{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T14:23:16Z","timestamp":1772806996339,"version":"3.50.1"},"reference-count":44,"publisher":"MDPI AG","issue":"2","license":[{"start":{"date-parts":[[2026,2,15]],"date-time":"2026-02-15T00:00:00Z","timestamp":1771113600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives: Pyometra is a life-threatening uterine infection of intact bitches and queens. Despite growing reports of multidrug-resistant (MDR) Escherichia coli in canine reproductive and urinary infections, no whole-genome data were previously available for pyometra isolates from Italy. This study aimed to characterise, by whole-genome sequencing and comparative genomics, the population structure, resistome and virulome of E. coli causing pyometra in companion animals from northern Italy in the context of European datasets. Methods: Four E. coli isolates (two canine, two feline) from pyometra cases underwent nanopore long-read sequencing. Genomes were compared with Brazilian and Finnish pyometra isolates using core- and accessory-genome analyses, pan-genome partitioning, phylogeny, and gene-based profiling of antimicrobial resistance and virulence determinants. Results: All Italian isolates belonged to phylogroup B2 and to recognised ExPEC sequence types (ST706\/O51:H1, ST141\/O2:H6, ST372\/O75:H31, ST646\/O22:H5). Phenotypically, they were uniformly resistant to several penicillins and early\/third-generation cephalosporins but remained susceptible to fluoroquinolones, aminoglycosides and trimethoprim\u2013sulphonamide. The combined 57-genome pan-genome was open yet strongly core-dominated; Italian strains shared an efflux- and regulator-centred intrinsic resistome and a rich ExPEC virulence repertoire (P, S, F1C and type 1 fimbriae, multiple siderophores, colibactin, Vat, haemolysin, CNF1) with Brazilian and Finnish isolates. Conclusions: Pyometra-associated E. coli from northern Italian pets belong to globally disseminated high-risk B2 lineages that combine extensive virulence with a largely intrinsic resistome, and currently retain susceptibility to several key drug classes, underscoring an important but vulnerable therapeutic window.<\/jats:p>","DOI":"10.3390\/antibiotics15020212","type":"journal-article","created":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T11:11:28Z","timestamp":1771240288000},"page":"212","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic Characterisation of Pyometra-Associated Escherichia coli in a Lombardy Veterinary Clinic: A Nanopore-Based Case Series"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2772-6410","authenticated-orcid":false,"given":"Gabriele","family":"Meroni","sequence":"first","affiliation":[{"name":"One Health Unit, Department of Biomedical Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7680-6068","authenticated-orcid":false,"given":"Alessio","family":"Soggiu","sequence":"additional","affiliation":[{"name":"One Health Unit, Department of Biomedical Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Davide","family":"Sciannimanico","sequence":"additional","affiliation":[{"name":"Freelance Veterinary Surgeon, Via A. Casati 28, 20862 Arcore, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raul Alexandru","family":"Pop","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Faculty of Veterinary Medicine, University of Agricultural Science and Veterinary Medicine, 3-5 M\u0103n\u0103\u015ftur Street, 400372 Cluj-Napoca, Romania"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luigi","family":"Bonizzi","sequence":"additional","affiliation":[{"name":"One Health Unit, Department of Biomedical Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0108-638X","authenticated-orcid":false,"given":"Piera Anna","family":"Martino","sequence":"additional","affiliation":[{"name":"One Health Unit, Department of Biomedical Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,15]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"110362","DOI":"10.1016\/j.vetmic.2024.110362","article-title":"Bacteria Associated with Canine Pyometra and Concurrent Bacteriuria: A Prospective Study","volume":"301","author":"Thomson","year":"2025","journal-title":"Vet. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1016\/j.cvsm.2018.03.001","article-title":"Pyometra in Small Animals","volume":"48","author":"Hagman","year":"2018","journal-title":"Vet. Clin. N. Am. Small Anim. Pract."},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Nascimento, A.E.d.J., Santos, L.C., and Silva, J.F. (2024). Molecular Factors Involved in the Pathogenesis of Pyometra in Domestic Cats (Felis catus). Animals, 14.","DOI":"10.3390\/ani14202987"},{"key":"ref_4","unstructured":"Hagman, R. (2004). New Aspects of Canine Pyometra. [Doctoral Thesis, Swedish University of Agricultural Sciences]."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"106157","DOI":"10.1016\/j.tvjl.2024.106157","article-title":"Antimicrobials Administration, Treatment Outcome and Bacterial Susceptibility in Canine Pyometra Cases Subjected to Ovariohysterectomy","volume":"306","author":"Bertero","year":"2024","journal-title":"Vet. J."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Xavier, R.G.C., Santana, C.H., de Castro, Y.G., de Souza, T.G.V., do Amarante, V.S., Santos, R.L., and Silva, R.O.S. (2023). Canine Pyometra: A Short Review of Current Advances. Animals, 13.","DOI":"10.3390\/ani13213310"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bellato, A., Robino, P., Stella, M.C., Scalas, D., Savarino, P., Zanatta, R., Re, G., and Nebbia, P. (2024). Ten-Year Antimicrobial Resistance Trend in Uropathogenic Escherichia coli (UPEC) Isolated from Dogs and Cats Admitted to a Veterinary Teaching Hospital in Italy. Microorganisms, 12.","DOI":"10.3390\/microorganisms12112175"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1111\/rda.12103","article-title":"Breed Variations in the Incidence of Pyometra and Mammary Tumours in Swedish Dogs","volume":"47","author":"Jitpean","year":"2012","journal-title":"Reprod. Domest. Anim."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1016\/j.theriogenology.2014.03.007","article-title":"Incidence of Pyometra in Swedish Insured Cats","volume":"82","author":"Hagman","year":"2014","journal-title":"Theriogenology"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1177\/1098612X15623114","article-title":"Pyometra in the Queen: To Spay or Not to Spay?","volume":"18","author":"Hollinshead","year":"2016","journal-title":"J. Feline Med. Surg."},{"key":"ref_11","first-page":"3708","article-title":"Cystic Endometrial Hyperplasia with Pyometra Complex and It\u2019s Surgical Management in Canine","volume":"12","author":"Kalim","year":"2023","journal-title":"Pharma Innov."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"289","DOI":"10.17221\/6864-VETMED","article-title":"Endometritis and Pyometra in Bitches: A Review","volume":"58","author":"Kempisty","year":"2013","journal-title":"Vet. Med."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e153111738996","DOI":"10.33448\/rsd-v11i17.38996","article-title":"Epidemiological Indicators of Canine Piometra: An Analysis of Main Components in the Case of Cases Assisted in the Northeast Region of Par\u00e1","volume":"11","author":"Silva","year":"2022","journal-title":"Res. Soc. Dev."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.theriogenology.2023.10.007","article-title":"Association between Bacterial Pathogenicity, Endometrial Histological Changes and Clinical Prognosis in Canine Pyometra","volume":"214","author":"Xavier","year":"2024","journal-title":"Theriogenology"},{"key":"ref_15","first-page":"153","article-title":"Comparative Analysis of Closed and Open-Cervix Canine Pyometra","volume":"51","author":"Vidya","year":"2020","journal-title":"J. Vet. Anim. Sci."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Jitpean, S., Ambrosen, A., Emanuelson, U., and Hagman, R. (2017). Closed Cervix Is Associated with More Severe Illness in Dogs with Pyometra. BMC Vet. Res., 13.","DOI":"10.1186\/s12917-016-0924-0"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1016\/j.theriogenology.2008.04.036","article-title":"Mucometra, Cystic Endometrial Hyperplasia, and Pyometra in the Bitch: Advances in Treatment and Assessment of Future Reproductive Success","volume":"70","author":"Verstegen","year":"2008","journal-title":"Theriogenology"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.4142\/jvs.2019.20.e39","article-title":"Fertility Outcome after Medically Treated Pyometra in Dogs","volume":"20","author":"Melandri","year":"2019","journal-title":"J. Vet. Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1111\/jsap.13894","article-title":"When\u2014And Whether\u2014Should We Spay\/Neuter Companion Dogs","volume":"66","author":"Romagnoli","year":"2025","journal-title":"J. Small Anim. Pract."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1007\/s11259-024-10355-7","article-title":"Comparative Genetic and Pathogenic Approaches of Escherichia coli Isolated Simultaneously from Pyometra and Urine of Bitches","volume":"48","author":"Lopes","year":"2024","journal-title":"Vet. Res. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41564-020-00834-3","article-title":"Community-Led, Integrated, Reproducible Multi-Omics with Anvi\u2019o","volume":"6","author":"Eren","year":"2021","journal-title":"Nat. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Gautreau, G., Bazin, A., Gachet, M., Planel, R., Burlot, L., Dubois, M., Perrin, A., M\u00e9digue, C., Calteau, A., and Cruveiller, S. (2020). PPanGGOLiN: Depicting Microbial Diversity via a Partitioned Pangenome Graph. PLoS Comput. Biol., 16.","DOI":"10.1371\/journal.pcbi.1007732"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"104453","DOI":"10.1016\/j.meegid.2020.104453","article-title":"Insights on the Genetic Features of Endometrial Pathogenic Escherichia coli Strains from Pyometra in Companion Animals: Improving the Knowledge about Pathogenesis","volume":"85","author":"Lopes","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Valat, C., Drapeau, A., Beurlet, S., Bachy, V., Boulouis, H.-J., Pin, R., Cazeau, G., Madec, J.-Y., and Haenni, M. (2020). Pathogenic Escherichia coli in Dogs Reveals the Predominance of ST372 and the Human-Associated ST73 Extra-Intestinal Lineages. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.00580"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/j.vetmic.2016.05.005","article-title":"Diversity of Class 1 and 2 Integrons Detected in Escherichia coli Isolates from Diseased and Apparently Healthy Dogs","volume":"194","author":"Siqueira","year":"2016","journal-title":"Vet. Microbiol."},{"key":"ref_26","first-page":"22","article-title":"Characterization of Extended Spectrum \u03b2-Lactamase Producing Escherichia coli Strains Isolated from Urogenital System of Dogs in Van Province of Turkey","volume":"24","author":"Kaplan","year":"2023","journal-title":"Iran. J. Vet. Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"11848","DOI":"10.1038\/s41598-024-62028-9","article-title":"Multidrug-Resistant Escherichia coli Causing Canine Pyometra and Urinary Tract Infections Are Genetically Related but Distinct from Those Causing Prostatic Abscesses","volume":"14","author":"Sroithongkham","year":"2024","journal-title":"Sci. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"3222","DOI":"10.1128\/AAC.47.10.3222-3232.2003","article-title":"Mutation Rate and Evolution of Fluoroquinolone Resistance in Escherichia coli Isolates from Patients with Urinary Tract Infections","volume":"47","author":"Karlsson","year":"2003","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.ijantimicag.2005.02.006","article-title":"Mechanisms of Quinolone Resistance in Escherichia coli and Salmonella: Recent Developments","volume":"25","author":"Hopkins","year":"2005","journal-title":"Int. J. Antimicrob. Agents"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Cattoir, V., Pourbaix, A., Magnan, M., Chau, F., de Lastours, V., Felden, B., Fantin, B., and Gu\u00e9rin, F. (2020). Novel Chromosomal Mutations Responsible for Fosfomycin Resistance in Escherichia coli. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.575031"},{"key":"ref_31","first-page":"mgen000930","article-title":"Identification of Genes Influencing the Evolution of Escherichia coli ST372 in Dogs and Humans","volume":"9","author":"Elankumuran","year":"2023","journal-title":"Microb. Genom."