{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T06:41:37Z","timestamp":1776321697173,"version":"3.50.1"},"reference-count":74,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T00:00:00Z","timestamp":1713916800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Goose erysipelas is a serious problem in waterfowl breeding in Poland. However, knowledge of the characteristics of Erysipelothrix rhusiopathiae strains causing this disease is limited. In this study, the antimicrobial susceptibility and serotypes of four E. rhusiopathiae strains from domestic geese were determined, and their whole-genome sequences (WGSs) were analyzed to detect resistance genes, integrative and conjugative elements (ICEs), and prophage DNA. Sequence type and the presence of resistance genes and transposons were compared with 363 publicly available E. rhusiopathiae strains, as well as 13 strains of other Erysipelothrix species. Four strains tested represented serotypes 2 and 5 and the MLST groups ST 4, 32, 242, and 243. Their assembled circular genomes ranged from 1.8 to 1.9 kb with a GC content of 36\u201337%; a small plasmid was detected in strain 1023. Strains 1023 and 267 were multidrug-resistant. The resistance genes detected in the genome of strain 1023 were erm47, tetM, and lsaE-lnuB-ant(6)-Ia-spw cluster, while strain 267 contained the tetM and ermB genes. Mutations in the gyrA gene were detected in both strains. The tetM gene was embedded in a Tn916-like transposon, which in strain 1023, together with the other resistance genes, was located on a large integrative and conjugative-like element of 130 kb designated as ICEEr1023. A minor integrative element of 74 kb was identified in strain 1012 (ICEEr1012). This work contributes to knowledge about the characteristics of E. rhusiopathiae bacteria and, for the first time, reveals the occurrence of erm47 and ermB resistance genes in strains of this species. Phage infection appears to be responsible for the introduction of the ermB gene into the genome of strain 267, while ICEs most likely play a key role in the spread of the other resistance genes identified in E. rhusiopathiae.<\/jats:p>","DOI":"10.3390\/ijms25094638","type":"journal-article","created":{"date-parts":[[2024,4,24]],"date-time":"2024-04-24T10:18:36Z","timestamp":1713953916000},"page":"4638","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Integrative and Conjugative Elements and Prophage DNA as Carriers of Resistance Genes in Erysipelothrix rhusiopathiae Strains from Domestic Geese in Poland"],"prefix":"10.3390","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5456-9652","authenticated-orcid":false,"given":"Marta","family":"Dec","sequence":"first","affiliation":[{"name":"Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0758-5190","authenticated-orcid":false,"given":"Aldert","family":"Zomer","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases and Immunology, Faculty of Veterinaty Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands"},{"name":"WOAH Reference Laboratory for Campylobacteriosis, WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective, 3584 CL Utrecht, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0441-6620","authenticated-orcid":false,"given":"John","family":"Webster","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":"Tomasz","family":"Nowak","sequence":"additional","affiliation":[{"name":"Diagnostic Veterinary Laboratory \u201cVet-Lab Brudzew Dr. Piotr Kwieci\u0144ski\u201d, 62-720 Brudzew, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5238-1007","authenticated-orcid":false,"given":"Dagmara","family":"St\u0119pie\u0144-Py\u015bniak","sequence":"additional","affiliation":[{"name":"Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8245-1646","authenticated-orcid":false,"given":"Renata","family":"Urban-Chmiel","sequence":"additional","affiliation":[{"name":"Department of Veterinary Prevention and Avian Diseases, University of Life Sciences in Lublin, 20-033 Lublin, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2024,4,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Zautner, A.E., Tersteegen, A., Schiffner, C.J., \u00d0ilas, M., Marquardt, P., Riediger, M., Delker, A.M., M\u00e4de, D., and Kaasch, A.J. (2022). Human Erysipelothrix rhusiopathiae infection via bath water\u2014Case report and genome announcement. Front. Cell Infect. Microbiol., 12.","DOI":"10.3389\/fcimb.2022.981477"},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Dec, M., \u0141agowski, D., Nowak, T., Pietras-O\u017cga, D., and