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

Xiulin Wan; Xinhui Li; Todd Osmundson; Chunling Li; He Yan

doi:10.7717/peerj.9293

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

PeerJ. 2020 Jun 22:8:e9293. doi: 10.7717/peerj.9293. eCollection 2020.

Authors

Xiulin Wan¹, Xinhui Li², Todd Osmundson³, Chunling Li⁴, He Yan¹

Affiliations

¹ School of Food Science and Engineering, South China University of Technology, Guangzhou, China.
² Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, United States of America.
³ Department of Biology, University of Wisconsin-La Crosse, La Crosse, United States of America.
⁴ Institute of Animal Health Guangdong Academy of Agricultural Sciences, Guangzhou, China.

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 bla _ROB-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.

Keywords: Antibiotic resistance genes; Glaesserella parasuis; Mobile genetic elements; Phylogeny; Whole-genome sequencing.

Grants and funding

This work was supported by the National Key Basic Research Program (Grant No. 2016YFD0500606), the Natural Science Foundation of China (Grant No. 31772776), Key-Area Research and Development Program of Guangdong Province (Grant No. 2019B020217002). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.