Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Advertisement

Scientific Reports
  • View all journals
  • Search
  • My Account Login
  • Content Explore content
  • About the journal
  • Publish with us
  • Sign up for alerts
  • RSS feed
  1. nature
  2. scientific reports
  3. articles
  4. article
Genomic profiling of extended-spectrum beta-lactamase-producing Escherichia coli isolated from poultry and poultry farm workers in Accra, Ghana
Download PDF
Download PDF
  • Article
  • Open access
  • Published: 05 February 2026

Genomic profiling of extended-spectrum beta-lactamase-producing Escherichia coli isolated from poultry and poultry farm workers in Accra, Ghana

  • Isaac J. Okyere1,4,
  • Grace O. Semevor1,
  • Anthony Ablordey2,
  • Sherry Johnson3 &
  • …
  • Eric S. Donkor1 

Scientific Reports , Article number:  (2026) Cite this article

We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Microbiology
  • Molecular biology

Abstract

Antimicrobial resistance (AMR), driven by the extensive use of antibiotics in human and animal health, poses a significant global threat. In Ghana, the contribution of poultry farming to the high prevalence of AMR remains underexplored. This study investigates the genomic characteristics and prevalence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli in poultry and human populations. A total of 300 cloacal swabs from poultry and 60 stool samples from poultry farm workers in peri-urban Accra were collected from 20 poultry farms and cultured. Bacterial isolates were identified through MALDI-TOF-MS, with ESBL production confirmed using the double disk synergy test. Whole-genome sequencing of 17 multi-drug resistant isolates selected was conducted on the MiSeq Illumina platform to characterize resistance genes, virulence genes, and sequence types. ESBL production was detected in 84.8% (n = 123/145) in isolates from poultry and 67.5% (n = 27/40) in isolates from humans. All isolates were resistant to cefotaxime, with significant resistance to tetracycline and sulfamethoxazole-trimethoprim also recorded. The blaCTX−M−15 gene was the most prevalent ESBL gene identified, with additional genes including blaCTX−M−27, blaOXA−1, blaOXA−181, blaTEM−1B, and blaDHA−1 also identified. Sequence typing revealed multiple resistance-associated sequence types, notably ST10 and ST155. Plasmid replicon analysis identified IncF, Col, and IncI1 groups, many co-occurring with multiple resistance genes. Virulome profiling revealed the presence of avian pathogenic E. coli (APEC)-associated genes such as iroN, iss, ompT, and hlyF. This study highlights the prevalence and genomic characteristics of ESBL-producing E. coli at the human–poultry interface in Ghana, emphasizing poultry as a potential reservoir for multidrug-resistant bacteria. The findings provide actionable insights for small- to medium-scale poultry farmers, including the importance of prudent antibiotic use, enhanced hygiene, and biosecurity practices, and underscore the need for ongoing genomic surveillance to guide interventions aimed at reducing the spread of antimicrobial resistance in Ghana.

Data availability

The raw sequencing data are available at the National Center for Biotechnology Information Sequence Read Archive under the BioProject ID PRJNA1208549. All other raw data supporting the reported results can be made available upon request from the corresponding author.

References

  1. Naghavi, M. et al. Global burden of bacterial antimicrobial resistance 1990–2021: a systematic analysis with forecasts to 2050. Lancet 404, 10459, 1199–1226. https://doi.org/10.1016/S0140-6736(24)01867-1 (2024).

    Google Scholar 

  2. Husna, A. et al. Extended-Spectrum β-Lactamases (ESBL): Challenges and Opportunities. Biomedicines. 11 11, 2937, (2023). https://doi.org/10.3390/biomedicines11112937

  3. Shaikh, S. et al. Antibiotic resistance and extended spectrum beta-lactamases: Types, epidemiology and treatment. Saudi J. Biol. Sci. 22, 1, 90–101. https://doi.org/10.1016/j.sjbs.2014.08.002 (2015).

    Google Scholar 

  4. Nkansa, M., Agbekpornu, H., Kikimoto, B. & Chandler, C. Antibiotic Use among Poultry Farmers in the Dormaa Municipality, Ghana. Report for Fleming Fund Fellowship Programme (London School of Hygiene & Tropical Medicine, 2020). https://doi.org/10.17037/PUBS.04658868

  5. Paintsil, E. K. et al. Antimicrobial usage in commercial and domestic poultry farming in two communities in the Ashanti region of Ghana. Antibiotic S (Basel). 10, 7, (800). https://doi.org/10.3390/antibiotics10070800 (2021).

