Species-specific cloned DNA probes for the identification of Campylobacter hyointestinalis

Predominant strains of thermophilic Campylobacter spp. in a German poultry slaughterhouse

Campylobacter causes bacterial diarrhoea in man and is a common foodborne pathogen, that has been associated mainly with poultry carcasses and processed poultry products as well as with drinking water. Genotyping of Campylobacter spp. from poultry was done in order to prove if predominant stable strains in the food chain are present. The influence of the slaughter process on the stability should be determined. Thermophilic Campylobacter spp. from eight poultry flocks were isolated from cloacal swabs, carcasses and offal at different abattoir processing steps to determine their stability. DNA-fingerprinting was done using Pulsed-Field Gel Electrophoresis (PFGE) with two enzymes (SmaI and KpnI) and ribotyping. More than 150 Campylobacter strains were ribotyped and these data were combined with the results of PFGE. Molecular typing showed that strains found in cloacal swabs before processing could also be isolated from carcasses and offal at different processing steps representing predominating stable strains. Strains with varying molecular pattern could additionally be detected at different processing steps. Both genotyping methods identified in agreement flock-specific strains. These remained stable through the slaughter of poultry and were not altered through the slaughter process. Despite the known genetic variability of thermophilic Campylobacter, stable predominant strains could be identified in the poultry slaughter process and those strains can thus enter the food chain.

Cloning of a sapB homologue (sapB2) encoding a putative 112-kDa Campylobacter fetus S-layer protein and its use for identification and molecular genotyping

A sap gene encoding a surface layer protein was isolated from a Campylobacter fetus ssp. fetus CIP 53.96T cosmid library. This sap gene, which shows significant homology with the sapB conserved region, was named sapB2. The complete ORF of 3339 nucleotides encodes a 1112-amino acid polypeptide with a calculated molecular mass of 112 kDa. High homology with the sapB gene was found in a region beginning 67 bp before the ORF and proceeding 546 bp into the ORF. Similarly, 98% homology with the sapA2 gene was observed in a 2038-bp region beginning 540 bp after the initiation codon. In the present study, we show that this sapB2 gene has two main interesting features: the 5' end of the region which presents high homology with the sapA2 homologue was found to be present in every C. fetus strain, and the fragment (IG01) comprising the region which presents homology with the sapB conserved region and the 5' end of the sapA2 homologue region, when used as a probe, can reveal genomic polymorphism among C. fetus strains. We exploited these features to develop a PCR assay for the specific detection of C. fetus and to set up a method for typing C. fetus isolates. The PCR assay was found to be species-specific. Oligonucleotide primers derived from the 5' end of sapA2 homologue region were used in a polymerase chain reaction test on genomic DNA extracted from 101 Campylobacter fetus, 18 Campylobacter non-fetus and seven non-Campylobacter strains. A 220-bp fragment was amplified only when C. fetus DNA was used as a target. In Southern blot analysis, the IG01 probe was found to hybridize only with DNA extracted from C. fetus strains. Moreover, IG01 hybridized with several fragments of HindIII-digested DNA, giving a specific pattern for each strain.

Rapid identification by PCR of the genus Campylobacter and of five Campylobacter species enteropathogenic for man and animals

The nucleotide sequences for the 16S ribosomal RNA gene were compared for 33 species comprising the epsilon subdivision of the Proteobacteria (genera: Campylobacter, Helicobacter, Arcobacter and Wolinella). Regions specific for the genus Campylobacter and for five Campylobacter species important in human and/or veterinary medicine were identified. From these regions, PCR primer pairs were designed for use in species-specific identification. Primer pairs were validated against strains representing all taxa of campylobacter-like organisms. They did not amplify products other than from their five target species (C. upsaliensis, C. helveticus, C. fetus, C. hyointestinalis and C. lari), and they generated amplicons of defined size from large numbers of strains of those species. A primer pair suitable for identification of the genus Campylobacter was also identified and validated. This generated amplicons from all species of Campylobacter as well as from unnamed groups known to be within the genus, but not from any species or unnamed strains of Helicobacter, Arcobacter or Wolinella.

