Application of polymerase chain reaction with arbitrary primer (AP-PCR) to strain identification of Porphyromonas (Bacteroides) gingivalis

Comparison of cluster analysis of Porphyromonas gingivalis by arbitrarily primed-polymerase chain reaction between healthy and chronic periodontitis subjects

Introduction

Periodontitis is a chronic destructive inflammatory disease of the oral cavity. The main causative agent is presence of biofilm formed due to different micro-organisms. Among different micro- organisms "red complex" bacteria is known to be the main causative agent in progression of periodontitis. Porphyromonas gingivalis out of the red the complex organism plays a major role in progression of periodontitis. P. gingivalisis present in both in healthy and diseased individuals. The difference in the strains will determine the virulence factor of the organism and also progression of disease. Only few studies have been done showing variation in strains present between healthy and diseased.

Aims

To check the difference in heterogeneity of P. gingivalis in chronic periodontitis and healthy individuals through Arbitrarily Primed-PCR (AP-PCR).

Materials and Methods

A total of 400 subjects (200 each of chronic periodontitisandhealthy individuals) were included. Sub-gingival plaque was collected in the Reduced transport fluid (RTF) medium and processed at the institutional central research laboratory. Presence of P. gingivalis was, confirmed by culture andphenotypical analysis. Further confirmed cases were processed for PCR after DNA extraction using 16S rRNA. Positive cases of P. gingivalis were subjected for AP-PCR for clonal analysis using the specific 272 primer.

Results

In 152(76%) and 98(49%) were confirmed for P. gingivalis in chronic periodontitis and healthy individual respectively by PCR. AP-PCR analysis showed 6 clusters with similarity index in CP and 3 clusters with similarity index in Healthy individuals.

Conclusion

The present study showed difference in clusters between chronic periodontitis and healthy individual'sthussuggestive variantin genetic heterogeneity of P. gingivalis strain between healthy and chronic periodontitis. AP- PCR appears to be a promising tool for clonal analysis of P. gingivalis.

Variability in Genomic and Virulent Properties of Porphyromonas gingivalis Strains Isolated From Healthy and Severe Chronic Periodontitis Individuals

Porphyromonas gingivalis has been extensively associated with both the onset and progression of periodontitis. We previously isolated and characterized two P. gingivalis strains, one from a patient exhibiting severe chronic periodontitis (CP3) and another from a periodontally healthy individual (H3). We previously showed that CP3 and H3 exhibit differences in virulence since H3 showed a lower resistance to cationic peptides compared with CP3, and a lower ability to induce proliferation in gingival epithelial cells. Here, we aimed to determine whether differences in virulence between these two strains are associated with the presence or absence of specific genes encoding virulence factors. We sequenced the whole genomes of both P. gingivalis CP3 and H3 and conducted a comparative analysis regarding P. gingivalis virulence genetic determinants. To do so, we performed a homology search of predicted protein sequences in CP3 and H3 genomes against the most characterized virulence genes for P. gingivalis available in the literature. In addition, we performed a genomic comparison of CP3 and H3 with all the 62 genomes of P. gingivalis found in NCBI's RefSeq database. This approach allowed us to determine the evolutionary relationships of CP3 and H3 with other virulent and avirulent strains; and additionally, to detect variability in presence/absence of virulence genes among P. gingivalis genomes. Our results show genetic variability in the hemagglutinin genes. While CP3 possesses one copy of hagA and two of hagC, H3 has no hagA and only one copy of hagC. Experimentally, this finding is related to lower in vitro hemmaglutination ability of H3 compared to CP3. Moreover, while CP3 encodes a gene for a major fimbrium subunit FimA type 4 (CP3_00160), H3 possess a FimA type 1 (H3_01400). Such genetic differences are in agreement with both lower biofilm formation ability and less intracellular invasion to oral epithelial cells exhibited by H3, compared with the virulent strain CP3. Therefore, here we provide new results on the genome sequences, comparative genomics analyses, and phenotypic analyses of two P. gingivalis strains. The genomics comparison of these two strains with the other 62 genomes included in the analysis provided relevant results regarding genetic determinants and their association with P. gingivalis virulence.

Overestimation of an Outbreak of Enterobacter cloacae in a Neonatal Intensive Care Unit in Germany, 2015

BACKGROUND

In August 2015, 17 neonates with Enterobacter cloacae (E. cloacae) colonization were identified in a neonatal intensive care unit (NICU) in Germany. Two developed severe brain abscesses. Despite temporary NICU closure in September, another infant with E. cloacae colonization was detected in October 2015.

METHODS

We defined potential cases as inpatients treated in the NICU or any pediatric/maternity ward in 2015 with E. cloacae in any specimen before molecular typing. Cases were at first confirmed by arbitrarily-primed-polymerase-chain-reaction and later by XbaI-macrorestriction/pulsed-field gel electrophoresis and next-generation-sequencing. Enhanced barrier precautions and cohorting were implemented for all potential cases and microbiologic screening was extended from NICU to all pediatric/maternity wards.

