Presence of Type I-F CRISPR/Cas systems is associated with antimicrobial susceptibility in Escherichia coli

Aydin, Seyid; Personne, Yoann; Newire, Enas; Laverick, Rebecca; Russell, Oliver M.; Roberts, Adam P.; Enne, Virve I.

doi:10.1093/jac/dkx137

Cited by 47 publications

(50 citation statements)

References 26 publications

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“…Similarly, type I-F CRISPR/Cas systems were more common in E. coli isolates that were antimicrobial sensitive (Aydin et al. 2017 ). Some of these CRISPR spacers aligned to sequences commonly found in IncFII and IncI1 plasmids, which are associated with clinical resistance (Aydin et al.…”

Section: Crispr/cas-based Plasmid Curing Systemsmentioning

confidence: 99%

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Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing

Buckner

Ciusa

Piddock

2018

FEMS Microbiology Reviews

168

103

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Antimicrobial resistance (AMR) is a global problem hindering treatment of bacterial infections, rendering many aspects of modern medicine less effective. AMR genes (ARGs) are frequently located on plasmids, which are self-replicating elements of DNA. They are often transmissible between bacteria, and some have spread globally. Novel strategies to combat AMR are needed, and plasmid curing and anti-plasmid approaches could reduce ARG prevalence, and sensitise bacteria to antibiotics. We discuss the use of curing agents as laboratory tools including chemicals (e.g. detergents and intercalating agents), drugs used in medicine including ascorbic acid, psychotropic drugs (e.g. chlorpromazine), antibiotics (e.g. aminocoumarins, quinolones and rifampicin) and plant-derived compounds. Novel strategies are examined; these include conjugation inhibitors (e.g. TraE inhibitors, linoleic, oleic, 2-hexadecynoic and tanzawaic acids), systems designed around plasmid incompatibility, phages and CRISPR/Cas-based approaches. Currently, there is a general lack of in vivo curing options. This review highlights this important shortfall, which if filled could provide a promising mechanism to reduce ARG prevalence in humans and animals. Plasmid curing mechanisms which are not suitable for in vivo use could still prove important for reducing the global burden of AMR, as high levels of ARGs exist in the environment.

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Section: Crispr/cas-based Plasmid Curing Systemsmentioning

confidence: 99%

“…Some of these CRISPR spacers aligned to sequences commonly found in IncFII and IncI1 plasmids, which are associated with clinical resistance (Aydin et al. 2017 ). This strongly suggests that antimicrobial-sensitive isolates can use CRISPR/Cas systems to degrade incoming AMR plasmids.…”

Section: Crispr/cas-based Plasmid Curing Systemsmentioning

confidence: 99%

Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing

Buckner

Ciusa

Piddock

2018

FEMS Microbiology Reviews

168

103

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“…Still, cells harboring cas genes of the two subtypes are extremely rare 6 61 . Unexpectedly, the E. coli I-F system is constitutively expressed under normal laboratory growth conditions 71 72 . Therefore, in principle, it is permanently acting against gene transfer.…”

Section: How Prokaryotes Bypass the Genetic Barrier Dictated By Crispmentioning

confidence: 99%

The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

Garcı́a-Martı́nez¹,

Maldonado²,

Guzmán³

et al. 2018

Microb Cell

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CRISPR-Cas represents a prokaryotic defense mechanism against invading genetic elements. Although there is a diversity of CRISPR-Cas systems, they all share similar, essential traits. In general, a CRISPR-Cas system consists of one or more groups of DNA repeats named CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), regularly separated by unique sequences referred to as spacers, and a set of functionally associated cas (CRISPR associated) genes typically located next to one of the repeat arrays. The origin of spacers is in many cases unknown but, when ascertained, they usually match foreign genetic molecules. The proteins encoded by some of the cas genes are in charge of the incorporation of new spacers upon entry of a genetic element. Other Cas proteins participate in generating CRISPR-spacer RNAs and perform the task of destroying nucleic acid molecules carrying sequences similar to the spacer. In this way, CRISPR-Cas provides protection against genetic intruders that could substantially affect the cell viability, thus acting as an adaptive immune system. However, this defensive action also hampers the acquisition of potentially beneficial, horizontally transferred genes, undermining evolution. Here we cover how the model bacterium Escherichia coli deals with CRISPR-Cas to tackle this major dilemma, evolution versus survival.

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“…Several studies have identified CRISPR-Cas systems in K. pneumoniae chromosomes as I-E and I-E * types (Ostria-Hernandez et al, 2015;Shen et al, 2017;Li et al, 2018) but little is known about CRISPR-Cas systems of plasmids in K. pneumoniae and other Enterobacteriaceae (Enas Newire et al, 2019). CRISPR-Cas systems are associated with relative antibiotic susceptibility in Streptococcus pyogenes and E. coli and the chromosomal CRISPR-Cas system is known to interfere with acquisition of antibioticresistant plasmids in E. coli (Zheng et al, 2014;Aydin et al, 2017). In this study, we examined 699 complete plasmid sequences from K. pneumoniae and 217 K. pneumoniae chromosomal sequences from the GenBank for the presence of CRISPR-Cas system and further analyzed the identified CRISPR-Cas systems and their spacers.…”

Section: Introductionmentioning

confidence: 99%

CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

Kamruzzaman

Iredell

2020

Front. Microbiol.

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CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPRassociated protein) is a microbial adaptive immune system involved in defense against different types of mobile genetic elements. CRISPR-Cas systems are usually found in bacterial and archaeal chromosomes but have also been reported in bacteriophage genomes and in a few mega-plasmids. Klebsiella pneumoniae is an important member of the Enterobacteriaceae with which they share a huge pool of antibiotic resistance genes, mostly via plasmids. CRISPR-Cas systems have been identified in K. pneumoniae chromosomes, but relatively little is known of CRISPR-Cas in the plasmids resident in this species. In this study, we searched for CRISPR-Cas system in 699 complete plasmid sequences (>50-kb) and 217 complete chromosomal sequences of K. pneumoniae from GenBank and analyzed the CRISPR-Cas systems and CRISPR spacers found in plasmids and chromosomes. We found a putative CRISPR-Cas system in the 44 plasmids from Klebsiella species and GenBank search also identified the identical system in three plasmids from other Enterobacteriaceae, with CRISPR spacers targeting different plasmid and chromosome sequences. 45 of 47 plasmids with putative type IV CRISPR had IncFIB replicon and 36 of them had an additional IncHI1B replicon. All plasmids except two are very large (>200 kb) and half of them carried multiple antibiotic resistance genes including bla CTX−M , bla NDM , bla OXA. To our knowledge, this is the first report of multi drug resistance plasmids from Enterobacteriaceae with their own CRISPR-Cas system and it is possible that the plasmid type IV CRISPR may depend on the chromosomal type I-E CRISPRs for their competence. Both chromosomal and plasmid CRISPRs target a large variety of plasmids from this species, further suggesting key roles in the epidemiology of large plasmids.

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Presence of Type I-F CRISPR/Cas systems is associated with antimicrobial susceptibility in Escherichia coli

Cited by 47 publications

References 26 publications

Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing

Strategies to combat antimicrobial resistance: anti-plasmid and plasmid curing

The CRISPR conundrum: evolve and maybe die, or survive and risk stagnation

CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

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