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Results for “Pathogen detection”

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At least 379 records · Page 21Linked to original sources

PubMed2005

Detection of Cyclospora cayetanensis oocysts in human fecal specimens by flow cytometry.

A diagnosis of cyclosporiasis typically involves stool examinations for the presence of Cyclospora oocysts by means of microscopy. In recent years, flow cytometry has been gaining in popularity as a novel method of detecting pathogens in environmental and clinical samples. The present study is an evaluation of a flow cytometric method for the detection and enumeration of Cyclospora oocysts in human fecal specimens associated with food-borne outbreaks of cyclosporiasis in Ontario, Canada. Flow cytometry results were generally very comparable to the original microscopy results for these specimens, in terms of both presence or absence of oocysts and relative oocyst concentrations. Of the 34 fecal specimens confirmed positive for Cyclospora by microscopy, 32 were also found positive by flow cytometry, and 2 others were considered equivocal. Of the eight fecal specimens reported to be negative by microscopy, two were found positive by flow cytometry and five others were considered equivocal. These two flow cytometry-positive samples and one of the equivocal samples were confirmed by microscopic reexamination, suggesting that flow cytometry may be more sensitive than microscopy. While the sample preparation time for flow cytometry is similar to or slightly longer than that for microscopy, the actual analysis time is much shorter. Further, because flow cytometry is largely automated, an analyst's levels of fatigue and expertise will not influence results. Flow cytometry appears to be a useful alternative to microscopy for the screening of large numbers of stool specimens for Cyclospora oocysts, such as in an outbreak situation.

Animals↗

PubMed1994

Leukocyte esterase urine strips for the screening of men with urethritis--use in developing countries.

BACKGROUND AND OBJECTIVES: The leukocyte esterase (LE) strip is a useful tool for the screening of men with urethritis. In developing countries, where laboratory facilities are limited, and sexually transmitted diseases endemic, simple and inexpensive diagnostic tests which perform well, would be of great value. METHODS: Men presenting with urethritis to a referral clinic for sexually transmitted diseases in Nairobi, Kenya participated in this cohort analytical study. First-void urine was collected for LE dipstick testing as part of the diagnostic work-up. The results of the dipstick measurement were compared with the laboratory detection of Chlamydia trachomatis and Neisseria gonorrhoeae. RESULTS: Of 200 men with symptoms of urethritis, 33 (17%) had a pathogen detected from the urethra or the urine. Chlamydia was detected in urine by PCR in 22 (11%), and gonorrhoea was cultured from the urethra in 11 (6%). Esterase activity (trace or greater) had a sensitivity of 76%, a specificity of 80%, a positive predictive value of 42% and a negative predictive value of 94% for the presence of chlamydia or gonorrhoea. CONCLUSIONS: The use of the LE dipstick for the screening of men with symptomatic urethritis can improve diagnostic accuracy and reduce the amount of empiric antimicrobial therapy. The low detection rate of chlamydia in these men with a clinical diagnosis of nongonococcal urethritis needs further study.

Adult↗

PubMed2026

Using Mapping-Profiles to Refine Strain-Level Metagenomic Classification.

Metagenomic classification at the strain level remains challenging due to high sequence similarity among closely related genomes, which leads to ambiguous read mappings and frequent false-positive strain detections. Reducing such errors improves the reliability of strain-level analyses, which is critical for applications such as pathogen detection. We introduce StrainRefine, a post-mapping refinement method that analyzes read-reference mapping profiles to resolve ambiguous assignments among highly similar genomes. The method represents candidate reference genomes using binary profiles that capture read-support patterns and measures similarity between references based on profile overlap. The method clusters references based on similar mapping profiles, filters weakly supported genomes, and reassigns reads to representative references, reducing redundant reporting of near-identical strains. StrainRefine substantially reduces false-positive strain detections while preserving recall and improving agreement between predicted and true abundance profiles. On large-scale metagenomic datasets, it achieves a substantially improved precision-recall balance compared with existing mapping-based approaches, with the standalone method obtaining the highest read-level classification accuracy on the most complex evaluated dataset. Unlike many strain-level tools designed for individual species, StrainRefine operates without prior assumptions about sample composition or curated species-specific reference collections, while still achieving comparable performance in single-species settings on species-specific reference databases. These results highlight mapping-profile similarity as an effective signal for improving strain-level metagenomic classification.

false-positive reduction↗

PubMed1998

Endoscopic evaluation of chronic human immunodeficiency virus-related diarrhea: is colonoscopy superior to flexible sigmoidoscopy?

