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PubMed2003

Genomic analysis of a recently identified virus (SEN virus) and genotypes D and H by polymerase chain reaction.

BACKGROUND/AIMS: SEN virus (SENV) was discovered in 1999 as a DNA virus with hepatotropic properties. Nine genotypes (A-I) have been identified with genotypes D and H being more prevalent in cases of chronic hepatitis. Attempts to determine whether SENV causes liver disease have been hampered by limited diagnostic testing. METHODS: In the present study, we developed two PCR based assays; a general SENV screening and genotype-specific assay. RESULTS: By screening PCR, the specificity for all SENV genotypes and SENV-related sequences was 20/20 (100%) with confirmation of the results being provided by genomic sequencing. With the genotype-specific PCR, specificities for SENV-D and SENV-H were 7/7 (100%) and 7/11 (64%), respectively. All screening PCR products were cloned and sequenced. The results of sequencing showed high genetic diversity in representative SENV genotypes. Five of twenty patients (25%) had mixed infections with several SENV genotypes. CONCLUSIONS: The screening PCR was useful for identifying cases of SENV infection. However, because of high genetic divergence and mixed co-infection, it was difficult to establish a specific method for genotype distinction. Hence, sequencing is still required for further investigations of SENV as a potential cause of liver disease.

Amino Acid Sequence↗
PubMed2002

Assessing the efficacy of a ram-genotyping programme to reduce susceptibility to scrapie in Great Britain.

Susceptibility to clinical scrapie is associated with polymorphisms in the PrP gene. The 'ARR' allele of this gene reduces susceptibility to clinical disease caused by all known strains of the transmissible spongiform encephalopathy (TSE) agent. The British government proposes to use a ram-genotyping scheme to breed genetic resistance to clinical scrapie into the national sheep population. We considered how best to target limited genotyping resources to achieve the maximum rate of genotype evolution. We created a metapopulation model of the British sheep industry, which includes the major pure-breeds of sheep and the cross-breeds produced by crossing these pure-bred animals. The main criterion for assessing the efficacy of different strategies was the time taken to increase the prevalence of the ARR allele in the slaughter-lamb population. Our model predicted that the most-effective strategy would be to target genotyping to those rams used for pure-breeding (i.e. mated with the same breed of ewe). This strategy was compared to two further strategies, in which the proportion of rams genotyped in each breed depended on the prevalence of the ARR/ARR genotype in that breed. A policy in which the proportion of animals genotyped is reduced as the ARR prevalence in that breed increases is efficient. The most-effective policy was targeting the hill sector in the early years and gradually switching to genotyping more terminal-sire and longwool rams as the resistance of the hill sector increases.

Animal Husbandry↗
PubMed1999

Four genotypic variants of a Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) are distinguishable by a hypervariable genomic region.

Four genotypes named SP2A, SP2B, SP2C and SP2D were obtained in vivo by infecting S. exigua larvae with limiting dilutions of the Spanish field isolate Spodoptera exigua Nucleopolyhedrovirus (Se-SP2) of SeMNPV. The cloning of variants SP2A, SP2B and SP2C took 1, 6, and 3 passages, respectively, before the DNA profiles showed all bands in equimolar concentrations, and they remained constant for at least six further passages indicating the stability of their genotypes. The SP2D variant isolation took over ten passages and it was genetically less stable. Physical maps of their genomes were constructed for the restriction enzymes BamHI, BglII, PstI, and XbaI. The region between 8-10 m.u. was highly variable and characteristic of each cloned genotype and, hence, can be used as RFLP markers for all four genotypic variants. This region, included in the PstI-MB fragment, was cloned and sequenced showing that all the Se-SP2 variants contained a homologous region (hr) with a variable number of 98 bp sequences tandemly repeated, which were used to distinguish genotypic variants from each other. The biological activity of the genotypic variants SP2A, SP2B, and SP2C when compared in terms of LD50 and LT50, were not significantly different. However, the SP2D genotypic variant was found to be significantly less infective (higher LD50). The emergence of new genotypes in the Se-SP2 field populations is discussed.

Animals↗
PubMed2002

High doses of interferon in combination with ribavirin are more effective than the standard regimen in patients with HCV genotype 1 chronic hepatitis.

