Comparative Genomics of Type 1 IncC Plasmids from China

Ma, Lun; Yin, Zhe; Zhang, Defu; Zhan, Zhe; Wang, Qian; Duan, Xiongbo; Gao, Han; Liang, Quanhui; Zhao, Yuzong; Feng, Jiao; Zhao, Yachao; Tong, Yigang; Dai, Erfu; Zhou, Dongsheng

doi:10.2217/fmb-2017-0072

Cited by 6 publications

(6 citation statements)

References 45 publications

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“…In addition to using the presence or absence of signature sequences orf1832 / orf1847 , rhs1 / rhs2 , i1, and i2, a phylogenetic analysis using recombination-free SNPs of core backbone regions can steadily discriminate type 1/2 hybrid from type 1 and type 2. As shown previously (Ma et al, 2017) and herein, additional resistance islands (e.g., the MDR regions and the bla CTX–M -carrying regions in this study) can be found in type 1, type 2, and type 1/2-hybrid plasmids.…”

Section: Discussionsupporting

confidence: 89%

“…As found in all the seven type 1 and type 1/2-hybrid plasmids except for p12085-Ct1 (type 1), the ARI-A islands (Figure 3) were identified as Tn 1696 (Partridge et al, 2001) derivatives. The Tn 1696 derivatives in pR148 and p205880-Ct1/2 were recognized as intact unit transposons Tn 6358 (Ma et al, 2017) and Tn 6395 , respectively, which differed from Tn 1696 mainly by insertion of In834 (Ma et al, 2017) and In1212 instead of In4 into a primary tnpAR – mer structure. The Tn 1696 derivatives in the other four plasmids could not be discriminated as intact transposons due to 3′-terminal truncations, which were in some cases accompanied with insertion of additional resistance modules: bla NDM– 1 -carrying ΔTn 125 (Poirel et al, 2012) in pQD1501-Ct1 and strAB -carrying ΔTn 6029 (Cain et al, 2010) in p427113-Ct1/2.…”

Section: Resultsmentioning

confidence: 99%

“…By contrast, the type 1 plasmid p12085-Ct1 and the type 2 plasmids pA1763-Ct2 and p397108-Ct2 harbored extremely simple backbones due to deletion of large backbone regions. In addition to insertion of accessory modules and deletion of backbone regions, large inversion (such as those in p427113-Ct1/2 and pA1763-Ct2) and translocation (such as those in pT5282-Ct2) events occurred within backbone regions during genomic diversification of IncC plasmids (Ma et al, 2017; Supplementary Figure S2).…”

Section: Discussionmentioning

confidence: 99%

“…Our previous study (Ma et al, 2017) has shown considerable genomic variation in a collection of three type 1 IncC plasmids from China together with pR148. This follow-up study presents the complete nucleotide sequences of 11 new IncC plasmids from China and a further comprehensive genomic comparison of these 11 plasmids together with pR148 and pR55, providing a deeper insight into parallel evolution of IncC plasmids from China.…”

Section: Introductionmentioning

confidence: 99%

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Type 1, 2, and 1/2-Hybrid IncC Plasmids From China

Cheng

Jiang

et al. 2019

Front. Microbiol.

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A collection of 11 IncC plasmids from China were fully sequenced herein and compared with reference plasmids pR148 and pR55. These 13 plasmids could be assigned into three different subgroups: type 1, type 2, and type 1/2 hybrid. Type 1/2-hybrid plasmids most likely emerged from homologous recombination between type 1 and type 2 plasmids. Different IncC plasmids had evolved to acquire quite different profiles of accessory modules and thus different collections of resistance genes. The accessory resistance modules included not only the blaCMY-carrying region, the ARI-A island, and the ARI-B island, but also various additional kinds of resistance islands such as the blaCTX–M-carrying regions and the MDR regions. Insertion of accessory modules was sometimes accompanied by deletion, inversion, and translocation of surrounding backbone regions. pR148 and pR55 were confirmed to have the most complete backbones for type 1 and type 2, respectively. This was the first report of a blaIMP–8-carrying IncC plasmid, and that of three novel mobile elements: a Tn1696-derived unit transposon Tn6395, a class 2 integron In2-76, and an insertion sequence ISEcl10.

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Section: Discussionsupporting

confidence: 89%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Type 1, 2, and 1/2-Hybrid IncC Plasmids From China

Cheng

Jiang

et al. 2019

Front. Microbiol.