  6. Enyetornye, B., Velayudhan, B. T. & Gottdenker, N. L. The poultry sector of Ghana: regime transitions and its implications for poultry health and management, World’s Poultry Science Journal, Dec. Accessed: Dec. 11, 2024. [Online]. Available: https://www.tandfonline.com/doi/abs/ (2024). https://doi.org/10.1080/00439339.2024.2437184

  7. Aworh, M. K. et al. Characteristics of antimicrobial resistance in Escherichia coli isolated from retail meat products in North Carolina. PLoS ONE. 19, 1, (e0294099). https://doi.org/10.1371/journal.pone.0294099 (2024).

  8. Cohen Stuart, J. et al. Comparison of ESBL contamination in organic and conventional retail chicken meat. Int. J. Food Microbiol. 154, 3, 212–214. https://doi.org/10.1016/j.ijfoodmicro.2011.12.034 (2012).

    Google Scholar 

  9. Overdevest, I. et al. Extended-spectrum β-lactamase genes of Escherichia coli in chicken meat and humans, the Netherlands. Emerg. Infect. Dis. 17, 7, 1216–1222. https://doi.org/10.3201/eid1707.110209 (2011).

    Google Scholar 

  10. Foster-Nyarko, E. et al. Genomic diversity of Escherichia coli isolates from backyard chickens and Guinea fowl in the Gambia. Microb. Genomics. 7 (1). https://doi.org/10.1099/mgen.0.000484 (2021).

  11. Asare Yeboah, E. E. et al. Genomic characterization of multi drug resistant ESBL-producing Escherichia coli isolates from patients and patient environments in a teaching hospital in Ghana. BMC Microbiol. 24, 1, (250). https://doi.org/10.1186/s12866-024-03406-1 (2024).

  12. Ayim-Akonor, M. et al. Antimicrobial Susceptibility Profile and Extended-Spectrum Beta-Lactamase Phenotype of E. coli Isolated From Poultry. International Journal of Microbiology. 1, 9468425, 2025, (2025). https://doi.org/10.1155/ijm/9468425

  13. Akenten, C. W. et al. Prevalence, Characterization, and antimicrobial resistance of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli from domestic Free-Range poultry in Agogo, Ghana. Foodborne Pathog. Dis. 20, 2, 59–66. https://doi.org/10.1089/fpd.2022.0060 (2023).

    Google Scholar 

  14. Falgenhauer, L. et al. Detection and characterization of ESBL-Producing Escherichia coli from humans and poultry in Ghana. Front. Microbiol., https://doi.org/10.3389/fmicb.2018.03358 (2019).

  15. Nhung, N. T., Chansiripornchai, N. & Carrique-Mas, J. J. Antimicrobial resistance in bacterial poultry pathogens: A review. Front. Vet. Sci. 4, 126 https://doi.org/10.3389/fvets.2017.00126 (2017).

  16. Alders, R. G. & Pym, R. E. Village poultry: still important to millions, eight thousand years after domestication. World’s Poult. Sci. J. 65, 2, 181–190. https://doi.org/10.1017/S0043933909000117 (2009).

    Google Scholar 

  17. Wong, J. T. et al. Small-scale poultry and food security in resource-poor settings: A review. Global Food Secur. 15, 43–52. https://doi.org/10.1016/j.gfs.2017.04.003 (2017).

    Google Scholar 

  18. WHO. Integrated Global Surveillance on ESBL-Producing E. Coli Using a One Health Approach: Implementation and Opportunities 1st edn (World Health Organization, 2021).

  19. Hindler, J. A. & Schuetz, A. N. CLSI and the AST subcommittee during COVID-19, 6, 1, (2021).

  20. O’Brien, T. F. & Stelling, J. M. WHONET: an information system for monitoring antimicrobial resistance. Emerg. Infect. Dis. 1, 2, (66). https://doi.org/10.3201/eid0102.950209 (1995).

  21. Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30, 15, 2114–2120. https://doi.org/10.1093/bioinformatics/btu170 (2014).