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Aurich, S., Wolf, S.A., Prenger-Berninghoff, E., Thrukonda, L., Semmler, T., and Ewers, C. (2023). Genotypic Characterization of Uropathogenic Escherichia coli from Companion Animals: Predominance of ST372 in Dogs and Human-Related ST73 in Cats. Antibiotics, 13.","DOI":"10.3390\/antibiotics13010038"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"3721","DOI":"10.1128\/JCM.01581-09","article-title":"Sharing of Escherichia coli Sequence Type ST131 and Other Multidrug-Resistant and Urovirulent E. Coli Strains among Dogs and Cats within a Household","volume":"47","author":"Johnson","year":"2009","journal-title":"J. Clin. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"17394","DOI":"10.1038\/s41598-019-54004-5","article-title":"An Escherichia coli ST131 Pangenome Atlas Reveals Population Structure and Evolution across 4,071 Isolates","volume":"9","author":"Decano","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1016\/j.chom.2022.04.008","article-title":"Persisting Uropathogenic Escherichia coli Lineages Show Signatures of Niche-Specific within-Host Adaptation Mediated by Mobile Genetic Elements","volume":"30","author":"Choi","year":"2022","journal-title":"Cell Host Microbe"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"e01291-22","DOI":"10.1128\/spectrum.01291-22","article-title":"Genomic and Temporal Trends in Canine ExPEC Reflect Those of Human ExPEC","volume":"10","author":"Elankumaran","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e00135-18","DOI":"10.1128\/CMR.00135-18","article-title":"Global Extraintestinal Pathogenic Escherichia coli (Expec) Lineages","volume":"32","author":"Manges","year":"2019","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1292\/jvms.60.287","article-title":"Distribution of Uropathogenic Virulence Factors among Escherichia coli Strains Isolated from Dogs and Cats","volume":"60","author":"Yuri","year":"1998","journal-title":"J. Vet. Med. Sci."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"49","DOI":"10.4142\/jvs.2011.12.1.49","article-title":"Virulence Factors and Genetic Variability of Uropathogenic Escherichia coli Isolated from Dogs and Cats in Italy","volume":"12","author":"Tramuta","year":"2011","journal-title":"J. Vet. Sci."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1016\/j.tvjl.2014.08.016","article-title":"Frequencies of Virulence Genes and Pulse Field Gel Electrophoresis Fingerprints in Escherichia coli Isolates from Canine Pyometra","volume":"202","author":"Maluta","year":"2014","journal-title":"Vet. J."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0378-1135(03)00063-4","article-title":"Uropathogenic Virulence Factors in Isolates of Escherichia coli from Clinical Cases of Canine Pyometra and Feces of Healthy Bitches","volume":"94","author":"Chen","year":"2003","journal-title":"Vet. Microbiol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.rvsc.2008.07.018","article-title":"da Virulence Factors in Escherichia coli Strains Isolated from Urinary Tract Infection and Pyometra Cases and from Feces of Healthy Dogs","volume":"86","author":"Siqueira","year":"2009","journal-title":"Res. Vet. Sci."},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Melo, R.T., Oliveira, R.P., Silva, B.F., Monteiro, G.P., Saut, J.P.E., Costa, L.R.M., Dias, S.D.C., and Rossi, D.A. (2022). Phylogeny and Virulence Factors of Escherichia coli Isolated from Dogs with Pyometra. Vet. Sci., 9.","DOI":"10.3390\/vetsci9040158"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Badis, A., Heleili, N., Merradi, M., Ayachi, A., Martino, P.A., Meroni, G., and Soggiu, A. (2025). Outbreak of Carbapenem-Resistant High-Risk Clone ST244 of Pseudomonas aeruginosa in Dogs and Cats in Algeria. Antibiotics, 14.","DOI":"10.20944\/preprints202502.0600.v1"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/2\/212\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T10:01:54Z","timestamp":1772791314000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/2\/212"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,15]]},"references-count":44,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2026,2]]}},"alternative-id":["antibiotics15020212"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics15020212","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,15]]}}}