A Rapid Identification Scheme for Helicobacter pylori and Other Species of Helicobacter Based on 23S rRNA Gene Polymorphisms

Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene

Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.

Anaerobic oral flora in the North American black bear (Ursus americanus) in eastern North Carolina

Microbial flora can provide insight into the ecology and natural history of wildlife in addition to improving understanding of health risks. This study examines the anaerobic oral flora of hunter killed black bears (Ursus americanus) in eastern North Carolina. Oral swabs from the buccal and lingual supragingival tooth surfaces of the first and second mandibular and maxillary molars of 22 black bears were inoculated onto Brucella Blood Agar plates supplemented with hemin and vitamin K after transport from the field using reduced oxoid nutrient broth. Sixteen anaerobic bacterial species, representing nine genera were identified using the RapID ANA II Micromethod Kit system and a number of organisms grown that could not be identified with the system. The most frequently identified anaerobes were Peptostreptococcus prevotii, Streptococcus constellatus, and Porphyromonas gingivalis. The diversity in the anaerobic oral flora of black bear in eastern North Carolina suggests the importance of including these organisms in basic health risk assessment protocols and suggests a potential tool for assessment of bear/habitat interactions.

Development of a simple and rapid method based on polymerase chain reaction-based restriction fragment length polymorphism analysis to differentiate Helicobacter, Campylobacter, and Arcobacter species

Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of amplified DNA fragment of the 16S and 23S rRNA genes was performed on 35 Helicobacter, 24 Campylobacter, and 15 Arcobacter strains. PCR amplification generated a 1004-bp fragment of 16S rDNA and a 2.6-Kbp fragment of 23S rDNA from each strain. The amplicons were digested with DdeI and HpaII, respectively. For both assays, distinctive profiles were obtained for each genus. 23S rDNA PCR-RFLP analysis with HpaII enzyme identified Campylobacter and Helicobacter strains at the species level. Analysis of 16S rRNA gene with DdeI enzyme was not useful for the specific identification of Campylobacter and Arcobacter, although it discriminated among Helicobacter species. The PCR-RFLP technique allowed for the discrimination among these three related genus with only one restriction enzyme; therefore it can be a simple, rapid, and useful method for routine identification.

Comparison of Helicobacter spp. in Cheetahs (Acinonyx jubatus) with and without gastritis

Chronic gastritis causes significant morbidity and mortality in captive cheetahs but is rare in wild cheetahs despite colonization by abundant spiral bacteria. This research aimed to identify the Helicobacter species that were associated with gastritis in captive cheetahs but are apparently commensal in wild cheetahs. Helicobacter species were characterized by PCR amplification and sequencing of the 16S rRNA, urease, and cagA genes and by transmission electron microscopy of frozen or formalin-fixed paraffin-embedded gastric samples from 33 cheetahs infected with Helicobacter organisms (10 wild without gastritis and 23 captive with gastritis). Samples were screened for mixed infections by denaturant gel gradient electrophoresis of the 16S rRNA gene and by transmission electron microscopy. There was no association between Helicobacter infection and the presence or severity of gastritis. Eight cheetahs had 16S rRNA sequences that were most similar (98 to 99%) to H. pylori. Twenty-five cheetahs had sequences that were most similar (97 to 99%) to "H. heilmannii" or H. felis. No cheetahs had mixed infections. The ultrastructural morphology of all bacteria was most consistent with "H. heilmannii," even when 16S rRNA sequences were H. pylori-like. The urease gene from H. pylori-like bacteria could not be amplified with primers for either "H. heilmannii" or H. pylori urease, suggesting that this bacteria is neither H. pylori nor "H. heilmannii." The cagA gene was not identified in any case. These findings question a direct role for Helicobacter infection in the pathogenesis of gastritis and support the premise that host factors account for the differences in disease between captive and wild cheetah populations.

