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CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated 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 bee...

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Autores principales: Kamruzzaman, Muhammad, Iredell, Jonathan R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965323/
https://www.ncbi.nlm.nih.gov/pubmed/31998256
http://dx.doi.org/10.3389/fmicb.2019.02934
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author Kamruzzaman, Muhammad
Iredell, Jonathan R.
author_facet Kamruzzaman, Muhammad
Iredell, Jonathan R.
author_sort Kamruzzaman, Muhammad
collection PubMed
description CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated 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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spelling pubmed-69653232020-01-29 CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae Kamruzzaman, Muhammad Iredell, Jonathan R. Front Microbiol Microbiology CRISPR-Cas (clustered regularly interspersed short palindromic repeats-CRISPR-associated 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. Frontiers Media S.A. 2020-01-10 /pmc/articles/PMC6965323/ /pubmed/31998256 http://dx.doi.org/10.3389/fmicb.2019.02934 Text en Copyright © 2020 Kamruzzaman and Iredell. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Kamruzzaman, Muhammad
Iredell, Jonathan R.
CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title_full CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title_fullStr CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title_full_unstemmed CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title_short CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae
title_sort crispr-cas system in antibiotic resistance plasmids in klebsiella pneumoniae
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6965323/
https://www.ncbi.nlm.nih.gov/pubmed/31998256
http://dx.doi.org/10.3389/fmicb.2019.02934
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