{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T15:31:29Z","timestamp":1773243089637,"version":"3.50.1"},"reference-count":51,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2023,1,23]],"date-time":"2023-01-23T00:00:00Z","timestamp":1674432000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Pork CRC","award":["2A-117"],"award-info":[{"award-number":["2A-117"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Erysipelothrix rhusiopathiae is a bacterial pathogen that is the causative agent of erysipelas in a variety of animals, including swine, emus, turkeys, muskox, caribou, moose, and humans. This study aims to investigate the population structure and genomic features of Australian isolates of E. rhusiopathiae in the Australian pig industry and compare them to the broader scope of isolates worldwide. A total of 178 isolates (154 Australian, seven vaccine isolates, six international isolates, and 11 of unknown origin) in this study were screened against an MLST scheme and publicly available reference isolates, identifying 59 new alleles, with isolates separating into two main single locus variant groups. Investigation with BLASTn revealed the presence of the spaA gene in 171 (96%) of the isolates, with three main groups of SpaA protein sequences observed amongst the isolates. Novel SpaA protein sequences, categorised here as group 3 sequences, consisted of two sequence types forming separate clades to groups 1 and 2, with amino acid variants at positions 195 (D\/A), 303 (G\/E) and 323(P\/L). In addition to the newly identified groups, five new variant positions were identified, 124 (S\/N), 307 (Q\/R), 323 (P\/L), 379 (M\/I), and 400 (V\/I). Resistance screening identified genes related to lincomycin, streptomycin, erythromycin, and tetracycline resistance. Of the 29 isolates carrying these resistance genes, 82% belonged to SpaA group 2-N101S (n = 22) or 2-N101S-I257L (n = 2). In addition, 79% (n = 23) of these 29 isolates belonged to MLST group ST 5. Our results illustrate that Australia appears to have a unique diversity of E. rhusiopathiae isolates in pig production industries within the wider global context of isolates.<\/jats:p>","DOI":"10.3390\/microorganisms11020297","type":"journal-article","created":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T01:29:45Z","timestamp":1674523785000},"page":"297","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Population Structure and Genomic Characteristics of Australian Erysipelothrix rhusiopathiae Reveals Unobserved Diversity in the Australian Pig Industry"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0441-6620","authenticated-orcid":false,"given":"John","family":"Webster","sequence":"first","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute PMB 4008, Narellan, NSW 2570, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bethany","family":"Bowring","sequence":"additional","affiliation":[{"name":"Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, Westmead, NSW 2145, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leah","family":"Stroud","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Infectious Diseases, Sydney South West Pathology Service, Liverpool, NSW 2170, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Marsh","sequence":"additional","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute PMB 4008, Narellan, NSW 2570, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Narelle","family":"Sales","sequence":"additional","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute PMB 4008, Narellan, NSW 2570, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7013-7326","authenticated-orcid":false,"given":"Daniel","family":"Bogema","sequence":"additional","affiliation":[{"name":"NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute PMB 4008, Narellan, NSW 2570, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,1,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.3389\/fmicb.2016.01759","article-title":"Bacterial Genomics Reveal the Complex Epidemiology of an Emerging Pathogen in Arctic and Boreal Ungulates","volume":"7","author":"Forde","year":"2016","journal-title":"Front. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.vetmic.2008.12.016","article-title":"Characterization of Erysipelothrix rhusiopathiae isolates from poultry, pigs, emus, the poultry red mite and other animals","volume":"137","author":"Eriksson","year":"2009","journal-title":"Vet. Microbiol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1007\/BF02227897","article-title":"Experimentelle, morphologische und klinische Studie \u00fcber die krankheitserregenden Mikroorganismen des Schweinerotlaufs, des Erysipeloids und der M\u00e4usesepsis","volume":"63","author":"Rosenbach","year":"1909","journal-title":"Z. Hyg. Infekt."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"418","DOI":"10.3389\/fmicb.2020.00418","article-title":"Genomic and immunogenic protein diversity of Erysipelothrix rhusiopathiae isolated from pigs in Great Britain: Implications for vaccine protection","volume":"11","author":"Forde","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2959","DOI":"10.1128\/JB.01500-10","article-title":"The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of Firmicutes and the organism\u2019s intracellular adaptations","volume":"193","author":"Ogawa","year":"2011","journal-title":"J. Bacteriol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"174","DOI":"10.3389\/fvets.2020.00174","article-title":"Erysipelothrix spp.: Past, present, and future directions in vaccine research","volume":"7","author":"Opriessnig","year":"2020","journal-title":"Front. Vet. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Yang, L., Zhu, Y., Peng, Z., Ding, Y., Jie, K., Wang, Z., Peng, Y., Tang, X., Wang, X., and Chen, H. (2020). Comparative Genome Analysis of a Pathogenic Erysipelothrix rhusiopathiae Isolate WH13013 from Pig Reveals Potential Genes Involve in Bacterial Adaptions and Pathogenesis. Vet. Sci., 7.","DOI":"10.3390\/vetsci7020074"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Kwok, A.H., Li, Y., Jiang, J., Jiang, P., and Leung, F.C. (2014). Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas\u2013Erysipelothrix rhusiopathiae SY1027. BMC Microbiol., 14.","DOI":"10.1186\/1471-2180-14-176"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e00130-17","DOI":"10.1128\/AEM.00130-17","article-title":"Clonal lineages of Erysipelothrix rhusiopathiae responsible for acute swine erysipelas in Japan identified by using genome-wide single-nucleotide polymorphism analysis","volume":"83","author":"Ogawa","year":"2017","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1128\/CVI.00206-10","article-title":"Characterization of Erysipelothrix species isolates from clinically affected pigs, environmental samples, and vaccine strains from six recent swine erysipelas outbreaks in the United States","volume":"17","author":"Bender","year":"2010","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1080\/03079457.2010.518313","article-title":"Characterization of Erysipelothrix rhusiopathiae isolates from laying hens and poultry red mites (Dermanyssus gallinae) from an outbreak of erysipelas","volume":"39","author":"Eriksson","year":"2010","journal-title":"Avian Pathol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1136\/vr.104421","article-title":"Erysipelothrix rhusiopathiae serotype 15 associated with recurring pig erysipelas outbreaks","volume":"182","author":"Gerber","year":"2018","journal-title":"Vet. Rec."},{"key":"ref_13","first-page":"560","article-title":"Erysipelothrix rhusiopathiae associated with recent widespread muskox mortalities in the Canadian Arctic","volume":"56","author":"Kutz","year":"2015","journal-title":"Can. Vet. J."},{"key":"ref_14","first-page":"101","article-title":"Erysipelothrix insidiosa recovered from sylvatic mammals in northwestern Canada during examinations for rabies and anthrax","volume":"18","author":"Langford","year":"1977","journal-title":"Can. Vet. J."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1046\/j.1439-0531.2002.00339.x","article-title":"Case study: Chronic erysipelas of the sow\u2013a subclinical manifestation of reproductive problems","volume":"37","author":"Hoffmann","year":"2002","journal-title":"Reprod. Domest. Anim."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.vetmic.2006.02.015","article-title":"Characterisation of Erysipelothrix rhusiopathiae isolates from pigs associated with vaccine breakdowns","volume":"115","author":"Eamens","year":"2006","journal-title":"Vet. Microbiol."},{"key":"ref_17","first-page":"239","article-title":"Cross protection of mice and swine inoculated with culture filtrate of attenuated Erysipelothrix rhusiopathiae and challenge exposed to strains of various serovars","volume":"48","author":"Sawada","year":"1987","journal-title":"Am. J. Vet. Res."},{"key":"ref_18","first-page":"1646","article-title":"Immunological characterization of a protective antigen of Erysipelothrix rhusiopathiae: Identification of the region responsible for protective immunity","volume":"67","author":"Shimoji","year":"1999","journal-title":"Infection"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1006\/mpat.1998.0216","article-title":"Properties of repeat domain found in a novel protective antigen, SpaA, of Erysipelothrix rhusiopathiae","volume":"25","author":"Makino","year":"1998","journal-title":"Microb. Pathog."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1186\/s13567-015-0216-x","article-title":"A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals","volume":"46","author":"Voss","year":"2015","journal-title":"Vet. Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"949","DOI":"10.1292\/jvms.11-0533","article-title":"Characterization of Erysipelothrix rhusiopathiae strains isolated from recent swine erysipelas outbreaks in Japan","volume":"74","author":"To","year":"2012","journal-title":"J. Vet. Med. Sci."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2490","DOI":"10.1016\/j.vaccine.2010.01.041","article-title":"Erysipelothrix rhusiopathiae: Association of Spa-type with serotype and role in protective immunity","volume":"28","author":"Ingebritson","year":"2010","journal-title":"Vaccine"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1007\/s13205-020-02451-7","article-title":"Draft genome sequence data and comparative analysis of Erysipelothrix rhusiopathiae vaccine strain VR-2","volume":"10","author":"Kovalchuk","year":"2020","journal-title":"3 Biotech"},{"key":"ref_24","unstructured":"Bell, S.M., Gatus, B.J., Pham, J.N., and Rafferty, D.L. (1999). Antibiotic Susceptibility Testing by the CDS Method: A Concise Laboratory Manual, South Eastern Area Laboratory Services."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1089\/cmb.2012.0021","article-title":"SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing","volume":"19","author":"Bankevich","year":"2012","journal-title":"J. Comput. Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: Ultrafast metagenomic sequence classification using exact alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1093\/bioinformatics\/btt086","article-title":"QUAST: Quality assessment tool for genome assemblies","volume":"29","author":"Gurevich","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1287","DOI":"10.12688\/f1000research.12232.1","article-title":"BlobTools: Interrogation of genome assemblies","volume":"6","author":"Laetsch","year":"2017","journal-title":"F1000Research"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/pro.3290","article-title":"Clustal Omega for making accurate alignments of many protein sequences","volume":"27","author":"Sievers","year":"2018","journal-title":"Protein Sci."