Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates

Authors: Nicholson, Tracy; Brunelle, Brian; Bayles, Darrell; Alt, David; Shore, Sarah

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2018
Publication Date: 11/1/2018
Citation: Nicholson, T.L., Brunelle, B.W., Bayles, D.O., Alt, D.P., Shore, S. 2018. Comparative genomic and methylome analysis of non-virulent D74 and virulent Nagasaki Haemophilus parasuis isolates. PLoS One. 13(11):e0205700. https://doi.org/10.1371/journal.pone.0205700.
DOI: https://doi.org/10.1371/journal.pone.0205700

Interpretive Summary: Haemophilus parasuis is a respiratory pathogen of swine and the etiological agent of Glässer's disease, causing significant economic losses to the swine industry worldwide. H. parasuis isolates can cause a range of illnesses from lethal systemic disease to subclinical carriage. This study reports the polished or closed whole-genome sequence annotation and genome-wide methylation patterns for a highly virulent H. parasuis strain known to cause lethal systemic disease, Nagasaki, and for a non-virulent H. parasuis strain known to contribute to subclinical carriage, D74. This study identifies many regions of difference between the genome sequences of the two strains that likely contribute to diseases outcomes. This information can be directly used to design improved vaccines and therapeutic interventions to eradicate H. parasuis from swine herds that do not rely on antimicrobial use.

Technical Abstract: Haemophilus parasuis is a respiratory pathogen of swine and the etiological agent of Glässer's disease. H. parasuis isolates can exhibit different virulence capabilities ranging from lethal systemic disease to subclinical carriage. To identify genomic differences between phenotypically distinct strains, we obtained the closed whole-genome sequence annotation and genome-wide methylation patterns for the highly virulent Nagasaki strain and for the non-virulent D74 strain. Evaluation of the virulence-associated genes contained within the genomes of D74 and Nagasaki led to the discovery of a large number of toxin-antitoxin (TA) systems within both genomes. Five predicted hemolysins were identified as unique to Nagasaki and seven putative contact-dependent growth inhibition toxin proteins were identified only in strain D74. Assessment of all potential vtaA genes revealed thirteen present in the Nagasaki genome and three in the D74 genome. Subsequent evaluation of the predicted protein structure revealed that none of the D74 VtaA proteins contain a collagen triple helix repeat domain and a much larger predicted amino acid size for two D74 VtaA protein compared to any predicted Nagasaki VtaA protein. Fifteen methylation sequence motifs were identified in D74 and fourteen methylation sequence motifs were identified in Nagasaki using SMRT sequencing analysis. Only one of the methylation sequence motifs were observed in both strains indicating an expected degree of diversity between D74 and Nagasaki. Subsequent analysis also revealed diversity in the restriction-modification systems harbored by D74 and Nagasaki. The collective information reported in this study will aid in the development of vaccines and intervention strategies to decrease the prevalence and disease burden caused by H. parasuis.