DNA-DNA hybridization and analysis of restriction endonuclease and rRNA gene patterns of atypical (catalase-weak/negative) Campylobacter jejuni from paediatric blood and faecal cultures.

Sixteen strains of atypical (catalase-weak or negative), hippurate-hydrolysing campylobacters from paediatric blood and faecal cultures were identified by DNA-DNA slot hybridization. All were closely related (greater than or equal to 67%) to Campylobacter jejuni and representative strains had G + C contents of 30 +/- 1 mol%. Numerical analysis of chromosomal DNA HaeIII digest patterns revealed two clusters of strains at the 55%S level corresponding to C. jejuni subsp. jejuni and C. jejuni subsp. doylei; most strains belonged to the latter subspecies. No two strains had identical patterns but within each subspecies two subgroups were identifiable, corresponding to Lior biotypes I and II. Southern blot hybridization analysis with a 16 + 23S rRNA cistron probe from Escherichia coli also showed differences between the various strains, and in a numerical analysis three groupings were formed at 70%S corresponding to C. jejuni subsp. jejuni Lior biotypes I and II, and C. jejuni subsp. doylei. Four of the subspecies doylei strains contained a 3.4-MDa plasmid. These analyses showed that catalase-negative C. jejuni subsp. jejuni were genomically distinguishable from C. jejuni subsp. doylei as were Lior biotypes within subsp. jejuni. Ability to produce catalase is not a feature common to all C. jejuni strains, and our results confirm that some strains of subspecies jejuni may be negative in that character although typical in other respects. DNA pattern heterogeneity was consistent with serological differences between strains.     

DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry)

Sixteen Frankia strains were isolated from Myrica pennsylvanica (bayberry) root nodules collected at diverse sites in New Jersey. Restriction pattern analysis of total genomic DNA was used to group the isolates into gel groups, and the genetic relatedness among the isolates was evaluated by DNA-DNA solution hybridization studies. Restriction pattern analysis provided a distinctive reproducible fingerprint for each isolate. Isolates fell into nine separate groups (strain types). More than one strain type was isolated from most sites. Isolates from two different gel groups were found in 3 of 10 nodules examined. Of the 16 isolates, 10 contained extrachromosomal DNA. Six different extrachromosomal DNA banding patterns were found. Genomically similar isolates carried related, but different, banding patterns. DNA hybridization studies indicated that isolates from a single plant species can be minimally related as determined by total genome homology. Homology ranged from 12 to 99%. Highly divergent strains were isolated from the same plant and found to cohabit the same nodule. Thus, this study demonstrated that Frankia strains which infect the same host plant are not only phenotypically different but also genetically diverse.     

DNA restriction patterns and DNA-DNA solution hybridization studies of Frankia isolates from Myrica pennsylvanica (bayberry).

Sixteen Frankia strains were isolated from Myrica pennsylvanica (bayberry) root nodules collected at diverse sites in New Jersey. Restriction pattern analysis of total genomic DNA was used to group the isolates into gel groups, and the genetic relatedness among the isolates was evaluated by DNA-DNA solution hybridization studies. Restriction pattern analysis provided a distinctive reproducible fingerprint for each isolate. Isolates fell into nine separate groups (strain types). More than one strain type was isolated from most sites. Isolates from two different gel groups were found in 3 of 10 nodules examined. Of the 16 isolates, 10 contained extrachromosomal DNA. Six different extrachromosomal DNA banding patterns were found. Genomically similar isolates carried related, but different, banding patterns. DNA hybridization studies indicated that isolates from a single plant species can be minimally related as determined by total genome homology. Homology ranged from 12 to 99%. Highly divergent strains were isolated from the same plant and found to cohabit the same nodule. Thus, this study demonstrated that Frankia strains which infect the same host plant are not only phenotypically different but also genetically diverse.     

Analysis of Actinobacillus pleuropneumoniae and related organisms by DNA-DNA hybridization and restriction endonuclease fingerprinting.