RESULTS

Of 41 potential cases (occurring between 08/04/2015 and 15/11/2015 in 4 wards), the isolates of 23 shared identical arbitrarily-primed-polymerase-chain-reaction patterns; 3 without plausible epidemiologic link. Pulsed-field gel electrophoresis analyses verified only 10 cases (all in the NICU); next-generation-sequencing analysis confirmed these results. In addition 6 cases without isolates available for genotyping were closely linked in place and time.

CONCLUSIONS

Forty-one suspected patients were cohorted and the NICU was temporarily closed. Further analyses revealed that only 16 cases belonged to the outbreak. Only close interdisciplinary collaboration and highly discriminatory genotyping methods allowed to clearly differentiate between cases and noncases in this E. cloacae outbreak.

Identification of multiple strains of Porphyromonas gingivalis using heteroduplex polymerase chain reaction in varying severity of chronic periodontitis

Aim

Research has demonstrated that there are multiple strains of Porphyromonas gingivalis with varying potency to cause periodontal disease. The current study aims at using heteroduplex polymerase chain reaction (PCR) to detect the strain diversity of P. gingivalis in periodontitis lesions of varying severity in a sample of the Indian population.

Materials and Methods

Subgingival plaque samples were collected from 60 individuals with varying severity of chronic periodontitis and 30 individuals with a clinically healthy periodontium. The samples were subjected to PCR analysis to identify P. gingivalis, followed by heteroduplex analysis to identify the strain diversity in a given sample. Bacterial culture was carried out as a comparative standard.

Results

Of the 56 samples that were positive for P. gingivalis by PCR, 54 samples yielded eight different heteroduplex patterns. Analysis of these patterns indicated that two strains of P. gingivalis were present in 41 individuals (45.6%) and three strains were present in 13 individuals (14.4%). Detection of P. gingivalis by PCR was significantly more in the periodontitis group as compared to the healthy group.

Conclusions

Species-specific PCR and heteroduplex analysis provide a simple and accurate method to analyse the strain diversity of P. gingivalis. P. gingivalis was detected in both healthy periodontal sites as well as sites with periodontitis. The presence of two or three P. gingivalis strains was seen in 60% of the samples.

Simple Protocol for Molecular Fingerprinting of Human Oral Microbiota Samples in Lab Classes

DNA fingerprinting is a major tool in identifying individuals and in evidence matching. However, this technique can be difficult to reproduce in practical classes. Here, we report on distinct PCR profiles obtained when amplifying saliva DNA of a score of distinct individuals with Random Amplified Polymorphic DNA (RAPD)-PCR primer BOXA1R. The RAPD-PCR method is simple and efficient for discrimination between bacterial strains and is used in this instance to obtain personalized fingerprints of each individual's oral microbiota. We present real results with undergraduate students confirming that this procedure is easily feasible in practical classes. Based on the results presented, we suggest a laboratory activity for undergraduate Molecular Biology or Microbiology students.

The Study of Genetic Relationship Among Third Generation Cephalosporin-resistant Salmonella enterica Strains by ERIC-PCR

Background and Objectives:

Salmonella is an important food-borne pathogen responsible for disease in humans and animals. The aim of this study was to investigate the genetic relationship among third generation cephalosporin-resistant Salmonella enterica strains by Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR.

Methods:

The study included all Salmonella isolates obtained from clinical cases in a pediatric hospital in Tehran, Iran during 2006 to 2009. Antimicrobial susceptibility testing was performed according to the Clinical and Laboratory Standards Institute. The genetic relationship between third generation cephalosporins-resistant Salmonella enterica strains was determined using ERIC-PCR.

Results:

Of 136 Salmonella enterica isolates recovered from pediatric patients, six isolates including four Salmonella enterica serotype Infantis and two Salmonella enterica serotype Enteritidis showed an extended-spectrum cephalosporins resistant phenotype. ERIC-PCR differentiated Salmonella enterica serotypes Infantis and Enteritidis into 2 distinct clusters arbitrarily named as E1 and E2. Profile E1 was found in two Salmonella enterica serotype Enteritidis isolates, and profile E2 was found in four Salmonella enterica serotype Infantis isolates.

Conclusion:

Extended-spectrum cephalosporins resistant Salmonella could be attributed to a few predominant serotypes including Enteritidis and Infantis in this study. Genetic analysis using ERIC-PCR showed that closely related clones are responsible for the occurrence of extended-spectrum cephalosporins resistant Salmonella infection in Tehran.

Genotypic characterization of Porphyromonas gingivalis isolated from subgingival plaque and blood sample in positive bacteremia subjects with periodontitis

AIM

The objective of this study was to investigate clonal relationship among Porphyromonas gingivalis isolated from subgingival plaque and blood samples in positive transient bacteremia subjects with periodontitis.