Herman, K. (2023). Serotypes, Antibiotic Susceptibility, Genotypic Virulence Profiles and SpaA Variants of Erysipelothrix rhusiopathiae Strains Isolated from Pigs in Poland. Pathogens, 12.","DOI":"10.3390\/pathogens12030409"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Whitman, W.B. (2015). Bergey\u2019s Manual of Systematics of Archaea and Bacteria, Bergey\u2019s Manual Trust. [1st ed.].","DOI":"10.1002\/9781118960608"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"835","DOI":"10.3201\/eid2904.221698","article-title":"Harbor Porpoise Deaths Associated with Erysipelothrix rhusiopathiae, the Netherlands, 2021","volume":"29","author":"IJsseldijk","year":"2023","journal-title":"Emerg. Infect. Dis."},{"key":"ref_5","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_6","first-page":"1833","article-title":"Serotypes of Erysipelothrix rhusiopathiae isolated from swine and from soil and manure of swine pens in the United States","volume":"39","author":"Wood","year":"1978","journal-title":"Am. J. Vet. Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"e69","DOI":"10.1038\/emi.2015.69","article-title":"Virulence determinants, antimicrobial susceptibility, and molecular profiles of Erysipelothrix rhusiopathiae strains isolated from China","volume":"4","author":"Ding","year":"2015","journal-title":"Emerg. Microbes Infect."},{"key":"ref_8","first-page":"100","article-title":"Swine Erysipelas: It\u2019s Epidemiology, Diagnosis, Treatment, Control, Preventive Measures and Comprehensive Review","volume":"12","author":"Dessalew","year":"2021","journal-title":"J. Vet. Sci. Technol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e240073","DOI":"10.1136\/bcr-2020-240073","article-title":"Erysipelothrix rhusiopathiae infection by geese to human transmission","volume":"14","author":"Meier","year":"2021","journal-title":"BMJ Case Rep."},{"key":"ref_10","first-page":"372","article-title":"An outbreak of erysipelas in commercial geese","volume":"36","author":"Bobrek","year":"2016","journal-title":"Pak. Vet. J."},{"key":"ref_11","unstructured":"Pattison, M., McMullin, P.F., Bradbury, J.M., Alexander, D.J., and Wieliczko, A. (2011). Choroby Drobiu, Edra Urban & Partner. [1st ed.]. (In Polish)."},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Bobrek, K., and Gawe\u0142, A. (2023). Antimicrobial Resistance of Erysipelothrix rhusiopathiae Strains Isolated from Geese to Antimicrobials Widely Used in Veterinary Medicine. Antibiotics, 12.","DOI":"10.3390\/antibiotics12081339"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Wu, C., Lv, C., Zhao, Y., Zhu, W., Liu, L., Wang, T., Kang, C., Yang, Y., Sun, X., and Zhang, Q. (2021). Characterization of Erysipelothrix Rhusiopathiae Isolates from Diseased Pigs in 15 Chinese Provinces from 2012 to 2018. Microorganisms, 9.","DOI":"10.3390\/microorganisms9122615"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.jgar.2020.02.017","article-title":"Genome sequence of multidrug-resistant Erysipelothrix rhusiopathiae ZJ carrying several acquired antimicrobial resistance genes","volume":"21","author":"Gu","year":"2020","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"ref_15","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_16","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_17","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1016\/j.gdata.2016.04.006","article-title":"Complete genome sequence of Erysipelothrix rhusiopathiae strain GXBY-1 isolated from acute swine erysipelas outbreaks in south China","volume":"8","author":"Tang","year":"2016","journal-title":"Genom. Data"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1292\/jvms.55.349","article-title":"Detection of plasmid DNA in Erysipelothrix rhusiopathiae isolated from pigs with chronic swine erysipelas","volume":"55","author":"Noguchi","year":"1993","journal-title":"J. Vet. Med. Sci."},{"key":"ref_19","first-page":"30","article-title":"Erysipelothrix rhusiopathiae: Plasmidy, usto\u012dchivost\u2019 k antibakterial\u2019nym preparatam [Erysipelothrix rhusiopathiae: Plasmids, resistance to antibacterial drugs]","volume":"41","author":"Pomerantsev","year":"1996","journal-title":"Antibiot. Khimioter."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2462","DOI":"10.1128\/AAC.00228-15","article-title":"First report of macrolide resistance gene erm(T) harbored by a novel small plasmid from Erysipelothrix rhusiopathiae","volume":"59","author":"Xu","year":"2015","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/j.diagmicrobio.2010.09.012","article-title":"Phenotypic and Molecular Characterization of Recent and Archived Erysipelothrix Spp. Isolated from Brazilian Swine","volume":"69","author":"Coutinho","year":"2011","journal-title":"Diagn. Microbiol. Infect. Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1128\/AAC.01126-07","article-title":"Lincomycin resistance gene lnu(D) in Streptococcus uberis","volume":"52","author":"Petinaki","year":"2008","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1292\/jvms.09-0448","article-title":"Antimicrobial susceptibility of Erysipelothrix rhusiopathiae isolated from pigs in Southern Japan with a modified agar dilution method","volume":"72","author":"Chuma","year":"2010","journal-title":"J. Vet. Med. Sci."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"54","DOI":"10.3390\/poultry2010007","article-title":"Antimicrobial Dilution Susceptibility Testing of Erysipelothrix rhusiopathiae According to CLSI Document VET06 Reveals High Resistance against Penicillin G, Erythromycin and Enrofloxacin","volume":"2","author":"Hess","year":"2023","journal-title":"Poultry"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"3046","DOI":"10.1093\/jac\/dkw290","article-title":"Novel chromosome-encoded erm(47) determinant responsible for constitutive MLSB resistance in Helcococcus kunzii","volume":"71","author":"Isnard","year":"2016","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.jbiotec.2014.09.011","article-title":"Complete genome sequence of Peptoniphilus sp. strain ING2-D1G isolated from a mesophilic lab-scale completely stirred tank reactor utilizing maize silage in co-digestion with pig and cattle manure for biomethanation","volume":"192","author":"Tomazetto","year":"2014","journal-title":"J. Biotechnol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Wang, S., Jiang, K., Du, X., Lu, Y., Liao, L., He, Z., and He, W. (2021). Translational Attenuation Mechanism of ErmB Induction by Erythromycin Is Dependent on Two Leader Peptides. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.690744"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Chen, L., Huang, J., Huang, X., He, Y., Sun, J., Dai, X., Wang, X., Shafiq, M., and Wang, L. (2021). Horizontal Transfer of Different erm(B)-Carrying Mobile Elements Among Streptococcus suis Strains with Different Serotypes. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.628740"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Urban-Chmiel, R., Marek, A., St\u0119pie\u0144-Py\u015bniak, D., Wieczorek, K., Dec, M., Nowaczek, A., and Osek, J. (2022). Antibiotic Resistance in Bacteria\u2014A Review. Antibiotics, 11.","DOI":"10.3390\/antibiotics11081079"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"102251","DOI":"10.1016\/j.anaerobe.2020.102251","article-title":"Phenotypic and genotypic antimicrobial resistance profiles of fecal lactobacilli from domesticated pigeons in Poland","volume":"65","author":"Dec","year":"2020","journal-title":"Anaerobe"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1006\/plas.1994.1077","article-title":"Nucleotide sequence of the 18-kb conjugative transposon Tn916 from Enterococcus faecalis","volume":"32","author":"Flannagan","year":"1994","journal-title":"Plasmid"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/femsle\/fnu050","article-title":"Complete genome sequence of BS49 and draft genome sequence of BS34A, Bacillus subtilis strains carrying Tn916","volume":"362","author":"Browne","year":"2015","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1016\/j.ijantimicag.2013.09.004","article-title":"Genetic analysis of Tn916-like elements conferring tetracycline resistance in clinical isolates of Clostridium difficile","volume":"43","author":"Dong","year":"2014","journal-title":"Int. J. Antimicrob. Agents."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"4185","DOI":"10.1038\/s41598-022-08097-0","article-title":"Genomic epidemiology of Streptococcus agalactiae ST283 in Southeast Asia","volume":"12","author":"Aiewsakun","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1093\/jac\/dkn255","article-title":"A novel transposon, Tn6009, composed of a Tn916 element linked with a Staphylococcus aureus mer operon","volume":"62","author":"Soge","year":"2008","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1111\/j.1574-6976.2011.00283.x","article-title":"Tn916-like genetic elements: A diverse group of modular mobile elements conferring antibiotic