    Google Scholar 

  22. Larsen, M. V. et al. Multilocus sequence typing of total-genome-sequenced bacteria. J. Clin. Microbiol. 50, 4, 1355–1361. https://doi.org/10.1128/JCM.06094-11 (2012).

    Google Scholar 

  23. Bortolaia, V. et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J. Antimicrob. Chemother. 75, 12, 3491–3500. https://doi.org/10.1093/jac/dkaa345 (2020).

    Google Scholar 

  24. Joensen, K. G. et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J. Clin. Microbiol. 52 (5), 1501–1510. https://doi.org/10.1128/JCM.03617-13 (2014).

    Google Scholar 

  25. Carattoli, A. et al. In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob. Agents Chemother. 58, 7, 3895–3903. https://doi.org/10.1128/AAC.02412-14 (2014).

    Google Scholar 

  26. Beghain, J., Bridier-Nahmias, A., Le Nagard, H., Denamur, E. & Clermont, O. ClermonTyping: an easy-to-use and accurate in Silico method for Escherichia genus strain phylotyping. Microb. Genom. 4, 7, (e000192). https://doi.org/10.1099/mgen.0.000192 (2018).

  27. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms | PLOS ONE. Accessed: Feb. 15, 2025. [Online]. Available: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0104984

  28. Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296. https://doi.org/10.1093/nar/gkab301 (2021).

    Google Scholar 

  29. Antimicrobial resistance, WOAH - World Organisation for Animal Health. Accessed: Feb. 15, 2025. [Online]. Available: https://www.woah.org/en/what-we-do/global-initiatives/antimicrobial-resistance/

  30. Murray, C. J. L. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 10325, 629–655. https://doi.org/10.1016/S0140-6736(21)02724-0 (2022).

    Google Scholar 

  31. Aliyu, A. B., Jalila, A., Saleha, A. A. & Zunita, Z. ESBL producing E. coli in chickens and poultry farms environment in Selangor, malaysia: A Cross-Sectional study on their occurrence and associated risk factors with environment and public health importance. Zoonoses Public. Health. 71, 8, 962–971. https://doi.org/10.1111/zph.13179 (2024).

    Google Scholar 

  32. Day, M. J. et al. Extended-spectrum β-lactamase-producing Escherichia coli in human-derived and foodchain-derived samples from England, Wales, and scotland: an epidemiological surveillance and typing study. Lancet. Infect. Dis. 19, 12, 1325–1335. https://doi.org/10.1016/S1473-3099(19)30273-7 (2019).

    Google Scholar 

  33. Halabi, M. K. et al. Antibiotic resistance pattern of extended spectrum beta lactamase producing Escherichia coli isolated from patients with urinary tract infection in Morocco. Front. Cell. Infect. Microbiol. 11 (720701). https://doi.org/10.3389/fcimb.2021.720701 (2021).

  34. Ibrahim, D. R. et al. Multidrug-Resistant ESBL-Producing E. coli in Clinical Samples from the UK. Antibiotics, 12,1, 169, (2023). https://doi.org/10.3390/antibiotics12010169

  35. Johnson, S., Bugyei, K., Nortey, P. & Tasiame, W. Antimicrobial drug usage and poultry production: case study in Ghana. Anim. Prod. Sci. 59 (1), 177–182. https://doi.org/10.1071/AN16832 (2019).

    Google Scholar 

  36. Chah, K. F. et al. Detection and molecular characterisation of extended-spectrum β-lactamase-producing enteric bacteria from pigs and chickens in Nsukka, Nigeria. J. Global Antimicrob. Resist. 15, 36–40. https://doi.org/10.1016/j.jgar.2018.06.002 (2018).

    Google Scholar 

  37. Ghenea, A. E. et al. TEM,CTX-M,SHV genes in ESBL-Producing Escherichia coli and Klebsiella pneumoniae isolated from clinical samples in a County clinical emergency hospital Romania-Predominance of CTX-M-15. Antibiot. (Basel). 11 (4, 503, ). https://doi.org/10.3390/antibiotics11040503 (2022).

  38. Manyahi, J. et al. Detection of CTX-M-15 beta-lactamases in Enterobacteriaceae causing hospital- and community-acquired urinary tract infections as early as 2004, in Dar Es Salaam, Tanzania. BMC Infect. Dis. 17, 1, (282). https://doi.org/10.1186/s12879-017-2395-8 (2017).

