Sequence Analysis Of Polymerase Chain Reaction Products Research Articles

Investigation of the presence of class 1, 2, 3 integrons and their relationships with antibiotic resistance in clinical Stenotrophomonas maltophilia isolates

Stenotrophomonas maltophilia is an opportunistic emergent pathogen causing hospital-acquired infections. It is resistant to majority of the broad spectrum antibiotics due to several mechanisms which significantly limit the treatment options. Although the relationship between integrons, mobile genetic elements which play role in transferring resistance genes, and the antibiotic resistance in different gram-negative bacteria have been investigated, the data are limited in Turkey especially for S.maltophilia. The aims of this study were to detect the presence of different classes of integrons and plasmids in clinical isolates of S.maltophilia and to investigate the antibiotic resistance profiles of those isolates. One hundred S.maltophilia strains isolated from various clinical samples (32 sputum, 25 tracheal aspirates, 9 urine and blood, 7 exudates and catheters, 4 sterile body fluids and wounds, 2 CSF, 1 conjunctiva) in our microbiology laboratory during January 2011-September 2012, were included in the study. The isolates were identified by VITEK2 Compact (BioMerieux, France) or Phoenix 100 (BD, USA) automatized systems, and the susceptibilities of the strains to levofloxacin, chloramphenicol, ceftazidime and trimethoprim/sulfamethoxazol (SXT) were evaluated via broth microdilution method according to the CLSI recommendations. Class 1 (intI-1), class 2 (intI-2), class 3 (intI-3) integron gene cassettes and integron 5'-3' conserved gene regions (intI-5'-3'CS) were investigated by polymerase chain reaction (PCR) using specific primers in all of the strains. Nucleotide sequence analysis of PCR products was performed in case of positive result, and the presence and size of plasmids were further investigated. The susceptibility rates of S.maltophilia strains to ceftazidime, chloramphenicol, SXT and levofloxacin were found as 24%, 66%, 93% and 95%, respectively, while MIC(50) and MIC(90) values were 64-128 µg/ml, 8-16 µg/ml, 1/19-2/38 µg/ml and 1-2 µg/ml, respectively. In PCR amplification with intI-1, intI-2 and intI-3 primers, 12%, 2% and 10% of the isolates yielded expectative bands, respectively. DNA sequence analysis of the amplified products revealed five isolates to harbour intI-1 gene, while intI class 2 and class 3 genes were not detected in any of the strains. Furthermore in PCR amplification with intI-5'CS and 3'CS primers, 20% of the strains yielded expected bands. Sequence analysis of these amplicons revealed the presence of quaternary ammonium compound resistance protein genes (qacL) in two, aminoglycoside adenyltransferase gene (aadA) in one and integron-associated recombination site (attI1) genes in five strains. Additionally, the presence of plasmids have been detected in 9 (9%) of the strains, however all of them was integron-negative. The sizes of plasmids were 2340, 1350, 2760, 18600, 20000, 3570-2540, 2510 and 5000-2540 base pairs, respectively. When the antibiotic susceptibility patterns of strains were compared with the presence of intI gene regions, no statistically significant relationship was observed (p> 0.05). In conclusion, the demonstration of integron class 1 genes and plasmids among clinical S.maltophilia strains is regarded as a warning data to indicate the potential for spread of those resistant strains in our hospital.

Tracking Plant, Fungal, and Bacterial DNA in Honey Specimens*

Consuming honey can result in adverse effects owing to poisoning by bacterial (botulism) or plant toxins. We have devised a method to extract polymerase chain reaction (PCR) amplifiable DNA of up to c. 400 bp in length based on dialysis of a 15-mL honey sample for 18 h against deionized water followed by sequential extraction using phenol, phenol/chloroform/isoamyl alcohol, chloroform/isoamyl alcohol, and ether. Sequence analysis of PCR products obtained using "universal" plant, fungal, and bacterial primers targeted to the ribosomal RNA genes has allowed us to identify six different orders of plants (Apiales, Fabales, Asterales, Solanales, Brassicales, and Sapindales), two orders of fungi (Entylomatales and Saccharomycetales), and six orders of bacteria (Sphingomonadales, Burkholderiales, Pseudomonadales, Enterobacteriales, Actinomycetales, and Bifidobacteriales) in a single honey specimen.

