Abstract
Multidrug-resistant Escherichia coli originating from poultry farms pose a significant One Health threat because of their emergence and spread connecting agricultural farms and the environment causing infections in humans. In this study, 38 isolates were collected, all of which exhibited resistance to penicillin, cephalosporins, fluoroquinolones and tetracycline, with an average Multiple Antibiotic Resistance (MAR) Index of 0.55. Among these 38 isolates, 7 isolates having ≥ 0.6 MAR index were subjected to whole genome sequencing - KEED-2 (ST117), KEED-3 (ST155), MTBW-1 (ST1011), MTBW-2 (ST167), PUND-1 (ST117), PUND-3 (ST17391) and VELW-1 (ST744). The analysis revealed the presence of antimicrobial-resistance genes such as tetracycline (tet(A)), quinolone (QnrS1) and aminoglycosides (aph(4)-Ia, aac(3)-IVa, aac(3)-IId, aph(3’’)-Ib, aph(3’)-Ia, aph(6)-Id). Notably, the CTX-M gene was present in KEED-2 (ST117), and the TEM-1B gene was present in MTBW-1 (ST1011) and VELW-1 (ST744). In this study, pandemic clones ST167, ST744 and ST17391 were identified, which has not been reported so far in poultry environments in India to the best of our knowledge, highlighting the need for continued surveillance and effective control measures, emphasising significance for the One Health framework.
Data availability
The sequence data for the samples has been submitted in the NCBI. The Sample ID KEED-2 has the Nucleotide accession IDJBEXCF000000000.1, Bioproject ID PRJNA224116, and Biosample ID SAMN42315190. KEED-3 corresponds to Nucleotideaccession ID JBEXCG000000000.1, Bioproject ID PRJNA1131611, and Biosample ID SAMN42315416. PUND-1 has the Nucleotideaccession ID JBRJJE000000000.1, Bioproject ID PRJNA1333720, and Biosample ID SAMN51805429. For PUND-3, the Nucleotideaccession ID is JBLOHC000000000.1, Bioproject ID is PRJNA1201741, and Biosample ID is SAMN45941455. The MTBW-1 samplehas the Nucleotide accession ID JBRZAD000000000.1, Bioproject ID PRJNA1355167, and Biosample ID SAMN53032474. MTBW-2is associated with Nucleotide accession ID JBRJJF000000000.1, Bioproject ID PRJNA1333795, and Biosample ID SAMN51805480.Finally, VELW-1 has the Nucleotide accession ID JBRJJG000000000.1, Bioproject ID PRJNA1333918, and Biosample IDSAMN51819988. MTB-3 (Metagenome sample) has the Bioproject ID PRJNA1347992.
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We thank Sri Ramachandra Institute of Higher Education and Research for providing the necessary facilities and support to carry out this research work.
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Rogith P - Writing - original draft, formal analysis, Images and software; Lakshmi Srijith - Writing and formal analysis; Karthic G - formal analysis; Ramanakishore VS - formal analysis; K S Sridharan - Review & Editing; Agastian Paul - Review & Editing; Kumar Perumal - Review, Editing & Supervision.
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P, R., Srijith, L., G, K. et al. Genomic analysis of ST117, 155, 1011, 167, 744, and 17391 in poultry-associated multidrug resistant Escherichia coli isolates from India. Sci Rep (2026). https://doi.org/10.1038/s41598-026-38232-0
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DOI: https://doi.org/10.1038/s41598-026-38232-0
