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PubMed2004

Direct detection of bacterial pathogens in representative dairy products using a combined bacterial concentration-PCR approach.

AIMS: To develop a simple, rapid method to concentrate and purify bacteria and their nucleic acids from complex dairy food matrices in preparation for direct pathogen detection using polymerase chain reaction (PCR). METHODS AND RESULTS: Plain non-fat yogurt and cheddar cheese were each seeded with Listeria monocytogenes or Salmonella enterica serovar. Enteritidis in the range of 10(1)-10(6) CFU per 11-g sample. Samples were then processed for bacterial concentration using high-speed centrifugation (9700 g) followed by DNA extraction, PCR amplification, and amplicon confirmation by hybridization. Bacterial recoveries after centrifugation ranged from 53 to >100% and 71 to >100% for serovar. Enteritidis and L. monocytogenes, respectively, in the non-fat yogurt samples; and from 77 to >100% and 69 to >100% for serovar. Enteritidis and L. monocytogenes, respectively, in the cheddar cheese samples. There were no significant differences in recovery efficiency at different inocula levels, and losses to discarded supernatants were always <5%, regardless of dairy product or pathogen. CONCLUSIONS: When followed by pathogen detection using PCR and confirmation by amplicon hybridization, detection limits of 10(3) and 10(1) CFU per 11-g sample were achieved for L. monocytogenes and serovar. Enteritidis, respectively, in both product types and without prior cultural enrichment. SIGNIFICANCE AND IMPACT OF THE STUDY: This study represents progress toward the rapid and efficient direct detection of pathogens from complex food matrices at detection limits approaching those that might be anticipated in naturally contaminated products.

Blotting, Southern↗
PubMed2002

Comparative evaluation of SIMPL silicone implants and NIT natural teat inserts to keep the teat canal patent after surgery.

The objective of this study was the comparative evaluation of SIMPL silicone implants and NIT natural teat inserts to keep the teat canal patent after teat surgery. The study was performed on 100 teats of 97 cows treated surgically for milk flow disorders. After surgery, 53 teats were administered with SIMPL and 47 with NIT, and rested for several days. Before treatment and 1 and 6 mo later quarter milk flow and milk yield were measured with Lactocorders; quarter milk was examined for somatic cell count (SCC), pathogens, and signs of mastitis (SCC > 100,000 and pathogens detected). Half a year after surgery milk flow, milk yield and SCC were equal from teats that had been inserted with SIMPL or NIT. The odds of detecting pathogens or signs of mastitis in the milk was lower in SIMPL than in NIT teats at this point in time. SIMPL teats stayed in the herd as long as NIT teats. Based on the results, it may be expected that teats inserted with a SIMPL or NIT do not differ long term in regards to milk flow, milk yield, SCC, and risk of removal from the herd. After the use of SIMPL, fewer pathogens may be detected in the milk long term than after the use of NIT.

Animals↗
PubMed1991

[Isolation of enteropathogenic microorganism from patients with infection of the digestive tract during 1976 to 1988 in Tenri Hospital].

Enteropathogenic microorganisms isolated from feces of 9,393 patients with diarrhea or enteritis in our hospital between 1976 and 1988 were analyzed. As the result of the examination of 5,443 outpatients, 1,811 strains of pathogens were isolated from 1,686 cases (31.0%). Several species including Salmonella spp., Escherichia coli serotype, Vibrio parahaemolyticus, were isolated before 1978, and the incidence of pathogens was low (14.8%). For the 10-year period since 1979, the incidence markedly increased to 34.4%, and the number of pathogens isolated also increased to about twice that before 1978. The main cause of the increase was Campylobacter species. The major pathogens detected since 1979 were Campylobacter spp., E. coli serotype, Salmonella spp., V. parahaemolyticus, etc., but Rota virus, Clostridium difficile, Aeromonas spp., Vibrio fluvialis, etc. have also been detected, showing an increase in the number and diversity of the detected pathogens. As the result of the examination of 3,950 inpatients, 835 strains of pathogens were isolated from 800 cases (20.3%). The incidence of C. difficile was the highest, 423 of 800, followed by E. coli serotype, Salmonella spp., Campylobacter spp., V. parahaemolyticus and Aeromonas spp., in that order. All the inpatients from whom C. difficile was isolated manifested diarrhea or enteritis after administration of antimicrobial agents. The pathogens causing communicable disease were Salmonella spp. serovar Typhi, Salmonella spp. serovar Paratyphi A, Shigella flexneri, Shigella sonnei and Entamoeba histolytica, which were isolated from 5, 1, 3, 2 and inpatients, respectively.

