Analysis of direct repeats and spacers of CRISPR/Cas systems type I-F in Brazilian clinical strains of Pseudomonas aeruginosa

Luz, Ana Carolina de Oliveira; Silva, Julia Mariana Assis da; Rezende, Antônio Mauro; Barros, Maria Paloma Silva de; Leal-Balbino, Tereza Cristina

doi:10.1007/s00438-019-01575-7

Cited by 7 publications

(7 citation statements)

References 38 publications

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“…In conclusion, this is the first study analyzing the presence of CRISPR/Cas systems in carbapenemase-producing P. aeruginosa isolates of Greek origin. In line with previous studies [34,35], our data confirmed the presence of type I-C, I-E and I-F systems in P. aeruginosa of clinical origin, and their strong association with specific lineages. Isolates, which belonged to the same clone, exhibited identical CRISPR/Cas systems underlined the fact that CRISPR arrays is a simple, but precise, genotyping tool that can be used to track pathogenic bacterium.…”

Section: Discussionsupporting

confidence: 92%

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Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital

et al. 2020

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The objective of this study was to analyze the characteristics that contribute to the successful dissemination of VIM-producing Pseudomonas aeruginosa (P. aeruginosa), belonging to ST111 and ST235, in a Greek hospital. A total of 120 non-repetitive P. aeruginosa, which had meropenem minimal inhibitory concentrations (MICs) greater than 2 mg/L, were studied. VIM-encoding genes were amplified and sequenced within their integrons. Isolates were typed by multilocus sequence typing (MLST). Six VIM-producers, representative of different integron structures and sequence types (STs), were completely sequenced using Illumina platform. Sixty-one P. aeruginosa were confirmed to produce VIM-type carbapenemases. ST111 dominated (n = 34) among VIM-producers, while 15 VIM-producers belonged to ST235. The blaVIM-like genes were located in three integron types, including In59, In595 and In1760, which were integrated into P. aeruginosa chromosomes. Whole genome sequencing (WGS) data demonstrated that ST111 and ST235 MBL producers carried several resistance and virulence genes. Additionally, the presence of type I-C and type I-E clustered regularly interspaced short palindromic repeats (CRISPR)/Cas locus was observed in ST235 and ST395 isolates, respectively. In conclusion, our findings confirmed the clonal spread of ST111 P. aeruginosa, carrying the VIM-2-encoding integron In59, in the University Hospital of Larissa (UHL). In addition, they highlighted the important role of high-risk clones, ST111 and ST235, in the successful dissemination and establishment into hospital settings of clinically important pathogens carrying resistance determinants.

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Section: Discussionsupporting

confidence: 92%

“…Unlike Pae91-Lar, the locus included two arrays of 13 and 18 spacers. Type I-F locus was found previously in 38.5% of clinical P. aeruginosa isolates recovered from two Brazilian hospitals [35].…”

Section: Resultsmentioning

confidence: 61%

Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital

et al. 2020

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“…The possession of three CRISPR/Cas systems simultaneously (I-F + I-E + III-U), as well as the combination of I-E and I-F CRISPR/Cas types, were specific characteristics of the ST654 isolates in our P. aeruginosa collection. The simultaneous presence of I-E and I-F CRISPR/Cas types was previously documented in several works on single isolates belonging to the STs 252, 387 and 3137 [ 12 , 16 , 17 , 50 ]. To the best of our knowledge, this is the first reported case of carrying three different CRISPR/Cas systems simultaneously in the genomes of clinical P. aeruginosa isolates.…”

Section: Discussionmentioning

confidence: 82%

“…The analysis of the CRISPR arrays in Brazilian P. aeruginosa isolates harboring I-F type systems showed that CRISPR loci exhibited a high plasticity and spacer diversity, but, at the same time, similarities between the strains and spacer rearrangements were observed [ 16 ]. These authors also reported the presence of I-F and I-E types in the same isolate simultaneously.…”