  39. Fam, N. et al. CTX-M-15-Producing Escherichia coli clinical isolates in Cairo (Egypt), including isolates of clonal complex ST10 and clones ST131, ST73, and ST405 in both community and hospital settings. Microb. Drug Resist. 17 (1), 67–73. https://doi.org/10.1089/mdr.2010.0063 (2011).

    Google Scholar 

  40. Agyekum, A. et al. blaCTX-M-15 carried by IncF-type plasmids is the dominant ESBL gene in Escherichia coli and Klebsiella pneumoniae at a hospital in Ghana. Diagn. Microbiol. Infect. Dis. 84 (4), 328–333. https://doi.org/10.1016/j.diagmicrobio.2015.12.010 (2016).

    Google Scholar 

  41. Akenten, C. W. et al. Carriage of ESBL-producing Klebsiella pneumoniae and Escherichia coli among children in rural ghana: a cross-sectional study. Antimicrob. Resist. Infect. Control. 12, 60 https://doi.org/10.1186/s13756-023-01263-7 (2023).

  42. Cissé, A. et al. Prevalence, Antimicrobial Susceptibility, and Resistance Genes of Extended-Spectrum β-Lactamase-Producing Escherichia coli from Broilers Sold in Open Markets of Dakar, Senegal. Microorganisms. 12, 11, 2357, (2024). https://doi.org/10.3390/microorganisms12112357

  43. Muhummed, A. et al. Fecal carriage of ESBL-producing E. coli and genetic characterization in rural children and livestock in the Somali region, ethiopia: a one health approach. Antimicrob. Resist. Infect. Control. 13, 148 https://doi.org/10.1186/s13756-024-01502-5 (2024).

  44. Sewunet, T. et al. Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia. J. Global Antimicrob. Resist. 29, 405–412. https://doi.org/10.1016/j.jgar.2021.09.017 (2022).

    Google Scholar 

  45. Sugumar, M., Kumar, K. M., Manoharan, A., Anbarasu, A. & Ramaiah, S. Detection of OXA-1 β-Lactamase gene of Klebsiella pneumoniae from blood stream infections (BSI) by conventional PCR and In-Silico analysis to understand the mechanism of OXA mediated resistance. PLOS ONE. 9 3, (e91800). https://doi.org/10.1371/journal.pone.0091800 (2014).

  46. Siu, L. K. et al. beta-lactamases in Shigella flexneri isolates from Hong Kong and Shanghai and a novel OXA-1-like beta-lactamase, OXA-30. Antimicrob. Agents Chemother. 44, 8, 2034–2038. https://doi.org/10.1128/AAC.44.8.2034-2038.2000 (2000).

    Google Scholar 

  47. Mahazu, S. et al. Possible dissemination of Escherichia coli sequence type 410 closely related to B4/H24RxC in Ghana. Front. Microbiol. https://doi.org/10.3389/fmicb.2021.770130 (2021).

    Google Scholar 

  48. Randall, L. P. et al. Prevalence of Escherichia coli carrying extended-spectrum β-lactamases (CTX-M and TEM-52) from broiler chickens and Turkeys in great Britain between 2006 and 2009. J. Antimicrob. Chemother. 66 (1), 86–95. https://doi.org/10.1093/jac/dkq396 (2011).

    Google Scholar 

  49. Huijbers, P. M. C. et al. Extended-spectrum and AmpC β-lactamase-producing Escherichia coli in broilers and people living and/or working on broiler farms: prevalence, risk factors and molecular characteristics. J. Antimicrob. Chemother. 69, 10, 2669–2675. https://doi.org/10.1093/jac/dku178 (2014).

    Google Scholar 

  50. Muteeb, G., Rehman, M. T., Shahwan, M. & Aatif, M. Origin of antibiotics and antibiotic Resistance, and their impacts on drug development: A narrative review. Pharmaceuticals (Basel). 16, 11, (1615). https://doi.org/10.3390/ph16111615 (2023).

  51. Pasquali, F. et al. Genetic diversity and antimicrobial resistance of extraintestinal E. coli populations Pre- and Post-Antimicrobial therapy on broilers affected by colisepticemia. Anim. : Open. Access. J. MDPI. 13,16 (2590). https://doi.org/10.3390/ani13162590 (2023).