Adolescent↗
PubMed2003

Detection of bacterial pathogens in environmental samples using DNA microarrays.

Polymerase chain reaction (PCR) is an important tool for pathogen detection, but historically, it has not been possible to accurately identify PCR products without sequencing, Southern blots, or dot-blots. Microarrays can be coupled with PCR where they serve as a set of parallel dot-blots to enhance product detection and identification. Microarrays are composed of many discretely located probes on a solid substrate such as glass. Each probe is composed of a sequence that is complimentary to a pathogen-specific gene sequence. PCR is used to amplify one or more genes and the products are then hybridized to the array to identify species-specific polymorphism within one or more genes. We illustrate this type of array using 16S rDNA probes suitable for distinguishing between several salmonid pathogens. We also describe the use of microarrays for direct detection of either RNA or DNA without the aid of PCR, although the sensitivity of these systems currently limits their application for pathogen detection. Finally, microarrays can also be used to "fingerprint" bacterial isolates and they can be used to identify diagnostic markers suitable for developing new PCR-based detection assays. We illustrate this type of array for subtyping an important food-borne pathogen, Listeria monocytogenes.

Actinomycetales Infections↗
PubMed2004

Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases.

Disease diagnosis is based on a number of factors, including laboratory tests for pathogen identification. Rapid development of genomic techniques for characterization of bacteria over the past decade has greatly simplified and improved pathogen detection and identification, but DNA-based methods have not yet entirely replaced traditional culture and phenotypic tests in the plant industry. The first section of this review focuses on rapid immunodiagnostic and DNA-based detection methods for known bacterial pathogens in plants or plant products, which often manifest no symptoms of disease. The second section covers the broader topic of disease diagnosis and new methods for identifying and characterizing bacteria.

Animals↗
PubMed1990

[Pneumonia in AIDS: pathogen spectrum and diagnostic value of various fiberoptic bronchoscopy methods for the detection of pathogens].

39 fibre-bronchoscopic examinations were performed prospectively in 29 AIDS-patients with pneumonia. Specimens were obtained from the central bronchial system with a protected brush and by suction, from the infiltrated peripheral area by catheter suction, protected brush, bronchoalveolar lavage (BAL) and transbronchial biopsy in randomized order. In patients with non-bacterial pneumonia, pneumocystis carinii (n = 20) was the most frequent pathogen. In this group BAL had a significantly higher rate of pathogen detection than other techniques. In patients with bacterial pneumonia (n = 10) the pathogens were found in all cases by suction from the central bronchial system. Fibre-bronchoscopy in patients with AIDS and pneumonia should include specimens from the central bronchial system and a bronchoalveolar lavage.

Acquired Immunodeficiency Syndrome↗
PubMed2003

[Application of multiplex semi-nested polymerase chain reaction in detection of pathogens in cerebrospinal fluid].

