a274f3ed3d0b99807d98db6b9889f353 antibiotics-15-00676.pdf 2d6be1a060e01677270c1cd22488fd43847e2b34 antibiotics-15-00676.pdf 8330d146b7da923902c696a9dbb23dc79580ff51009f2011c0342ce3b872752a antibiotics-15-00676.pdf Title: Prevalence and Genomic Characterization of ESBL-Producing Escherichia coli in Livestock and Farmers in Catalonia, Spain Subject: Background and objectives: Extended-spectrum -lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae represent an increasing One Health concern because food-producing animals may act as reservoirs of antimicrobial-resistant bacteria with potential transmission to humans. Therefore, this study aimed to assess the prevalence and genomic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in livestock and farmers, and to evaluate genomic overlap between animal and human ESBL-producing Escherichia coli to explore potential shared origins and interspecies transmission. Methods: We conducted a cross-sectional study in Osona (Catalonia, Spain), sampling livestock (swine, cattle, poultry, and horses) and farmers. ESBL-, AmpC-, and carbapenemase-producing Enterobacteriaceae were identified and characterized using whole genome sequencing (WGS). Genomic analyses included sequence typing (ST), serotyping, virulence-associated genes, antimicrobial resistance determinants, and plasmid replicon profiling. Results: A total of 945 animals were analysed. ESBL-producing Enterobacteriaceae were predominantly detected in swine, with 63.5% (127/200) of animals testing positive, including four ESBL + AmpC-producing isolates and two carbapenem-resistant Enterobacteriaceae. No ESBL-, AmpC- or carbapenemase-producing isolates were identified in cattle (0/360) or poultry (0/171), and a low prevalence was observed in horses (7.0%, 15/214). A total of 64 farm workers were analysed. ESBL-producing E. coli were detected in 46.7% (7/15) of swine farmers and 8.3% (2/24) of cattle farmers, while no ESBL-producing isolates were found among poultry farmers (0/8) or equine caretakers (0/17). A total of 162 isolates were analyzed by WGS, showing high genetic diversity. Among the 127 Escherichia coli isolates, the most prevalent were ST10 (18/127, 14.2%), followed by ST453 (7/127, 5.5%), ST515 (7/127, 5.5%), and ST10562 (7/127, 5.5%). Virulence-associated gene profiles were heterogeneous, although genes related to stress tolerance and intestinal colonization predominated among ESBL-producing E. coli isolates from swine, including terC (54/127, 42.5%), csgA (41/127, 32.3%), nlpI (41/127, 32.3%), and fimH (39/127, 30.7%). ESBL production among E. coli isolates from swine was primarily mediated by blaCTX-M genes (89/127, 70.1%), with additional contributions from blaSHV (34/127, 26.8%) and blaTEM (40/127, 31.5%). Among swine isolates, IncX1 (100/127, 78.7%), IncFIB(AP001918) (82/127, 64.6%), IncI1-I(Alpha) (69/127, 54.3%), and IncFII (54/127, 42.5%) were the most frequently detected plasmid replicons. Two carbapenem-resistant isolates carrying blaOXA-48 were identified in swine, including E. coli ST58 and K. oxytoca ST145, both associated with IncL plasmids. Conclusions: Swine appear to constitute the primary reservoir of ESBL-producing E. coli. The genomic relatedness observed between animal and human isolates supports shared exposure to a common ecological pool of multidrug-resistant bacteria. The identification of blaOXA-48-producing Enterobacterales associated with IncL plasmids further highlights the public health relevance of livestock-associated antimicrobial resistance. However, the cross-sectional design precludes inference of transmission pathways or transmission directionality. Longitudinal studies are needed to elucidate the dynamics of interspecies transmission. Keywords: antimicrobial resistance; ESBL-producing Escherichia coli; prevalence; genomic; rectal colonization; livestock; Spain Author: Marina Serras-Pujol, Noemí Párraga-Niño, Marian Navarro, Anna Vilamala, Emma Puigoriol, Elisenda Arqué, Judit Serra-Pladevall, Luisa Pedro-Botet and Esteban Reynaga Creator: LaTeX with hyperref Producer: pdfTeX-1.40.25; modified using OpenPDF 1.4.2 CreationDate: Fri Jul 10 08:31:50 2026 CEST ModDate: Fri Jul 10 08:51:45 2026 CEST Custom Metadata: yes Metadata Stream: no Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 17 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 3343120 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- ZCHBYA+VnURWPalladioL Type 1 Custom yes yes yes 124 0 ABKRJY+URWPalladioL-Ital Type 1 Custom yes yes yes 125 0 CAMXTK+EURM10 Type 1 Builtin yes yes yes 126 0 XJLBJU+URWPalladioL-Bold Type 1 Custom yes yes yes 127 0 SFUDNE+URWPalladioL-BoldItal Type 1 Custom yes yes yes 128 0 PFULRJ+URWPalladioL-Roma Type 1 Custom yes yes yes 129 0 FIADMR+CMSY10 Type 1 Builtin yes yes yes 196 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2026-09-16 04:08:37 CEST RepresentationInformation: antibiotics-15-00676.