scholarly journals Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing

2016 ◽  
Vol 36 (6) ◽  
Author(s):  
Gang Li ◽  
Mengyu Shen ◽  
Shuai Le ◽  
Yinling Tan ◽  
Ming Li ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Single Molecule ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Read Length ◽  
Genome Comparison ◽  
Genomic Analyses

As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin–antitoxin (T–A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.

scholarly journals Comparative genome analysis of a multidrug-resistant Pseudomonas aeruginosa sequence type 277 clone that harbours two copies of the blaSPM-1 gene and multiple single nucleotide polymorphisms in other resistance-associated genes

2019 ◽  
Author(s):  
Ana Paula Barbosa do Nascimento ◽  
Fernando Medeiros Filho ◽  
Hério Sousa ◽  
Hermes Senger ◽  
Rodolpho Mattos Albano ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Single Nucleotide Polymorphisms ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Genomic Islands ◽  
Genome Comparison ◽  
Nucleotide Polymorphisms ◽  
Emerging Pathogens ◽  
Single Nucleotide

AbstractPseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of blaSPM-1 gene, encoding a metallo-beta-lactamase, in addition to other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify physiological key aspects that may lead to the exposure of new targets for therapy. This study was designed to characterize the genome of Pseudomonas aeruginosa CCBH4851 through the detection of genomic features and genome comparison with other Pseudomonas aeruginosa strains. The CCBH4851 closed genome showed features that were consistent with data reported for the specie. However, comparative genomics revealed the absence of genes important for pathogenesis. On the other hand, CCBH4851 genome contained acquired genomic islands that carry additional virulence and antimicrobial resistance-related genes. The presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations could influence the multidrug-resistant behavior of CCBH4851. Overall, the characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed several features that could directly impact the profile of virulence and antibiotic resistance of this pathogen in infectious outbreaks.

scholarly journals High quality 3C de novo assembly and annotation of a multidrug resistant ST-111 Pseudomonas aeruginosa genome: Benchmark of hybrid and non-hybrid assemblers

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
José Arturo Molina-Mora ◽  
Rebeca Campos-Sánchez ◽  
César Rodríguez ◽  
Leming Shi ◽  
Fernando García
Keyword(s):  
Pseudomonas Aeruginosa ◽  
De Novo Assembly ◽  
De Novo ◽  
Multidrug Resistant ◽  
High Quality

scholarly journals Complete Genome Sequences of Two Pseudomonas aeruginosa Strains Isolated from Children with Bacteremia

2017 ◽  
Vol 5 (35) ◽  
Author(s):  
Luis F. Espinosa-Camacho ◽  
Gabriela Delgado ◽  
Guadalupe Miranda-Novales ◽  
Gloria Soberón-Chávez ◽  
Luis D. Alcaraz ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Mexico City ◽  
Single Molecule ◽  
Complete Genome ◽  
Genome Sequences ◽  
Class 1 Integron ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Class 1

ABSTRACT Two Pseudomonas aeruginosa strains isolated from children with bacteremia in Mexico City were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. The strains consist of a 7.0- to 7.4-Mb chromosome, with a high content of mobile elements, and variation in the genetic content of class 1 integron In1409.

scholarly journals Multi-tissue transcriptome analysis using hybrid-seq revealed potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (Azadirachtin indica)

2020 ◽  
Author(s):  
Huiyan Wang ◽  
Ning Wang ◽  
Yixin Huo
Keyword(s):  
Real Time ◽  
Single Molecule ◽  
Biosynthetic Pathway ◽  
De Novo ◽  
Analysis Data ◽  
Sequencing Data ◽  
Neem Tree ◽  
Illumina Hiseq ◽  
Oxidosqualene Cyclase ◽  
Azadirachtin A

