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At least 397 records · Page 22Linked to original sources
PubMed2003

Confirmation of viable E. coli O157:H7 by enrichment and PCR after rapid biosensor detection.

Many rapid tests have been developed for the detection of Escherichia coli O157:H7 from complex matrices such as food and water. However, many of these methods rely on traditional culture steps for confirmation, which can take an extra 24-48 h. The fiber optic biosensor has been used to rapidly detect pathogens from complex matrices. In this paper, we demonstrate a method using a rapid biosensor assay, recovery through a short enrichment, and PCR to detect and confirm the presence of at least 10(3) CFU/ml of E. coli O157:H7 in a sample in less than 10 h.

Biosensing Techniques↗
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↗
PubMed2006

Direct screening of clinical specimens for multiple respiratory pathogens using the Genaco Respiratory Panels 1 and 2.

We report here on the results of a pilot study comparing our clinical diagnostic virology laboratory's current methods of respiratory pathogen detection against the Genaco Respiratory Infections Panels 1 and 2. These assays employ xMap (Luminex) liquid phase bead conjugated array technology to facilitate automated detection of PCR and RT-PCR products, which provides potential for levels of assay multiplexing above those currently practical with either conventional gel-resolved or real-time methods. In the study presented here we used the Genaco panels to simultaneously screen previously analyzed clinical specimens (nasopharyngeal washings) for twenty-one important pathogens. Our results indicate the Genaco panels met or exceeded our current methods' sensitivity and specificity although allowing for detection of a wider range of infectious agents than practical by current diagnostic laboratory practices. In addition, the Genaco panels provided data on the presence of multiple respiratory pathogens in single specimens, which would otherwise be missed in most instances. To our knowledge, this study represents the first trial of these panels on standard clinical specimens in a routine diagnostic setting.

Bacteria↗
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↗
PubMed2000

A multiplex approach to molecular detection of Brucella abortus and/or Mycobacterium bovis infection in cattle.

A multiplex amplification and detection platform for the diagnosis of Mycobacterium bovis and Brucella abortus infection simultaneously in bovine milk and nasal secretions was developed. This system (designated the bovine pathogen detection assay [BPDA]-PCR) consists of duplex amplification of species-specific targets (a region of the BCSP31K gene of B. abortus and a repeat-sequence region in the hsp65 gene of M. bovis, respectively). This is followed by a solid-phase probe capture hybridization of amplicons for detection. On the basis of spiking experiments with normal milk, the analytical sensitivity of the assay was 800 CFU equivalents/ml of milk for B. abortus and as low as 4 CFU equivalents per ml of milk for M. bovis. BPDA-PCR was validated with 45 liver samples from lemmings experimentally infected with B. abortus. The assay sensitivity, based on culture status as a "gold standard," was 93.9%. In this experiment, BPDA-PCR also identified five culture-negative liver samples as positive (41.7%). Field studies for the evaluation of BPDA-PCR were performed with samples from dairy animals from geographically distinct regions (India, Mexico, and Argentina). A high prevalence of shedding of B. abortus (samples from India) and M. bovis (samples from Mexico) was identified by BPDA-PCR. In samples from India, B. abortus shedding was identified in 86% of milk ring test-positive animals (n = 15) and 80% of milk ring test-negative cows (n = 5). In samples from Mexico, M. bovis was identified by PCR in 32.6% of pools (n = 46) of milk that each contained milk from 10 animals and in 56.2% of nasal swabs (n = 121) from cattle from tuberculin test-positive herds. In contrast, the Argentine cattle (n = 70) had a modest prevalence of M. bovis shedding in nasal swabs (2.9%) and milk (1.4%) and of B. abortus in milk (11.4%). On the basis of these analyses, we identify BPDA-PCR as an optimal tool for both screening of herds and testing of individual animals in a disease eradication program. A combination of the duplex assay, screening of milk samples in pools, and the proposed algorithm provides a highly sensitive, cost-effective, and economically viable alternative to serological testing.

Animals↗
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↗
PubMed2000

[Identification of bacterial strain at each episode of recurrent acute otitis media].