BACKGROUND/AIMS: The aim of the present, open-labelled, controlled study was to determine whether 5 MU of interferon (IFN) alpha 2b combined with a standard dose of ribavirin might increase the rate of viral clearance in all patients with chronic HCV hepatitis or at least in those with an unfavourable genotype. METHODS: A total of 298 previously untreated patients with chronic hepatitis C were randomized to 5 or 3 MU of interferon alpha 2b 3 times per week with 1000-1200 mg of ribavirin daily (148 and 150 patients, respectively). Patients were treated for 12 months and observed for 6 months posttreatment. RESULTS: In patients infected with HCV genotype 1, the sustained virologic response was 37.8% (95% CI 27.3-48.1) with IFN 5 MU and 19.2% (95% CI 10.1-28.2) with IFN 3 MU (P=0.008). Out of 45 sustained responders with genotype 1, 31 (69%) had received 5 MU and 14 (31.1%) the standard 3 MU dose of IFN in combination with ribavirin (P=0.01). Of the 86 responders infected with genotype non-1, 39 (45.3%) were from the 5 MU IFN group and 47 (54.6%) were from the 3 MU IFN group; these figures were not significant. At the multivariate analysis of baseline features for all patients, the variables with an independent effect for a sustained response were genotype non-1 (odds ratio (OR) 3.98, 95% CI 2.36-6.40), and the histological grading (score 0-2) (OR 2.48, 95% CI 1.12-5.51) and staging (score 0-1) (OR 1.73, 95% CI 1.02-2.95). For patients with genotype 1 only the high regimen of IFN entered the model (OR 2.39, 95% CI 1.13-5.05), whereas for patients with genotype non-1 an age of <40 years (OR 2.64, 95% CI 1.23-5.70) and staging (score 0-1) (OR 2.38, 95% CI 1.07-5.28) were independent predictors of a sustained response. CONCLUSIONS: Our study suggests that when treating naive patients with genotype 1, there is a significant increase in the rate of sustained virologic clearance by increasing the dose of IFN given in combination with ribavirin.

Adult↗
PubMed2002

[Prevalence of hepatitis C virus genotypes in the area of El Ferrol (La Coruña, Spain)].

BACKGROUND: To determine the prevalence of hepatitis C virus (HCV) genotypes in the area of El Ferrol, as well as their distribution according to risk factors. METHODS: A total of 479 patients with hepatitis C were studied, including 254 with no known risk factors, 161 intravenous drug abusers (IVDA) and 64 with a history of blood transfusions. The presence of HCV RNA was studied by RT-PCR, and a reverse hybridization method (INNO-LiPA) was used for genotyping. RESULTS: Genotype distribution was as follows: 1b, 269 (56.2%); 1a, 79 (16.5%); 3a, 59 (12.3%); 4c/4d, 35 (7.3%); 1, 19 (4.0%); 2a/2c, 3 (0.6%); 4, 3 (0.6%); 2b, 2 (0.4%). In 10 patients (2.1%) genotype could not be determined. In patients with no known risk factor, the predominant genotype was 1b, detected in 191 of the 254 patients in this group (75.2%). Distribution of genotypes was more varied in the IVDA group, with the most frequent being 1a in 49 (30.4%) and 3a in 43 (26.7%). In the 64 patients who had received transfusions, 1b was predominant, detected in 54 of 64 patients (84.4%). CONCLUSIONS: The predominant HCV genotype in our area is 1b. Differences in genotype distribution were observed in the population groups studied, according to their underlying risk factors.

Adolescent↗
PubMed1998

Effects of glutathione S-transferase (GST) M1 and GSTT1 genotypes on urothelial cancer risk.

The M1 member of the mu class of the glutathione S-transferase (GSTM1) gene is present in about 50% of individuals. GSTT1, a member of the theta class, which has been recently shown to be polymorphic, is expressed in 35-90% of individuals. In this study, 145 Japanese patients with urothelial transitional cell carcinoma and 145 healthy controls, frequency-matched for age and gender, were compared for frequencies of GSTM1 and GSTT1 genotypes. The urothelial cancer risk increased due to the GSTM1 null genotype (odds ratio (OR) 1.71, 95% confidence interval (CI) 1.05-2.79). On the other hand, the OR tended to decrease due to the GSTT1 null genotype, although not significantly. Among individuals of the GSTM1 null genotype, those of the GSTT1-positive genotype had a two-fold risk (OR 2.62, 95% CI 1.36-5.05) compared with the GSTT1 null genotype (OR 1.25, 95% CI 0.62-2.51). A significant interaction between the GSTM1 genotype and smoking status was found; the GSTM1 null genotype was associated with an increased risk of urothelial cancer among smokers (OR 1.98, 95% CI 1.10-3.57).

