Whole-genome analysis reveals exchange of ESBL-E. coli genomes between migratory sheep and surrounding farm environments

Whole-genome analysis reveals exchange of ESBL-E. coli genomes between migratory sheep and surrounding farm environments | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Whole-genome analysis reveals exchange of ESBL-E. coli genomes between migratory sheep and surrounding farm environments Baldev Gulati, Shivasharanappa Nayakvadi, Manas Madhukar, Sangeetha T R, and 8 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9564623/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract The spillover of pathogenic organisms across the livestock-environmental interface is a major OneHealth concern. To investigate the co-occurrence, antimicrobial resistance profiles, and genomic characteristics of ESBL-E. coli in healthy migratory sheep flocks and associated farm environments, a cross-sectional study was conducted in South Karnataka, India. 9124 animals from 60 farms were included in the study, and 701 samples from sheep and environmental were analysed, during 2023-2025. The occurrence of ESBL-E. coli was comparable in sheep and environmental samples, and exhibited high multidrug resistance patterns. Whole-genome-sequencing and comparative genomic analysis of ESBL-E. coli isolates revealed substantial diversity in antimicrobial resistance genes including resistance-nodulation-cell division family efflux pumps, alterations in β-lactam target proteins such as penicillin-binding proteins, and a wide range of β-lactamase genes, including CTX-M, TEM, DHA, AmpC, and SHV variants. Several plasmid replicon types were detected in both sheep and environmental isolates, suggesting potential plasmid-mediated horizontal gene transfer at the livestock-environment interface. Notably, phenotypic resistance to imipenem was detected in 16.6% of sheep isolates, and stx genes were identified in 19% of isolates, raising additional public health concerns. Overall, the detection of multidrug-resistant ESBL-E. coli in migratory sheep and their surrounding environments, together with shared resistomes, plasmids, and lineages, underscores the role of small non-sedentary ruminants as overlooked nodes in AMR dissemination and highlights the need for targeted OneHealth surveillance strategies. Biological sciences/Microbiology/Bacteriology Biological sciences/Microbiology/Environmental microbiology/Soil microbiology Biological sciences/Microbiology/Environmental microbiology/Water microbiology Biological sciences/Genetics/Genomics/Comparative genomics ESBL-producing Escherichia coli Multidrug resistance (MDR) Migratory sheep Farm environment Whole-genome sequencing (WGS) Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Full Text Additional Declarations There is NO Competing Interest. Tables 1 and 2 are available in the Supplementary Files section. Supplementary Files 23032026SupplementarytablesTIGSNIVEDI.xlsx Supplementary Tables 22032026TIGSNIVEDISupplementaryFigures.docx Supplementary Figures TIGSNIVEDIMAINTABLES11032026.docx Tables 1 and 2 Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9564623","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":636453953,"identity":"908cc7d2-500c-4995-b89a-a55f67ae5dec","order_by":0,"name":"Baldev Gulati","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0klEQVRIiWNgGAWjYBACAxDxgIGBhx/ESCggVksCgwGPZAOIYUCCFgaDA3AuAWAuffyaRELNHxnj86sTPzwwYJDnFzuAX4tlX06ZRMIxAx6zG283SwAdZjhzdgIBh53hSZNIYANpObsBpCXB4DZRWv4Z8BjPOLv5B5Fa2I9JJLYZ8Bjw924jzhbLHh5mi8Q+Yx6JG7zbLBIMJAj7xZyH/eGND9/k7Pn7z26++aPCRp5fmoAWYLxD40ICrFKCkHIQYH8AofkPEKN6FIyCUTAKRiIAAA9oQJ8w3OwHAAAAAElFTkSuQmCC","orcid":"","institution":"ICAR-NIVEDI (National Institute of Veterinary Epidemiology and Disease Informatics)","correspondingAuthor":true,"prefix":"","firstName":"Baldev","middleName":"","lastName":"Gulati","suffix":""},{"id":636453954,"identity":"8def199c-bf8e-4257-af35-0fb58cad8a68","order_by":1,"name":"Shivasharanappa Nayakvadi","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Shivasharanappa","middleName":"","lastName":"Nayakvadi","suffix":""},{"id":636453955,"identity":"703e6868-f072-4150-b4ec-a7623b8e20b9","order_by":2,"name":"Manas Madhukar","email":"","orcid":"https://orcid.org/0009-0005-4608-6422","institution":"Tata Institute for Genetics and Society","correspondingAuthor":false,"prefix":"","firstName":"Manas","middleName":"","lastName":"Madhukar","suffix":""},{"id":636453956,"identity":"e08a0aca-9191-4425-ad38-eefb051f04f4","order_by":3,"name":"Sangeetha T R","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Sangeetha","middleName":"T","lastName":"R","suffix":""},{"id":636453957,"identity":"57b7d09b-21f1-4986-9c6e-5c7fbc7da61a","order_by":4,"name":"Aishwarya S R","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Aishwarya","middleName":"S","lastName":"R","suffix":""},{"id":636453958,"identity":"9d83dc35-4b44-45d7-bf63-06e92b3b7319","order_by":5,"name":"Kavya