The objective of this study was to determine the degree of genetic relatedness of Actinobacillus pleuropneumoniae to selected members of the family Pasteurellaceae, with particular emphasis on species commonly associated with swine. Free-solution DNA-DNA hybridization studies revealed that representative strains of all 12 serotypes of A. pleuropneumoniae formed a homogeneous group, sharing 74 to 90% sequence homology with A. pleuropneumoniae serotype 1. All serotypes of A. pleuropneumoniae tested demonstrated a high degree of genetic relatedness (66 to 79%) to the type species of the genus Actinobacillus, A. lignieresii. Little homology (less than 20%) was detected between A. pleuropneumoniae strains and selected Haemophilus spp. and Pasteurella spp. Since free-solution hybridization methods are technically demanding and require large amounts of highly purified DNA, restriction endonuclease fingerprinting (REF) was examined to determine whether it could be a useful taxonomic tool for classification of members of the family Pasteurellaceae. REF profiles were compared, and the degree of similarity between organisms was quantitated by calculating Jaccard similarity coefficients. There was a significant positive relationship between the REF Jaccard coefficients and the DNA homology values determined from free-solution hybridization experiments.     

PCR/restriction fragment length polymorphism (RFLP) typing of human and poultry Campylobacter jejuni strains

AIMS: The PCR/RFLP typing of 156 isolates Campylobacter jejuni originating from poultry and humans was performed (101 human and 55 poultry strains). METHODS AND RESULTS: On the basis of restrictive digest, six types were identified with AfaI, seven types with MboI and five types with HaeIII. With a combination of these three enzymes, 22 types were found. In human strains, the most frequently occurring types were Cj.4 (28%), Cj.1 (19%), Cj. 13 (13%) and Cj. 2 (5%). In the case of poultry strains, the most frequent types were Cj. 1 (34%), Cj. 11 (22%), C.j. 21 (16%) and Cj. 15 (11%). CONCLUSIONS: The findings support the hypothesis that poultry is a significant source but not sole source of Campylobacter sp. in relation to humans. SIGNIFICANCE AND IMPACT OF THE STUDY: The typing of Campylobacter sp. forms the basis for an evaluation of the current state and risk assessment of various Campylobacter sp. sources in relation to humans.     

Advantages of peptide nucleic acid oligonucleotides for sensitive site directed 16S rRNA fluorescence in situ hybridization (FISH) detection of Campylobacter jejuni, Campylobacter coli and Campylobacter lari

Traditionally fluorescence in situ hybridization (FISH) has been performed with labeled DNA oligonucleotide probes. Here we present for the first time a high affinity peptide nucleic acid (PNA) oligonucleotide sequence for detecting thermotolerant Campylobacter spp. using FISH. Thermotolerant Campylobacter spp, including the species Campylobacter coli, Campylobacter jejuni and Campylobacter lari, are important food and water borne pathogens. The designed PNA probe (CJE195) bound with higher affinity to a previously reported low affinity site on the 16S rRNA than the corresponding DNA probe. PNA also overcame the problem of the lack of affinity due to the location of the binding site and the variation of the target sequence within species. The PNA probe specificity was tested with several bacterial species, including other Campylobacter spp. and their close relatives. All tested C. coli, C. jejuni and C. lari strains were hybridized successfully. Aging of the Campylobacter cultures caused the formation of coccoid forms, which did not hybridize as well as bacteria in the active growth phase, indicating that the probe could be used to assess the physiological status of targeted cells. The PNA FISH methodology detected C. coli by membrane filtration method from C. coli spiked drinking water samples.     

