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

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

JOURNAL=Frontiers in Veterinary Science

VOLUME=6

YEAR=2019

URL=https://www.frontiersin.org/journals/veterinary-science/articles/10.3389/fvets.2019.00128

DOI=10.3389/fvets.2019.00128

ISSN=2297-1769

ABSTRACT=<p>We report for the first time the occurrence of integrative conjugative elements (ICEs) in <italic>Riemerella anatipestifer</italic> (<italic>R.anatipestifer</italic>) isolated from diseased ducks in China. For this purpose, a total of 48 genome sequences were investigated, which comprised 30 publicly available <italic>R. anatipestifer</italic> genome sequences, and 18 clinical isolates genomes sequences. Two ICEs, named ICE<italic>Ran</italic>RCAD0133-1 and ICE<italic>Ran</italic>RCAD0179-1 following the classic nomenclature system, were identified in <italic>R. anatipestifer</italic> through the use of bioinformatics tools. Comparative analysis revealed that three ICEs in <italic>Ornithobacterium rhinotracheale</italic> showed a high degree of conservation with the core genes of ICE<italic>Ran</italic>RCAD0133-1, while 13 ICEs with high similarity to ICE<italic>Ran</italic>RCAD0179-1 were found in <italic>Bacteroidetes</italic>. Based on the definition of ICE family, ICE<italic>Ran</italic>RCAD0179-1 was grouped in CTn<italic>DOT/ERL</italic> family; however, ICE<italic>Ran</italic>RCAD0133-1, which had no significant similarity with known ICEs, might be classified into a novel ICE family. The sequences of ICE<italic>Ran</italic>RCAD0133-1 and ICE<italic>Ran</italic>RCAD0179-1 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 ICE<italic>Ran</italic>RCAD0179-1 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 CTn<italic>DOT</italic>/<italic>ERL</italic> family ancestor. Collectively, this study is the first identification and characterization of ICEs in <italic>R. anatipestifer</italic>; and provides new insights into the genetic diversity, evolution, adaptation, antimicrobial resistance, and virulence of <italic>R. anatipestifer</italic>.</p>