scholarly journals Characterization of Tn6349, a novel mosaic transposon carrying poxtA, cfr and other resistance determinants, inserted in the chromosome of an ST5-MRSA-II strain of clinical origin

2019 ◽  
Vol 74 (10) ◽  
pp. 2870-2875 ◽  
Author(s):  
Marco Maria D’Andrea ◽  
Alberto Antonelli ◽  
Andrea Brenciani ◽  
Vincenzo Di Pilato ◽  
Gianluca Morroni ◽  
...  
Keyword(s):  
Sanger Sequencing ◽  
Bioinformatics Analysis ◽  
Strain Analysis ◽  
Inverse Pcr ◽  
Original Structure ◽  
Insertion Sequences ◽  
Resistance Determinants ◽  
Genetic Context ◽  
Index Strain

AbstractObjectivesTo characterize the genetic element carrying the poxtA oxazolidinone resistance gene found in the poxtA index strain Staphylococcus aureus AOUC-0915 isolated from a cystic fibrosis patient.MethodsThe genetic context of poxtA was investigated by bioinformatics analysis of WGS data of strain AOUC-0915, followed by PCR and confirmatory Sanger sequencing for repetitive regions. Conjugation and electrotransformation experiments were carried out to assess horizontal transferability using S. aureus and Enterococcus faecalis recipients. Production of phage particles was evaluated by PCR using DNA preparations obtained after phage induction. Excision of the transposon carrying poxtA was evaluated by inverse PCR experiments for detection of circular intermediates.ResultspoxtA was found to be associated with a 48 kb composite transposon of original structure, named Tn6349, inserted into a φN315-like prophage. The transposon was bounded by two IS1216 insertion sequences, carried several resistance genes [erm(B), cfr, poxtA and fexB] and exhibited a mosaic structure made by a derivative of plasmid pE35048-oc (previously described in an Enterococcus faecium clinical isolate) and Tn6657, a novel composite transposon carrying the poxtA and fexB genes. Excision ability of Tn6349 as a circular intermediate was demonstrated. Transferability of Tn6349 or modules thereof to S. aureus or E. faecalis by either conjugation or electrotransformation was not detected. Induction of the φN315-like prophage carrying Tn6349 was not observed.ConclusionsThis study describes the structure of Tn6349, a novel composite transposon carrying several resistance determinants to anti-ribosomal drugs, including cfr and poxtA, from an oxazolidinone-resistant MRSA strain. Analysis of Tn6349 revealed a modular structure that could favour the mobilization of its resistance determinants.

scholarly journals Tn5393d, a Complex Tn5393 Derivative Carrying the PER-1 Extended-Spectrum β-Lactamase Gene and Other Resistance Determinants

2005 ◽  
Vol 49 (8) ◽  
pp. 3289-3296 ◽  
Author(s):  
Elisabetta Mantengoli ◽  
Gian Maria Rossolini
Keyword(s):  
Artificial Chromosome ◽  
Alcaligenes Faecalis ◽  
Mercury Resistance ◽  
Original Structure ◽  
E Coli ◽  
Resistance Determinants ◽  
Extended Spectrum ◽  
Additional Resistance ◽  
Lactamase Gene ◽  
Genetic Context

ABSTRACT In Alcaligenes faecalis FL-424/98, a clinical isolate that produces the PER-1 extended-spectrum β-lactamase, the bla PER-1 gene was found to be carried on a 44-kb nonconjugative plasmid, named pFL424, that was transferred to Escherichia coli by electroporation. Investigation of the genetic context of the bla PER-1 gene in pFL424 by means of a combined cloning and PCR mapping approach revealed that the gene is associated with a transposonlike element of the Tn3 family. This 14-kb element is a Tn5393 derivative of original structure, named Tn5393d, which contains the transposition module and the strAB genes typical of other members of the Tn5393 lineage plus additional resistance determinants, including the bla PER-1 gene and a new allelic variant of the aphA6 aminoglycoside phosphotransferase gene, named aphA6b, whose product is active against kanamycin, streptomycin, and amikacin. Tn5393d apparently originated from the consecutive insertion of two composite transposons into a Tn5393 backbone carrying the aphA6b and the bla PER-1 genes, respectively. The putative composite transposon carrying bla PER-1, named Tn4176, is made of two original and nonidentical insertion sequences of the IS4 family, named IS1387a and IS1387b, of which one is interrupted by the insertion of an original insertion sequence of the IS30 family, named IS1066. In pFL424, Tn5393d is inserted into a Tn501-like mercury resistance transposon. Transposition of Tn5393d or modules thereof containing the bla PER-1 gene from pFL424 to small multicopy plasmids or to a bacterial artificial chromosome was not detected in an E. coli host harboring both replicons.

