Environmental risk quotient of the antibiotic, phenotypic, and genotypic profiles for antibiotic resistance of Escherichia coli collected from manure and wastewater at swine farms in Prachinburi Province, Thailand

Currently, antimicrobial drug resistance is a problem that deserves thoughtful consideration. Especially in the swine production industry, many pig farms tend to release wastewater into natural water sources, which villagers use for their livelihood. This study aimed to demonstrate the occurrence of phenotypic and genotypic resistance characteristics of E. coli, as well as antibiotic residues in manure and wastewater on swine farms in Prachinburi Province, Thailand. Samples were collected in 2020 and 2021 during the rainy and summer seasons. The results of a questionnaire showed that farmers used antibiotics for disease treatment and prevention at a ratio of 2/4 (50%). The most common antibiotic used was amoxicillin (4/4, 100%), followed by Enrofloxacin (75%) and colistin (25%). The analysis of antibiotic residue in wastewater by Liquid Chromatography-Mass Spectrometry (LCMS, LC-MS) during the rainy season revealed that amoxicillin (54%) was the highest, followed by florfenicol (14%) and tiamulin (13%). While oxytetracycline (59%), amoxicillin (20%), and florfenicol (11%) were the highest in the summer. The study of Risk Quotient (RQ) indicated that water resources present a risk of antibiotic contamination by sulfonamides, trimethoprim, β-lactam, quinolones, and tetracycline at high levels (ΣRQ >1) during both seasons. The minimal inhibitory concentrations (MICs) were determined by an antibiotic susceptibility test (AST), analyzed by microdilution technique, and VITEK® 2 Compact. The test result indicated that a total of 143 isolates were found in manure (45/143), pre-treatment (51/143), and final effluent (post-treatment, 47/143). ESBL-positive resistance was detected at 13%. However, an immensely high percentage of antimicrobial resistance was found for ampicillin (90%), whereas imipenem did not show any drug resistance (0%). The average MIC value towards colistin in all samples was 2.71 μg/ml, while mcr1 was not found in any samples. Furthermore, MDR was expressed in E. coli at as high as 76.22% (109/143). The highest MDR pattern detected was AMP-TET–FFC–SXT. The PCR technique detected that the diversity and abundance of AMR genes were not significantly different from animal manure and wastewater at the swine farms. The bla-TEM was found more frequently than bla-PS. While the tetracycline group (tetA, tetB) and aminoglycoside (aadA1, aadA2, aadB) represented a major proportion, respectively. The PFGE study revealed the possibility of similar genetic morphology from the different isolates found in this study.