MATERIAL AND METHODS

Unrelated patients with general chronic periodontitis or general aggressive periodontitis requiring scaling and root planing (SRP) were included in the study. Genotyping of each isolate was performed using pulsed field gel electrophoresis technique. Genetic relatedness of strains isolated within an individual or between different patients was determined by dendogram analysis.

RESULTS

Following SRP, from 16 patients, seven patients showed positive P. gingivalis bacteremia and nine were negative. Thirty-two strains were isolated from subgingival plaque and blood samples before and during induced transient bacteremia. The majority of the patients harboured one clonal type. Two patients showed different clones in plaque and blood samples suggesting that more than one clone can be found in subgingival plaque. P. gingivalis isolates from periodontitis patients after transient bacteremia following SRP, revealed a high heterogeneity among isolates.

CONCLUSION

In 6/16 subjects the same P. gingivalis isolate was found in the blood and in oral cavity. P. gingivalis heterogeneity suggests no association of a unique clonal type with transient bacteremia.

Random amplified polymorphic DNA (RAPD) analysis of Mycobacterium tuberculosis strains in India

The usefulness of random amplification of polymorphic DNA (RAPD) analysis for typing Indian strains of M. tuberculosis was investigated. M. tuberculosis H37Rv, M. tuberculosis DT and 42 clinical isolates of M. tuberculosis were subjected to RAPD-PCR using 7 random decamer primers. All 7 primers were found to be differentiated and produced specific RAPD profiles. The polymorphic amplicons served as RAPD markers for M. tuberculosis. The dendrograms, obtained by different primers, showed the discriminatory ability of the primers. RAPD analysis provided a rapid and easy means of identifying polymorphism in M. tuberculosis isolates, and it was found to be a valuable alternative epidemiological tool. In addition, the results of the present study showed heterogeneity in the M. tuberculosis strains in the population studied.

Molecular identification of Astragalus membranaceus at the species and locality levels

Astragalus membranaceus (Fisch.) Bunge, a commonly used Chinese medicinal material, from certain localities contains more favourable trace elements and fewer harmful trace elements than those from other localities. Therefore, there is a need to distinguish Astragalus membranaceus from different localities. Internal transcribed spacer 1 (ITS1) of the nuclear ribosomal RNA gene of 23 Astragalus membranaceus samples were sequenced to confirm the species of the samples. Arbitrarily primed polymerase chain reaction (APPCR) was then used to obtain unique fingerprints for each sample using several primers. The presence and absence of bands were used for calculating mean similarity indexes among the samples. It was found that the Heilongjiang samples were markedly distinguishable from samples of other localities. In addition, bands common for samples from the same locality were also identified and used to distinguish samples from Neimengu and Shanxi. Therefore, Astragalus membranaceus from these provinces, the major cultivation places in China, can be differentiated.

Genetic variation of a fimbrial protein from Porphyromonas gingivalis and its distribution in patients with periodontal diseases

Pg-II fim from various strains of Porphyromonas gingivalis was classified on the basis of each nucleotide sequence, while the distribution of Pg-II fim types in 141 subgingival plaque samples was analyzed using PCR assays. Pg-II fim was divided into two types as follows: strains OMZ409, HG405, 381, ATCC 33277 and BH18/10 (type 1) and strains OMZ314 and HW24D-1 (type 2). The presence of P. gingivalis was demonstrated in 2.8% of healthy subjects and 56.1% of patients with periodontal diseases, and Pg-II fim was detected in 91.8% of the P. gingivalis-positive subjects. We also analyzed the distribution of the Pg-II fim types among Pg-II fim-positive patients, with the following results: type 1 (38.2%), type 2 (56.4%) and types 1 and 2 (5.4%). These findings strongly suggest that P. gingivalis organisms possessing Pg-II fim type 2 was principally detected in patients with periodontal diseases.

Multilocus sequence analysis of Porphyromonas gingivalis indicates frequent recombination

In this study, the genetic relationship of 19 Porphyromonas gingivalis isolates from patients with periodontitis was investigated by multilocus sequence analysis. Internal 400-600 bp DNA fragments of the 10 chromosomal genes ef-tu, ftsQ, hagB, gpdxJ, pepO, mcmA, dnaK, recA, pga and nah were amplified by PCR and sequenced. No two isolates were identical at all 10 loci. Phylogenetic analyses indicated a panmictic population structure of P. gingivalis. Split decomposition analysis, calculation of homoplasy ratios and analyses of clustered polymorphisms all indicate that recombination plays a major role in creating the genetic heterogeneity of P. gingivalis. A standardized index of association of 0.0898 indicates that the P. gingivalis genes analysed are close to linkage equilibrium.

