scholarly journals Transposon Tn7 Is Widespread in Diverse Bacteria and Forms Genomic Islands

2006 ◽  
Vol 189 (5) ◽  
pp. 2170-2173 ◽  
Author(s):  
Adam R. Parks ◽  
Joseph E. Peters
Keyword(s):  
Genomic Island ◽  
Genomic Islands ◽  
Specific Site ◽  
Island Formation ◽  
Diverse Species ◽  
Functionally Diverse ◽  
Bacterial Transposon

ABSTRACT We find that relatives of the bacterial transposon Tn7 are widespread in disparate environments and phylogenetically diverse species. These elements form functionally diverse genomic islands at the specific site of Tn7 insertion adjacent to glmS. This work presents the first example of genomic island formation by a DDE type transposon.

AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid

2021 ◽  
Author(s):  
Antony T Vincent ◽  
Laurent Intertaglia ◽  
Victor Loyer ◽  
Valérie E Paquet ◽  
Émilie Adouane ◽  
...  
Keyword(s):  
Genomic Island ◽  
Insertion Site ◽  
Aeromonas Salmonicida ◽  
Genomic Islands ◽  
The Other ◽  
Fish Pathogen ◽  
Integrase Gene ◽  
New Variant ◽  
Cat Gene ◽  
Unique Genes

Abstract Genomic islands (Aeromonas salmonicida genomic islands, AsaGEIs) are found worldwide in many isolates of Aeromonas salmonicida subsp. salmonicida, a fish pathogen. To date, five variants of AsaGEI (1a, 1b, 2a, 2b and 2c) have been described. Here, we investigate a sixth AsaGEI, which was identified in France between 2016 and 2019 in 20 A. salmonicida subsp. salmonicida isolates recovered from sick salmon all at the same location. This new AsaGEI shares the same insertion site in the chromosome as the other AsaGEI2s as they all have a homologous integrase gene. This new AsaGEI was thus named AsaGEI2d, and has 5 unique genes compared to the other AsaGEIs. The isolates carrying AsaGEI2d also bear the plasmid pAsa7, which was initially found in an isolate from Switzerland. This plasmid provides resistance to chloramphenicol thanks to a cat gene. This study reveals more about the diversity of the AsaGEIs.

scholarly journals Genomic Islands in the Corynebacterium efficiens Genome

2005 ◽  
Vol 71 (6) ◽  
pp. 3126-3130 ◽  
Author(s):  
Ren Zhang ◽  
Chun-Ting Zhang
Keyword(s):  
Thermal Stability ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Genomic Island ◽  
Genomic Islands ◽  
Aspartate Kinase ◽  
Gene Encoding ◽  
Profile Method ◽  
Adaptive Mutations ◽  
Thermal Stability Of

ABSTRACT Corynebacterium efficiens is a gram-positive nonpathogenic bacterium which can grow and produce glutamate at 40°C or above. By using the cumulative GC profile method, we have identified four genomic islands which have many unifying genomic island-specific features in the C. efficiens genome. The presence of the gene encoding an aspartate kinase in a genomic island helps explain the unexpected low thermal stability of this enzyme; i.e., the adaptive mutations have not occurred extensively due to the recent horizontal gene transfer.

scholarly journals Stability of a Pseudomonas putida KT2440 Bacteriophage-Carried Genomic Island and Its Impact on Rhizosphere Fitness

2012 ◽  
Vol 78 (19) ◽  
pp. 6963-6974 ◽  
Author(s):  
Jose M. Quesada ◽  
María Isabel Soriano ◽  
Manuel Espinosa-Urgel
Keyword(s):  
Pseudomonas Putida ◽  
Genomic Island ◽  
Mobile Element ◽  
Direct Repeat ◽  
Promoter Sequence ◽  
Repeat Sequence ◽  
Genomic Islands ◽  
Pseudomonas Putida Kt2440 ◽  
Bacterial Populations ◽  
Content Type