This study was undertaken to investigate whether each episode of recurrent acute otitis media (rAOM) is caused by the same strain of bacteria or different strains at each episode. Seventy infants less than 3-years of age, having experienced rAOM for a period shorter than 8 weeks, were selected and included in the present study. The total number of AOM episodes experienced by this group was 282. At each subsequent episode of AOM, otorrhea and nasopharyngeal swabs were taken for bacterial culture and determination of the MIC for antibiotics. When S. pneumoniae was identified, its serotype, and its pbp, ermAM, and mefE genes were also investigated to determine the bacterial species and strains. S. pneumoniae was the most frequently cultured bacteria with 26 penicillin-sensitive S. pneumoniae (PSSP), 65 penicillin-insensitive S. pneumoniae (PISP), and 50 penicillin-resistant S. pneumoniae (PRSP). H. influenzae was the next most frequently cultured bacteria of which 65 were sensitive to penicillin, 27 were found to be beta-bactamase-negative-ampicillin-resistant (BLNAR) and 17 were found to be beta-bactamase positive. Bacteria cultured from each pair of two successive episodes of AOM were compared as to the identity of the bacteria during the two episodes. In 150 out of 202 pairs (74%), the cultured pathogen was different. In 22 cases in which either PISP or PRSP was the pathogen detected in two consecutive AOM episodes, 15 cases (68%) were found in which the involved strain differed between the two episodes. This study indicates that the pathogen involved in rAOM is likely to differ at each episode of AOM, not only in cases caused by PSSP, but also in those caused by PRSP.

Acute Disease↗
PubMed2003

Demonstration of labeless detection of food pathogens using electrochemical redox probe and screen printed gold electrodes.

The demonstration of a labeless immunosensor for the detection of pathogenic bacteria using screen printed gold electrodes (SPGEs) and a potassium hexacyanoferrate(II) redox probe is reported. Gold electrodes were produced using screen printing and the gold surfaces were modified by a thiol based self assembled monolayer (SAM) to facilitate antibody immobilisation. SAMs based on the use of thioctic acid (TA), mercaptopropionic acid (MPA) and mercaptoundecanoic acid (MUA) were evaluated. Following antibody immobilisation via the optimum SAM, the redox behaviour and diffusion co-efficient (D) of the potassium hexacyanoferrate(II) probe was monitored in the absence and presence of analyte. In the presence of analyte, a change in the apparent diffusion co-efficient of the redox probe was observed, attributable to impedance of the diffusion of redox electrons to the electrode surface due to the formation of the antibody-bacteria immunocomplex. No change in the diffusion co-efficient was observed when a non-specific antibody (mouse IgG) was immobilised and antigen added. The system has been demonstrated with Listeria monocytogenes and Bacillus cereus.

Antibodies, Bacterial↗
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% (&#x3b1;&#x2009;=&#x2009;0.05, &#x3b2;&#x2009;=&#x2009;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&#x2009;<&#x2009;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↗
PubMed2006

Development of a rapid real-time PCR assay for detection and quantification of four familiar species of Chlamydiaceae.

Chlamydiae are one of the causative agents of various diseases in animals and human beings, which include abortion, pneumonia, gastroenteritis, encephalomyelitis, conjunctivitis, arthritis and sexually transmitted diseases. Much work has been carried out to attempt to develop an efficient pathogen detection strategy. Here, we presented a Chlamydiaceae-specific 23S rRNA-based real-time PCR assay for simultaneous detection and quantification of four members of Chlamydiaceae family, C. trachomatis, C. psittaci, C. pneumoniae and C. pecorum, using SYBR Green and Lightcycler. The assay was characterized using plasmid constructs of the bacteria and verified on standard strains of all four species of the Chlamydiaceae and a large cohort of clinical samples collected from human and animals by comparison with fluorescence immunohistochemistry method. The results showed that the present real-time PCR assay was of high specificity and sensitivity. It was capable of detecting as few as 250fg of chlamydial DNA (equivalent to 10(-1)IFU) and was applicable to both liquid cultures and clinical samples. This assay may therefore offer a rapid, economic and reliable means for screening of the chlamydiaceae pathogens.

Animals↗
PubMed2004

A new approach to apple proliferation detection: a highly sensitive real-time PCR assay.

