Sequencing and comparative genomics analysis of the IncHI2 plasmids pT5282-mphA and p112298-catA and the IncHI5 plasmid pYNKP001-dfrA

Liang, Quanhui; Yin, Zhe; Zhao, Yachao; Liang, Liqi; Feng, Jiao; Zhan, Zhe; Wang, Hui; Song, Yajun; Tong, Yigang; Wu, Weili; Chen, Weijun; Wang, Jinglin; Jiang, Lingxiao; Zhou, Dongsheng

doi:10.1016/j.ijantimicag.2017.01.021

Cited by 40 publications

(54 citation statements)

References 39 publications

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“…The clades correspond to the R27-like and pNDM-CIT-like plasmids, which suggest a parallel evolution in different ecological niches (Poirel et al 2011). Both clades and the same subclusters were identified by Kubasova et al (2016) using core backbone regions, and Liang et al (2017) using traI and trhC genes.…”

Section: Molecular Clock Testmentioning

confidence: 83%

“…Recently, Liang et al (2017) proposed, based in similar results, a scheme for typing IncHI plasmids into five separately clustering subgroups, which includes the three mentioned for taxa, IncHI4 for clade pNDM-CIT, and IncHI5 for clade pKOX-R1. Nevertheless IncHI1 and IncHI4 belong to same taxon, as occurs with IncHI3 and IncHI5.…”

Section: Inchi Plasmid Homologymentioning

confidence: 99%

“…Even if new clades are presents, divergence time will not be very different from the already mentioned. Three of those new sequenced plasmids were studied by Liang et al (2017) and by Sun et al (2016) and genetic conservation was observed within the core sequences of representatives IncHI2 plasmids, but differences in MDR modules; the comparison will be made in the corresponding section (3.3.6).…”

Section: Molecular Clock Testmentioning

confidence: 99%

“…Identities with Tra genes were 99%, except for one, with 96% (p704SK6_1; GB: CP022144). One of them, (pYNKP001-dfrA; GB: KY270853), studied by Liang et al (2017), will be compared in the corresponding section (3.5.7).…”

Section: Molecular Clock Testmentioning

confidence: 99%

“…Supporting this supposition, in the plasmid pP10164-2, studied by Sun et al (2016), beside rcnR/pcoE1/pcoS genes (99,9% of identities with homologous in pCFSAN2050-2), is emplaced the complete Silver operon (94% of identities with R478). In plasmid pT5282-mphA, studied by Liang et al (2017), remains only silR gene (100% of identities with pP10164-2).…”

Section: Triple Operon Copper Resistance/silver Resistance/tn7mentioning

confidence: 99%

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Comparative genomics and phylogeny of sequenced IncHI plasmids

Alvarez¹

2018

Preprint

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Conjugative plasmids from the IncHI incompatibility group are relevant vectors for multidrug resistance. Is the objective of this article the screening of the phylogeny of the first 44 publicly available sequences of IncHI plasmids from Enterobacteriaceae , because since there, a few hundred were registered in Genebank. A comparison of the similarities and differences between them revealed extensive conservation of their coding sequences. However, each genome had accessory regions with features of degradation or resistance to antibacterial agents. This article elucidates the IncHI1, IncHI2 and IncHI3 subgroup plasmids from the evolutive line based on multiple drug-resistant modules, explains the origin of the IncHI1 pAKU1-like composite transposon lineage, typifies the subgroup IncHI3, which is distantly related to IncHI1 and IncHI2 in phylogenetic analyses, confirms the relations within the transfer regions of H-group plasmids, and points to the divergence time of evolution with phylogenetic trees. Homology between subgroups, as measured by the molecular clock test, indicated that the contemporary IncHI1 and IncHI2 transfer region lineages diverged from an ancestral clone approximately 8,000 years ago (17,000 years ago if the divergent IncHI3 plasmids are included), although the IncH backbone was older. The uniformity of the composite transposon shared by most IncHI1 subgroup plasmids might be functionally equivalent to the heavy metal resistance that is mediated by some operons in the IncHI2 subgroup plasmids. A comparison of the DNA among these closely related plasmids provided insights on the horizontal and vertical transfers that were involved in their development.

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Section: Molecular Clock Testmentioning

confidence: 83%

Section: Inchi Plasmid Homologymentioning

confidence: 99%