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Antibiotic Susceptibility Testing of Isolates

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The antibiotic susceptibility of the all isolates was determined by the disk diffusion method on Mueller–Hinton agar (Becton–Dickinson, Sparks, MD, USA) according to the recommendations of the Clinical and Laboratory Standards Institute (CLSI). The disk diffusion assay was run with 15 antibiotics: bacitracin (10 U), enrofloxacin (5 μg) (OXOID), streptomycin (10 μg), spiramycin (100 μg), sulfadiazine (25 μg), chloramphenicol (30 μg) (BD), doxycycline (30 μg), erythromycin (15 μg), gentamicin (10 μg), neomycin (30 μg), penicillin (10 U), tetracycline (30 μg), cefoxitin (30 μg), trimethoprim/sulfamethoxazole (1.25 μg/23.75 μg, respectively), and vancomycin (30 µg and 5 µg) (BIO-RAD, Hercules, CA, USA). S. aureus strain ATCC 25923 and Enterococcus faecalis strain ATCC 29212 were used as controls in the susceptibility test.
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Antibiotic Susceptibility Profiling

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Twenty antibiotic agents (Hangzhou Binhe Microorganism Reagent Co., Ltd) were used, including cefotazime (30 µg), cephradine (30 µg), ceftriaxone (30 µg), ceftazidime (30 µg), amox-icillin (20 µg) and ampicillin (10 µg), ofloxacin (5 µg), ciprofloxacin (5 µg), enrofloxacin (10 µg), norfloxacin (10 µg), spectinomycin (100 µg), gentamicin (10 µg), streptomycin (10 µg), amikacin (30 µg), kanamycin (30 µg), doxycycline (30 µg), lincomycin (30 µg), azithromycin (15 µg), polymyxin B (300 µg) and trimethoprim (23.75/1.25 µg).
Each purified isolates of tested bacteria were evenly spread onto a tryptic soy agar plate (TSA, BD TM , USA) that had been coated with nicotinamide adenine dinucleotide liquid (NAD, Guangzhou Saiguo Biotech, China) and bovine serum (Zhejiang Tianhang Biotechnology, China). The antimicrobial discs were placed onto the surface of the agar. The plates were then incubated at 37 o C for about 24 h. The inhibition zone diameter was measured and compared with standardized CLSI interpretive criteria to designate the isolate as sensitive, intermediate or resistant to the drug (CLSI, 2018) . In this study, the isolates that showed intermediate were classified as resistant.
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Antibiotic Resistance Screening in Environmental Isolates

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Samples were first plated on Chromocult agar, and then presumptive E. coli colonies were transferred onto MacConkey lactose (MKL) agar for confirmation before replating on Chromocult was performed to ensure pure isolates. We selected up to four E. coli colonies from soil and fecal samples and two from water and surface samples to test for AR. More isolates from soil samples than from water or surfaces were used because we expected higher microbial diversity in soil. Antibiotic sensitivity was assessed using the Kirby-Bauer disc diffusion method (43 (link)) and 12 antibiotics: ampicillin, amoxicillin/clavulanate, cefotaxime, cephalothin, chloramphenicol, ciprofloxacin, enrofloxacin, gentamicin, streptomycin, sulfisoxazole, trimethoprim-sulfamethoxazole, and tetracycline (Becton, Dickinson, Franklin Lakes, NJ). Zones of inhibition were measured after a 24-h incubation period using digital calipers.
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Antimicrobial Susceptibility Testing Protocol

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Antimicrobial susceptibility testing was performed using the agar diffusion test according to the standards given by the Clinical and Laboratory Standards Institute49 ,50 . The antimicrobial agents tested included chloramphenicol (30 μg), clindamycin (2 μg), oxacillin (1 µg, sulfamethoxazole/trimethoprime (1, 25/23, 75 μg), tetracycline (30 μg), enrofloxacin (5 µg), erythromycin (15 µg), clarithromycin (15 µg) vancomycin (30 µg) (Becton Dickinson, Heidelberg, Germany).
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