Deoxyribonucleic Acid Relatedness Research Articles

The first case of pulmonary disease caused by Mycobacterium septicum in China

Mycobacterium septicum is a rapidly growing Mycobacterium (RGM) that rarely causes pulmonary disease globally. We describe a case of M. septicum pulmonary disease, which to our knowledge is the first reported in China. The isolates were identified as M. septicum and were susceptible in vitro to amikacin, ciprofloxacin, ofloxacin, levofloxacin, kanamycin, and sulfamethoxazole.

A Fast Real-Time Polymerase Chain Reaction Method for Sensitive and Specific Detection of the Neisseria gonorrhoeae porA Pseudogene

Ever since the advent of molecular methods, the diagnostics of Neisseria gonorrhoeae has been troubled by false negative and false positive results compared with culture. Commensal Neisseria species and Neisseria meningitidis are closely related to N. gonorrhoeae and may cross-react when using molecular tests comprising too-low specificity. We have devised a real-time polymerase chain reaction (PCR), including an internal amplification control, that targets the N. gonorrhoeae porA pseudogene. DNA was automatically isolated on a BioRobot M48. Our subsequent PCR method amplified all of the different N. gonorrhoeae international reference strains (n = 34) and N. gonorrhoeae clinical isolates (n = 176) but not isolates of the 13 different nongonococcal Neisseria species (n = 68) that we tested. Furthermore, a panel of gram-negative bacterial (n = 18), gram-positive bacterial (n = 23), fungal (n = 1), and viral (n = 4) as well as human DNA did not amplify. The limit of detection was determined to be less than 7.5 genome equivalents/PCR reaction. In conclusion, the N. gonorrhoeae porA pseudogene real-time PCR developed in the present study is highly sensitive, specific, robust, rapid and reproducible, making it suitable for diagnosis of N. gonorrhoeae infection.

Taxonomic study of bacteria isolated from Lebanese spring waters: proposal for Pseudomonas cedrella sp. nov. and P. orientalis sp. nov.

Deoxyribonucleic acid relatedness studies (S1 nuclease method) have shown that 15 strains isolated from three Lebanese spring waters, belonging to the genus Pseudomonas, formed two homogeneous DNA groups, with a within-group DNA relatedness ranging from 70 to 100%. These groups are referred to as Pseudomonas cedrella sp. nov. and Pseudomonas orientalis sp.nov. These strains were previously grouped on the basis of a numerical analysis in phenons Ve, Vd, Vg, and VI. DNA relatedness with 65 strains representing 24 species of the genus Pseudomonas sensu stricto was below 50%. The highest DNA binding value (50%) was found with P. marginalis species. A comparison of the complete 16S rRNA gene sequences of the strains representing the two new deoxyribonucleic acid hybridization groups, i.e., strains CFML 96–198 T and CFML 96–170 T, and the sequence of other strains of the genus Pseudomonas revealed that these strains (CFML 96–198 T and CFML 96–170 T) fell within the' Pseudomonas fluorescens intrageneric cluster'. The G+C contents of the DNA of P. cedrella CIP 105541 T and P. orientalis CIP 105540 T were 59 and 60 mol%, respectively. The two species can be differentiated from each other by the fact that P. cedrella strains hydrolyze erythritol and D-lyxose. P. cedrella grouped together a total of nine strains from phenotypic groups Ve, Vg, and VI. P. orientalis grouped together six strains from both phenotypic groups Vd and Ve.

Taxonomic Study of Bacteria Isolated from Natural Mineral Waters: Proposal of Pseudomonas jessenii sp. nov. and Pseudomonas mandelii sp. nov.