Identification of Campylobacter coli isolates from animals and humans by bacterial restriction endonuclease DNA analysis

Ninety-nine Campylobacter coli isolates were examined by bacterial restriction endonuclease DNA analysis (BRENDA) with HindIII. Isolates from poultry from the same environment had identical patterns, patterns of isolates carried by suckling piglets were generally the same as those of isolates recovered from their dams, and one human patient yielded the same BRENDA type when sampled 6 weeks later. The 14 human isolates examined produced 11 distinct BRENDA types. Forty-three C. coli isolates from pigs were represented by 20 BRENDA types. Ten C. coli isolates from the feces of gulls yielded five different BRENDA types. Thirty-two C. coli isolates from live chickens and processed chicken yielded five different BRENDA types. Three human isolates had identical DNA patterns; two were from brothers living in the same house, and the third was from a human with no apparent relationship to the brothers. Another human isolate was identical to a poultry isolate. None of the pig strains had DNA patterns resembling those of human strains, nor were the DNA patterns like those of any strains recovered from poultry or gulls. Four C. coli isolates were subcultured onto agar 23 times over a period of 45 days, and their BRENDA patterns were preserved. BRENDA shows great promise for use in epidemiological studies of C. coli.     

Characterization of Dutch porcine Serpulina (Treponema) isolates by restriction endonuclease analysis and DNA hybridization.

Genomes of 55 Dutch porcine Serpulina (Treponema) hyodysenteriae and non-pathogenic Serpulina isolates were characterized by restriction endonuclease analysis (REA) and DNA hybridization. The Dutch porcine isolates were compared with American Type Culture Collection (ATCC) strains of S. hyodysenteriae and S. innocens and isolates of S. hyodysenteriae with known serotypes (reference strains). REA of the Dutch S. hyodysenteriae isolates resulted in two main patterns, while the non-pathogenic isolates had many distinct REA patterns, all different from the S. hyodysenteriae strains. The S. hyodysenteriae reference strains all had distinct REA patterns, different from the Dutch strains. Upon Southern hybridization with a S. hyodysenteriae DNA fragment encoding a flagellar protein, all S. hyodysenteriae strains could be divided in two groups. The non-pathogenic Serpulina strains had many distinct hybridization patterns and hybridized less intensely. Upon hybridization with a S. hyodysenteriae DNA fragment encoding a haemolysin, DNA of all S. hyodysenteriae strains reacted in the same band. DNA of non-pathogenic Dutch Serpulina strains and S. innocens did not hybridize. It was concluded that there are two main genotypes of S. hyodysenteriae in the Netherlands. This could be of importance for recombinant DNA vaccine development.     

PCR-based restriction fragment length polymorphism (RFLP) analysis and serotyping of Campylobacter jejuni isolates from diarrheic patients in China and Japan

Abstract A molecular typing approach for Campylobacter jejuni was applied with restriction fragment length polymorphism (RFLP) analysis of a 702-bp PCR-amplified portion of the flagellin-A ( flaA ) gene. We analyzed a total of 179 strains, including 69 independent clinical isolates from diarrheic patients in Japan, 85 isolates in China, and 25 heat-stable (HS) serotype strains by Penner and Hennessy ((1980) J. Clin. Microbiol. 12, 732–737). Six Afa I, seven Mbo I, and five Hae III RFLPs were found in the 702-bp flaA segment from the 179 strains. Using a combination of these three enzymes, 25 separate RFLP groups were recognized. While 59 of 154 (38.3%) strains obtained in Japan and China were nontypeable by the HS antigenic scheme, all but two of 154 (98.7%) could be typed by RFLP typing. All 11 isolates of HS-19 strains, which are frequently isolated from Guillain-Barré syndrome (GBS) patients, showed an identical RFLP pattern (Cj-1), and Cj-1 consisted only of HS-19 strains. This suggests that the HS-19:Cj-l strain is distinct among C. jejuni strains. This molecular typing method provides a rapid and reliable typing scheme for epidemiological studies of C. jejuni , and may also be useful for the analysis of C. jejuni subtypes from GBS patients.     

