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At least 433 records · Page 24Linked to original sources
PubMed1994

Identification of the Staphylococcus sciuri species group with EcoRI fragments containing rRNA sequences and description of Staphylococcus vitulus sp. nov.

Strains of a new species, Staphylococcus vitulus, were isolated from food and a variety of mammals. This species was recognized on the basis of the results of an analysis of genomic EcoRI fragments containing portions of the rRNA operons. The patterns of hybridized fragments obtained from strains belonging to the new taxon were sorted into a distinguishable cluster and were distinct from the Staphylococcus lentus and Staphylococcus sciuri patterns. The results of DNA-DNA hybridization reactions demonstrated that strains in this cluster were more closely related to S. lentus and S. sciuri than to other Staphylococcus species and yet were significantly different. While these strains had some of the phenotypic characteristics of the S. sciuri species group, the newly recognized taxon could be distinguished by its very small colonies on P agar, absence of alkaline phosphatase activity, and lack of acid production from L-arabinose, maltose, N-acetylglucosamine, D-mannose, and raffinose. The type strain of the new species is strain DD 756 (= ATCC 51145).

Animals↗
PubMed1997

Comparison of the 16S/23S ribosomal intergenic regions of "Candidatus Liberobacter asiaticum" and "Candidatus Liberobacter africanum," the two species associated with citrus huanglongbing (greening) disease.

16S/23S intergenic spacer regions from the rRNA operons of two strains of "Candidatus Liberobacter asiaticum" and one strain of "Candidatus Liberobacter africanum" were cloned and sequenced. The intergenic spacers of the two "Candidatus L. asiaticum" strains studied are identical and contain the genes for isoleucine tRNA (tRNA(Ile)) and alanine tRNA (tRNA(Ala)) separated by 11 nucleotides. The intergenic spacer of the "Candidatus L. africanum" strain contains only one tRNA gene (tRNA(Ala)). The level of homology between the intergenic spacers of the two liberobacter species is 79.46%. Ribosomal operons with 16S/23S spacer regions other than those studied might be present in the two "Candidatus Liberobacter" species.

Base Sequence↗
PubMed2001

Comparison of sequence analysis of 16S-23S rDNA spacer regions, AFLP analysis and DNA-DNA hybridizations in Bradyrhizobium.

The sequences of the 16S-23S rDNA intergenic spacer region of 62 strains of Bradyrhizobium, including representatives of the three valid species, were determined. The majority of strains had a single rRNA operon type and all contained a tRNA(Ala) and a tRNA(Ile) gene. Analysis of the sequence data produced groupings in line with previously obtained AFLP data. DNA-DNA hybridizations were performed to determine to what extent spacer sequences and AFLP profiles reflected the overall genomic similarities. Strains belonging to the same AFLP group, and strains with spacer sequences diverging less than 4%, were found to belong to the same genospecies. More remote relationships (DNA homology levels of 40-60%) between species were reflected in the spacer sequence analysis, but not in the AFLP analysis. For the genus Bradyrhizobium, 16S-23S rDNA spacer sequence analysis provides taxonomic information similar, but not always identical to that obtained by DNA-DNA hybridizations. Our results indicate that this genus consists of a group of four highly related genospecies (Bradyrhizobium japonicum, Bradyrhizobium liaoningense and two other genospecies) and at least three other genospecies, one of which is Bradyrhizobium elkanii.

Bradyrhizobium↗
PubMed2001

Pulmonary colonisation with Pneumocystis carinii in an immunosuppressed HIV-negative patient: detection and typing of the fungus by PCR.

Mostly Pneumocystis carinii isolates from patients with acute pneumocystosis (PCP) have been typed until now. This report describes the typing of P. carinii organisms obtained from an HIV-negative patient without PCP. The patient underwent a broncho-alveolar lavage (BAL) to investigate an abnormal chest X-ray. He was diagnosed with sarcoidosis. However, a low level of P. carinii organisms undetectable by microscopy was detected in BAL fluid by two subsequent nested PCR assays: one assay amplifying a portion of the mitochondrial large subunit RNA gene and a second one amplifying the internal transcribed spacers (ITS) 1 and ITS 2 of the nuclear rRNA operon. This low level of the fungus did not reflect acute PCP. Indeed, the clinical outcome was improvement despite the absence of specific treatment. The patient was considered to be only colonised by the fungus. Analysis of sequences of ITS PCR products led to identification of genotype Gg. This information constitutes the first data concerning P. carinii ITS genotype from a patient without acute PCP and HIV. This type has been described previously in AIDS patients diagnosed with PCP. These results show that PCR and ITS genotyping could represent efficient tools for the further investigation of the role played by HIV-negative patients with pulmonary colonisation in the human reservoir of P. carinii.