Distribution of Bacteroides forsythus genotypes in a Japanese periodontitis population

Bacteroides forsythus is an important pathogen in periodontal diseases and has been associated with advanced and refractory periodontitis. The difficulties associated with culturing this species have meant that the distribution and pathogenic mechanisms of B. forsythus remain unclear. In this study, the arbitrarily primed polymerase chain reaction (AP-PCR) method was used to investigate the genotype distribution of B. forsythus in a Japanese periodontitis population, as well as the relationship between AP-PCR genotypes and periodontal status. B. forsythus reference strain, ATCC 43037T and 137 clinical bacterial isolates from 64 subjects were separated into 11 distinct AP-PCR genotypes using a single randomly-sequenced primer, 5'-CCGGCGGCG-3' (A-05). The majority (80.9%) of B. forsythus strains examined belonged to AP-PCR genotypes I, II, III and IV (accounting for 39.7%, 20.6%, 10.3% and 10.3%, respectively). Types I and III primarily consisted of isolates from chronic periodontitis subjects (80.8% and 85.7%, respectively), while Types II and IV consisted mainly of isolates from aggressive periodontitis subjects (85.7% and 100%, respectively). Except for three subjects who harbored two different B. forsythus genotypes in the oral cavity, all subjects only infected with one genotype intraindividually. These results demonstrate that the AP-PCR method is useful for genotypic analysis of B. forsythus. This species showed a genetic diversity among the investigated population. A clonal nature of B. forsythus infection is suggested. Furthermore, different AP-PCR genotypes of B. forsythus appear to be associated with different types of periodontitis.

Prevalence of putative periodontopathogens from periodontal patients and healthy subjects in Sao Paulo, SP, Brazil

A. actinomycetemcomitans, B. forsythus, P. gingivalis, C. rectus, E. corrodens, P. intermedia, F. nucleatum, and T. denticola were identified from subgingival plaque from 50 periodontal patients and 50 healthy subjects. PCR products from each species showed a specific band and could be used to identify periodontal organisms from clinical specimens. Identical negative or positive results between PCR and culture occurred in 66% (A. actinomycetemcomitans) to 93% (F. nucleatum) of the samples. PCR detection odds ratio values for A. actinomycetemcomitans, B. forsythus, C. rectus, E. corrodens, P. intermedia, and T. denticola were significantly associated with disease having a higher OR values for B. forsythus (2.97, 95% CI 1.88 - 4.70). Cultures showed that A. actinomycetemcomitans, B. forsythus and P. intermedia were associated with periodontitis, however, P. gingivalis, C. rectus, E. corrodens and F. nucleatum were not significantly associated with the disease.

Genetic diversity of Porphyromonas gingivalis and its possible importance to pathogenicity

During recent years much effort has been put into understanding the genetic composition of the oral populations of black-pigmented anaerobic bacteria. One of them, Porphyromonas gingivalis, is a putative periodontopathogenic organism considered to be particularly relevant in the etiology of adult periodontitis. It has been shown in studies using molecular typing methods that most bacterial populations consist of numerous genetic clones, and that only a small proportion of these clones cause disease. Elucidation of a possible association of genotypic profiles with either disease or clinical healthy condition is important for understanding the pathogenic characteristics of bacteria. Studies addressing this issue as it relates to P. gingivalis are reviewed in the present article. Genotypic characterization of P. gingivalis strains has revealed extensive heterogeneity in natural populations of this bacterium. Some of the potential virulence factors of P. gingivalis have been purified and cloned and methods have been established to identify their genes. Although no studies have clearly defined the relationship between a specific genotype of P. gingivalis and periodontal status of the host, it seems that molecular typing tools, which are undergoing rapid improvements, will allow us to distinguish between virulent and avirulent strains of the same species in the near future.

Identification of Porphyromonas gingivalis strains by heteroduplex analysis and detection of multiple strains

Heteroduplex analysis has been used extensively to identify allelic variation among mammalian genes. It provides a rapid and reliable method for determining and cataloging minor differences between two closely related DNA sequences. We have adapted this technique to distinguish among strains or clonal types of Porphyromonas gingivalis. The ribosomal intergenic spacer region (ISR) was amplified directly from a subgingival plaque sample by PCR with species-specific primers, avoiding the need for culturing the bacteria. The PCR products were then directly compared by heteroduplex analysis with known strains of P. gingivalis for identification. We identified 22 distinct but closely related heteroduplex types of P. gingivalis in 1,183 clinical samples. Multiple strains were found in 34% of the samples in which P. gingivalis was detected. Heteroduplex types were identified from these multistrain samples without separating them by culturing or molecular cloning. PCR with species-specific primers and heteroduplex analysis makes it possible to reliably and sensitively detect and identify strains of P. gingivalis in large numbers of samples.

