Study reveals new mechanism for rapid evolution of multi-drug resistant infections in patients UniofOxford NatureComms
PAO1 as a reference strain. Antibiotics were assayed along the following 2-fold dilution series between: ciprofloxacin , aztreonam , ceftazidime , meropenem , piperacillin/tazobactam and gentamicin . Growth inhibition was defined as ODisolates on each antibiotic . When an isolate reached the measurable limit of the MIC assay , the MIC was recorded as double of the upper limit in the raw data file of MIC results .
5–64 µg/mL, and a colistin resistance phenotype was determined as an MIC above 2 µg/mL All isolates were sequenced in the MiSeq or NextSeq illumina platforms yielding a sequencing coverage of 21X–142X. Raw reads were quality controlled with the ILLUMINACLIP and SLIDINGWINDOW in trimmomatic v. 0.39. Quality controlled reads were assembled for each isolate with SPAdes v. 3.13.1 with default parameters. These assemblies were further polished using pilon v. 1.
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