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2026-09-15 14:52:08 CEST Size: 3343120 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 442 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: false NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Item: Title: Material and Methods Children: Item: Title: Selection of Farms Item: Title: Collection of Animal Samples Item: Title: Collection of Human Samples Item: Title: Microbiological Analysis of Samples Item: Title: DNA Extraction and Quantification Item: Title: Whole Genome Sequencing Item: Title: Statistical Analysis Item: Title: Results Children: Item: Title: Prevalence of ESBL/AmpC- and Carbapenemase-Producing Enterobacteriaceae Item: Title: Comparative Phylogenomics Children: Item: Title: Sequence Types Item: Title: Serotypes (O:H) Item: Title: Virulence-Associated Genes Item: Title: Antimicrobial Resistance Genes Item: Title: Plasmid Replicon Types Item: Title: Discussion Item: Title: References Info: Title: Prevalence and Genomic Characterization of ESBL-Producing Escherichia coli in Livestock and Farmers in Catalonia, Spain Author: Marina Serras-Pujol, Noemí Párraga-Niño, Marian Navarro, Anna Vilamala, Emma Puigoriol, Elisenda Arqué, Judit Serra-Pladevall, Luisa Pedro-Botet and Esteban Reynaga Subject: Background and objectives: Extended-spectrum -lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae represent an increasing One Health concern because food-producing animals may act as reservoirs of antimicrobial-resistant bacteria with potential transmission to humans. Therefore, this study aimed to assess the prevalence and genomic characteristics of ESBL- and carbapenemase-producing Enterobacteriaceae in livestock and farmers, and to evaluate genomic overlap between animal and human ESBL-producing Escherichia coli to explore potential shared origins and interspecies transmission. Methods: We conducted a cross-sectional study in Osona (Catalonia, Spain), sampling livestock (swine, cattle, poultry, and horses) and farmers. ESBL-, AmpC-, and carbapenemase-producing Enterobacteriaceae were identified and characterized using whole genome sequencing (WGS). Genomic analyses included sequence typing (ST), serotyping, virulence-associated genes, antimicrobial resistance determinants, and plasmid replicon profiling. Results: A total of 945 animals were analysed. ESBL-producing Enterobacteriaceae were predominantly detected in swine, with 63.5% (127/200) of animals testing positive, including four ESBL + AmpC-producing isolates and two carbapenem-resistant Enterobacteriaceae. No ESBL-, AmpC- or carbapenemase-producing isolates were identified in cattle (0/360) or poultry (0/171), and a low prevalence was observed in horses (7.0%, 15/214). A total of 64 farm workers were analysed. ESBL-producing E. coli were detected in 46.7% (7/15) of swine farmers and 8.3% (2/24) of cattle farmers, while no ESBL-producing isolates were found among poultry farmers (0/8) or equine caretakers (0/17). A total of 162 isolates were analyzed by WGS, showing high genetic diversity. Among the 127 Escherichia coli isolates, the most prevalent were ST10 (18/127, 14.2%), followed by ST453 (7/127, 5.5%), ST515 (7/127, 5.5%), and ST10562 (7/127, 5.5%). Virulence-associated gene profiles were heterogeneous, although genes related to stress tolerance and intestinal colonization predominated among ESBL-producing E. coli isolates from swine, including terC (54/127, 42.5%), csgA (41/127, 32.3%), nlpI (41/127, 32.3%), and fimH (39/127, 30.7%). ESBL production among E. coli isolates from swine was primarily mediated by blaCTX-M genes (89/127, 70.1%), with additional contributions from blaSHV (34/127, 26.8%) and blaTEM (40/127, 31.5%). Among swine isolates, IncX1 (100/127, 78.7%), IncFIB(AP001918) (82/127, 64.6%), IncI1-I(Alpha) (69/127, 54.3%), and IncFII (54/127, 42.5%) were the most frequently detected plasmid replicons. Two carbapenem-resistant isolates carrying blaOXA-48 were identified in swine, including E. coli ST58 and K. oxytoca ST145, both associated with IncL plasmids. Conclusions: Swine appear to constitute the primary reservoir of ESBL-producing E. coli. The genomic relatedness observed between animal and human isolates supports shared exposure to a common ecological pool of multidrug-resistant bacteria. The identification of blaOXA-48-producing Enterobacterales associated with IncL plasmids further highlights the public health relevance of livestock-associated antimicrobial resistance. However, the cross-sectional design precludes inference of transmission pathways or transmission directionality. Longitudinal studies are needed to elucidate the dynamics of interspecies transmission. 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