Porphyromonas gingivalis strain variability and periodontitis

To determine if there is variability in virulence among strains of Porphyromonas gingivalis in human periodontitis, their distribution in a group of subjects with clear indicators of periodontitis and in a healthy, age-matched control group was examined. The presence of heteroduplex types of P. gingivalis in the two groups was determined with a PCR-based assay. This assay relied on detection of polymorphisms in the ribosomal internal spacer region (ISR). ISR fragments generated by PCR with P. gingivalis-specific primers were hybridized to fragments from reference strains, and the formation of heteroduplexes from the hybridization of nonidentical sequences was observed by polyacrylamide gel electrophoresis. Characteristic fingerprints from comparison with a panel of reference strains allowed the identification of heteroduplex types in clinical samples. One hundred thirty adults with periodontitis and 181 controls were sampled. With this approach, 11 heteroduplex types of P. gingivalis were detected in the population. Sufficient numbers were available for statistical analysis of six of these types. Heteroduplex type hW83 was found to be very strongly associated with periodontitis (P = 0.0000), and two additional types, h49417 and hHG1691, were also significantly associated with disease. The remaining types, h23A4, h381, and hA7A1, were detected more frequently in subjects with periodontitis than in healthy subjects, but the difference was not significant. These data indicate that virulence in human periodontitis varies among strains of P. gingivalis, and they identify an apparently highly virulent subgroup.

Sequencing of the ribosomal intergenic spacer region for strain identification of Porphyromonas gingivalis

The ribosomal intergenic spacer regions (ISRs) of 19 laboratory strains and 30 clinical samples of Porphyromonas gingivalis were amplified by PCR and sequenced to provide a strain identifier. The ISR is a variable region of DNA located between the conserved 16S and 23S rRNA genes. This makes it an ideal locus for differentiation of strains within a species: primers specific for the conserved flanking genes were used to amplify the ISR, which was then sequenced to identify the strain. We have constructed a P. gingivalis ISR sequence database to facilitate strain identification. ISR sequence analysis provides a strain identifier that can be easily reproduced among laboratories and catalogued for unambiguous comparison.

Identical clonal types of Porphyromonas gingivalis or Prevotella nigrescens recovered from infected root canals and subgingival plaque

Clinical samples from 10 infected root canals and from subgingival plaque in 10 patients were screened by anaerobic culture for black-pigmented anaerobes. A total of 17 Porphyromonas gingivalis and 9 Prevotella nigrescens were obtained from four patients and were identified by species-specific polymerase chain reaction (PCR) amplification. The arbitrarily primed PCR reaction used to examine the genetic diversity of the isolates revealed that the P. gingivalis or P. nigrescens simultaneously present in the root canal system and in subgingival plaque of all four patients were genotypically indistinguishable. These data indicate that the endodontium and the periodontium can be colonized by the same clonal types of black-pigmented anaerobes.

Evaluation of two commercial kits and arbitrarily primed PCR for identification and differentiation of Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, and Haemophilus paraphrophilus

The closely related species Actinobacillus actinomycetemcomitans, Haemophilus aphrophilus, and Haemophilus paraphrophilus are common findings in oral microbiota. The aims of this study were to evaluate the applicability of the Rapid NH and API ZYM kits and arbitrarily primed PCR (AP-PCR) in the identification and differentiation of the three species from each other. The material included 62 clinical isolates and three reference strains of A. actinomycetemcomitans representing the 5 serotypes and 18 AP-PCR genotypes. Haemophilus species included 12 clinical isolates and 11 reference strains of H. aphrophilus, H. paraphrophilus, and 5 other species. For the PCR amplification, the oligonucleotide 5'-CAGCACCCAC-3' was used as a primer. Contrary to the consistent performance of API ZYM, the Rapid NH system was able to identify only 10 of 65 (15%) A. actinomycetemcomitans isolates, whereas all Haemophilus species were correctly identified. The API ZYM test differentiated A. actinomycetemcomitans from H. aphrophilus and H. paraphrophilus by negative beta-galactosidase and alpha-glucosidase reactions and a positive esterase lipase reaction. However, the API ZYM test was unable to differentiate H. aphrophilus from H. paraphrophilus, it also could not differentiate A. actinomycetemcomitans serotypes from each other. Among the H. aphrophilus isolates three AP-PCR genotypes and among H. paraphrophilus isolates only one AP-PCR genotype, distinct from those of A. actinomycetemcomitans, were found. The Rapid NH test showed poor ability to identify clinical isolates of all A. actinomycetemcomitans serotypes. Moreover, AP-PCR genotyping proved to be a rapid method for the species differentiation of A. actinomycetemcomitans, H. aphrophilus, and H. paraphrophilus.

Genetic relationships among Pseudomonas stutzeri strains based on molecular typing methods

Detailed characterization of the genetic variability among strains belonging to Pseudomonas stutzeri was achieved using different rapid molecular typing methods based on polymerase chain reaction (PCR), Southern blot and Western blot. Consensus motifs complementary to fragments of repetitive elements dispersed throughout the genomes of bacteria were used as primers and allowed differentiation at subspecies levels. Further and simple differentiation was also achieved based on the direct amplification of spacer regions between 16S and 23S rRNA, combined with single-strand conformation polymorphism (SSCP) analysis of the generated fragments. These methods are fast, sensitive, reliable for determining relationships, and have demonstrated a great genetic diversity among the strains of Ps. stutzeri studied in agreement with the heterogeneous phenotypic traits of the species.

