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Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands

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Abstract

Riemerella anatipestifer is a gram-negative bacterium that leads to severe contagious septicemia in ducks, turkeys, chickens, and wild waterfowl. Here, a pan-genome with 32 R. anatipestifer genomes is re-established, and the mathematical model is calculated to evaluate the expansion of R. anatipestifer genomes, which were determined to be open. Average nucleotide identity (ANI) and phylogenetic analysis preliminarily clarify intraspecies variation and distance. Comparative genomic analysis of R. anatipestifer found that horizontal gene transfer events, which provide an expressway for the recruitment of novel functionalities and facilitate genetic diversity in microbial genomes, play a key role in the process of acquiring and transmitting antibiotic-resistance genes in R. anatipestifer. Furthermore, a new antibiotic-resistance gene cluster was identified in the same loci in 14 genomes. The uneven distribution of virulence factors was also confirmed by our results. Our study suggests that the ability to acquire foreign genes (such as antibiotic-resistance genes) increases the adaptability of R. anatipestifer, and the virulence genes with little mobility are highly conserved in R. anatipestifer.

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Acknowledgments

This work was supported by the National Key Research and Development Program of China [Grant No. 2017YFD050080]; China Agricultural Research System [Grant No. CARS-42-17]; International S&T Cooperation Program of Sichuan Province [Grant No. 2017HH0026]; Science and Technology Innovation Program of Guizhou Academy of Agricultural Science [Grant No. (2017)03]

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  1. Dekang Zhu and Zhishuang Yang contributed equally to this work.

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  1. Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China

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

  2. Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, Sichuan, China

    Dekang Zhu, Zhishuang Yang, Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Xiaoyue Chen & Anchun Cheng

  3. Guizhou Animal Husbandry and Veterinary Research Institute, Guiyang, Guizhou, China

    Jinge Xu

  4. Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China

    Mingshu Wang, Renyong Jia, Shun Chen, Mafeng Liu, Xinxin Zhao, Qiao Yang, Ying Wu, Shaqiu Zhang, Yunya Liu, Ling Zhang, Yanling Yu & Anchun Cheng

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Zhu, D., Yang, Z., Xu, J. et al. Pan-genome analysis of Riemerella anatipestifer reveals its genomic diversity and acquired antibiotic resistance associated with genomic islands. Funct Integr Genomics 20, 307–320 (2020). https://doi.org/10.1007/s10142-019-00715-x

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