Bronchoalveolar Lavage Fluid↗
PubMed1997

Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome.

The photosynthetic bacterium Rhodobacter sphaeroides 2.4.1T has two chromosomes, CI (approximately 3.0 Mb) and CII (approximately 0.9 Mb). In this study a low-redundancy sequencing strategy was adopted to analyse 23 out of 47 cosmids from an ordered CII library. The sum of the lengths of these 23 cosmid inserts was approximately 495 kb, which comprised approximately 417 kb of unique DNA. A total of 1145 sequencing runs was carried out, with each run generating 559 +/- 268 bases of sequence to give approximately 640 kb of total sequence. After editing, approximately 2.8% bases per run were estimated to be ambiguous. After the removal of vector and Escherichia coli sequences, the remaining approximately 565 kb of R. sphaeroides sequences were assembled, generating approximately 291 kb of unique sequences. BLASTX analysis of these unique sequences suggested that approximately 131 kb (45% of the unique sequence) had matches to either known genes, or database ORFs of hypothetical or unknown function (dORFs). A total of 144 strong matches to the database was found; 101 of these matches represented genes encoding a wide variety of functions, e.g. amino acid biosynthesis, photosynthesis, nutrient transport, and various regulatory functions. Two rRNA operons (rrnB and rrnC) and five tRNAs were also identified. The remaining 160 kb of DNA sequence which did not yield database matches was then analysed using CODONPREFERENCE from the GCG package. This analysis suggested that 122 kb (42% of the total unique DNA sequence) could encode putative ORFs (pORFs), with the remaining 38 kb (13%) possibly representing non-coding intergenic DNA. From the data so far obtained, CII does not appear to be specialized for encoding any particular metabolic function, physiological state or growth condition. These data suggest that CII contains genes which are functionally as diverse as those found on any other bacterial chromosome and also contains sequences (pORFs), which may prove to be unique to this organism.

Base Sequence↗
PubMed2001

A chromosome map of the European stone fruit yellows phytoplasma.

A physical map of the European stone fruit yellows phytoplasma strain GSFY1 chromosome was constructed using PFGE-purified genomic DNA from diseased tobacco and tomato plants. The map was generated with single and double digestions of the chromosome with SmaI, BssHII, ApaI, BamHI and XhoI restriction endonucleases and the fragments were resolved by PFGE. Reciprocal double digestions were used to locate 26 restriction sites on the chromosome. Southern blot analysis was also used to assist in the arrangement of the contiguous restriction fragments obtained. From the restriction fragments generated by double digestion, the circular chromosome was calculated to be approximately 635 kb. Loci of two rRNA operons, the operon containing the tuf gene, genes encoding an immunodominant membrane protein and a putative nitroreductase, and randomly cloned DNA fragments IH184 and AT67 were placed on the map. Digestion of chromosomal DNA of strain GSFY1 with MluI gave a complex restriction pattern, suggesting that this isolate consists of a population with heterogeneity with respect to MluI restriction sites. The GSFY1 physical map was different from that of the closely related apple proliferation phytoplasma but the genetic arrangement was similar.

Blotting, Southern↗
PubMed1998

Granulocytic ehrlichiosis: an emerging or rediscovered tick-borne disease?