The present paper describes a new approach for diagnosis of apple proliferation (AP) phytoplasma in plant material using a multiplex real-time PCR assay simultaneously amplifying a fragment of the pathogen 16S rRNA gene and the host, Malus domestica, chloroplast gene coding for tRNA leucine. For the first time, such an approach, with an internal analytical control, is described in a diagnostic procedure for plant pathogenic phytoplasmas enabling distinction between uninfected plant material and false-negative results caused by PCR inhibition. Pathogen detection is based on the highly conserved 16S rRNA gene to ensure amplification of different AP phytoplasma strains. The newly designed primer/probe set allows specific detection of all examined AP strains, without amplifying other fruit tree phytoplasmas or more distantly related phytoplasma strains. Apart from its specificity, real-time PCR with serial dilutions of initial template DNA ranging over almost five orders of magnitude (undiluted to 80,000-fold diluted) demonstrated linear amplification over the whole range, while conventional PCR showed a reliable detection only up to 500-fold or 10,000-fold dilutions, respectively. Compared to existing analytical diagnostic procedures for phytoplasmas, a rapid, highly specific and highly sensitive diagnostic method becomes now available.

DNA, Bacterial↗
PubMed2005

[Detection and quantification of nucleic acids in infections diseases: utility and limitations].

The amplification of nucleic acids is often used for the diagnosis and the follow-up of infectious diseases. The interpretation of PCR results varies according to the pathogens detected, the site of infection and the clinical presentation. PCR tests might be the reference method or only an help for the diagnosis. With the development of antiviral treatments quantitative PCR tests are now essential for the evaluation of treatment efficacy. A discussion with the laboratory is important for the correct interpretation of PCR results.

Communicable Diseases↗
PubMed1995

Using oligonucleotide probe arrays to access genetic diversity.

As the Human Genome Project and related efforts identify and determine the DNA sequences of human genes, it is important that highly reliable and efficient mechanisms are found to access individual genetic variation. It is only through a greater understanding of genetic diversity that the true benefit of the Human Genome Project will be realized. One approach, hybridization to high-density arrays of oligonucleotides, is a fast and effective means of accessing this genetic variation. Light-directed chemical synthesis has been used to generate miniaturized, high-density arrays of oligonucleotide probes. Application-specific oligonucleotide probe array designs have been developed for the rapid screening of characterized genes. Dedicated instrumentation and software have been developed for array hybridization, fluorescence detection and data acquisition and analysis. In a specific and challenging application, oligonucleotide probe arrays have been used to screen the reverse transcriptase and protease genes of the highly polymorphic HIV-1 genome to explore genetic diversity and detect mutations conferring resistance to antiviral drugs. Results from this application strongly suggest that oligonucleotide probe arrays will be a powerful tool for rapid investigations in sequence checking, pathogen detection, expression monitoring and DNA molecular recognition.

Base Sequence↗
PubMed1999

Use of the clinical microbiology laboratory for the diagnosis and management of infectious diseases related to the oral cavity.

Our knowledge regarding the pathogenesis of infections relative to the oral cavity is rapidly expanding, similar to our overall understanding of how infectious diseases impact our daily lives. The complexity of the flora within the oral cavity is quite unique and often makes diagnosis difficult; however, it is becoming more apparent that accurate diagnostic testing is important from the standpoint of focusing appropriate therapy on pathogens within this crucial body site, and avoiding overuse of antimicrobial agents in settings of infection where they have no demonstrated benefit. New diagnostic methods are being developed to detect pathogens and rapidly delineate resistance patterns. Many will be based on new genetic assays, but they must be cost effective, sensitive, and specific. Another growing challenge is to provide adequate lab support to outpatient offices and clinics, without compromising the specimen culture or turnaround times. So many patients are being seen away from hospital laboratories that we need ways to diagnose sinusitis, pharyngitis, abscess, and other infections of the oral cavity without killing the anaerobes and other significant facultative bacteria, and without ruining the direct stains by overgrowth or inflammatory cell degradation during specimen transport. These results need to be available quickly enough to give useful information for office diagnosis in order to effect therapy. To optimize both diagnosis and treatment, a key to the future will be better communication between the clinical practitioner and laboratory, with an increasing emphasis on training expertise in medical microbiology and infectious diseases.

Abscess↗
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↗