The taxonomic position of 23 strains isolated from mineral waters and previously grouped in the authentic pseudomonads on the basis of a phenotypic analysis (cluster IX, subclusters XIIIa and XIIIc of VERHILLE, S., ELOMARI, M., COROLER, L., IZARD, D., LECLERC, H. (Syst. Appl. Microbiol, 20, 137-149, 1997) has been genotypically further studied in the present work. On the basis of hybridization results, these strains were gathered into two new genomic groups for which we propose the names of Pseudomonas jessenii sp. nov. (Type strain CIP 105274) and Pseudomonas mandelii sp. nov. (Type strain CIP 105273). Deoxyribonucleic acid relatedness levels showed homologies ranging from 78 to 100% for Pseudomonas jessenii and from 77 to 100% for Pseudomonas mandelii. Furthermore, hybrization rates with 66 representative well characterized species or only partially characterized species of the genus Pseudomonas were below 53%, with delta Tm values of 7 degrees C and more. The mol% G + C content ranged from 57 to 58. The two new species presented basic morphological characteristics common to all pseudomonads. Various phenotypic features, such as denitrification, growth at 4 degrees C or 41 degrees C, trigonelline assimilation, alpha-L-glutamyl-L-histidine arylarmidase activity, growth on benzoate and meso-tartrate were found to differentiate Pseudomonas jessenii from Pseudomonas mandelii and from other Pseudomonas species. Pseudomonas jessenii encompassed a total of 9 strains from both phenotypic groups IX and XIIIa. Pseudomonas mandelii clustered a total of 13 strains from both phenotypic groups IX and XIIIc. Their clinical significance is unknown. The 16S rDNA of each type strain was sequenced and compared with the known sequences of the representative strains of the genus Pseudomonas. A phylogenetic tree was constructed to determine the intrageneric relationships within the genus Pseudomonas.

Catalase-positive Eikenelia corrodens and Eikenella-like isolates of human and canine origin

Ten catalase-positive isolates and one catalase-negative isolate that had been assigned to Eikenella corrodens were compared to the nomenclatural type strain regarding selected phenotypic and molecular features and chromosomal deoxyribonucleic acid (DNA) relatedness using the spectrophotometric method. Five catalase-positive human isolates were assigned to the genomic species Eikenella corrodens on the basis of high DNA relatedness levels. Three others, among them strain Chen UB 204, exhibited only moderate degrees of DNA relatedness to the type strain and with each other. Two catalase-positive isolates from dogs were closely interrelated, but yielded only low degrees of DNA binding with Eikenella corrodens and the Eikenella-like human isolates. These findings confirm that the human eikenellas comprise more than one genomic species and that the canine strains represent a distinct taxonomic entity. The differentiation of the strains investigated by conventional phenotypic features, hydrolytic enzyme reactions, and cellular carbohydrate patterns was considered.

Unusual Yersinia enterocolitica strains recovered from domestic animals and people in New Zealand

Twenty five isolates of Yersinia recovered from the faeces of cattle, sheep, goats and people in New Zealand were characterised biochemically and serologically and were found to be unrelated to any known Yersinia species. Two phenotypes were identified biochemically. Testing against all known O-factors of Yersinia showed that the isolates were serologically unique and two new serotypes were proposed, O:77 and O:78. Deoxyribonucleic acid relatedness studies indicated that the strains formed a homogeneous group, closely related to Yersinia enterocolitica. The definitive status of the isolates has not yet been decided.

Pseudomonas rhodesiae sp. nov., a New Species Isolated from Natural Mineral Waters

Summary Deoxyribonucleic acid relatedness studies (S1 nuclease method) showed that 7 strains of the cluster IIa previously described by Elomari et al. (J. Appl. Bacteriol 78, 71-81, (1995)) formed a homogenous deoxyribonucleic acid hybridization group. This group of strains forms a new species: Pseudomonas rhodesiae sp. nov. A total of 67 strains representing known or partially characterized sprecies of the genus Pseudomonas had 7 to 48 % DNA hybridization with Pseudomonas rhodesiae. This new species composed of strains isolated from natural mineral waters, were Gram negative, rod shaped, and motile by means of a single polar flagellum. They were not able to accumulate poly-γ-hydroxybutyrate, were capable of respiratory but not fermentative metabolism. They grew at 4°C but not a 41°C, produced fluorescent pigment, catalase, cytochrome oxidase and lecithinase, and possessed arginine dihydrolase system. They did not hydrolyse gelatin and starch, and were able to use glucose, trehalose, 2-ketogluconate, inositol, L-valine and γ-alanine. They possessed L-pyrrolidone arylamidase, L-histidyl-L-serine arylamidase but did not have osidase, esterase = C12, esterase = C14, esterase = C16, and glycyl-L-tryptophane arylamidase. The average guanine + cytosine (G + C) content of the deoxyribonucleic acid was 59 ± 1 mol%. The type strain of P. rhodesiae has been deposited as CIP 1046641. The clinical significance of Pseudomonas rhodesiae is unknown.

