{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T05:37:23Z","timestamp":1792820243283,"version":"4.5.0"},"reference-count":52,"publisher":"Springer Science and Business Media LLC","issue":"6","license":[{"start":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T00:00:00Z","timestamp":1787961600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Universidade Federal De Minas Gerais","id":[{"id":"https:\/\/ror.org\/0176yjw32","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Vet Res Commun"],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The objective of this study was to perform genomic, phylogenomic, and phenotypic characterization of bacterial isolates from a captive\n                    <jats:italic>Cacatua alba<\/jats:italic>\n                    to investigate their antimicrobial resistance profiles, virulence-associated genes, and genomic relationships with publicly available strains. Bacterial isolates obtained from the lungs and encephalon were identified as\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    (AV037),\n                    <jats:italic>Enterobacter hormaechei<\/jats:italic>\n                    (AV038), and\n                    <jats:italic>Cupriavidus gilardii<\/jats:italic>\n                    (AV039). Comparative genomic analyses, phylogenomic reconstruction, and antimicrobial susceptibility testing (AST) were performed. Genomic analysis identified multiple antimicrobial resistance-associated genes in AV037, AV038, and AV039, with genes associated with efflux pumps, particularly those in the resistance-nodulation-cell division (RND) family, as the predominant resistance-associated mechanism identified. Most identified genes are intrinsic to the respective bacterial species and do not necessarily confer phenotypic antimicrobial resistance when present alone. Phenotypic testing confirmed multidrug-resistant (MDR) profiles, with resistance to \u03b2-lactams and aminoglycosides. Susceptibility to carbapenems was preserved in AV037 and AV038, whereas AV039 exhibited resistance to meropenem. Phylogenomic analysis demonstrated that AV037 and AV038 clustered with strains recovered from diverse hosts and geographic regions. In contrast, AV039 clustered predominantly with environmental and human-associated isolates, including strains harboring the\n                    <jats:italic>mcr-5<\/jats:italic>\n                    gene. These findings are consistent with previous reports describing the recovery of\n                    <jats:italic>C. gilardii<\/jats:italic>\n                    from both environmental and clinical sources. Overall, this study documents the occurrence of MDR bacteria carrying resistance and virulence-associated determinants in a captive\n                    <jats:italic>C. alba<\/jats:italic>\n                    , highlighting the value of genomic surveillance to improve our understanding of the distribution of clinically relevant bacterial isolates across different ecological settings.\n                  <\/jats:p>","DOI":"10.1007\/s11259-026-11490-z","type":"journal-article","created":{"date-parts":[[2026,8,29]],"date-time":"2026-08-29T10:30:45Z","timestamp":1787999445000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Genomic analysis of Escherichia coli, Enterobacter hormaechei, and Cupriavidus gilardii isolated from Cacatua alba"],"prefix":"10.1007","volume":"50","author":[{"given":"Julia Penna","family":"de Andrade","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henrique","family":"da Silva Vieira","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Camilla Faria","family":"Soares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marcela Laryssa Oliveira","family":"Duarte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andr\u00e9 Almeida","family":"Fernandes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hannah Luiza