  52. Aworh, M. K., Kwaga, J. K. P., Hendriksen, R. S., Okolocha, E. C. & Thakur, S. Genetic relatedness of multidrug resistant Escherichia coli isolated from humans, chickens and poultry environments. Antimicrob. Resist. Infect. Control. 10 (1, 58, ). https://doi.org/10.1186/s13756-021-00930-x (2021).

  53. Bergeron, C. R. et al. Chicken as reservoir for extraintestinal pathogenic Escherichia coli in Humans, Canada. Emerg. Infect. Dis. 18,3, (415). https://doi.org/10.3201/eid1803.111099 (2012).

  54. Manges, A. R. et al. Multilocus sequence typing and virulence gene profiles associated with Escherichia coli from human and animal sources. Foodborne Pathog Dis. 12, 4, 302–310. https://doi.org/10.1089/fpd.2014.1860 (2015).

    Google Scholar 

  55. Müller, C. M. et al. Type 1 Fimbriae, a colonization factor of uropathogenic Escherichia coli, are controlled by the metabolic sensor CRP-cAMP. PLoS Pathog. 5 https://doi.org/10.1371/journal.ppat.1000303 (2009). 2, e1000303.

  56. Sváb, D. et al. The long Polar fimbriae (lpf) Operon and its flanking regions in bovine Escherichia coli O157:H43 and STEC O136:H12 strains. Pathog Dis. 68 https://doi.org/10.1111/2049-632X.12038 (2013).

  57. Prorok-Hamon, M. et al. Colonic mucosa-associated diffusely adherent afaC + Escherichia coli expressing LpfA and Pks are increased in inflammatory bowel disease and colon cancer. Gut 63 (5, 761). https://doi.org/10.1136/gutjnl-2013-304739 (2013).

  58. Hojati, Z., Zamanzad, B., Hashemzadeh, M., Molaie, R. & Gholipour, A. The FimH gene in uropathogenic Escherichia coli strains isolated from patients with urinary tract infection. Jundishapur J. Microbiol. 8, (e17520). https://doi.org/10.5812/jjm.17520 (2015).

  59. Gomes, T. A. T. et al. Diarrheagenic Escherichia coli. Braz J. Microbiol. 47, 1, 3–30. https://doi.org/10.1016/j.bjm.2016.10.015 (2016).

    Google Scholar 

  60. Nataro, J. P. & Kaper, J. B. Diarrheagenic Escherichia coli. Clin. Microbiol. Rev. 11, 1, 142–201. https://doi.org/10.1128/cmr.11.1.142 (1998).

    Google Scholar 

  61. Trabulsi, L. R., Keller, R. & Gomes, T. A. T. 10.321/eid0805.Typical and atypical enteropathogenic Escherichia coli. Emerg. Infect. Dis. 8, 5, 508–513. https://doi.org/10.3201/eid0805.010385 (2002).

    Google Scholar 

  62. Kathayat, D., Lokesh, D., Ranjit, S. & Rajashekara, G. Avian Pathogenic Escherichia coli (APEC): An Overview of Virulence and Pathogenesis Factors, Zoonotic Potential, and Control Strategies. Pathogens 10, 4, 467, (2021). https://doi.org/10.3390/pathogens10040467

  63. Thomrongsuwannakij, T., Blackall, P. J., Djordjevic, S. P., Cummins, M. L. & Chansiripornchai, N. A comparison of virulence genes, antimicrobial resistance profiles and genetic diversity of avian pathogenic Escherichia coli (APEC) isolates from broilers and broiler breeders in Thailand and Australia, Avian Pathology, Sept. Accessed: Oct. 01, 2025. [Online]. Available: https://www.tandfonline.com/doi/abs/ (2020). https://doi.org/10.1080/03079457.2020.1764493

  64. Ewers, C., Janssen, T. & Wieler, L. H. [Avian pathogenic Escherichia coli (APEC)]. Berl Munch. Tierarztl. Wochenschr. 116, 9–10 (2003).

    Google Scholar 

  65. Zhang, H. et al. Dissecting the metal resistance genes contributed by Virome from mining-affected metal contaminated soils. Front. Environ. Sci. https://doi.org/10.3389/fenvs.2023.1182673 (2023).