resistance","volume":"35","author":"Roberts","year":"2011","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1128\/jb.179.4.1117-1125.1997","article-title":"Specific DNA cleavage mediated by the integrase of conjugative transposon Tn916","volume":"179","author":"Taylor","year":"1997","journal-title":"J. Bacteriol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2147","DOI":"10.1128\/AEM.06193-11","article-title":"Behavior and target site selection of conjugative transposon Tn916 in two different strains of toxigenic Clostridium difficile","volume":"78","author":"Mullany","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Qin, X., Galloway-Pe\u00f1a, J.R., Sillanpaa, J., Roh, J.H., Nallapareddy, S.R., Chowdhury, S., Bourgogne, A., Choudhury, T., Muzny, D.M., and Buhay, C.J. (2012). Complete genome sequence of Enterococcus faecium strain TX16 and comparative genomic analysis of Enterococcus faecium genomes. BMC Microbiol., 12.","DOI":"10.1186\/1471-2180-12-135"},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Lin, I.H., Liu, T.T., Teng, Y.T., Wu, H.L., Liu, Y.M., Wu, K.M., Chang, C.H., and Hsu, M.T. (2011). Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: Genome plasticity, adaptation and virulence. PLoS ONE, 6.","DOI":"10.1371\/journal.pone.0020519"},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Raftis, E.J., Forde, B.M., Claesson, M.J., and O\u2019Toole, P.W. (2014). Unusual genome complexity in Lactobacillus salivarius JCM1046. BMC Genom., 15.","DOI":"10.1186\/1471-2164-15-771"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1146\/annurev-genet-112414-055018","article-title":"Integrative and Conjugative Elements (ICEs): What They Do and How They Work","volume":"49","author":"Johnson","year":"2015","journal-title":"Annu. Rev. Genet."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1111\/j.1574-6976.2009.00168.x","article-title":"The diversity of conjugative relaxases and its application in plasmid classification","volume":"33","author":"Francia","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1016\/j.vetmic.2015.02.014","article-title":"Presence and new genetic environment of pleuromutilin-lincosamide-streptogramin A resistance gene lsa(E) in Erysipelothrix rhusiopathiae of swine origin","volume":"177","author":"Zhang","year":"2015","journal-title":"Vet. Microbiol."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1186\/s13756-019-0563-x","article-title":"New genetic context of lnu(B) composed of two multi-resistance gene clusters in clinical Streptococcus agalactiae ST-19 strains","volume":"8","author":"Zhou","year":"2019","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/j.envpol.2018.03.024","article-title":"Estimating the contribution of bacteriophage to the dissemination of antibiotic resistance genes in pig feces","volume":"238","author":"Wang","year":"2018","journal-title":"Environ. Pollut."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Webster, J., Bowring, B., Stroud, L., Marsh, I., Sales, N., and Bogema, D. (2023). Population Structure and Genomic Characteristics of Australian Erysipelothrix rhusiopathiae Reveals Unobserved Diversity in the Australian Pig Industry. Microorganisms, 11.","DOI":"10.3390\/microorganisms11020297"},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Forde, T.L., Kollanandi Ratheesh, N., Harvey, W.T., Thomson, J.R., Williamson, S., Biek, R., and Opriessnig, T. (2020). Genomic and Immunogenic Protein Diversity of Erysipelothrix rhusiopathiae Isolated from Pigs in Great Britain: Implications for Vaccine Protection. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00418"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"106352","DOI":"10.1016\/j.dib.2020.106352","article-title":"Draft genome sequence data of Erysipelothrix rhusiopathiae vaccine strain VR-2","volume":"33","author":"Kovalchuk","year":"2020","journal-title":"Data Brief."},{"key":"ref_50","unstructured":"CLSI Supplement Vet06 (2017). Methods for Antimicrobial Susceptibility Testing of Infrequently Isolated or Fastidious Bacteria Isolated from Animals, Clinical and Laboratory Standards Institute. [1st ed.]."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.vetmic.2018.09.014","article-title":"Identification of serovar 1a, 1b, 2, and 5 strains of Erysipelothrix rhusiopathiae by a conventional gel-based PCR","volume":"225","author":"Shiraiwa","year":"2018","journal-title":"Vet. Microbiol."