Gonsalves","family":"Coelho","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vict\u00f3ria Veiga","family":"Alves","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bertram","family":"Brenig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vasco Ariston","family":"de Carvalho Azevedo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fl\u00e1via Figueira","family":"Aburjaile","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nelson Rodrigo","family":"da Silva Martins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,29]]},"reference":[{"key":"11490_CR1","unstructured":"Andrew S (2010) FastQC: a quality control tool for high throughput sequence data. Braham Bioinformatics"},{"issue":"5\u20136","key":"11490_CR2","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1016\/j.micpath.2008.08.005","volume":"45","author":"EM Ant\u00e3o","year":"2008","unstructured":"Ant\u00e3o EM, Glodde S, Li G, Sharifi R, Homeier T, Laturnus C et al (2008) The chicken as a natural model for extraintestinal infections caused by avian pathogenic Escherichia coli (APEC). Microb Pathog 45(5\u20136):361\u2013369. https:\/\/doi.org\/10.1016\/j.micpath.2008.08.005","journal-title":"Microb Pathog"},{"issue":"15","key":"11490_CR3","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114\u20132120. https:\/\/doi.org\/10.1093\/bioinformatics\/btu170","journal-title":"Bioinformatics"},{"key":"11490_CR5","unstructured":"Brazilian Committee on Antimicrobial Susceptibility Testing \u2013 BrCAST (2025) Tabelas de pontos de corte para interpreta\u00e7\u00e3o de CIMs e di\u00e2metros de halos. Vers\u00e3o 15.0, 2025 do EUCAST. Available at: https:\/\/brcast.org.br\/documentos\/documentos-3\/"},{"key":"11490_CR56","doi-asserted-by":"publisher","unstructured":"Campos ACDC, Andrade NL, Couto N, Mutters NT, de Vos M, Rosa ACP et al (2020) Characterization of fosfomycin heteroresistance among multidrug-resistant Escherichia coli isolates from hospitalized patients in Rio de Janeiro, Brazil. J Glob Antimicrob Resist 22:584\u2013593. https:\/\/doi.org\/10.1016\/j.jgar.2020.04.026","DOI":"10.1016\/j.jgar.2020.04.026"},{"key":"11490_CR6","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","volume":"20","author":"A Chklovski","year":"2023","unstructured":"Chklovski A, Parks DH, Woodcroft BJ, Tyson GW (2023) CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 20:1203\u20131212. https:\/\/doi.org\/10.1038\/s41592-023-01940-w","journal-title":"Nat Methods"},{"key":"11490_CR7","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1080\/03079457.2020.1845300","volume":"50","author":"H Christensen","year":"2021","unstructured":"Christensen H, Bachmeier J, Bisgaard M (2021) New strategies to prevent and control avian pathogenic Escherichia coli (APEC). Avian Pathol 50:370\u2013381. https:\/\/doi.org\/10.1080\/03079457.2020.1845300","journal-title":"Avian Pathol"},{"key":"11490_CR8","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.vetmic.2012.08.019","volume":"163","author":"AW Confer","year":"2013","unstructured":"Confer AW, Ayalem S (2013) The OmpA family of proteins: roles in bacterial pathogenesis and immunity. Vet Microbiol 163:207\u2013222. https:\/\/doi.org\/10.1016\/j.vetmic.2012.08.019","journal-title":"Vet Microbiol"},{"issue":"11","key":"11490_CR9","doi-asserted-by":"publisher","first-page":"2606","DOI":"10.1099\/ijs.0.018341-0","volume":"60","author":"V Cuadrado","year":"2010","unstructured":"Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ERB (2010) Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 60(11):2606\u20132612. https:\/\/doi.org\/10.1099\/ijs.0.018341-0","journal-title":"Int J Syst Evol Microbiol"},{"issue":"5","key":"11490_CR10","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1007\/s10123-026-00811-6","volume":"29","author":"A da Silva","year":"2026","unstructured":"da Silva A, Luna FS, Nogueira JF, Rosa DS, de Figueir\u00eado PI, da Cruz BADS et al (2026) Phenotypical-genetic virulence and resistance in atypical avian pathogenic Escherichia coli. Int Microbiol 29(5):631\u2013640. https:\/\/doi.org\/10.1007\/s10123-026-00811-6","journal-title":"Int Microbiol"},{"key":"11490_CR11","doi-asserted-by":"publisher","unstructured":"Delgado MA, Vincent PA, Farias RN, Salom\u00f3n RA (2005) YojI of Escherichia coli functions as a Microcin J25 efflux pump. J Bacteriol 187. https:\/\/doi.org\/10.1128\/jb.187.10.3465-3470.2005","DOI":"10.1128\/jb.187.10.3465-3470.2005"},{"issue":"9","key":"11490_CR13","doi-asserted-by":"publisher","first-page":"171","DOI":"10.3390\/vetsci8090171","volume":"8","author":"VV Ebani","year":"2021","unstructured":"Ebani VV, Guardone L, Bertelloni F, Perrucci S, Poli A, Mancianti F (2021) Survey on the presence of bacterial and parasitic zoonotic agents in the feces of wild birds. Vet Sci 8(9):171. https:\/\/doi.org\/10.3390\/vetsci8090171","journal-title":"Vet Sci"},{"issue":"7","key":"11490_CR14","doi-asserted-by":"publisher","first-page":"2274","DOI":"10.1128\/jb.179.7.2274-2280.1997","volume":"179","author":"R Edgar","year":"1997","unstructured":"Edgar R, Bibi E (1997) MdfA, an Escherichia coli multidrug resistance protein with an extraordinarily broad spectrum of drug recognition. J Bacteriol 179(7):2274\u20132280. https:\/\/doi.org\/10.1128\/jb.179.7.2274-2280.1997","journal-title":"J Bacteriol"},{"key":"11490_CR15","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1186\/s13059-019-1832-y","volume":"20","author":"DM Emms","year":"2019","unstructured":"Emms DM, Kelly S (2019) OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol 20:238. https:\/\/doi.org\/10.1186\/s13059-019-1832-y","journal-title":"Genome Biol"},{"key":"11490_CR16","doi-asserted-by":"publisher","first-page":"105424","DOI":"10.1016\/j.rvsc.2024.105424","volume":"180","author":"E Esposito","year":"2024","unstructured":"Esposito E, Scarpellini R, Celli G, Marliani G, Zaghini A, Mondo E (2024) Wild birds as potential bioindicators of environmental antimicrobial resistance: A preliminary investigation. Res Vet Sci 180:105424. https:\/\/doi.org\/10.1016\/j.rvsc.2024.105424","journal-title":"Res Vet Sci"},{"issue":"2","key":"11490_CR17","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1016\/j.bjid.2012.09.011","volume":"17","author":"RG Ferrari","year":"2013","unstructured":"Ferrari RG, Galiana A, Cremades R, Rodr\u00edguez JC, Magnani M, Tognim MCB et al (2013) Expression of the marA, soxS, acrB and ramA genes related to the AcrAB\/TolC efflux pump in Salmonella enterica strains with and without quinolone resistance-determining regions gyrA gene mutations. Braz J Infect Dis 17(2):125\u2013130. https:\/\/doi.org\/10.1016\/j.bjid.2012.09.011","journal-title":"Braz J Infect Dis"},{"issue":"1","key":"11490_CR18","doi-asserted-by":"publisher","first-page":"68","DOI":"10.3390\/antibiotics10010068","volume":"10","author":"W Gwenzi","year":"2021","unstructured":"Gwenzi W, Chaukura N, Muisa-Zikali N, Teta C, Musvuugwa T, Rzymski P et al (2021) Insects, Rodents, and Pets as Reservoirs, Vectors, and Sentinels of Antimicrobial Resistance. Antibiotics 10(1):68. https:\/\/doi.org\/10.3390\/antibiotics10010068","journal-title":"Antibiotics"},{"issue":"15","key":"11490_CR20","doi-asserted-by":"publisher","first-page":"2199","DOI":"10.3390\/ani14152199","volume":"14","author":"H Hai","year":"2024","unstructured":"Hai H, Yang M, Cheng Z, Ma K, Shang F (2024) Potential Role of SdiA in Biofilm Formation and Drug Resistance in Avian Pathogenic Escherichia coli. Anim (Basel) 14(15):2199. https:\/\/doi.org\/10.3390\/ani14152199","journal-title":"Anim (Basel)"},{"key":"11490_CR19","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.3390\/biology2041242","volume":"2","author":"J Haiko","year":"2013","unstructured":"Haiko J, Westerlund-Wildtr\u00f6m B (2013) The Role of the Bacterial Flagellum in Adhesion and Virulence. Biology 