The Ehrlichieae are gram-negative obligately intracellular bacterial pathogens. They can be divided into at least three genogroups on the basis of 16S rRNA gene sequences, but are also classified by target cell specificity. A group of granulocytic ehrlichiae primarily infect neutrophils and fall into genogroup II. The granulocytic ehrlichiae are subdivided by their target hosts, i.e., Ehrlichia phagocytophila in cattle and sheep, E. equi in horses, and the agents of human (HGE) and llama (LGE) granulocytic ehrlichioses. However, these subdivisions may give a false impression, as all these species are closely related both antigenically and on the basis of 16S rRNA operon sequence. In addition, cross-species transmission can occur naturally or by experimental infection. The vectors for these granulocytic ehrlichiae are hard-bodied ixodid ticks, and the reservoir hosts are probably wild rodents, deer and sheep. In each host, this illness presents as a febrile disease which can be followed by immunosuppression leading to secondary infections.

Animals↗
PubMed1995

Typing of Staphylococcus aureus strains by PCR-amplification of variable-length 16S-23S rDNA spacer regions: characterization of spacer sequences.

To develop a rapid and accurate method of typing large numbers of clinical isolates of Staphylococcus aureus, the spacer region C of the rRNA operon [1391-507 (16S-23S)] was enzymically amplified from 322 strains. When the products were separated by denaturing PAGE, 15 variable-length rrn alleles were demonstrated, ranging in size from 906 to 1223 bp. The variable-length HpaII-digested region C [(region E; 1446-196 (16S-23S)] amplification products were cloned into M13mp18RF to sequence separate variable-length alleles. A total of 17 region E inserts were sequenced, aligned and divided into nine alleles by length (938-1174) and sequence properties. The 16S-23S spacer rDNA varied in length (303-551 bp) and in properties; three alleles contained a tRNAIle gene alone, two alleles contained a tRNAIle and a tRNAAla gene, and four alleles lacked tRNA genes. The sequences of two alleles showed less than 1% variation when isolated from two or three S. aureus strains. The 48 penicillin- and methicillin-sensitive strains were divided into 26 ribotypes; in contrast, the 274 methicillin-resistant S. aureus (MRSA) strains were divided into nine ribotypes (A-I) with 97% typing as either ribotype A or B (rrnL was missing in B). The sequence conservation of the rrn operons argues for the use of the 16S-23S spacer region as a stable and direct indicator of the evolutionary divergence of S. aureus strains.

Alleles↗
PubMed1996

Gene arrangement and organization in a approximately 76 kb fragment encompassing the oriC region of the chromosome of Mycobacterium leprae.

A continuous 75627 bp segment of the Mycobacterium leprae chromosome spanning the oriC region was sequenced. The gene order at this locus was similar to that found in the replication origin region of many other prokaryotes, particularly Mycobacterium tuberculosis and Streptomyces coelicolor. As in the case of several Gram-positive bacteria, essential genes involved in basic cellular functions, such as DNA or RNA metabolism (dnaA, dnaB, dnaN, gyrB, gyrA, pcnB, recF, rnpA, ssb), cell wall synthesis (ponA, pbpA) and probably cell division (gidB, rodA) were found. Strikingly, the gidA gene was absent from this part of the genome and there was no rRNA operon near oriC. The gyrA gene harbours an intein coding sequence indicating that protein splicing is required to produce the mature A subunit of DNA gyrase. Among the many other noteworthy features were ORFs encoding putative serine/threonine protein kinases and a protein phosphatase, three tRNA genes, one M. leprae-specific repetitive element and a glnQ pseudogene.

Amino Acid Sequence↗
PubMed2004

A putative transposase gene in the 16S-23S rRNA intergenic spacer region of Mycoplasma imitans.

Examination of the nucleotide sequences of the 16S-23S intergenic transcribed spacer (ITS) region of Mycoplasma imitans and Mycoplasma gallisepticum identified a putative transposase gene located only in the ITS of M. imitans, which can be used as a genetic marker to distinguish these two species. The relative size of the PCR products of the ITS region allowed a clear distinction to be made between strains of M. imitans and M. gallisepticum, both of which could be readily discriminated from the type strains of all the other recognized avian Mycoplasma species. In addition, the putative transposase gene assigned in the ITS of M. imitans was shown to include a sequence homologous to that of the P75 gene of M. gallisepticum. This is believed to be the first description of an insertion element in the rRNA operon region of a mycoplasma species.

Animals↗
PubMed2005

The vlhA loci of Mycoplasma synoviae are confined to a restricted region of the genome.