A probability matrix for the identification of campylobacters, helicobacters and allied taxa

A probabilistic identification matrix for campylobacteria, comprising 76 phenotypic characters and 37 taxa, is described. The accuracy and integrity of the matrix was evaluated using established computer-assisted methods. Certain taxa (for example, Campylobacter concisus and Camp. gracilis) demonstrated significant phenotypic diversity; previous data corroborated these findings. Differentiation between a few pairs of taxa proved difficult, although discriminatory characteristics were noted in each of these cases. The results indicate that most campylobacteria can be identified accurately and objectively with phenotypic tests when probabilistic methods of data assessment are employed.

Identification methods for campylobacters, helicobacters, and related organisms

The organisms which are referred to as campylobacteria are associated with a diverse range of diseases and habitats and are important from both clinical and economic perspectives. Accurate identification of these organisms is desirable for deciding upon appropriate therapeutic measures, and also for furthering our understanding of their pathology and epidemiology. However, the identification process is made difficult because of the complex and rapidly evolving taxonomy, fastidious nature, and biochemical inertness of these bacteria. These problems have resulted in a proliferation of phenotypic and genotypic methods for identifying members of this group. The purpose of this review is to summarize the problems associated with identifying campylobacteria, critically appraise the methods that have been used for this purpose, and discuss prospects for improvements in this field.

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.

Detection of genomic heterogeneity in Streptococcus suis isolates by DNA restriction fragment length polymorphisms of rRNA genes (ribotyping)

Whole-cell chromosomal digests of 54 isolates of Streptococcus suis encompassing all known serotypes from a geographically varied collection were examined by PstI restriction fragment length polymorphisms and then hybridized with a digoxigenin-11-dUTP-labeled cDNA probe transcribed from a mixture of 16S and 23S rRNAs from Escherichia coli MRE600. The hybridization patterns showed genetic heterogeneity within and between S. suis serotypes. Most isolates (87%) representing 28 serotypes contained a common band at approximately 1.8 kb. However, 13% of the isolates representing seven serotypes lacked the 1.8-kb band, indicating that the species as currently defined is diverse. Nonetheless, the 1.8-kb band may be a useful genotypic marker for identification of most S. suis isolates. We tested the ability of this technique to discriminate between virulent and avirulent S. suis type 2 isolates. A virulent strain of S. suis type 2 could be distinguished from avirulent strains by the presence of specific bands. No correlation was obvious between band pattern and hemolysin production.

Specific in situ hybridization of the intracellular organism of porcine proliferative enteropathy

The identity of the intracellular bacteria found in the enterocytes of pigs with proliferative enteropathy was investigated using specific DNA probes to various Campylobacter species and to a novel organism, ileal symbiont intracellularis. The ilea from pigs (Nos. 1-7) that were diagnosed by routine histopathology as having proliferative enteropathy were used. Diagnosis was made on the basis of proliferation of the enterocytes on hematoxylin and eosin-stained sections and the presence of large numbers of intracellular curved organisms on Warthin-Starry silver-stained sections. Four of these pigs (Nos. 1-4) had the chronic form of the disease, porcine intestinal adenomatosis, and three (Nos. 5-7) had the acute form, proliferative hemorrhagic enteropathy. An additional three normal pigs (Nos. 8-10) were obtained from three separate farms with no history of proliferative enteropathy. Frozen ileal sections were examined by in situ hybridization with DNA probes specific for ileal symbiont intracellularis and the three porcine intestinal Campylobacter species, C. coli, C. hyointestinalis, and C. mucosalis. In all seven pigs with either the intestinal adenomatosis or hemorrhagic enteropathy form of the disease, a DNA probe specific for ileal symbiont intracellularis hybridized to localized foci in the apical cytoplasm of ileal enterocytes. These hybridization sites corresponded to the location of intracellular bacteria in silver-stained sections of adjacent tissue. Sections from the three normal pigs tested with this probe and from all pigs tested with the Campylobacter species-specific DNA probes showed no specific hybridization reactions. The identity of the intracellular organism in these diseased pigs is ileal symbiont intracellularis.

