scholarly journals Virulence analysis of 81 of Pseudomonas aeruginosa genomes available in public sequence databases

2019 ◽  
Author(s):  
Marcin Brzozowski ◽  
Joanna Barbara Jursa-Kulesza ◽  
Danuta Kosik-Bogacka
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Virulence Genes ◽  
Opportunistic Infections ◽  
Pearson Correlation ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Secretion Systems ◽  
Wide Range ◽  
Genes Encoding ◽  
Sequence Databases

Abstract Background Pseudomonas aeruginosa is a pathogen capable of causing a wide range of severe opportunistic infections. Its genome contains numerous virulence genes encoding secretion systems of different types, structures responsible for adhesion and motility, toxins, proteases, siderophores, and others. The aim of this study is to analyse virulence, population structure, and distribution of highly divergent genes among 81 P. aeruginosa strains available in whole genome sequence databases. Results For this purpose, 260 virulence genes were searched in 81 different P. aeruginosa whole genomes that were available in databases. We identified most of the virulence genes as core and softcore genes. The most of the highly divergent sequences encoding pyoverdines, flagella and pilA were acknowledged as accessory, because of the differences in sequence among different alleles of those genes. Phylogenetic tree revealed the existence of three genetic groups of P. aeruginosa. Strains of the first clade were characterised as ExoS positive, whiles genomes of the second clade were ExoU positive. The member of third clade, PA7 strain was the only strain deprived of all T3SS genes. The analysis of pyoverdine locus facilitated finding a new pyoverdine type similar to pyoverdine type III. This newly described variant was present in 7 different strains. It contained a gene that was probably created by the fusion of pilD and pilI genes. In order to determine the coexistence of genes encoding exoenzymes, flagella and pyoverdines, Pearson correlation coefficients were calculated. There were significant correlations between genes encoding ExoS/ExoU-type strains and genes encoding type-A/type-B flagella. The correlation also occurred between Conclusion This study facilitates describing genetic differences of various P. aeruginosa strains based on Pseudomonas aeruginosa whole genome information from online databases. We conclude that most P. aeruginosa virulence genes are present in more than 95% of available genomes of the species. There are correlations of occurrence of different P. aeruginosa accessory virulence genes.

scholarly journals Whole Genome Sequence Analysis of Brucella melitensis Phylogeny and Virulence Factors

2021 ◽  
Vol 12 (3) ◽  
pp. 698-710
Author(s):  
Peter Rabinowitz ◽  
Bar Zilberman ◽  
Yair Motro ◽  
Marilyn C. Roberts ◽  
Alex Greninger ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Pathogenic Bacteria ◽  
Virulence Genes ◽  
Brucella Melitensis ◽  
Geographic Region ◽  
Clinical Severity ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Pan Genome ◽  
Wide Range

Brucellosis has a wide range of clinical severity in humans that remains poorly understood. Whole genome sequencing (WGS) analysis may be able to detect variation in virulence genes. We used Brucella melitensis sequences in the NCBI Sequence Read Archive (SRA) database to assemble 248 whole genomes, and additionally, assembled 27 B. melitensis genomes from samples of human patients in Southern Israel. We searched the 275 assembled genomes for the 43 B. melitensis virulence genes in the Virulence Factors of Pathogenic Bacteria Database (VFDB) and 10 other published putative virulence genes. We explored pan-genome variation across the genomes and in a pilot analysis, explored single nucleotide polymorphism (SNP) variation among the ten putative virulence genes. More than 99% of the genomes had sequences for all Brucella melitensis virulence genes included in the VFDB. The 10 other virulence genes of interest were present across all the genomes, but three of these genes had SNP variation associated with particular Brucella melitensis genotypes. SNP variation was also seen within the Israeli genomes obtained from a small geographic region. While the Brucella genome is highly conserved, this novel and large whole genome study of Brucella demonstrates the ability of whole genome and pan-genome analysis to screen multiple genomes and identify SNP variation in both known and novel virulence genes that could be associated with differential disease virulence. Further development of whole genome techniques and linkage with clinical metadata on disease outcomes could shed light on whether such variation in the Brucella genome plays a role in pathogenesis.

scholarly journals Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Syed A. K. Shifat Ahmed ◽  
Michelle Rudden ◽  
Sabrina M. Elias ◽  
Thomas J. Smyth ◽  
Roger Marchant ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Quorum Sensing ◽  
Virulence Factors ◽  
Genomic Islands ◽  
Clinical Strain ◽  
Whole Genome ◽  
Synonymous Mutations ◽  
Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

scholarly journals Whole-Genome Sequence of Multidrug-ResistantPseudomonas aeruginosaStrain BAMCPA07-48, Isolated from a Combat Injury Wound

2016 ◽  
Vol 4 (4) ◽  
Author(s):  
Fatemeh Sanjar ◽  
S. L. Rajasekhar Karna ◽  
Tsute Chen ◽  
Ping Chen ◽  
Johnathan J. Abercrombie ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Valuable Resource ◽  
Combat Injury ◽  
Pathogen Surveillance

We report here the complete genome sequence ofPseudomonas aeruginosastrain BAMCPA07-48, isolated from a combat injury wound. The closed genome sequence of this isolate is a valuable resource for pathogenome characterization ofP. aeruginosaassociated with wounds, which will aid in the development of a higher-resolution phylogenomic framework for molecular-guided pathogen-surveillance.

scholarly journals Cyclic Di-GMP and VpsR Induce the Expression of Type II Secretion in Vibrio cholerae

