Physical and genetic analyses of IncI2 plasmid R721: Evidence for the presence of shufflon

Komano, Teruya; Fujitani, Shoji; Funayama, Noriko; Kanno, Akira; Sakuma, Keita

doi:10.1016/0147-619x(90)90057-j

Cited by 14 publications

(9 citation statements)

References 9 publications

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“…1). Shufflons are a multiple inversion system, originally described for IncI1 plasmid R64 (33) and later also found in IncI2 plasmids (34). The R64 shufflon consists of four DNA segments designated A, B, C, and D (33).…”

Section: Resultsmentioning

confidence: 99%

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

Chen

Chavda

Laham

et al. 2013

Antimicrob Agents Chemother

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h Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have spread worldwide and become a significant public health threat. bla KPC , the plasmid-borne KPC gene, was frequently identified on numerous transferable plasmids in different incompatibility replicon groups. Here we report the complete nucleotide sequence of a novel bla KPC-3 -harboring IncI2 plasmid, pBK15692, isolated from a multidrug-resistant K. pneumoniae ST258 strain isolated from a New Jersey hospital in 2005. pBK15692 is 78 kb in length and carries a backbone that is similar to those of other IncI2 plasmids (pR721, pChi7122-3, pHN1122-1, and pSH146-65), including the genes encoding type IV pili and shufflon regions. Comparative genomics analysis of IncI2 plasmids reveals that they possess a conserved plasmid backbone but are divergent with respect to the integration sites of resistance genes. In pBK15692, the bla KPC-3 -harboring Tn4401 was inserted into a Tn1331 element and formed a nested transposon. A PCR scheme was designed to detect the prevalence of IncI2 and pBK15692-like plasmids from a collection of clinical strains from six New Jersey and New York hospitals isolated between 2007 and 2011. IncI2 plasmids were found in 46.2% isolates from 318 clinical K. pneumoniae strains. Notably, 59 pBK15692-like plasmids (23%) have been identified in 256 KPC-bearing K. pneumoniae strains, and all carried KPC-3 and belong to the epidemic ST258 clone. Our study revealed that the prevalence of IncI2 plasmids has been considerably underestimated. Further studies are needed to understand the distribution of this plasmid group in other health care regions and decipher the association between IncI2 plasmids and bla KPC-3 -bearing ST258 strains.

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Section: Resultsmentioning

confidence: 99%

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

Chen

Chavda

Laham

et al. 2013

Antimicrob Agents Chemother

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“…The shufflon is a multiple-inversion system first discovered in 1986 in the IncI1 plasmid R64 and subsequently identified in other IncI1 plasmids, IncIγ and IncI2 plasmids (Komano et al, 1987(Komano et al, , 1990Takahashi et al, 2011). Shufflons have now also been identified in more distantly related IncK (Cottell et al, 2014) and IncZ (Venturini et al, 2013) plasmids.…”

Section: Introductionmentioning

confidence: 98%

IncI shufflons: Assembly issues in the next-generation sequencing era

Brouwer

Tagg

Mevius

et al. 2015

Plasmid

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“…Shufflons have also been identified in IncI1γ 3 , IncI2 4, 5 , IncK 6, 7 and IncZ plasmids 8, 9 . Shufflons generate variants of the PilV protein, a minor component of the thin pilus.…”

Section: Introductionmentioning

confidence: 99%

“…As of September 2016, 76,793 records of genome sequences were submitted in the Assembly Database of the National Center for Biotechnology Information. Moreover, NGSs not only provide draft and complete genome sequences but are also used for quantitative analyses, including transcriptomic and metagenomic approaches 5, 26–28 . However, NGS short reads are too difficult to assemble because of frequent recombination regions, which include shufflon regions of bacterial plasmids 3, 29 .…”

Section: Introductionmentioning

confidence: 99%

Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

Sekizuka

Kawanishi

Ohnishi

et al. 2017

Sci Rep

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A multiple DNA inversion system, the shufflon, exists in incompatibility (Inc) I1 and I2 plasmids. The shufflon generates variants of the PilV protein, a minor component of the thin pilus. The shufflon is one of the most difficult regions for de novo genome assembly because of its structural diversity even in an isolated bacterial clone. We determined complete genome sequences, including those of IncI2 plasmids carrying mcr-1, of three Escherichia coli strains using single-molecule, real-time (SMRT) sequencing and Illumina sequencing. The sequences assembled using only SMRT sequencing contained misassembled regions in the shufflon. A hybrid analysis using SMRT and Illumina sequencing resolved the misassembled region and revealed that the three IncI2 plasmids, excluding the shufflon region, were highly conserved. Moreover, the abundance ratio of whole-shufflon structures could be determined by quantitative structural variation analysis of the SMRT data, suggesting that a remarkable heterogeneity of whole-shufflon structural variations exists in IncI2 plasmids. These findings indicate that remarkable rearrangement regions should be validated using both long-read and short-read sequencing data and that the structural variation of PilV in the shufflon might be closely related to phenotypic heterogeneity of plasmid-mediated transconjugation involved in horizontal gene transfer even in bacterial clonal populations.

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Physical and genetic analyses of IncI2 plasmid R721: Evidence for the presence of shufflon

Cited by 14 publications

References 9 publications

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

IncI shufflons: Assembly issues in the next-generation sequencing era

Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

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Physical and genetic analyses of IncI2 plasmid R721: Evidence for the presence of shufflon

Cited by 14 publications

References 9 publications

Complete Nucleotide Sequence of a bla KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

Complete Nucleotide Sequence of a bla KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

IncI shufflons: Assembly issues in the next-generation sequencing era

Elucidation of quantitative structural diversity of remarkable rearrangement regions, shufflons, in IncI2 plasmids

Contact Info

Product

Resources

About

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals

Complete Nucleotide Sequence of a bla _KPC -Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals