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PubMed1984

Pathogens detected in the faeces of children with diarrhoea in a Sydney hospital.

During a 54-week period, faecal samples taken from 350 children under 5 years of age, who were admitted with acute diarrhoea to the infectious diseases ward of a Sydney hospital, were examined for pathogens. Rotavirus was detected as the sole agent in the specimens of 58 patients (16.6%), enteroviruses in those of 26 patients (7.4%), salmonellae in those of 19 patients (5.4%) and Campylobacter jejuni in those of 15 patients (4.3%). Shigellae were not detected. The results are discussed and, in view of the changing patterns of infection, it is suggested that there is a continuing need for research into the causes of enteritis in Australia.

Australia↗
PubMed1994

[The use of PCR for detecting pathogenic microorganisms in water].

This replication method, which was introduced in 1985, has been used to find and identify microorganisms in the environment, among others in samples of soil, sediments and waters. A gene or a DNA fragment specific to a microorganism is replicated in vitro by a chain reaction catalyzed by DNA polymerase (PCR: Polymerase Chain Reaction) and analyzed by electrophoretic procedures. At the moment in most legislations bacteriological criteria for drinking water depend on E. coli and other bacteria referring to fecal contamination (fecal coliforms and enterococci). Absence of these bacteria does not necessarily exclude contamination of water with protozoa or virus. Detection of the latter by common methods is difficult and time-consuming. Application of PCR to these purposes is interesting. During the last years several protocols have been developed such as methods for the detection of E. coli, bacteria referring to fecal contamination, pathogens like Legionella pneumophila as well as Salmonella and Shigella, enterovirus and protozoa i.e. Giardia. Compared to the traditional methods an obvious advantage of the new methods lies in their velocity, sensitivity and specificity. This review introduces to several different applications of PCR. Although this method is still restricted to specialized laboratories at the moment, it will gain importance as a complement to traditional methods for the detection of pathogenic microorganisms in water as soon as simple tests will be available.

Animals↗
PubMed2000

Adding injury to insult: pathogen detection and responses.

Genomic approaches to the study of the expression of plant genes induced in response to disease and attack are now showing that there is an intimate association between pathogen perception and general stress detection.

Gene Expression Regulation, Plant↗
PubMed2005

Empyema: the use of broad range 16S rDNA PCR for pathogen detection.

BACKGROUND: An increase in the incidence of thoracic empyema in children has been reported. The causative pathogen is often unknown as pleural fluid is frequently sterile at the time of culture. The role of unusual organisms is unclear. AIMS: (1) To compare the detection of organisms in pleural fluid from children with empyema using a molecular technique (16S rDNA polymerase chain reaction (PCR)) and bacterial culture. (2) To compare the concordance of organisms identified using the two techniques and the influence of prior antibiotic treatment on positive detection rate. METHODS: Pleural fluid from children admitted with empyema between January 2000 and February 2002 was cultured and additionally analysed using broad range 16S rDNA PCR. RESULTS: Pleural fluid was cultured from 32 patients, aged 1 month-16 years. Median duration of previous antibiotic therapy was 8 days (range 1-42 days). Six samples were culture positive and 22 were PCR positive. A causal organism was detected by PCR alone, after considering results from the local hospital, in 14 patients. There was complete concordance in organisms cultured and detected by PCR. Additional organisms detected by PCR were predominantly S pneumoniae, S pyogenes, and anaerobes. CONCLUSIONS: Analysis of pleural fluid by broad range 16S rDNA PCR in addition to culture, increases organism identification in empyema.

Adolescent↗
PubMed1998

Rapid pathogen detection using a microchip PCR array instrument.

An array of PCR microchips for rapid, parallel testing of samples for pathogenic microbes is described. The instrument, called the Advanced Nucleic Acid Analyzer (ANAA), utilizes 10 silicon reaction chambers with thin-film resistive heaters and solid-state optics. Features of the system include efficient heating and real-time monitoring, low power requirements for battery operation, and no moving parts for reliability and ruggedness. We analyzed cultures of Erwinia herbicola vegetative cells, Bacillus subtilis spores, and MS2 virions, which simulated pathogenic microbes such as Yersinia pestis, Bacillus anthracis spores, and Venezuelan equine encephalitis, respectively. Detection of microbes was achieved in as little as 16 min with detection limits of 10(5)-10(7) organisms/L (10(2)-10(4) organisms/mL).