Aged↗
PubMed1998

Angiotensin-converting enzyme genotypes and risk for myocardial infarction in women.

OBJECTIVES: We tested for an association between the angiotensin-converting enzyme (ACE) DD polymorphic genotype and myocardial infarction (MI) in a sample group composed exclusively of women. BACKGROUND: The human ACE gene occurs with either an insertion (I allele) or a deletion (D allele) of a 287-base pair (bp) Alu element. Part of the variance in serum ACE levels may be accounted for by this polymorphism. Also, the DD genotype has been associated with an increased risk of MI in predominantly male populations. However, the risk in women is poorly defined. METHODS: Genomic DNA was extracted from buffy coat blood using a phenol/chloroform method. Angiotensin-converting enzyme alleles were identified using primers to bracket the insertion region in intron 16. Amplification using polymerase chain reaction allowed identification of a 490-bp (I allele) or a 190-bp (D allele) product, or both. RESULTS: Allelic and genotypic frequencies in control subjects were similar to those reported in mostly male populations, and frequencies of genotypes were in the Hardy-Weinberg equilibrium. In contrast, the distribution of genotypes in patients with MI diverged from the equilibrium. Specifically, DD genotypic frequency was increased in women with (n = 141) versus without (n = 338) a previous MI (39% vs. 29%, odds ratio [OR] 1.54, 95% confidence interval 1.02 to 2.32, p < 0.04). Risk was particularly increased in women <60 years old (OR 2.04, p < 0.05). In contrast, the DD genotype did not predict angiographic coronary artery disease. CONCLUSIONS: Consistent with findings in male-dominated populations, a modest association of the ACE DD genotype with MI was found in women. The basis for this association requires further study.

Aged↗
PubMed1998

Impact of CYP2E1 genotype in renal cell and urothelial cancer patients.

Genetic polymorphisms of enzymes involved in carcinogen metabolism have been found to influence susceptibility to cancer. Ethanol-inducible CYP2E1 is an enzyme of major toxicological interest because it metabolizes several drugs, precarcinogens and solvents to reactive metabolites. In the present study, we investigated the cytochrome P450 2E1 genetic polymorphism in renal cell/urothelial cancer patients from two German regions, Jena and Halle, different with respect to their environmental pollution degree in comparison with healthy controls from the same regions. DNA of peripheral white blood cells was isolated both from 224 renal cell/urothelial cancer patients and 304 controls. We focussed on polymorphisms in the promoter region and intron 6 of the CYP2E1 gene. The polymorphisms were identified as RFLP's by amplification of the appropriate DNA fragment and subsequent digestion with the restriction enzymes PstI, RsaI and DraI. In Jena as well as in Halle, the frequency distributions of the PstI/RsaI, DraI and combined DraI + PstI/RsaI genotypes showed no significant differences between controls and renal cell/urothelial cancer patients. We did not find significant differences between Jena and Halle. 86.2% of all subjects with a homozygote PstI/RsaI genotype also carried a heterozygote DraI genotype, whereas 5.1% of the subjects with a heterozygote PstI/RsaI genotype also carried a heterozygote DraI genotype. Renal cell cancer as well as urothelial cancer risk was not elevated in patients with heterozygote DraI, PstI/RsaI and combined DraI + PstI/RsaI genotypes (odds ratios slightly insignificantly increased). Interestingly enough, an association between these polymorphisms and renal cell cancer risk was found in the female subgroup but not in the male subgroup. The basis of these sex-specifically increased risks are different frequencies concerning heterozygote and homozygote genotypes in controls and cancer patients. In controls, the heterozygote genotype frequency was lower in females than in males. In renal cell cancer patients, the results were quite the contrary. Summing up, our results demonstrate an lack between CYP2E1 genetic polymorphism and renal cell/urothelial cancer risk.

Carcinoma, Renal Cell↗
PubMed2001

CMV gB genotypes and outcome of vertical transmission: study on dried blood spots of congenitally infected babies.