Phylogenetic analysis of gastric and enterohepatic Helicobacter species based on partial HSP60 gene sequences

Analysis of 16S rRNA gene sequences has been the method generally used to study the evolution and phylogeny of bacteria. Phylogenetic analysis of the 16S rRNA gene has shown the position of the genus Helicobacter in the epsilon-subclass of the Proteobacteria. Because 16S rRNA-based phylogeny does not always correspond to the results of polyphasic taxonomy, and the related species cannot always be separated, new phylogenetic markers for Helicobacter species are needed. In this study, conserved partial (600 bp) 60 kDa heat-shock protein (HSP60) sequences were used to study the phylogeny of 37 strains of gastric and enterohepatic Helicobacter species, including type strains of 15 Helicobacter species with validly published names, reference strains of flexispira taxa and Helicobacter felis, Helicobacter bizzozeronii and Helicobacter salomonis and canine flexispira strains. The partial HSP60 gene sequence proved to be a useful phylogenetic marker for the genus Helicobacter, providing a means of differentiating all 15 Helicobacter species analysed. In the resulting phylogenetic tree, gastric Helicobacter species and enterohepatic species with flexispira morphology formed tight, separate clusters. In general, HSP60 sequence similarities between Helicobacter species were significantly lower than the corresponding 16S rRNA gene sequence similarities, indicating a better resolution for species identification. In addition, a specific PCR method for identifying H. salomonis was developed based on the partial HSP60 sequence.

Helicobacter sp. flexispira 16S rDNA taxa 1, 4 and 5 and Finnish porcine Helicobacter isolates are members of the species Helicobacter trogontum (taxon 6)

The term 'flexispira' refers to micro-organisms with a particular morphology: fusiform-shaped with helical periplasmic fibrils and bipolar tufts of sheathed flagella. Two flexispira taxa have been formally named, Helicobacter bilis and Helicobacter trogontum, a third named species is Helicobacter aurati and eight additional 16S rRNA sequence-based flexispira taxa have been described by Dewhirst et al. (Int J Syst Evol Microbiol 50, 1781-1787, 2000) and given the provisional designation Helicobacter sp. flexispira taxa 1-5, 7, 8 and 10. In the present study, seven gastric or intestinal flexispira isolates from seven Finnish pigs originating from different farms were characterized. Morphologically, all these porcine isolates had typical flexispira morphology. Analysis of the 16S rDNA sequences of five isolates showed that they were most closely related to the sequences of flexispira taxa 4 and 5 and H. trogontum (taxon 6), but less closely related to taxa 1-3 and 8, H. bilis and H. aurati. Phenotypic characterization, analysis of RFLPs of 16S and 23S rDNAs and SDS-PAGE profiles revealed that all of the porcine isolates, reference strains of flexispira taxa 1, 4 and 5 and the type strain of H. trogontum (ATCC 700114T) had highly related characteristics that differed from those of the reference strains of taxa 2, 3 and 8 and H. bilis. Furthermore, a high DNA-DNA binding rate was found, in dot-blot hybridization studies, between the Finnish porcine strains, taxa 1, 4 and 5 reference strains and H. trogontum ATCC 700114T. In conclusion, polyphasic characterization of novel porcine flexispira isolates and previously described taxa 1, 4 and 5 reference strains showed that they all belong to a validly described species, H. trogontum, and that the taxonomy of known flexispiras is less complicated than proposed on the basis of 16S rDNA sequence analysis.

Isolation and characterization of Campylobacter, Helicobacter, and Anaerobiospirillum strains from a puppy with bloody diarrhea

We carried out a microscopic examination of stools from a 2-month-old female puppy with bloody diarrhea, and this revealed large numbers of different spiral-shaped bacteria. To isolate these organisms, a rectal swab specimen was inoculated onto plates of Skirrow's agar and incubated at 37 degrees C for 6 days in a microaerobic atmosphere. Finally, a total of six different spiral-shaped bacteria (strains G1104, 94105, FR106, B0101, 3J102, and J2103) were isolated. Based on their morphology, biochemical traits, whole-cell protein profiles, and analysis of their 16S rDNA sequences, they were identified as Campylobacter upsaliensis, Helicobacter cinaedi, 'Flexispira rappini', two Anaerobiospirillum spp. with different morphologies, and Helicobacter sp., respectively. Analysis of 16S rRNA gene sequence data for strains 94150 (H. cinaedi) and FR106 (F. rappini) revealed that this approach has limitations when identifying isolates to the species level because of a high degree of sequence homology between these species (>99%) and considerable sequence variation among different isolates within these species. The dog was treated orally with amoxicillin for 3 days, which resolved the diarrhea. However, 1 day after the last dose the bloody diarrhea recurred but regarded to six more days amoxicillin treatment. This suggests a bacterial cause for the diarrhea. The approach to identification to microaerobic spiral-shaped bacteria in diarrheic dogs can be applied further to characterize their role in diarrhea illness.