P","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Kavya","middleName":"","lastName":"P","suffix":""},{"id":636453959,"identity":"1dd3fd16-7356-46a6-af07-c926dab99253","order_by":6,"name":"Sharanagouda Patil","email":"","orcid":"","institution":"National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Sharanagouda","middleName":"","lastName":"Patil","suffix":""},{"id":636453960,"identity":"9c89af24-dfa2-4e8c-ae13-ece574b066e9","order_by":7,"name":"JAGADISH HIREMATH","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"JAGADISH","middleName":"","lastName":"HIREMATH","suffix":""},{"id":636453961,"identity":"46de93d6-1a15-48e1-a95a-3fb05430bbc2","order_by":8,"name":"Rajeswari Shome","email":"","orcid":"","institution":"ICAR-National Institute of Veterinary Epidemiology and Disease Informatics","correspondingAuthor":false,"prefix":"","firstName":"Rajeswari","middleName":"","lastName":"Shome","suffix":""},{"id":636453962,"identity":"4d5d96aa-0e95-4ae1-b136-ce588a85dedf","order_by":9,"name":"Ramith Ramu","email":"","orcid":"","institution":"4Department of Biotechnology and Bioinformatics, School of Life sciences, JSS Academy of Higher Education \u0026 Research","correspondingAuthor":false,"prefix":"","firstName":"Ramith","middleName":"","lastName":"Ramu","suffix":""},{"id":636453963,"identity":"43ea302a-25f9-4f05-9309-4526660b22c4","order_by":10,"name":"Rakesh Mishra","email":"","orcid":"https://orcid.org/0000-0001-6636-7380","institution":"Tata Institute for Genetics and Society","correspondingAuthor":false,"prefix":"","firstName":"Rakesh","middleName":"","lastName":"Mishra","suffix":""},{"id":636453964,"identity":"bae49aee-b8ae-4568-be0b-08a015c8a71a","order_by":11,"name":"Shivranjani Moharir","email":"","orcid":"https://orcid.org/0000-0001-8713-4543","institution":"Tata Institute for Genetics and Society","correspondingAuthor":false,"prefix":"","firstName":"Shivranjani","middleName":"","lastName":"Moharir","suffix":""}],"badges":[],"createdAt":"2026-04-29 10:46:35","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9564623/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9564623/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":108955429,"identity":"50f932eb-3bc1-4226-b82f-c05fd8540f85","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":298358,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGraphical abstract showing the study design with respect to sampling strategy, experimental approach and data analysis: \u003c/strong\u003eThe figure illustrates workflow of the study. 701 samples were collected sheep rectal swab, soil, feed, and water) from two districts, Chitradurga and Tumakur, in South Indian state of Karnataka. \u003cem\u003eE. coli \u003c/em\u003ewas isolated on selective media, with ESBL-producing strains confirmed using standard disc diffusion methods. A molecular screen for ESBL, tetracycline, and virulence genes was performed using PCR. Whole Genome Sequencing (WGS) was performed on 72 samples to enable in-depth characterization of ARGs, virulence genes, sequence types (MLST), and phylogeny.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/02e4683f45c68c37ac546944.png"},{"id":108955438,"identity":"8c30d7b5-9777-4139-bea7-6eaf8e10e534","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":93219,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePhenotypic Antibiotic Resistance Profiles of ESBL-Producing \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eIsolates from sheep and the environmental samples: (a) Heatmap showing the phenotypic resistance patterns for different antibiotics for the sheep and environment derived \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. \u003c/strong\u003eThe resistance profiles using AST disc diffusion assay for the 72 \u003cem\u003eE. coli \u003c/em\u003eisolates are shown in the heatmap, with annotation bars at the bottom indicating the district, village, sample type and sample ID. Multiple Antibiotic Resistance (MAR) index for each of the 72 samples is depicted in the form of a bar plot on the top. The vertical axis lists the tested antibiotics, categorized into - lactam and non-- lactam classes. Red cells indicate ‘resistance’, and white cells indicate ‘no resistance’ found in isolates for the specific antibiotics. \u003cstrong\u003e(b) Bar diagram showing the percent prevalence of phenotypic antibiotic resistance observed in the \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates: \u003c/strong\u003eThe data is stratified by source, showing the percentage of phenotypically resistant \u003cem\u003eE coli \u003c/em\u003eisolates derived from sheep (orange bar) and environment (green bar). Total 72 isolates were tested against the 14 antibiotics depicted on X axis, using the standard AST disc diffusion assay. \u003cstrong\u003e(c) Bar plot depicting the average MAR index of sheep and environmental isolates.