Transmission of mutans streptococci between mothers and children with cleft lip and/or palate

OBJECTIVE

The aim of this study was to investigate the transmission of Streptococcus mutans between children with cleft lip and/or palate and their mothers.

DESIGN

Saliva samples of 21 mother-child pairs were collected and cultured on plates containing a selective growth medium for mutans streptocci. At least five separate colonies of each colony morphotype were isolated. A polymerase chain reaction (PCR) with randomly chosen primers was used to type the isolates.

RESULTS

The number of morphotypes and PCR types was significantly lower in the children than in the mothers. Significant correlations were found between the number of morphotypes and PCR types, in the children as well as in the mothers. In only 38% of the mother-child pairs were the same PCR types found in mother and child.

CONCLUSIONS

This suggests that S. mutans had been transmitted from mother to child in one-third of the population studied. No correlations were found among the number of colony-forming units, the number of colony-colony-morphotypes, and the number of PCR types of the mothers and transmission. Similar PCR types in mother and child were found significantly more often in children who had more than one PCR type. The results indicate that transmission of S. mutans from mother to child is not frequent in children with oral cleft. This may have consequences for preventive treatment of cleft lip and/or palate children and their mothers.

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.

New strategies on molecular biology applied to microbial systematics

Systematics is the study of diversity of the organisms and their relationships comprising classification, nomenclature and identification. The term classification or taxonomy means the arrangement of the organisms in groups (rate) and the nomenclature is the attribution of correct international scientific names to organisms and identification is the inclusion of unknown strains in groups derived from classification. Therefore, classification for a stable nomenclature and a perfect identification are required previously. The beginning of the new bacterial systematics era can be remembered by the introduction and application of new taxonomic concepts and techniques, from the 50's and 60's. Important progress were achieved using numerical taxonomy and molecular taxonomy. Molecular taxonomy, brought into effect after the emergence of the Molecular Biology resources, provided knowledge that comprises systematics of bacteria, in which occurs great evolutionary interest, or where is observed the necessity of eliminating any environmental interference. When you study the composition and disposition of nucleotides in certain portions of the genetic material, you study searching their genome, much less susceptible to environmental alterations than proteins, codified based on it. In the molecular taxonomy, you can research both DNA and RNA, and the main techniques that have been used in the systematics comprise the build of restriction maps, DNA-DNA hybridization, DNA-RNA hybridization, sequencing of DNA sequencing of sub-units 16S and 23S of rRNA, RAPD, RFLP, PFGE etc. Techniques such as base sequencing, though they are extremely sensible and greatly precise, are relatively onerous and impracticable to the great majority of the bacterial taxonomy laboratories. Several specialized techniques have been applied to taxonomic studies of microorganisms. In the last years, these have included preliminary electrophoretic analysis of soluble proteins and isoenzymes, and subsequently determination of deoxyribonucleic acid base composition and assessment of base sequence homology by means of DNA-RNA hybrid experiments beside others. These various techniques, as expected, have generally indicated a lack of taxonomic information in microbial systematics. There are numberless techniques and methodologies that make bacteria identification and classification study possible, part of them described here, allowing establish different degrees of subspecific and interspecific similarity through phenetic-genetic polymorphism analysis. However, was pointed out the necessity of using more than one technique for better establish similarity degrees within microorganisms. Obtaining data resulting from application of a sole technique isolatedly may not provide significant information from Bacterial Systematics viewpoint.

Identification of microorganisms using random primed PCR

The polymerase chain reaction has facilitated the use of molecular approaches in microbiology including new strategies for the rapid identification of micro-organisms. Approaches based on the use of random primers and standard conditions, allows characteristic DNA fingerprints to be generated from any micro-organism even in the absence of information about its DNA sequence. Different primers can be used to produce genus-specific, species-specific, or even strain-specific DNA fingerprints. This article covers the background to this strategy, describes three different approaches to generating DNA fingerprints using random primers, and provides experimental detail for one method, RAPD.

RAPD fingerprinting for the distinction ofPrevotella intermediasensu stricto fromPrevotella nigrescens

A collection of 70 oral strains including reference strains and clinical isolates identified as Prevotella intermedia sensu lato was constituted to cover a large clinical and geographical diversity. Electrophoresis of the enzyme malate dehydrogenase allowed the identification of the 70 study strains as Prevotella intermedia sensu stricto (n= 36), Prevotella nigrescens (n= 31) and three unclassified strains. By using four primers, DNA fingerprints were generated from 20 strains as random amplified polymorphic DNA (RAPD). Matching co-migrating amplicon positions by pairwise comparison allowed the clustering of the fingerprints as two groups coincident with the P. intermedia/P. nigrescens assignment by enzyme electrophoresis of malate dehydrogenase. Our data suggest that isolates identified asP. intermedia sensu lato by conventional criteria can be speciated asP. intermedia sensu stricto or P. nigrescens by RAPD fingerprinting.

