Occurrence and Molecular Characterization of Extended-Spectrum Beta-Lactamase (ESBL)-Producing Escherichia coli in Broilers in Indonesia

Abstract

Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) are widespread in the food chain, but nationwide surveillance in Indonesian broiler production is limited. This study investigated the occurrence, antimicrobial resistance, phylogenetic diversity, and molecular characteristics of ESBL-E. coli from broilers in Indonesia. A total of 2182 E. coli isolates from broiler cecal samples across three regions during the period 2018–2020 were analyzed. Antimicrobial susceptibility testing and ESBL phenotyping were performed following the CLSI guidelines. ESBL resistance genes and phylogenetic groups were detected using multiplex/quadruplex PCR. ESBL-E. coli (9.9%) was most frequently observed in the western (15.2%) region, followed by the central (8.0%) and eastern (7.2%) regions. A total of 85 resistance patterns were identified, with 98.5% exhibiting multidrug resistance. The blaCTX-M gene was detected in 97.5% of isolates, predominantly blaCTX-M-1 (97.5%), while blaCTX-M-9 was found in 2.5%. The blaTEM gene was present in 33.0% of ESBL isolates; however, blaSHV and blaOXA-1 were absent. Phylogenetic group A predominated (42.0%), followed by E (22.5%), B1 (20.5%), F (10.5%), C (2.5%), and D (2.0%). This study demonstrates a significant occurrence of ESBL-E. coli in Indonesian broilers with regional variation and blaCTX-M predominance. The high rate of multidrug resistance poses a serious public health concern, emphasizing the urgent need for antimicrobial stewardship and enhanced surveillance programs.