Ribosomal RNA gene restriction fragment diversity amongst Lior biotypes and Penner serotypes of Campylobacter jejuni and Campylobacter coli

Diversity based on ribosomal RNA gene-restriction endonuclease digest patterns was detected amongst 42 strains of Campylobacter jejuni and 18 strains of C. coli including representatives of 53 different Penner serotypes. HaeIII ribopatterns were coded for numerical analysis which showed that all except two were different including those of several strains of the same serotype (P2 and P20). At the 30% similarity level, four groupings were formed in the analysis of which three corresponded to C. jejuni, C. coli and C. lari phenotypes respectively. Eight strains (13%) were atypical as their phenotypic and ribopattern associations did not correspond. Ribopattern fragments of 3.0, 5.0 and 9.3 kb were characteristic of the majority of C. jejuni, whereas 1.5, 2.2-, 2.3- and 4.7-kb fragments were commonly present in C. coli. These fragments provided novel species-specific markers. We conclude that HaeIII ribotyping was as discriminatory as Penner serotyping of C. jejuni and C. coli and may even provide a basis for distinguishing between strains of the same serotype and for identifying new groups within the thermophilic campylobacters.     

Fingerprinting of Campylobacter jejuni by using resolution-optimized binary gene targets derived from comparative genome hybridization studies

The aim of this investigation was to exploit the vast comparative data generated by comparative genome hybridization (CGH) studies of Campylobacter jejuni in developing a genotyping method. We examined genes in C. jejuni that exhibit binary status (present or absent between strains) within known plasticity regions, in order to identify a minimal subset of gene targets that provide high-resolution genetic fingerprints. Using CGH data from three studies as input, binary gene sets were identified with "Minimum SNPs" software. "Minimum SNPs" selects for the minimum number of targets required to obtain a predefined resolution, based on Simpson's index of diversity (D). After implementation of stringent criteria for gene presence/absence, eight binary genes were found that provided 100% resolution (D=1) of 20 C. jejuni strains. A real-time PCR assay was developed and tested on 181 C. jejuni and Campylobacter coli isolates, a subset of which have previously been characterized by multilocus sequence typing, flaA short variable region sequencing, and pulsed-field gel electrophoresis. In addition to the binary gene real-time PCR assay, we refined the seven-member single nucleotide polymorphism (SNP) real-time PCR assay previously described for C. jejuni and C. coli. By normalizing the SNP assay with the respective C. jejuni and C. coli ubiquitous genes, mapA and ceuE, the polymorphisms at each SNP could be determined without separate reactions for every polymorphism. We have developed and refined a rapid, highly discriminatory genotyping method for C. jejuni and C. coli that uses generic technology and is amenable to high-throughput analyses.     

Identification of Campylobacter coli isolates from animals and humans by bacterial restriction endonuclease DNA analysis.

Ninety-nine Campylobacter coli isolates were examined by bacterial restriction endonuclease DNA analysis (BRENDA) with HindIII. Isolates from poultry from the same environment had identical patterns, patterns of isolates carried by suckling piglets were generally the same as those of isolates recovered from their dams, and one human patient yielded the same BRENDA type when sampled 6 weeks later. The 14 human isolates examined produced 11 distinct BRENDA types. Forty-three C. coli isolates from pigs were represented by 20 BRENDA types. Ten C. coli isolates from the feces of gulls yielded five different BRENDA types. Thirty-two C. coli isolates from live chickens and processed chicken yielded five different BRENDA types. Three human isolates had identical DNA patterns; two were from brothers living in the same house, and the third was from a human with no apparent relationship to the brothers. Another human isolate was identical to a poultry isolate. None of the pig strains had DNA patterns resembling those of human strains, nor were the DNA patterns like those of any strains recovered from poultry or gulls. Four C. coli isolates were subcultured onto agar 23 times over a period of 45 days, and their BRENDA patterns were preserved. BRENDA shows great promise for use in epidemiological studies of C. coli.     