  66. Kormutakova, R., Klucar, L. & Turna, J. DNA sequence analysis of the tellurite-resistance determinant from clinical strain of Escherichia coli and identification of essential genes. Biometals 13 (2), 135–139. https://doi.org/10.1023/A:1009272122989 (2000).

    Google Scholar 

  67. Karatzas, K. A. G., Suur, L. & O’Byrne, C. P. Characterization of the intracellular glutamate decarboxylase system: analysis of its Function, Transcription, and role in the acid resistance of various strains of Listeria monocytogenes. Appl. Environ. Microbiol. 78,10 (3571). https://doi.org/10.1128/AEM.00227-12 (2012).

  68. Yang, H., He, M. & Wu, C. Cross protection of lactic acid bacteria during environmental stresses: stress responses and underlying mechanisms. LWT 144 (111203). https://doi.org/10.1016/j.lwt.2021.111203 (2021).

  69. Reig, M. & Toldrá, F. Veterinary drug residues in meat: concerns and rapid methods for detection. Meat Sci. 78 (1–2), 60–67. https://doi.org/10.1016/j.meatsci.2007.07.029 (2008).

    Google Scholar 

  70. Goetting, V., Lee, K. A. & Tell, L. A. Pharmacokinetics of veterinary drugs in laying hens and residues in eggs: a review of the literature. J. Vet. Pharmacol. Ther. 34, 6, 521–556. https://doi.org/10.1111/j.1365-2885.2011.01287.x (2011).

    Google Scholar 

  71. Yang, Q. E. et al. IncF plasmid diversity in multi-drug resistant Escherichia coli strains from animals in China. Front. Microbiol. https://doi.org/10.3389/fmicb.2015.00964 (2015).

    Google Scholar 

  72. Mathers, A. J., Peirano, G. & Pitout, J. D. D. The role of epidemic resistance plasmids and international high-risk clones in the spread of multidrug-resistant Enterobacteriaceae. Clin. Microbiol. Rev. 28, 3, 565–591. https://doi.org/10.1128/CMR.00116-14 (2015).

    Google Scholar 

  73. Rozwandowicz, M. et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J. Antimicrob. Chemother. 73, 5, 1121–1137. https://doi.org/10.1093/jac/dkx488 (2018).

    Google Scholar 

  74. Liao, X. P. et al. Comparison of plasmids coharboring 16S rRNA Methylase and Extended-Spectrum β-Lactamase genes among Escherichia coli isolates from pets and poultry. J. Food. Prot. 76, 12, 2018–2023. https://doi.org/10.4315/0362-028X.JFP-13-200 (2013).

    Google Scholar 

  75. Adelowo, O. O. et al. A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in Southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance. PLoS One. 15, (e0229451). https://doi.org/10.1371/journal.pone.0229451 (2020).

  76. Liu, B. T. et al. Dissemination and characterization of plasmids carrying oqxAB-blaCTX-M genes in Escherichia coli isolates from Food-Producing animals. PLOS ONE. 8, (e73947). https://doi.org/10.1371/journal.pone.0073947 (2013).

  77. Soncini, J. G. M. et al. Genomic insights of high-risk clones of ESBL-producing Escherichia coli isolated from community infections and commercial meat in Southern Brazil. Sci. Rep. 12 (1, 9354, ). https://doi.org/10.1038/s41598-022-13197-y (2022).

  78. Carattoli, A. Plasmids and the spread of resistance. Int. J. Med. Microbiol. 303, 6, 298–304. https://doi.org/10.1016/j.ijmm.2013.02.001 (2013).

    Google Scholar 

Download references

Acknowledgements

We are grateful to the poultry farm owners, workers, and the laboratory and technical staff of the Department of Medical Microbiology, University of Ghana Medical School.

