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PubMed1995

Probes and polymerase chain reaction for detection of food-borne bacterial pathogens.

DNA-hybridization and the polymerase chain reaction (PCR) are techniques commonly used to detect pathogenic bacteria. In this paper, the use of these techniques for detection of Salmonella, E. coli, V. cholerae, non-O1 Vibrio, Yersinia enterocolitica, Campylobacter, Listeria monocytogenes, Staphylococcus aureus, Bacillus cereus, Clostridium perfringens, and C. botulinum is reviewed with emphasis on application in food microbiology. In food control, DNA-techniques have most often been used in a 'culture confirmation' fashion, i.e. bacteria are enriched and sometimes even purified by traditional culture procedures and thereafter identified by the use of DNA-based methods. The most desirable approach is, however, to detect organisms directly in the food, but major problems remain to be solved before this can be routinely performed.

Bacteria↗

PubMed2006

Development of a multiplex-PCR for rapid detection of the enteric pathogens Lawsonia intracellularis, Brachyspira hyodysenteriae, and Brachyspira pilosicoli in porcine faeces.

AIMS: To develop an assay to simultaneously detect Lawsonia intracellularis, Brachyspira hyodysenteriae and Brachyspira pilosicoli in pig faeces. METHODS AND RESULTS: A multiplex-polymerase chain reaction (M-PCR) was designed to amplify a 655-base pair (bp) portion of the L. intracellularis 16S rRNA gene, a 354-bp portion of the B. hyodysenteriae NADH oxidase gene, and a 823-bp portion of the B. pilosicoli 16S rRNA gene. Specificity was assessed using 80 strains of Brachyspira spp. and 30 other enteric bacteria. Bacterial DNA was extracted from faeces using the QIAamp DNA Stool Mini Kit. The M-PCR was tested in parallel with culture and/or PCR on 192 faecal samples from eight piggeries. Faeces also were seeded with known cell concentrations of the three pathogenic species, and the limits of detection of the M-PCR tested. The M-PCR was specific, with limits of detection of 10(2)-10(3) cells of the respective species per gram of faeces. CONCLUSIONS: The M-PCR is a rapid, sensitive and specific test for detecting three important enteric bacterial pathogens of pigs. SIGNIFICANCE AND IMPACT OF THE STUDY: The availability of a new diagnostic M-PCR will allow rapid detection and control of three key porcine enteric pathogens.

Animals↗

PubMed1996

[Application of molecular biological methods for diagnosis and epidemiology of human fungal infections].

For mycological diagnosis molecular methods can be applied to detect the pathogen directly without prior cultivation and to identify species and subspecies. For the detection of infecting agents specific DNA probes and/or the polymerase chain reaction (PCR) are widely used, whereas normally only PCR can provide sufficient sensitivity for the direct detection of pathogens in clinical material. Prospects and limitations of PCR approaches for the detection of pathogenic fungi reported in the literature will be discussed. DNA polymorphisms which are useful for species identification and epidemiological strain typing of medically relevant fungi can be detected by such methods as the analysis of restriction fragment length polymorphisms (RFLP), and Southern hybridization with appropriate DNA probes, and as karyotyping by pulsed field gel electrophoresis (PFGE). These techniques which could be applied successfully to different epidemiological studies are, however, laborious and time consuming. By using a PCR-fingerprinting method which can be performed much simpler polymorphic DNA regions are amplified with different non-specific primers. Distinctive and reproducible sets of amplification products were observed for 26 different Candida and 8 other fungal species. The number and size of the amplification products obtained were characteristic for each species. By comparing species-specific PCR-fingerprints of clinical isolates with those of reference strains, clinical isolates could be identified to the species level even if they could not be identified by conventional typing methods. With all primers, PCR-fingerprints also displayed intraspecies variability. Therefore, PCR-fingerprinting can also be applied for epidemiological strain characterization among medically relevant fungi.

Blotting, Southern↗

PubMed2001

Role of bronchoalveolar lavage in immunocompromised patients with pneumonia treated with a broad spectrum antibiotic and antifungal regimen.