Bacillus subtilis↗
PubMed1995

How many stool examinations are necessary to detect pathogenic intestinal protozoa?

Recent reports have suggested that examination of one stool specimen is sufficient to detect protozoa in symptomatic patients. To verify this hypothesis, we examined specimens submitted to the regional laboratory of a large, prepaid health plan that provides primary care to a membership representative of the general population in northern California. We examined the number and results of stool specimen examinations in the two-month period before detection of Entamoeba histolytica in 125 infected persons, of Giardia lamblia in 154 infected persons, and of Dientamoeba fragilis in 60 persons infected with this parasite. About 13% of the entire group had a single stool specimen examined, 19% had two examined, 65% had three examined, and 6% had more than three examined. Most infections were detected in the first specimen or specimens submitted, but many were not detected until later examination. Thirteen patients with E. histolytica (10.4%) required 4-9 examinations. The sensitivity of one examination was compared with that of three examinations; with the additional examinations, the yield increased 22.7% (95% confidence interval [CI] = 11.8-33.5%) for E. histolytica, 11.3% (95% CI = 6.9-81.8%) for G. lamblia, and 31.1% (95% CI = 17.7-54.4%) for D. fragilis. Our results suggest that a single stool specimen examination will miss many pathogenic protozoan infections in symptomatic persons.

Animals↗
PubMed2025

nf-UnO pipeline: A metagenomic co-assembly pipeline for novel pathogen detection from mNGS outbreak sets.

SUMMARY: nf-UnO is a pipeline implemented in Nextflow to identify novel pathogens from metagenomic shotgun sequencing of epidemiologically related foodborne outbreak specimens. nf-UnO uses MIDAS2, metagenomic co-assembly, multiple binning programs, and read mapping to metagenomically assembled genomes to detect potential etiological agents found in common across outbreak specimens. AVAILABILITY AND IMPLEMENTATION: https://github.com/uel3/nf-UnO.

Metagenomics↗
PubMed1999

[Pathogen detection in blood culture. Contamination, colonization or infection].

Sepsis is a severe and life-threatening disease that requires a rapid and reliable diagnosis. The detection of microorganisms in blood culture and the results of in vitro anti-microbial susceptibility testing are prerequisites for a directed and cost-effective antimicrobial therapy. Microbiological results are difficult to interpret if contamination of the blood culture with colonizing or environmental germs cannot be ruled out. The source of contamination is predominantly inappropriate withdrawal of blood. Occasionally, contamination of blood cultures occurs in the laboratory. A potentially relevant blood culture result is already indicated by the isolated pathogen itself. In addition, a short time between the collection of blood and the isolation of the microorganism as well as the detection of the same pathogen in several blood cultures even more suggest a clinically relevant result.

Bacteriological Techniques↗
PubMed1997

Prevalence of six periodontal pathogens detected by DNA probe method in HIV vs non-HIV periodontitis.

OBJECTIVE: The aim of the study was to examine the prevalence of selected periodontal pathogens associated with HIV and non-HIV related periodontal lesions. METHODS: Subgingival plaque samples were obtained from both HIV-seropositive and HIV-seronegative patients affected with periodontal disease. DNA probes were used to detect Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Bacteroides forsythus, Eikenella corrodens and Campylobacter rectus. RESULTS: A actinomycetemcomitans, P. intermedia and B. forsythus (P < 0.05) were more prevalent in HIV-seronegative patients with rapidly progressive periodontitis. Only C. rectus was slightly more prevalent in HIV-seropositive subjects with periodontal diseases, but this was not significant.

AIDS-Related Opportunistic Infections↗
PubMed1975

Vibrio parahaemolyticus -- a marine pathogen detected in South African coastal waters.