OBJECTIVES: In patients with chronic human immunodeficiency virus (HIV)-related diarrhea undergoing lower endoscopy, the decision to perform flexible sigmoidoscopy or colonoscopy is controversial. The purpose of this study is twofold: 1) to evaluate the diagnostic yield of colonoscopy in a large group of patients with chronic HIV-related diarrhea and negative stool studies, and 2) to determine whether colonoscopy is superior to flexible sigmoidoscopy in this setting. METHODS: All HIV-infected patients with chronic diarrhea who were referred for diagnostic colonoscopy at Bellevue Hospital Center between January 1992 and December 1996 were identified. Patient charts, pathology reports, and endoscopy records were reviewed. RESULTS: During the 5-yr study period, 317 consecutive patients with chronic unexplained diarrhea undergoing colonoscopy were identified. A potential cause of diarrhea was found in 116 patients (36.6%). Cytomegalovirus was the most common pathogen detected (24%). The yield of colonoscopy was significantly higher in patients with a CD4 count of <100 cells/mm3 than in those with higher CD4 counts (44.8% vs 6.4%, p < 0.0001). Thirty percent of pathogens and 75% of lymphomas were identified only on biopsies taken from the proximal colon, well beyond the reach of the flexible sigmoidoscope. Importantly, 94% of the pathogens that were found only in the proximal colon were organisms for which effective therapy is currently available. CONCLUSIONS: Colonoscopy is superior to flexible sigmoidoscopy in HIV-infected patients with chronic unexplained diarrhea. If flexible sigmoidoscopy had been performed instead of colonoscopy, 30% of pathogens would have been missed and 75% of lymphomas would have escaped detection.

AIDS-Related Opportunistic Infections↗

PubMed2005

Detection of sexually transmitted pathogens in patients with hematospermia.

BACKGROUND: Although the current literature attributes most cases of hematospermia to an infectious agent, identification of the specific pathogens involved has been limited. OBJECTIVES: To determine the prevalence of different pathogens in patients presenting with hematospermia to our sexually transmitted disease clinic. METHODS: Between January 1999 and January 2000, 16 patients presented to our STD clinic with hematospermia after other noninfectious pathologies had been excluded by a referring physician. After obtaining informed consent, subjects completed a questionnaire addressing symptoms and sexual behavior. First-void urine samples, as well as genitourinary and serum specimens were tested for Chlamydia trachomatis, Ureaplasma urealyticum and herpes simplex virus. Standard bacterial cultures were also performed. RESULTS: Laboratory testing detected a pathogen in 12 of the 16 males presenting with hematospermia. The sexually transmitted pathogens detected were herpes simplex virus in 5 patients (42%), Chlamydia trachomatis in 4 (33%), Enterococcus fecalis in 2 (17%), and Ureaplasma urealyticum in 1 (8%). In all cases in which a pathogen was identified, the appropriate antimicrobial agent was administered. Symptoms resolved for each patient following antimicrobial therapy. During a 1 year follow-up, all 12 patients remained free of disease. CONCLUSIONS: Recent advances in microbiologic diagnostic techniques have facilitated the detection of pathogens in patients with hematospermia, thereby enhancing the efficacy of treatment.

Adolescent↗

PubMed1992

A DNA probe specific to pathogenic Entamoeba histolytica.

A DNA sequence, IE-gen1 (3.1 kb), was isolated from the pathogenic strain of E. histolytica NIH-200. IE-gen1 was identified by the subtractive hybridization of a genomic library to a cDNA probe prepared from NIH-200 trophozoites. The IE-gen1 probe specifically detected pathogenic E. histolytica in slot blots of genomic DNA and Northern blots, but not other Entamoeba species and additional human parasites. This genomic probe could detect with complete specificity DNA from about 10(3) organisms. The IE-gen1 probe could be related to highly specialized loci in pathogenic E. histolytica, and is likely to be a valuable DNA reagent for clinical diagnosis and epidemiological investigations.