2:1242\u20131267. https:\/\/doi.org\/10.3390\/biology2041242","journal-title":"Biology"},{"key":"11490_CR21","doi-asserted-by":"publisher","first-page":"1127948","DOI":"10.3389\/fmicb.2023.1127948","volume":"14","author":"M Han","year":"2023","unstructured":"Han M, Liu C, Xie H, Zheng J, Zhang Y, Li C et al (2023) Genomic and clinical characteristics of carbapenem-resistant Enterobacter cloacae complex isolates collected in a Chinese tertiary hospital during 2013\u20132021. Front Microbiol 14:1127948. https:\/\/doi.org\/10.3389\/fmicb.2023.1127948","journal-title":"Front Microbiol"},{"key":"11490_CR22","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1007\/s00408-011-9323-2","volume":"189","author":"J Hennigs","year":"2011","unstructured":"Hennigs J, Baumann HJ, Schiedel S, Tennstedt P, Sobottka I, Bokemeyer C et al (2011) Characterization of Enterobacter cloacae pneumonia: a single-center retrospective analysis. Lung 189:475\u2013483. https:\/\/doi.org\/10.1007\/s00408-011-9323-2","journal-title":"Lung"},{"key":"11490_CR23","doi-asserted-by":"publisher","unstructured":"Holdsworth SR, Law CJ (2013) Multidrug resistance protein MdtM adds to the repertoire of antiporters involved in alkaline pH homeostasis in Escherichia coli. BMC Microbiol 13. https:\/\/doi.org\/10.1186\/1471-2180-13-113","DOI":"10.1186\/1471-2180-13-113"},{"key":"11490_CR24","doi-asserted-by":"publisher","first-page":"124","DOI":"10.12688\/wellcomeopenres.14826.1","volume":"3","author":"KA Jolley","year":"2018","unstructured":"Jolley KA, Bray JE, Maiden MCJ (2018) Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 3:124. https:\/\/doi.org\/10.12688\/wellcomeopenres.14826.1","journal-title":"Wellcome Open Res"},{"issue":"4","key":"11490_CR25","doi-asserted-by":"publisher","first-page":"467","DOI":"10.3390\/pathogens10040467","volume":"10","author":"D Kathayat","year":"2021","unstructured":"Kathayat D, Lokesh D, Ranjit S, Rajashekara G (2021) Avian Pathogenic Escherichia coli (APEC): An Overview of Virulence and Pathogenesis Factors, Zoonotic Potential, and Control Strategies. Pathogens 10(4):467. https:\/\/doi.org\/10.3390\/pathogens10040467","journal-title":"Pathogens"},{"key":"11490_CR26","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1186\/s12879-016-1838-y","volume":"16","author":"T Kobayashi","year":"2016","unstructured":"Kobayashi T, Nakamura I, Fujita H, Tsukimori A, Sato A, Fukushima S et al (2016) First case report of infection due to Cupriavidus gilardii in a patient without immunodeficiency: a case report. BMC Infect Dis 16:493. https:\/\/doi.org\/10.1186\/s12879-016-1838-y","journal-title":"BMC Infect Dis"},{"issue":"W1","key":"11490_CR27","doi-asserted-by":"publisher","first-page":"W78","DOI":"10.1093\/nar\/gkae268","volume":"52","author":"I Letunic","year":"2024","unstructured":"Letunic I (2024) Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 52(W1):W78\u2013W82. https:\/\/doi.org\/10.1093\/nar\/gkae268","journal-title":"Nucleic Acids Res"},{"key":"11490_CR28","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1007\/s12275-017-6408-5","volume":"55","author":"MF Lin","year":"2017","unstructured":"Lin MF, Lin YY, Lan CY (2017) Contribution of EmrAB efflux pumps to colistin resistance in Acinetobacter baumannii. J Microbiol 55:130\u2013136. https:\/\/doi.org\/10.1007\/s12275-017-6408-5","journal-title":"J Microbiol"},{"key":"11490_CR29","doi-asserted-by":"publisher","first-page":"5035","DOI":"10.2147\/IDR.S367073","volume":"15","author":"H Liu","year":"2022","unstructured":"Liu H, Wang D, Tang M, Jia P, Huo Y, Wei E et al (2022) Genetic Characterization of Enterobacter hormaechei Co-Harboring bla\u2009<\u2009sub>NDM-1\u2009and mcr-9 Causing Upper Respiratory Tract Infection. Infect Drug Resist 15:5035\u20135042. https:\/\/doi.org\/10.2147\/IDR.S367073","journal-title":"Infect Drug