BACKGROUND: In a retrospective study the value of bronchoalveolar lavage (BAL) in the diagnosis of pneumonia was investigated in 95 immunocompromised patients suffering from haematological disorders and receiving a regimen of broad spectrum antibiotics and antifungal agents (BSAR). METHODS: With the exception of four afebrile patients, all had fever, raised C reactive protein (CRP) levels, and new infiltrates visible on chest radiography. All patients underwent BAL to identify the organism causing the pneumonia and surveillance cultures were performed regularly for pathogens at different sites. Following classification of the isolates, patients with positive cultures were subdivided into two groups, pathogenic or contaminated. We investigated whether relevant pathogens were cultured only from the BAL fluid and whether they were susceptible to BSAR. RESULTS: Although 77 of the 95 patients were thrombocytopenic, bleeding during BAL occurred in only 15% of all patients. Ten days after the procedure the fever improved in 88% of patients, radiographic findings improved in 71%, and CRP levels improved in 75% of patients; 22% of patients died within 28 days. Pathologically relevant isolates were found in 65% of all patients. Respiratory pathogens were detected only in the BAL fluid of 29 of the 95 patients (35% Gram positive species, 40% Gram negative species, 11% Mycobacterium, 11% fungi, and 3% cytomegalovirus). In 16 of these 29 patients (55%) the pathogens cultured only from the BAL fluid were resistant to treatment. Pathogens detected only in the BAL fluid were not susceptible to a standard broad spectrum antibiotic and antifungal regimen including teicoplanin, ceftriaxon, tobramycin, and amphotericin B in 12 of the 29 patients (41%). CONCLUSIONS: Our data suggest that 12 patients were treated with broad spectrum antimicrobial agents which were not directed at the appropriate organism on in vitro sensitivity tests without BAL. BAL is a relatively safe procedure in the diagnosis of pneumonia, supplying important information in immunocompromised patients as well as in immunocompromised patients receiving BSAR.

Acute Disease↗

PubMed2006

A microbial diagnostic microarray technique for the sensitive detection and identification of pathogenic bacteria in a background of nonpathogens.

A major challenge in microbial diagnostics is the parallel detection and identification of low-bundance pathogens within a complex microbial community. In addition, a high specificity providing robust, reliable identification at least at the species level is required. A microbial diagnostic microarray approach, using single nucleotide extension labeling with gyrB as the marker gene, was developed. We present a novel concept applying competitive oligonucleotide probes to improve the specificity of the assay. Our approach enabled the sensitive and specific detection of a broad range of pathogenic bacteria. The approach was tested with a set of 35 oligonucleotide probes targeting Escherichia coli, Shigella spp., Salmonella spp., Aeromonas hydrophila, Vibrio cholerae, Mycobacterium avium, Mycobacterium tuberculosis, Helicobacter pylori, Proteus mirabilis, Yersinia enterocolitica, and Campylobacter jejuni. The introduction of competitive oligonucleotides in the labeling reaction successfully suppressed cross-reaction by closely related sequences, significantly improving the performance of the assay. Environmental applicability was tested with environmental and veterinary samples harboring complex microbial communities. Detection sensitivity in the range of 0.1% has been demonstrated, far below the 5% detection limit of traditional microbial diagnostic microarrays.

Bacteria↗

PubMed1991

[The use of stains for the detection of the pathogenetic factors of Escherichia and Salmonella].

The authors have modified the technique for using three stains to detect enterobacterial pathogenicity factors. The methods have been tried with 306 Escherichia and Salmonella strains. The most accurate results were obtained when azure eosin was layered onto culture growth surface and when Congo red was added into solid medium. Crystal violet layering yielded less specific results. The techniques listed above helped detect pathogenicity factors of up to 25-30 percent of Escherichia and up to 17 percent of Salmonella strains. The methods are recommended to be used in complex with other tests in practical studies.

Escherichia↗

PubMed2006

Detection and differentiation between pathogenic and saprophytic Leptospira spp. by multiplex polymerase chain reaction.