scholarly journals Tn6249, a New Tn6162Transposon Derivative Carrying a Double-Integron Platform and Involved with Acquisition of theblaVIM-1Metallo-β-Lactamase Gene in Pseudomonas aeruginosa

2014 ◽  
Vol 59 (3) ◽  
pp. 1583-1587 ◽  
Author(s):  
Vincenzo Di Pilato ◽  
Simona Pollini ◽  
Gian Maria Rossolini
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genomic Island ◽  
Mercury Resistance ◽  
Original Structure ◽  
Content Type ◽  
Lactamase Gene ◽  
Genetic Context ◽  
Generation Sequencing ◽  
Index Strain

ABSTRACTThe In70.2 integron platform appears to be a conserved structure involved in the dissemination of theblaVIM-1metallo-β-lactamase gene inPseudomonas aeruginosa. The genetic context of the In70.2 integron platform fromP. aeruginosaVR-143/97, the VIM-1-producing index strain isolated in Italy in 1997, was fully characterized by a next-generation sequencing approach refined by conventional sequencing. The In70.2 integron platform from VR-143/97 was found to be associated with a defective Tn402-like transposon inserted into theurf2gene of a Tn3family transposon of an original structure, named Tn6249, which also carried a partially deletedmeroperon and an In90 integron platform in a tail-to-tail orientation. Tn6249was inserted into a PACS171b-like genomic island, which was in turn inserted into theendAgene of thePseudomonaschromosomal backbone. Tn6249showed a similar structure and a conserved location with respect to that of Tn6060, a Tn3family transposon associated with In70.2 and carrying a double-integron platform, which was detected in a VIM-1-producingP. aeruginosastrain isolated in Australia in 2008. Both Tn6249and Tn6060are apparently derived from Tn6162, a mercury resistance transposon carrying an integron platform, which was found inP. aeruginosaisolates from different geographic locations. The conservation of the genetic context of Tn6249and Tn6060suggests anin situevolution of these elements after the insertion of a Tn6162-like ancestor into the PACS171b-like genomic island (GI) present in the genome of a successful widespreadP. aeruginosaclonal lineage.

scholarly journals Characterization of Small ColE-Like Plasmids Mediating Widespread Dissemination of the qnrB19 Gene in Commensal Enterobacteria

2009 ◽  
Vol 54 (2) ◽  
pp. 678-682 ◽  
Author(s):  
Lucia Pallecchi ◽  
Eleonora Riccobono ◽  
Samanta Sennati ◽  
Antonia Mantella ◽  
Filippo Bartalesi ◽  
...  
Keyword(s):  
Urban Areas ◽  
Resistance Determinant ◽  
Plasmid Replication ◽  
Insertion Sequences ◽  
Healthy Children ◽  
High Prevalence ◽  
Flanking Regions ◽  
Genetic Context ◽  
Widespread Dissemination

ABSTRACT In this work, we have characterized two small ColE-like plasmids (pECY6-7, 2.7 kb in size, and pECC14-9, of 3.0 kb), encoding the QnrB19 quinolone resistance determinant, that were carried by several clonally unrelated quinolone-resistant commensal Escherichia coli strains isolated from healthy children living in different urban areas of Peru and Bolivia. The two plasmids are closely related to each other and carry the qnrB19 gene as the sole resistance determinant, located in a conserved genetic context between the plasmid RNAII sequence (which controls plasmid replication) and the plasmid Xer site (involved in plasmid dimer resolution). ISEcp1-like or other putative insertion sequences are not present in the qnrB19-flanking regions or elsewhere on the plasmids. Since we previously observed a high prevalence (54%) of qnrB genes in the metagenomes of commensal enterobacteria from the same population of healthy children, the presence of pECY6-7- and pECC14-9-like plasmids in those qnrB-positive metagenomes was investigated by PCR mapping. Both plasmids were found to be highly prevalent (67% and 16%, respectively) in the qnrB-positive metagenomes, suggesting that dissemination of these small plasmids played a major role in the widespread dissemination of qnrB genes observed in commensal enterobacteria from healthy children living in those areas.

