Comparative analysis of CRISPR‐Cas systems in <i>Klebsiella</i> genomes

Shen, Jianjian; Lv, Li; Wang, Xudong; Xiu, Zhilong; Chen, Guoqiang

doi:10.1002/jobm.201600589

Cited by 41 publications

(53 citation statements)

References 43 publications

(64 reference statements)

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“…A total of 217 K. pneumoniae complete chromosomal sequences were extracted from GenBank (June 2019) and we identified that 81 of these (37%) carried CRISPR-Cas system on the chromosome. Of these 81, 45 were I-E and 36 were I-E * type ( Supplementary Table S3), consistent with previous reports (Ostria-Hernandez et al, 2015;Shen et al, 2017;Li et al, 2018). CP030878.1, CP020068.1, CP0016921.1, CP028929.1, CP024507.1, CP020854.1), ( * * CP018708.1, CP018702.1, CP018696.1, CP018720.1), ( * * * CP018687.1, CP018714.1, CP017986.1), (#CP022612.1, CP012754.1, CP006799.1), (##MG845201.1, MG845200.1) and (###CP030858.1, CP008933.1) and marked with asterisk or hashtag were the representative from each group showed in the figure.…”

Section: Analysis Of Crispr-cas System In K Pneumoniae Chromosomessupporting

confidence: 90%

“…Several previous studies identified and analyzed chromosomal CRISPR-Cas systems in K. pneumoniae by analyzing 52 (Ostria-Hernandez et al, 2015), 68 (Shen et al, 2017) and 97 (Li et al, 2018) complete and draft genome sequences. Here, we analyzed 217 complete K. pneumoniae chromosomes available in GenBank for the distribution of CRISPR-Cas systems, their types, acquired spacers and relationship between presence and absence of CRISPR and plasmids.…”

Section: Discussionmentioning

confidence: 99%

“…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).…”

Section: Introductionmentioning

confidence: 99%

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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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Section: Analysis Of Crispr-cas System In K Pneumoniae Chromosomessupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

Kamruzzaman

Iredell

2020

Front. Microbiol.

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“…A representative set of putative novel cas genes was extracted from the genome of isolate INF256 (read accession: ERR1008719, genome assembly available in Figshare) and tBLASTx was used to detect the presence of NTUH--K2044--and INF256--like cas genes among all genomes (identity ≥85%, coverage ≥25%). Note that the INF256 cas genes were subsequently found to be highly similar to those of strain Kp52.145 reported during the course of this study 100 .…”

Section: Crispr/cas and Restriction--modification Systemssupporting

confidence: 76%

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones ofKlebsiella pneumoniae

Wyres

Wick

Judd

et al. 2018

Preprint

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Klebsiella pneumoniae (Kp) has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare--associated infections 1 and community--acquired invasive infections, particularly pyogenic liver abscess 2 . The majority of MDR hospital outbreaks are caused by a subset of Kp clones with a high prevalence of acquired antimicrobial resistance (AMR) genes, while the majority of community--acquired invasive infections are caused by 'hypervirulent' clones that rarely harbour acquired AMR genes but have high prevalence of key virulence loci 3-5 . Worryingly, the last few years have seen increasing reports of convergence of MDR and the key virulence genes within individual Kp strains 6 , but it is not yet clear whether these represent a transient phenomenon or a significant ongoing threat. Here we perform comparative genomic analyses for 28 distinct Kp clones, including 6 hypervirulent and 8 MDR, to better understand their evolutionary histories and the risks of convergence. We show that MDR clones are highly diverse with frequent chromosomal recombination and gene content variability that far exceeds that of the hypervirulent clones. Consequently, we predict a much greater risk of virulence gene acquisition by MDR Kp clones than of resistance gene acquisition by hypervirulent clones. Kp MDR evolution is largely driven through acquisition of AMR genes on diverse mobilisable plasmids 7 which are particularly prevalent among the subset of clones that have become globally disseminated and frequently cause hospital outbreaks 8 ; e.g. clonal group (CG) 258 which is implicated in global spread of the Kp carbapenemases 9 . Kp pathogenicity is driven by a wide array of interacting factors 10-12 that are present in all strains, including the type III fimbriae (mrk) and the surface polysaccharides (capsule and lipopolysaccharide (LPS)) 12,13 which exhibit antigenic variation between strains. The majority of hypervirulent Kp, distinguished clinically as causing invasive infections even outside the hospital setting 14 , are associated with just two 4,15 of the >130 predicted capsular serotypes 16 , K1 and K2, that are considered particularly antiphagocytic and serum resistant 15,17 . Hypervirulent Kp are also associated with high prevalence of several other key virulence factors; the rmpA/rmpA2 genes that upregulate capsule expression to generate hypermucoidy 18,19 ; the colibactin genotoxin that induces eukaryotic cell death and promotes invasion to the blood from the intestines 20,21 ; and the yersiniabactin, aerobactin and salmochelin siderophores that promote survival in the blood by enhancing iron sequestration 11,[22][23][24] . Yersiniabactin synthesis is encoded by the ybt locus, which is usually mobilised by an integrative, conjugative element known as ICEKp. It is present in 40% of the general Kp population and seems to be frequently acquired and lost from MDR clones 25 . Fourteen distinct ybt+ICEKp variants are recognised, one of which also carries the colibactin synthesis locus (c...

