Complete Genome Analysis of a Haemophilus parasuis Serovar 12 Strain from China

Abstract

Haemophilus parasuis is the etiological agent of Glässer's disease in pigs and 15 standard serovars were identified. The widespread disease causes great economic loss in the swine industry worldwide. Aiming to investigate the differences in genome composition and functions among various strains, a highly virulent strain ZJ0906 of H. parasuis serovar 12 from China was analyzed and compared with serovar 5 SH0165. Strain ZJ0906 genome is 2,324,740 base pairs with 40.06% genomic GC content. It contains 2,484 open reading frames (ORF) predicted by Glimmer 3.02, of which 2,352 (∼94.7%) were annotated by NCBI nr blast, 1,745 by COG database and 1,829 by KEGG database. 109 potential virulence factors were annotated in strain ZJ0906 and 3 of which are potentially related to antibiotic resistance. Strain ZJ0906 genome is ∼55 kilobases longer than SH0165 genome, with an extra 211 predicted ORFs. VFDB, ARDB, and PAIDB blast searches showed that ZJ0906 and SH0165 shared a nearly identical panel of potential virulence factors, drug resistant genes and four PAI-like regions which showed high homology to Enterococcus, Escherichia and Salmonella. Synteny analysis showed that gene rearrangements are frequent between the two strains, which may lead to variations in pathogenicity and cross-protection among serovars. KEGG pathway analyses showed strain ZJ0906 shared similar metabolic pathways to strain SH0165. Molecular identification of these genomic elements and potential virulence factors pave the way to the better understanding of mechanisms underlying metabolic capabilities and pathogenicity of H. parasuis and prospective vaccine targets besides the widely used method of inactivated bacteria.

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis

“…The 212 isolates in the collection originate from the UK (n = 121 from 70 geographically dispersed farms), Argentina (n = 1), Belgium (n = 1), China (n = 2), Denmark (n = 29), Germany (n = 6), Greece (n = 1), Italy (n = 2), Japan (n = 7), Spain (n = 21), Sweden (n = 4), Switzerland (n = 2) and the USA (n = 6), with nine isolates of unknown origin. Our analysis included the reference strains of the 15 serovars and the published genomes of the US strain 29755, and the Chinese strains SH0165 and ZJ0906 [ 40 , 41 , 60 ]. The dates of collection ranged between 1991–2008 for European isolates and 1955–1992 for the reference strains [ 61 ].…”

“…The table describing the isolate collection and metadata (including accession numbers for the isolates) can be found in Additional file 1 : Table S1. This collection includes the reference strains currently used in the serotyping scheme and three published genomes of 29755, SH0165 and ZJ0906 in the analyses [ 40 , 41 , 60 ]. There are currently multiple isolates used as reference strains for the same serovar in different serotyping laboratories, and so we have sequenced 27 reference strains from three different laboratories [ 61 ].…”

Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

“…Recently, wholegenome sequencing (WGS) has emerged as a powerful tool for predicting antibiotic resistance and pathogenic potential in G. parasuis. For instance, Li et al (2013) reported two G. parasuis strains with potential resistance towards the antibiotics ciprofloxacin, trimethoprim, and penicillin, based on the presence of associated resistance genes; Nicholson et al (2018) reported genomic differences in the toxin-antitoxin systems between phenotypically distinct G. parasuis strains from Japan and Sweden; and Bello-Orti et al (2014) noted the role of mobile genetic elements and strain-specific accessory genes in fostering high genomic diversity between pathogenic strains of the same serovar from diseased pigs in Japan, China, and the USA.…”

Peer Review #1 of "Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants (v0.2)"

“…parasuis. For instance, Li et al (2013) reported two G. parasuis strains with potential resistance towards the antibiotics ciprofloxacin, trimethoprim, and penicillin, based on the presence of associated resistance genes; Nicholson et al (2018) reported genomic differences in the toxinantitoxin systems between phenotypically distinct G. parasuis strains from Japan and Sweden;…”