Abstract Background: Azadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The manufacture of azadirachtin A depends on extraction from neem tissues, which is not ecofriendly and sustainable. The low yield and discontinuous supply impeded the further application. The biosynthetic pathway of azadirachtin A is still well-known.Results: We attempted to explore azadirachtin A biosynthetic pathway and identified key involved genes by analyzing transcriptome data of five neem tissues through hybrid-seq (Illumina HiSeq and Pacific Biosciences Single Molecule Real Time (PacBio SMRT)) technology. A total 219 and 397 up-regulated differentially expressed genes (DEGs) in leaf and fruit tissues than other tissues (root, stem and flower) were isolated. After phylogenetic analysis and domain prediction, 22 candidates encoding 2,3-oxidosqualene cyclase (OSC), alcohol dehydrogenase (ADH), cytochrome P450 (CYP450), acyltransferase (ACT) and esterase (EST) proposed to be involved in azadirachtin A biosynthesis were finally selected. De novo assembled sequences were verified by Quantitative Real-Time PCR (qRT-PCR) analysis.Conclusions: By integrating and analysis data from Illumina HiSeq and PacBio SMRT platform, 22 DEGs were finally selected as candidates involved in azadirachtin A biosynthesis. The obtained reliable and accurate sequencing data provided important novel information for understanding neem genome. Our data shed new light on the understanding of other triterpenoids biosynthesis in neem trees and provide reference for exploring other valuable natural product biosynthesis in plants.

scholarly journals Emergence of XDR high-risk Pseudomonas aeruginosa ST309 in South America: a global comparative genomic analysis

2021 ◽  
Author(s):  
Érica L. Fonseca ◽  
Sérgio M. Morgado ◽  
Raquel V. Caldart ◽  
Fernanda Freitas ◽  
Ana Carolina P. Vicente
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Antimicrobial Resistance ◽  
South America ◽  
Resistance Genes ◽  
Genomic Islands ◽  
Intrinsic Resistance ◽  
Heterogeneous Distribution ◽  
Antimicrobial Resistance Genes ◽  
Genomic Analyses

ABSTRACTPseudomonas aeruginosa has been considered one of the major nosocomial pathogens associated with elevated morbidity and mortality worldwide. Outbreaks have been associated with few high-risk pandemic P. aeruginosa lineages, presenting a remarkable antimicrobial resistance. However, the biological features involved with the persistence and spread of such lineages among clinical settings remain to be unravel. This study reports the emergence of the ST309 P. aeruginosa lineage in South America/Brazil, more precisely, in the Amazon region. Global genomic analyses were performed with the Brazilian strain (PA834) and more 41 complete and draft ST309 genomes publicly available, giving insights about ST309 epidemiology and its resistome and mobilome. Antimicrobial susceptibility tests revealed that the Brazilian PA834 strain presented the XDR phenotype, which was mainly due to intrinsic resistance mechanisms. Genomic analyses revealed a heterogeneous distribution of acquired antimicrobial resistance genes among ST309 genomes, which included blaVIM-2, blaIMP-15 and qnrVC1, all of them associated with class 1 integrons. The mobilome mining showed the presence of Integrative and Conjugative Elements, transposons and genomic islands harbouring a huge arsenal of hevy metal resistance genes. Moreover, these elements also carried genes involved with virulence and adaptive traits. Therefore, the presence of such genes in ST309 lineage possibly accounted for the global spread and persistence of this emerging clone, and for its establishment as a pandemic lineage of clinical importance.

scholarly journals Pathogenicity Genomic Island-Associated CrpP-Like Fluoroquinolone-Modifying Enzymes among Pseudomonas aeruginosa Clinical Isolates in Europe

2020 ◽  
Vol 64 (7) ◽  
Author(s):  
José Manuel Ortiz de la Rosa ◽  
Patrice Nordmann ◽  
Laurent Poirel
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genomic Island ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Genomic Islands ◽  
Clinical Isolates ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
Content Type ◽  
Genes Encoding

ABSTRACT Many transferable quinolone resistance mechanisms have been identified in Gram-negative bacteria. The plasmid-encoded 65-amino-acid-long ciprofloxacin-modifying enzyme CrpP was recently identified in Pseudomonas aeruginosa isolates. We analyzed a collection of 100 clonally unrelated and multidrug-resistant P. aeruginosa clinical isolates, among which 46 were positive for crpP-like genes, encoding five CrpP variants conferring variable levels of reduced susceptibility to fluoroquinolones. These crpP-like genes were chromosomally located as part of pathogenicity genomic islands.