ABSTRACTThe stability of seven genomic islands ofPseudomonas putidaKT2440 with predicted potential for mobilization was studied in bacterial populations associated with the rhizosphere of corn plants by multiplex PCR. DNA rearrangements were detected for only one of them (GI28), which was lost at high frequency. This genomic island of 39.4 kb, with 53 open reading frames, shows the characteristic organization of genes belonging to tailed phages. We present evidence indicating that it corresponds to the lysogenic state of a functional bacteriophage that we have designated Pspu28. Integrated and rarely excised forms of Pspu28 coexist in KT2440 populations. Pspu28 is self-transmissible, and an excisionase is essential for its removal from the bacterial chromosome. The excised Pspu28 forms a circular element that can integrate into the chromosome at a specific location,attsites containing a 17-bp direct repeat sequence. Excision/insertion of Pspu28 alters the promoter sequence and changes the expression level of PP_1531, which encodes a predicted arsenate reductase. Finally, we show that the presence of Pspu28 in the lysogenic state has a negative effect on bacterial fitness in the rhizosphere under conditions of intraspecific competition, thus explaining why clones having lost this mobile element are recovered from that environment.

scholarly journals Genomic islands targeting dusA in Vibrio species are distantly related to Salmonella Genomic Island 1 and mobilizable by IncC conjugative plasmids

2021 ◽  
Author(s):  
Romain Durand ◽  
Florence Deschênes ◽  
Vincent Burrus
Keyword(s):  
Antibiotic Resistance ◽  
Genomic Island ◽  
Functional Characterization ◽  
Antibiotic Resistance Genes ◽  
Promoter Sequence ◽  
Genomic Islands ◽  
Helper Plasmid ◽  
Reading Frame ◽  
Conjugative Plasmids ◽  
Fresh Perspective

Salmonella Genomic Island 1 (SGI1) and its variants are significant contributors to the spread of antibiotic resistance among Gammaproteobacteria . All known SGI1 variants integrate at the 3’ end of trmE , a gene coding for a tRNA modification enzyme. SGI1 variants are mobilized specifically by conjugative plasmids of the incompatibility groups A and C (IncA and IncC). Using a comparative genomics approach based on genes conserved among members of the SGI1 group, we identified diverse genomic islands (GIs) distantly related to SGI1 in several species of Vibrio , Aeromonas , Salmonella , Pokkaliibacter , and Escherichia . Unlike SGI1, these GIs target two alternative chromosomal loci, the 5’ end of dusA and the 3’ end of yicC . Although these elements share many features with SGI1, they lack antibiotic resistance genes and carry alternative integration/excision modules. Functional characterization of MGI Vch USA3, a dusA -specific GI, revealed promoters that respond to AcaCD, the master activator of IncC plasmid transfer genes. Quantitative PCR and mating assays confirmed that MGI Vch USA3 excises from the chromosome and is mobilized by an IncC helper plasmid from Vibrio cholerae to Escherichia coli . MGI Vch USA3 encodes the AcaC homolog SgaC that associates with AcaD to form a hybrid activator complex AcaD/SgaC essential for its excision and mobilization. We identified the dusA -specific recombination directionality factor RdfN required for the integrase-mediated excision of dusA -specific GIs from the chromosome. Like xis in SGI1, rdfN is under the control of an AcaCD-responsive promoter. Although the integration of MGI Vch USA3 disrupts dusA , the GI provides a new promoter sequence and restores the reading frame of dusA for proper expression of the tRNA-dihydrouridine synthase A. Phylogenetic analysis of the conserved proteins encoded by SGI1-like elements targeting dusA , yicC , and trmE gives a fresh perspective on the possible origin of SGI1 and its variants.

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.

scholarly journals Acquisition and Evolution of the exoU Locus in Pseudomonas aeruginosa

2006 ◽  
Vol 188 (11) ◽  
pp. 4037-4050 ◽  
Author(s):  
Bridget R. Kulasekara ◽  
Hemantha D. Kulasekara ◽  
Matthew C. Wolfgang ◽  
Lisa Stevens ◽  
Dara W. Frank ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Type Iii Secretion ◽  
Genomic Island ◽  
Genomic Islands ◽  
Targeted Mutagenesis ◽  
Host Cells ◽  
System A ◽  
Transmissible Plasmid ◽  
Genomic Regions ◽  
Functional Analyses