A Case of Generalized Bovine Tuberculosis in a Sheep

The present report describes a rare case of generalized bovine-type tuberculosis in a slaughtered 4-year-old ewe discovered during routine surveillance at an abattoir. A postmortem examination revealed lesions in the ewe's thoracic and abdominal cavities, ranging from encapsulated, mineralized foci to extensive, soft, caseous tissue. Lesions in the lungs, liver, and lymph nodes were consistent with mycobacterial infection. A histopathological examination detected granulomatous lesions in all tissue samples. The presence of Mycobacterium tuberculosis complex genome was confirmed through a polymerase chain reaction (PCR) analysis of tissues, using IS6110 primers, followed by a nucleotide sequence analysis of PCR products. Acid-fast bacteria, characterized as Mycobacterium bovis, were isolated from lesions following 38 days of incubation.

Detection of tick blood parasites in Egypt using PCR assay I—Babesia bovis and Babesia bigemina

Babesia bovis and Babesia bigemina are distributed all over the world; the etiologic agents of the animal babesiosis are considered the most important tick-borne disease. The present research work was the first attempt to determine the prevalence of B. bovis and B. bigemina infection in ticks, in Egypt, by using polymerase chain reaction (PCR). Questing 5,243 hard and soft ticks were collected from different localities throughout the Giza Governorate. Furthermore, DNA from 500 different individual tick species was extracted and PCR was performed. Primers verified from the sequence of Mexico strain of both species were used. Two fragments of 275 and 175 bp of B. bovis and B. bigemina, respectively, were generated. Fragments of the pathogens were recovered with PCR and sequenced. The prevalence of B. bovis and B. bigemina in Boophilus annulatus ticks were 55% and 66%, respectively. Also, presence of 12% dual infection with B. bovis and B. bigemina was observed. Sequence analysis of PCR product of these pathogens shares a high degree of similarity in sequence compared to similar species found in GenBank.

Anaplasma phagocytophilum and Borrelia burgdorferi in rabbits from southeastern China

A total of 54 wild rabbits captured from southeastern China were examined for Anaplasma phagocytophilum and Borrelia burgdorferi sensu lato by polymerase chain reaction (PCR) assays. One and three samples were positive for A. phagocytophilum and B. burgdorferi, respectively. Sequence analyses of PCR products identified a variant of A. phagocytophilum and a B. garinii genotype. This is the first detection of the two tick-borne agents in Chinese rabbits, the role of which in the maintenance of the agents deserve further investigations.

Molecular detection of Anaplasma platys and Ehrlichia canis in dogs from the North of Portugal

Tick-transmitted rickettsial pathogens belonging to the Ehrlichia and Anaplasma genera can infect dogs and humans. In this study, four dogs from the North of Portugal, in which an ehrlichial disease was suspected clinically, were tested by molecular methods. After DNA extraction from blood on filter paper, a 345 bp fragment of the Ehrlichia/Anaplasma 16S rRNA gene was amplified by the polymerase chain reaction (PCR). Sequence analysis of PCR products revealed one dog infected with Ehrlichia canis and three with Anaplasma platys. One of these latter animals was co-infected with Babesia canis subspecies vogeli. This is the first report of the genetic characterisation of both A. platys and E. canis in naturally infected dogs from the North of Portugal.

Molecular characterization of Cryptosporidium from animal sources in Qinghai province of China

