Species-specific Nested Polymerase Chain Reaction Research Articles

Treponema species associated with abscesses of endodontic origin

Spirochetes have been frequently observed in abscesses of endodontic origin, but they have rarely been identified. This study sought to investigate the prevalence of eight oral treponemes in acute periradicular abscesses using a species-specific nested polymerase chain reaction assay. Purulent exudate was collected by aspiration from 19 cases diagnosed as acute periradicular abscesses and DNA extracted from the samples was initially amplified using universal 16S rDNA primers. A second round of amplification used the first polymerase chain reaction products to detect a specific fragment of the 16S rDNA of each Treponema species. The species-specific nPCR assay used in this study allowed the detection of Treponema denticola in 79%(15 of 19), Treponema socranskii in 26%(5 of 19), Treponema pectinovorum in 21% (4 of 19), Treponema amylovorum in 16% (3 of 19), and Treponema medium in 5% (1 of 19) of the cases. Spirochetal DNA was found in 89% of the cases (17 of 19). The number of Treponema species per case ranged from 1 to 3 (mean, 1.5). Treponema vincentii, Treponema lecithinolyticum and Treponema maltophilum were not detected in any pus sample. The present data lend support to the assertion that Treponema species, particularly T. denticola and T. socranskii, may be involved in the pathogenesis of acute periradicular abscesses.

Positive and Negative Bacterial Associations Involving Dialister pneumosintes in Primary Endodontic Infections

Dialister pneumosintes is an anaerobic Gram-negative rod that has been recently implicated as a candidate endodontic pathogen. In this study, samples taken from abscessed teeth and infected root canals associated with asymptomatic or symptomatic periradicular lesions were examined for the occurrence of bacterial associations involving D. pneumosintes. DNA was extracted from the samples, and the presence of D. pneumosintes and 16 other bacterial species was determined by means of species-specific nested polymerase chain reaction. Positive and negative associations involving D. pneumosintes were investigated by computing the odds ratio of D. pneumosintes being found in a sample from endodontic infection in co-infection with one of the other target species. The association between the pairs containing D. pneumosintes and the occurrence of pain also was evaluated. D. pneumosintes was always detected in mixed infections with at least two of the other target species. D. pneumosintes was positively associated with Treponema denticola, Porphyromonas endodontalis, Fusobacterium nucleatum, Peptostreptococcus micros, Campylobacter rectus, Prevotella intermedia, T. pectinovorum, and T. vincentii. Negative associations were observed with Bacteroides forsythus, P. gingivalis, and Actinomyces israelii. No pair containing D. pneumosintes was found to be significantly associated with symptomatic cases (p > 0.01). The findings of this study lend considerable support to the notion of D. pneumosintes being an important endodontic pathogen, usually in a mixed infection. Positive associations of this species with other highly prevalent species, such as T. denticola and P. endodontalis, suggest that bacterial synergism can occur and thereby play an important role in the pathogenesis of different forms of periradicular lesions.

Bacteroides forsythus in Primary Endodontic Infections as Detected by Nested PCR

The purpose of this study was to investigate the prevalence of Bacteroides forsythus in primary endodontic infections using a species-specific nested polymerase chain reaction assay. Samples were collected from 50 teeth having carious lesions, necrotic pulps, and different forms of periradicular diseases. DNA extracted from the samples was initially amplified using universal 16S rDNA primers. A second round of amplification used the first polymerase chain reaction products to detect a specific fragment of B. forsythus 16S rDNA. B. forsythus was detected in 13 of 22 asymptomatic cases (59.1%), 4 of 10 root canals associated with acute apical periodontitis (40%), and 9 of 18 cases diagnosed as acute periradicular abscesses (50%). There was no relationship between the presence of B. forsythus and the occurrence of symptoms. In general, this bacterial species was detected in 26 of 50 samples of endodontic infections (52%). The findings of this study support the assertion that this bacterial species is associated with infections of endodontic origin and suggest that B. forsythus may be involved in the pathogenesis of different forms of periradicular lesions.

Treponema socranskii in Primary Endodontic Infections as Detected by Nested PCR

Spirochetes have been frequently observed in root canal infections, but they were rarely identified. The purpose of this study was to investigate the prevalence of Treponema socranskii in primary endodontic infections using a species-specific nested polymerase chain reaction assay. Samples were collected from 60 teeth having carious lesions, necrotic pulps, and different forms of periradicular diseases. DNA extracted from the samples was initially amplified using universal 16S rDNA primers. A second round of amplification used the first polymerase chain reaction products to detect a specific fragment of T. socranskii 16S rDNA. T. socranskii was detected in 11 of 28 asymptomatic cases (39.3%), five of 12 root canals associated with acute apical periodontitis (41.7%), and five of 20 cases diagnosed as acute periradicular abscesses (25%). There was no relationship between the presence of T. socranskii and the occurrence of symptoms. In general, this spirochete was detected in 21 of 60 samples of endodontic infections (35%). Findings suggest that T. socranskii can be involved in the pathogenesis of different forms of periradicular lesions.

Campylobacter gracilis and Campylobacter rectus in primary endodontic infections.

A species-specific nested polymerase chain reaction (PCR) assay was used to investigate the occurrence of Campylobacter gracilis and C. rectus in primary root canal infections. Samples were collected from 57 single-rooted teeth with carious lesions, necrotic pulps and radiographic evidence of periradicular disease. Twenty-eight cases were diagnosed as chronic asymptomatic periradicular lesions, 12 cases as acute apical periodontitis, and 17 cases as acute periradicular abscess. DNA was extracted from the samples and initially amplified using universal 16S rDNA primers. A second round of amplification using the first PCR products was performed to specifically detect C. gracilis or C. rectus in the samples. Campylobacter gracilis and C. rectus were, respectively, detected in 21.4 (6 of 28) and 30% (6 of 20) of the root canals associated with chronic asymptomatic periradicular lesions. Campylobacter gracilis was found in 16.7% (2 of 12) of the cases diagnosed as acute apical periodontitis, whilst C. rectus was found in 33.3% (two of six cases). In the abscessed cases, C. gracilis and C. rectus were detected in 23.5 (4 of 17) and 11.8% (2 of 17) of the cases, respectively. No association of these species with clinical symptoms was observed (P > 0.01) In general, species-specific nPCR allowed the detection of C. gracilis in 21.1% (12 of 57) and C. rectus in 23.3% (10 of 43)of the samples taken from primary endodontic infections. Findings confirmed the assertion that both C. gracilis and C. rectus participate in infections of endodontic origin and suggest a pathogenetic role with regard to periradicular diseases.

Dialister pneumosintes can be a suspected endodontic pathogen.

Dialister pneumosintes is a nonmotile, nonfermentative, non-spore-forming, obligately anaerobic, gram-negative bacillus that has been associated with some infections in the human body. A species-specific nested polymerase chain reaction assay was used to investigate the occurrence of D pneumosintes in primary root canal infections. Samples were collected from 32 teeth with carious lesions, necrotic pulps, and radiographic evidence of periradicular bone destruction. Twenty-two teeth were asymptomatic, and 10 cases were diagnosed as acute apical periodontitis. DNA extracted from the samples was initially amplified with universal 16S ribosomal DNA primers. A second round of amplification used the first polymerase chain reaction products to specifically detect D pneumosintes. This bacterial species was detected in 17 of 22 asymptomatic cases (77.3%) and in 4 of 10 root canals associated with acute apical periodontitis (40%). No relationship was found between the presence of this bacterial species and the occurrence of symptoms. In general, D pneumosintes was detected in 21 of 32 root canal samples (65.6%). This study is the first to report a high prevalence of D pneumosintes in root canal infections of humans. Because of this high prevalence and the apparent pathogenicity of the microorganism, we suggest the inclusion of D pneumosintes in the selected group of putative endodontic pathogens.

Parasitic procrastination: late‐presenting ovale malaria and schistosomiasis

A 29-year-old woman with ovale malaria (most likely contracted, together with asymptomatic schistosomiasis, in East Africa two years previously) had fever, nausea and confusion, jaundice, anaemia, thrombocytopenia, hyponatraemia and hypokalaemia. She was initially diagnosed with and treated for blood-smear-positive vivax malaria. Because of the unusual clinical presentation, blood was analysed by a malaria species-specific nested polymerase chain reaction (PCR) assay which identified Plasmodium ovale as the only infecting species. This case illustrates (i) that a detailed travel history remains a vital part of clinical assessment, (ii) ovale malaria can have an exceptionally long incubation period and features of a moderately severe acute infection, and (iii) PCR assay may prove a valuable adjunct to blood film examination in the diagnosis and speciation of malaria.

Detection of Candida species by polymerase chain reaction (PCR) in blood samples of experimentally infected mice and patients with suspected candidemia