ABSTRACT ExoU is a potent Pseudomonas aeruginosa cytotoxin translocated into host cells by the type III secretion system. A comparison of genomes of various P. aeruginosa strains showed that that the ExoU determinant is found in the same polymorphic region of the chromosome near a tRNALys gene, suggesting that exoU is a horizontally acquired virulence determinant. We used yeast recombinational cloning to characterize four distinct ExoU-encoding DNA segments. We then sequenced and annotated three of these four genomic regions. The sequence of the largest DNA segment, named ExoU island A, revealed many plasmid- and genomic island-associated genes, most of which have been conserved across a broad set of β- and γ-Proteobacteria. Comparison of the sequenced ExoU-encoding genomic islands to the corresponding PAO1 tRNALys-linked genomic island, the pathogenicity islands of strain PA14, and pKLC102 of clone C strains allowed us to propose a mechanism for the origin and transmission of the ExoU determinant. The evolutionary history very likely involved transposition of the ExoU determinant onto a transmissible plasmid, followed by transfer of the plasmid into different P. aeruginosa strains. The plasmid subsequently integrated into a tRNALys gene in the chromosome of each recipient, where it acquired insertion sequences and underwent deletions and rearrangements. We have also applied yeast recombinational cloning to facilitate a targeted mutagenesis of ExoU island A, further demonstrating the utility of the specific features of the yeast capture vector for functional analyses of genes on large horizontally acquired genetic elements.

scholarly journals Genomic Analysis of a Serotype 5Streptococcus pneumoniaeOutbreak in British Columbia, Canada, 2005–2009

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Ruth R. Miller ◽  
Morgan G. I. Langille ◽  
Vincent Montoya ◽  
Anamaria Crisan ◽  
Aleksandra Stefanovic ◽  
...  
Keyword(s):  
British Columbia ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Island ◽  
Wide Spectrum ◽  
Health Agency ◽  
Genomic Islands ◽  
Great Promise ◽  
Whole Genome ◽  
Serotype 5

Background.Streptococcus pneumoniaecan cause a wide spectrum of disease, including invasive pneumococcal disease (IPD). From 2005 to 2009 an outbreak of IPD occurred in Western Canada, caused by aS. pneumoniaestrain with multilocus sequence type (MLST) 289 and serotype 5. We sought to investigate the incidence of IPD due to thisS. pneumoniaestrain and to characterize the outbreak in British Columbia using whole-genome sequencing.Methods. IPD was defined according to Public Health Agency of Canada guidelines. Two isolates representing the beginning and end of the outbreak were whole-genome sequenced. The sequences were analyzed for single nucleotide variants (SNVs) and putative genomic islands.Results. The peak of the outbreak in British Columbia was in 2006, when 57% of invasiveS. pneumoniaeisolates were serotype 5. Comparison of two whole-genome sequenced strains showed only 10 SNVs between them. A 15.5 kb genomic island was identified in outbreak strains, allowing the design of a PCR assay to track the spread of the outbreak strain.Discussion. We show that the serotype 5 MLST 289 strain contains a distinguishing genomic island, which remained genetically consistent over time. Whole-genome sequencing holds great promise for real-time characterization of outbreaks in the future and may allow responses tailored to characteristics identified in the genome.

scholarly journals Novel Type IV Secretion System Involved in Propagation of Genomic Islands

2006 ◽  
Vol 189 (3) ◽  
pp. 761-771 ◽  
Author(s):  
Mario Juhas ◽  
Derrick W. Crook ◽  
Ioanna D. Dimopoulou ◽  
Gerton Lunter ◽  
Rosalind M. Harding ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Genomic Island ◽  
Secretion System ◽  
Type Iv Secretion ◽  
Genomic Islands ◽  
Phenotypic Traits ◽  
Type Iv Secretion System ◽  
Genome Plasticity ◽  
Secretion Systems ◽  
Type Iv

ABSTRACT Type IV secretion systems (T4SSs) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other virulence traits. A gene cluster of the Haemophilus influenzae genomic island ICEHin1056 has been identified as a T4SS involved in the propagation of genomic islands. This T4SS is novel and evolutionarily distant from the previously described systems. Mutation analysis showed that inactivation of key genes of this system resulted in a loss of phenotypic traits provided by a T4SS. Seven of 10 mutants with a mutation in this T4SS did not express the type IV secretion pilus. Correspondingly, disruption of the genes resulted in up to 100,000-fold reductions in conjugation frequencies compared to those of the parent strain. Moreover, the expression of this T4SS was found to be positively regulated by one of its components, the tfc24 gene. We concluded that this gene cluster represents a novel family of T4SSs involved in propagation of genomic islands.