Genetic diversity of Helicobacter pylori indexed with respect to clinical symptomatology, using a 16S rRNA and a species-specific DNA probe

DNA probes are described which identify group and fingerprint strains of the human gastric pathogen Helicobacter pylori, on the basis of well-defined band homologies. A 544 bp internal fragment of the 16S ribosomal RNA gene was generated by polymerase chain reaction (PCR) with primers derived from the Escherichia coli rRNA gene sequence. In genomic Southern blots this probe detected restriction site variation around these loci, generating simple but strain-specific molecular fingerprints. A small conserved chromosomal fragment of 1.2 kbp, Hps, species-specific for H. pylori, was obtained by cloning random HindIII fragments into pUC19. It was useful for dot-blot identification, and also separated isolates into one major and two minor groups. When results for these two probes were combined, a baseline characterization of genotype was obtained. A band-matching database of molecular fingerprints for the type strain and 63 clinical isolates of H. pylori from asymptomatic, ulcer and gastritis contexts is presented. No significant association between the genotypes at this level of definition and the associated clinical symptomatology of the isolates was detected.

Use of DNA analysis of Pasteurella haemolytica biotype T isolates to monitor transmission in bighorn sheep (Ovis canadensis canadensis)

Pneumonia has been identified as a major cause of poor lamb survival in indigenous herds of Rocky Mountain bighorn sheep (Ovis canadensis canadensis) in central Idaho. Pasteurella haemolytica was isolated from five adult Rocky Mountain bighorn ewes captured from a free-ranging herd in central Idaho. The lambs from two of these ewes delivered by cesarean section were free of P. haemolytica until 40 days of age and after repeated contact with their dams. The lambs subsequently developed signs of pneumonia, and P. haemolytica was isolated from nasal, pharyngeal, and transtracheal wash samples from each lamb. All P. haemolytica biotype T isolates from the ewes and lambs, as well as those from a 9-month-old lamb of the same herd from which samples for culture were obtained 2 years earlier, were subjected to HaeIII restriction enzyme analysis (REA) and ribotyping. Two ribotypes and seven REA patterns were visually distinguishable by these procedures. Similarity coefficients (SAB) of 0.09 to 0.95 were calculated for the seven REA patterns. The REA patterns of the isolates from the lambs were identical (SAB = 1.0). The isolates from the lambs also had SAB values of 1.0, which was indicative of identity with one of the seven isolates cultured from the ewes at the time of capture and with the organism isolated from the 9-month-old lamb. These procedures have the discriminatory capabilities necessary to monitor the transmission of specific strains of bacteria within and between animal populations.

Uncommon Campylobacter species in infant Macaca nemestrina monkeys housed in a nursery

Studies were conducted to characterize 18 isolates of Campylobacter spp. that could not be identified as either Campylobacter jejuni or C. coli. The isolates were cultured from specimens from 13 of 18 infant nonhuman primates during a prospective epidemiologic study reported previously. Phenotypic tests, DNA hybridization, and analysis of DNA coding for rRNA identified the isolates as C. butzleri (seven isolates), C. hyointestinalis (seven isolates), and C. fetus subsp. fetus or C. fetus subsp. fetus-like organisms (four isolates). Ribotype and polyacrylamide gel electrophoresis patterns indicated that there was heterogeneity among the isolates of C. butzleri and C. fetus subsp. fetus-like organisms.

Oligodeoxynucleotide probes for Campylobacter fetus and Campylobacter hyointestinalis based on 16S rRNA sequences

Deoxyoligonucleotide probes were constructed for the identification of Campylobacter fetus and Campylobacter hyointestinalis based on 16S rRNA sequence data. Probes were targeted to hypervariable regions of 16S rRNA. Specificity of oligonucleotide probes was tested in a colony blot assay with type strains of 15 Campylobacter and Arcobacter species as well as in a slot blot format using genomic DNA extracted from field strains of C. fetus and C. hyointestinalis. Two oligonucleotides were constructed for C. fetus that hybridized with equal specificity with each of 57 biochemically confirmed isolates of C. fetus but not with any other Campylobacter species. The C. hyointestinalis probe reacted with 47 of 48 biochemically confirmed field isolates of C. hyointestinalis. In Southern blot hybridization of BglII digests of genomic DNA, the respective probes reacted within three restriction fragments of either C. hyointestinalis (7.2, 8.2, and 10.1 kb) or C. fetus (7.0, 7.7, and 9.0 kb). This suggests multiple copies of genes encoding 16S rRNA.

