Phylogeny Analysis of gyrB Gene and 16S rRNA Genes of Pseudomonas aeruginosa Isolated from Iraqi Patients

2021 ◽  
pp. 2517-2521
Author(s):  
Sana MH AL-Shimmary ◽  
Nadira S. Mohamed ◽  
Safaa A. S. Al-Qaysi ◽  
Asmaa M Salih Almohaidi
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Efficient System ◽  
16S Rrna Analysis ◽  
Gyrb Sequence ◽  
Genetic Sequences

Infection caused by Pseudomonas aeruginosa is one of the major problems in hospitalized patients which are related to the high mortality. The DNA gyrase B, gyrB reading gene sequence method provides a fast and efficient system for bacterial identification and diagnosis, taxonomic analysis and monitoring of bacteria in the natural environment. Evolution analysis was performed using gene nucleotide sequences for gyrB and 16S rRNA genes. PCR amplifiers were used for the genes under study and their genetic sequences were read. The evolutionary tree was drawn based on the genetic sequences of the classification of P. aeruginosa, compared to the analysis of the 16S rRNA genes, gyrB sequences showed a greater evolutionary deviation of bacteria and may be useful for distinguishing between closely related species. Sequence analysis of 16S rRNA is accurate for identifying unknown bacteria to the genus level. However, the variable gyrB sequence analysis can identify unknown bacteria to the species level. Together with the 16S rRNA analysis, gyrB sequence analysis is considered a useful tool to build the evolutionary relationships of bacteria, especially for the classification of converging bacterial species and controlling the invasive Patho Micobial infection treatment in the hospital.

scholarly journals Identification and classification of the genus Bacteroides by multilocus sequence analysis

Microbiology ◽  
2011 ◽  
Vol 157 (12) ◽  
pp. 3388-3397 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Moriya Ohkuma
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Sequence Similarity ◽  
Single Gene ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Rrna Gene

Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5 % gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.

scholarly journals Molecular characterization of Pseudomonas aeruginosa isolates from Sudanese patients: A cross-sectional study

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1135
Author(s):  
Reem H. Amoon ◽  
Amna H. Abdallha ◽  
Ahmed Osman Sharif ◽  
Ehssan H. Moglad ◽  
Hisham N. Altyb ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Bacterial Disease ◽  
Clinical Specimens

Background:16S rRNA gene sequence analysis is a robust tool for characterization of new pathogens in clinical specimens with suspected bacterial disease. The aim of this study was to characterizePseudomonas aeruginosaisolated from clinical specimens by sequencing the 16S rRNA gene.Methods:Forty bacterial isolates were obtained from different clinical specimens (wound, urine and sputum) using enrichment selective media and biochemical tests to characterize and identify the bacteria asP. aeruginosa.DNA was extracted fromP. aeruginosausing the Chelex method. A universal primer was used to amplify 16S rRNA genes by a conventional PCR technique. The amplified PCR products were sequenced, and the sequences were viewed by Finch TV program version 1.4.0. The identity and similarity of the nucleotide sequence of the isolated strains was detected by comparing them with published sequences using BLASTn. Phylogenetic trees were constructed using Phylogeny.fr software.Results:Sequence analysis by BLASTn displayed high similarity and identity withP. aeruginosafrom China KX461910, Australia JN609194 and with otherP. aeruginosaisolates from the GenBank database.Conclusions:Our observation of isolates from different origin sites, further show the utility of 16s rRNA PCR amplification. This reveals the high specify of the primers and accuracy of the PCR. Thus, 16S rRNA sequencing can be used to identify genetically atypicalP. aeruginosaisolates from different origins.

scholarly journals Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes

2017 ◽  
Vol 15 (5) ◽  
pp. 766-774 ◽  
Author(s):  
Mehdi Roshdi Maleki ◽  
Hossein Samadi Kafil ◽  
Naser Harzandi ◽  
Seyyed Reza Moaddab
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Distribution Systems ◽  
Water Distribution ◽  
Nontuberculous Mycobacteria ◽  
Cetylpyridinium Chloride ◽  
Water Distribution Systems ◽  
Single Species ◽  
16S Rrna Genes ◽  
Rrna Genes