BACKGROUND: The role of the virulence of the infecting cytomegalovirus (CMV) strain in the transmission of the virus from mother to fetus and the outcome of the fetal infection has not received much attention yet. Molecular analysis of the gene coding for the surface glycoprotein B (gB) has been used to investigate the relationship between genotype and virulence in groups of immunosuppressed patients. OBJECTIVES: (1) to assess the prevalence of different gB genotypes in babies with congenital CMV infection; (2) to investigate the possible relationship between genotype and severity of congenital CMV disease; (3) to evaluate the possibility of using dried blood on Guthrie cards (DBS) for genotyping. STUDY DESIGN: CMV DNA was extracted from DBS and from urine/saliva samples collected in the first two weeks of life of 98 congenitally infected babies, half of which were symptomatic at birth. Genotyping was performed through RFLP analysis of the region corresponding to the cleavage site of the gB protein. RESULTS: The most prevalent genotype was gB1 (42%) followed by gB3 (26%), gB2 (19%) and gB4 (13%). Rates of disease and CNS damages were higher among children infected by gB1 (35%, 17%) and gB3 (31%, 28%) than in those infected by gB2 and gB4 (20%, 17% and 13%, 15%, respectively). These differences however did not reach the statistical significance. The parallel typing of DBS and urine/saliva strains gave a full concordance of results. CONCLUSIONS: All four major CMV gB genotypes (gB1-4) can cause a congenital infection but none seems to be associated to the development and the severity of disease. The possibility of using the neonatal DBS for genotyping opens a way to the examination of large numbers of cases of congenital CMV infection.

Blood Specimen Collection↗
PubMed1999

HCV genotyping by three methods: analysis of discordant results based on sequencing.

BACKGROUND: Correct genotyping of hepatitis C virus (HCV) RNA-positive serum samples may have important clinical and therapeutic implications. OBJECTIVES: Three methods were compared to improve accuracy of HCV genotyping. STUDY DESIGN: A panel of 144 HCV RNA-positive sera prospectively tested by a modified Okamoto's type-specific reverse transcription-nested polymerase chain reaction (RT-nPCR) (Okamoto H, Tokita H, Sakamoto M, Kojima M, Iizuka H, Mishiro S. J Gen Virol 1993; 74: 2385-2390) was retrospectively analyzed by two recently described methods which were reported to identify all HCV types and the majority of HCV subtypes: (i) a restriction fragment length polymorphism (RFLP) analysis of PCR products amplified from the 5' untranslated region (5'UTR) of the viral genome (Pohjanpelto P, Lappalainen M, Widell A, Asikainen K, Paunio M. Clin Diagn Virol 1996; 7: 7-16); and (ii) a type-specific RT-nPCR relevant to the core region (Ohno T, Mizokami M, Wu R, Saleh M, Ohba K, Orito E, Mukaide M, Williams R, Lau J. J Clin Microbiol 1997; 35: 201-207). The panel (according to results given by the modified Okamoto's method) consisted of: (i) 105 sera belonging to five different HCV subtypes; (ii) 20 specimens containing a mixture of > or = 2 genotypes; and (iii) 19 untypeable clinical samples. RESULTS: There was agreement of the three methods for 78/144 (54.2%) blood samples, whereas discordant results were obtained for the remaining 66 samples, 56 of which could be typed by sequencing. Of these, 51 (91.7%) were correctly typed by RFLP, 37 (66.0%) by Ohno's and 27 (48.2%) by the modified Okamoto's procedure. The overall genotyping sensitivity of each method over the total number of 134 samples whose genotype was ascertained, was 96.2% for RFLP, 85.8% for Ohno's and 78.3% for the modified Okamoto's procedure. CONCLUSIONS: RFLP analysis, notwithstanding some limitations in subtyping efficiency of genotype 1 samples, appears superior to the two RT-nPCR methods because: (i) it is able to type a larger number of samples; (ii) it is more efficient in identifying genotypes 2a/c, which are widespread in Italy; (iii) it is highly sensitive (together with Ohno's method) in recognizing genotypes 3 and 4.

5' Untranslated Regions↗
PubMed2005

Pancreaticobiliary cancers with deficient methylenetetrahydrofolate reductase genotypes.

BACKGROUND & AIMS: Methyl group deficiency might promote carcinogenesis by inducing DNA breaks and DNA hypomethylation. We hypothesized that deficient methylenetetrahydrofolate reductase (MTHFR) genotypes could promote pancreatic cancer development. METHODS: First, we performed a case-control study of germline MTHFR polymorphisms (C677T, A1298C) in 303 patients with pancreatic cancer and 305 matched control subjects. Pancreatic neoplasms frequently lose an MTHFR allele during tumorigenesis; we hypothesized that such loss could promote carcinogenesis. We therefore evaluated the cancer MTHFR genotypes of 82 patients with pancreaticobiliary cancers and correlated them to genome-wide measures of chromosomal deletion by using 386 microsatellite markers. Finally, MTHFR genotypes were correlated with global DNA methylation in 68 cancer cell lines. RESULTS: Germline MTHFR polymorphisms were not associated with an increased likelihood of having pancreatic cancer. Fractional allelic loss (a measure of chromosomal loss) trended higher in cancers with 677T genotypes than in cancers with other genotypes (P = .055). Among cancers with loss of an MTHFR allele, cancers with 677T MTHFR alleles had more deletions at folate-sensitive fragile sites (36.9%) and at tumor suppressor gene loci (68.5%) than 677C cancers (28.7% and 47.8%, P = .079 and .014, respectively). LINE1 methylation was lower in cancers with less functional 677T/TT genotypes (24.4%) than in those with 677CT (26.0%) and CC/C genotypes (32.5%) (P = .014). CONCLUSION: Cancers with defective MTHFR genotypes have more DNA hypomethylation and more chromosomal losses. Deficient MTHFR function due to loss of an MTHFR allele by an evolving neoplasm might, by promoting chromosomal losses, accelerate cancer development.