scholarly journals Bioinformatics analysis and characterization of a secretory cystatin from Thelohanellus kitauei

AMB Express ◽  
2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fengli Zhang ◽  
Yalin Yang ◽  
Chenchen Gao ◽  
Yuanyuan Yao ◽  
Rui Xia ◽  
...  
Keyword(s):  
Bioinformatics Analysis

Detection and characterization of two insertion sequences in Vibrio alginolyticus

2011 ◽  
Vol 62 (1) ◽  
pp. 69-75 ◽  
Author(s):  
Chunhua Ren ◽  
Xiao Jiang ◽  
Hongyan Sun ◽  
Peng Luo ◽  
Chang Chen ◽  
...  
Keyword(s):  
Vibrio Alginolyticus ◽  
Insertion Sequences

Characterization of a mutated KCNJ5 gene, G387R, in unilateral primary aldosteronism

2021 ◽  
Vol 67 (4) ◽  
pp. 203-215
Author(s):  
Jeff S Chueh ◽  
Kang-Yung Peng ◽  
Vin-Cent Wu ◽  
Shuo-Meng Wang ◽  
Chieh-Kai Chan ◽  
...  
Keyword(s):  
Primary Aldosteronism ◽  
Bioinformatics Analysis ◽  
Genomic Analysis ◽  
Ion Current ◽  
Mutant Channel ◽  
Transfected Cells ◽  
Aldosterone Production ◽  
Mutant Cells ◽  
Electrophysiological Experiment

Somatic mutation in the KCNJ5 gene is a common driver of autonomous aldosterone overproduction in aldosterone-producing adenomas (APA). KCNJ5 mutations contribute to a loss of potassium selectivity, and an inward Na+ current could be detected in cells transfected with mutated KCNJ5. Among 223 unilateral primary aldosteronism (uPA) individuals with a KCNJ5 mutation, we identified 6 adenomas with a KCNJ5 p.Gly387Arg (G387R) mutation, previously unreported in uPA patients. The six uPA patients harboring mutant KCNJ5-G387R were older, had a longer hypertensive history, and had milder elevated preoperative plasma aldosterone levels than those APA patients with more frequently detected KCNJ5 mutations. CYP11B2 immunohistochemical staining was only positive in three adenomas, while the other three had co-existing multiple aldosterone-producing micronodules. The bioinformatics analysis predicted that function of the KCNJ5-G387R mutant channel could be pathological. However, the electrophysiological experiment demonstrated that transfected G387R mutant cells did not have an aberrantly stimulated ion current, with lower CYP11B2 synthesis and aldosterone production, when compared to that of the more frequently detected mutant KCNJ5-L168R transfected cells. In conclusion, mutant KCNJ5-G387R is not a functional KCNJ5 mutation in unilateral PA. Compared with other KCNJ5 mutations, the observed mildly elevated aldosterone expression actually hindered the clinical identification of clinical unilateral PA. The KCNJ5-G387R mutation needs to be distinguished from functional KCNJ5 mutations during genomic analysis in APA evaluation because of its functional silence.

scholarly journals Molecular characterization and bioinformatics analysis of Ncoa7B, a novel ovulation-associated and reproduction system-specific Ncoa7 isoform

Reproduction ◽  
2008 ◽  
Vol 135 (3) ◽  
pp. 321-333 ◽  
Author(s):  
Ketty Shkolnik ◽  
Shifra Ben-Dor ◽  
Dalia Galiani ◽  
Ariel Hourvitz ◽  
Nava Dekel
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
Oxidative Dna Damage ◽  
Bioinformatics Analysis ◽  
Cdna Clones ◽  
Nuclear Receptor Coactivator ◽  
Reproduction System ◽  
Preovulatory Follicles ◽  
Multiple Signaling