A multiplex polymerase chain reaction (PCR) was developed for diagnosing leptospirosis and differentiating pathogenic and saprophytic leptospires. Specific primers were designed to amplify 23S rDNA from pathogenic Leptospira and saprophytic Leptospira spp. PCR products from 27 pathogenic and 5 (including 1 intermediate) saprophytic serovars were 615 and 316 base pairs (bp), respectively. After the restriction enzyme's digestion of PCR products, the fragments by SacI of pathogenic serovars and by PstI of saprophytic serovars were 339 and 276 bp and 202 and 114 bp, respectively. The PCR primers enabled amplification of DNA from L. meyeri serovar Ranarum as a pathogenic Leptospira spp. The PCR assay could detect 1 to 2 cells of leptospires and not amplify DNA from other 18 bacterial species. The sensitivity and specificity of this PCR in rat kidney, using isolation as gold standard, were 98.6% and 100%, respectively. The most appropriate sample preparation of blood for detecting DNA was buffy coat. Among the sample preparations from 7 laboratory-confirmed leptospirosis cases, leptospiral DNA was detected in all 7 buffy coat preparations, whereas leptospiral DNA was detected in only 3 plasma or serum samples. The PCR assay may be useful as a diagnostic tool for leptospirosis.

Animals↗

PubMed2001

Development of an ELISA procedure to detect swine carriers of pathogenic Yersinia enterocolitica.

An enzyme immunoassay (ELISA) was developed to detect antibodies in pigs against the lipopolysaccharidic antigen of the three serotypes of Yersinia enterocolitica mostly associated with human infections. Recent epidemiological evidence has demonstrated that pigs and pork are important sources of yersiniosis in humans. The purpose of this study was to clarify the use of an ELISA to detect swine carriers of this enteroinvasive bacteria by examining seroconversion and tissue distribution of Y. enterocolitica following experimental infection and then screening pigs at a slaughterhouse by bacterial culture and ELISA. It was observed that seroconversion occurred in animals experimentally inoculated with Y. enterocolitica but not with other enterobacteria. It was also found that 27% of swine at a slaughterhouse carried the bacterium in their tonsils and/or intestinal tract, whereas 66% showed serological evidence of previous infection. About 6% of swine at slaughter were culture-positive, but seronegative. Although, similar numbers of swine showed serological evidence of previous infection by each of the three Y. enterocolitica serotypes tested, virtually all culture isolates belonged to serotype O:3. This ELISA appears as a valuable control tool that can be used, in conjunction with culture, to identify pigs or herds infected by strains of Y. enterocolitica associated with human infections.

Abattoirs↗

PubMed2003

Detection of Listeria monocytogenes from a model food by fluorescence resonance energy transfer-based PCR with an asymmetric fluorogenic probe set.

It has been shown that fluorescence resonance energy transfer (FRET)-based PCR, including the TaqMan assay and molecular beacons, has potential for rapid detection of pathogens. In these promising real-time detection assays a single internal oligonucleotide probe labeled on both the 5' (reporter) and 3' (quencher) ends is used for selective generation of fluorescence. In this paper, we describe the use of a previously reported novel probe design for FRET-based PCR detection of Listeria monocytogenes in pure culture and in a model food commodity. In the assay described here an asymmetric probe set is used; this probe set consists of a long 5' fluorescein-labeled reporter probe and a short, complementary 3' DABCYL-labeled quencher oligonucleotide, which are used in a 5' nuclease amplification and detection assay. By using the listeriolysin O (hly) and p60 (iap) genes as amplification targets, the performance of two primer-probe sets in amplification and subsequent detection of target DNA was evaluated. In studies performed with pure cultures of L. monocytogenes, the PCR profiles indicated that the relative change in fluorescence intensity was correlated with both the initial number of cells and the accumulation of specific amplicons for both hly and iap gene fragments. Experiments were also done to determine the applicability of the method to the detection of L. monocytogenes by targeting hly DNA and its short-lived mRNA product in a model food commodity. Twenty-five-milliliter samples of reconstituted nonfat dry milk (NFDM) were seeded with L. monocytogenes and processed to concentrate the bacteria by centrifugation, and this was followed by nucleic acid extraction and amplification with hly-specific primers. Endpoint detection of PCR and reverse transcription-PCR amplicons could be achieved at inoculum levels of 10(3) and 10(4) CFU of L. monocytogenes/25 ml of NFDM, respectively. This study demonstrated that this asymmetric FRET-based amplification and detection protocol provides an alternative approach for endpoint detection of nucleic acid amplification products as applied to detection of pathogens in a model food.