A review of DNA sequencing techniques

2002 ◽  
Vol 35 (2) ◽  
pp. 169-200 ◽  
Author(s):  
Lilian T. C. França ◽  
Emanuel Carrilho ◽  
Tarso B. L. Kist
Keyword(s):  
Dna Sequencing ◽  
Real Time ◽  
Single Molecule ◽  
Fluorescent Dyes ◽  
Read Length ◽  
Chemical Methods ◽  
Single Molecule Sequencing ◽  
Exonuclease Digestion ◽  
Speed Accuracy ◽  
Sanger Method

1. Summary 1692. Introduction 1703. Sanger's method and other enzymic methods 1703.1 Random approach 1713.2 Direct approach 1713.3 Enzyme technology 1753.4 Sample preparation 1753.5 Labels and DNA labelling 1763.5.1 Radioisotopes 1763.5.2 Chemiluminescent detection 1763.5.3 Fluorescent dyes 1773.6 Fragment separation and analysis 1803.6.1 Electrophoresis 1803.6.2 Mass spectrometry – an alternative 1824. Maxam & Gilbert and other chemical methods 1835. Pyrosequencing – DNA sequencing in real time by the detection of released PPi 1876. Single molecule sequencing with exonuclease 1907. Conclusion 1928. Acknowledgements 1929. References 193The four best known DNA sequencing techniques are reviewed. Important practical issues covered are read-length, speed, accuracy, throughput, cost, as well as the automation of sample handling and preparation. The methods reviewed are: (i) the Sanger method and its most important variants (enzymic methods); (ii) the Maxam & Gilbert method and other chemical methods; (iii) the PyrosequencingTM method – DNA sequencing in real time by the detection of released pyrophosphate (PPi); and (iv) single molecule sequencing with exonuclease (exonuclease digestion of a single molecule composed of a single strand of fluorescently labelled deoxynucleotides). Each method is briefly described, the current literature is covered, advantages, disadvantages, and the most suitable applications of each method are discussed.

scholarly journals Complete Genome Sequence of Pseudomonas aeruginosa PA1, Isolated from a Patient with a Respiratory Tract Infection

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Shuguang Lu ◽  
Shuai Le ◽  
Gang Li ◽  
Mengyu Shen ◽  
Yinling Tan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Tract Infection ◽  
Respiratory Tract ◽  
Respiratory Tract Infection ◽  
Genome Sequence ◽  
Single Molecule ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
De Novo ◽  
Sequence Coverage

We report the 6,498,072-bp complete genome sequence of Pseudomonas aeruginosa PA1, which was isolated from a patient with a respiratory tract infection in Chongqing, People's Republic of China. Whole-genome sequencing was performed using single-molecule real-time (SMRT) technology, and de novo assembly revealed a single contig with 396-fold sequence coverage.

scholarly journals Complete Genome Sequences of Four Extensively Drug-Resistant Pseudomonas aeruginosa Strains, Isolated from Adults with Ventilator-Associated Pneumonia at a Tertiary Referral Hospital in Mexico City

2017 ◽  
Vol 5 (36) ◽  
Author(s):  
Luis F. Espinosa-Camacho ◽  
Gabriela Delgado ◽  
Gloria Soberón-Chávez ◽  
Luis D. Alcaraz ◽  
Jorge Castañon ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Single Molecule ◽  
Genomic Islands ◽  
Ventilator Associated Pneumonia ◽  
Drug Resistant ◽  
Tertiary Referral Hospital ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Extensively Drug Resistant ◽  
Class 1

ABSTRACT Four extensively drug-resistant Pseudomonas aeruginosa strains, isolated from patients with pneumonia, were sequenced using PacBio RS-II single-molecule real-time (SMRT) technology. Genome sequence analysis identified great variability among mobile genetic elements, as well as some previously undescribed genomic islands and new variants of class 1 integrons (In1402, In1403, In1404, and In1408).

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