Vibrio parahaemolyticus has been detected in the Natal and Eastern Cape costal water of South Africa. As a proven cause of gastro-enteritis or a potential pathogen to humans, it is an organism of importance to public health. Outlines of the history, pathogenicity and identification are given, as well as the results of the local investigation of this organism.

Culture Media↗
PubMed2006

Nucleotide-binding oligomerization domain-like receptors: intracellular pattern recognition molecules for pathogen detection and host defense.

The nucleotide binding oligomerization domain-like receptor (NLR) family of pattern recognition molecules is involved in a diverse array of processes required for host immune responses against invading pathogens. Unlike TLRs that mediate extracellular recognition of microbes, several NLRs sense pathogens in the cytosol and upon activation induce host defense signaling pathways. Although TLRs and NLRs differ in their mode of pathogen recognition and function, they share similar domains for microbial sensing and cooperate to elicit immune responses against the pathogen. Genetic variation in several NLR genes is associated with the development of inflammatory disorders or increased susceptibility to microbial infection. Further understanding of NLRs should provide critical insight into the mechanisms of host defense and the pathogenesis of inflammatory diseases.

Adaptor Proteins, Signal Transducing↗
PubMed2006

Pathogen detection, testing, and control in fresh broccoli sprouts.

BACKGROUND: The recent increased interest in consuming green vegetable sprouts has been tempered by the fact that fresh sprouts can in some cases be vehicles for food-borne illnesses. They must be grown according to proper conditions of sanitation and handled as a food product rather than as an agricultural commodity. When sprouts are grown in accordance with the criteria proposed from within the sprout industry, developed by regulatory agencies, and adhered to by many sprouters, green sprouts can be produced with very low risk. Contamination may occur when these guidelines are not followed. METHODS: A one year program of microbial hold-and-release testing, conducted in concert with strict seed and facility cleaning procedures by 13 U.S. broccoli sprout growers was evaluated. Microbial contamination tests were performed on 6839 drums of sprouts, equivalent to about 5 million consumer packages of fresh green sprouts. RESULTS: Only 24 (0.75%) of the 3191 sprout samples gave an initial positive test for Escherichia coli O157:H7 or Salmonella spp., and when re-tested, 3 drums again tested positive. Composite testing (e.g., pooling up to 7 drums for pathogen testing) was equally sensitive to single drum testing. CONCLUSION: By using a "test-and-re-test" protocol, growers were able to minimize crop destruction. By pooling drums for testing, they were also able to reduce testing costs which now represent a substantial portion of the costs associated with sprout growing. The test-and-hold scheme described herein allowed those few batches of contaminated sprouts to be found prior to packaging and shipping. These events were isolated, and only safe sprouts entered the food supply.

Brassica↗
PubMed2005

Porous silicon-based biosensor for pathogen detection.

A porous silicon-based biosensor for rapid detection of bacteria was fabricated. Silicon (0.01 ohmcm, p-type) was anodized electrochemically in an electrochemical Teflon cell containing ethanoic hydrofluoric acid solution to produce sponge-like porous layer of silicon. Anodizing conditions of 5 mA/cm2 for 85 min proved best for biosensor fabrication. A single-tube chemiluminescence-based assay, previously developed, was adapted to the biosensor for detection of Escherichia coli. Porous silicon chips were functionalized with a dioxetane-Polymyxin B (cell wall permeabilizer) mixture by diffusion and adsorption on to the porous surface. The reaction of beta-galactosidase enzyme from E. coli with the dioxetane substrate generated light at 530 nm. Light emission for the porous silicon biosensor chip with E. coli was significantly greater than that of the control and planar silicon chip with E. coli (P<0.01). Sensitivity of the porous silicon biosensor was determined to be 101-102 colony forming units (CFU) of E. coli. The porous silicon-based biosensor was fabricated and functionalized to successfully detect E. coli and has potential applications in food and environmental testing.

Biosensing Techniques↗
PubMedDate not supplied

Competitive inhibition and attachment assays in cell cultures to detect pathogenic binding components of mycoplasmas: a review.