Animals↗

PubMed2006

Detection of individual microbial pathogens by proximity ligation.

BACKGROUND: Nucleic acid amplification allows the detection of single infectious agents. Protein-based assays, although they provide information on ongoing infections, have substantially less detection sensitivity. METHODS: We used proximity ligation reactions to detect proteins on bacteria and virus particles via nucleic acid amplification. Antibodies recognizing viral or bacterial surface proteins were equipped with DNA strands that could be joined by ligation when several antibodies were bound in proximity to surface proteins of individual infectious agents. RESULTS: Detection sensitivities similar to those of nucleic acid-based detection reactions were achieved directly in infected samples for a parvovirus and an intracellular bacterium. CONCLUSIONS: This method enables detection of ligated DNA strands with good sensitivity by real-time PCR and could be of value for early diagnosis of infectious disease and in biodefense.

Animals↗

PubMed2005

Rapid detection of food-borne pathogens by using molecular techniques.

Traditional methods of identification of food-borne pathogens, which cause disease in humans, are time-consuming and laborious, so there is a need for the development of innovative methods for the rapid identification of food-borne pathogens. Recent advances in molecular cloning and recombinant DNA techniques have revolutionized the detection of pathogens in foods. In this study the development of a PCR-based technique for the rapid identification of the food-borne pathogens Salmonella and Escherichia coli was undertaken. Suitable primers were designed based on specific gene fimA of Salmonella and gene afa of pathogenic E. coli for amplification. Agarose gel electrophoresis and subsequent staining with ethidium bromide were used for the identification of PCR products. The size of the amplified product was 120 bp as shown by comparison with marker DNA. These studies have established that fimA and afa primers were specific for detecting Salmonella and pathogenic E. coli, respectively, in the environmental samples. Thus a rapid, sensitive and reliable technique for the detection of Salmonella and pathogenic E. coli was developed.

Adhesins, Escherichia coli↗

PubMed1995

Culture of intestinal biopsy specimens and stool culture for detection of bacterial enteropathogens in patients infected with human immunodeficiency virus. The Berlin Diarrhea/Wasting Syndrome Study Group.

The diagnostic yields of stool cultures and biopsy specimens for the detection of enteric bacterial pathogens in 213 human immunodeficiency virus-infected patients were compared. Forty-five percent (19 of 42) of the pathogens were detected exclusively by stool culture, 2% (1 of 42) of the isolates were detected exclusively by culture of biopsy specimens, and 53% (22 of 42) were detected by both methods. Repeated stool cultures remain the most important means of diagnosing enteric bacterial pathogens, which were encountered in 20% (40 of 213) of all patients. The additional culture of biopsy specimens should be reserved for patients with suspected mycobacteriosis.

AIDS-Related Opportunistic Infections↗

PubMed1995

Detection of the turkey pathogens Mycoplasma meleagridis and M. iowae by amplification of genes coding for rRNA.

PCR-based diagnostic tests using oligonucleotides specific to 16S rRNA were designed for the specific detection of the turkey pathogens Mycoplasma meleagridis and M. iowae. This method of detection was shown to be rapid, species specific, and unaffected by strain variation or the presence of other organisms. Detection of M. meleagridis in clinical samples by PCR was achieved and later confirmed by culture and growth inhibition. Definitive identification by culture and growth inhibition required up to 3 weeks, whereas positive results from PCR testing were obtained within a day and negative samples were confirmed within 4 days.

Animals↗

PubMed2004

Simultaneous detection of marine fish pathogens by using multiplex PCR and a DNA microarray.