The presence of Cryptosporidium oocysts in 20 zoo animals of the Xining Zoo, 16 farm yaks and 42 farm goats in Qinghai province, China was investigated by an immunofluorescence test (IFT). The species and/or genotypes were determined by nested polymerase chain reaction (PCR) and sequence analysis of a fragment of the small subunit (SSU) rRNA gene. Cryptosporidium oocysts were found in 16 zoo animals, 2 yaks, and 15 goats by IFT. The IFT positive samples were further investigated by PCR, and 16 of them were found to be positive by that method also. Sequence analysis of the PCR products derived from Cryptosporidium oocysts from Black leopard (Panthera pardus), Heijing He (Grus nigricollis), Barbary sheep (Ammotragus lervia), Takin (Budorcas taxicolor), Lesser panda (Ailurus fulgens), and White-eared pheasant (Crossoptilon crossoptilon) fecal samples matched that of Cryptosporidium parvum mouse genotype. Sequence analyses of other PCR products were consistent with cervine genotype Cryptosporidium from Ibex (Capra ibex), a novel Cryptosporidium genotype from a wild yak (Bos mutus), C. bovis-like genotype from one goat sample and also a novel Cryptosporidium genotype from one other separate goat sample. The present work reports the first data on Cryptosporidium infections in animals from the Qinghai province of mountainous central western China and the first findings of the 'cervine' genotype in Capra ibex, C. bovis-like genotype and the new Cryptosporidium spp. in farm goat and in wild yak.

Occurrence of strawberry marginal chlorosis caused by “Candidatus Phlomobacter fragariae” in Japan

In February 2004, a disease of strawberry (Fragaria × ananassa Duch.), causing little-leaf, proliferation, malformation of fruits, and marginal chlorosis of leaves, occurred in Ehime Prefecture, Japan. The causal pathogen was identified as a phloem-restricted bacterium-like organism, “Candidatus Phlomobacter fragariae,” based on polymerase chain reaction (PCR) detection, electron microscopy, and sequence analysis of PCR products. This is the first report of strawberry marginal chlorosis in Asia.

Association of uncultivated oral phylotypes AU126 and X112 with periodontitis

To discuss the relationship between uncultivated pathogenic bacteria and periodontitis. Specific polymerase chain reaction (PCR) primers were designed for phylotypes AU126 and X112; PCRs were applied to determine the prevalence of these phylotypes in 35 patients with chronic periodontitis, 26 patients with plaque-induced gingivitis and 20 healthy control subjects. The specificity of each primer is validated on the basis of the results from sequence analysis of PCR products. AU126 and X112 were detected in the subgingival plaque samples in all the three groups. The prevalence of AU126 in subgingival plaque in chronic periodontitis (77.1%) and plaque-induced gingivitis (61.5%) is relatively higher than that in the healthy subjects (10.0%), and the difference is statistically significant (P < 0.01). The prevalence of X112 in subgingival plaque in periodontitis patients (85.7%) is higher than that in healthy subjects (30.0%), the difference (P < 0.01) being equally statistically significant. The difference between the chronic periodontitis group and the plaque-induced gingivitis group (50.0%) is statistically significant (P < 0.05). It might be assumed that the novel uncultivated AU126 phylotype could possibly be related to chronic periodontitis and plaque-induced gingivitis, and that X112 might play a role in the progress of lesion from gingivitis to periodontitis.

Occurrence of two newly named oral treponemes -Treponema parvum and Treponema putidum- in primary endodontic infections

Recent evidence from molecular genetic studies has revealed that oral Treponema species are involved in infections of endodontic origin. This study assessed the occurrence of two newly named oral treponemes - Treponema parvum and Treponema putidum - in primary endodontic infections using a culture-independent identification technique. Genomic DNA was isolated directly from clinical samples, and a 16S rRNA gene-based nested polymerase chain reaction (PCR) assay was used to determine the presence of T. parvum and T. putidum. Species-specific primer pairs were developed by aligning closely related 16S rRNA gene sequences. The specificity for each primer pair was validated by running PCR against a panel of oral bacteria and by sequence analysis of PCR products from positive clinical samples. T. parvum was detected in 52% of the root canals associated with chronic apical periodontitis, in 20% of the cases diagnosed as acute apical periodontitis, and in no abscessed case. In general, T. parvum was detected in 26% of the samples from primary endodontic infections. T. putidum was found in only one case of acute apical periodontitis (2% of the total number of cases investigated). The devised nested PCR protocol was able to identify both T. parvum and T. putidum directly in clinical samples and demonstrated that these two treponemes can take part in endodontic infections.