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“…Coexistence of two to four different resistance plasmids has been observed in C. freundii . 36 , 38 , 39 We recently determined the complete nucleotide sequences of four plasmids p112298-KPC (belonging to an unknown incompatibility group; accession number KP987215), 36 p112298-NDM (IncX3 type; KP987216), 36 p112298-catA (IncHI2; KY270851) and p112298-tetA (type 1 IncC) 40 coexisting in a clinical C. freundii isolate 112,298. In this follow-up study, high-throughput genomic sequencing disclosed the co-occurrence of five resistance plasmids pP10159-1, pP10159-2, pP10159-3, pP10159-4 and pP10159-5 in a clinical C. freundii isolate P10159.…”

Section: Discussionmentioning

confidence: 99%

Comparative genomics of five different resistance plasmids coexisting in a clinical multi-drug resistant <em>Citrobacter freundii</em> isolate

Ouyang

Sun²,

Zhou

et al. 2018

IDR

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BackgroundPlasmid-mediated multi-drug resistance (MDR) has been widely found in Citro-bacter freundii. C. freundii P10159 was isolated from a human case of postoperative urinary tract infection in a Chinese teaching hospital.MethodsThe complete nucleotide sequences of five resistance plasmids pP10159-1, pP10159-2, pP10159-3, pP10159-4 and pP10159-5 from C. freundii P10159 were determined through high-throughput genome sequencing, and then compared with related plasmids sequences. Plasmid transfer, CarbaNP test of carbapenemase activity, and bacterial antimicrobial susceptibility test were performed to characterize resistance phenotypes mediated by these plasmids.ResultspP10159-1 carrying blaNDM-1and pP10159-2 harboring blaIMP-4 plus qnrS1 were almost identical to IncX3 plasmid pNDM-HN380 and IncN1 plasmid pP378-IMP, respectively. The blaKPC-2-carrying plasmids pP10159-3, pHS062105-3 and pECN49-KPC were highly similar to each other, and constituted a novel group of plasmids belonging to an unknown incomparability group. The MDR plasmids pP10159-4 and pP10159-5 had the backbones highly similar to IncHI4 plasmid pNDM-CIT and type 2 IncC plasmid pR55, respectively, but their accessory resistance regions differed from pNDM-CIT and pR55, respectively. The five plasmids from the P10159 isolate contained a total of 24 different genes or gene loci, which contributed to resistance to 13 distinct antibiotic molecules or toxic compounds.ConclusionThis is the first report of co-occurrence of five different resistance plasmids, with determination of their complete sequences. Data presented here provide a deeper insight into co-selection and maintenance of multiple plasmids and an extremely large number of resistance genes in a single bacterial isolate.

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Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria

Ambrose

Harmer

Hall

2018

Plasmid

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The large, broad host range IncC plasmids are important contributors to the spread of key antibiotic resistance genes and over 200 complete sequences of IncC plasmids have been reported. To track the spread of these plasmids accurate typing to identify the closest relatives is needed. However, typing can be complicated by the high variability in resistance gene content and various typing methods that rely on features of the conserved backbone have been developed. Plasmids can be broadly typed into two groups, type 1 and type 2, using four features that differentiate the otherwise closely related backbones. These types are found in many different countries in bacteria from humans and animals. However, hybrids of type 1 and type 2 are also occasionally seen, and two further types, each represented by a single plasmid, were distinguished. Generally, the antibiotic resistance genes are located within a small number of resistance islands, only one of which, ARI-B, is found in both type 1 and type 2. The introduction of each resistance island generates a new lineage and, though they are continuously evolving via the loss of resistance genes or introduction of new ones, the island positions serve as valuable lineage-specific markers. A current type 2 lineage of plasmids is derived from an early type 2 plasmid but the sequences of early type 1 plasmids include features not seen in more recent type 1 plasmids, indicating a shared ancestor rather than a direct lineal relationship. Some features, including ones essential for maintenance or for conjugation, have been examined experimentally.

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Comparative Genomics of Type 1 IncC Plasmids from China

Abstract: Complex rearrangement and homologous recombination events have occurred during evolution of p112298-tetA, making it significantly differ modularly from the other three plasmids with respect to both plasmid backbone and exogenous resistance regions.

Cited by 6 publications

References 45 publications

Type 1, 2, and 1/2-Hybrid IncC Plasmids From China

Type 1, 2, and 1/2-Hybrid IncC Plasmids From China

Comparative genomics of five different resistance plasmids coexisting in a clinical multi-drug resistant <em>Citrobacter freundii</em> isolate

Evolution and typing of IncC plasmids contributing to antibiotic resistance in Gram-negative bacteria

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