Randomly amplified polymorphic DNA analysis confirms the biotyping scheme of Porphyromonas gingivalis

Osmotic stress-induced genetic rearrangements in Escherichia coli H10407 detected by randomly amplified polymorphic DNA analysis

Randomly amplified polymorphic DNA (RAPD) analysis is a DNA polymorphism assay commonly used for fingerprinting genomes. After optimizing the reaction conditions, samples of Escherichia coli H10407 DNA were assayed to determine the influence of osmotic and/or oligotrophic stress on variations in RAPD banding patterns. Genetic rearrangements or DNA topology variations could be detected as changes in agarose gel electrophoresis banding profiles. A new amplicon generated using DNA extracted from bacteria prestarved by an osmotic stress and resuscitated in rich medium was observed. Enrichment improved recovery of mutator cells and allowed them to be detected in samples, suggesting that DNA modifications, such as stress-induced alterations and supercoiling phenomena, should be taken into consideration before beginning RAPD analyses.

An Examination of ‘Unidentified’Prevotella (Formerly PINLO) using RAPD-PCR and Partial 16S rRNA Gene Sequencing

Prevotella intermedia- and Prevotella nigrescens-like organisms (PINLO) have been described as organisms which are phenotypically and biochemically similar to P. intermedia and P. nigrescens and the species P. pallens was created to include some of them. Other PINLO groups which do not fit the definition of P. pallens exist, and in this study these 'unidentified' Prevotella sp. were compared with P. corporis, P. intermedia, P. nigrescens and P. pallens using commercial identification kits, GLC, RAPD-PCR and partial 16S rRNA gene sequencing. The Rapid ID 32 A and the RapID ANA II system both identified all 'unidentified' Prevotella as P. intermedia. Similarly they gave this identification to all the species tested (with the exception of P. corporis using the RapID ANA II system) clearly demonstrating biochemical similarities. Gas liquid chromatography (GLC) analysis of the volatile end-products of fermentation could not distinguish between strains. RAPD-PCR using arbitrary primer L10 demonstrated intra-species homogeneity within PINLO strains with amplification profiles which differed from other Prevotella species tested. Cluster analysis of the amplification profiles confirmed species divisions and yielded a distinct 'unidentified' Prevotella cluster. Comparison of partial 16S rDNA sequences displayed 98% sequence similarity between the 'unidentified' Prevotella strains, although 2 strains, HST 1156 and HST 2160 displayed 100% identity. The highest similarity between groups was seen between 'unidentified' Prevotella strains and P. corporis (approximately 94% similarity). The DNA techniques used here confirm that 'unidentified' Prevotella strains are distinct from the other species of Prevotella tested, including P. pallens. Partial 16S rDNA sequence comparisons suggested a close relationship with P. corporis.

Bacteroides fragilis isolates compared by AP-PCR

Bacteroides fragilis is a component of the normal intestinal flora and an important pathogen in nonintestinal endogenous infections. It has been associated with enteric infections and has already been detected in polluted water. In order to evaluate the genetic diversity of B. fragilis, a total of 31 isolates and two reference strains were examined. This collection included strains from nonintestinal infections [12], intestinal infections [5], intestinal microflora [10], aquatic environments [4], and the reference strains ATCC 25285 and ATCC 23745. DNA fingerprints were detected using two separate PCR reactions with different arbitrary primers. The computer-assisted system Taxotron (Institut Pasteur, Dr P. Grimont) was used to analyze the profiles obtained and dendrograms were generated. By using a distance of 0.65 as the threshold, two clusters (hereafter referred to as genotypes I and II) were defined. Strains of differents origins could be distributed into both genotypes. We were unable to detect any obvious correlation between a given genotype and the specific disease or the source of the corresponding strains.

Identification of oral mitis group streptococci by arbitrarily primed polymerase chain reaction

"Mitis group" streptococci are commensal but may play some role in dental caries, septicemia or endocarditis. Rapid genotypic identification would aid studies of dental plaque ecology, or diagnostic use. AP-PCR with 58 unpaired arbitrary primers was used to characterize 7 Streptococcus gordonii, 11 Streptococcus sanguis, 2 Streptococcus crista, 5 Streptococcus parasanguis, 18 Streptococcus oralis, and 36 Streptococcus mitis (22 biovar 1 and 14 biovar 2). S. parasanguis 16S rRNA variable region primer RR2 produced species-specific bands with all S. gordonii and S. sanguis. Human V beta 1 T-cell receptor primer 434 yielded concordant genotypic identification of all phenotypically defined S. crista and S. parasanguis, 83% of S. oralis, and 74% of S. mitis biovar 1. Amplicon patterns for S. mitis biovar 2 were heterogeneous. Findings suggest that primers RR2 and 434 in succession will allow rapid identification of genotypic groups corresponding closely to mitis group species established by phenotype.