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1038\/s41587-019-0072-8","article-title":"Assembly of long, error-prone reads using repeat graphs","volume":"37","author":"Kolmogorov","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Huang, Y.T., Liu, P.Y., and Shih, P.W. (2021). Homopolish: A method for the removal of systematic errors in nanopore sequencing by homologous polishing. Genome Biol., 22.","DOI":"10.1186\/s13059-021-02282-6"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., and Korobeynikov, A. (2020). Using SPAdes De Novo Assembler. Curr. Protoc. Bioinform., 70.","DOI":"10.1002\/cpbi.102"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: A genome comparison visualizer","volume":"27","author":"Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1093\/bioinformatics\/btab007","article-title":"Clinker & clustermap.js: Automatic generation of gene cluster comparison figures","volume":"37","author":"Gilchrist","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_58","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_59","doi-asserted-by":"crossref","first-page":"102405","DOI":"10.1016\/j.psj.2022.102405","article-title":"Antibiotic resistance of Riemerella anatipestifer and comparative analysis of antibiotic-resistance gene detection methods","volume":"102","author":"Xihui","year":"2023","journal-title":"Poult. Sci."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for predictions of phenotypes from genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1093\/jac\/dkaa390","article-title":"Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder","volume":"76","author":"Johansson","year":"2021","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"W16","DOI":"10.1093\/nar\/gkw387","article-title":"PHASTER: A better, faster version of the PHAST phage search tool","volume":"44","author":"Arndt","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3691","DOI":"10.1093\/bioinformatics\/btv421","article-title":"Roary: Rapid large-scale prokaryote pan genome analysis","volume":"31","author":"Page","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_64","doi-asserted-by":"crossref","unstructured":"Price, M.N., Dehal, P.S., and Arkin, A.P. (2010). FastTree 2\u2014Approximately maximum-likelihood trees for large alignments. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009490"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_66","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\u2014Erysipelothrix rhusiopathiae SY1027. BMC Microbiol., 14.","DOI":"10.1186\/1471-2180-14-176"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"774836","DOI":"10.3389\/fvets.2022.774836","article-title":"Pathological and Genomic Findings of Erysipelothrix rhusiopathiae Isolated from a Free-Ranging Rough-Toothed Dolphin Steno bredanensis (Cetacea: Delphinidae) Stranded in Korea","volume":"9","author":"Lee","year":"2022","journal-title":"Front. Vet. Sci."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Nesbitt, K., Bloodgood, J., Mullis, M.M., Deming, A.C., Colegrove, K., and Kiel Reese, B. (2022). Draft Genome Sequences of Erysipelothrix sp. Strains Isolated from Stranded Septic Bottlenose Dolphins in Alabama, USA. Microbiol. Resour. Announc., 11.","DOI":"10.1128\/mra.00273-22"},{"key":"ref_69","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_70","doi-asserted-by":"crossref","first-page":"e00592-20","DOI":"10.1128\/MRA.00592-20","article-title":"Draft Genome Sequence of Erysipelothrix rhusiopathiae, Isolated from a Canine Case of Diskospondylitis","volume":"9","author":"Little","year":"2020","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_71","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_72","doi-asserted-by":"crossref","unstructured":"Eisenberg, T., M\u00fchldorfer, K., Erhard, M., Fawzy, A., Kehm, S., Ewers, C., Semmler, T., Blom, J., Lipski, A., and Rau, J. (2022). Erysipelothrix anatis sp. nov., Erysipelothrix aquatica sp. nov. and Erysipelothrix urinaevulpis sp. nov., three novel species of the genus, and emended description of Erysipelothrix. Int. J. Syst. Evol. Microbiol., 72.","DOI":"10.1099\/ijsem.0.005454"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1007\/s10482-014-0342-x","article-title":"Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae)","volume":"107","author":"Bang","year":"2015","journal-title":"Antonie Leeuwenhoek"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"740","DOI":"10.4315\/JFP-21-431","article-title":"Fattening Pigs Are a Reservoir of Florfenicol-Resistant Enterococci Harboring Oxazolidinone Resistance Genes","volume":"85","author":"Haussmann","year":"2022","journal-title":"J. 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