PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Pathogen detection”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources
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↗
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↗
PubMed2001

Utility of paired BACTEC MYCO/F LYTIC blood culture vials for detection of bacteremia, mycobacteremia, and fungemia.

In previous bloodstream infection studies in Malawi, we inoculated blood from a single venesection into a single BACTEC MYCO/F LYTIC (MFL) vial. Inoculation of one vial, however, would be expected to reduce the sensitivity of bloodstream pathogen detection with MFL vials. To ascertain the degree of this loss of sensitivity, blood was drawn from each of 228 febrile, adult inpatients in Malawi and 5 ml of each blood sample was inoculated into each of two MFL vials. Of 228 paired vials, 51 (22%) were both positive, 172 (75%) were both negative, and 5 (3%) had discordant results. Bloodstream infection would have been detected in 11 (92%) of 12 patients with mycobacteremia and 38 (92%) of 41 patients with bacteremia had only one MFL vial been inoculated. Our study shows that a second MFL vial does not significantly increase diagnostic sensitivity.

Bacteremia↗
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↗
PubMed2000

[Evaluation of the usefulness of selected virulence markers for identification of virulent Yersinia enterocolitica strains. II. Genotypic markers associated with the pYV plasmid].

Pathogenic strains of Yersinia enterocolitica bear virulence associated plasmid pYV. Unfortunately plasmid pYV is easily lost by these bacteria incubated at elevated temperatures (37 degrees C) or long stored at room temperatures. This sometimes makes difficult the detection of the virulence plasmid, especially by its isolation or biochemical tests. On the other hand, observations done by some authors suggest that polymerase chain reaction (PCR) could be useful for demonstration of the pYV plasmid of Yersinia strains. Accordingly to this observation the aim of the presented study was to check the usefulness of plasmid-localised genes virF and yadA, detected by PCR, for the identification of the virulent strains of Y. enterocolitica. In the presented study one hundred and fifty two clinical strains of Y. enterocolitica belonging to serogroup O3 were investigated by the PCR for the presence of genes virF and yadA. Bacterial strains were first tested for the presence of pYV plasmid. In addition the phenotypic features: calcium dependence, Congo red binding and autoagglutination were determined. In this way the virulence plasmid was found in 130 of 152 examined strains. For PCR studies also forty plasmid-cured strains of Y. enterocolitica and 32 non-Y. enterocolitica, Enterobacteriaceae strains were included. The obtained results show that the tested genes were present only in Yersinia strains possessing the pYV plasmid and no one non-specific PCR product was observed. The detection level of these genes in nested PCR permits to detect pathogenic Y. enterocolitica in suspension composed of 1 x 10(3) CFU/ml of pYV+ bacilli and 3 x 10(9) CFU/ml plasmid-cured, isogenic bacteria. In the study it was shown that genes virF and yadA were useful virulence markers, which could be helpful in clinical studies for the detection of the virulence plasmid in Y. enterocolitica strains long stored or incubated at elevated temperatures.

Adhesins, Bacterial↗
PubMed1999

Use of polymerase chain reaction to detect Proteus mirabilis and Ureaplasma urealyticum in urinary calculi.

In this study, we evaluated the efficacy of the polymerase chain reaction (PCR) in detecting urea-splitting microorganisms in desiccated urinary tract infection stones. Seventy-eight urinary tract stones were tested for the presence of Proteus mirabilis and Ureaplasma urealyticum by means of PCR with species-specific primers. Twenty-seven stone samples were composed of struvite and/or carbonate apatite (infection stone); 40 were calcium oxalate and/or calcium phosphate; seven were mixed, with struvite/carbonate apatite and calcium oxalate; and four were uric acid stones. PCR was performed with DNA extracted from pulverized stone pieces. Initial assays using the pulverized stone specimens spiked with microorganisms showed that PCR could not detect U. urealyticum at densities below 10(3) color changing units (CCU), or P. mirabilis at densities below 10(4) colony-forming units (CFU). PCR was negative for U. urealyticum and P. mirabilis in all metabolic stones from patients. P. mirabilis was detected by PCR in 10 of 34 patients with infection stones. Preoperative urine cultures grew P. mirabilis in three of these 10 patients, and were negative for P. mirabilis in the other seven. U. urealyticum was detected by PCR in stone samples from four patients, two of which were also PCR-positive for P. mirabilis. All four of these patients had infection stones: two had residual stones, and the other two had recurrence of urinary stones after their operations. These results demonstrate that microorganisms in urinary stones can be detected by PCR even when the voided urine culture is negative. Investigations into the role of bacterial infection in stone formation will require further improvements in the sensitivity of PCR assays for pathogen detection.

Adult↗
PubMed1995

Genital tract infections in sexually active women in Barbados.

Ninety-eight women attending three different clinics were prospectively studied for the presence of genital tract infections, including Chlamydia trachomatis. Of these 98 women, 35 were presenting to a polyclinic with symptoms of genital tract infection, 55 were attending an antenatal clinic for their first visit, and 8 referred to a colposcopy clinic because of an abnormal Papanicolaou smear were included. Gonorrhoea was detected in one patient, syphilis in two, and Trichomonas vaginalis in six. Candida albicans and Chlamydia trachomatis were each detected in 18 patients, while the most common condition was bacterial vaginosis, detected in 35 patients. The prevalence of these infections was lowest in patients referred for colposcopy and highest in the women attending the antenatal clinic. Chlamydia trachomatis was the most common sexually-transmitted pathogen detected in this population. These data emphasise the need for an aggressive approach to the diagnosis and treatment of chlamydial infection in females.

Adolescent↗
PubMed2001

Monitoring of microbial hazards at farms, slaughterhouses, and processing lines of swine in Korea.

This study was executed to investigate microbiological hazards at swine farms, slaughterhouses, dressing operations, and local markets for the application of the hazard analysis critical control point system in Korea by analyzing total aerobic plate count (APC) and presence of pathogens. Six integrated pig farms and meat packers were selected from six different provinces, and samples were collected from pig carcasses by swabbing and excision methods at the slaughterhouses, processing rooms, and local markets, respectively. APCs of water in water tanks were relatively low, 1.9 to 3.1 log10 CFU/ml; however, they were increased to 4.6 to 6.9 log10 CFU/ml when sampled from water nipples in the pigpen. APCs of feeds in the feed bins and in the pigpens were 4.4 to 5.4 and 5.2 to 6.7 log10 CFU/g, respectively. Salmonella spp., Staphylococcus aureus, and Clostridium perfringens were detected from water and feed sampled in pigpens and pigpen floors. S. aureus was the most frequently detected pathogenic bacteria in slaughterhouses and processing rooms. Listeria monocytogenes and Yersinia enterocolitica were also detected from the processing rooms of the Kyonggi, Kyongsang, and Cheju provinces. Even though APCs were maintained at the low level of 3.0 log10 CFU/g during slaughtering and processing steps, those of final pork products produced by the same companies showed relatively high numbers when purchased from the local market. These results indicated that the cold chain system for transporting and merchandising of pork products was deficient in Korea. Water supply and feed bins in swine farms and individual operations can be identified as critical control points to reduce microbiological hazards in swine farms, slaughterhouses, and processing plants.

Abattoirs↗