting of positive test results by laboratories and STD cases by health-care providers to health departments can facilitate rapid sex partner notification and outbreak detection. By 1998, private providers, including those affiliated with commercial or Medicaid managed care organizations (MCOs) (2,3) were caring for approximately 70% of persons with chlamydia and 55% of persons with gonorrhea. To assess the quality of STD care at a MCO-affiliated multisite facility, the testing, treatment, and reporting practices of gonorrhea- and chlamydia-associated urethritis in male patients were evaluated. This report summarizes the evaluation, which indicated that the providers tested most men with urethritis symptoms, prescribed CDC-recommended therapy to all patients, and reported most laboratory-confirmed chlamydia and gonorrhea cases of urethritis to the state health department. Several interventions introduced at this large group practice may have encouraged these favorable STD practices.

Adult↗
PubMed2002

Managing a large outbreak of cryptosporidiosis: how to investigate and when to decide to lift a 'boil water' notice.

The largest outbreak of cryptosporidiosis reported in the United Kingdom, involving 575 confirmed cases (of which 474 met an agreed case definition), occurred in the county of Devon during August and September of 1995. The descriptive epidemiology supports the hypothesis that the outbreak was associated with the consumption of cold tap water in the area served by a particular water treatment works. Cryptosporidium oocysts were detected in treated water samples at the time of the outbreak. Although the epidemiological analysis provided strong circumstantial evidence of a waterborne outbreak, the data were not recorded in a manner that made them admissible in criminal proceedings taken by the Drinking Water Inspectorate against the water company involved. The need to carry out an analytical study in conjunction with the identification and characterisation of the pathogen in the drinking water and the practicalities of agreeing criteria for lifting a 'boil water' notice are discussed.

Adolescent↗
PubMed2004

New approaches to development of mucosal vaccine against enteric bacterial pathogens; preventing campylobacteriosis.

Although vaccination, after having been more than 200 years in medical practice, has proven to be the most effective and the cheapest way to prevent infectious diseases, they remain still the main cause of human premature deaths. As many pathogens enter the human body through the mucosal surfaces, the mucosal way of immunization is considered to be the most promising strategy to decrease the number of human infections. Moreover, the oral delivery system eliminates the necessity of injection what is extremely important for pediatric immunization programs. However, most of recently constructed subunit vaccines based on purified bacterial/viral antigens are rather poorly immunogenic. This review presents some novel ways to enhance and modulate host immune responses by combining antigens with specific adjuvants or by employing specific delivery systems. We also discuss some recent technologies, based on mining the genomic sequences of bacterial pathogens, which accelarate and improve identification of new candidates for vaccine construction. As an example, we focus on the progress in the development of vaccine against Campylobacter spp. Campylobacter jejuni is now recognized as a leading cause of bacterial enteritis in human.

Adjuvants, Immunologic↗
PubMed1977

Disorders of phagocyte function: biochemical aspects.

Intensive laboratory investigation of patients with recurrent infections, and with infections with microbial species not usually considered to be pathogenic, have led to the identification of several defects in granulocyte function. The two functions of granulocytes which have received most attention in the past decade have been locomotion (especially response to chemotactic stimulation) and microbicidal activity. Defective granulocyte chemotaxis has been demonstrated in patients with clinical manifestations suggesting abnormalities related to vasoactive amines, i.e., patients with eczema and extreme IgE hyperimmunoglobulinemia. The depressed granulocyte chemotactic responsiveness found in these patients can be reproduced in vitro when histamine and beta adrenergic agents are incubated with control granulocytes. Since these compounds have been shown to increase levels of intracellular cyclic AMP in other cells, there appears to be an association between cyclic nucleotide metabolism and regulation of granulocyte locomotion. Defective granulocyte microbicidal activity is found in patients with chronic granulomatous disease and it has been shown that there is little increase in oxidative metabolism during phagocytosis by these cells. Methods for quantitating the oxidative metabolism of granulocytes and monocytes include oxygen uptake, reduction of nitroblue tetrazolium, formate oxidation, and chemiluminescence response during phagocytosis. Since products of oxygen metabolism, i.e., hydrogen peroxide, superoxide or singlet oxygen do not accumulate in granulocyte phagocytic vacuoles, intracellular microbes are not killed (except bacterial species that produce hydrogen peroxide). The biochemical basis for defective oxidative metabolism in granulocytes from patients with chronic granulomatous disease appears to be associated with abnormal nucleotide oxidase activity.

Blood Bactericidal Activity↗
PubMed1995

[A system of processing data of clinical microbiology laboratories].

