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Front. Microbiol. | doi: 10.3389/fmicb.2019.01184

Novel Yersinia enterocolitica prophages and a comparative analysis of genomic diversity

Junrong Liang1,  Xin Wang2*, Zengqiang Kou3, Shuai Qin1, Yuhuang Chen4,  Zhenpeng Li1, Chuchu Li1, 5,  Duan Ran1, Huijing Hao6, Tao Zha7,  Wenpeng Gu8,  Yuanming Huang1, Meng Xiao1 and  Huaiqi Jing1
  • 1Chinese Center For Disease Control and Prevention, China
  • 2Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention (China CDC), China
  • 3Shandong Center for Disease Control and Prevention, China
  • 4Nansha Maternity and Child Health Care Hospital, China
  • 5Jiangsu University, China
  • 6Women and Children's Department of Shunyi Hospital, China
  • 7Wuhan Centre for Disease Prevention and Control, China
  • 8Yunnan Provincial Center for Disease Control and Prevention, China

Yersinia enterocolitica is a major agent of foodborne diseases worldwide. Prophage plays an important role in the genetic evolution of the bacterial genome. Little is known about the genetic information about prophages in the genome of Y. enterocolitica, and no pathogenic Y. enterocolitica prophages have been described. In this study, we induced and described the genomes of six prophages from pathogenic Y. enterocolitica for the first time. Phylogenetic analysis based on whole genome sequencing revealed that these novel Yersinia phages are genetically distinct from the previously reported phages, showing considerable genetic diversity. Interestingly, the prophages induced from O:3 and O:9 Y. enterocolitica showed different genomic sequences and morphology but highly conserved among the same serotype strains, which classified into two diverse clusters. The three long-tailed Myoviridae prophages induced from serotype O:3 Y. enterocolitica were highly conserved, shared ≥ 99.99% identity and forming genotypic cluster A; the three Podoviridae prophages induced from the serotype O:9 strains formed cluster B, also shared more than 99.90% identity with one another. Cluster A was most closely related to O:5 non-pathogenic Y. enterocolitica prophage PY54 (61.72% identity). The genetic polymorphism of these two kinds of prophages and highly conserved among the same serotype strains, suggested a possible shared evolutionary past for these phages: originated from distinct ancestors and entered pathogenic Y. enterocolitica as extrachromosomal genetic components during evolution when facing selective pressure. These results are critically important for further our understanding of phage roles in host physiology and the pathology of disease.

Keywords: Yersinia enterocolitica, Phage (bacteriophage), Podoviridae, Myoviridae prophage, Comparative genomic analyses

Received: 06 Feb 2019; Accepted: 09 May 2019.

Edited by:

Feng Gao, Tianjin University, China

Reviewed by:

Jens A. Hammerl, Federal Institute for Risk Assessment (BfR), Germany
Sherwood R. Casjens, The University of Utah, United States  

Copyright: © 2019 Liang, Wang, Kou, Qin, Chen, Li, Li, Ran, Hao, Zha, Gu, Huang, Xiao and Jing. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Xin Wang, National Institute for Communicable Disease Control and Prevention (China CDC), Chinese Center for Disease Control and Prevention, Beijing, China, wangxin@icdc.cn