Genetic relatedness between oral and intestinal isolates of Porphyromonas endodontalis by analysis of random amplified polymorphic DNA

Genomic fingerprints from the DNA of 27 strains of Porphyromonas endodontalis from diverse clinical and geographic origins were generated as random amplified polymorphic DNA (RAPD) using the technique of PCR amplification with a single primer of arbitrary sequence. Cluster analysis of the combined RAPD data obtained with three selected 9- or 10-mer-long primers identified 25 distinct RAPD types which clustered as three main groups identifying three genogroups. Genogroups I and II included exclusively P. endodontalis isolates of oral origin, while 7/9 human intestinal strains of genogroup III which linked at a similarity level of 52% constituted the most homogeneous group in our study. Genotypic diversity within P. endodontalis, as shown by RAPD analysis, suggests that the taxon is composed of two oral genogroups and one intestinal genogroup. This hypothesis remains to be confirmed.

Identification of Legionella species by random amplified polymorphic DNA profiles

Random amplified polymorphic DNA (RAPD) was used for the identification of Legionella species. Primer SK2 (5'-CGGCGGCGGCGG-3') and standardized RAPD conditions gave the technique a reproducibility of 93 to 100%, depending on the species tested. Species-specific patterns corresponding to the 42 Legionella species were consequently defined by this method; the patterns were dependent on the recognition of a core of common bands for each species. This specificity was demonstrated by testing 65 type strains and 265 environmental and clinical isolates. No serogroup-specific profiles were obtained. A number of unidentified Legionella isolates potentially corresponding to new species were clustered in four groups. RAPD analysis appears to be a rapid and reproducible technique for identification of Legionella isolates to the species level without further restriction or hybridization.

Arbitrarily primed polymerase chain reaction fingerprinting for the genotypic identification of mutans streptococci from humans

Determining whether two strains of bacteria are unique, identical or clonally related depends upon comparisons of phenotypic and/or genotypic traits. Individual isolates can then be grouped according to differences or similarities among those traits. One method of genotyping strains of bacteria is commonly referred to as chromosomal DNA fingerprinting. Previously, we generated chromosomal DNA fingerprints of mutans streptococci to study the transmission of this organism within families. Here, we developed and evaluated an arbitrarily primed polymerase chain reaction (AP-PCR) method for the genotypic characterization of mutans streptococci. Results were compared to those derived from the more conventional chromosomal DNA fingerprinting method. First, we showed that randomly selected clinical isolates displayed a unique banding profile by both methods; the mean similarity indices between DNA fragment patterns were 0.69 for chromosomal DNA fingerprinting and 0.74 for AP-PCR. This indicated that AP-PCR demonstrated less diversity than chromosomal DNA fingerprinting. Subsequently, we tested the agreement between chromosomal DNA fingerprinting and AP-PCR in determining genotypic similarities among 21 mutans streptococci strains obtained from 10 mother-child pairs, and 5 mutans streptococci strains from 5 fathers. The Kappa value for agreement was 0.88. We conclude that AP-PCR, which generates patterns of 8 to 12 amplicons, is capable of distinguishing strains of mutans streptococci among non-related individuals. Moreover, AP-PCR can discern both homogeneity and heterogeneity of mutans streptococci genotypes among mother and child pairs. Overall, we found that AP-PCR gave results comparable to those of chromosomal DNA fingerprinting.

The first clinical isolate of Legionella parisiensis, from a liver transplant patient with pneumonia

A bluish white autofluorescent strain of Legionella was isolated from the tracheal aspirate of a female liver transplant patient who developed hospital-acquired pneumonia. This strain had biochemical characteristics compatible with those of L. cherrii, L. anisa, and L. parisiensis and could not be differentiated from L. bozemanii and L. parisiensis by the direct fluorescent-antibody assay. Phylogenetic analysis of partial 16S rRNA gene sequences of this strain (ATCC 700174) revealed the closest homology to the species L. parisiensis (99.5%). An L. parisiensis species-specific profile was also identified by a random amplified polymorphic DNA technique. This is the first report of L. parisiensis isolation from humans.

Similarity of salivary and subgingival Prevotella intermedia and Prevotella nigrescens isolates by arbitrarily primed polymerase chain reaction

The distribution and the genetic similarity of Prevotella intermedia and Prevotella nigrescens in saliva and in subgingival samples recovered from the same subject were studied in 16 subjects with different periodontal status. The isolates (4 salivary and 4 subgingival P. intermedia/nigrescens group isolates per subject) were identified to species level by hybridization with species-specific oligonucleotide probes, and the clonal analysis was performed using arbitrarily primed polymerase chain reaction (AP-PCR) (all isolates) and ribotyping (isolates from 5 subjects). In addition, the applicability of AP-PCR in differentiating between P. intermedia and P. nigrescens species was tested using 18 P. intermedia and 20 P. nigrescens isolates from 34 subjects. P. intermedia was detected in 7 and P. nigrescens in 14 of the 16 subjects. In all subjects the same species was found both in saliva and in subgingival plaque. In 15 of the 16 subjects, similar AP-PCR types of P. intermedia and/or P. nigrescens between salivary and subgingival samples were found. The salivary and subgingival isolates that were similar by AP-PCR were indistinguishable also by ribotyping. The AP-PCR analysis revealed a P. intermedia or P. nigrescens species-specific AP-PCR product in most isolates. This study indicates that both P. intermedia and P. nigrescens were found both in salivary and in subgingival samples, and both sampling sites within the same individual were usually colonized with identical AP-PCR types of the species. Thus, in addition to a subgingival sample a salivary sample seems to be suitable for detection and clonal analysis of these species. The AP-PCR method proved to be a simple method applicable for differentiation and clonal analysis of P. intermedia and P. nigrescens.

