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Results for “Pathogen detection”

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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↗

PubMed1987

Cryptosporidiosis in well-nourished and malnourished children.

During a 5-month period, 513 stool samples submitted to the enteric laboratory at the University Hospital of the West Indies were examined for Cryptosporidium. Oocysts were detected in 4.9% of all stools, 7.3% of diarrhoeal stools, 19.5% of stools from malnourished children and 23.7% of stools from malnourished children with diarrhoea. Cryptosporidium was the sole pathogen detected in all 25 positive stools, and was the second most frequent enteric isolate. All cases of cryptosporidiosis occurred in children less than 2.5 years of age. All 15 malnourished children were admitted to hospital where they presented with dehydration (87%), vomiting (93%), fever (100%) and diarrhoea which lasted an average of 15.3 days. Two of these children died. In contrast, dehydration (20%), vomiting (40%) and fever (50%) were less common and diarrhoea less protracted in well-nourished children, four of whom were admitted to hospital. This preliminary report suggests that cryptosporidial gastroenteritis presents with increased frequency and severity in malnourished compared with well-nourished Jamaican children.

Child, Preschool↗

PubMed2024

Beyond water and soil: Air emerges as a major reservoir of human pathogens.

Assessing the risk of human pathogens in the environment is crucial for controlling the spread of diseases and safeguarding human health. However, conducting a thorough assessment of low-abundance pathogens in highly complex environmental microbial communities remains challenging. This study compiled a comprehensive catalog of 247 human-pathogenic bacterial taxa from global biosafety agencies and identified more than 78 million genome-specific markers (GSMs) from their 17,470 sequenced genomes. Subsequently, we analyzed these pathogens' types, abundance, and diversity within 474 shotgun metagenomic sequences obtained from diverse environmental sources. The results revealed that among the four habitats studied (air, water, soil, and sediment), the detection rate, diversity, and abundance of detectable pathogens in the air all exceeded those in the other three habitats. Air, sediment, and water environments exhibited identical dominant taxa, indicating that these human pathogens may have unique environmental vectors for their transmission or survival. Furthermore, we observed the impact of human activities on the environmental risk posed by these pathogens, where greater amounts of human activities significantly increased the abundance of human pathogenic bacteria, especially in water and air. These findings have remarkable implications for the environmental risk assessment of human pathogens, providing valuable insights into their presence and distribution across different habitats.

Humans↗

PubMed2026

The Next Step: The Role of Metagenomic Next-Generation Sequencing in Microbial Detection of Culture-Negative Cardiovascular Infections.

Cardiovascular infections, including those that involve native and prosthetic heart valves, implantable cardiac devices, mechanical circulatory assist devices, and vascular grafts, are associated with significant morbidity and mortality risks. Optimal management of these complex infections requires pathogen-directed antimicrobial therapy. However, standard culture-based methods often fail to identify causative organisms due to prior antimicrobial use, infections due to fastidious organisms, or biofilm-associated infections. Emerging evidence suggests that microbial cell-free DNA (mcfDNA) and metagenomic testing can enhance pathogen detection, particularly in culture-negative cases. However, their results require careful clinical interpretation, often necessitating input from infectious diseases specialists. In this review, we examine published evidence regarding metagenomic testing for cardiovascular infections and its impact on patient care. We propose a framework for microbiological adjudication of mcfDNA results, introduce standardized definitions for clinical impact assessment, and provide guidance on integrating mcfDNA testing into diagnostic evaluation of patients with culture-negative cardiovascular infections.

Humans↗

PubMed1989

Diagnostic studies of nosocomial diarrhea in children: assessing their use and value.

During a 17-month period (01/11/85-05/31/86) 225 cases of nosocomial diarrhea were identified in a children's hospital. Diarrhea was considered to be nosocomial if it began at least 72 hours after the patient's hospital admission or within 3 days after discharge. One or more routine diagnostic studies for identification of a pathogen were performed in 195 (87%) cases. The most commonly performed test was the bacterial stool culture. None of these samples yielded a bacterial pathogen. The only pathogens detected by routine laboratory studies were rotavirus (61/137 [45%] samples were positive for rotavirus by ELISA) and Clostridium difficile (9/54 [17%] positive for toxin). Of the patients whose tests were positive for rotavirus 56 were younger than 2 years of age, and all were identified in the winter and spring. When multiple stool samples were tested by the diagnostic laboratory, rotavirus was identified in an additional 14 patients whose initial stool samples were negative for rotavirus. All patients whose tests were positive for C. difficile toxin had received antibiotics within the previous 3 months. Ova/parasites were not detected in 53 of the tested stools. We also identified enteric adenovirus in six patients. Viruses were identified in 95 (42%) of the 225 cases of nosocomial gastroenteritis. Nosocomial diarrhea is common in a children's hospital. Rotavirus is the most commonly identified pathogen. Rotavirus testing is valuable in children with nosocomial diarrhea who are younger than 2 years of age, especially in the winter and spring. Multiple samples may be necessary to identify rotavirus. C. difficile toxin assay should be considered for patients who are receiving or who have received antibiotics.(ABSTRACT TRUNCATED AT 250 WORDS)