Mycoplasma synoviae, a major pathogen of poultry, contains a single expressed, full-length vlhA gene encoding its haemagglutinin, and a large number of vlhA pseudogenes that can be recruited by multiple site-specific recombination events to generate chimaeric variants of the expressed gene. The position and distribution of the vlhA pseudogene regions, and their relationship with the expressed gene, have not been investigated. To determine the relationship between these regions, a physical map of the M. synoviae genome was constructed using the restriction endonucleases SmaI, I-CeuI, BsiWI, ApaI and XhoI and radiolabelled probes for rrnA, recA and tufA. A cloned fragment encoding the unique portion of the expressed vlhA gene and two PCR products containing conserved regions of the ORF 3 and ORF 6 vlhA pseudogenes were used to locate the regions containing these genes on the map. The chromosome of M. synoviae was found to be 890.4 kb and the two rRNA operons were in the same orientation. Both the expressed vlhA gene and the vlhA pseudogenes were confined to the same 114 kb region of the chromosome. These findings indicate that, unlike Mycoplasma gallisepticum, in which the vlhA genes are located in several loci around the chromosome and in which antigenic variation is generated by alternating transcription of over 40 translationally competent genes, M. synoviae has all of the vlhA sequences clustered together, suggesting that close proximity is needed to facilitate the site-specific recombinations used to generate diversity in the expressed vlhA gene.

Animals↗
PubMed1993

Transmission of oral bacterial species between spouses.

The transmission of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis and mutans streptococci was studied between 4 married couples who suffered from advanced periodontitis. Of the 20 couples investigated, the 4 in which both spouses harbored A. actinomycetemcomitans and P. gingivalis were chosen for the transmission study. Three of these couples also harbored mutans streptococci. A. actinomycetemcomitans isolates (8-24 per subject) and mutans streptococcal isolates (5-23 per subject) were serotyped by immunodiffusion technique. For ribotyping, chromosomal DNA from A. actinomycetemcomitans isolates (4-5 per subject) and mutans streptococcal isolates (4-11 per subject) was digested with restriction endonucleases ClaI or BglI and HindIII or SmaI, respectively. P. gingivalis isolates (2-15 per subject) were ribotyped by using ClaI, BglI and SmaI. The blotted restriction fragments were hybridized to the plasmid pKK3535, which contains the rRNA operon of the E. coli chromosome. The spouses in 2 couples shared the same sero- and ribotypes of A. actinomycetemcomitans and S. mutans. P. gingivalis ribotypes were identical in 2 couples. The result suggests transmission of oral bacteria between spouses.

Adult↗
PubMed1994

Transmission of oral Prevotella melaninogenica between a mother and her young child.

Most likely, young children acquire their oral microflora by frequent transfer of bacteria between family members. The possible transmission of obligately anaerobic Prevotella melaninogenica recovered from 11 mother-child pairs was examined by ribotyping. One to 18 isolates (mean 13) per child from different oral sampling sites and 4 to 17 (mean 10) isolates per mother from stimulated salivary samples, collected on 2 occasions, were analyzed. On sampling, the mean ages of the children were 4 months and 32 months, respectively. Restriction endonucleases KpnI and ClaI were chosen for the digestion of chromosomal DNA. DNA fragments were electrophoretically separated, blotted onto a nylon membrane and hybridized with rRNA operon of Escherichia coli. DNA-DNA hybrids were detected immunologically. Extensive genetic heterogeneity, 101 distinct ribotypes, was observed among 248 P. melaninogenica isolates studied. Both mothers and children harbored several (up to 7) ribotypes which, apart from 3 ribotypes, were distinguishable in unrelated subjects. Several P. melaninogenica ribotypes were detected on both sampling occasions over 2 years apart. Identical ribotypes were found in 6 of the 11 mother-child pairs, 1 to 2 similar ribotypes per pair. This suggests the transmission of P. melaninogenica between the mother and her child, probably via maternal saliva. However, the unique ribotypes found in these children also indicate that other sources besides the mother influence the oral colonization of young children.

Adult↗
PubMed2005

Insights into the genomes of archaea mediating the anaerobic oxidation of methane.

The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.

