Dataset Information

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years.

ABSTRACT: IncX3 plasmids are correlated with the dissemination and acquisition of carbapenem resistance in Enterobacteriaceae and have been prevalent in China over the last 10 years. Since the distribution characteristics of IncX3 plasmids across China as well as their evolutionary traits for 10 years remain unclear, here we conducted a retrospective literature review and in silico comparative analysis of IncX3 plasmids in publicly available IncX3 plasmid genomes. IncX3 plasmids distributed in 17 provinces or cities were extracted for analysis, which tend to be specifically associated with hospital-isolated Escherichia coli ST410 from phylogroup A. Although the backbones of IncX3 plasmids have remained highly conservative over the last 10 years, the bla _NDM resistance genetic contexts on these plasmids could fall into five subtypes, among which AR_N1_I has been identified in Enterobacter cloacae174 chromosome and AR_N5_I was simultaneously located on IncF and IncA/C plasmids. This suggests that the bla _NDM resistance gene environment can spread between different plasmids, between different bacterial genera, or between strains and plasmids, highlighting that it is imperative to adopt more stringent infection control measures targeting IncX3 plasmid spread.

SUBMITTER: Liu B

PROVIDER: S-EPMC8681339 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years.

Liu Baomo B Guo Yingyi Y Liu Ningjing N Wang Jiong J Li Feifeng F Yao Likang L Zhuo Chao C

Frontiers in microbiology 20211203

IncX3 plasmids are correlated with the dissemination and acquisition of carbapenem resistance in Enterobacteriaceae and have been prevalent in China over the last 10 years. Since the distribution characteristics of IncX3 plasmids across China as well as their evolutionary traits for 10 years remain unclear, here we conducted a retrospective literature review and in silico comparative analysis of IncX3 plasmids in publicly available IncX3 plasmid genomes. IncX3 plasmids distributed ...[more]

PMID: 34925253

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Project description:Carbapenem-resistant Enterobacterales poses a global urgent antibiotic resistance threat because of its ability to transfer carbapenemase genes to other bacteria via horizontal gene transfer mediated by mobile genetic elements such as plasmids. Oxacillinase-181 (OXA-181) is one of the most common OXA-48-like carbapenemases, and OXA-181-producing Enterobacterales has been reported in many countries worldwide. However, systematic research concerning the overall picture of plasmids harboring bla OXA-181 in Enterobacterales is currently scarce. In this study, we aimed to determine the phylogeny and evolution of bla OXA-181-positive (gene encoding OXA-181) plasmids. To characterize the plasmids harboring bla OXA-181 in Enterobacterales, we identified 81 bla OXA-181-positive plasmids from 35,150 bacterial plasmids downloaded from the NCBI RefSeq database. Our results indicated that diverse plasmid types harbored bla OXA-181 but was predominantly carried by IncX3-type plasmids. We systematically compared the host strains, plasmid types, conjugative transfer regions, and genetic contexts of bla OXA-181 among the 66 bla OXA-181-positive IncX3 plasmids. We found that IncX3 plasmids harboring bla OXA-181 were mostly ColKP3-IncX3 hybrid plasmids with a length of 51 kb each and were mainly distributed in Escherichia coli and Klebsiella pneumoniae. Most of the IncX3 plasmids harboring bla OXA-181 were human origin. Almost all the bla OXA-181-positive IncX3 plasmids were found to carry genes coding for relaxases of the MOBP family and VirB-like type IV secretion system (T4SS) gene clusters, and all the 66 IncX3 plasmids were found to carry the genes encoding type IV coupling proteins (T4CPs) of the VirD4/TraG subfamily. Most IncX3 plasmids harbored both bla OXA-181 and qnrS1 in their genomes, and the two antibiotic resistance genes were found to a composite transposon bracketed by two copies of insertion sequence IS26 in the same orientation. Our findings provide important insights into the phylogeny and evolution of bla OXA-181-positive IncX3 plasmids and further address their role in acquiring and spreading bla OXA-181 genes in Enterobacterales.

