CRISPR Arrays Away from <i>cas</i> Genes

Shmakov, Sergey; Уткина, И. И.; Wolf, Yuri I.; Makarova, Kira S.; Severinov, Konstantin; Koonin, Eugene V.

doi:10.1089/crispr.2020.0062

Cited by 26 publications

(27 citation statements)

References 47 publications

(69 reference statements)

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“…The enrichment or depletion of COG functional categories for the subset of transposons in completely sequenced bacterial genomes were calculated as described previously ( 132 ). Briefly, the ORFs in these genomes were annotated by comparison to the COG database of multiple sequence alignments ( 58 ) using the PSI-BLAST parameters described above.…”

Section: Methodsmentioning

confidence: 99%

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

Benler

Faure

Altae-Tran

et al. 2021

mBio

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Section: Methodsmentioning

confidence: 99%

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

Benler

Faure

Altae-Tran

et al. 2021

mBio

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“…In light of the high sequence identity of the isolated array repeats on the mosaic plasmids to the repeats in the complete CRISPR-Cas systems of closely related genomes, and the absence of transposable elements in the vicinity of isolated arrays, the most probable route of the evolution of the isolated CRISPR array is the loss of cas genes in a CRISPR-Cas locus [30]. It remains unclear whether the array isolated in this study is functional; however, it is known to be active through trans utilization by Cas proteins.…”

Section: Discussionmentioning

confidence: 99%

Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-β-Lactamase in Klebsiella pneumoniae in Russia

Starkova

Lazareva²,

Avdeeva

et al. 2021

Antibiotics

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The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a new threat to healthcare. In this study, we analyzed nine CR-hvKp isolates of different sequence-types (ST) recovered from patients with nosocomial infections in two hospitals in Saint Petersburg. Whole-genome sequencing showed that eight of them harbored large mosaic plasmids carrying resistance to carbapenems and hypervirulence simultaneously, and four different types of hybrid plasmids were identified. BLAST analysis showed a high identity with two hybrid plasmids originating in the UK and Czech Republic. We demonstrated that hybrid plasmids emerged due to the acquisition of resistance genes by virulent plasmids. Moreover, one of the hybrid plasmids carried a novel New Delhi metallo-beta-lactamase (NDM) variant, differing from NDM-1 by one amino acid substitution (D130N), which did not provide significant evolutionary advantages compared to NDM-1. The discovery of structurally similar plasmids in geographically distant regions suggests that the actual distribution of hybrid plasmids carrying virulence and resistance genes is much wider than expected.

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“…One hundred eighty putative predicted arrays were found (without filtering) using metaCRT in the 18 genomes of ST-2 A. baumannii clinical strains (Supplementary Table 3). After the complete process of filtering designed by Shmakov et al (2020) and removing the low-complexity sequences (Zhang and Ye, 2017), only 40 CRISPR arrays were selected (Table 1): 18 CRISPR arrays were present in the 2000 strains and 22 in 2 www.python.org the 2010 strains. All the strains, except in the Ab161_GEIH-2000 strain, presented at least one CRISPR array.…”

Section: Clustered Regularly Interspaced Short Palindromic Repeats Ar...mentioning

confidence: 99%

Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection

et al. 2022

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To optimize phage therapy, we need to understand how bacteria evolve against phage attacks. One of the main problems of phage therapy is the appearance of bacterial resistance variants. The use of genomics to track antimicrobial resistance is increasingly developed and used in clinical laboratories. For that reason, it is important to consider, in an emerging future with phage therapy, to detect and avoid phage-resistant strains that can be overcome by the analysis of metadata provided by whole-genome sequencing. Here, we identified genes associated with phage resistance in 18 Acinetobacter baumannii clinical strains belonging to the ST-2 clonal complex during a decade (Ab2000 vs. 2010): 9 from 2000 to 9 from 2010. The presence of genes putatively associated with phage resistance was detected. Genes detected were associated with an abortive infection system, restriction–modification system, genes predicted to be associated with defense systems but with unknown function, and CRISPR-Cas system. Between 118 and 171 genes were found in the 18 clinical strains. On average, 26% of these genes were detected inside genomic islands in the 2000 strains and 32% in the 2010 strains. Furthermore, 38 potential CRISPR arrays in 17 of 18 of the strains were found, as well as 705 proteins associated with CRISPR-Cas systems. A moderately higher presence of these genes in the strains of 2010 in comparison with those of 2000 was found, especially those related to the restriction–modification system and CRISPR-Cas system. The presence of these genes in genomic islands at a higher rate in the strains of 2010 compared with those of 2000 was also detected. Whole-genome sequencing and bioinformatics could be powerful tools to avoid drawbacks when a personalized therapy is applied. In this study, it allows us to take care of the phage resistance in A. baumannii clinical strains to prevent a failure in possible phage therapy.

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CRISPR Arrays Away from cas Genes

Cited by 26 publications

References 47 publications

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

Cargo Genes of Tn 7 -Like Transposons Comprise an Enormous Diversity of Defense Systems, Mobile Genetic Elements, and Antibiotic Resistance Genes

Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-β-Lactamase in Klebsiella pneumoniae in Russia

Genomic Analysis of Molecular Bacterial Mechanisms of Resistance to Phage Infection

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