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

Marina Tyumentseva,Aleksandr Tyumentsev,Vasiliy Akimkin,Mikhail Zamyatin,Konstantin Karbyshev,Anna Mironova,Anna Prelovskaya,Lyudmila Petrova,Yulia Mikhaylova,Andrey Shelenkov

doi:10.3390/antibiotics10111301

Abstract

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.

Highlights

We demonstrated that the number of antibiotic resistance genes, plasmid number and the number of genes encoding virulence factors did not differ between the P. aeruginosa isolates with different types of CRISPR/Cas systems
We found significant correlations between the number of antibiotic resistance genes and the number of virulence genes in P. aeruginosa isolates with different types of CRISPR/Cas systems
Summarizing the results of the research performed, here we presented an assay of a clinical Russian P. aeruginosa population consisting of 51 clinical isolates collected from a multidisciplinary medical center during the period of 2017–2020; the majority of isolates possessed a large number of antimicrobial resistance determinants

Summary

Introduction

Most of the strains are able to enhance their resistance by the acquisition of resistance determinants using horizontal gene transfer, which results in the emergence of multidrug-resistant (MDR), or even pan drug-resistant, strains of P. aeruginosa. Due to this capacity, it was included in the group 4.0/). Of “superbugs” and added to the WHO’s Global List of critical, priority-level strains that require scientific research and the development of new antibiotics [2]. The population of P. aeruginosa is characterized by an epidemic structure, i.e., frequent recombination, the conservation of the common gene pool in strains from various sources and the spreading of epidemic clones characterized by the conservation of structural genomic regions [3].

Methods

Results

Discussion

Conclusion