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“…Spacer analysis was performed by BLAST and Geneious 18 . A phylogenetic UPGMA-based tree was constructed for CRISPR using MEGA7 19, 20 . Direct repeats and PAM conservation were assessed using WebLogo, RNA secondary structure was predicted using RNAfold 21–23 .…”

Section: Methodsmentioning

confidence: 99%

Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

Newire

Aydin

Juma

et al. 2019

Preprint

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During an investigation of CRISPR carriage in clinical, multi-drug resistant, Klebsiella pneumoniae, a novel CRISPR-Cas system (which we have designated Type IV-B) was detected on plasmids from two K. pneumoniae isolates from Egypt (isolated in 2002-2003) and a single K. pneumoniae isolate from the UK (isolated in 2017). Sequence analysis of other genomes available in GenBank revealed that this novel Type IV-B CRISPR-Cas system was present on 28 other plasmids from various Enterobacteriaceae hosts and was never found on the chromosome. Type IV-B is found exclusively on IncHI1B/IncFIB plasmids and is associated with multiple putative transposable elements. Type IV-B has a single repeat-spacer array (CRISPR1) upstream of the cas loci with some spacers matching regions of conjugal transfer genes of IncFIIK/IncFIB(K) plasmids suggesting a role in plasmid incompatibility. Expression of the cas loci was confirmed in available clinical isolates by RT-PCR; indicating the system is active. To our knowledge, this is the first report describing a new subtype within Type IV CRISPR-Cas systems exclusively associated with IncHI1B/IncFIB plasmids.ImportanceHere, we report the identification of a novel subtype of Type IV CRISPR-Cas that is expressed and exclusively carried by IncHI1B/IncFIB plasmids in Enterobacteriaceae, demonstrating unique evolutionarily juxtaposed connections between CRISPR-Cas and mobile genetic elements (MGEs). Type IV-B encodes a variety of spacers showing homology to DNA from various sources, including plasmid specific spacers and is therefore thought to provide specific immunity against plasmids of other incompatible groups (IncFIIK/IncFIB(K)). The relationship between Type IV-B CRISPR-Cas and MGEs that surround and interrupt the system is likely to promote rearrangement and be responsible for the observed variability of this type. Finally, the Type IV-B CRISPR-Cas is likely to co-operate with other cas loci within the bacterial host genome during spacer acquisition.

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Comparative analysis of CRISPR‐Cas systems in Klebsiella genomes

Cited by 41 publications

References 43 publications

CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

CRISPR-Cas System in Antibiotic Resistance Plasmids in Klebsiella pneumoniae

Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones ofKlebsiella pneumoniae

Identification of a Type IV CRISPR-Cas system located exclusively on IncHI1B/IncFIB plasmids in Enterobacteriaceae

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