Rapid genotyping of Escherichia coli O157 isolates by random amplification of polymorphic DNA

Although several typing methods have been described for Shiga-like toxin-producing Escherichia coli O157, the methods are somewhat cumbersome. Using 22 isolates of Escherichia coli O157 and five other Escherichia coli isolates, two primers (M13 core sequence and 970-11) were found to give excellent differentiation between isolates using random amplified polymorphic DNA (RAPD). Using only the presence or absence of variable bands, a matrix of 20 variable characters was identified. From these characters, similarity coefficients were calculated and a phenogram constructed. All of the Escherichia coli O157 isolates were easily distinguished from the non-O157 Escherichia coli isolates. Using a 95% similarity cutoff, we found 13 RAPD types among the 22 Escherichia coli O157 isolates. Isolates thought to be identical by toxin and phage typing as well as by epidemiological association were distinguished, and others thought to be distinct by lack of epidemiological association were identical. RAPD using M13 and 970-11 primers is a potentially useful typing tool for Escherichia coli isolates of serotype O157 and possibly other Escherichia coli isolates.

Isolation of Porphyromonas gingivalis strain from tubal-ovarian abscess

An unusual case of involvement of Porphyromonas gingivalis is described. Two anaerobic isolates, identified as Fusobacterium nucleatum and P. gingivalis, were recovered from the pus of a tubal-ovarian abscess in a 35-year-old woman. Identification of the P. gingivalis isolate was confirmed by randomly amplified polymorphic DNA fingerprinting.

Clonal diversity of the taxon Porphyromonas gingivalis assessed by random amplified polymorphic DNA fingerprinting

A total of 97 strains of the periopathogen Porphyromonas gingivalis were collected. This collection included laboratory strains and clinical isolates of human origin with diverse clinical and geographical origins. Biological diversity was further increased by including 32 strains isolated from the oral cavities of nine different animal species. Genomic fingerprints of the 129 strains were generated as random amplified polymorphic DNAs (RAPDs) by the technique of PCR amplification with a single primer of arbitrary sequence. Four nonameric oligonucleotides were used as single primers, and the banding patterns of the DNA products separated on agarose gels were compared after ethidium ethidium bromide staining. Distance coeffients based on the positions of the major DNA fragments were calculated, and dendrograms were generated. We identified 102 clonal types (CTs) that could be assembled into three main groups by cluster analysis by the unweighted pair group method with mathematic averages. Group I (n = 79 CTs) included all 97 human strains and 6 monkey isolates. The strains in group II (n = 22 CTs) and III (n = 1 CT) were strongly differentiated from those in group I and included only strains of animal origin; they likely represent two cryptic species within the present P. gingivalis taxon. We observed that strains from Old World monkeys clustered together with the human genotype, whereas strains from New World monkeys clustered with the animal genotype. Our results with human strains also indicated that (i) the population structure is basically clonal, (ii) no dominant or widespread CT could be observed, and (iii) no relationship could be established between specific clusters of CTs and the periodontal status of the host. Our results corroborate previous findings by B. G. Loos, D. W. Dyer, T. S. Whittam, and R. K. Selander (Infect. Immun. 61:204-212, 1993) and suggest that P. gingivalis should be considered a commensal of the oral cavity acting as an opportunistic pathogen. Our results are not consistent with the hypothesis that only a few virulent clones of P. gingivalis are associated with disease.

Typing Listeria monocytogenes: a comparison of random amplification of polymorphic DNA with 5 other methods

One hundred Listeria monocytogenes strains were typed by random amplification of polymorphic DNA (RAPD) with three different primers, and the results were compared with those obtained by serotyping, ribotyping, multilocus enzyme electrophoresis, restriction enzyme analysis and phage typing. The RAPD patterns of strains appear to be stable during epidemics even over periods of several years. Reproducibility of the RAPD patterns was good. The discriminatory power of RAPD typing was the best among all the methods tested. RAPD is therefore a very promising tool in the study of listeriosis epidemiology. However, the problems related to the standardization of the technique first have to be resolved before the wide use of RAPD is possible.

Polymerase chain reaction using arbitrary primer for the design and construction of a DNA probe specific for Porphyromonas gingivalis

In this work, we used a novel approach for the design and construction of DNA probes which requires no knowledge of target DNA sequence. We demonstrated that species-specific genetic markers, identified as such among monomorphic, randomly amplified DNA segments generated by the polymerase chain reaction with arbitrary primer can be labelled to yield so-called "anonymous probes". We report here on the construction of such an anonymous probe, 1146 bp long, specific for the Gram-negative anaerobe Porphyromonas gingivalis, a suspected major etiologic agent of chronic periodontitis in adults.