OBJECTIVE: To establish a new method of multiplex semi-nested polymerase chain reaction (PCR) to detect pathogens in cerebrospinal fluid (CSF). METHODS: According to the analysis of the conservative and variable regions in bacterial 16S rRNA genes, we designed universal primers for all bacteria and specific primers for most gram-positive and gram-negative bacteria. All primers were added into the same reaction systems successively of a two-step PCR assay to amplify the different bacterial DNA in CSF, and the results were compared with common culture method with sensitivity and the specificity both detected at the same time. RESULTS: Both gram-positive and gram-negative bacteria amplified DNA fragment about 1,032 bp after first-step amplification with universal primers. In the second step, specific fragments of 336 bp and 127 bp were amplified in gram-positive and gram-negative bacteria respectively besides fragments of 1,032 bp; The detection limit for E. coli was 8 cfu/ml. The comparison of 62 CSF samples detected by both multiplex semi-PCR and conventional culture method revealed sensitivity, specificity, positive and negative values of 93.8%, 95.7%, 88.2%, and 97.8% respectively for PCR. CONCLUSION: The result suggested that the multiplex semi-nested PCR we established was sensitive, specific and rapid method for clinical laboratory to detect pathogens in CSF.

Cerebrospinal Fluid↗
PubMed2005

Diagnostic system for rapid and sensitive differential detection of pathogens.

Naturally emerging and deliberately released pathogens demand new detection strategies to allow early recognition and containment. We describe a diagnostic system for rapid, sensitive, multiplex discrimination of microbial gene sequences and report its application for detecting 22 respiratory pathogens in clinical samples.

Bacterial Infections↗
PubMed2005

Monte Carlo simulation of pathogen behavior during the sprout production process.

Food-borne disease outbreaks linked to the consumption of raw sprouts have become a concern over the past decade. A Monte Carlo simulation model of the sprout production process was created to determine the most-effective points for pathogen control. Published literature was reviewed, and relevant data were compiled. Appropriate statistical distributions were determined and used to create the Monte Carlo model with Analytica software. Factors modeled included initial pathogen concentration and prevalence, seed disinfection effectiveness, and sampling of seeds prior to sprouting, sampling of irrigation water, or sampling of the finished product. Pathogen concentration and uniformity of seed contamination had a large effect on the fraction of contaminated batches predicted by the simulation. The model predicted that sprout sampling and irrigation water sampling at the end of the sprouting process would be more effective in pathogen detection than seed sampling prior to production. Day of sampling and type of sample (sprout or water) taken had a minimal effect on rate of detection. Seed disinfection reduced the proportion of contaminated batches, but in some cases it also reduced the ability to detect the pathogen when it was present, because cell numbers were reduced below the detection limit. Both the amount sampled and the pathogen detection limit were shown to be important variables in determining sampling effectiveness. This simulation can also be used to guide further research and compare the levels of effectiveness of different risk reduction strategies.

Colony Count, Microbial↗
PubMed2003

Detection of pathogenic Listeria spp. in zoo animal faeces: use of immunomagnetic separation and a chromogenic isolation medium.

Faecal samples, collected from 200 healthy animals in Antwerp Zoo, were examined for the presence of pathogenic Listeria spp. A two-stage standard isolation (ISO) method was combined with immunomagnetic separation (IMS). ALOA agar, a chromogenic isolation medium, differentiating Listeria spp. on the basis of beta-glucosidase and phosphatidylinositol-specific phospholipase C (PIPLC) activity, was compared with PALCAM agar. Confirmation of the isolates was based on conventional biochemical tests and a disc test, which detects a specific aminopeptidase produced by all Listeria spp. except Listeria monocytogenes. Listeria spp. were isolated from 42 (21.0%), L. monocytogenes from 14 (7.0%), and Listeria ivanovii from two (1.0%) faecal samples. The application of IMS after primary enrichment detected pathogenic Listeria spp. in 12 (6.0%) samples. The ISO method, combining primary and secondary enrichment, detected pathogenic Listeria spp. in 15 (7.5%) samples. The sensitivity of IMS compared to the ISO method was 73.3% and the specificity was 99.5%. ALOA agar was superior to PALCAM agar for isolation of Listeria spp. The disc test identified all L. monocytogenes isolates. IMS after primary enrichment was a suitable screening method, but secondary enrichment increased the number of positive samples.

