scholarly journals Genomic Context of the Two Integrons of ST-111 Pseudomonas aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

2020 ◽  
Author(s):  
Jose Arturo Molina-Mora ◽  
Diana Chinchilla-Montero ◽  
Raquel García Batán ◽  
Fernando García
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Comparative Genomics ◽  
High Risk ◽  
Genomic Region ◽  
Genomic Islands ◽  
Genomic Context ◽  
Intrinsic Resistance ◽  
Pan Genome ◽  
Class 1 ◽  
Genomic Regions

Abstract Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections mainly in immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems, due to the activity of VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons located inone out of the 57 PaeAG1 genomic islands. However, the genomic context associated to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we first assessed the transcriptional activity of VIM-2 and IMP-18 genes when exposed to imipenem (a carbapenem) by RT-qPCR. To select related genomes to PaeAG1, we implemented a pan-genome analysis to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes. We also studied the PaeAG1 genomic islands content in the related strains and finally we described the architecture and possible evolutionary steps of the genomic regions around the VIM-2- and IMP-18-carrying integrons.Expression of VIM-2 and IMP-18 genes was demonstrated to be induced after imipenem exposure. In a subsequent comparative genomics analysis with 211 strains, the P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile, including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes. Finally, landscape reconstruction of genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in the same known region found in other two ST-111 strains. Also, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Altogether, we provide new insights about the genomic determinants associated with the resistance to carbapenems in this high-risk P. aeruginosa using comparative genomics.

From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

2020 ◽  
Author(s):  
Jose Arturo Molina-Mora ◽  
Raquel García Batán ◽  
Fernando García
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Genome Analysis ◽  
Genomic Region ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Genomic Context ◽  
Intrinsic Resistance ◽  
Pan Genome ◽  
Genomic Regions

Abstract Background Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections among immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials, including critical strains due to resistance to carbapenems, a last-resort antibiotic. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems due to the activity of both VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons, belonging to one out of the 57 PaeAG1 genomic islands. However, the genomic context related to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we implemented a comparative genomic approach to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes using a pan-genome analysis. We also studied the PaeAG1 genomic islands content in other strains and the architecture of genomic regions around the VIM-2- and IMP-18-carrying integrons. Results With 211 strains, the up-dated P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile (ST), including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes, but content was related to phylogenetic relationships. Finally, landscape reconstruction of specific genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in a known genomic region completely found in other two ST-111 strains. In addition, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Conclusions We provide new insights about the genomic determinants associated with the resistance to carbapenems in the high-risk PaeAG1 using comparative genomics. With the pan-genome analysis and the comparison of PaeAG1 genomic islands in other strains, it was possible to describe the genomic landscape of the two MBLs-carrying integrons, including an old-acquaintance element carrying VIM-2 and a new IMP-18-carrying integron.

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 Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

2020 ◽  
Author(s):  
Carola Berger ◽  
Christian Rückert ◽  
Jochen Blom ◽  
Korneel Rabaey ◽  
Jörn Kalinowski ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Comparative Genomics ◽  
Environmental Isolate ◽  
Genomic Islands ◽  
Pathogenic Potential ◽  
Accessory Genome ◽  
Potential Pathogen ◽  
The Difference ◽  
Highly Virulent

Abstract BackgroundNew strains of Pseudomonas aeruginosa are continuously being isolated and sequenced to increase the genomic accessibility of this important pathogen. This has led to the generation of an impressive dataset of closed P. aeruginosa genomes. To understand the difference between the strains, investigations are focused on the accessory genome, thereby constantly extending the known pan genome of P. aeruginosa as a species. Apart from follow-up studies, many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. ResultsPseudomonas spp. KRP1 could clearly be identified as a P. aeruginosa isolate, via comparative genomics. By using different genomic island prediction programs, we could identify a total of 25 genomic islands that cover ~12% of the genome of P. aeruginosa KRP1. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of its genomic information with the highly virulent PSE9 and LESB58 strains. For both of these clones, their increased virulence has been directly linked to their accessory genome before. ConclusionsHere we show, how the integrated use of previously published genomic data today, can help to replace expensive and time consuming wetlab work to determine the pathogenetic potential of environmental isolates. This knowledge is vital to understand what makes an isolate a potential pathogen as it helps design effective treatment.