Identification of Pseudomonas anguilliseptica isolated from several fish species in France

Since 1990, outbreaks of haemorrhagic septicemia, frequently associated with keratitls, have occurred on gilthead sea bream Sparus aurata, farmed along the French Mediterranean and Atlantic coasts. Several bacterial isolates obtained from diseased sea bream, sea bass Dicentrarchus labrax, and turbot Scophthalmus maximus showed phenotypic similarities with the Pseudomonas anguilliseptica Mlakabayashi & Egusa, 1972 type strain NCIMB 194gT The French isolates were con~pared with the type strain by determining levels of deoxyribonucleic acid (DNA) relatedness (S1 nuclease method), guanine + cytosine content (thermal denaturation method), and by performing phenotypic tests. All of the isolates formed a tight genomic species with higher than 90% DNA relatedness to the type strain. This study demonstrates the phenotypic and genomic homogeneity of P. anguilliseptlca and confirms that this bacterial species exhibits no host specificity. It thus represents a potential hazard for many farmed fish species and could cause serious economic losses.

Lyme Disease Spirochetes in a Wild Fox (Vulpes vulpes schrencki) and in Ticks

Lyme disease spirochetes were demonstrated in a wild female fox (Vulpes vulpes schrencki) and in Ixodes persulcatus ticks collected from the fox on Sapporo, Hokkaido, Japan. Spirochetes were detected in I. persulcatus, as well as skin lesions, brain, heart, kidney, and liver of the fox. Five of seven isolates reacted with a monoclonal antibody against Borrelia afzelii specific Osp B. Deoxyribonucleic acid (DNA) relatedness of a brain isolate was 89% to B. afzelii, and ranged from 50 to 67% to three other species. Immunoglobulin G antibodies to B. afzelii, B. garinii and B. burgdorferi sensulato, when tested in an enzyme-linked immunosorbent assay (ELISA), were negative in the fox. There were no antibodies against seven serovars of Leptospira interrogans.

Classification of Pasteurella field strains isolated from farms in germany using traditional methods and DNA-DNA hybridization

410 Pasteurella (P.) field strains isolated from calves and piglets were classified according to Bisgaard et al. (1). 376 strains were assigned to P. multocida ssp. multocida, 34 of them were ornithine- and trehalose+, and 61 of them ornithine- and trehalose-. 4 strains belonged to P. multocida ssp. septica, 4 to P. multocida ssp. gallicida, 6 to P. avium biovar 2 and 20 to P. canis biovar 2. There was no difference in the prevalence of the species in calves and pigs. The fact that strains belonging to P. multocida ssp. septica were isolated only from calves and P. multocida ssp. multocida ornithine- and trehalose- were mostly isolated from piglets could indicate a certain host specificity of these isolates. In genotypic investigations 20 field isolates of P. multocida belonging to different Carter serotypes, as well as serologically negative strains were compared to reference strains in terms of deoxyribonucleic acid (DNA) relatedness. The data obtained by filter hybridization revealed a considerable degree of genotypic intraspecies heterogeneity within P. multocida. No correlations to the respective serotypic classification could be detected.

Genetic heterogeneity among nutritionally deficient streptococci

The nutritionally deficient (variant) streptococci (NDS) share the auxotrophic characteristic of requiring pyridoxal or thiol group supplementation for growth. The deoxyribonucleic acid relatedness of these organisms among themselves is unknown. Improved speciation of NDS would lead to a better knowledge of their pathogenesis and possible insight into improved clinical management. Therefore, DNA-DNA hybridization and biotyping of 23 nutritionally deficient streptococci were performed. Biochemical testing using the API Rapid Strept Identification method revealed that the organisms in this study were characterized among three broad biotype groups. Only one strain was nontypeable. DNA-DNA hybridization among the nutritionally deficient streptococci that we compared revealed genetic heterogeneity. Only four (17%) of 23 isolates were highly homologous; all were of biotypes 2 and 3. Reference viridans streptococcal strains had minimal homology to the NDS strains. The data indicate that the NDS are genetically heterogeneous.

