The qPCR array contained 384 primer sets as previously described (10), including some additional primer sets: 16S rRNA gene (AY2), blaCTX-M (AY326 and AY360), blaOXA (AY361), blaSHV (AY272), blaTEM (AY3), blaVIM (AY260), mecA (AY284), qnrSrtF11 (AY6), sul1 (AY110), tetM (AY357), vanA (AY4; AY368), mcr-1 (AY80), and intI1 (AY45) (table S2). The concentration and quality of the DNA samples were verified using the Qubit 3.0 Fluorometer (Thermo Fisher Scientific, USA). Only the samples fulfilling the quality criteria were processed. The qPCR array uses a microfluidic SmartChip Multisample Nanodispenser (WaferGen at the time of the study, now Takara) to load primer sets and samples from 384-well plates into a SmartChip (Takara) with 5 184-reaction wells. The same 384-well plate of primers was used for all experiments, and three technical replicates were run for each sample. Samples were diluted to have the same mass of DNA per reaction. Following amplification on the SmartChip Real-Time PCR cycler, Ct values were calculated using default parameters provided with the SmartChip analysis software.

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