Animals↗
PubMed2001

The effect of liming on the microbiological quality of urban sludge.

Treatments applied to sludge in order to stabilise and dehydrate them may give notable inactivation of microorganisms. This is observed when sludge is exposed either to high temperature or drastic pH when residual sludge is limed. The control of virological, parasitological and bacteriological sludge quality by detecting pathogenic microorganisms is slow and too expensive to be commonly practised. Thus, it is possible to replace pathogenic microorganisms detection by that of contamination indicators. The aim of this study was to determine the influence of liming on the behaviour of pathogenic microorganisms detected in urban sludge. The detection of Salmonella and helminth eggs was carried out in liquid sludge (2-3% dryness) and solid sludge (23% dryness) with added lime (0-45% weight/dry weight) and stored for 24 h-46 weeks. The results showed that liming modified some characteristics such as temperature, dryness and pH of the sludge. It appeared that, whatever the percentage of added lime, the temperature of liquid sludge did not change while it increased by about 9 degrees C when 30-45% lime was added to solid sludge. In the same way, the dryness of liquid sludge did not change during the liming, whereas the dryness of 45% limed solid sludge increased from 23% to 31%. Finally, 15%, 30% and 45% liming gave a pH of at least 10, 11.5 and 12, respectively, although the pH increase depended on the sludge type. The efficiency of liming was considered to be related to the pH and not to the percentage of added lime. Three factors determined the efficiency of pathogen elimination: (a) the pH reached by the sludge, (b) the period of liming activity and (c) the dryness of the sludge. Salmonella were eliminated from liquid sludge in 24 h at pH 10.7 and from solid sludge in 24 h at pH 10.0. Viable helminth egg concentration decreased to 3 eggs/10 g DM in liquid sludge in 14 d at pH 11.9 and 60 d at pH 11.6. In solid sludge, egg reduction was achieved in 24 h at pH 12.5, 7 d at pH 12.0 and 14 d at pH 11.5. From this study, it appeared that liming resulted in a much better microbiological quality of liquid sludge if its pH was maintained at 11.6 over 60 d or at pH 11.9 for 14 d. Solid sludge needed to be maintained at pH 11.5 for 14 d, pH 12.0 for 7 d or pH 12.5 for 24 h to achieve similar results.

Animals↗
PubMed2001

Rapid duplex PCR assay for the detection of pathogenic Yersinia enterocolitica strains.

For the detection of pathogenic Yersinia enterocolitica strains, a duplex PCR has been developed based on differences observed between the fingerprint profiles of pathogenic and non-pathogenic strains. The profiles were obtained by using a primer derived from the Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences. From the sequence of one pathogen-specific amplified fragment, a discriminative primer has been designed bridging the sequence of the highly conserved core region and 3' end of the ERIC element. In combination with three other primers, all located within the detected open reading frame that resembled the sequence of the bipA gene, this primer was applied in a duplex PCR assay to simultaneously detect Y. enterocolitica and to discriminate between pathogenic and non-pathogenic strains. The same primer combinations were used in an on line rapid cycling real-time PCR assay. The used SYBR Green I format allowed for the easy translation of the PCR conditions and confirmation of the resulting amplicons. The time of analysis was reduced to approximately 60 min.

Amino Acid Sequence↗
PubMed2006

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

BACKGROUND: Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites) and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. RESULTS: PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV) as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication). CONCLUSION: PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

Computational Biology↗
PubMedDate not supplied

Feasibility of fluorescent detection of pathogens on pork carcasses.

