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1

Screening Carbapenem Resistance Genes

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Eleven carbapenem resistance genes (blaIMP, blaVIM, blaNDM, blaSPM, blaAIM, blaDIM, blaGIM, blaSIM, blaKPC, blaBIC, and blaOXA–48) (Poirel et al., 2011 (link)) were screened using PCR detection from the presumptive carbapenemase-producing bacteria. The amplicons were sequenced (Macrogen) and identified using NCBI BLAST1. For the screened carbapenemase-producing bacteria, MDR to 16 antibiotics was determined using Kirby-Bauer disk diffusion, and resistance to colistin was determined using broth dilution methods. For MDR, the following antibiotic disks were used: ampicillin-sulbactam (10/10 μg), cefotaxime (30 μg), ceftazidime (30 μg), chloramphenicol (30 μg) ciprofloxacin (5 μg), colistin (2 mg/L), doripenem (10 μg), fosfomycin (200 μg), gentamicin (10 μg), levofloxacin (5 μg), meropenem (10 μg), netilmicin (10 μg), piperacillin (100 μg), tetracycline (30 μg), tobramycin (10 μg), and trimethoprim-sulfamethoxazole (1.25/23.75 μg) (Liofilchem, Roseto degli Abruzzi, Italy). Resistance to the antibiotics was determined according to the Clinical and Laboratory Standards Institute (CLSI) guideline (Clinical Laboratory Standars and Institue, 2016 ). Subsequently, MICs of 16 antibiotics for E. coli strain N7 were evaluated using the broth dilution method (Hasselmann, 2003 (link)).
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2

Antimicrobial Susceptibility Testing for Bacterial Isolates

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Antimicrobial susceptibility testing for the bacterial isolates was carried out using the Kirby-Bauer method, as recommended by the Clinical and Laboratory Standards Institute (CLSI). 15 The following antibiotics were tested: imipenem (10 μg), meropenem (10 μg), doripenem (10 μg), ceftazidime (30 μg), cefepime (30 μg), piperacillin (100 μg), piperacillin/tazobactam (100/10 μg), gentamicin (10 μg), amikacin (30 μg), tobramycin (10 μg), ciprofloxacin (5 μg), aztreonam (30 μg), polymyxin B (300 units), and colistin (10 μg) (Mast Group Ltd, UK). The minimum inhibitory concentrations (MICs) of carbapenems (imipenem [IMI], meropenem [MRP], and doripenem [DOR]) were obtained by an E-test (Liofilchem, Italy), as described in the manufacturer's instructions. Carbapenem resistance was determined based on the MIC breakpoints. When an isolate was resistant to three carbapenems (imipenem, meropenem, and doripenem), that isolate was considered high-level carbapenem resistant. If an isolate was resistant to three or more classes of antimicrobial agents (i.e., penicillins/cephalosporins, carbapenems, aminoglycosides, and fluoroquinolones), that isolate was considered multidrug resistant (MDR). In accordance with the CLSI guidelines, P. aeruginosa ATCC 27853 and Escherichia coli ATCC 25922 were used as control strains in all susceptibility assays.
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