Cloned DNA probes specific for the intracellular Campylobacter-like organism of porcine proliferative enteritis

Although the etiology of porcine proliferative enteritis is not understood, the consistent presence of intracellular Campylobacter-like organisms (CLOs) in proliferating pig intestinal epithelial cells suggests that the organism is involved in the disease process. In order to obtain information about this organism, we generated and characterized specific DNA probes to the intracellular CLO which was purified without culturing. Intracellular CLOs were isolated from mucosa by homogenization, filtration, and absorption to wheat germ agglutinin-Sepharose. The DNA was purified, and a CLO genomic library was constructed. The specificity of recombinant plasmids was confirmed by both dot blot hybridization and Southern analysis of normal and diseased mucosa, as well as of a variety of Campylobacter species. Several of the CLO-specific probes hybridized with porcine mucosa obtained from pigs with proliferative enteritis but not with nondiseased mucosa. The probes hybridized equally with mucosa or DNA obtained from each of the two clinical forms of proliferative enteritis, i.e., proliferative hemorrhagic enteropathy and porcine intestinal adenomatosis. The CLO-specific probes failed to hybridize with any of the commonly isolated porcine Campylobacter species, including Campylobacter hyointestinalis, C. mucosalis, and C. coli. Therefore, the intracellular CLO of porcine proliferative enteritis may be an as yet unidentified or uncultured species.

Identification of epidemic strains of Streptococcus suis by genomic fingerprinting

A natural outbreak of Streptococcus suis meningitis in two closed swine herds was studied. DNA fingerprinting, serotyping, and biochemical profiles were assessed. Multiple serotypes were recovered from these herds. In farm A, 50 S. suis strains were isolated from 330 swabs collected. Eighteen strains belonged to serotype 2, and 32 strains belonged to serotypes 3, 5, 6, 8, 9, and 11. In farm B, 16 S. suis strains were recovered from a total of 70 samples. Eight strains belonged to serotype 7 and eight belonged to serotypes 2, 3, 5, and 8. In each epidemiological situation, a single strain characterized by a distinctive restriction fragment pattern predominated among affected penmates. The epidemic serotype 2 strain was detected in farm A in weaned pigs between the ages of 5 and 7 weeks. In contrast, the pathogenic strain in farm B belonged to serotype 7 and was isolated from pigs up to 3 weeks of age. The results from both farms strongly suggest a lateral spread of these organisms. No vertical transmission could be shown in either herd. It was concluded that genomic fingerprinting is an appropriate method to distinguish outbreak isolates of S. suis from nonoutbreak strains, within the same serotype or from epidemiologically unrelated clusters of strains.

Southern blot analysis of strain variation in Campylobacter mucosalis

A panel of three DNA probes were derived at random from a genomic DNA library of Campylobacter mucosalis strain E8384-4. Each probe hybridized specifically to C. mucosalis DNA from bacteria fixed to nylon membranes. The probes did not hybridize to DNA from other Campylobacter species or to other bacteria even at 100-fold higher amounts. Each probe hybridized to all of 24 isolates of C. mucosalis which had been collected over time from different geographic locations. Southern blot analysis of selected C. mucosalis isolates was carried out to determine if the probes would be useful for differentiating among various isolates. It indicated that restriction fragment length polymorphisms (RFLPs) exist at the loci identified by our probes. These differences were used to characterize seven C. mucosalis isolates recovered from pigs in Minnesota. The results suggest that RFLP analysis may be a useful tool for epidemiological studies of C. mucosalis.

Characterization of prototype and clinically defined strains of Streptococcus suis by genomic fingerprinting

A collection of Streptococcus suis strains from animal and human infections was examined for DNA-banding patterns after restriction endonuclease digestion and agarose gel electrophoresis. The endonuclease HaeIII produced the most discriminating restriction profiles among 23 serotypes studied. DNA from serotypes 9, 11, 12, and 16 was resistant to HaeIII cleavage. DNA from serotypes 9 through 16 was cleaved with HindIII and showed substantial genomic differences. We also examined 106 epidemiologically unrelated strains isolated from cases of pig meningitis or pneumonia and 5 strains isolated from cases of human meningitis in order to compare genomic fingerprinting and serotyping as epidemiological tools. Heterogeneity was found among fingerprints of serologically identical isolates, indicating genetic diversity within some serotypes. DNA fingerprints of some serotype 2 strains from different sources appeared identical, suggesting a clonal relationship among strains of this serotype. The data suggest that this technique represents an important tool for examining the natural history of disease caused by S. suis.