Resist"},{"issue":"3","key":"11490_CR30","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1111\/j.1469-0691.2011.03570.x","volume":"18","author":"AP Magiorakos","year":"2012","unstructured":"Magiorakos AP, Srinivasan A, Carey RB, Carmeli Y, Falagas ME, Giske CG et al (2012) Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: An international expert proposal for interim standard definitions for acquired resistance. Clin Microbiol Infect 18(3):268\u2013281. https:\/\/doi.org\/10.1111\/j.1469-0691.2011.03570.x","journal-title":"Clin Microbiol Infect"},{"issue":"10","key":"11490_CR31","doi-asserted-by":"publisher","first-page":"4647","DOI":"10.1093\/molbev\/msab199","volume":"38","author":"M Manni","year":"2021","unstructured":"Manni M, Berkeley MR, Seppey M, Sim\u00e3o FA, Zdobnov EM (2021) BUSCO Update: novel and streamlined workflows along with broader and deeper phylogenetic coverage for scoring of eukaryotic, prokaryotic, and viral genomes. Mol Biol Evol 38(10):4647\u20134654. https:\/\/doi.org\/10.1093\/molbev\/msab199","journal-title":"Mol Biol Evol"},{"key":"11490_CR32","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1016\/j.vetmic.2018.05.017","volume":"221","author":"LC Melo","year":"2018","unstructured":"Melo LC, Oresco C, Leigue L, Netto HM, Melville PA, Benites NR et al (2018) Prevalence and molecular features of ESBL\/pAmpC-producing Enterobacteriaceae in healthy and diseased companion animals in Brazil. Vet Microbiol 221:59\u201366. https:\/\/doi.org\/10.1016\/j.vetmic.2018.05.017","journal-title":"Vet Microbiol"},{"issue":"5","key":"11490_CR33","doi-asserted-by":"publisher","first-page":"443","DOI":"10.1111\/j.1348-0421.2005.tb03748.x","volume":"49","author":"T Niga","year":"2013","unstructured":"Niga T, Ito H, Oyamada Y, Yamagishi J, Kadono M, Nishino T et al (2013) Cooperation between Alteration of DNA Gyrase Genes and Over-Expression of MexB and MexX Confers High-Level Fluoroquinolone Resistance in Pseudomonas aeruginosa Strains Isolated from a Patient Who Received a Liver Transplant Followed by Treatment with Fluoroquinolones. Microbiol Immunol 49(5):443\u2013446. https:\/\/doi.org\/10.1111\/j.1348-0421.2005.tb03748.x","journal-title":"Microbiol Immunol"},{"key":"11490_CR34","doi-asserted-by":"publisher","first-page":"2319","DOI":"10.1128\/JB.184.8.2319-2323.2002","volume":"184","author":"K Nishino","year":"2002","unstructured":"Nishino K, Yamaguchi A (2002) EvgA of the two-component signal transduction system modulates production of the YhiUV multidrug transporter in Escherichia coli. J Bacteriol 184:2319\u20132323","journal-title":"J Bacteriol"},{"issue":"8","key":"11490_CR35","doi-asserted-by":"publisher","first-page":"1059","DOI":"10.3390\/pathogens10081059","volume":"10","author":"A Nowazek","year":"2021","unstructured":"Nowazek A, Dec M, Stepien-Pysniak D, Urban-Chmiel R, Marek A, Rozanski P (2021) Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland. Pathogens 10(8):1059. https:\/\/doi.org\/10.3390\/pathogens10081059","journal-title":"Pathogens"},{"key":"11490_CR36","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1186\/s12917-024-04197-3","volume":"20","author":"K Papageorgiou","year":"2024","unstructured":"Papageorgiou K, Stoikou A, Delis G, Giantsis IA, Stamelou E, Sofia M et al (2024) First detection of Cupriavidus gilardii in a bovine neonatal diarrhea outbreak. BMC Vet Res 20:345. https:\/\/doi.org\/10.1186\/s12917-024-04197-3","journal-title":"BMC Vet Res"},{"key":"11490_CR37","doi-asserted-by":"publisher","unstructured":"Perreten V, Schwarz FV, Teuber M, Levy SB (2001) Mdt(A), a new efflux protein conferring multiple antibiotic resistance in lactococcus lactis and Escherichia coli. Antimicrob Agents Chemother 45. https:\/\/doi.org\/10.1128\/AAC.45.4.1109-1114.2001","DOI":"10.1128\/AAC.45.4.1109-1114.2001"},{"key":"11490_CR38","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1128\/CMR.19.2.382-402.2006","volume":"19","author":"LJV