J Vet Sci.  2024 May;25(3):e44. 10.4142/jvs.24031.

Whole genome sequencing analysis Microbiology on antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia

• Latif H
• Pazra DF
• Basri C
• Wibawan IWT
• Rahayu P

• KMID: 2556477
• DOI: http://doi.org/10.4142/jvs.24031

Abstract

Importance
The emergence and rapid increase in the incidence of multidrug-resistant (MDR) bacteria in pig farms has become a serious concern and reduced the choice of effective antibiotics.
Objective
This study analyzed the phylogenetics and diversity of antibiotic resistance genes (ARGs) and molecularly identified the source of ARGs in antibiotic-resistant Escherichia coli isolated from pig farms in Banten Province, Indonesia.
Methods
Forty-four antibiotic-resistant E. coli isolates from fecal samples from 44 pig farms in Banten Province, Indonesia, were used as samples. The samples were categorized into 14 clusters. Sequencing was performed using the Oxford Nanopore Technologies MinION platform, with barcoding before sequencing with Nanopore Rapid sequencing gDNAbarcoding (SQK-RBK110.96) according to manufacturing procedures. ARG detection was conducted using ResFinder, and the plasmid replicon was determined using PlasmidFinder.
Results
Three phylogenetic leaves of E. coli were identified in the pig farming cluster in Banten Province. The E. coli isolates exhibited potential resistance to nine classes of antibiotics. Fiftyone ARGs were identified across all isolates, with each cluster carrying a minimum of 10 ARGs. The ant(3'')-Ia and qnrS1 genes were present in all isolates. ARGs in the E. coli pig farming cluster originated mainly from plasmids, accounting for an average of 89.4%.
Conclusions and Relevance
The elevated potential for MDR events, coupled with the dominance of ARGs originating from plasmids, increases the risk of ARG spread among bacterial populations in animals, humans, and the environment.

Keyword

Antibiotic resistance; antibiotic resistance genes; Escherichia coli; multidrug-resistant; pig farm