Animals↗

PubMed1996

Enzyme-linked immunomagnetic electrochemical detection of Salmonella typhimurium.

There is a need for rapid methods to detect pathogenic bacteria in food products as alternatives to the current laborious and time-consuming culture procedures. We report a microbial detection technique that combines the selectivity of antibody-coated superparamagnetic beads with the rapidity and sensitivity of electrochemical detection in a format termed enzyme-linked immunomagnetic electrochemistry. In it, Salmonella typhimurium were sandwiched between antibody-coated magnetic beads and an enzyme-conjugated antibody. With the aid of a magnet, the beads (with or without bound bacteria) were localized onto the surface of disposable graphite ink electrodes in a multi-well plate format. Enzyme substrate was added and conversion of substrate to an electroactive product was measured using electrochemical detection. The electrochemical response was directly proportional to the number of captured bacteria. Using this technique, a minimum detectable level of 8 x 10(3) cells/ml of Salmonella typhimurium in buffer was achieved in ca. 80 min.

Electrochemistry↗

PubMed2000

[Report of questionnaire survey for methicillin-resistant Staphylococcus aureus and penicillin-resistant Streptococcus pneumoniae in the Kinki District].

An epidemiological investigation for methicillin-resistant Staphylococcus aureus (MRSA) and penicillin-resistant Streptococcus pneumoniae (PRSP) was performed at 22 medical institutes in Kinki area by the questionnaire from Kinki Infection Working Group in 1998. The isolation frequencies of MRSA and PRSP, including penicillin-intermediate resistant S. pneumoniae (PISP), were 61.5 and 45.8%, respectively. As compared to the previous data of MRSA in the Kinki area of 1997, the increase of MRSA was recognized. A single infection with MRSA was 49.5% and simultaneous pathogen detected with MRSA was Candida species. On the other hand, a single infection with PRSP including PISP, was 36.4% and simultaneous pathogen with PRSP was Haemophilus influenzae. Vancomycin, teicoplanin, ST and arbekacin showed good activity against MRSA. PRSP and PISP had low activity to ampicillin and erythromycin.

Humans↗

PubMed1995

A rapid method to determine bacterial contamination on hatching eggs. 3. Use of commercial DNA probe kits for detection of specific pathogens after six hours of incubation.

The usefulness of commercially available DNA probe kits for the detection of Escherichia coli and Salmonella spp. after only 6 h of incubation, was determined. It was established that the commercially available probe kits used could detect E. coli at initial levels of approximately 4.5 x 10(2) colony-forming units (cfu) per ml after only 6 h of incubation in nutrient broth (NB). Initial bacterial levels as low as 4.5 x 10(1) cfu/ml could be detected when the NB was incubated for 18 h. Salmonella Enteritidis, at initial levels of 2.86 x 10(2) cfu/ml could be detected after 6 h of incubation at 37 degrees C in NB, while initial levels as low as 2.86 x 10(-1) cfu/ml could be detected after 18 h at 37 degrees C in both NB and selected media, as specified by the manufacturers of the probe kits. Commercially available DNA probe kits can therefore be used to detect specific pathogens on the surface of hatching eggs and these probes can be used in conjunction with an egg-washing system, which is used to determine total bacterial contamination, although a longer incubation period greatly improves the sensitivity of these tests.

Animals↗

PubMed2004

Engagement of the pathogen survival response used by group A Streptococcus to avert destruction by innate host defense.

Neutrophils are a critical component of human innate host defense and efficiently kill the vast majority of invading microorganisms. However, bacterial pathogens such as group A Streptococcus (GAS) successfully avert destruction by neutrophils to cause human infections. Relatively little is known about how pathogens detect components of the innate immune system to respond and survive within the host. In this study, we show that inactivation of a two-component gene regulatory system designated Ihk-Irr significantly attenuates streptococcal virulence in mouse models of soft tissue infection and bacteremia. Microarray analysis of wild-type and irr-negative mutant (irr mutant) GAS strains revealed that Ihk-Irr influenced expression of 20% of all transcripts in the pathogen genome. Notably, at least 11 genes involved in cell wall synthesis, turnover, and/or modification were down-regulated in the irr mutant strain. Compared with the wild-type strain, significantly more of the irr mutant strain was killed by human neutrophil components that destroy bacteria by targeting the cell envelope (cell wall and/or membrane). Unexpectedly, expression of ihk and irr was dramatically increased in the wild-type strain exposed to these same neutrophil products under conditions that favored cell envelope damage. We report a GAS mechanism for detection of innate host defense that initiates the pathogen survival response, in which cell wall synthesis is critical. Importantly, our studies identify specific genes in the pathogen survival response as potential targets to control human infections.

