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1

Antibiotic Susceptibility Testing Protocol

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Susceptibility testing was performed by Kirby Bauer disk diffusion method using 22 antibiotics: amikacin, ampicillin, cefpodoxime, ceftazidime, ceftriaxone, cefuroxime, ciprofloxacin, ertapenem, imipenem, nalidixic acid, nitrofurantoin, tetracycline, trimethoprim/sulfamethoxazole (Becton Dickinson, NJ), ampicillin-sulbactam, aztreonam, cefazoline, cefepime, cefotaxime, ceftiofur, chloramphenicol, kanamycin, and streptomycin (Oxoid), according to the Clinical and Laboratory Standards Institute, CLSI.18 ESCs and ciprofloxacin-resistant isolates were selected and cryopreserved for further analysis. Multiresistance was defined as the resistance to three or more structural classes of antibiotics19 (link) and M100 from CLSI (30th edition, 2020) was used for interpretation and antimicrobial class classification (Glossary I).20 Isolates showing an intermediate resistant pattern were included in the resistant group for the analysis of antibiotic susceptibility but excluded from the minimal inhibitory concentration (MIC) assays. MICs were performed manually using the microdilution method on isolates that showed resistance to cefotaxime, ciprofloxacin, and nalidixic acid as recommended by CLSI.21 Concentrations from 0.125 (μg/mL) to 256 (μg/mL) were evaluated for each antibiotic.
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Antimicrobial Susceptibility Testing of Isolates

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Antimicrobial susceptibility testing (AST) was conducted on the isolates using the disk-diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI) [11 ]. Antimicrobial substances included ampicillin, amoxicillin/clavulanic acid, cefazolin, cefotaxime, cefepime, nalidixic acid, ciprofloxacin, sulfamethoxazole-trimethoprim, fosfomycin, azithromycin, nitrofurantoin, streptomycin, kanamycin, gentamicin, chloramphenicol, and tetracycline (Becton, Dickinson, Heidelberg, Germany). Results were interpreted according to CLSI breakpoints for human clinical isolates [11 ]. Multidrug resistance (MDR) was defined as resistance to three or more classes of antimicrobials, counting beta-lactams as one class.
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Antimicrobial Susceptibility Testing of Citrobacter and E. coli

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AST was performed using the disk diffusion method according to the guidelines of the Clinical and Laboratory Standards Institute (Clinical and Laboratory Standards Institute, 2020 ). Antimicrobial substances included ampicillin, amoxicillin/clavulanic acid, cefazolin, cefotaxime, cefepime, nalidixic acid, ciprofloxacin, sulfamethoxazole‐trimethoprim, fosfomycin, azithromycin, nitrofurantoin, streptomycin, kanamycin, gentamicin, chloramphenicol, and tetracycline (Becton, Dickinson). Results were interpreted according to CLSI breakpoints for human clinical isolates (Clinical and Laboratory Standards Institute, 2020 ). In the absence of clinical breakpoints for azithromycin resistance in Citrobacter spp. and E. coli, a zone diameter of ≤12 mm was interpreted as resistant, based on data reported by Meerwein et al. (2020 ).
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Kirby-Bauer Disk Diffusion for Antibiotic Susceptibility

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Kirby-Bauer disk diffusion method was used to assess antimicrobial susceptibility as recommended by the CLSI guidelines [13 (link), 14 ]. Ampicillin (AMP: 10 μg), ciprofloxacin (CEP: 30 μg), nitrofurantoin (NIF: 300 μg, BD), norfloxacin (NOR: 10 μg), amoxicillin-clavulanic acid (AMC: 20/10 μg), gentamicin (G: 10 μg), trimethoprim-sulfamethoxazole (STX: 1.25/23.75 μg) cefotaxime (CTX: 30 μg), cefoxitin (FOR: 30 μg), ceftriaxone (CTR: 30 μg), tetracycline (TE: 30 μg), and meropenem (MEM: 10 μg). Zone of inhibition was measured after overnight incubation at 37°C. Nonsusceptibility to three or more classes of antibiotics defined multidrug resistance.
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Antimicrobial Susceptibility of SAR Bari Strain

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Antimicrobial susceptibility of the SAR Bari strain was determined by a BD PHOENIX 100 instrument (Becton Dickinson, Franklyn Lake, NJ). Data were elaborated by the BD Epicenter Expert System according to EUCAST rules (http://www.eucast.org). The PMIC/ID-88 (BD) panel was used to test susceptibility to ampicillin, cefoxitin, ceftaroline, ciprofloxacin, clindamycin, daptomycin, erythro-mycin, fosfomycin, fusidic acid, gentamicin, imipenem, linezolid, moxifloxacin, mupirocin, nitro-furantoin, oxacillin, penicillin, rifampin, teicoplanin, tetracyclin, tigecycline, trimethoprim/ sulfamethoxazole, and vancomycin. The Epsilometer Test (ETest) was used for testing resistance to ciprofloxacin, daptomycin, erythromycin, gentamicin, moxifloxacin, tetracyclin, tigecycline, trimethoprim/sulfamethoxazole, and vancomycin (bioMérieux, Marcy-L’Étolie, France and Liofilchem, Roseto degli Abruzzi, Italy). All tests were repeated on four independent technical replicates. MIC interpretative breakpoints were defined according to EUCAST recommendations. Staphylococcus aureus ATCC 29213 was used as a control strain.
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Antibiotic Susceptibility Testing of Enterobacteriaceae

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The disk diffusion was performed, and after 16–18 hours of incubation at 37°C, zone of inhibition was measured and interpreted as recommended by the CLSI.11 Using a sterile wire loop, three to five pure colonies were picked from MacConkey agar and emulsified in nutrient broth. Standard inoculums adjusted to 0.5 McFarland using McFarland Densitometer were swabbed onto Muller-Hinton agar (dispensed on 100 mm plate). Drug susceptibility testing of all Enterobacteriaceae was performed using disk diffusion method against amoxicillin (30 µg, BD), amoxicillin-clavulanic acid (30 µg, BD), chloramphenicol (30 µg, BD), gentamicin (10 µg, BD), sulfamethoxazole-trimethoprim (1.25 µg, BD), cefotaxime (30 µg, BD), cefoxitin (30 µg, Oxoid), tetracycline (30 µg, BD), nitrofurantoin (300 µg, BD), norfloxacin (5 µg, BD), imipenem (10 µg, Oxoid), and meropenem (10 µg, Oxoid). In this study, multidrug resistance was defined as simultaneous resistance to two or more drugs of different classes of antimicrobial agents.
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7

Antibiotic Resistance Profiling of Pathogens

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The antimicrobial resistance/susceptibility was performed by using the disk diffusion method according to the guidelines set by ‘‘The Clinical and Laboratory Standards Institute” (CLSI, 2019).14 Twelve antimicrobial agents were used: amikacin (AN, 30 μg), ampicillin (AM, 10 μg), gentamicin (GM, 10 μg), trimethoprim/sulfamethoxazole (SXT, 23.75/1.25 μg), ceftriaxone (CRO, 30 μg), cefotaxime (CTX, 30 μg), dicloxacillin (CLOX, 1 μg), cephalotin (CF, 30 μg), chloramphenicol (C, 30 μg), penicillin (10, U), nitrofurantoin (NF, 100 μg), and netilmycin (NET, 30 μg) (BD, Brea, CA). Pseudomonas aeruginosa ATCC 27853 and A. baumannii ATCC 19606 were used as controls. Results were inferred as susceptible, intermediate, or resistant by measuring the diameter of the inhibition zone. The frequency of antibiotic resistance was calculated and represented in percentages (%).
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