Isolation and Analysis of Nucleotide Sequences of the 16S rRNA Gene of Pseudomonas aeruginosa Isolated from Clinical Samples

2021 ◽  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Nucleotide Sequences ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The 16S Rrna Gene

scholarly journals Ochrobactrum pseudintermedium sp. nov., a novel member of the family Brucellaceae, isolated from human clinical samples

2007 ◽  
Vol 57 (5) ◽  
pp. 1007-1013 ◽  
Author(s):  
Corinne Teyssier ◽  
Hélène Marchandin ◽  
Hélène Jean-Pierre ◽  
Agnès Masnou ◽  
Ghislaine Dusart ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Family ◽  
Ochrobactrum Intermedium ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

Three novel Gram-negative, non-fermenting aerobic bacilli were isolated from human clinical samples. They shared more than 99.8 % of the 16S rRNA gene nucleotide positions. The strains were related to Ochrobactrum intermedium with about 97.48 % 16S rRNA gene sequence similarity. In 16S rRNA gene-, dnaK- and rpoB-based phylogenies, the strains were grouped in a lineage that was distinct from other Ochrobactrum species in the family Brucellaceae. Fatty acid composition, polar lipids, quinone system, DNA–DNA relatedness, genome organization, and physiological and biochemical data differentiated these isolates from recognized species of the genus Ochrobactrum. The three clinical strains therefore represent a novel species within the genus Ochrobactrum, for which the name Ochrobactrum pseudintermedium sp. nov., is proposed. The type strain is ADV31T (=CIP 109116T=DSM 17490T). The DNA G+C content of strain ADV31T was 54.5 mol%.

scholarly journals Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes

2010 ◽  
Vol 60 (6) ◽  
pp. 1271-1279 ◽  
Author(s):  
Hélène Marchandin ◽  
Corinne Teyssier ◽  
Josiane Campos ◽  
Hélène Jean-Pierre ◽  
Frédéric Roger ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The Novel ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Gram Negative ◽  
The Family ◽  
The 16S Rrna Gene

Three strains of a hitherto unknown, Gram-negative, tiny, anaerobic coccus were collected from human clinical samples originating from skin and soft tissues. The three isolates displayed at least 99.9 % identity in their 16S rRNA gene sequences and more than 99.8 % identity in their dnaK gene sequences. The isolates were affiliated to the family Veillonellaceae, the coccobacillus Dialister micraerophilus being the most closely related species, but there was no more than 91.1 % identity in the 16S rRNA gene sequence between this species and the three isolates. Phylogeny based on the 16S rRNA gene confirmed that the three strains represent a novel and robust lineage within the current family Veillonellaceae. A similar genomic structure was demonstrated for the three isolates by PFGE-based analysis. Morphology and metabolic end products, as well as genotypic and phylogenetic data supported the proposal of the novel genus Negativicoccus gen. nov., with the novel species Negativicoccus succinicivorans sp. nov. [type strain ADV 07/08/06-B-1388T (=AIP 149.07T=CIP 109806T=DSM 21255T=CCUG 56017T) as type species]. Phylogenetic analyses based on the 16S rRNA gene sequences of members of the phylum Firmicutes and other phyla indicated that the family Veillonellaceae forms a robust lineage clearly separated from those of the classes ‘Bacilli’, ‘Clostridia’, Thermolithobacteria and ‘Erysipelotrichi’ in the phylum Firmicutes. Therefore, we propose that this family is a class-level taxon in the phylum Firmicutes, for which the name Negativicutes classis nov. is proposed, based on the Gram-negative type of cell wall of its members, with the type order Selenomonadales ord. nov. In this order, a novel family, Acidaminococcaceae fam. nov., is proposed and description of the family Veillonellaceae is emended.

Assessment of real-time PCR for diagnosis ofMycoplasma pneumoniaepneumonia in pediatric patients

2006 ◽  
Vol 52 (2) ◽  
pp. 125-129 ◽  
Author(s):  
Miyuki Morozumi ◽  
Akira Ito ◽  
Somay Y Murayama ◽  
Keiko Hasegawa ◽  
Reiko Kobayashi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Mycoplasma Pneumoniae ◽  
Real Time Pcr ◽  
High Sensitivity ◽  
Community Acquired Pneumonia ◽  
Clinical Samples ◽  
Rrna Gene ◽  
The 16S Rrna Gene

We developed a real-time PCR to detect Mycoplasma pneumoniae with a primer set designed for the 16S rRNA gene. Clinical samples (n = 937) were collected from children with community-acquired pneumonia between April 2002 and March 2004 at 12 Japanese medical institutions. Sensitivity of real-time PCR was calculated as 10 colony-forming units per reaction tube using a pMP01 plasmid carrying a 225-bp target DNA fragment of the 16S rRNA gene in M. pneumoniae M129, a standard strain. Results, obtained within 2 h, were compared with those of conventional culture and serologic methods. Of all cases tested, 151 (16.4%) and 129 (13.8%) were positive for M. pneumoniae by real-time PCR and by culture, respectively. Among the 151 cases, almost all of those tested serologically by passive agglutination showed a rise in M. pneumoniae antibody titre between acute and convalescent sera. We conclude that this real-time PCR can identify M. pneumoniae rapidly and fulfills the need for rapid identification, high sensitivity, and high specificity.Key words: real-time PCR, Mycoplasma pneumoniae identification, pediatrics, community-acquired pneumonia, Mycoplasma pneumoniae culture.