The direct immunofluorescent detection of pathogens on pork skin is evaluated. Calibrate contamination of pork skin with Salmonella Typhimurium (ST) and Listeria monocytogenes (Lm) is developed in 2 h at 4 degrees C. Then a specific indirect immunofluorescent staining protocol is optimized in order to obtain specific and intensive signals able to be detected by electronic cameras (deported microscopy). Despite the individual staining of ST and Lm is possible on pork skin and is specific and bright, the deported microscopy failed to detect these particles. After respectively 3 and 6 h, we obtain micro-colonies of ST and Lm. Due to the limited power of the video camera used, only the microscope permits the detection on the skin. However, our work gives standard conditions to mime the pathogens contamination and staining directly on a biological matrix such as pork skin. This work is a first step in the development of direct and rapid detection of pathogens on biological matrix.

Animals↗
PubMed2003

Pathogenic Yersinia DNA is detected in bowel and mesenteric lymph nodes from patients with Crohn's disease.

Previously, we detected pathogenic (invasive) DNA in the appendices of two patients who later developed Crohn's disease (CD). This subsequent investigation is the first to evaluate a series of specimens from CD patients for the presence of pathogenic DNA. A total of 54 intestinal resection specimens from 52 patients with confirmed CD were evaluated. Lesional tissue was tested by polymerase chain reaction analysis for the presence of genes occurring only in pathogenic Primer pairs are specific for each species, with no known cross reactions with other bacteria. Forty normal bowel specimens, 30 cases of acute appendicitis, and 50 cases of various active colitides served as disease controls. Medical records were reviewed following polymerase chain reaction and histologic evaluation. A total of 17 of 54 resections (31%) contained DNA by polymerase chain reaction. Mesenteric lymph nodes were also positive in eight of these cases. All controls were negative. -positive patients had carried the diagnosis of CD for a median of 10 years before resection (range 1 month to 40 years). We report the first documentation of DNA in a series of CD cases. Further studies are needed, including serial study, over time, of -positive CD patients, as well as prospective studies of newly diagnosed CD patients for evidence of infection. Like previous studies associating infectious organisms with CD, much work remains to elucidate whether the presence of DNA is an epiphenomenon or actually a factor in the pathogenesis of CD.

Adult↗
PubMed2004

Detection of pathogenic leptospiral DNA in urine by polymerase chain reaction.

Diagnosis of leptospirosis is currently based on serological tests detecting antibodies against the spirochete. The standard method is the microscopic agglutination test (MAT), which is serovar-specific, requires a period of antibody development, and increases the risk of exposure to viable organisms. Therefore, the present study aimed to develop a rapid, sensitive, specific, and safe method based on the PCR technique to detect pathogenic Leptospira in urine samples. Nested PCR using two sets of primers, external and internal primers, were shown to specifically amplify 16S rRNA target of patho-genic Leptospira. No amplification was observed when DNA from non-pathogenic Leptospira and other non-Leptospira bacteria were used as DNA templates. The method was able to detect as few as 10 leptospires in urine. Therefore, nested PCR approach may be a useful tool for prompt and definitive diagnosis of leptospirosis.

Agglutination Tests↗
PubMed2003

Towards a unified system for detecting waterborne pathogens.

Currently, there is no single method to collect, process, and analyze a water sample for all pathogenic microorganisms of interest. Some of the difficulties in developing a universal method include the physical differences between the major pathogen groups (viruses, bacteria, protozoa), efficiently concentrating large volume water samples to detect low target concentrations of certain pathogen groups, removing co-concentrated inhibitors from the sample, and standardizing a culture-independent endpoint detection method. Integrating the disparate technologies into a single, universal, simple method and detection system would represent a significant advance in public health and microbiological water quality analysis. Recent advances in sample collection, on-line sample processing and purification, and DNA microarray technologies may form the basis of a universal method to detect known and emerging waterborne pathogens. This review discusses some of the challenges in developing a universal pathogen detection method, current technology that may be employed to overcome these challenges, and the remaining needs for developing an integrated pathogen detection and monitoring system for source or finished water.

Animals↗