In the present work, we employed bioinformatics search tools to select ovulation-associated cDNA clones with a preference for those representing putative novel genes. Detailed characterization of one of these transcripts, 6C3, by real-time PCR and RACE analyses led to identification of a novel ovulation-associated gene, designatedNcoa7B. This gene was found to exhibit a significant homology to theNcoa7gene that encodes a conserved tissue-specific nuclear receptor coactivator. UnlikeNcoa7,Ncoa7Bpossesses a unique and highly conserved exon at the 5′ end and encodes a protein with a unique N-terminal sequence. Extensive bioinformatics analysis has revealed thatNcoa7Bhas one identifiable domain, TLDc, which has recently been suggested to be involved in protection from oxidative DNA damage. An alignment of TLDc domain containing proteins was performed, and the closest relative identified wasOXR1, which also has a corresponding, highly related short isoform, with just a TLDc domain. Moreover,Ncoa7Bexpression, as seen to date, seems to be restricted to mammals, while other TLDc family members have no such restriction. Multiple tissue analysis revealed that unlikeNcoa7, which was abundant in a variety of tissues with the highest expression in the brain,Ncoa7BmRNA expression is restricted to the reproductive system organs, particularly the uterus and the ovary. The ovarian expression ofNcoa7Bwas stimulated by human chorionic gonadotropin. Additionally, using real-time PCR, we demonstrated the involvement of multiple signaling pathways forNcoa7Bexpression on preovulatory follicles.

scholarly journals Mutations in NOTCH3 Gene may Promote the Clinical Presentation of Spinocerebellar Ataxia Type 37 Caused by Mutations in DAB1 Gene

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhao-Wei Wang ◽  
Li-Ping Wang ◽  
Ye Du ◽  
Qi Liu
Keyword(s):  
Spinocerebellar Ataxia ◽  
Sanger Sequencing ◽  
Autosomal Dominant ◽  
Bioinformatics Analysis ◽  
Clinical Presentation ◽  
Cerebellar Atrophy ◽  
Gene Mutations ◽  
Brain Magnetic Resonance Imaging ◽  
Diagnostic Methods ◽  
Spinocerebellar Ataxia Type

Background: Autosomal dominant spinocerebellar ataxia type 37 (SCA37) and Cerebral autosomal dominant arteriopathy with subcortical infarct and leukoencephalopathy (CADASIL) result from DAB1 and NOTCH3 gene mutations, respectively.Methods: In addition to conventional diagnostic methods, next-generation sequencing (NGS) and Sanger sequencing were performed to define and confirm the DAB1 and NOTCH3 gene mutation for a Chinese pedigree. Bioinformatics analysis was also applied for the mutated DAB1 and NOTCH3 protein using available software tools.Results: Brain magnetic resonance imaging shows diffuse leukoencephalopathy and cerebellar atrophy in the proband. NGS and Sanger sequencing identified two novel heterozygous mutations: NM_021080:c.318T > G (p.H106Q) in the DAB1 gene and NM_000435:c.3298C > T (p.R1100C) in the NOTCH3 gene. Bioinformatics analysis suggested that the DAB1 and NOTCH3 gene mutations are disease-causing and may be responsible for the phenotypes.Conclusion: This is the first report of a pedigree with both SAC37 and CADASIL phenotypes carrying corresponding gene mutations. Mutations in the NOTCH3 gene may promote the clinical presentation of spinocerebellar ataxia type 37 caused by mutations in the DAB1 gene. In addition to general examinations, it is vital for physicians to apply molecular genetics to get an accurate diagnosis in the clinic, especially for rare diseases.

scholarly journals Molecular Characterization of the Transcription Factors in Susceptible Poplar Infected with Virulent Melampsora larici-populina

2019 ◽  
Vol 20 (19) ◽  
pp. 4806 ◽  
Author(s):  
Qiaoli Chen ◽  
Jianan Wang ◽  
Danlei Li ◽  
Zhiying Wang ◽  
Feng Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Calcium Binding ◽  
Bioinformatics Analysis ◽  
Pathological Process ◽  
Compatible Interaction ◽  
Time Points ◽  
Time Periods ◽  
Two Phases ◽  
Transcript Profiles

Transcription factors (TFs) have been shown to play important roles in determining poplar susceptibility. In this study, the transcript profiles of five resistance-related TF groups at different time points were investigated to study the roles of TFs in the compatible interaction between ‘Robusta’ (Populus nigra × P. deltoides) and the virulent E4 race of Melampsora larici-populina. The susceptibility test indicated that the parasitic process of E4 could be divided into two representative time periods: the infection phase and the production phase. Bioinformatics analysis showed that in these two phases, E4 infection induced a network of TFs in ‘Robusta’. Although some TFs responded rapidly and positively, most TFs did not respond to E4, especially during the infection phase. The ethylene, jasmonic acid, and auxin pathways were downregulated, while a calcium-binding protein was upregulated. No other significantly changed phytohormone-related genes were found, which was consistent with the pathological process in the absence of an immune response, suggesting that the lack of response of most TFs during the infection phase of E4 is related to the susceptibility of ‘Robusta’.

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