Deoxyribonucleic acid relatedness among strains of the moderately halophilic speciesDeleya halophila

The genomic relatedness among 16 strains assigned to the moderately halophilic speciesDeleya halophila and other 20 representative strains of halophilic and nonhalophilic species was estimated by determination of deoxyribonucleic acid (DNA) base composition and by DNA-DNA hybridization studies. The guanine-plus-cytosine (G + C) base contents, determined from the melting temperature of DNAs ofD. halophila strains, were 66.0–68.8 mol %. DNA-DNA homology studies, determined by membrane filter technique, indicate that the 16 strains ofD. halophila comprise a genetically homogeneous group. High homology (≥70–100%) was obtained between the type strainD. halophila CCM 3662 and the otherD. halophila strains studied; however, very low DNA relatedness was found between the representative strains ofD. halophila and otherDeleya species (≤13-0%), as well as other moderately halophilic, marine, or nonhalophilic bacteria investigated.

Deoxyribonucleic Acid Relatedness among Members of the Genus Frankia

The diversity among 43 isolates of the genus Frankia was studied by determining levels of deoxyribonucleic acid relatedness (SI nuclease method) and DNA base compositions. The guanine + cytosine contents ranged from 66 to 75 mol%. At least nine genomic species were differentiated, including three genomic species among strains compatible with members of the genus Alnus, five genomic species among strains compatible with members of the family Elaeagnaceae, and one genomic species among strains compatible with members of the genus Casuarina. Genomic species 1, which contained proposed type strain CpI1 and nine strains that were compatible with members of the genus Alnus and were 64 to 97 % related to strain ACoN24d, is Frankia alni. Four genomic species contained single strains that were 0 to 30% related to the other genomic species. Typical strains isolated from members of the genus Casuarina were found to be very homogeneous (69 to 100% related to strain ORS020606) and clearly separated from atypical strains. The nine genomic species delineated in this study cannot be named since no phenotypic tests are available for identification.

Synonymy of Alcaligenes aquamarinus, Alcaligenes faecalis subsp. homari, and Deleya aesta: Deleya aquamarina comb. nov. as the Type Species of the Genus Deleya

Alcaligenes aquamarinus and Alcaligenes faecalis subsp. homari proved to be identical to Deleya aesta in respiratory quinone type, cellular fatty acid profiles, and biochemical and physiological characteristics and as determined by deoxyribonucleic acid-deoxyribonucleic acid relatedness studies. The name Alcaligenes aquamarinus has priority. Therefore, the name Deleya aquamarina comb. nov. is proposed for the type species of the genus Deleya; the type strain should be changed from strain IAM 12551 (= ATCC 27128) (type strain of Deleya aesta) to strain IAM 12550 (= ATCC 14400) (type strain of Alcaligenes aquamarinus).

Mesophilobacter marinus gen. nov., sp. nov.: An Aerobic Coccobacillus Isolated from Seawater

The name Mesophilobacter marinus gen. nov., sp. nov. is proposed for 11 strains of aerobic, mesophilic, nonmotile, oxidase-positive, penicillin-resistant, moderately halophilic, gram-negative coccobacilli that were isolated from seawater. The genus Mesophilobacter is closely related to the genera Acinetobacter, Moraxella, and Psychrobacter, but the levels of deoxyribonucleic acid relatedness to members of these genera are low. The mesophilobacters have optimal growth temperatures of 33 to 37°C and can grow in broth containing 7% sodium chloride. The ubiquinone system is Q-8, and the major cellular fatty acids are C16:1, C18:1, and C16:0 acids. The guanine-plus-cytosine contents of the deoxyribonucleic acids are 44.0 to 46.9 mol%. The type strain of this species is strain 14S-4 (= IAM 13185).

Numerical Taxonomy and Deoxyribonucleic Acid Relatedness of Environmental and Clinical Vibrio Species Isolated in Indonesia

Numerical taxonomic methods were used to analyze taxonomic data gathered for 229 Vibrio strains isolated from fecal, seawater, and seafood specimens collected in Jakarta, Indonesia. Simple matching and Jaccard coefficients yielded similar results. Most of the clinical isolates were identified as Vibrio parahaemolyticus, V. cholerae, or V. mimicus. Environmental isolates included V. alginolyticus and one strain of V. vulnificus. Clusters of V. parahaemolyticus included both clinical and environmental isolates. Biotypes of V. parahaemolyticus were not associated with a specific source. Reference strains of other Vibrio species did not cluster with any of the isolates examined in this study. Four groups remained initially unidentified and were further subjected to deoxyribonucleic acid hybridization analysis, which enabled their identification as V. parahaemolyticus, V. alginolyticus, or possible new Vibrio spp. Descriptions of Vibrio species already published proved useful in identifying and classifying most of the isolates from a tropical climate.