Cross Infection↗

PubMed2025

Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics.

Widespread interest in the development of population-wide pathogen and antimicrobial resistance (AMR) monitoring has revealed wastewater's microbial footprint as a marker of public health. Near-source wastewater remains a difficult sample type for microbiome analyses but represents a closer link to human health than the downstream products of its treatment. Few studies integrate methods for non-targeted monitoring applications, and critically, current methods cannot connect AMR genes to species, nor resolve full genomes. We address these challenges by developing a pipeline that enables untargeted metagenomics, metatranscriptomics, and novel long-read metagenomics (LRG). We achieve untargeted pathogen detection, limited by highly abundant resident species, while retaining microbial information with near-source sampling. Furthermore, LRG identifies antibiotic resistance gene-containing microbes and enables assembly of culture-independent genomes with previously unreported AMR genes. We establish an integrated approach to broadly monitor pathogens in wastewater, while demonstrating the importance of LRG to illuminate microbial AMR at the species level.

Journal Article↗

PubMed1988

[The place of 67Ga scintigraphy in the primary diagnosis and follow-up evaluation of opportunistic pneumonia in patients with AIDS].

Opportunistic pneumonias are a life-threatening complication in patients with AIDS. Early diagnosis and therapy is necessary to improve prognosis. This study was designed to assess the value of 67Ga scintigraphy in the primary detection and follow-up of these special pneumonias. 67Ga scintigraphy was performed in 40 patients: 10 normal controls and 30 HIV-positive patients with AIDS or AIDS-related complex (ARC). 67Ga scan results were compared with current chest radiographs and the results of pathogen detection. The evaluation of positive scans was based on a quantification of the pulmonary uptake, expressed as a pulmonary/soft-tissue uptake ratio. Only 8/30 patients had a normal scan, 22/30 showed diffuse (13/22) or focal (9/22) increases of pulmonary uptake. In 7/8 patients with normal scans the chest radiograph was negative as well. The one patient with negative scan but positive chest radiograph had pulmonary Kaposi's sarcoma. In 11/22 patients the 67Ga scan and chest radiograph were positive simultaneously. In the other 11/22 patients with positive scans chest radiographs were initially negative but showed pathology in 5 cases within 1-2 weeks. The reason for positive scans in most cases was an opportunistic lung infection; other forms of pneumonia were only observed in two cases. The defined uptake ratio demonstrated to be a highly sensitive parameter for monitoring pneumonia and the effects of therapy in follow-up studies. In conclusion, quantitative 67Ga scintigraphy proved to be a reliable and highly sensitive method for primary detection and follow-up of opportunistic pneumonias in patients with AIDS.

Acquired Immunodeficiency Syndrome↗

PubMed1990

Value of 67gallium scintigraphy in primary diagnosis and follow-up of opportunistic pneumonia in patients with AIDS.

Opportunistic pneumonias are a life-threatening complication in patients with AIDS. Early diagnosis and therapy is necessary to improve the prognosis. This study was designed to assess the value of 67gallium scintigraphy in the primary detection and follow-up of these special pneumonias. 67Gallium scintigraphy was performed in 40 patients: 10 normal controls and 30 HIV-positive patients with AIDS or AIDS-related complex (ARC). 67Gallium scan results were compared with current chest x-rays and the results of pathogen detection. The evaluation of positive scans was based on a quantification of the pulmonary uptake, expressed as a pulmonary/soft tissue uptake ratio. Only 8 of 30 patients had a normal scan, while 22 of 30 showed diffuse (13/22) or focal (9/22) increases of pulmonary uptake. In seven of eight patients with normal scans the chest radiograph was negative as well. The one patient with negative scan but positive chest radiograph had pulmonary Kaposi's sarcoma. In 11 of 22 patients, the 67gallium scan and chest x-ray were positive simultaneously. In the other 11 of 22 patients with positive scans, chest radiographs were initially negative but showed pathology in five cases within 1-2 weeks. The reason for positive scans in most cases was an opportunistic lung infection; other forms of pneumonia were observed only in two cases. The defined uptake ratio was demonstrated to be a highly sensitive parameter for monitoring pneumonia and the effects of therapy in follow-up studies. In conclusion, quantitative 67gallium scintigraphy proved to be a reliable and highly sensitive method for primary detection and follow-up of opportunistic pneumonias in patients with AIDS.