Project description:There is an increasing need to understand the structural drivers of immigrant health inequities, including xenophobic and racist policies at the state level in the United States. Databases aggregate state policies related to immigration and research using single year indices examines state policy and immigrant health. Yet none of these sources use a theoretically informed social determinants of immigrant health approach to consider state environments longitudinally, include both exclusionary and inclusionary policies, and are relevant to immigrants from any region of the world or ethnic group. Using an established social determinants of immigrant health framework, a measure of structural xenophobia was created using fourteen policies across five domains: access to public health benefits, higher education, labor and employment, driver's licenses and identification, and immigration enforcement over a ten-year period (2009-2019). To create the Immigration Policy Climate (IPC) index, we used data from state legislatures as well as policy databases from foundations, advocacy organizations, and scholarly articles. We identified and coded 714 US state policies across the 50 US States and the District of Columbia from 2009 to 2019. We calculated annual IPC index scores (range: 12 - 12) as a continuous measure (negative scores: exclusionary; positive scores: inclusionary). Results show that the US has an exclusionary immigration policy climate at the state-level (mean IPC score of -2.5). From 2009 to 2019, two-thirds of state-level immigration policies are exclusionary towards immigrants. About 75% of states experienced a 4-point change or less on the IPC index, and no state changed from largely exclusive to largely inclusive. By aggregating comprehensive, detailed data and a measure of state-level immigration policies over time, the IPC index provides population health researchers with rigorous evidence with which to assess structural xenophobia and an opportunity for longitudinal research on health inequities and immigrant health.

Project description:PurposePlasmids of the incompatibility group X type 3 (IncX3) were described carrying various carbapenemase genes in carbapenemase-producing Enterobacteriaceae (CPE) worldwide and in the United Arab Emirates (UAE), as well. To understand the driving force behind the emergence of such plasmids in the UAE, the relationship between IncX3 plasmids encountered locally and globally was investigated.MethodsCPE strains isolated in the UAE during 2009-2014 were screened by X3 PCR-based replicon typing. The clonal relationship of CPE carrying IncX3 plasmids was determined by multi-locus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). Complete sequence of selected IncX3 plasmids was determined. Phylogenetic relationship between the carbapenemase carrying IncX3 plasmids from the UAE and of those reported worldwide was established by comparing the plasmid backbones.Results10.2% of the 295 CPE tested were identified to carry IncX3 plasmids: 13 Escherichia coli, 13 Klebsiella pneumoniae, two Enterobacter cloacae, one Citrobacter freundii and one Morganella morganii isolate, respectively. Most of them were non-clonal; with small clusters of triplets and pairs of E. coli and K. pneumoniae, and a cluster of five K. pneumoniae ST11 exhibiting >90% similar PFGE patterns, respectively. The 30 isolates harbored either bla NDM-1, bla NDM-4, bla NDM-5, bla NDM-7, bla OXA-181 or bla KPC-2 carbapenemase genes on IncX3 plasmids. Phylogenetic analysis of the backbone region of IncX3 plasmids carrying various beta-lactamase genes from the UAE (n=23) and that of North-America, Europe, Asia and Australia (n=35) revealed three clusters based on the carbapenemase genes carried: plasmids harboring bla OXA-181 and bla NDM-5 formed two distinct groups, whereas backbones of plasmids with bla NDM-1, bla NDM-4 and bla NDM-7 clustered together. Each cluster contained plasmids of diverse geographical origin.ConclusionThe findings suggest that different carbapenemase gene carrying IncX3 plasmids encountered in the UAE do not evolve locally, rather are subtypes of this epidemic plasmid emerging in this country due to international transfer.

Dataset Information

In silico Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years.

Publications

<i>In silico</i> Evolution and Comparative Genomic Analysis of IncX3 Plasmids Isolated From China Over Ten Years.

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