scholarly journals Species and Genetic Diversity of Representatives of the Anaplasmataceae Family Found in the Sympatry Zone of the Ixodes, Dermacentor and Haemaphysalis Genera Ticks

2019 ◽  
Vol 4 (2) ◽  
pp. 127-135
Author(s):  
E. K. Doroshchenko ◽  
O. V. Lisak ◽  
V. A. Rar ◽  
O. V. Suntsova ◽  
Yu. S. Savinova ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Nucleotide Sequences ◽  
Rrna Gene ◽  
Potential Reservoir ◽  
Ixodes Ticks ◽  
Sympatry Zone ◽  
Reservoir Hosts ◽  
The 16S Rrna Gene

Introduction.On the territory of the Ekhirit-Bulagatsky district of the Irkutsk region zones of sympatry of four Ixodes ticks species are found, where the species and genetic diversity of infectious agents transmitted through tick bites may be more pronounced than in foci with a mono-dominant type of ticks’ population. In this connection, the study of the species and genetic diversity of representatives of the Anaplasmataceae family in the sympatry zone of the Ixodes ticks of closely related species was of scientific interest.Objective:To study the species and genetic diversity of members of the Anaplasmataceae family in the zones of sympatry of Ixodes ticks Ixodes persulcatus, Dermacentor silvarum, D. nuttalli and Haemaphysalis concinna, to identify the main carriers and potential reservoir hosts of ehrlichia and anaplasma.Methods.In the course of the study, 1106 specimens of adult ticks and 49 samples of small mammalian livers from the Ekhirit-Bulagatsky area were analyzed. Anaplasma and ehrlichia DNA were detected by two-round PCR in the presence of genus- and species-specific primers from the 16S rRNA gene region. The nucleotide sequences of the 16S rRNA gene and the fragment of the groESL operon were identified in some samples. Sequencing was carried out according to the Sanger method. Comparative analysis was performed using the BLASTN program and ClustalW method. Epidemiological data analysis was performed using parametric methods of statistical processing of the material.Results.The DNA of Ehrlichia muris and Anaplasma phagocytophilum were detected in all studied species of ticks in their sympatry area. However, the rate of infection of taiga ticks was significantly higher than that of H. concinna and Dermacentor spp. Potential reservoir hosts of the Anaplasmataceae family members can be classified as Microtus oeconomus, M. gregalis, Myodes rutilus and Sorex spp. When analyzing the nucleotide sequences of the 16S rRNA gene, three genetic variants of anaplasma were detected. The nucleotide sequences of the A. phagocytophilum groESL operon belonged to two genetic groups.

scholarly journals Comparison of P1 and 16S rRNA genes for detection of Mycoplasma pneumoniae by nested PCR in adults in Zhejiang, China

2015 ◽  
Vol 9 (03) ◽  
pp. 244-253 ◽  
Author(s):  
Zibo Zhou ◽  
Xiangzhi Li ◽  
Xiaojian Chen ◽  
Lili Yao ◽  
Changwang Pan ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Mycoplasma Pneumoniae ◽  
Nested Pcr ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Positive Rate ◽  
The 16S Rrna Gene

Introduction: Mycoplasma pneumoniae (M. pneumoniae) is the most common atypical pathogen that causes respiratory infections in humans. Laboratory tests are important in the diagnosis of M. pneumoniae because of the atypical features in clinical signs and symptoms. Nowadays, both the P1 adhesin gene and 16S ribosomal (r) RNA (rRNA) gene of M. pneumoniae have been widely detected by polymerase chain reaction (PCR). The purpose of the present study was to evaluate the most suitable target in the detection of M. pneumonia via nested PCR. Methodology: Both the P1 adhesin gene and 16S rRNA gene for nested PCR reaction conditions were optimized through an orthogonal test and single-factor experiment. Then, the sensitivity of the two sets of targets was evaluated. Finally, based on the optimal conditions, 55 clinical samples of throat swabs collected from adult patients in 2013 were examined by established nested PCR. Result: The results revealed that PCR detection of the 16S rRNA gene was more sensitive than the P1 adhesin gene because the detection limits for both the P1 gene and 16S rRNA gene were at least 100 fg and 10 fg of M. pneumoniae DNA, respectively. Furthermore, the positive rate for detection of the 16S rRNA gene (30/55; 54.5%) was higher than that of the P1 adhesin gene (25/55; 45.5%). Conclusion: Our results indicate that the 16S rRNA gene is more suitable for diagnosis of M. pneumoniae infection than the P1 adhesin gene due to its higher sensitivity and positive rate in clinical samples.

scholarly journals PSEUDOMONAS AERUGINOSA STRAIN 21SG A DEGRADER OF CHLORPHENOXYACETIC ACIDS

ÈKOBIOTEH ◽  
2020 ◽  
Vol 3 (3) ◽  
pp. 311-317
Author(s):  
V.V. Korobov ◽  
◽  
N.V. Zharikova ◽  
T.R. Iasakov ◽  
E.I. Zhurenko ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Comparative Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Morphometric Characteristics ◽  
Rrna Gene Sequence ◽  
The 16S Rrna Gene

A new strain of Pseudomonas aeruginosa 21SG, a chlorphenoxyacetic acid degrader, was isolated. The culture was determined on the basis of physiological, biochemical, cultural, morphological and morphometric characteristics, as well as the results of a comparative analysis of the 16S rRNA gene sequence. We studied the growth of a periodic culture of P. aeruginosa 21SG on chlorophenoxyacetic acids and presented the dynamics of a decrease in the concentration of substrates. The metabolic stages of 2,4,5-trichlorophenoxyacetic acid were revealed.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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