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At least 163 records · Page 9Linked to original sources

PubMed1997

Molecular diagnosis of Ureaplasma urealyticum in an immunocompetent patient with destructive reactive polyarthritis.

Polymerase chain reaction (PCR) amplification, which is a useful method for detecting infectious agents in joints, has potential utility in the molecular diagnosis of venereal-associated arthritis. Among pathogens detected by this technique, Ureaplasma urealyticum, which is primarily associated with reactive arthritis (ReA), is also implicated in septic arthritis in immunocompromised patients. We report here a case of destructive polyarthritis, initially suggestive of septic arthritis, in an immunocompetent patient whose PCR positivity for U. urealyticum DNA in one joint, in conjunction with the disease outcome and histologic findings, led to the diagnosis of destructive ReA.

Adult↗

PubMed1987

Clinical relevance of culture versus screens for the detection of microbial pathogens in urine specimens.

The use of screens to detect "significant levels" of pathogenic microorganisms in urine specimens offers the advantages of both rapidly reporting results and controlling costs. Many of these screens, however, are insensitive at microbial counts below 10(5) colony-forming units (CFU)/ml of urine. It is increasingly apparent that patients with almost any type of urinary tract infection (except for most patients who are asymptomatic or who have pyelonephritis) may have urine concentrations of pathogens as low as 10(2) to 10(3) CFU/ml. This review documents factors that can contribute to diminished concentrations of microorganisms in urine, lists patient populations in whose urine microorganisms in concentrations well below 10(5) CFU/ml have been associated with infection, and makes recommendations for selection of laboratory tests, including rapid screens, for the diagnosis and management of urinary tract infections.

Age Factors↗

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↗

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↗

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↗

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↗

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↗

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↗

PubMed1987

Cryptosporidiosis in Ogun State, south-west Nigeria.

During the period of one month in the rainy season in Ogun State in south-west Nigeria 479 stool samples (420 of which were diarrhoea stool samples) were examined for cryptosporidiosis. Oocysts were detected in 2.3% of all stools, in 2.6% of diarrhoeal stools and in 5.3% out of 150 children with diarrhoea. Cryptosporidium was the sole pathogen detected in six of 11 cases. In addition to cryptosporidia also Entamoeba histolytica, Blastocystis hominis, Giardia lamblia, Ascaris lumbricoides, and Trichuris trichiura could be found. Compared to other studies in tropical countries, the frequency of infection was lower in south-west Nigeria.

Adult↗

PubMed2026

Mapping Wastewater Pathogens and Their Associated Environmental and Public Health Risk Factors: A Systematic Review and Meta-Analysis.

BACKGROUND: Wastewater-based epidemiology (WBE) has emerged as a critical tool for public health surveillance, yet its application across diverse pathogens and geographical settings remains inconsistent. This systematic review synthesizes global evidence on wastewater surveillance to identify associated risk factors. METHODS: Following PRISMA 2020 guidelines (PROSPERO: CRD420261297382), a systematic search was conducted across PubMed, Scopus, Google Scholar, and Web of Science for studies published between 2000 and 2025. RESULTS: Thirty-nine peer-reviewed studies were included. The evidence base is geographically skewed toward the European Region (48.7%) and the Americas (23.1%), with significant underrepresentation in LMICs. Viruses were the primary biological target (89.7%), followed by bacteria (7.7%) and parasites (2.6%). A proportion meta-analysis of 31 eligible studies demonstrated a pooled wastewater pathogen detection prevalence of 62% (95% CI: 47.5-74.6%), with the European Region yielding the highest regional estimate (73%) and the African Region the lowest (8.3%). Conventional PCR and sequencing methods showed higher pooled detection rates (92.4% and 90.1%, respectively) than RT-qPCR (47.9%). CONCLUSION: WBE provides a robust early-warning system indicating a need for broader pathogen diversity, incorporating bacterial and parasitic surveillance and expansion into rural and resource-limited regions.

Contamination↗

PubMed1987

[Infectious diarrhea in children. Results of a prospective study concerning various epidemiological and clinical aspects of infectious diarrhea in children].

Over a 3-year period (from October 1981 to September 1984) 352 pediatric patients were treated for infectious diarrhea at the Division for Pediatric Infectious Diseases, Department of Pediatrics, University of Berne, Switzerland. Routine diagnostic tests on stool samples included cultures for Salmonella, Shigella, Campylobacter and Yersinia, and enzyme-linked immunosorbent assay (Rotazyme) for rotaviruses. In selected cases special tests for parasitic pathogens were also performed. The patients were divided into three etiologic groups to compare epidemiological, clinical and laboratory characteristics; group 1 = rotavirus, group 2 = no detectable pathogen, and group 3 = bacterial agents. Specific etiology of diarrhea was established in 210 of the 352 patients (59.5%). Rotaviral gastroenteritis represented the most common diagnosis (42.5%), whereas Salmonella was isolated from fecal cultures in 9% and Campylobacter jejuni in 3%. A parasitic etiology was documented in only 1%. In 5 patients two pathogens were recovered from stools: rotavirus and Salmonella in 4 cases and Salmonella and Campylobacter in 1 case. Relevant features of rotavirus, Salmonella and Campylobacter gastroenteritis in childhood are described in detail.