},{"key":"ref_30","first-page":"e000131","article-title":"ARIBA: Rapid antimicrobial resistance genotyping directly from sequencing reads","volume":"3","author":"Hunt","year":"2017","journal-title":"Microb. Genom."},{"key":"ref_31","unstructured":"Bushnell, B. (2022, January 12). BBTools Software Package. Available online: https:\/\/sourceforge.net\/projects\/bbmap."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2640","DOI":"10.1093\/jac\/dks261","article-title":"Identification of acquired antimicrobial resistance genes","volume":"67","author":"Zankari","year":"2012","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_33","unstructured":"Seeman, T. (2021, April 06). ABRicate. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_34","unstructured":"Seeman, T. (2020, February 24). mlst. Available online: https:\/\/github.com\/tseemann\/mlst."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"W246","DOI":"10.1093\/nar\/gkw359","article-title":"PHYLOViZ Online: Web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees","volume":"44","author":"Vaz","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_36","unstructured":"Webster, J., and Bogema, D. (2022, February 23). Core_gene_phylo, v1.0.0. Github. Available online: https:\/\/github.com\/Jwebster89\/Core_gene_phylo."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s13059-020-02090-4","article-title":"Producing polished prokaryotic pangenomes with the Panaroo pipeline","volume":"21","author":"MacAlasdair","year":"2020","journal-title":"Genome Biol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Didelot, X., and Wilson, D.J. (2015). ClonalFrameML: Efficient inference of recombination in whole bacterial genomes. PLoS Comput. Biol., 11.","DOI":"10.1371\/journal.pcbi.1004041"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Mai, U., Sayyari, E., and Mirarab, S. (2017). Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0182238"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/s41592-018-0293-7","article-title":"Inferring bacterial recombination rates from large-scale sequencing datasets","volume":"16","author":"Lin","year":"2019","journal-title":"Nat. Methods"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1292\/jvms.16-0164","article-title":"Pathogenic characterization of Erysipelothrix rhusiopathiae Met-203 type SpaA strains from chronic and subacute swine erysipelas in Japan","volume":"79","author":"Uchiyama","year":"2017","journal-title":"J. Vet. Med. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1128\/CVI.00099-07","article-title":"Genetic and antigenic diversity of the surface protective antigen proteins of Erysipelothrix rhusiopathiae","volume":"14","author":"To","year":"2007","journal-title":"Clin. Vaccine Immunol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"7670505","DOI":"10.1155\/2018\/7670505","article-title":"Microcrystalline cellulose for delivery of recombinant protein-based antigen against erysipelas in mice","volume":"2018","author":"Jeon","year":"2018","journal-title":"BioMed Res. Int."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"4333","DOI":"10.1128\/IAI.00549-13","article-title":"Characterization and identification of a novel candidate vaccine protein through systematic analysis of extracellular proteins of Erysipelothrix rhusiopathiae","volume":"81","author":"Shi","year":"2013","journal-title":"Infect. Immun."},{"key":"ref_46","first-page":"mgen000412","article-title":"Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics","volume":"6","author":"Formenti","year":"2020","journal-title":"Microb. Genom."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"3383","DOI":"10.1038\/s41598-021-82959-x","article-title":"Comparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species","volume":"11","author":"Grazziotin","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Smith, J.T., Eckhardt, E.M., Hansel, N.B., Eliato, T.R., Martin, I.W., and Andam, C.P. (2021). Genomic epidemiology of methicillin-resistant and-susceptible Staphylococcus aureus from bloodstream infections. BMC Infect. Dis., 21.","DOI":"10.1186\/s12879-021-06293-3"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"e00515-19","DOI":"10.1128\/mSystems.00515-19","article-title":"Distinct but intertwined evolutionary histories of multiple Salmonella enterica subspecies","volume":"5","author":"Park","year":"2020","journal-title":"Msystems"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1111\/j.1751-0813.2011.00822.x","article-title":"Quarantine, exports and animal disease in Australia 1901\u20132010","volume":"89","author":"Turner","year":"2011","journal-title":"Aust. Vet. J."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1128\/AAC.25.3.385","article-title":"Antibiotic resistance of Erysipelothrix rhusiopathiae isolated from pigs with chronic swine erysipelas","volume":"25","author":"Takahashi","year":"1984","journal-title":"Antimicrob. Agents Chemother."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/2\/297\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:14:10Z","timestamp":1760120050000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/11\/2\/297"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,1,23]]},"references-count":51,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2023,2]]}},"alternative-id":["microorganisms11020297"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms11020297","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,1,23]]}}}