Adenocarcinoma↗
PubMed2004

Power calculations for selective genotyping in QTL mapping in backcross mice.

Selective genotyping concerns the genotyping of a portion of individuals chosen on the basis of their phenotypic values. Often individuals are selected for genotyping from the high and low extremes of the phenotypic distribution. This procedure yields savings in cost and time by decreasing the total number of individuals genotyped. Previous work by Darvasi et al. (1993) has shown that the power to detect a QTL by genotyping 40-50 % of a population is roughly equivalent to genotyping the entire sample. However, these power studies have not accounted for different strategies of analysing the data when phenotypes of individuals in the middle are excluded, nor have they investigated the genome-wide type I error rate under these different strategies or different selection percentages. Further, these simulation studies have not considered markers over the entire genome. In this paper, we present simulation studies of power for the maximum likelihood approach to QTL mapping by Lander & Botstein (1989) in the context of selective genotyping. We calculate the power of selectively genotyping the individuals from the middle of the phenotypic distribution when performing QTL mapping over the whole mouse genome.

Animals↗
PubMed2002

The occurrence of five major Newcastle disease virus genotypes (II, IV, V, VI and VIIb) in Bulgaria between 1959 and 1996.

Partial sequence and restriction enzyme cleavage site analyses of the fusion protein gene were used to genotype 47 Newcastle disease virus strains isolated between 1959 and 1996 in Bulgaria. Viruses belonged to five major genotypes that appeared to be associated with epizootics characterized by temporal and/or geographical restrictions. Genotype IV viruses (responsible for the European branch of the first panzootic) dominated the scene up to the early 1980s, interspersed with sporadic outbreaks caused by genotype II (US strains causing pneumoencephalitis) viruses. Genotype V viruses (transmitted by psittacines from South America) were first shown in 1973 and persisted until the late 1980s. Genotype VI (earliest members from the Middle-East 1968/70 outbreaks) was represented by scattered isolations between 1974 and 1996. A genotype VIIb (recent Middle East epizootic) virus was isolated as early as in 1984. Newcastle disease epizootics in Bulgaria were highlighted by multiple infection with more than one genotype at any one time.

Animals↗
PubMed2000

Investigations into genotypic variations of peanut carbohydrates.

Carbohydrates are known to be important precursors in the development of roasted peanut quality. However, little is known about their genotypic variation. A better understanding of the role of carbohydrates in roasted peanut quality requires first an understanding of the genotypic variation in the soluble carbohydrate components. Ion exchange chromatography was used to isolate 20 different carbohydrate components in 52 genotypes grown in replicated trials at two locations. Inositol, glucose, fructose, sucrose, raffinose, and stachyose were quantitated, and 12 unknown peaks were evaluated on the basis of the peak height of the unknown relative to the cellobiose internal standard peak height. Peaks tentatively identified as verbascose and ajugose could not be properly integrated because of tailing. Of the 18 carbohydrates that were estimated, 9 exhibited significant variation between test environments, 5 among market types, 14 among genotypes within market types, and 11 exhibited some significant form of genotype x environment interaction. Genotypes accounted for 38-78% of the total variation for the known components, suggesting that broad-sense heritability for these components is high. The observed high genotypic variation in carbohydrate components is similar to the high genotypic variation observed for the sweetness attribute in roasted peanuts, which raises the question regarding possible interrelationships. The establishment of such interrelationships could be most beneficial to peanut breeding programs to ensure the maintenance of flavor quality in future peanut varieties.

Arachis↗
PubMed2000

VP7 and VP4 genotypes among rotavirus strains recovered from children with gastroenteritis over a 3-year period in Valencia, Spain.