Captive rhesus monkeys (Macaca mulatta) are commonly infected with Helicobacter cinaedi

Helicobacter cinaedi may cause proctocolitis or bacteremia in homosexual men infected with human immunodeficiency virus or occasionally in other immunocompromised hosts. There are scattered reports of H. cinaedi isolated from a variety of animal hosts, but to date only hamsters have been found to be a common natural reservoir. Microaerophillic cultures of feces from 5 of 16 asymptomatic rhesus monkeys (Macaca mulatta) (31%) were positive for a curved gram-negative rod. A polyphasic taxonomic approach was used to identify the organism as H. cinaedi. These results show that H. cinaedi frequently colonizes asymptomatic captive rhesus monkeys, which may serve as another potential reservoir for human infection.

Comparison of 23S polymerase chain reaction-restriction fragment length polymorphism and amplified fragment length polymorphism techniques as typing systems for thermophilic campylobacters

In this study, we evaluated the combination of polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and amplified fragment length polymorphism (AFLP) molecular typing techniques for the analysis of thermophilic campylobacter species isolated from clinical and poultry samples. 23S PCR-RFLP analysis performed to fingerprint 69 strains exhibited an excellent level of typability. Eleven different types were defined at 100% linkage level following numerical analysis of band patterns. Differentiation of Campylobacter jejuni and Campylobacter coli at species level was achieved although no significant relationship could be observed between the profiles and the origin of the strains. Simplified AFLP analysis of the isolates disclosed the presence of 66 different banding patterns. The resulting dendrogram showed a high diversity among the strains studied. All the isolates were grouped within eight main types with a 69% homology degree among them. Differentiation at subspecies level was possible but no significant relationship could be observed between the AFLP profiles and the origin of the strains. When used in combination, 23S PCR-RFLP and single-enzyme AFLP methods can be applied to determine taxonomic and epidemiological relationships among thermophilic campylobacters.

A phylogenetic analysis of Bacillus thuringiensis serovars by RFLP-based ribotyping

AIMS

To determine the 23S and 5S rRNA gene fingerprints in order to reveal phylogenetic relationships among Bacillus thuringiensis strains.

METHODS AND RESULTS

Eighty-six B. thuringiensis strains which include 80 serovar type strains, five intraserovar strains and a non-serotypeable strain, wuhanensis, were tested. Total DNA was digested with EcoRI and HindIII. The 23S and 5S rRNA gene restriction fragment length polymorphisms showed 82 distinctive ribopatterns. The dendrogram generated by numerical analysis showed 10 phylogenetic groups and six ungrouped serovars at the 95.5% DNA relatedness rate. A second dendrogram was constructed using a combination of the data from this study and from a previous study on 16S rRNA gene fingerprinting. It revealed eight distinct phylogenetic groups and three ungrouped serovars at the 94% DNA relatedness rate.

CONCLUSION

This method permitted the classification and positioning of a wide variety of B. thuringiensis strains on a phylogenetic tree. Bacillus thuringiensis strains appear to be relatively homogeneous and to share a high degree of DNA relatedness.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study contributes a further step to the definition of valid taxonomic sublevels for the B. thuringiensis species.

Accurate diagnosis of Helicobacter pylori. Polymerase chain reaction tests

Although PCR has improved considerably the sensitivity of the diagnosis of H. pylori infection, many studies have not shown conclusively the full potential of PCR in clinical diagnosis. In daily clinical practice, PCR does not have to be performed to establish H. pylori infection. PCR is still classified primarily as a research technique in the Helicobacter field. PCR or similar technology will expand in the future when automation and commercialized kits are available to most laboratories. The development of a noninvasive PCR test may prove useful because it may lead ultimately to the determination of the source and route of transmission of this important pathogen.