2017 ◽  
Vol 199 (19) ◽  
Author(s):  
Rudolph E. Sloup ◽  
Ashley E. Konal ◽  
Geoffrey B. Severin ◽  
Michelle L. Korir ◽  
Mira M. Bagdasarian ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Protein Complexes ◽  
Second Messenger ◽  
Type Ii Secretion ◽  
Type Ii ◽  
Secretion Systems ◽  
Content Type ◽  
Severe Diarrhea ◽  
Wide Range ◽  
Genes Encoding

ABSTRACT Vibrio cholerae is a human pathogen that alternates between growth in environmental reservoirs and infection of human hosts, causing severe diarrhea. The second messenger cyclic di-GMP (c-di-GMP) mediates this transition by controlling a wide range of functions, such as biofilms, virulence, and motility. Here, we report that c-di-GMP induces expression of the extracellular protein secretion (eps) gene cluster, which encodes the type II secretion system (T2SS) in V. cholerae. Analysis of the eps genes confirmed the presence of two promoters located upstream of epsC, the first gene in the operon, one of which is induced by c-di-GMP. This induction is directly mediated by the c-di-GMP-binding transcriptional activator VpsR. Increased expression of the eps operon did not impact secretion of extracellular toxin or biofilm formation but did increase expression of the pseudopilin protein EpsG on the cell surface. IMPORTANCE Type II secretion systems (T2SSs) are the primary molecular machines by which Gram-negative bacteria secrete proteins and protein complexes that are folded and assembled in the periplasm. The substrates of T2SSs include extracellular factors, such as proteases and toxins. Here, we show that the widely conserved second messenger cyclic di-GMP (c-di-GMP) upregulates expression of the eps genes encoding the T2SS in the pathogen V. cholerae via the c-di-GMP-dependent transcription factor VpsR.

scholarly journals Whole-Genome Sequence of Pseudomonas aeruginosa Strain 4014, Isolated from Soil in France

2018 ◽  
Vol 7 (10) ◽  
Author(s):  
Julien Crovadore ◽  
Damien Grizard ◽  
Romain Chablais ◽  
Bastien Cochard ◽  
Philippe Blanc ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Human Pathogen ◽  
Content Type ◽  
Multiple Antibiotics

We report here the draft genome sequence of strain 4014 of Pseudomonas aeruginosa, a common human pathogen, isolated from soil in France. This sequence predicts resistance to multiple antibiotics, including vancomycin.

scholarly journals Transcriptomic Analysis of the Sulfate Starvation Response of Pseudomonas aeruginosa

2007 ◽  
Vol 189 (19) ◽  
pp. 6743-6750 ◽  
Author(s):  
Tewes Tralau ◽  
Stéphane Vuilleumier ◽  
Christelle Thibault ◽  
Barry J. Campbell ◽  
C. Anthony Hart ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Pseudomonas Aeruginosa ◽  
Stress Proteins ◽  
Large Family ◽  
Opportunistic Pathogen ◽  
Transport Systems ◽  
Sulfur Source ◽  
Secretion Systems ◽  
Starvation Response ◽  
Wide Range

ABSTRACT Pseudomonas aeruginosa is an opportunistic pathogen that causes a number of infections in humans, but is best known for its association with cystic fibrosis. It is able to use a wide range of sulfur compounds as sources of sulfur for growth. Gene expression in response to changes in sulfur supply was studied in P. aeruginosa E601, a cystic fibrosis isolate that displays mucin sulfatase activity, and in P. aeruginosa PAO1. A large family of genes was found to be upregulated by sulfate limitation in both isolates, encoding sulfatases and sulfonatases, transport systems, oxidative stress proteins, and a sulfate-regulated TonB/ExbBD complex. These genes were localized in five distinct islands on the genome and encoded proteins with a significantly reduced content of cysteine and methionine. Growth of P. aeruginosa E601 with mucin as the sulfur source led not only to a sulfate starvation response but also to induction of genes involved with type III secretion systems.

scholarly journals Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Amjad B. Khalil ◽  
Neelamegam Sivakumar ◽  
Muhammad Arslan ◽  
Hamna Saleem ◽  
Sami Qarawi
Keyword(s):  
Saudi Arabia ◽  
Hot Spring ◽  
Gc Content ◽  
Morphological Characterization ◽  
Thermophilic Bacterium ◽  
Whole Genome Sequence ◽  
Strictly Aerobic ◽  
Whole Genome ◽  
Aerobic Bacterium ◽  
Wide Range

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

scholarly journals Whole-Genome Sequence of Stenotrophomonas maltophilia ZBG7B Reveals Its Biotechnological Potential

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Kok-Gan Chan ◽  
Teik-Min Chong ◽  
Tan-Guan-Sheng Adrian ◽  
Heng Leong Kher ◽  
Kar-Wai Hong ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Bacterial Strain ◽  
Stenotrophomonas Maltophilia ◽  
Draft Genome ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Biotechnological Potential ◽  
Vineyard Soil ◽  
Genes Encoding ◽  
Prediction Of Function

Stenotrophomonas maltophilia ZBG7B was isolated from vineyard soil of Zellenberg, France. Here, we present the draft genome sequence of this bacterial strain, which has facilitated the prediction of function for several genes encoding biotechnologically important enzymes, such as xylosidase, xylanase, laccase, and chitinase.

scholarly journals Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

2020 ◽  
Author(s):  
Xueping LI ◽  
Jianhong Li ◽  
Yonghong Qi ◽  
Yonggang Liu ◽  
Minquan Li
Keyword(s):  
Molecular Mechanisms ◽  
Gc Content ◽  
Whole Genome Sequence ◽  
Effective Control ◽  
Sequence Length ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Fusarium Equiseti ◽  
Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

Sign in / Sign up

Export Citation Format

Share Document