scholarly journals Characterization and Comparative Analysis of the Staphylococcus aureus Genomic Island vSaβ: an In Silico Approach

2019 ◽  
Vol 201 (22) ◽  
Author(s):  
Anita J. Kläui ◽  
Renate Boss ◽  
Hans U. Graber
Keyword(s):  
Staphylococcus Aureus ◽  
In Silico ◽  
Serine Proteases ◽  
Genomic Island ◽  
Bacterial Species ◽  
Opportunistic Pathogen ◽  
Genomic Islands ◽  
Protease Gene ◽  
Sequencing Data ◽  
Content Type

ABSTRACT Staphylococcus aureus is a widespread opportunistic pathogen to humans and animals. Of its genome, 20 to 25% varies between strains and consists of phages, pathogenicity islands, transposons, and genomic islands. S. aureus harbors up to three genomic islands, vSaα, vSaβ, and vSaγ. The vSaβ region of S. aureus can encode a number of virulence-associated factors, such as serine proteases, leukocidins, enterotoxins, bacteriocins, or a hyaluronate lyase. In this study, the vSaβ regions of 103 clinically relevant S. aureus strains were characterized in silico and compared to the three predefined vSaβ types. We here suggest a superordinate system of 15 different vSaβ types, of which 12 were newly defined. Each vSaβ type has a distinct structure with a distinct set of genes, which are both highly conserved. Between the different types, gene content and composition vary substantially. Based on our data, a strain’s vSaβ type is strongly coupled with its clonal complex, suggesting that vSaβ was acquired in an ancestral S. aureus strain, arguably by phage mediation, before differentiation into clonal complexes. In addition, we addressed the issue of ambiguous nomenclature in the serine protease gene cluster and propose a novel, phylogeny-based nomenclature of the cluster contained in the vSaβ region. IMPORTANCE With the rapid increase of available sequencing data on clinically relevant bacterial species such as S. aureus, the genomic basis of clinical phenotypes can be investigated in much more detail, allowing a much deeper understanding of the mechanisms involved in disease. We characterized in detail the S. aureus genomic island vSaβ and defined a superordinate system to categorize S. aureus strains based on their vSaβ type, providing information about the strains’ virulence-associated genes and clinical potential.

scholarly journals Salmonella Genomic Island 1 is Broadly Disseminated within Gammaproteobacteriaceae

2020 ◽  
Vol 8 (2) ◽  
pp. 161 ◽  
Author(s):  
Max Laurence Cummins ◽  
Mohammad Hamidian ◽  
Steven Philip Djordjevic
Keyword(s):  
Escherichia Coli ◽  
Genomic Island ◽  
Multiple Drug Resistance ◽  
Genomic Islands ◽  
Multiple Drug ◽  
Class 1 Integron ◽  
The United Kingdom ◽  
Class 1 ◽  
Providencia Stuartii ◽  
Conserved Gene

Salmonella genomic island 1 (SGI1) is an integrative mobilisable element that plays an important role in the capture and spread of multiple drug resistance. To date, SGI1 has been found in clinical isolates of Salmonella enterica serovars, Proteus mirabilis, Morganella morganii, Acinetobacter baumannii, Providencia stuartii, Enterobacter spp, and recently in Escherichia coli. SGI1 preferentially targets the 3´-end of trmE, a conserved gene found in the Enterobacteriaceae and among members of the Gammaproteobacteria. It is, therefore, hypothesised that SGI1 and SGI1-related elements (SGI1-REs) may have been acquired by diverse bacterial genera. Here, Bitsliced Genomic Signature Indexes (BIGSI) was used to screen the NCBI Sequence Read Archive (SRA) for putative SGI1-REs in Gammaproteobacteria. Novel SGI-REs were identified in diverse genera including Cronobacter spp, Klebsiella spp, and Vibrio spp and in two additional isolates of Escherichia coli. An extensively drug-resistant human clonal lineage of Klebsiella pneumoniae carrying an SGI1-RE in the United Kingdom and an SGI1-RE that lacks a class 1 integron were also identified. These findings provide insight into the origins of this diverse family of clinically important genomic islands and expand the knowledge of the potential host range of SGI1-REs within the Gammaproteobacteria.

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