A microattachment assay for quantitating adherence of radiolabelled Mycoplasma pneumoniae to human WiDr cell culture monolayers is described. Preincubating the WiDr cell monolayers with a protein-rich extract of M. pneumoniae inhibited the subsequent attachment of radiolabelled organisms. Competitive attachment inhibition provided a quantitative procedure to determine M. pneumoniae-binding components in the extract. The microattachment assays also measured attachment inhibition by the sialoglycoconjugates ceruloplasmin, orosomucoid and gangliosides, indicating that these reagents may be structural analogues of the mammalian cell receptor. Attachment of virulent M. pneumoniae strains to glutaraldehyde-treated monolayers was reduced approximately 60% and showed a different temperature dependence compared with untreated cells. These results suggest that maximal attachment of virulent M. pneumoniae may require two or more different receptors and binding components.

Adhesiveness↗
PubMed2003

A handheld real time thermal cycler for bacterial pathogen detection.

The handheld advanced nucleic acid analyzer (HANAA) is a portable real time thermal cycler unit that weighs under 1 kg and uses silicon and platinum-based thermalcycler units to conduct rapid heating and cooling of plastic reaction tubes. Two light emitting diodes (LED) provide greater than 1 mW of electrical power at wavelengths of 490 nm (blue) and 525 nm (green), allowing detection of the dyes FAM and JOE/TAMRA. Results are displayed in real time as bar graphs, and up to three, 4-sample assays can be run on the charge of the 12 V portable battery pack. The HANAA was evaluated for detection of defined Escherichia coli strains, and wild-type colonies isolated from stream water, using PCR for the lac Z and Tir genes. PCR reactions using SYBR Green dye allowed detection of E. coli ATCC 11775 and E. coli O157:H7 cells in under 30 min of assay time; however, background fluorescence associated with dye binding to nonspecific PCR products was present. DNA extracted from three isolates of Bacillus anthracis Ames, linked to a bioterrorism incident in Washington DC in October 2001, were also successfully tested on the HANAA using primers for the vrrA and capA genes. Positive results were observed at 32 and 22 min of assay time, respectively. A TaqMan probe specific to the aroQ gene of Erwinia herbicola was tested on the HANAA and when 500 cells were used as template, positive results were observed after only 7 min of assay time. Background fluorescence associated with the use of the probe was negligible. The HANAA is unique in offering real time PCR in a handheld format suitable for field use; a commercial version of the instrument, offering six reaction chambers, is available as of Fall 2002.

Bacillus anthracis↗
PubMed2005

Relative value of surrogate indicators for detecting pathogens in lakes and reservoirs.

This study investigated the relative behavior of pathogens, fecal indicator organisms, and particles of varying size during transport through a reservoir following a storm event inflow in Myponga Reservoir, South Australia. During the inflow, samples were collected from the river and at various locations within the reservoir to determine the fate and transport of microroganisms as they progressed through the water body. Microbiological analysis included the indicator organisms Escherichia coli, enterococci, Clostridium perfringens, aerobic spores, and somatic coliphages, the protozoan pathogens Cryptosporidium spp. and Giardia spp., and the potential physical surrogates of pathogen contamination including particle size and turbidity. Of the microbial indicator groups, C. perfringens spores were the most highly correlated with Cryptosporidium spp. concentrations (Spearman Rho = 0.58), closely followed by enterococci (Spearman Rho = 0.57). Cryptosporidium spp. oocysts were predominantly associated with small sized particles (range of 14.3-27.7 microm). All of the microbial indicator groups tested were associated with larger sized particle ranges (> 63.3 microm) except C. perfringens spores which were associated with particles in the size range of 45.5-63.3 microm. Although indicators may rank correlate with Cryptosporidium spp., the variation in settling rates of different microorganisms has significant implications for the use of surrogates to estimate pathogen attenuation within reservoirs. For example, concentrations of Cryptosporidium spp. oocysts were reduced by a factor of 3 on reaching the dam wall, whereas enterococci were reduced by a factor of 10.

Animals↗