Detection of Genomic Polymorphism in Plasmodium falciparum using an arbitrarily primed PCR assay

Modifications of the arbitrarily primed polymerase chain reaction assay (i.e. a low annealing temperature and a very slow increase in the temperature during the elongation steps during the amplification cycles) allowed it to be used with the AT-rich Plasmodium falciparum DNA. The analysis of the products by polyacrylamide-urea gels, after silver staining, resulted in high resolution and sensitivity. Eighteen single and six combined pairs of arbitrary primers were tested. Two produced polymorphic patterns complex enough to differentiate between close Colombian isolates in a single assay. This method may be useful in studying the distribution and migration of strains in endemic areas, and for identifying intralaboratory cross-contamination of cultures.

Characterization of Serpulina hyodysenteriae isolates of serotypes 8 and 9 by random amplification of polymorphic DNA analysis

A PCR-based DNA fingerprinting method termed RAPD (Random Amplification of Polymorphic DNA), or AP-PCR (for Arbitrary Primed PCR) was used to detect sequence diversity among reference strains and isolates of Serpulina hyodysenteriae. RAPD fingerprinting of 20 S. hyodysenteriae isolates of serotypes 8 or 9 from Quebec was generated with 2 different 10-base primers used independently. Reference strains and field isolates belonging to serotypes 8 or 9 revealed polymorphisms in RAPD fingerprints with both primers. Interspecies polymorphisms were observed by RAPD analysis of S. hyodysenteriae representing serotypes 1 to 9, S.innocens, and 5 other weakly beta-hemolytic intestinal spirochetes. A dendrogram based on the analysis of RAPD profiles of the strains tested with one of the primers (#17), permitted the clustering of these strains into 11 divisions. The predominance of particular RAPD profiles among S. hyodysenteriae isolates isolated from cases of swine dysentery in different herds suggested that certain S. hyodysenteriae types could be epidemiologically important. Our results indicate that RAPD could be used as a typing method for S. hyodysenteriae and as an epidemiological method for identifying spirochetes isolated from swine.

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.

Generation of polymerase chain reaction-specific probes for library screening using single degenerate primers

Degenerate oligonucleotide primers were made to peptide sequences from hydroxylamine oxidoreductase (HAO) from Nitrosomonas europaea. The primers were used singly in PCR reactions to amplify portions of the gene for HAO from genomic DNA. Southern hybridizations using fragments amplified with each primer showed that they labeled the same genomic DNA fragments. The PCR-amplified fragments were successfully used to screen a gene library for clones containing the HAO gene. The method of isolating genes by PCR with single primers has general utility.

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.

Stress response of Porphyromonas gingivalis

The heat shock response of Porphyromonas gingivalis was examined by 1- and 2-dimensional polyacrylamide gel electrophoresis after metabolic labeling with [14C]-amino acids. When P. gingivalis cells were shifted from 37 degrees C to 42 degrees C, elevated synthesis of 4 proteins with the apparent molecular weight of 92, 80, 74, and 62 kDa was observed, and synthesis of a 50-kDa protein decreased during heat shock. The 74- and 62-kDa proteins were identified as homologs of Escherichia coli DnaK and GroEL respectively by Western immunoblotting. On 2-dimensional Western blots, 2 forms of DnaK and 4 forms of GroEL were identified due to their slightly different isolelectric points. dnaK and groEL gene homologs were identified in several P. gingivalis strains and some other black-pigmented oral species. DnaK and GroEL homolog proteins were induced when P. gingivalis cells were challenged by ethanol. These proteins were not induced by oxidative stress or change in pH.

DNA fingerprinting of medically important microorganisms by use of PCR

Selected segments of any DNA molecule can be amplified exponentially by PCR. This technique provides a powerful tool to detect and identify minimal numbers of microorganisms. PCR is applicable both in diagnosis and in epidemiology. By amplification of hypervariable DNA domains, differences can be detected even among closely related strains. PCR fingerprinting is a valuable tool for medical microbiologists, epidemiologists, and microbial taxonomists. The current state of PCR-mediated genotyping is reviewed, and a comparison with conventional molecular typing methods is included. Because of its speed and versatility, PCR fingerprinting will play an important role in microbial genetics, epidemiology, and systematics.

Clonal analysis of Porphyromonas gingivalis by the arbitrarily primed polymerase chain reaction

Genetic analysis of Porphyromonas gingivalis strains may distinguish between virulent and nonvirulent strains and also may be used to trace individual strains in epidemiological studies. The present study examined the utility of the arbitrarily primed polymerase chain reaction for genotypic fingerprinting of P. gingivalis. DNA was extracted according to conventional methods. Ten-base oligonucleotide primers with arbitrary sequences were used with the polymerase chain reaction to amplify P. gingivalis genomic DNA. The amplification products were analyzed by agarose gel electrophoresis. The primer GACCGCTTGT grouped 73 P. gingivalis strains into 23 genotypes, including 16 genotypes containing a single strain each. The primer AGGGGTCTTG identified 45 different genotypes, 33 of which contained a single strain. P. gingivalis strains ATCC 33277T and 381 belonged to the same genotype. Likewise, strains W50 and W83 were of the same genetic clone. The present study indicates that the arbitrarily primed polymerase chain reaction represents a valuable and easy method for clonal analysis of P. gingivalis.