We coupled multiplex PCR and a DNA microarray to construct an assay suitable for the simultaneous detection of five important marine fish pathogens (Vibrio vulnificus, Listonella anguillarum, Photobacterium damselae subsp. damselae, Aeromonas salmonicida subsp. salmonicida, and Vibrio parahaemolyticus). The array was composed of nine short oligonucleotide probes (25-mer) complementary to seven chromosomal loci (cyt, rpoN, gyrB, toxR, ureC, dly, and vapA) and two plasmid-borne loci (fatA and A.sal). Nine primer sets were designed to amplify short fragments of these loci (100 to 177 bp) in a multiplex PCR. PCR products were subsequently labeled by nick translation and hybridized to the microarray. All strains of the five target species (n = 1 to 21) hybridized to at least one species-specific probe. Assay sensitivities ranged from 100% for seven probes to 83 and 67% for the two remaining probes. Multiplex PCR did not produce any nonspecific amplification products when tested against 23 related species of bacteria (n = 40 strains; 100% specificity). Using purified genomic DNA, we were able to detect PCR products with < 20 fg of genomic DNA per reaction (equivalent to four or five cells), and the array was at least fourfold more sensitive than agarose gel electrophoresis for detecting PCR products. In addition, our method allowed the tentative identification of virulent strains of L. anguillarum serotype O1 based on the presence of the fatA gene (67% sensitivity and 100% specificity). This assay is a sensitive and specific tool for the simultaneous detection of multiple pathogenic bacteria that cause disease in fish and humans.

Animals↗

PubMedDate not supplied

Rapid detection and identification of pathogenic fungi by polymerase chain reaction amplification of large subunit ribosomal DNA.

We describe a polymerase chain reaction (PCR) based approach to the detection and identification of pathogenic fungi which has potential for the diagnosis of systemic mycoses. Primers to sequences of the large subunit ribosomal DNA genes, which are universally conserved within the fungal kingdom, were capable of amplifying DNA from 43 strains representing 20 species (12 genera) of medically important fungi. Sequence analysis of the products obtained from Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans allowed us to design species-specific primers which only amplified homologous DNA. The use of these two PCRs in tandem allows the detection (universal PCR) and identification (species-specific PCR) of a fungal pathogen within 8 h from simulated clinical specimens.

Base Sequence↗

PubMed2005

Rapid detection and identification of pathogens in blood cultures by fluorescence in situ hybridization and flow cytometry.

Septicemia is one of the leading causes of death in hospitalized patients. The timely detection and identification of microorganisms from the patient's blood has great diagnostic, prognostic and economic significance. Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes has been proven to be a fast method for the identification of human pathogenic bacteria and yeasts. Data presented herein reveal that the combination of FISH and flow cytometry (FC-FISH) is a rapid and reliable technique for identification of pathogens (Gram-negative rods, Candida spp.) directly from blood cultures without further cultivation and biotyping. Moreover, detection of growing pathogens (e.g., Stenotrophomonas maltophilia) in blood cultures is achieved more rapidly by FC-FISH compared to standard detection methods. Therefore, FC-FISH allows rapid detection and identification of pathogens in blood cultures.

Bacteria↗

PubMed2005

Detection of single bacterial pathogens with semiconductor quantum dots.

Semiconductor quantum dots (QDs) have been used in a simple fluorometric assay to detect single cells of the pathogenic Escherichia coli O157:H7 serotype. Composed of CdSe/ZnS core/shell QDs conjugated to streptavidin, this system exhibits 2 orders of magnitude more sensitivity than a similar assay using a common organic dye. Selectivity for this pathogenic bacterial strain over a common lab strain (E. coli DH5alpha), which is gained from the use of specific biotinylated antibodies, is also demonstrated for QD labeling. Under continuous excitation, these QDs retain high fluorescence intensities for hours, whereas a typical organic dye bleaches within seconds, allowing for more rapid and accurate identification of E. coli O157:H7 in single-cell fluorescence-based assays. This indirect QD labeling method, based on antibody-antigen and streptavidin-biotin interactions, is flexible enough to expand to other systems and has great potential for use in simultaneous multicolor detection schemes.

Biotin↗

PubMed2003

Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens.

Fusarium wilt, caused by Fusarium oxysporum f. sp. lycopersici, and Verticillium wilt, caused by either Verticillium albo-atrum or Verticillium dahliae, are devastating diseases of tomato (Lycopersicon esculentum) found worldwide. Monitoring is the cornerstone of integrated pest management of any disease. The lack of rapid, accurate, and reliable means by which plant pathogens can be detected and identified is one of the main limitations in integrated disease management. In this paper, we describe the development of a molecular detection system, based on DNA array technology, for rapid and efficient detection of these vascular wilt pathogens. We show the utility of this array for the sensitive detection of these pathogens from complex substrates like soil, plant tissues and irrigation water, and samples that are collected by tomato growers in their greenhouses.

DNA, Bacterial↗