Amendment of the Genus Saccharothrix Labeda et al. 1984 and Descriptions of Saccharothrix espanaensis sp. nov., Saccharothrix cryophilis sp. nov., and Saccharothrix mutabilis comb. nov.

The description of the genus Saccharothrix is amended to include strains having either a type PII (phosphatidylethanolamine) or a type PIV (phosphatidylethanolamine and glucosamine-containing phospholipids) phospholipid pattern. A new antibiotic-producing species, Saccharothrix espanaensis (type strain, NRRL 15764), is described. Nocardiopsis mutabilis Shearer et al. 1983 is transferred to the amended genus as Saccharothrix mutabilis comb. nov. “Nocardiopsis mutabilis subsp. cryophilis” Takahashi et al. 1986 is described as a new species, Saccharothrix cryophilis, based on its physiological properties and lack of high levels of deoxyribonucleic acid relatedness to the previously described Saccharothrix species.

Relationships amongVibrio costicolastrains assessed by DNA-DNA hybridization

Deoxyribonucleic acid (DNA)-DNA hybridization was used to determine the relationships among 14 strains of Vibrio costicola isolated from cured meats or hypersaline waters. Our results indicate that the strains investigated should be considered members of the same genomic species, with homologies of 60% or higher with the V. costicola strains used as reference. Low DNA relatedness was found with other marine vibrios or moderately halophilic bacteria tested. The guanine-plus-cytosine base contents of DNAs from the 14 V. costicola strains were 47.6 to 51.1 mol%.

Taxonomic Relationship of Black-Pigmented Bacillus subtilis Strains and a Proposal for Bacillus atrophaeus sp. nov.

The taxonomic position of Bacillus subtilis strains that produce soluble black pigment is unclear. To assess the genetic relatedness between the pigmented and nonpigmented strains, deoxyribonucleic acid (DNA) reassociation was measured spectrophotometrically. Among the 40 pigmented strains examined, two distinct DNA relatedness groups were found. A total of 25 strains (group 1) showed 24 to 34% DNA relatedness and 15 strains (group 2) showed 70 to 100% relatedness to Bacillus subtilis type strain NRRL NRS-744. The intragroup DNA relatedness values for each group ranged from 85 to 100%; the intergroup relatedness values ranged from 20 to 35%. A multilocus enzyme electrophoresis analysis revealed a low level of similarity between group 1 and group 2 or the nonpigmented group. The group 2 strains and the nonpigmented strains clustered in a common group, indicating the close genetic relationship of these organisms. My results strongly suggest that group 2 is a pigmented variant of B. subtilis, but group 1 is a new species, for which the name Bacillus atrophaeus is proposed. The type strain of the new species is strain NRRL NRS-213.

Campylobacter mustelae, a New Species Resulting from the Elevation of Campylobacter pylori subsp. mustelae to Species Status

The name Campylobacter pylori subsp. mustelae was recently proposed for strains belonging to the genus Campylobacter that were isolated from the gastric mucosa of ferrets because of the high levels of deoxyribonucleic acid relatedness (85 to 100%) of these strains to the type strain of Campylobacter pylori. Subsequent deoxyribonucleic acid relatedness studies done independently in three laboratories by three different methods indicate that the original results were in error. Strains isolated from ferrets in the United States, England, and Australia are members of a single species that is substantially different from C. pylori (10 to 20% relatedness at 50°C and 3 to 10% relatedness at 65°C as determined by the hydroxyapatite method; less than 10% relatedness at 65°C as determined by the nylon membrane blot method; and 30 to 49% relatedness at 66 to 68°C as determined by the spectrophotometric method). The strains isolated from ferrets also differ from human C. pylori strains in their ability to reduce nitrates, their negative leucine arylamidase reaction, their susceptibility to nalidixic acid, and their resistance to cephalothin. The strains from ferrets possess both polar and lateral flagella, whereas only polar flagella have been demonstrated in human C. pylori strains. Thus, the strains isolated from ferrets are members of a species that is distinct from C. pylon, and we propose elevating C. pylori subsp. mustelae to species status as Campylobacter mustelae sp. nov.