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/33949eaa8eee8b1ec86d565b.png"},{"id":108978202,"identity":"1f5e21b5-6348-4e84-8928-1e6a506e6ce7","added_by":"auto","created_at":"2026-05-11 11:34:55","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":87979,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePCR based characterization of ESBL producing genes, tetracycline resistance genes and virulence genes: (a) Heatmap showing the presence or absence of four ESBL genes- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eTEM\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e, \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSHV\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e, \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eAmpC \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eand \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eCTXM \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003ein 72 \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment. (b) Bar plot showing the percent prevalence of the four ESBL genes- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eTEM\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e, \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eSHV\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e, \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eAmpC \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eand \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eCTXM \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003ein 72 \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment. (c) Heatmap showing the presence or absence of the tetracycline resistance genes \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003etetA \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eand \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003etetB \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenes in 72 \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. (d) Bar plot showing the percent prevalence of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003etetA \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eand \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003etetB \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenes in the sheep and environmental \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. (e) Heatmap showing the presence or absence of the virulence genes- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003estx1 and stx2 \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenes in 72 \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. (f) Bar plot showing the percent prevalence of \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003estx1 and stx2 \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003egenes in the sheep and environmental \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/8681877d0f7b4888a283ef03.png"},{"id":108977773,"identity":"9fb0be4b-2879-4dba-b888-0a8c77d58f71","added_by":"auto","created_at":"2026-05-11 11:32:51","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":146312,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDistribution pattern of antimicrobial resistance genes (ARGs) in \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment. Boxplots representing the alpha diversity calculated for ARG hits in sheep (orange colour) and the environmental (green colour) isolates using the (a) Shannon and (b) Simpson indices. \u003c/strong\u003eEach black dot represents the alpha diversity index of the individual isolate, and error bars indicate 95% confidence interval. No statistically significant difference was observed in the ARG hits alpha diversity between the sheep and environmental isolates. \u003cstrong\u003e(c) Heatmap showing the ARGs detected in sheep and environmental isolates. \u003c/strong\u003eGenes associated with the ESBL drug class are highlighted in red font, and grey cells indicate the absence of ARG in that sample. Carbapenem associated ARGs are marked with red triangle.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/b10b57635e11ca67a748a894.png"},{"id":108955430,"identity":"1145f72e-552a-4b32-8b2e-8cfbdf82eb63","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":225102,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDistribution pattern of antibiotic-resistant drug classes in ESBL- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment. Boxplots representing the alpha diversity calculated for resistant drug class hits in sheep (orange colour) and the environmental (green colour) isolates using the (a) Shannon and (b) Simpson indices\u003c/strong\u003e. Each black dot represents the alpha diversity index of the individual isolate, and error bars indicate 95% confidence interval. No statistically significant difference was observed in the alpha diversity of drug classes hits between the sheep and environmental isolates. \u003cstrong\u003e(c) Heatmap showing the relative abundance of the antibiotic-resistant drug classes detected in sheep and environmental isolates.