Between September 1996 and May 1999, the incidence and distribution of the main human rotavirus G genotypes (VP7 associated: G1-G4) and P genotypes (VP4 associated: P[8], P[4], P[6] and P[9]) among children with rotavirus gastroenteritis were determined using reverse transcription and polymerase chain reaction (RT-PCR)-based genotyping methods. From a total of 145 rotavirus strains examined, we identified the G type in 131 (90.3%) and the P type in 127 (87.5%) of the samples. An overall predominance of genotypes P[8] G1 (42.7%) and P[8] G4 (32.4%) was found during the period of study, with much lower incidence of genotypes P[4] G2 (5.5%) and P[8] G3 (2%). P[6] and P[9] types were not detected, neither were unusual combinations of P and G types. A significant genotypic shift was observed: whereas P[8] G4 was the most prevalent genotype during the first year of the study (60%), the genotype P[8] G1 gradually increased to account for 62.3% of the strains analysed in the following winter season. Mixed G types revealing dual infections G1/G4 and G3/G4 were found at low frequency (2%).

Acute Disease↗
PubMed2003

Effects of soybean genotype and growing location on oil and fatty acids in tofu.

Soyfood products like tofu are becoming popular among American consumers due to health benefits. In order to increase production to meet consumer demands, it is imperative that factors that effect quantity and quality of tofu be characterized. The present study was conducted to determine the effects of soybean genotypes and growing locations on contents of oil and fatty acids in tofu which was prepared from twelve soybean genotypes (BARC-8, BARC-9, Enrei, Hutcheson, MD86-5788, Nakasennari, S90-1056, Suzuyutaka, V71-370, V81-1603, Ware, and York) grown at three southern U.S. locations (Huntsville, Alabama; Princess Anne, Maryland; and Petersburg, Virginia) during 1995. The results showed that tofu quality was determined by the soybean genotype. The tofu made from seeds of high seed-protein and low seed-oil genotypes (BARC-8 and BARC-9) resulted in tofu with low contents of oil (15.8 and 11.3 g/100g, respectively) and total saturated fatty acids (2.59 and 160 g/100g, respectively). Tofu made from seeds of conventional grain type genotypes, such as Hutcheson, resulted in higher oil (24.0 g/100g) and total saturated fatty acids (3.80 g/100g) contents in tofu. Effects of growing environment on contents of oil were not significant but tofu made from seeds grown in Alabama had significantly higher content of total saturated fatty acids (3.50 g/100g) as compared to that made from seeds grown in Maryland (2.88 g/100g) or Virginia (2.96 g/100g). Tofu made from seeds of large and medium-seeded genotypes had higher contents of total monounsaturated fatty acids in tofu as compared to that made from small-seeded genotypes. Highly positive correlation existed between contents of oil, 18:1, 18:2, total saturated, and total unsaturated fatty acids in the seeds and their contents in the tofu (+0.80, +0.75, +0.79, +0.62, +0.68, respectively). These results indicated that tofu quality is governed by soybean genotype, seed size and growing location.

Alabama↗
PubMed2003

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.

Acute Disease↗
PubMed2003

Prevalence of Porphyromonas gingivalis fimA genotypes in Caucasians.

The aim of the present study was to determine the prevalence of Porphyromonas gingivalis fimA genotypes in Caucasian patients with periodontitis. A total of 102 patients harboring P. gingivalis subgingivally were enrolled into the study. Pooled subgingival plaque samples of the six most severely affected sites were taken and analysed by fimA-specific polymerase chain reaction (PCR) and restriction analysis. Moreover, 26 P. gingivalis isolates were analysed by sequence analysis of the fimA gene. Sequence analysis revealed five major fimA genotypes (fimA types I-V) and allowed further subtyping of fimA genotypes II and IV into two subgroups each. The overall prevalences of fimA genotypes as assessed by PCR and restriction analysis among the P. gingivalis-positive patients with periodontitis were: type I, 25.5%; type II, 38.2%; type III, 4.9%; type IV, 18.6%; type V, 3.9%; and non-typable, 6.9%. Two patients were colonized by both type II and type IV, or type III and type IV fimA genotypes, respectively. Patients harboring different fimA genotypes showed no significant difference in severity of periodontal disease, as assessed by pocket probing depth and bleeding on probing following adjustment for smoking habit and age. The results indicate that predominant fimA genotypes in Caucasian periodontitis patients are types I, II, and IV. However, there was no difference in the association of the various fimA genotypes with disease severity.

Age Factors↗