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 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).

scholarly journals Recombination suppression and selection affect local ancestries in genomes of a migratory songbird

2021 ◽  
Author(s):  
Jun Ishigohoka ◽  
Karen Bascón-Cardozo ◽  
Andrea Bours ◽  
Janina Fuß ◽  
Arang Rhie ◽  
...  
Keyword(s):  
Zebra Finch ◽  
Genetic Relatedness ◽  
De Novo ◽  
Balancing Selection ◽  
Genomic Region ◽  
Genomic Islands ◽  
Background Selection ◽  
Recombination Suppression ◽  
Migratory Songbird ◽  
Genomic Regions

The patterns of genetic relatedness among individuals vary along the genome, representing fluctuation of local ancestry. The factors responsible for this variation have not been well studied in wild animals with ecological and behavioural relevance. Here, we characterise the genomic architecture of genetic relatedness in the Eurasian blackcap, an iconic songbird species in ecology and quantitative genetics of migratory behaviour. We identify 23 genomic regions with deviated local relatedness patterns, using a chromosome-level de novo assembly of the blackcap genome and whole-genome resequencing data of 179 individuals from nine populations with diverse migratory phenotypes. Five genomic regions show local relatedness patterns of polymorphic inversions, three of which are syntenic to polymorphic inversions known in the zebra finch. Phylogenetic analysis reveals these three polymorphic inversions evolved independently in the blackcap and zebra finch indicating convergence of polymorphic inversions. Population genetic analyses in these three inversions in the blackcap suggest balancing selection between two haplotypes in one locus and background selection in the other two loci. One genomic region with deviated local relatedness is under selection against gene flow by population-specific reduction in recombination rate. Other genomic islands including 11 pericentromeric regions consist of evolutionarily conserved and non-conserved recombination cold-spots under background selection. Two of these regions with non-conserved recombination suppression are known to be associated with population-specific migratory phenotypes, where local relatedness patterns support additional effects of population-specific selection. These results highlight how different forms of recombination suppression and selection jointly affect heterogeneous genomic landscape of local ancestries.

scholarly journals Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa

Open Biology ◽  
2016 ◽  
Vol 6 (3) ◽  
pp. 150175 ◽  
Author(s):  
Piklu Roy Chowdhury ◽  
Martin Scott ◽  
Paul Worden ◽  
Peter Huntington ◽  
Bernard Hudson ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
De Novo ◽  
Direct Repeat ◽  
Genomic Islands ◽  
Opportunistic Pathogens ◽  
Class 1 Integron ◽  
Integrative Conjugative Element ◽  
Class 1 ◽  
Specific Proteins ◽  
Almost All

Pseudomonas aeruginosa are noscomially acquired, opportunistic pathogens that pose a major threat to the health of burns patients and the immunocompromised. We sequenced the genomes of P. aeruginosa isolates RNS_PA1, RNS_PA46 and RNS_PAE05, which displayed resistance to almost all frontline antibiotics, including gentamicin, piperacillin, timentin, meropenem, ceftazidime and colistin. We provide evidence that the isolates are representatives of P. aeruginosa sequence type (ST) 235 and carry Tn 6162 and Tn 6163 in genomic islands 1 (GI1) and 2 (GI2), respectively. GI1 disrupts the endA gene at precisely the same chromosomal location as in P. aeruginosa strain VR-143/97, of unknown ST, creating an identical CA direct repeat. The class 1 integron associated with Tn 6163 in GI2 carries a bla GES-5 – aacA4 – gcuE15 – aphA15 cassette array conferring resistance to carbapenems and aminoglycosides. GI2 is flanked by a 12 nt direct repeat motif, abuts a tRNA-gly gene, and encodes proteins with putative roles in integration, conjugative transfer as well as integrative conjugative element-specific proteins. This suggests that GI2 may have evolved from a novel integrative conjugative element. Our data provide further support to the hypothesis that genomic islands play an important role in de novo evolution of multiple antibiotic resistance phenotypes in P. aeruginosa .

scholarly journals Diverse Mobilized Class 1 Integrons Are Common in the Chromosomes of Pathogenic Pseudomonas aeruginosa Clinical Isolates

2012 ◽  
Vol 56 (4) ◽  
pp. 2169-2172 ◽  
Author(s):  
Elena Martinez ◽  
Carolina Marquez ◽  
Ana Ingold ◽  
John Merlino ◽  
Steven P. Djordjevic ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Genomic Islands ◽  
Clonal Line ◽  
Class 1 Integron ◽  
Content Type ◽  
Class 1 Integrons ◽  
Class 1 ◽  
Genomic Locations

ABSTRACTEleven clinical class 1 integron-containingPseudomonas aeruginosaisolates from Australia and Uruguay were investigated for the genomic locations of these elements. Several novel class 1 integrons/transposons were found in at least four distinct locations in the chromosome, including genomic islands. These elements seem to be undergoing successful dispersal by lateral gene transfer since integrons were identified across several lineages and more than one clonal line.

scholarly journals Comparative Genomics of Closely Related Tetragenococcus halophilus Strains Elucidate the Diversity and Microevolution of CRISPR Elements

2021 ◽  
Vol 12 ◽  
Author(s):  
Minenosuke Matsutani ◽  
Takura Wakinaka ◽  
Jun Watanabe ◽  
Masafumi Tokuoka ◽  
Akihiro Ohnishi
Keyword(s):  
Comparative Genomics ◽  
Starter Culture ◽  
Soy Sauce ◽  
Fermented Foods ◽  
Type I ◽  
Bacterial Strains ◽  
Tetragenococcus Halophilus ◽  
Bacteriophage Infection ◽  
Class 1 ◽  
Genomic Regions

Tetragenococcus halophilus – a halophilic lactic acid bacterium – is frequently used as a starter culture for manufacturing fermented foods. Tetragenococcus is sometimes infected with bacteriophages during fermentation for soy sauce production; however, bacteriophage infection in starter bacteria is one of the major causes of fermentation failure. Here, we obtained whole-genome sequences of the four T. halophilus strains YA5, YA163, YG2, and WJ7 and compared them with 18 previously reported genomes. We elucidated five types of clustered regularly interspaced short palindromic repeat (CRISPR) loci in seven genomes using comparative genomics with a particular focus on CRISPR elements. CRISPR1 was conserved in the four closely related strains 11, YA5, YA163, and YG2, and the spacer sequences were partially retained in each strain, suggesting that partial deletions and accumulation of spacer sequences had occurred independently after divergence of each strain. The host range for typical bacteriophages is narrow and strain-specific thus these accumulation/deletion events may be responsible for differences in resistance to bacteriophages between bacterial strains. Three CRISPR elements, CRISPR1 in strains 11, YA5, YA163, and YG2, CRISPR2 in strain WJ7, and CRISPR2 in strain MJ4, were inserted in almost the same genomic regions, indicating that several independent insertions had occurred in this region. As these elements belong to class 1 type I-C CRISPR group, the results suggested that this site is a hotspot for class 1, type I-C CRISPR loci insertion. Thus, T. halophilus genomes may have acquired strain-specific bacteriophage-resistance through repeated insertion of CRISPR loci and accumulation/deletion events of their spacer sequences.

scholarly journals Dissemination of High-Risk Clones of Extensively Drug-Resistant Pseudomonas aeruginosa in Colombia

2015 ◽  
Vol 59 (4) ◽  
pp. 2421-2425 ◽  
Author(s):  
Adriana Correa ◽  
Rosa del Campo ◽  
Marcela Perenguez ◽  
Victor M. Blanco ◽  
Mercedes Rodríguez-Baños ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Sequence Type ◽  
Single Locus ◽  
Drug Resistant ◽  
Class 1 Integron ◽  
Content Type ◽  
Extensively Drug Resistant ◽  
Single Locus Variant ◽  
Class 1

ABSTRACTThe ability ofPseudomonas aeruginosato develop resistance to most antimicrobials represents an important clinical threat worldwide. We report the dissemination in several Colombian hospitals of two predominant lineages of extensively drug-resistant (XDR) carbapenemase-producingP. aeruginosastrains. These lineages belong to the high-risk clones sequence type 111 (ST111) and ST235 and harborblaVIM-2on a class 1 integron andblaKPC-2on a Tn4401transposon, respectively. Additionally,P. aeruginosaST1492, a novel single-locus variant of ST111, was identified. Clonal dissemination and the presence of mobile genetic elements likely explain the successful spread of XDRP. aeruginosastrains in Colombia.

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