Misidentifying helicobacters: the Helicobacter cinaedi example

Whole-cell protein electrophoresis and biochemical examination by means of a panel of 64 tests were used to identify 14 putative helicobacters to the species level. The results were confirmed by means of DNA-DNA hybridization experiments and were used to discuss misidentification of helicobacters based on 16S rRNA gene sequence data. The data indicated that comparison of near-complete 16S ribosomal DNA sequences does not always provide conclusive evidence for species level identification and may prove highly misleading. The data also indicated that "Helicobacter westmeadii" is a junior synonym of Helicobacter cinaedi and that Helicobacter sp. strain Mainz belongs to the same species. H. cinaedi occurs in various animal reservoirs, including hamsters, dogs, cats, rats, and foxes. Appropriate growth conditions and identification strategies will be required to establish the genuine significance of this widely distributed Helicobacter species.

Campylobacter coli strains with enlarged flagellin genes isolated from river water

A group of campylobacters isolated from river water were found to possess unusually large flagellin genes. Both phenotype and serology were consistent with identification as Campylobacter coli. Phylogenetic analysis of small (16S, rrs) and large subunit (23S, rrl) rRNA genes of a representative strain, NCTC 13006, demonstrated high levels of relatedness with C. jejuni and C. coli (99.1 and 98.3% similarity for 16S; 99.3 and 99.4% similarity for 23S). Large flagellin proteins were demonstrated by SDS-PAGE analysis. The flaA and flaB genes were sequenced and aligned with known campylobacter flagellin amino acid sequences. The encoded FlaA protein of the new group exhibited a high degree of divergence from other Campylobacter species. Within the central variable region of FlaA, a further hypervariable domain was identified containing characteristic repeated motifs. Separate pairwise alignments performed for the variable regions of the polypeptide indicated these large fla genes were more closely related to those of C. upsaliensis than to those of C. coli or C. jejuni.

Evaluation of a molecular identification scheme based on 23S rRNA gene polymorphisms for differentiating canine and feline gastric Helicobacter spp

A scheme for the rapid identification of Helicobacter spp. using restriction fragment length polymorphism digestion profiles of PCR amplified 23S rRNA genes is described. The efficacy of this scheme for speciation of the closely related gastric species H. felis, H. bizzozeronii and H. salomonis was evaluated. It was difficult to distinguish between some RFLP profiles obtained and often, more than one profile was seen with each species examined. Some evidence was found that the 23S rRNA gene copies of these species may not be identical. Moreover, the identification scheme was ineffective in discriminating these species from each other, although they could be differentiated, as a group, from other Helicobacter spp. The results indicate that this scheme should be carefully evaluated with a number of isolates if it is to be applied to additional, highly related Helicobacter spp.

Characterization of Helicobacter felis by pulsed-field gel electrophoresis, plasmid profiling and ribotyping

BACKGROUND

Helicobacter felis, an organism naturally infecting both canine and feline gastric mucosa, has been largely used as in animal models to study the ecology and treatment of human Helicobacter pylori infections. H. felis has not yet been studied at the genetic level.

METHODS

The aims of this study were to modify an in situ DNA isolation method suitable for H. felis and, by the use of pulsed-field gel electrophoresis (PFGE), plasmid profiling, and ribotyping, to determine the degree of genetic variation among H. felis strains isolated from cats and dogs from various geographic locations, and to determine the genome size of H. felis. Furthermore, the ability of these new H. felis strains to colonize mice was tested.

RESULTS

Most H. felis strains were distinguishable from each other, and 20 distinct PFGE types were detected. Four pairs of strains within a country and animal species produced identical patterns. All strains tested were found to carry several plasmids and plasmid profiling was equally discriminatory to PFGE. Ribotyping was not able to discriminate all the strains.

CONCLUSIONS

The genome size of H. felis was found to be approximately 1.6 Mb.