The COBAS BACT automized system (Hoffman la Roche, Switzerland) was used in the practical work of the laboratory of clinical microbiology. The analyzer performed two functions i.e. the identification of gram-negative pathogens of the family Enterobacteriaceae and the rapid assay of their susceptibility to antibacterial drugs. The primary computer processing was embedded in the COBAS BACT machine. An information system providing the automatization of the secondary processing of the results of microbiological tests was developed. It included not only a system of the data bases for storage of the information and accumulation of the statistical data on the assays and their results but also the automized position of the microbiologist providing the possibility of the statistical information accumulation and reading. The CLIPPER program was used as a basis for the system development. The results of the secondary computer processing are illustrated by the actualities of the determination of the etiological factor of postoperative meningitis and septicemia carried out in 1993.

Clinical Laboratory Information Systems↗
PubMed1994

[Lice and methods of control].

The morphology and biology of sucking lice (Anoplura) and biting lice (Mallophaga) are described. A table shows the main species for given hosts and provides simplified keys for identification. Lice have a direct pathogenic effect (damage to skin and cutaneous appendages, fall in productivity) and an indirect effect (transmission of Rickettsia prowazeki, R. quintana and Borrelia recurrentis in human beings; African and classical swine fever virus, equine infectious anaemia virus and Dipylidium caninum in animals). Control methods, current active insecticides (and those being tested) and appropriate formulations are outlined.

Animals↗
PubMed1993

Enterocytozoon bieneusi detection in a patient with human immunodeficiency virus infection and chronic diarrhoea: response to albendazole treatment.

Diarrhoea is a common symptom among HIV-infected subjects. An infective cause is often missed. However, more recent knowledge about pathogens has led to the identification of newly recognized unusual microorganisms, such as Microsporidia. We report a case of infestation with these agents in an HIV-infected subject with chronic diarrhoea.

AIDS-Related Opportunistic Infections↗
PubMed1993

Costs of clinical mastitis and mastitis prevention in dairy herds.

A stratified random sample of 50 Ohio dairy herds, monitored for 1 year between March 1988 and May 1989, was used to estimate the component costs of clinical mastitis per cow-year overall and by organism, the component costs of an episode of clinical mastitis overall and by organism, and the incidence of clinical mastitis by organism. Each herd was visited monthly by a veterinarian who conducted on-farm interviews and completed standardized data-collection forms designed to elicit economic information about the on-farm costs of clinical mastitis and mastitis prevention. Producers collected milk samples prior to treatment of clinical mastitis cases. Culturing methods allowed identification of 18 specific mastitis pathogen classifications. Annual costs estimated were on a per cow-year and clinical episode basis. The monthly mean population of cows monitored was 4,068. Mastitis prevention cost $14.50/cow-year, whereas the cost incurred by producers because of clinical cases of mastitis was $37.91. Organisms prevalent in the cows' environment caused the most costly types of mastitis. Disregarding contaminated samples and episodes for which no milk samples were taken, mastitis for which 2 organisms were isolated accounted for 35.5% of costs of clinical mastitis, followed by cases for which Escherichia coli (21.3%) was isolated, cases for which culturing yielded no growth (8.6%), and cases for which esculin-positive Streptococcus spp (6.4%), Klebsiella spp (5.7%), esculin-negative CAMP-negative Streptococcus spp (5.1%), Enterobacter spp (4.8%), coagulase-negative Staphylococcus spp (4.1%), coagulase-positive Staphylococcus spp (3.0%), S agalactiae (2.5%), and Bacillus spp (1.2%) were isolated.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2001

Identification and antimicrobial susceptibility of Alcaligenes xylosoxidans isolated from patients with cystic fibrosis.

In the past decade, potential pathogens, including Alcaligenes species, have been increasingly recovered from cystic fibrosis (CF) patients. Accurate identification of multiply antibiotic-resistant gram-negative bacilli is critical to understanding the epidemiology and clinical implications of emerging pathogens in CF. We examined the frequency of correct identification of Alcaligenes spp. by microbiology laboratories affiliated with American CF patient care centers. Selective media, an exotoxin A probe for Pseudomonas aeruginosa, and a commercial identification assay, API 20 NE, were used for identification. The activity of antimicrobial agents against these clinical isolates was determined. A total of 106 strains from 78 patients from 49 CF centers in 22 states were studied. Most (89%) were correctly identified by the referring laboratories as Alcaligenes xylosoxidans. However, 12 (11%) strains were misidentified; these were found to be P. aeruginosa (n = 10), Stenotrophomonas maltophilia (n = 1), and Burkholderia cepacia (n = 1). Minocycline, imipenem, meropenem, piperacillin, and piperacillin-tazobactam were the most active since 51, 59, 51, 50, and 55% of strains, respectively, were inhibited. High concentrations of colistin (100 and 200 microg/ml) inhibited 92% of strains. Chloramphenicol paired with minocycline and ciprofloxacin paired with either imipenem or meropenem were the most active combinations and inhibited 40 and 32%, respectively, of strains. Selective media and biochemical identification proved to be useful strategies for distinguishing A. xylosoxidans from other CF pathogens. Standards for processing CF specimens should be developed, and the optimal method for antimicrobial susceptibility testing of A. xylosoxidans should be determined.

Alcaligenes↗