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5 protocols using eravacycline

1

Compound Sourcing and Preparation

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All compounds were obtained from the Cayman Chemical Company with some exceptions. Eravacycline was obtained from MedChemExpress. Flufenoxuron, kanamycin, tetracycline, ampicillin, haloperidol, and risperidone were purchased from the Sigma-Aldrich.
All compounds were dissolved in the recommended solvent (DMSO, DMF, alcohol, or water). Compounds were diluted in serum-free DMEM-N2 to the desired concentrations before addition to media.
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2

Profiling Carbapenem-resistant A. baumannii in China

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From January 2020 to December 2022, 287 non-duplicate A. baumannii isolates, including 147 CRAB and 140 carbapenem-susceptible A. baumannii (CSAB) isolates, were collected from various clinically sampled infections of inpatients at Yangjiang People’s Hospital, a tertiary hospital with 2000 beds in Guangdong Province of China. Bacterial species were identified using a VITEK 2 compact system (BioMérieux, Marcy l’Etoile, France). All strains in this study were cultured on Mueller-Hinton (MH) broth (Oxoid, Basingstoke, UK), or in MH agar plates and Luria-Bertani (LB) broth (Oxoid, Basingstoke, UK) at 37°C. All procedures performed were approved by the Ethical Committee of Yangjiang People’s Hospital and were in accordance with the 1964 Helsinki Declaration and its later amendments. The novel fluorocycline antibiotic, eravacycline (catalog no. HY-16980A), was purchased from MedChem Express (MCE, Shanghai, China). The other antimicrobials were purchased from Meilunbio (Dalian, China). Escherichia coli ATCC 25922 was used for quality control.
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3

Antimicrobial Susceptibility Testing of Eravacycline and Tigecycline

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Antimicrobial susceptibility testing was performed by the broth microdilution method according to the Clinical and Laboratory Standards Institute (CLSI) guidelines.19 All isolates tested were stored in a −80 °C refrigerator. Eravacycline and tigecycline (MedChemExpress, Shanghai, China) were freshly prepared in sterile water on the day of use. The final inoculum of 1.5×108 CFU/mL was acquired by adjusting the turbidity of the incubated mixture to 0.5 McFarland standards using normal saline.20 (link) Aliquots (100 μL) of the colony suspension were inoculated into 96-well broth microdilution panels (Corning, NY, USA) containing 200 μL aliquots of Eravacycline and tigecycline (<0.0625, 0.0625, 0.125, 0.25, 0.5, 1, 2, 4, 8, and 16 mg/L). And 96-well broth microdilution panels were read visually after incubation for 16–20 hours at 37 °C. The results of this study were interpreted according to the criteria of the European Committee on Antimicrobial Susceptibility (EUCAST) (http://www.eucast.org) and the Food and Drug Administration (FDA) (https://www.fda.gov/).21 ,22
E. coli ATCC 25922 was used as a quality control strain.
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4

Reconstitution of E. coli 70S Ribosomes

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In vitro reconstituted E. coli 70S ribosomes were generated from the E. coli K12 strain BW25113, as described previously56 (link). Antibiotic–ribosome samples were generated by incubating antibiotic cocktails 1–5 with E. coli 70S ribosomes in buffer A (50 mM HEPES-KOH, pH 7.5, 25 mM Mg(OAc)2, 80 mM NH4Cl, 100 mM KOAc, 1 mM DTT, 0.05% DDM) at 37 °C for 15 min, before being frozen at −80 °C until use. Final antibiotic concentrations for complexes formed with each cocktail was: cocktail 1 contained 200 μM omadacycline (MedChemExpress), 200 μM spectinomycin (Santa Cruz Biotechnology), 200 μM streptomycin (Santa Cruz Biotechnology), 200 μM evernimicin, 200 μM hygromycin B (Cayman Chemical); cocktail 2 contained 100 μM capreomycin (Sigma Aldrich), 100 μM kasugamycin (Sigma Aldrich) and 100 μM retapamulin (Sigma Aldrich); cocktail 3 contained 100 μM tetracycline (Sigma Aldrich), 100 μM viomycin (Sigma Aldrich), 100 μM streptomycin (Santa Cruz Biotechnology), 100 μM lincomyin (Sigma Aldrich) and 100 μM avilamycin (Cayman Chemical); cocktail 4 contained 10 μM apramycin (Sigma Aldrich), 10 μM eravacycline (MedChemExpress) and 100 μM clindamycin (Santa Cruz Biotechnology); cocktail 5 contained 100 μM pentacycline (Tetraphase), 10 μM gentamicin (Carl Roth) and 100 μM tiamulin (Sigma Aldrich).
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5

Rifamycin Compound Library Evaluation

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The 10 compounds in rifamycin
class used in this study were kindly provided by the Korea Chemical
Bank (www.chembank.org)
of the Korea Research Institute of Chemical Technology (Table S27). Rifamycin S (S4425), dirithromycin
(S4213), gamithromycin (S5328), spiramycin (S5744), kitasamycin (S3645),
acetylspiramycin (S3618), and josamycin (S4421) were purchased from
Selleckchem. Telithromycin (HYA0062), erythromycin ethylsuccinate
(HYB0957), tylosin (HYB0519A), midecamycin (HYB1908), tilmicosin (HYB0905),
tulathromycin A (HY15662), cadazolid (HY100436), radezolid (HY14800),
delplazolid (HY100180), lefamulin (HY16908A), pleuromutilin (HYN2301),
azamulin (HYW019847), valnemulin (HYB0027), chlortetracycline (HYB1327A),
demeclocycline (HY121268), eravacycline (HY16980), rolitetracycline
(HY18257), minocycline (HY17412A), meclocycline (HYB1366), omadacycline
(HY14865), and sarecycline (HY13858A) were purchased from MedChemExpress.
Troleandomycin (ab141568) was purchased from Abchem. Eperezolid (B3390)
was purchased from APExBIO. BODIPYTR Cadeverine (D6251) was purchased
from Invitrogen. Other compounds and E. coli O128:B12
LPS were purchased from Sigma-Aldrich.
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