Adolescent↗

PubMed2026

Invisible Threats, Relentless Hunters: Biosurveillance of Airborne Plant Pathogens.

Airborne dispersal enables plant pathogens to travel across fields, regions, and continents, fueling rapid epidemics and emerging disease threats. Biosurveillance, the systematic monitoring of airborne inoculum, offers the opportunity to detect pathogens before symptoms appear and informs timely, risk-based management. Recent advances in air sampling, molecular diagnostics, metagenomics, and imaging technologies have expanded the scale and resolution of pathogen monitoring, from single-species qPCR assays to community-level aerobiome surveys. Integration of biosurveillance data with decision-support systems, remote sensing, and artificial intelligence is transforming early-warning capabilities and providing novel insights into pathogen ecology, evolution, and fungicide resistance. Yet major challenges remain, including assay standardization, data interpretation, and translation into actionable tools for growers. This review synthesizes current approaches, highlights case studies in which biosurveillance has advanced disease management, and outlines future directions toward coordinated surveillance networks and precision agriculture applications.

Air Microbiology↗

PubMed1991

Immunological methods for detection of foodborne pathogens and their toxins.

Improved methods to detect microorganisms and their toxins introduced during the last decade involve among others recombinant DNA techniques and various immuno-assays such as the enzyme-linked immunosorbent assay and the latex agglutination. Immuno-assays are based on a quantitative reaction of an antigen (bacterial metabolite, e.g., toxin) with its antibody. Therefore, they are suited for detection of microorganisms based on their production of specific antigens and for quantitative detection of bacterial toxins. Sensitivity and specificity of immuno-assays are mainly determined by the antiserum used. In this respect the use of well selected monoclonal antibodies can be of advantage. With the enzyme-linked immunosorbent assay and latex agglutination test quantities of 0.1-1 ng of antigen/ml can be detected. Of both techniques the latex agglutination method has several advantages; the method is simple, inexpensive and rapid. Since each immuno-assay is sensitive to non-specific reactions, recognition of false positive results is necessary. The most appropriate method for this is to add an inhibitor to the test sample which blocks specifically the paratope of the immunoglobulin. Another general disadvantage of immuno-assays is that only the antigenicity is determined and this may differ from the actual toxicity. Therefore, antibodies should be used that react with the toxic centre(s) of the molecule, which can be accomplished by using well selected monoclonal antibodies.

Animals↗

PubMed2026

Computed tomography-guided precision biopsy combined with metagenomic next-generation sequencing for etiological diagnosis in patients with blood culture-negative systemic infections.

ObjectiveTo evaluate the diagnostic efficacy of computed tomography-guided percutaneous biopsy combined with metagenomic next-generation sequencing in patients with blood culture-negative systemic infections and to assess the clinical impact of using this combined strategy for etiological confirmation and guidance of targeted antimicrobial therapy.MethodsThis single-center retrospective observational cohort study enrolled 78 patients who met the Sepsis-3 consensus criteria for suspected systemic infection and had negative conventional microbiological work-ups (at least two sets of blood cultures) between April 2022 and March 2025. All patients underwent computed tomography-guided biopsy of radiologically identified infectious foci, with specimens processed concurrently for conventional culture and metagenomic next-generation sequencing. Diagnostic performance was benchmarked against the final comprehensive clinical diagnosis, and the influence of metagenomic next-generation sequencing findings on antimicrobial therapy modification was analyzed. Sample size calculation, based on a prior study estimating an metagenomic next-generation sequencing detection rate of 85% (α = 0.05, β = 0.2), indicated a minimum of 68 cases; accordingly, 78 patients were enrolled.ResultsComputed tomography-guided biopsy was technically successful in all 78 patients (100%). The pathogen detection rate of metagenomic next-generation sequencing (91.0%, 71/78) was significantly higher than that of conventional culture (55.1%, 43/78; p < 0.001). Using the final clinical diagnosis as the reference standard, metagenomic next-generation sequencing achieved a sensitivity of 94.7% (95% confidence interval: 86.9-98.5), specificity of 100.0% (95% confidence interval: 29.2-100.0), positive predictive value of 100.0% (95% confidence interval: 94.9-100.0), and negative predictive value of 42.9% (95% confidence interval: 9.9-81.6). Among the 35 culture-negative specimens, metagenomic next-generation sequencing established a definitive microbiological diagnosis in 28 cases (80.0%) and detected polymicrobial infections in 11 cases (14.1% of the cohort). Antimicrobial therapy was rationally adjusted based on metagenomic next-generation sequencing results in 69.2% (54/78) of the patients.ConclusionsThe integration of computed tomography-guided precision biopsy with metagenomic next-generation sequencing offers a highly effective diagnostic approach for blood culture-negative systemic infections. This synergistic strategy improves etiological diagnosis by providing high-yield target specimens that enable comprehensive, unbiased pathogen screening, facilitates differentiation between infectious and non-infectious etiologies, and supplies critical evidence for guiding precision antimicrobial therapy. These findings highlight the growing role of interventional radiology in the contemporary framework of precision infectious disease management.

Humans↗