Identification and molecular cloning of a gene encoding a fibronectin-binding protein (CadF) from Campylobacter jejuni

Campylobacter jejuni , a Gram-negative bacterium, is a common cause of gastrointestinal disease. By analogy with other enteric pathogens such as Salmonella and Shigella , the ability of C. jejuni to bind to host cells is thought to be essential in the pathogenesis of enteritis. Scanning electron microscopy of infected INT407 cells suggested that C. jejuni bound to a component of the extracellular matrix. Binding assays using immobilized extracellular matrix proteins and soluble fibronectin showed specific and saturable binding of fibronectin to C. jejuni . Ligand immunoblot assays using ¹²⁵I-labelled fibronectin revealed specific binding to an outer membrane protein with an apparent molecular mass of 37 kDa. A rabbit antiserum, raised against the gel-purified protein, reacted with a 37 kDa protein in all C. jejuni isolates ( n  = 15) as tested by immunoblot analysis. Antibodies present in convalescent serum from C. jejuni -infected individuals also recognized a 37 kDa protein. The gene encoding the immunoreactive 37 kDa protein was cloned and sequenced. Sequencing of overlapping DNA fragments revealed an open reading frame (ORF) that encodes a protein of 326 amino acids with a calculated molecular mass of 36 872 Da. The deduced amino acid sequence of the ORF exhibited 52% similarity and 28% identity to the root adhesin protein from Pseudomonas fluorescens . Isogenic C. jejuni mutants which lack the 37 kDa outer membrane protein, which we have termed CadF, displayed significantly reduced binding to fibronectin. Biotinylated fibronectin bound to a protein with an apparent molecular mass of 37 kDa in the outer membrane protein extracts from wild-type C. jejuni as judged by ligand-binding blots. These results indicate that the binding of C. jejuni to fibronectin is mediated by the 37 kDa outer membrane protein which is conserved among C. jejuni isolates.     

Identification of 'Campylobacter upsaliensis' and other catalase-negative campylobacters from paediatric blood cultures by numerical analysis of electrophoretic protein patterns

Twenty-one strains of catalase-negative campylobacters from paediatric blood cultures were characterized by one-dimensional SDS-PAGE of cellular proteins. A further 11 Campylobacter strains were included for reference purposes. The partial protein patterns were used as the basis of a numerical analysis, which showed that 17 hippurate-negative strains had a high similarity to 'C. upsaliensis' (r greater than or equal to 0.82) irrespective of their geographical location, and that three hippurate-positive isolates had a high similarity (r greater than or equal to 0.87) to C. jejuni subsp. jejuni. One hippurate-positive CNW strain was not identified. The analysis of SDS-PAGE protein patterns proved an excellent method of characterizing these thermophilic campylobacter as they were difficult to identify by traditional methods.     

Characterization of the DNA of rodent herpesviruses by restriction endonuclease analysis and hybridization.

Restriction endonuclease analysis, dot-blot hybridization, and dried gel hybridization were used to differentiate mouse cytomegalovirus, rat cytomegalovirus, and mouse herpesvirus strain 76. Viral DNA was obtained directly from virus-infected mouse or rat cells. Restriction endonuclease digestion was performed by standard methods with BamHI, EcoRI, HindIII, and PstI, and DNA was analyzed by electrophoresis on agarose gels. Cross-hybridization was used to determine the degree of genetic homology among the three viruses. Electrophoretic patterns revealed clear differences between mouse cytomegalovirus and rat cytomegalovirus restriction profiles. Extensive comigration of DNA was observed for rat cytomegalovirus and mouse herpesvirus strain 76. Both viruses also shared common DNA sequences. These results suggest that mouse herpesvirus strain 76 is probably a rat cytomegalovirus strain infecting mice.     

