First Report of Integrative Conjugative Elements in Riemerella anatipestifer Isolates From Ducks in China.

Dekang Zhu,Ying Wu,Qiao Yang,Mingshu Wang,Renyong Jia,Yanling Yu,Anchun Cheng,Jinge Xu,Yunya Liu,Xiaoyue Chen,Mafeng Liu,Xinxin Zhao,Shun Chen,Zhishuang Yang,Jianbang Wan,Shaqiu Zhang,Ling Zhang

doi:10.3389/fvets.2019.00128

Dekang Zhu, Ying Wu + Show 15 more

Open Access

https://doi.org/10.3389/fvets.2019.00128

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Abstract

We report for the first time the occurrence of integrative conjugative elements (ICEs) in Riemerella anatipestifer (R.anatipestifer) isolated from diseased ducks in China. For this purpose, a total of 48 genome sequences were investigated, which comprised 30 publicly available R. anatipestifer genome sequences, and 18 clinical isolates genomes sequences. Two ICEs, named ICERanRCAD0133-1 and ICERanRCAD0179-1 following the classic nomenclature system, were identified in R. anatipestifer through the use of bioinformatics tools. Comparative analysis revealed that three ICEs in Ornithobacterium rhinotracheale showed a high degree of conservation with the core genes of ICERanRCAD0133-1, while 13 ICEs with high similarity to ICERanRCAD0179-1 were found in Bacteroidetes. Based on the definition of ICE family, ICERanRCAD0179-1 was grouped in CTnDOT/ERL family; however, ICERanRCAD0133-1, which had no significant similarity with known ICEs, might be classified into a novel ICE family. The sequences of ICERanRCAD0133-1 and ICERanRCAD0179-1 were 70890 bp and 49166 bp in length, had 33.14 and 50.34% GC content, and contained 77 CDSs and 51 CDSs, respectively. Cargo genes carried by these two ICEs were predicted to encode: R-M systems, IS elements, a putative TonB-dependent receptor, a bacteriocin/lantibiotic efflux ABC transporter, a tetracycline resistance gene and more. In addition, phylogenetic analyses revealed that ICERanRCAD0179-1 and related ICEs were derived from a common ancestor, which may have undergone divergence prior to integartation into the host bacterial chromosome, and that the core genes co-evolved via a related evolutionary process or experienced only a low degree of recombination events during spread from a common CTnDOT/ERL family ancestor. Collectively, this study is the first identification and characterization of ICEs in R. anatipestifer; and provides new insights into the genetic diversity, evolution, adaptation, antimicrobial resistance, and virulence of R. anatipestifer.

Highlights

Integrative conjugative elements (ICEs), a type of selftransmissible mobile genetic elements (MGEs) are widely distributed in bacterial genomes
integrative conjugative elements (ICEs) elements identified in R.anatipestifer were named ICERan in accordance with the nomenclature system proposed by Burrus, the different ICERan elements were allocated to different strain numbers, ICERanRCAD0133-1, and ICERanRCAD0179-1 [23, 24]
Comparison analysis of ICERanRCAD0133-1 and ICERanRCAD0179-1 was carried out through the BLASTn and BLASTp, which indicated that these two ICEs were not similar in DNA sequences or protein productions encoded by core genes and were not classified into the same ICE family [11]

Summary

Introduction

Integrative conjugative elements (ICEs), a type of selftransmissible mobile genetic elements (MGEs) are widely distributed in bacterial genomes. ICEs are major mediators for horizontal gene transfer (HGT), which contribute to microbial evolution and adjustment to new niche [1, 2]. ICEs have the capability to excise from their host chromosome and reintegrate into a new host’s chromosome at a target site where they replicate as a part of the host chromosome. Each type of ICE contains a set of core genes involved in its integration and excision, regulation and maintenance, and conjugative transfer [3]. The remaining components of ICEs are accessory genes, which endow the host bacteria with multiple phenotypes that can be beneficial for the recipient bacteria, such as colonization of a eukaryotic host, nitrogen fixation or promotion of virulence and biofilm formation, or resistance to antibiotics and heavy metals [4]. Homologous recombination among unrelated or distantly related ICEs probably occurs in ICE recipients, resulting in a diverse set of novel hybrid ICEs, which leads to the diversity of ICEs among bacterial genomes [5, 6]

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