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/e0cc94d09f0fc3847495348f.png"},{"id":108978076,"identity":"dd3d5c05-1c73-460a-8f0f-080b6cd06dc3","added_by":"auto","created_at":"2026-05-11 11:33:58","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":74971,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eHeatmap showing the distribution pattern of the drug class resistance mechanism observed in ESBL- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/427efd2e5e273251e1429a20.png"},{"id":108977774,"identity":"26ebef52-bd16-4026-93ae-f4c547920ec8","added_by":"auto","created_at":"2026-05-11 11:32:51","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":90842,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDistribution pattern of virulence genes observed in ESBL- \u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from sheep and environment. Boxplots representing the alpha diversity calculated for virulence genes hits in sheep (orange colour) and the environmental (green colour) isolates using the (a) Shannon and (b) Simpson indices\u003c/strong\u003e. Each black dot represents the alpha diversity index of the individual isolate, and error bars indicate 95% confidence interval. No statistically significant difference was observed in the alpha diversity of virulence genes hits between the sheep and environmental isolates. \u003cstrong\u003e(c) Heatmap showing the virulence genes detected in sheep and environmental isolates.\u003c/strong\u003e\u003c/p\u003e","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/a9bc212408262aae90ccf320.png"},{"id":108955432,"identity":"fdf852f6-c8a0-4006-93cf-52843d267609","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":106586,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePlasmids and serotypes detected in ESBL-\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates from Sheep and environment. (a) Venn diagram showing the shared and unique plasmids in 48 sheep and 16 environmental ESBL-\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. \u003c/strong\u003eOf the total 45 plasmids detected, 16 were unique to sheep isolates, 8 were unique to environmental isolates, and 21 were shared between both the sources. \u003cstrong\u003e(b) Venn diagram showing the shared and unique H-serotypes in 45 sheep and 17 environmental ESBL-\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. \u003c/strong\u003eOf the total 28 H serotypes detected, 13 were unique to sheep isolates, 3 were unique to environmental isolates, and 12 were shared between both the sources. \u003cstrong\u003e(c) Venn diagram showing the shared and unique O- serotypes in 45 Sheep and 17 environmental ESBL-\u003c/strong\u003e\u003cem\u003e\u003cstrong\u003eE. coli \u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003eisolates. \u003c/strong\u003eOf the total 61 O serotypes detected, 33 were unique to sheep isolates, 13 were unique to environmental isolates, and 15 were shared between both the sources.\u003c/p\u003e","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/09697e2919a48357bacc8aa1.png"},{"id":108955437,"identity":"efc54fea-783e-4114-a278-f1e8b9de5c09","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"png","order_by":9,"title":"Figure 9","display":"","copyAsset":false,"role":"figure","size":349747,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eNested pie-chart showing Achtman 7 gene MLSTs and phylogroups. \u003c/strong\u003ePlot illustrates the distribution of Achtman 7-gene Sequence Types (STs) and phylotypes across isolates from this study and comparative datasets from human derived isolates from Southern India, Slovenia Europe and Anguilla North America and sheep isolates from USA. Outermost layer labels indicate the identified Sequence Types (STs), followed by inner ring representing the sampling district (Chitradurga or Tumakuru), further followed by a ring denoting the sample source or type. Core annotations denote the sample IDs.\u003c/p\u003e","description":"","filename":"9.png","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/e927c26e421e6cb68f3d723c.png"},{"id":108980014,"identity":"f112b0a5-ce5f-4cc6-b23b-55221d795db5","added_by":"auto","created_at":"2026-05-11 12:03:02","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1495659,"visible":true,"origin":"","legend":"Article File","description":"","filename":"TIGSNIVEDIManuscipt29042026.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1_covered_9fb11fbd-0e4f-46fd-bc27-dc15bd7ee862.pdf"},{"id":108955434,"identity":"32458a66-0bfa-43bf-97b9-a178949b8a48","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":3593812,"visible":true,"origin":"","legend":"Supplementary Tables","description":"","filename":"23032026SupplementarytablesTIGSNIVEDI.