Detection of Brucella DNA in sera from patients with brucellosis by polymerase chain reaction

To overcome the limitations of current diagnostic methods for brucellosis, accurate and simple methods must be sought. In this study, sera of patients diagnosed with brucellosis were examined by polymerase chain reaction (PCR) for the detection of Brucella DNA. Results showed that an amplicon of 223 bp was obtained in 96% (24/25) of tested sera using primers derived from the nucleotide sequence of a gene encoding the 31-kDa Brucella abortus antigen. However, when serum DNA templates were examined by another PCR, an amplicon of 731 bp was obtained in 60% (15/25) of the tested samples using Brucella melitensis–specific primers derived from a polymorphic locus adjacent to the 3′ end of IS711. The specificity of each PCR was demonstrated by inclusion of reference Brucella DNA strains and by DNA sequence analysis of PCR products. These results suggest that serum analysis by PCR is a convenient and safe method for rapid and accurate diagnosis of brucellosis and that B. melitensis is the leading cause of brucellosis in Saudi Arabia.

Identification of Borrelia burgdorferi sensu lato, Anaplasma and Ehrlichia species, and spotted fever group Rickettsiae in ticks from Southeastern Europe.

Prevalence data for tick-borne pathogens are used to assess the risk for human health. In this study the presence and identity of Borrelia burgdorferi sensu lato, Ehrlichia, Anaplasma, and Rickettsia species in Bulgarian Ixodes ricinus ticks and in non- Ixodes ticks from Turkey and Albania was determined by polymerase chain reaction (PCR) and reverse line blot hybridization. In the adult Bulgarian ticks, the prevalence of Borrelia burgdorferi sensu lato infection was approximately 40%, while Borrelia afzelii was the predominant species, representing more than half of all Borrelia-positive ticks. Ehrlichia and Anaplasma species were detected in 35% of the adult Ixodes ricinus ticks and in 10% of the nymphs. Sequence analysis of PCR products reacting with the Anaplasma phagocytophila probe revealed a 16S rRNA gene identical to that of the Anaplasma phagocytophila prototype strain. Ehrlichia and Anaplasma species were found in approximately 7% of the non- Ixodes ticks. Sequence analysis of some of these samples revealed the presence of Anaplasma ovis, Ehrlichia canis, and a species closely resembling Ehrlichia chaffeensis. About half of all adult ticks examined and approximately 20% of all nymphs were infected with Rickettsia species. In Ixodes ricinus ticks, Rickettsia helvetica and a Rickettsia species designated as IRS3 were found in high prevalence. Rickettsia conorii was found in virtually all non- Ixodes tick species from Albania and Turkey. The results of this study show that many tick-borne diseases are most probably endemic in the Balkan area. Furthermore, the results suggest that there is a considerable chance for simultaneous transmission of tick-borne pathogens to human beings.

Polymerase Chain Reaction (PCR) Amplification of Parvoviral DNA from the Brains of Dogs and Cats with Cerebellar Hypoplasia

Cerebellar hypoplasia in cats is caused most commonly by an in utero or perinatal infection with feline panleukopenia virus (parvovirus). Cerebellar hypoplasia has been reported infrequently in dogs, but no viral etiology has been identified to date. DNA was extracted from archival, paraffin-embedded, cerebellar tissue from 8 cats and from 2 canine littermates with cerebellar hypoplasia, 2 canine littermates with cerebellar cortical abiotrophy, 6 dogs with congenital cerebellar vermal defects, 1 dog with congenital hydranencephaly, and 15 dogs and cats with various encephalitdes. The DNA extracted from each cerebellum was subject to polymerase chain reaction (PCR) amplification by 3 primer pairs specific for parvovirus DNA. Sequence analysis of PCR products from each of the 8 cats and 2 dogs with cerebellar hypoplasia confirmed their identity with parvoviral DNA. The 6 dogs with cerebellar vermal defects, 2 dogs with cortical abiotrophy, 1 dog with congenital hydranencephaly, and all control samples were PCR negative for parvovirus. Parvoviral structural proteins were not identified by immunohistochemistry in either dog with cerebellar hypoplasia. This study shows that parvoviral DNA can be amplified from feline and canine archival brain tissue and that cerebellar hypoplasia in dogs might be associated with in utero parvovirus infection.

