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

Abstract

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

Molecular characterization of Glaesserella parasuis strains circulating in North American swine production systems

“…Phylogenetic analysis revealed three primary lineages, LI, LII and LIII. This is in contrast with a recently published study from China [ 23 ] that showed G. parasuis isolates clustering into two main primary lineages comprised of STs not found in the present study, highlighting the high genetic variation found within the species.…”

“…Among the genes, bcr (bicyclomycin resistance ) , ksgA (kasugamycin resistance), bacA (bacitracin resistance ) , sul2 (sulfonamide resistance, and aph (3’’)-Ib (streptomycin resistance) were detected in almost 100% of the isolates. Consistent with this study, bcr , ksgA , and bacA genes were highly prevalent in G. parasuis isolates in a recent study [ 23 ]. Some of these highly prevalent genes encode resistance to antibiotics not commonly used in swine production.…”

“…In this study, WGS was performed on 218 G. parasuis isolates predominantly from North America. The size and GC content were within range with other published G. Parasuis genomes [ 23 ]. Phylogenetic analysis revealed three primary lineages, LI, LII and LIII.…”

Identification of Glaesserella parasuis and Differentiation of Its 15 Serovars Using High-Resolution Melting Assays

“…There is a broad genetic variability within the G. parasuis species mediated through plasmids and/or transposons [ 22 ]. A phylogenic analysis reported the existence of two main lineages, namely, lineages I and II, revealing an association with serovars, countries, and multilocus sequence types.…”

“…A G. parasuis strain from Switzerland was identified to be part of lineage I, which mainly comprises serovars 5, 12, and 14. Lineage II predominantly includes serovars 2 and 10 [ 22 ]. Recently published studies about the distribution of G. parasuis in North America, Europe, and Asia found that the geographic prevalence of molecular serovars varied slightly among different countries; however, due to the variable sizes of the examined samples, no differences in serovar prevalence could be determined [ 23 ].…”