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/d62b1b3ad109f8eef462893a.xlsx"},{"id":108955431,"identity":"0559e9f2-8b12-45b8-915d-b6d5325b9c4c","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":14542118,"visible":true,"origin":"","legend":"Supplementary Figures","description":"","filename":"22032026TIGSNIVEDISupplementaryFigures.docx","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/36499bba1c332c9f66cafbc6.docx"},{"id":108955439,"identity":"44fe7de0-12a5-4ff0-8c3a-e1760e1fb1ea","added_by":"auto","created_at":"2026-05-11 08:07:25","extension":"docx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":21545,"visible":true,"origin":"","legend":"Tables 1 and 2","description":"","filename":"TIGSNIVEDIMAINTABLES11032026.docx","url":"https://assets-eu.researchsquare.com/files/rs-9564623/v1/c63c44c84a4511a32d79c9cd.docx"}],"financialInterests":"\u003cp\u003eThere is \u003cstrong\u003eNO\u003c/strong\u003e Competing Interest.\u003c/p\u003e\n\u003cp\u003eTables 1 and 2 are available in the Supplementary Files section.\u003c/p\u003e","formattedTitle":"Whole-genome analysis reveals exchange of ESBL-E. coli genomes between migratory sheep and surrounding farm environments","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"ESBL-producing Escherichia coli, Multidrug resistance (MDR), Migratory sheep, Farm environment, Whole-genome sequencing (WGS)","lastPublishedDoi":"10.21203/rs.3.rs-9564623/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9564623/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"The spillover of pathogenic organisms across the livestock-environmental interface is a major OneHealth concern. To investigate the co-occurrence, antimicrobial resistance profiles, and genomic characteristics of ESBL-E. coli in healthy migratory sheep flocks and associated farm environments, a cross-sectional study was conducted in South Karnataka, India. 9124 animals from 60 farms were included in the study, and 701 samples from sheep and environmental were analysed, during 2023-2025. The occurrence of ESBL-E. coli was comparable in sheep and environmental samples, and exhibited high multidrug resistance patterns. Whole-genome-sequencing and comparative genomic analysis of ESBL-E. coli isolates revealed substantial diversity in antimicrobial resistance genes including resistance-nodulation-cell division family efflux pumps, alterations in β-lactam target proteins such as penicillin-binding proteins, and a wide range of β-lactamase genes, including CTX-M, TEM, DHA, AmpC, and SHV variants. Several plasmid replicon types were detected in both sheep and environmental isolates, suggesting potential plasmid-mediated horizontal gene transfer at the livestock-environment interface. Notably, phenotypic resistance to imipenem was detected in 16.6% of sheep isolates, and stx genes were identified in 19% of isolates, raising additional public health concerns. Overall, the detection of multidrug-resistant ESBL-E. coli in migratory sheep and their surrounding environments, together with shared resistomes, plasmids, and lineages, underscores the role of small non-sedentary ruminants as overlooked nodes in AMR dissemination and highlights the need for targeted OneHealth surveillance strategies.","manuscriptTitle":"Whole-genome analysis reveals exchange of ESBL-E. coli genomes between migratory sheep and surrounding farm environments","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-05-11 08:07:13","doi":"10.21203/rs.3.rs-9564623/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"nature-communications","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"NCOMMS","sideBox":"Learn more about [Nature Communications](http://www.nature.com/ncomms/)","snPcode":"","submissionUrl":"https://mts-ncomms.nature.com/","title":"Nature Communications","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Nature Communications","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"da6698fd-a0e0-4846-8f6a-b49b03acca0c","owner":[],"postedDate":"May 11th, 2026","published":true,"recentEditorialEvents":[{"type":"editorInvitedReview","content":"This content is not available.","date":"2026-05-10T12:44:55+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewerAgreed","content":"This content is not available.","date":"2026-05-08T06:50:19+00:00","index":1,"fulltext":"This content is not available."},{"type":"reviewersInvited","content":"3","date":"2026-05-07T21:39:43+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2026-05-05T08:11:19+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2026-04-29T19:01:33+00:00","index":"","fulltext":""},{"type":"submitted","content":"Nature Communications","date":"2026-04-29T10:43:41+00:00","index":"","fulltext":""}],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":67743159,"name":"Biological sciences/Microbiology/Bacteriology"},{"id":67743160,"name":"Biological sciences/Microbiology/Environmental microbiology/Soil microbiology"},{"id":67743161,"name":"Biological sciences/Microbiology/Environmental microbiology/Water microbiology"},{"id":67743162,"name":"Biological sciences/Genetics/Genomics/Comparative genomics"}],"tags":[],"updatedAt":"2026-05-11T08:07:13+00:00","versionOfRecord":[],"versionCreatedAt":"2026-05-11 08:07:13","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9564623","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9564623","identity":"rs-9564623","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}