Genomic landscape of Escherichia coli from swine to identify antibiotic resistance, pathogenicity, and dissemination potential: Implications for environmental and public health.
Abstract
Background
The emergence of antimicrobial-resistant Escherichia coli in livestock, particularly swine, represents a growing concern for animal, environmental, and public health. Unorganized swine production systems may act as reservoirs for multidrug-resistant strains with zoonotic potential.
Methods
This study analyzed E. coli isolates recovered from swine in Karnataka, India using antimicrobial susceptibility testing and PCR screening for ESBL/AmpC genes (blaCTX-M, blaTEM, blaSHV, blaAmpC). Ten positive isolates were subjected to whole-genome sequencing (WGS) using the Illumina MiSeq platform and bioinformatic analyses included the identification of antimicrobial resistance genes (ARGs), virulence factors (VFs), mobile genetic elements (MGEs), plasmid replicons, and biofilm-associated genes. Molecular typing (MLST, serotyping, CH typing, Clermont phylogrouping) and comparative phylogenomic analysis were performed with 53 global swine-origin E. coli genomes.
Results
Multiplex PCR confirmed 25/29 isolates as E. coli and PCR identified ESBL and/or AmpC genes in 10 E. coli isolates (three - single ESBL genes, four- multiple ESBL genes, one -ESBL+ AmpC co-occurrence and two carrying only AmpC). WGS revealed 48 unique ARGs, with blaTEM-1B and sul1 being most prevalent, ESBL (blaCTX-M) and AmpC (blaCMY) genes were identified in two and three isolates, respectively. The integron-integrase genes (intI1/intI2) associated with dfrA17 in two isolates suggests involvement of MGEs in resistance gene carriage and virulome analysis identified 34 conserved virulence genes. High genetic diversity with nine sequence types, multiple phylogroups (A, B1, C, F, G), seven serotype combinations, and CH typing revealed alleles such as fimH58 and fumC4. High Simpson's diversity indices (0.978 for MLST; 0.952 for serotypes) confirmed this heterogeneity. Comparative phylogenomics indicated clustering of Indian isolates (e.g., ST624, ST117) with global lineages.
Conclusion
The co-occurrence of diverse resistance determinants, VFs, and MGEs in swine E. coli highlights their genomic diversity. These findings underscore the need for integrated genomic surveillance and antimicrobial stewardship within a One Health framework.