Molecular cloning of feline CD34

In humans, baboons, dogs and mice CD34 is a cell surface molecule that is expressed on primitive hematopoietic cells and in all these species CD34 positive cells can be used to effect long-term haematopoietic reconstitution. CD34 positive haematopoietic cells therefore provide a convenient and relatively small cell population to target when attempting gene therapy via the haematopoietic system. In order to develop the mucopolysaccharidosis type VI (MPS VI) cat as a model for haematopoietic cell-mediated gene therapy we have isolated the feline CD34 gene as a first step in the generation of antibodies for purification of feline CD34 positive cells. The coding sequence for feline CD34 was isolated from brain cDNA using the polymerase chain reaction (PCR) with oligonucleotides designed to conserved regions of known CD34 gene sequences as primers. Sequence analysis of PCR products revealed the complete amino acid sequence of feline CD34 and allowed analysis of sequence conservation with CD34 from other species. Northern blot analysis showed a 2.6 kb CD34 transcript was present in feline brain, spleen, heart, testis and thymus, and to a lesser extent, in liver. A full-length cDNA clone of the feline CD34 coding sequence was assembled and expressed in CHO-K1 cells. The isolation and expression of the feline CD34 cDNA should facilitate the production of antibodies suitable for the purification of CD34 positive cells.

Colonic spirochetosis of colony-raised rhesus macaques associated with Brachyspira and Helicobacter

Colonic spirochetosis is an inflammatory bowel disease that affects a broad range of hosts, including human and non-human primates. The disease in humans and non-human primates is characterized by intimate attachment of the anaerobic spirochetes Brachyspira aalborgi and B. pilosicoli, and some unclassified flagellated microbes along the apical membrane of colonic enterocytes. Although the presence of spiral-shaped bacteria with single polar flagella and blunted ends in colonic spirochetosis is well established, the identities of many of these organisms is still unknown. Recently, Helicobacter species with a morphology similar to the flagellated bacteria present in colonic spirochetosis have been cultured from intestinal specimens obtained from rhesus macaques, some with idiopathic colitis. The purpose of the present study was to determine whether or not the flagellated bacteria seen in the colons of rhesus macaques with colonic spirochetosis are Helicobacter. The presence of flagellated bacteria alone ( n=2) or together with spirochetes ( n=1) in formalin-fixed and paraffin-embedded colons of three rhesus macaques with the naturally occurring disease was demonstrated by immunohistochemical staining and ultrastructural examination. Total DNA extracted from affected and control intestinal specimens was amplified by polymerase chain reaction (PCR) using Helicobacter 16S rRNA gene-specific primers. Comparative nucleotide sequence analysis of PCR products cloned from positive reactions indicated that two distinct Helicobacter genomospecies were present either alone or in combination with Brachyspira in the colons of rhesus macaques with microscopic lesions indicative of colonic spirochetosis.

Diagnosis of group A coxsackieviral infection using polymerase chain reaction

Aims: To examine the relation between enteroviral infection, especially group A coxsackieviral infection, and acute febrile illness over two summers using tissue culture and polymerase chain reaction (PCR). Methods: Throat...

Detection of HTLV-I tax-rex and pol gene sequences of thymus gland in a large group of patients with myasthenia gravis.

We report in this study the use of polymerase chain reaction (PCR) for the amplification of the genomic DNA, isolated from thymic tissue, using the primers flanking HTLV-I/II tax-rex genes and the sequence method to analyze the HTLV-I pol sequence of 27 Italian patients with myasthenia gravis. These molecular methods showed that 92.5% of patients tested positive for tax gene and 55% for pol genes; 55.5% samples were positive for both the tax gene of HTLV-I/II, and the pol gene of HTLV-I. Histologic investigation of the thymus showed that 15 samples had thymic hyperplasia, 93% tested positive for the tax gene, and 40% tested positive for both the tax and pol genes of HTLV-I. In contrast, 91.6% of thymoma-positive samples were positive for tax gene I/II and 75% positive for both genes, tax and pol type I. The sequence analysis of PCR product for tax and pol genes confirmed that these amplified products were HTLV-I, with minimal variations. Our date suggested that either HTLV-I or part of the virus genome is involved in the etiopathogenesis of myasthenia gravis.