Amino Acid Sequence↗
PubMed1991

Differentiation of lactococci by rRNA gene restriction analysis.

Strains of the subspecies of Lactococcus lactis could be differentiated by rRNA gene restriction fragment length polymorphisms (RFLP). 16S rRNA-specific oligonucleotide as well as polynucleotide DNA probes were used for the detection of restriction fragments. In addition, a site-specific probe was designed for the intergenic spacer region of 23S and 5S rRNA genes. For all lactococcal strains the putative presence of six rRNA operons was confirmed. A non-radioactive hybridization assay was used based on hybrid detection by chemiluminescence. Specific patterns were found for any of the strains investigated. Subspecies-specific restriction fragments could be identified in addition to the strain-specific patterns.

Base Sequence↗
PubMed2002

Physical and genetic map of the Bacteroides fragilis YCH46 chromosome.

The chromosome of Bacteroides fragilis strain YCH46 was shown to be a single circular DNA molecule of about 5.3 Mb having 16 NotI, seven AscI, and six I-CeuI sites. A physical map of the chromosome was constructed by four independent experimental approaches: linking clone analysis, cross-Southern hybridization, partial restriction digestion, and two-dimensional pulsed-field gel electrophoresis. Six rRNA operons and 10 known genes were localized on the physical map.

Bacteroides fragilis↗
PubMed1995

Characterisation of Pasteurella multocida isolated from fowl cholera outbreaks on turkey farms.

Biochemical profiles, restriction endonuclease analysis (REA) and ribotyping were used to investigate Pasteurella multocida isolates from outbreaks of fowl cholera on 7 turkey farms in New South Wales. While only a single isolate was available from 5 of the farms, multiple isolates, 4 and 12 respectively, were available from the other 2 farms. The available field evidence suggested that 8 outbreaks had occurred with one farm suffering 2 outbreaks. The isolates obtained were all confirmed as Pasteurella multocida. Biochemical profiles allocated the isolates to 4 groups, 3 being variants of P multocida subsp multocida and the fourth being P multocida subsp septica. REA performed with HpaII established 7 groups. Ribotyping using the HpaII digests probed with the 16S rRNA operon of Haemophilus paragallinarum recognised the same 7 groups as REA. Unlike the biochemical profiles, both REA and ribotyping provided a fine subdivision that identified outbreaks as either related or unrelated. The REA and ribotyping patterns as well as biochemical profiles were stable for all isolates from the outbreaks in which multiple isolates were obtained from either the same bird or from different birds. REA and ribotyping were found to be superior to biotyping methods for the investigation of fowl cholera outbreaks.

Animals↗
PubMed2005

Reduced azole susceptibility in genotype 3 Candida dubliniensis isolates associated with increased CdCDR1 and CdCDR2 expression.

Candida dubliniensis is a recently identified yeast species primarily associated with oral carriage and infection in individuals infected with the human immunodeficiency virus. The species can be divided into at least four genotypes on the basis of the nucleotide sequence of the internal transcribed spacer region of the rRNA operon. Previous studies have shown that a small number of clinical isolates belonging to genotype 1 are resistant to the commonly used antifungal drug fluconazole. The aim of the present study was to investigate the molecular mechanisms responsible for reduced susceptibility to azole drugs in C. dubliniensis genotype 3 isolates obtained from a patient with fluconazole-recalcitrant oral candidiasis. Four isolates from a single clinical sample, one susceptible, the other three exhibiting reduced susceptibilities to fluconazole, itraconazole, ketoconazole, voriconazole, and posaconazole, were examined. Results showed that reduced susceptibility to azole drugs was associated with an increase in the expression of the multidrug transporters CdCDR1 and CdCDR2 which correlated with reduced intracellular accumulation of radiolabeled fluconazole and an increase in the activity of energy-dependent efflux mechanisms. In contrast to observations made in previous studies, overexpression of the multidrug transporter CdMDR1 was not observed. Despite a thorough investigation of all commonly encountered mechanisms of azole resistance, no other mechanism could be associated with reduced susceptibility to azole drugs in the clinical isolates studied. This is the first report of CdCDR2 involvement in azole resistance in C. dubliniensis.

ATP-Binding Cassette Transporters↗