Nontuberculous mycobacteria (NTM) have emerged as an important cause of opportunistic nosocomial infections. NTM has frequently been isolated from hospital water distribution systems. The aim of this study was to survey the risk of NTM infections and determine the prevalence of NTM species in the hospital water distribution systems in Tabriz, Iran. One hundred and twenty samples of water from different sources of Tabriz hospitals were collected. The samples were filtered through 0.45-µm pore size membranes and decontaminated with 0.01% cetylpyridinium chloride. The sediment was inoculated onto Lowenstein–Jensen medium and incubated for 8 weeks. For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. NTM were detected in 76 (63.3%) of 120 samples. Potentially pathogenic mycobacteria and saprophytic mycobacteria were isolated. Mycobacterium gordonae was the only single species that was present in all types of water. The prevalence of NTM in Tabriz hospitals' water compared with many investigations on hospital waters was high. This indicates that the immunocompromised patients and transplant recipients are at risk of contamination which necessitates considering decontamination of water sources to prevent such potential hazards.

scholarly journals Multilocus sequence analysis of Ensifer and related taxa

2007 ◽  
Vol 57 (3) ◽  
pp. 489-503 ◽  
Author(s):  
Miet Martens ◽  
Manuel Delaere ◽  
Renata Coopman ◽  
Paul De Vos ◽  
Monique Gillis ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Housekeeping Genes ◽  
16S Rrna Genes ◽  
New Combination ◽  
Rrna Genes ◽  
Multilocus Sequence Analysis ◽  
Bootstrap Support ◽  
Rrna Gene ◽  
Separate Species

Multilocus sequence analysis (MLSA) was performed on representatives of Ensifer (including species previously assigned to the genus Sinorhizobium) and related taxa. Neighbour-joining (NJ), maximum-parsimony (MP) and maximum-likelihood (ML) phylogenies of dnaK, gltA, glnA, recA, thrC and 16S rRNA genes were compared. The data confirm that the potential for discrimination of Ensifer species is greater using MLSA of housekeeping genes than 16S rRNA genes. In incongruence-length difference tests, the 16S rRNA gene was found to be significantly incongruent with the other genes, indicating that this gene should not be used as a single indicator of relatedness in this group. Significant congruence was detected for dnaK, glnA and thrC. Analyses of concatenated sequences of dnaK, glnA and thrC genes yielded very similar NJ, MP and ML trees, with high bootstrap support. In addition, analysis of a concatenation of all six genes essentially produced the same result, levelling out potentially conflicting phylogenetic signals. This new evidence supports the proposal to unite Ensifer and Sinorhizobium in a single genus. Support for an alternative solution preserving the two genera is less strong. In view of the opinions expressed by the Judicial Commission, the name of the genus should be Ensifer, as proposed by Young [Young, J. M. (2003). Int J Syst Evol Microbiol 53, 2107–2110]. Data obtained previously and these new data indicate that Ensifer adhaerens and ‘Sinorhizobium morelense’ are not heterotypic synonyms, but represent separate species. However, transfer to the genus Ensifer is not possible at present because the species name is the subject of a pending Request for an Opinion, which would affect whether a novel species in the genus Ensifer or a new combination based on a basonym would be created.

scholarly journals The Influence of DNA Extraction Procedure and Primer Set on the Bacterial Community Analysis by Pyrosequencing of Barcoded 16S rRNA Gene Amplicons

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Ingo C. Starke ◽  
Wilfried Vahjen ◽  
Robert Pieper ◽  
Jürgen Zentek
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Dna Extraction ◽  
16S Rrna Genes ◽  
Read Length ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Variable Regions ◽  
Extraction Procedures ◽  
Primer Sets

In this study, the effect of different DNA extraction procedures and primer sets on pyrosequencing results regarding the composition of bacterial communities in the ileum of piglets was investigated. Ileal chyme from piglets fed a diet containing different amounts of zinc oxide was used to evaluate a pyrosequencing study with barcoded 16S rRNA PCR products. Two DNA extraction methods (bead beating versus silica gel columns) and two primer sets targeting variable regions of bacterial 16S rRNA genes (8f-534r versus 968f-1401r) were considered. The SEED viewer software of the MG-RAST server was used for automated sequence analysis. A total of 5.2×105 sequences were used for analysis after processing for read length (150 bp), minimum sequence occurrence (5), and exclusion of eukaryotic and unclassified/uncultured sequences. DNA extraction procedures and primer sets differed significantly in total sequence yield. The distribution of bacterial order and main bacterial genera was influenced significantly by both parameters. However, this study has shown that the results of pyrosequencing studies using barcoded PCR amplicons of bacterial 16S rRNA genes depend on DNA extraction and primer choice, as well as on the manner of downstream sequence analysis.

