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Haemophilus parasuis  is an economically important bacterial pathogen of swine. Extensive genetic and phenotypic heterogeneity among  H. parasuis  strains have been observed, which hinders the deciphering of the population structure and its association with clinical virulence. In this study, two highly divergent clades were defined according to iron–sulphur cluster regulator ( iscR )-based phylogeny analysis of 148 isolates. Clear separation of serovars and potential virulence markers (PVMs) were observed between the two clades, which are indicative of independent evolution of the two lineages. Previously suggested virulence factors showed no correlation with clinical virulence, and were probably clade or serovar specific genes emerged during different stage of evolution. PVMs profiles varied widely among isolates in the same serovar. Higher strain diversity in respect of PVMs was found for isolates from multi-strain infected farms than those from single strain infected ones, which indicates that multi-strain infection in one farm may increase the frequency of gene transfer in  H. parasuis . Systemic isolates were more frequently found in serovar 13 and serovar 12, while no correlation between clinical virulence and  iscR -based phylogeny was observed. It shows that  iscR  is a reliable marker for studying population structure of  H. parasuis , while other factors should be included to avoid the interference of gene exchange of  iscR  between isolates. The two lineages of  H. parasuis  may have undergone independent evolution, but show no difference in clinical virulence. Wide distribution of systemic isolates across the entire population poses new challenge for development of vaccine with better cross-protection. Our study provides new information for better deciphering the population structure of  H. parasuis , which helps understanding the extreme diversity within this pathogenic bacterium.

Association betweeniscR-based phylogeny, serovars and potential virulence markers ofHaemophilus parasuis