Seroprevalence and comparison of isolates of endometriotropic bovine herpesvirus-4.

Sixty-eight cases of suppurative, ulcerative endometritis associated with Bovine Herpesvirus-4 (BHV-4) in postparturient dairy cows (62 Holsteins and 6 Jerseys, mean age 4.2 years) were confirmed by a combination of histopathology, fluorescent antibody assays, electron microscopic evaluation of uterus, and polymerase chain reaction (PCR). All cases occurred in the 3- to 28-day postpartum period, and histologic lesions among various cows were consistent when compared with postpartum interval. The endometrial lining epithelium was necrotic and ulcerated from 3 to 7 days postpartum, with only mild inflammation in the lamina propria and submucosa. From 1 to 4 weeks postpartum, the ulcers were confluent to diffuse. Epithelium was replaced by fibrinonecrotic, suppurative mats, resulting in severe bacterial pyometra by day 24. Seroprevalence to BHV-4 in one dairy with a history of 18 mortality cases was 36% (107 of 296). In a random sample of 8 cows from this herd, none had serologic titers in blood sampled 2 weeks prepartum, but 3 of 8 seroconverted with significant titers of 1:8 to 1:16 at 2 weeks postpartum. By 10 weeks postpartum, all 8 cows returned to negative serologic status. Two of 6 cats from the premises also had positive titers. Random serum samples taken from 480 dairy cattle at sale barns indicated 76 (16%) were positive by serum neutralization. Clinical signs, postparturient timing, and histologic lesions were very similar to those previously reported in Belgium with BHV-4. But sequence analysis of PCR products of the glycoprotein B region of 4 separate field isolates of endometriotropic BHV-4 suggests these field isolates were more closely related to the North American nonvirulent strain DN-599 than to the endometriotropic European strain V.

Detection of infectious enteroviruses and adenoviruses in tap water in urban areas in Korea

We investigated the viral contamination of tap water at 11 urban sites in Korea between 1997 and 1998 over a period of 11 months. A total of 23 tap water samples were examined for infectious enteroviruses and adenoviruses by a cell culture technique followed by polymerase chain reaction (PCR) amplification. To identify the recovered viruses, sequence analysis of PCR products was performed. Infectious enteroviruses and adenoviruses were detected in 11 (47.8%) and 9 (39.1%) of the samples, respectively. Both enteroviruses and adenoviruses were detected in five samples (21.7%). The level of viral contamination was quite high, ranging from 2×10 −3 to 2.9×10 −2 Most Probable Number of Infectious Unit L −1, far above the recommended virus level in drinking water set by the US EPA. Poliovirus type 1 derived from vaccine was frequently detected and the remainder comprised coxsackievirus B type or echovirus type 6, which were causative agents of aseptic meningitis in Korea in 1997 and 1998, respectively. Several types of adenovirus were detected in tap water samples and some water samples were found to contain adenoviruses which were closely related to enteric adenovirus types 40 and 41.

Variation of the agr locus in Staphylococcus aureus isolates from cows with mastitis

Staphylococcus aureus isolates from mastitic cow’s milk were examined for production of α-hemolysin and protein A and their accessory gene regulator ( agr locus) was analyzed. An inverse relationship between α-hemolysin and protein A production was found in most of the 76 isolates, suggesting that the isolates tested may be classified into group I (high α-hemolysin/low protein A), II (low α-hemolysin/high protein A), or III (low α-hemolysin/low protein A). The agr locus, which consists of hld, agrB, agrD, agrC, and agrA, was detected in most of the 78 isolates including two reference strains (Wood 46 and Cowan I) by polymerase chain reaction (PCR). When the PCR products for agr locus of 22 isolates from groups I and II were digested with restriction enzyme MboI, seven bands of the expected lengths were recognized in strain Wood 46, but not in the other isolates tested. Nucleotide sequence analysis of PCR products from six isolates revealed that the agr locus sequence of strain Wood 46 corresponded to that of the published sequence data, but the other five isolates from groups I and II diverged at agrB and agrD sequences and thus the deduced amino acid sequences. These variations of agr locus in S. aureus bovine isolates differed from those reported by Ji et al. [Science 276 (1997) 2027].