Funding

This work was funded by the National Institutes of Health, USA, through the “Application of Data Science to Build Research Capacity in Zoonoses and Food-Borne Infections in West Africa (DS-ZOOFOOD) Training Programme” hosted at the Department of Medical Microbiology, University of Ghana Medical School (Grant Number: UE5TW012566). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Author information

Authors and Affiliations

  1. Department of Medical Microbiology, University of Ghana Medical School, Korle Bu, P.O. Box KB 4236, Accra, Ghana

    Isaac J. Okyere, Grace O. Semevor & Eric S. Donkor

  2. Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, P.O. Box LG 581, Accra, Ghana

    Anthony Ablordey

  3. School of Veterinary Medicine, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 68, Accra, Ghana

    Sherry Johnson

  4. Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY, 13210, USA

    Isaac J. Okyere

Authors
  1. Isaac J. Okyere
    View author publications

    Search author on:PubMed Google Scholar

  2. Grace O. Semevor
    View author publications

    Search author on:PubMed Google Scholar

  3. Anthony Ablordey
    View author publications

    Search author on:PubMed Google Scholar

  4. Sherry Johnson
    View author publications

    Search author on:PubMed Google Scholar

  5. Eric S. Donkor
    View author publications

    Search author on:PubMed Google Scholar

Contributions

Conceptualization, ESD, SJ, AA, IJO; methodology, IJO, ESD, GOS, AA, SJ; software, IJO.; validation, IJO, GOS, ESD, SJ, AA; formal analysis, IJO.; investigation, IJO, GOS, ESD, SJ, AA.; resources, ESD.; data curation, IJO, GOS; writing—original draft preparation, IJO, GOS, ESD, SJ, AA; writing—review and editing, IJO, ESD, SJ, AA; visualization, IJO, GOS; supervision, ESD, SJ, AA; project administration, ESD, SJ, AA; funding acquisition, ESD. All authors have read and agreed to the published version of the manuscript.

Corresponding author

Correspondence to Eric S. Donkor.

Ethics declarations

Competing interests

The authors declare no competing interests.

Informed consent

Informed consent was obtained from all subjects involved in the study.

Institutional review board

The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical and Protocol Review Committee of the College of Health Sciences, University of Ghana (CHS-Et/M.2-P 4.6/2021–2022).

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Okyere, I.J., Semevor, G.O., Ablordey, A. et al. Genomic profiling of extended-spectrum beta-lactamase-producing Escherichia coli isolated from poultry and poultry farm workers in Accra, Ghana. Sci Rep (2026). https://doi.org/10.1038/s41598-026-36471-9

Download citation

  • Received: 21 October 2025

  • Accepted: 13 January 2026

  • Published: 05 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-36471-9

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

Keywords

  • Antimicrobial resistance
  • Extended-spectrum beta-lactamase
  • Whole-genome sequencing
  • Poultry farming
  • Escherichia coli
  • Ghana
Download PDF

Advertisement

Explore content

  • Research articles
  • News & Comment
  • Collections
  • Subjects
  • Follow us on Facebook
  • Follow us on Twitter
  • Sign up for alerts
  • RSS feed

About the journal

  • About Scientific Reports
  • Contact
  • Journal policies
  • Guide to referees
  • Calls for Papers
  • Editor's Choice
  • Journal highlights
  • Open Access Fees and Funding

Publish with us

  • For authors
  • Language editing services
  • Open access funding
  • Submit manuscript

Search

Advanced search

Quick links

  • Explore articles by subject
  • Find a job
  • Guide to authors
  • Editorial policies

Scientific Reports (Sci Rep)

ISSN 2045-2322 (online)

nature.com sitemap

About Nature Portfolio

  • About us
  • Press releases
  • Press office
  • Contact us

Discover content

  • Journals A-Z
  • Articles by subject
  • protocols.io
  • Nature Index

Publishing policies

  • Nature portfolio policies
  • Open access

Author & Researcher services

  • Reprints & permissions
  • Research data
  • Language editing
  • Scientific editing
  • Nature Masterclasses
  • Research Solutions

Libraries & institutions

  • Librarian service & tools
  • Librarian portal
  • Open research
  • Recommend to library

Advertising & partnerships

  • Advertising
  • Partnerships & Services
  • Media kits
  • Branded content

Professional development

  • Nature Awards
  • Nature Careers
  • Nature Conferences

Regional websites

  • Nature Africa
  • Nature China
  • Nature India
  • Nature Japan
  • Nature Middle East
  • Privacy Policy
  • Use of cookies
  • Legal notice
  • Accessibility statement
  • Terms & Conditions
  • Your US state privacy rights
Springer Nature

© 2026 Springer Nature Limited

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology