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10 protocols using etest

1

MIC determination of C. difficile isolates

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For each isolate, the MIC for AMP, PEN, AMC, MEP, TET, CHL, ERY, CLI, MOX, CIP, MEZ, VAN and LZD was determined by Etest® (bioMérieux, Nürtingen, Germany). For quality control, Clostridioides (Clostridium) difficile ATCC® 700057 was included. As there are no quality control ranges provided by CLSI for CHL and TET for C. difficile ATCC® 700057, Bacterioides fragilis ATCC® 25285 was used additionally as quality control for these antimicrobial agents [19 ]. For ERY and CIP, no quality control ranges were available.
Etest® was performed following the instructions for anaerobes (manual available as package insert online [17 ]) with the following adaptation: the inoculum was prepared by inoculating colonies of a 24 h old lawn culture grown on a Schaedler agar plate (Oxoid, Wesel, Germany) in 0.5 mL NaCl (0.85%).
For the classification of the results as susceptible/intermediate/resistant respectively WT or NWT (see Table 5), the MICs obtained were rounded up to the next two-fold standard dilution if they were in between two steps as indicated by the Etest® instructions [17 ].
The breakpoints used according to CLSI and EUCAST as well as the epidemiological cut-off values (ECOFF) from EUCAST can be found in Table 5 [18 ,19 ,20 ]. As there is no official breakpoint nor an ECOFF for LZD, no classification in susceptible/resistant or WT/NWT was performed.
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2

Antimicrobial Susceptibility Testing Protocol

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Antimicrobial susceptibility testing was performed at the clinical microbiology laboratories according to the EUCAST methodology for MIC determination using gradient tests (Etest, Oxoid) [17 ]. Müller–Hinton fastidious broth agar plates produced by the Substrate department at Karolinska University Hospital and by Clinical Microbiology, Labmedicin, Lund, were used. Bacterial inoculum of 0.5 McFarland and gradient test were applied on agar plates, and inhibition of growth was judged with naked eye after 18 h (± 2 h) of incubation in 35 °C (± 1 °C) in 4–6% CO2 environment.
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3

Antibiotic Susceptibility Testing Protocol

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The MIC was determined by epsilometric test (Etest®, BioMérieux, Marcy l’Etoile, France) for ertapenem (0.002–32), meropenem (0.002–32), ciprofloxacin (0.002–32), ceftriaxone (0.016–256) and piperacillin/tazobactam (0.016–256), following the recommendations of the manufacturer. Quality control was performed by testing E. coli ATCC 25,922® and P. aeruginosa ATCC® 27,853, with all results within expected ranges.
Samples were subcultured onto blood agar and then onto MacConkey agar to ensure viability and purity. Individual colonies were picked from 18 to 24 h plates and suspended in 0.85% saline to a turbidity of a 0.5 McFarland standard. Cotton swabs were used to transfer the inoculum to the plates with Mueller Hinton agar (Oxoid, Basingstoke, Inglaterra), which were dried before the Etest® strips were applied. For each strain, the five antibiotics were arranged in a single plate. Plates were incubated for 18–24 h at 35 °C. Readings and interpretations were performed according to National Committee for Clinical Laboratory Standards (NCCLS).11
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4

Antimicrobial Resistance Profiling of CC464 Isolates

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We determined antimicrobial susceptibility for 21 representative CC464 isolates with genotypic polymorphisms across the range of detected resistance markers. We used Mueller-Hinton agar with 5% defibrinated horse blood and 20 mg/L β-nicotinamide adenine dinucleotide for antimicrobial susceptibility testing using the disk diffusion method for ciprofloxacin (5 μg/disk), gentamicin (10 μg/disk), tetracycline (5 μg/disk), kanamycin (5 μg/disk), amikacin (30 μg/disk), tobramycin (10 μg/diskc), and streptomycin (30 μg/disk) (29 (link),30 ). We determined MIC of ampicillin (AMP) by Etest (Oxoid, http://www.oxoid.com) and interpreted the MICAMP and disk susceptibility results using guidelines from the European Committee on Antimicrobial Susceptibility Testing and Clinical and Laboratory Standards Institute and interpreted them as described previously (29 (link)). We used the antimicrobial drug–susceptible isolate ARI3025 as a control. We subcultured the ST5136 isolate ARI4158 on antibiotic-free blood agar plate (ARI4158_20) 22 times to assess the stability of its antimicrobial resistance genes.
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5

Determining SXT MICs using Etest

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We determined SXT MICs using Etest (bioMerieux) for ST5 isolates. Isolates were cultured on horse blood agar (HBA; Oxoid, United Kingdom) for 18 h at 37°C with 5% CO2. Suspensions (0.5 McFarland in 0.85% physiological saline) were lawn inoculated onto Mueller-Hinton (MH) agar (Oxoid) and incubated at 35°C for 18 h. Etest SXT MICs were reported as the trimethoprim MICs in micrograms per milliliter as per manufacturer’s instructions (the EUCAST trimethoprim-sulfamethoxazole resistance breakpoint is >4/76 μg/ml) (38 ).
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6

Determining Ciprofloxacin Resistance in Isolates

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For isolates found resistant to ciprofloxacin on primary antimicrobial susceptibility, E-test (Oxoid) strips were used to determine the MIC of isolates to ciprofloxacin (CIP 32 μg/mL - 0.002 μg/mL). Also, E. coli ATCC®25922TM was used as a quality control strain (American Type Culture Collection Global Bioresource Center, Manassas, VA, USA). Results were interpreted according to CLSI 2018 guidelines (susceptible, MIC ≤ 1 μg/mL, intermediate, MIC = 2 μg/mL, resistant, MIC ≥ 4 μg/mL).12
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7

Salmonella Identification and Antimicrobial Susceptibility

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Methods for the identification of Salmonella from blood culture have been described previously [20 (link),24 (link)]. In brief, positive blood cultures were subcultured on Columbia blood agar, chocolate agar, and MacConkey agar (Oxoid, UK). Salmonella isolates were identified biochemically by API 20E tests (bioMérieux, France) and serotyped following the White–Kauffmann–Le Minor scheme. Ground meat samples were incubated overnight in Selenite broth (Oxoid) and subsequently cultured on Xylose Lysine Deoxycholate agar (Oxoid). Identification was performed as for blood culture isolates.
Ciprofloxacin minimum inhibitory concentrations (MICs) were determined by Etest (Oxoid) according to the European Committee for Antimicrobial Susceptibility Testing (EUCAST) guidelines [25 (link)]. Isolates were classed as ciprofloxacin susceptible (MIC ≤0.06 μg/mL), intermediate/diminished susceptibility (MIC >0.06 and <1 μg/mL) or resistant (MIC ≥1 μg/mL).
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8

BLNAR Transformation and β-Lactam Resistance

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Various strains of H. in uenzae (Table 1) were then transformed with either pLS88 or pADUTAS17. Competent cell preparation and transformation of BLNAR strains were performed using electroporation as previously described by Mitchell et al [6], using cooled 2 mm electroporation cuvettes and the electroporator (BioRad micropulser) was set at 2.5 kV. Selection of positive colonies was made using BHI supplemented with vitox, 15 µg/mL NAD and 15 µg/mL haemin concentrations containing 50 µg/mL kanamycin (Thermo Scienti c, ABD).
Determination of MIC concentration of wild type and transformant BLNAR strains against the β-lactam antibiotics MIC concentrations of both wild type and transformant BLNAR strains (Table 1) containing plasmid expressed nonmutated ftsI gene were determined to analyze the change in MIC concentrations against βlactam antibiotics, cefotaxime, and ampicillin. For this purpose, E-Test (OXOID, UK) method was used according to the manufacturer's instructions.
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9

Antimicrobial Susceptibility Testing Protocol

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Antimicrobial susceptibility testing was performed for a range of clinically relevant antimicrobials with different MOAs (Table 1). Minimum Inhibitory Concentrations (MICs) were determined by ETESTs (bioMérieux) according to the manufacturer's instructions.
Briefly, pure bacterial cultures were diluted in saline to 0.5 MacFarland standard, 100 µl of solution was inoculated and spread onto Isosensitest plates (Oxoid, CM0471), and an ETEST strip was placed on top. Plates were incubated for 16-18 hours at 37°C before the result was read.
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10

Antibiotic Susceptibility of Bacteroides fragilis

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Four antibiotics belonging to different classes werE tested: erythromycin (macrolides), gentamicin (aminoglycosides), tetracycline and penicillin.
Minimum inhibitory concentrations (MIC) for erythromycin, penicillin, gentamycin and tetracycline were determined using E test (Oxoid, Hants, UK). A 0.5 McFarland bacterial inoculum was prepared and the surface of Brucella agar (BRU) plates was flooded with bifidobacterium suspension. Subsequently, the surface of the agar was allowed to dry before the strips were applied and plates incubated in anaerobiosis for 48 h at 37 °C. The MIC was considered as the lowest concentration at which the border of the elliptical inhibition zone intersected the scale on the strip. Bacteroides fragilis E-022248 (=DSM 2151=ATCC 25285) was used as a control for susceptibility testing on BRU (tested in three repeats for all antibiotics). Antibiotic susceptibility was evaluated by comparing MIC values to breakpoints suggested by EFSA (EFSA 2008) . Breakpoints for penicillin were taken from NCCLS guidelines (National Committee for Clinical Laboratory Standards 2003).
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