AIDS-Related Complex↗

PubMed1989

Direct and sensitive detection of a pathogenic protozoan, Toxoplasma gondii, by polymerase chain reaction.

We applied the polymerase chain reaction to detection of the pathogenic protozoan Toxoplasma gondii based on our identification of a 35-fold-repetitive gene (the B1 gene) as a target. Using this procedure, we were able to amplify and detect the DNA of a single organism directly from a crude cell lysate. This level of sensitivity also allowed us to detect the B1 gene from purified DNA samples containing as few as 10 parasites in the presence of 100,000 human leukocytes. This is representative of the maximal cellular infiltration (10(5)/ml) in 1 ml of cerebrospinal fluid obtained from patients with toxoplasmic encephalitis. The B1 gene is present and conserved in all six T. gondii strains tested to date, including two isolates from patients with acquired immunodeficiency syndrome. No signal was detected by using this assay and DNAs from a variety of other organisms, including several which might be found in the central nervous system of an immunocompromised host. This combination of sensitivity and specificity should make detection of the B1 gene based on polymerase chain reaction amplification a very useful method for diagnosis of toxoplasmosis both in immunocompromised hosts and in congenitally infected fetuses.

Animals↗

PubMed1990

Clinical and parasitologic aspects of cryptosporidiosis in nonhuman primates.

Eighty-one cases of acute cryptosporidiosis were diagnosed among 157 (52%) infant primates, predominantly Macaca nemestrina, housed in the nursery unit of the Washington Regional Primate Research Center. The mean age at onset of oocyst passage was 38 +/- 25 days. The outbreak was confined to the nursery and no cases were detected among juvenile or adult primates housed in other rooms within the colony. All but one animal manifested symptoms of enteric infection, including severe diarrhea and dehydration. Infected animals excreted oocysts for a mean of 36 days (range 7-78 days). No reinfections occurred. Cryptosporidium was the second most common enteric pathogen detected in the population, after Campylobacter jejuni. The risk of infection was related to the length of time the animal was housed in the nursery and to social interaction with other monkeys. These findings are relevant to the understanding of the epidemiology of cryptosporidiosis among human infants and children in environments with close social interactions and minimal learned personal hygiene practices.

Animals↗

PubMed1992

Reverse transcription and polymerase chain reaction amplification of rRNA for detection of Helicobacter species.

Sequence data on Helicobacter pylori 16S rRNA were used to select two 22-base oligonucleotide primers for use in a polymerase chain reaction (PCR) for detection of H. pylori. H. pylori cells were treated with lysis buffer, boiled, and chloroform extracted. Reverse transcription of rRNA was followed by PCR amplification (RT-PCR) of the synthesized cDNA and 16S rRNA gene. The amplified PCR products were analyzed by agarose gel electrophoresis and Southern blotting. Using ethidium bromide-stained agarose gels, we were able to detect the expected 500-bp DNA fragment from as few as two H. pylori organisms per reaction. The specificity of the RT-PCR assay was tested with 27 clinical isolates and related reference strains; although the number of bacterial cells used per reaction was 10(5)-fold greater than the number of H. pylori organisms used, amplification was detected only with bacteria in the same genus, H. cinaedi and H. mustelae. Ten H. pylori organisms per biopsy specimen were detected on agarose gels when organisms were added to samples prepared from a processed colon biopsy sample. RT-PCR results were consistent with urea breath test and culture results in 14 of 15 gastric biopsy specimens; the specificity was 100%. RT-PCR of rRNA from H. pylori increased the sensitivity of pathogen detection at least 25- to 50-fold compared with that of previous PCR assays. This low level of detection by RT-PCR assay may prove to be well suited for verifying eradication following therapy.

Base Sequence↗