Animals↗

PubMed1997

Impact of molecular biology on the detection of foodborne pathogens.

Molecular biological methods that use antibodies and nucleic acids to detect specific foodborne bacterial pathogens were scarcely known a decade and a half ago. Few scientists could have predicted that these tools of basic research would come to dominate the field of food diagnostics. Today, a large number of cleverly designed assay formats using these technologies are available commercially for the detection in foods of practically all major established pathogens and toxins, as well as of many emerging pathogens. These tests range from very simple antibody-bound latex agglutination assays to very sophisticated DNA amplification methods. Although molecular biological assays are more specific, sensitive, and faster than conventional (often cultural) microbiological methods, the complexities of food matrices continue to offer unique challenges that may preclude the direct application of these molecular biological methods. Consequently, a short cultural enrichment period is still required for food samples prior to analysis with these assays. The greater detection sensitivity of molecular biological methods may also affect existing microbiological specifications for foods; this undoubtedly will have repercussions on the regulatory agencies, food manufacturers, and also consumers.

Antibodies, Bacterial↗

PubMed1985

Cryptosporidium and diarrhoea in southern Indian children.

Cryptosporidium was detected more frequently in stool samples from southern Indian children with acute diarrhoea than from matched controls. It was seldom the only pathogen detected and was not associated with clearcut clinical features. The frequency of the protozoon in children under six months of age was higher in controls than in patients with acute diarrhoea. These features suggest that Cryptosporidium is unlikely to be a major cause of acute diarrhoea in this population. Frequency of Cryptosporidium was higher in children who had been given antibiotics and in those with prolonged episodes of diarrhoea. Administration of antibiotics may lead to conditions within the intestinal lumen that favour colonisation by the organism and prolongation of diarrhoeal episodes.

Acute Disease↗

PubMed2006

[RNA amplification from low numbers of bacteria in human blood to solve low sensitivity problem of conventional PCR amplification].

Blood culture from a febrile patient is often unsuccessful when a number of bacteria is lower than 10 CFU/ml in circulation. Theoretically, PCR amplification of bacteria in this low bacterial level in human blood is beyond the sensitivity of PCR method. RNA based Amplification (NASBA) method is more sensitive than PCR base assay because living bacteria carries several hundred to thousand RNA molecules in a cell. Increasing evidences also revealed another problem that human blood stream is often contaminated with bacterial genome. This often cause false positive results and bring difficulty of the interpretation to determine causative agent. Direct DNA amplification should be limited to severe causative agent such as Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitides, and etc. and also applied only for slow growing and fastidious pathogens such as mycoplasmae, chlamydiae, bartonellae, mycobacteria, and etc. Most cases blood culture should be carried out first and genetic amplification should be selected as a next step to detect pathogens from a blood culture bottle, because in these cases, patients are not in life threatening stages. These attempts also decrease the chance to detect circulating bacterial DNA fragment in blood stream.

Bacterial Infections↗

PubMedDate not supplied

Occurrence and significance of Cryptosporidium infection in Calcutta.

During a 2-year study, Cryptosporidium oocysts were detected in 32 (5.6%) of 566 hospitalized paediatric diarrhoea cases and 2 (1.2%) of 167 non-diarrhoeic individuals. Cryptosporidium was the sole pathogen detected in 17 (3.0%) of the 32 positive cases; in the other 15 it occurred in combination with one or more other established enteropathogen(s). The frequency of detection of the parasite was highest in the 0-6 months age group; no sex-specific difference was discernible. The detection rate of the parasite was highest during the monsoon and post-monsoon months. Most of the patients had watery stools with a mild to moderate degree of dehydration, with the diarrhoea lasting for less than 7 d.