Piddock","year":"2006","unstructured":"Piddock LJV (2006) Clinically relevant chromosomally encoded multidrug resistance efflux pumps in bacteria. Clin Microbiol Rev 19:382\u2013402","journal-title":"Clin Microbiol Rev"},{"issue":"3","key":"11490_CR39","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1046\/j.1365-2958.2002.02773.x","volume":"43","author":"S Rahmati","year":"2002","unstructured":"Rahmati S, Yang S, Davidso AL, Zechiedrich EL (2002) Control of the AcrAB multidrug efflux pump by quorum-sensing regulator SdiA. Mol Microbiol 43(3):677\u2013685. https:\/\/doi.org\/10.1046\/j.1365-2958.2002.02773.x","journal-title":"Mol Microbiol"},{"key":"11490_CR40","doi-asserted-by":"publisher","first-page":"1070406","DOI":"10.3389\/fbinf.2023.1070406","volume":"3","author":"DLN Rodrigues","year":"2023","unstructured":"Rodrigues DLN, Ariute JC, Rodrigues da Costa FM, Benko-Iseppon AM, Barh D, Azevedo V et al (2023) PanViTa: Pan Virulence and resistance analysis. Front Bioinform 3:1070406. https:\/\/doi.org\/10.3389\/fbinf.2023.1070406","journal-title":"Front Bioinform"},{"key":"11490_CR41","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1128\/JB.182.6.1754-1756.2000","volume":"182","author":"EY Rosenberg","year":"2000","unstructured":"Rosenberg EY, Ma D, Nikaido H (2000) AcrD of Escherichia coli Is an Aminoglycoside Efflux Pump. J Bacteriol 182:1754\u20131756. https:\/\/doi.org\/10.1128\/JB.182.6.1754-1756.2000","journal-title":"J Bacteriol"},{"issue":"5","key":"11490_CR42","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1128\/mSphere.00631-19","volume":"4","author":"C Ruiz","year":"2019","unstructured":"Ruiz C, McCarley A, Espejo ML, Cooper KK, Harmon DE (2019) Comparative genomics reveals a well-conserved intrinsic resistome in the emerging multidrug-resistant pathogen Cupriavidus gilardii. MSphere 4(5):10\u20131128","journal-title":"MSphere"},{"key":"11490_CR53","doi-asserted-by":"publisher","unstructured":"Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068\u20132069. https:\/\/doi.org\/10.1093\/bioinformatics\/btu153","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"11490_CR44","doi-asserted-by":"publisher","unstructured":"Stahlhofer SR, Peripolli V, Lopes PD, Balbinot AC, Zuffo JP, Pires PGD, Millezi AF (2026) Evaluation of resistance and virulence factors in Salmonella enterica subsp. enterica serovar Thompson isolates in the poultry chain. Br Poult Sci 1\u201312. https:\/\/doi.org\/10.1080\/00071668.2025.2588244","DOI":"10.1080\/00071668.2025.2588244"},{"issue":"9","key":"11490_CR45","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","volume":"30","author":"A Stamakis","year":"2014","unstructured":"Stamakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312\u20131313. https:\/\/doi.org\/10.1093\/bioinformatics\/btu033","journal-title":"Bioinformatics"},{"key":"11490_CR12","unstructured":"The European Committee on Antimicrobial Susceptibility Testing (EUCAST) (2026) When there are no breakpoints. Version 10 July 2026. https:\/\/www.escmid.org\/fileadmin\/eucast\/pdf\/guidance_documents\/When_there_are_no_breakpoints_revision_20260710.pdf. Accessed 20 Jul 2026"},{"issue":"24","key":"11490_CR46","doi-asserted-by":"publisher","first-page":"e01613","DOI":"10.1128\/AEM.01613-20","volume":"86","author":"LJ Toombs-Ruane","year":"2020","unstructured":"Toombs-Ruane LJ, Benschop J, French NP, Biggs PJ, Midwinter AC, Marshall JC et al (2020) Carriage of extended-spectrum-beta-lactamase- and ampC beta-lactamase-producing Escherichia coli strains from humans and pets in the same households. Appl Environ Microbiol 86(24):e01613\u2013e01620. https:\/\/doi.org\/10.1128\/AEM.01613-20","journal-title":"Appl Environ Microbiol"},{"key":"11490_CR47","doi-asserted-by":"publisher","DOI":"10.1101\/2023.06.01.543064","author":"N Walas","year":"2023","unstructured":"Walas N, M\u00fcller NF, Parker E, Henderson A, Capone D, Brown J et al (2023) Phylodynamics uncovers the transmission of antibiotic-resistant Escherichia coli between canines and humans in an urban environment. https:\/\/doi.org\/10.1101\/2023.06.01.543064","journal-title":"bioRxiv doi"},{"key":"11490_CR48","doi-asserted-by":"publisher","unstructured":"Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6). https:\/\/doi.org\/10.1371\/journal.pcbi.1005595","DOI":"10.1371\/journal.pcbi.1005595"},{"issue":"18","key":"11490_CR49","doi-asserted-by":"publisher","first-page":"6363","DOI":"10.1128\/JB.187.18.6363-6369","volume":"187","author":"B Woebking","year":"2005","unstructured":"Woebking B, Reuter G, Shilling RA, Velamakanni S, Shahi S, Venter H et al (2005) Drug-lipid A interactions on the Escherichia coli ABC transporter MsbA. J Bacteriol 187(18):6363\u20136369. https:\/\/doi.org\/10.1128\/JB.187.18.6363-6369","journal-title":"J Bacteriol"},{"key":"11490_CR50","volume-title":"Bacterial Priority Pathogens List, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance","author":"World Health Organization","year":"2024","unstructured":"World Health Organization (2024) Bacterial Priority Pathogens List, 2024: bacterial pathogens of public health importance to guide research, development and strategies to prevent and control antimicrobial resistance. World Health Organization, Geneva"},{"key":"11490_CR51","doi-asserted-by":"publisher","first-page":"e01858","DOI":"10.1128\/aac.01858-24","volume":"69","author":"L Xie","year":"2025","unstructured":"Xie L, Li J, Peng Q, Liu X, Lin F, Dai X et al (2025) Contribution of RND superfamily multidrug efflux pumps AdeABC, AdeFGH, and AdeIJK to antimicrobial resistance and virulence factors in multidrug-resistant Acinetobacter baumannii AYE. Antimicrob. Agents Chemother 69:e01858\u2013e01824. https:\/\/doi.org\/10.1128\/aac.01858-24","journal-title":"Agents Chemother"},{"key":"11490_CR52","doi-asserted-by":"publisher","first-page":"e01577","DOI":"10.1128\/aem.01577-23","volume":"89","author":"R Zhang","year":"2023","unstructured":"Zhang R, Wang Y (2023) EvgS\/EvgA, the unorthodox two-component system regulating bacterial multiple resistance. Appl Environ Microbiol 89:e01577\u2013e01523. https:\/\/doi.org\/10.1128\/aem.01577-23","journal-title":"Appl Environ Microbiol"}],"container-title":["Veterinary Research Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11259-026-11490-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11259-026-11490-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s11259-026-11490-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,24]],"date-time":"2026-10-24T04:44:11Z","timestamp":1792817051000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s11259-026-11490-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,29]]},"references-count":52,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,12]]}},"alternative-id":["11490"],"URL":"https:\/\/doi.org\/10.1007\/s11259-026-11490-z","relation":{},"ISSN":["0165-7380","1573-7446"],"issn-type":[{"value":"0165-7380","type":"print"},{"value":"1573-7446","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,29]]},"assertion":[{"value":"8 June 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 August 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"All procedures were approved by the Ethics Committee on Animal Use (CEUA) of the Universidade Federal de Minas Gerais (UFMG), protocol N\u00ba. 172\/2025, in compliance with Brazilian legislation (Law No. 11,794\/2008, Decree N\u00ba. 6,899\/2009) and CONCEA guidelines.","order":1,"name":"Ethics","label":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"This manuscript does not contain any individual person\u2019s data, images, or videos requiring consent for publication.","order":2,"name":"Ethics","label":"Informed Consent","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.","order":3,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"544"}}