Pseudomonas aeruginosa serotype O12 outbreak studied by arbitrary primer PCR

A total of 16 colonizing and infecting ofloxacin-resistant Pseudomonas aeruginosa strains and two strains isolated from ventilation equipment fluids, all with similar colonial morphologies and with minor but distinct susceptibility differences, were suspected of belonging to a single outbreak and were studied by arbitrary primer (AP) PCR. Thirteen nonrelated strains were included to evaluate the discriminatory capacity of the technique. AP PCR fingerprinting was compared with serotyping, phage typing, and antibiotic susceptibility testing. AP PCR was performed independently with three different primers. The different AP PCR typing systems yielded almost identical patterns for the epidemic strains and enabled us to differentiate most of the nonrelated strains from each other and from the outbreak strains. The combination of AP PCR typing and the phenotyping techniques that we used enabled us to conclude that an outbreak was occurring. In general, the typeability of AP PCR was greater than those of phage typing and serotyping, while the discriminatory powers of the three methods were comparable.

Study of the influence of plasmids on the arbitrary primer polymerase chain reaction fingerprint of Escherichia coli strains

To study the effect of plasmids on the arbitrary primer-polymerase chain reaction fingerprint of bacterial strains, the Escherichia coli strains DH5, Top10, and W3110 were transformed with plasmids of different sizes: respectively, pUC19, pCEP and two clinically important plasmids carrying resistance to several antibiotics. Total DNA, i.e. both chromosomal and plasmid DNA, was prepared from transformed cells by boiling the cell suspensions and by phenol-chloroform extraction; chromosomal DNA was prepared by the same methods from the non-transformed, plasmid-free strains; plasmid DNA of pUC19 was purchased; plasmid DNA of pCEP was purified from the transformed strains by caesium chloride density gradient centrifugation. Arbitrarily primed polymerase chain reaction was carried out for all of these preparations. Amplification carried out independently with three different primers resulted in similar patterns for the chromosomal preparations whether or not plasmid was present. Amplification of plasmid DNA gave different patterns, characterized by fragments larger than those obtained when total or chromosomal DNA were used as the target. These data illustrate that the plasmids studied here do not influence the chromosomal arbitrarily primed PCR fingerprint, although plasmids alone are amplified in the absence of chromosomal DNA. Experiments comparing different relative concentrations of plasmid and chromosomal DNA indicate that under natural conditions the amount of chromosomal DNA per cell is sufficient to inhibit observable amplification of the plasmid(s) present.

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

The application of the arbitrarily primed PCR (AP-PCR) procedure to generate randomly amplified polymorphic DNA (RAPD) fingerprints for the study of the taxon Porphyromonas gingivalis was investigated. Nine human strains and seven animal strains of P. gingivalis as well as eighteen strains other than P. gingivalis were analysed. Four nanomer primers of random sequence were evaluated for their ability to distinguish genetic diversity. Three primers generated RAPD fingerprints that allowed the sixteen strains to be differentiated; two of the primers yielded species-specific markers, and two of the primers permitted biotype distinction. Cluster analysis of the RAPD fingerprints revealed two major phenetic groups that matched the human and animal biotypes. Our results indicate that AP-PCR (i) can generate strain-specific fingerprints, (ii) confirms genetic heterogeneity and the biotype grouping of the P. gingivalis taxon, and (iii) enables identification of potential genetic markers at the species, biotype and subtype levels and is thus a promising tool for bacterial systematics. Our results also underline the potential of AP-PCR for epidemiological studies of periodontal pathogens.

Phenotypic characterization of human and animal biotypes within the species Porphyromonas gingivalis

Ninety-nine strains of Gram-negative black-pigmented anaerobic rods, grown on Todd-Hewitt blood agar plates, were identified and characterized according to a typing scheme including UV fluorescence, catalase, trypsin-like and haemagglutinating activities, biochemical tests with the ATB 32A kit, and gas-liquid chromatography. To determine the taxonomic position of the Porphyromonas gingivalis biotypes, 68 strains (31 of human origin and 37 of animal origin) were compared to 31 strains of closely related species or of uncertain generic status. Most animal strains were isolated in our laboratory by subculturing samples from the oral cavity of five mammalian species (bear, cat, coyote, dog and wolf). Those strains differed from human P. gingivalis strains in that they were positive for catalase, beta-galactosidase and glutamyl-glutamic acid arylamidase; from Bacteroides macacae by more rapid pigmentation, positive haemagglutination, failure to produce propionic acid, and negative alpha-galactosidase; and from Bacteroides salivosus by more rapid pigmentation, positive haemagglutination and failure to produce propionic acid. These data demonstrate that phenotypic heterogeneity within the taxon P. gingivalis can be resolved into two biotypes, each corresponding to a human source or an animal source.