ABSTRACT

Background and Aim: Antimicrobial resistance (AMR) is a growing global health concern, particularly at the human–animal–environment interface where livestock production may facilitate the circulation of antibiotic resistance genes (ARGs). Pig slaughterhouses are recognized as potential reservoirs of resistant bacteria, yet genomic information regarding commensal Escherichia coli from healthy human populations living nearby remains scarce in Indonesia. Pregnant women represent an important sentinel population because intestinal carriage of resistant bacteria may contribute to neonatal colonization and early-life infections. This study aimed to characterize ARG profiles and their genomic locations in commensal E. coli isolated from healthy pregnant women residing near pig slaughterhouses in Banten Province, Indonesia. 

Materials and Methods: Rectal swab samples were collected from 100 healthy pregnant women attending primary healthcare centers located within a 5-km radius of pig slaughterhouses. Ninety-four E. coli isolates were recovered and subjected to whole-genome sequencing using the Oxford Nanopore Technologies MinION platform. Bioinformatic analyses were performed to identify ARGs and determine their chromosomal or plasmid localization. 

Results: Thirty distinct ARGs belonging to 10 antimicrobial classes were detected. Beta-lactamase genes exhibited the greatest diversity, with chromosomally encoded blaEC-15, blaEC, and blaEC-18 predominating. Aminoglycoside resistance genes represented the second most diverse group, whereas plasmid-associated genes such as sul2, qnrS1, and tet(A) were among the most frequently identified mobile resistance determinants. Overall, chromosomal ARGs were more prevalent than plasmid-borne genes. Although most isolates carried resistance determinants affecting fewer than three antimicrobial classes, 12.8% exhibited potential multidrug resistance. Shared plasmid-mediated ARGs previously reported in livestock reservoirs from the same region suggested localized circulation of resistance elements across sectors. 

Conclusion: Commensal E. coli from healthy pregnant women living near pig slaughterhouses harbored diverse ARGs, predominantly chromosomal beta-lactamase genes, together with several plasmid-mediated determinants shared with livestock-associated reservoirs. These findings highlight the interconnected nature of AMR dissemination and support the incorporation of pregnant women into integrated One Health surveillance programs. Genome-based monitoring may facilitate early detection of emerging resistance and guide region-specific interventions to mitigate AMR spread. 

Keywords: antibiotic resistance genes, antimicrobial resistance, commensal Escherichia coli, multidrug resistance, One Health, pig slaughterhouses, pregnant women, whole-genome sequencing.