Section: Introductionmentioning

confidence: 99%

CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia

et al. 2021

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Pseudomonas aeruginosa is a member of the ESKAPE opportunistic pathogen group, which includes six species of the most dangerous microbes. This pathogen is characterized by the rapid acquisition of antimicrobial resistance, thus causing major healthcare concerns. This study presents a comprehensive analysis of clinical P. aeruginosa isolates based on whole-genome sequencing data. The isolate collection studied was characterized by a variety of clonal lineages with a domination of high-risk epidemic clones and different CRISPR/Cas element patterns. This is the first report on the coexistence of two and even three different types of CRISPR/Cas systems simultaneously in Russian clinical strains of P. aeruginosa. The data include molecular typing and genotypic antibiotic resistance determination, as well as the phylogenetic analysis of the full-length cas gene and anti-CRISPR genes sequences, predicted prophage sequences, and conducted a detailed CRISPR array analysis. The differences between the isolates carrying different types and quantities of CRISPR/Cas systems were investigated. The pattern of virulence factors in P. aeruginosa isolates lacking putative CRISPR/Cas systems significantly differed from that of samples with single or multiple putative CRISPR/Cas systems. We found significant correlations between the numbers of prophage sequences, antibiotic resistance genes, and virulence genes in P. aeruginosa isolates with different patterns of CRISPR/Cas-elements. We believe that the data presented will contribute to further investigations in the field of bacterial pathoadaptability, including antimicrobial resistance and the role of CRISPR/Cas systems in the plasticity of the P. aeruginosa genome.

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“…So far, numerous studies have been conducted describing the CRISPR-Cas systems in P. aeruginosa, both at the structural and functional levels [16][17][18][19][20][21][22][23], but not throughout the entire Pseudomonas genus. The search for CRISPR structures in the genomes of the Pseudomonas genus is significant as it contributes to the study of the diversity and distribution of these genetic elements in various environments.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes

Parra-Sánchez,

Antequera-Zambrano,

Martínez-Navarrete

et al. 2023

Genes

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Pseudomonas is a bacterial genus with some saprophytic species from land and others associated with opportunistic infections in humans and animals. Factors such as pathogenicity or metabolic aspects have been related to CRISPR-Cas, and in silico studies into it have focused more on the clinical and non-environmental setting. This work aimed to perform an in silico analysis of the CRISPR-Cas systems present in Pseudomonas genomes. It analyzed 275 complete genomic sequences of Pseudomonas taken from the NCBI database. CRISPR loci were obtained from CRISPRdb. The genes associated with CRISPR (cas) and CAS proteins, and the origin and diversity of spacer sequences, were identified and compared by BLAST. The presence of self-targeting sequences, PAMs, and the conservation of DRs were visualized using WebLogo 3.6. The CRISPR-like RNA secondary structure prediction was analyzed using RNAFold and MFold. CRISPR structures were identified in 19.6% of Pseudomonas species. In all, 113 typical CRISPR arrays with 18 putative cas were found, as were 2050 spacers, of which 52% showed homology to bacteriophages, 26% to chromosomes, and 22% to plasmids. No potential self-targeting was detected within the CRISPR array. All the found DRs can form thermodynamically stable secondary RNA structures. The comparison of the CRISPR/Cas system can help understand the environmental adaptability of each evolutionary lineage of clinically and environmentally relevant species, providing data support for bacterial typing, traceability, analysis, and exploration of unconventional CRISPR.

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Analysis of direct repeats and spacers of CRISPR/Cas systems type I-F in Brazilian clinical strains of Pseudomonas aeruginosa

Cited by 7 publications

References 38 publications

Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital

Unravelling the Features of Success of VIM-Producing ST111 and ST235 Pseudomonas aeruginosa in a Greek Hospital

CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia

Comparative Analysis of CRISPR-Cas Systems in Pseudomonas Genomes

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