Comparison of 16S ribosomal RNA genes inClavibacter michiganensissubspecies with other coryneform bacteria

1995 ◽  
Vol 41 (10) ◽  
pp. 925-929 ◽  
Author(s):  
Xiang Li ◽  
Solke H. De Boer
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Clavibacter Michiganensis ◽  
Arthrobacter Simplex ◽  
16S Rrna Analysis ◽  
Coryneform Bacteria ◽  
Clavibacter Michiganensis Subsp ◽  
Complete Sequences

Nearly complete sequences (97–99%) of the 16S rRNA genes were determined for type strains of Clavibacter michiganensis subsp. michiganensis, Clavibacter michiganensis subsp. insidiosus, Clavibacter michiganensis subsp. sepedonicus, and Clavibacter michiganensis subsp. nebraskensis. The four subspecies had less than 1% dissimilarity in their 16S rRNA genes. Comparative studies indicated that the C. michiganensis subsp. shared relatively high homology with the 16S rRNA gene of Clavibacter xyli. Further comparison with representatives of other Gram-positive coryneform and related bacteria with high G + C% values showed that this group of bacteria was subdivided into three clusters. One cluster consisted of the Clavibacter michiganensis subsp., Clavibacter xyli, Arthrobacter globiformis, Arthrobacter simplex, and Frankia sp.; another cluster consisted of members of the corynebacteria–mycobacteria–nocardia (CMN) group of Mycobacteriaceae including Tsukamurella paurometabolum; and Propionibacterium freudenreichii alone formed a unique cluster, which was remote from other coryneform bacteria analyzed. The three clusters may reflect a systematic rank higher than the genus level among these bacteria.Key words: Clavibacter, coryneform bacteria, phylogeny, 16S rRNA analysis.

scholarly journals Comparative Genetic Analysis of Mycobacterium ulcerans and Mycobacterium marinum Reveals Evidence of Recent Divergence

2000 ◽  
Vol 182 (22) ◽  
pp. 6322-6330 ◽  
Author(s):  
Timothy P. Stinear ◽  
Grant A. Jenkin ◽  
Paul D. R. Johnson ◽  
John K. Davies
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Genetic Relationship ◽  
Mycobacterium Marinum ◽  
Mycobacterium Ulcerans ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Mobile Dna ◽  
Apparent Paradox ◽  
Close Genetic Relationship

ABSTRACT Previous studies of the 16S rRNA genes from Mycobacterium ulcerans and Mycobacterium marinum have suggested a very close genetic relationship between these species (99.6% identity). However, these organisms are phenotypically distinct and cause diseases with very different pathologies. To investigate this apparent paradox, we compared 3,306 nucleotides from the partial sequences of eight housekeeping and structural genes derived from 18M. ulcerans strains and 22 M. marinumstrains. This analysis confirmed the close genetic relationship inferred from the 16S rRNA data, with nucleotide sequence identity ranging from 98.1 to 99.7%. The multilocus sequence analysis also confirmed previous genotype studies of M. ulceransthat have identified distinct genotypes within a geographical region. Single isolates of both M. ulcerans and M. marinum that were shown by the sequence analysis to be the most closely related were then selected for further study. One- and two-dimensional pulsed-field gel electrophoresis was employed to compare the architecture and size of the genome from each species. Genome sizes of approximately 4.4 and 4.6 Mb were obtained forM. ulcerans and M. marinum, respectively. Significant macrorestriction fragment polymorphism was observed between the species. However, hybridization analysis of DNA cleaved with more frequently cutting enzymes identified significant preservation of the flanking sequence at seven of the eight loci sequenced. The exception was the 16S rRNA locus. Two high-copy-number insertion sequences, IS2404 and IS2606, have recently been reported in M. ulcerans, and significantly, these elements are not present in M. marinum. Hybridization of theAseI restriction fragments from M. ulcerans with IS2404 and IS2606 indicated widespread genome distribution for both of these repeated sequences. Taken together, these data strongly suggest that M. ulcerans has recently diverged from M. marinumby the acquisition and concomitant loss of DNA in a manner analogous to the emergence of M. tuberculosis, where species diversity is being driven mainly by the activity of mobile DNA elements.

Sign in / Sign up

Export Citation Format

Share Document