In this study, we have established and evaluated a genus-specific polymerase chain reaction (PCR) and species-specific nested PCRs for the detection of Candida species in blood samples of neutropenic mice and patients suspected of candidemia. DNA segments of the gene encoding cytochrome P450 L1A1 were targeted for amplification by using genus and species-specific primers. As compared to the genus-specific PCR, the species-specific nested PCRs improved the sensitivity by 10 times with the detection limit < 10 yeast cells. Of the 18 blood samples tested daily over a period of 8 days following Candida albicans infection in neutropenic mice, four samples were positive by genus-specific PCR and 11 were positive by species-specific nested PCR. The PCR results were correlated with culture findings obtained on blood samples. Two of the three blood culture-positive samples were positive by genus-specific PCR and all the three with species-specific nested PCR. Among 15 mice, which were negative by blood culture but had C. albicans isolated from visceral organs, 2 and 8 mice yielded positive results by genus-specific PCR and species-specific nested PCR, respectively. Consistent with the results of the animal study, species-specific nested PCR yielded much higher positivity as compared to culture (52.2% versus 21.2%) in patients suspected for candidemia. Moreover, 8 specimens which were negative for Candida by genus-specific PCR became positive by species-specific nested PCR. No correlation was apparent between PCR positivity and Candida antigen titers. The results suggest that nested PCR is a sensitive technique for the detection of Candida species from blood samples, and thus it may have application in the diagnosis of suspected cases of candidemia and candidiasis.

Detection of ehrlichial infection by PCR in dogs from Yamaguchi and Okinawa Prefectures, Japan.

Species-specific nested polymerase chain reaction (PCR) was used to detect the presence of possible canine ehrlichial agents (Ehrlichia canis, E. chaffeensis, E. ewingii, E. equi and E. platys) and monocytic ehrlichial agents found in Japan (E. muris and a recently discovered Ehrlichia species detected from Ixodes ovatus) in blood samples from dogs in Yamaguchi and Okinawa Prefecture, Japan. Partial sequence of E. platys was detected from 1 of 67 dogs (1.5%) tested from Yamaguchi Prefecture and 24 out of 87 (27.6%) in the subtropical Okinawa Prefecture. Dogs in Okinawa and Miyako Islands had a higher positive rate (69.2 and 45.0%, respectively) than Ishigaki Island (11.1%). Another dog in Yamaguchi Prefecture had a positive PCR reaction to the Ehrlichia sp. detected from I. ovatus. No other Ehrlichia were found in these samples.

A genus- and species-specific nested polymerase chain reaction malaria detection assay for epidemiologic studies.

A nested polymerase chain reaction (PCR) assay that uses Plasmodium genus-specific primers for the initial PCR (nest 1) amplification and either genus- or species-specific primers for the nest 2 amplifications was tested on laboratory and field samples. With in vitro cultured Plasmodium falciparum-infected blood samples, it was capable of detecting six parasites/microl of blood using DNA prepared from 25-microl blood spots on filter paper. The assay was evaluated on fingerprick blood samples collected on filter paper from 129 individuals living in a malaria-endemic area in Malaysia. Malaria prevalence by genus-specific nested PCR was 35.6% (46 of 129) compared with 28.7% (37 of 129) by microscopy. The nested PCR detected seven more malaria samples than microscopy in the first round of microscopic examination, malaria in three microscopically negative samples, six double infections identified as single infections by microscopy and one triple infection identified as a double infection by microscopy. The nested PCR assay described is a sensitive technique for collecting accurate malaria epidemiologic data. When coupled with simple blood spot sampling, it is particularly useful for screening communities in remote regions of the world.

Frequency of the Asn-108 and Thr-108 point mutations in the dihydrofolate reductase gene in Plasmodium falciparum from southwest Colombia.

Several point mutations in the dihydrofolate reductase (DHFR) gene of Plasmodium falciparum have been correlated with in vitro anti-folate drug resistance of laboratory and field isolates. Furthermore, two different point mutations that generate amino acid substitutions at the same position of the enzyme have been observed in all the isolates studied to date. These point mutations change a serine (Ser-108) in the wild type to an asparagine (Asn-108 mutation) or to a threonine (Thr-108 mutation). Using the polymerase chain reaction (PCR), it is possible to identify isolates that present these mutations. We used a mutation-specific PCR to screen 71 samples from several geographic locations of Colombia for the Asn-108 mutation (pyrimethamine resistance). In this initial screening 53 of 71 yielded amplification product with the DHFR mutation-specific primers. We further analyzed the 18 samples that did not amplify using a mutation-specific nested PCR. Of those 18 samples, seven amplified with primers specific for the Thr-108 mutation (proguanil resistance), one with the wild type (Ser-108), and 10 did not amplify. Of these 10 samples, three were identified as P. falciparum using a species-specific diagnostic nested PCR base on sequences from the small ribosomal RNA subunit gene. Overall, 51.6% of the samples amplified for the Asn-108 mutation, 10.9% for the Thr-108 mutation, 35.9% with the wild type specific primer, and 4.8% did not amplify with any of the DHFR primers. We observed variability in the frequency of the mutation between the different geographic location. The frequency of the Asn-108 and Thr-108 mutations in the state of Narifio was 25% each, while in Valle del Cauca the frequencies were 59% and 11%, respectively. These results contrast with observations in Brazil in which the Asn-108 mutation was found in 90% of the blood samples screened.