Age Factors↗

PubMed2006

Dendritic cells in the recognition of intestinal microbiota.

Mucosal dendritic cells (DCs) constantly survey the luminal microenvironment which contains commensal microbiota and potentially harmful organisms regulating pathogen recognition and adaptive as well as innate defense activation. Distinct mechanisms are beginning to emerge by which intestinal antigen sampling and handling is achieved ensuring specificity and contributing to redundancy in pathogen detection. Distinct DC subsets are associated with these mechanisms and regulate specific innate or adaptive immune responses to help distinguish between commensal microbiota, pathogens and self antigens. Understanding DC biology in the mucosal immune system may contribute to the unraveling of infection routes of intestinal pathogens and may aid in developing novel vaccines and therapeutic strategies for the treatment of infectious and inflammatory diseases.

Animals↗

PubMed2005

[Role of gastro-esophageal reflux (GER) and swallowing latency in aspiration pulmonary diseases].

We evaluated the role of gastro-esophageal reflux (GER) in aspiration pulmonary disease. To explore swallowing function, we measured the latent time (LT) on the swallowing provocation test in patient with non-aspiration pneumonia (PN, n=5), aspiration pneumonia (AP, n=8), post-gastrectomy aspiration pneumonia (PGAP, n=8), gastro-esophageal reflux disease (GERD, n=12) and normal group (NR, n=7). LT was prolonged in the AP (2.83 +/- 1.66 sec p < 0.01), PGAP (2.58 +/- 1.40 sec p < 0.05) and GERD (2.40 +/- 1.70 sec p < 0.05) groups compared with NR (1.04 +/- 0.56 sec) group, but not prolonged in PN (1.46 +/- 0.75 sec) group. LT was also prolonged when swallowing was provoked during inspiration both in AP (3.61 +/- 2.60 sec vs. 2.73 +/- 2.19 sec, p < 0.05) and NR (2.13 -/+ 1.12 sec vs. 1.49 +/- 1.30 sec, p < 0.01). Protected specimen brushing (PSB) was employed to detect pathogenic organisms in the PN (n=70), AP (AP, n=27) and PGAP (n=15) groups. Gram-negative rods were most frequently detected in the PGAP (p=0.008) group. We conclude that GER plays an important role in aspiration pulmonary disease not only as a source of aspirating agent but also as a disturbing factor of swallowing function.

Adult↗

PubMed2005

[The pathogenicity of amoebae-resisting chlamydiales].

During the last 15 years, several new bacterial species related to Chlamydia have been discovered within amoebae. Their ability to grow within these professionnal phagocytes suggests that they are also resistant to destruction by other phagocytic cells such as alveolar macrophages and that they may be excellent candidates as new agents of pneumonia. There are growing evidence that these Chlamydia-like organisms play a role as etiological agent of lower respiratory tract infections. Thus, Parachlamydia is apparently an agent of inhalation pneumonia and--at least in the immunocompromised host--of community-acquired pneumonia, whereas Simkania is considered as a common agent of bronchiolitis and an emerging agent of pneumonia. Nevertheless, their pathogenic potential remains underestimated since these obligate intracellular bacteria grow only poorly or not at all on the culture media generally used to detect pathogen in diagnostic laboratories.

Amoeba↗

PubMed2005

Detection of human metapneumovirus RNA sequences in nasopharyngeal aspirates of young French children with acute bronchiolitis by real-time reverse transcriptase PCR and phylogenetic analysis.

Human metapneumovirus (HMPV) was the unique viral pathogen detected by a real-time reverse transcriptase PCR (RT-PCR) assay in 6 (6.4%) of 94 consecutive French children hospitalized for acute bronchiolitis from September 2001 to June 2002. This virus was identified as the third etiological cause of bronchiolitis, after respiratory syncytial virus and rhinovirus (35 [37%] and 21 [22%] of 94 cases, respectively). Phylogenetic analysis of F-gene sequences demonstrated the cocirculation of distinct HMPV genotypes during this study. These findings highlight the need to implement a rapid HMPV RT-PCR detection assay for the clinical diagnosis of respiratory infections in pediatric patients with bronchiolitis.

Acute Disease↗