Genotyping of Campylobacter jejuni strains from Danish broiler chickens by restriction fragment length polymorphism of the LPS gene cluster

AIMS: To apply and evaluate LG (LPS genes) genotyping, which is a genotyping method based on a cluster of genes involved in the synthesis of surface lipopolysaccharides (LPS) in Campylobacter species, for typing of Campylobacter jejuni isolates obtained from Danish broiler chickens. Furthermore, the LG genotyping method was used to study the genetic stability of four C. jejuni strains after gastrointestinal passage through experimentally infected chickens. METHODS AND RESULTS: In the present study, the LG genotyping method was modified with respect to the restriction enzymes used. To validate the method, 63 Penner serotype reference strains and 107 C. jejuni chicken isolates, representing the most common Penner serotypes of C. jejuni in Danish poultry, were selected for typing. The method was successfully used for typing all isolates and the LG genotype profiles were reproducible. There were no changes in the LG genotype of the C. jejuni strains obtained after experimental passage through chickens. CONCLUSIONS: All C. jejuni strains obtained from broiler chickens were typeable by the LG genotyping method. Application of the RsaI restriction enzyme improved the method in terms of ease and consistency of analyses and increase of discriminatory power. SIGNIFICANCE AND IMPACT OF THE STUDY: The LG genotyping method is a valuable tool for typing C. jejuni isolates obtained from poultry. However, the association between Penner serotyping based on passive haemagglutination of heat-stable antigens and LG genotyping was low when applied to poultry isolates. This is in contrast to previous studies on isolates of human origin that reported a high correlation between results obtained by the two typing methods (Shi et al. 2002).     

The isolation and characterization of Campylobacter jejuni subsp. jejuni from domestic geese (Anser anser)

AIMS: The objectives of this study were to determine the presence of thermophilic Campylobacter spp. in free range domestic geese, and to characterize isolated strains using phenotyping criteria and SDS-PAGE of whole-cell proteins. METHODS AND RESULTS: Forty cloacal swabs from two different flocks of domestic geese were examined. All Camp. jejuni strains isolated from geese were biotyped using the Lior biotyping scheme. Twelve Camp. jejuni isolates were also tested for their susceptibility to 17 different antibacterial agents by a disc diffusion METHOD: Fourteen of the isolates were also subjected to SDS-PAGE. All of the geese examined were found to harbour Camp. jejuni. Six geese carried more than one species of Campylobacter. All strains examined were susceptible to various antibiotics but resistant to penicillin G and cephalothin. Eleven strains (92%) were resistant to sodium cefuroxime, and eight (67%) were resistant to cloxacillin, ampicillin and colistin sulphate. Three strains (25%) were resistant to tetracycline, and one strain was resistant to sulfamethoxazole/trimethoprim and kanamycin. Nine strains were subtyped as Camp. jejuni subsp. jejuni biotype II and the remaining ones as biotype I. There were 96% and 100% similarities between all the strains examined by SDS-PAGE. CONCLUSION: This study showed that Camp. jejuni were common in the intestinal tract of domestic geese. SIGNIFICANCE AND IMPACT OF THE STUDY: Geese should be considered as potential reservoirs for human and animal campylobacteriosis. The antibiotic resistance data from this study also showed that fluoroquinolone resistance, which appears to be a problem in poultry isolates in some countries, is not yet a problem in these geese.     

DNA base compositions and base sequence relatedness of atypical Campylobacter jejuni strains from clinical material

Abstract The relationships of nitrate-negative campylobacters (NNC) resembling Campylobacter jejuni were investigated by DNA base composition estimation (T _m method) and DNA-DNA hybridization (S1 endonuclease assay). The 8 NNC strains which were from clinical material formed a homogeneous DNA group with a high level of relatedness (approx. 70%) to typical (nitrate-positive) C. jejuni , but were less similar (approx. 35%) to Campylobacter coli , and only slightly related (≥ 10%) to Campylobacter fetus, Campylobacter laridis and Campylobacter sputorum . The NNC strains showed small but consistent genome differences from typical C. jejuni . As these differences can be correlated with several bacteriological test differences, we conclude that the NNC strains constitute a distinct subspecies within C. jejuni .