The RNA was adjusted to a concentration of 140 ng μL−1. A total quantity of 280 ng RNA was then used for one-step reverse transcription using High Capacity RNA-to-cDNA Master Mix (Applied Biosystems). For quantitative real-time PCR, amplification was performed with Power SYBR Green Master Mix in a Step One Plus Thermal Cycler (Applied Biosystems). Forty cycles were run with denaturation at 95 °C for 15 s,

annealing at 55 °C for 30 s and extension at 60 °C for 45 s. rpsL was used as reference gene to normalize the relative amount of mRNA. The mRNA levels SCH772984 order of a specific gene were expressed by comparing with the expression of the reference gene on that strain and also in PAO1, and the expression levels were calculated on a standard curve (Oh et al., 2003). RT-PCR was carried out in triplicates. Primers used for RT-PCR investigations are described in Table S1. PAO1 and PAOMY-Mgm had similar growth rates in LB or in LB supplemented with 0.1 mg L−1 ciprofloxacin. Competition experiments were carried out in a Bioscreen (Labsystem C, Bie og Berntsen) with and without antibiotic. We attempted to start with a ratio 1 : 1 of PAO1 and PAOMY-Mgm in each well. The inoculums in the start of the experiment were 3.5 × 108 CFU mL−1 for PAO1 and 2.4 × 108 CFU mL−1 for PAOMY-Mgm. A total quantity of 140 µL of each strain culture was transferred in 2 × 10 wells in microtitre plate, the growth was carried out at 37 °C, continuously shaking, and OD600 nm

measurements were CX-5461 supplier performed every 30 min for 24 h. The experiment was carried out for 5 days (start day 0, end day 4), and in each day 1 : 1000 dilutions of the cultures were transferred to a new microtitre plate for exponential growth throughout very the experiment. Each day, the culture was serially diluted and plated on LB agar and on LB agar supplemented with 30 mg L−1 gentamicin, a concentration which is inhibitory for PAO1, but not for the PAOMY-Mgm mutant. The CFU mL−1 of PAOMY-Mgm was calculated on gentamicin plates and the PAO1 and PAOMY-Mgm mixture on LB plates. The

CFU of PAO1 was calculated by subtracting the number of CFU mL−1 on gentamicin plates from the number of CFU mL−1 on LB plates. The ratio of PAO1 : PAOMY-Mgm, PAO1 : PAOMYgm and PAO1 : PAOMMgm was followed for 4 days. The efflux pumps transcriptional regulators nfxB, mexR, mexZ and mexT, and the ciprofloxacin target genes gyrA, gyrB, parC and parE, were sequenced in selected isolates from the antibiotic resistance development study and from the growth competition study. DNA was purified using Promega Wisart purification kit (Promega). Polymerase Dynazyme EXT (Finnzymes, Espoo, Finland) was used for PCR amplification. The sequencing was done on an automatic DNA sequencer ABI3700 (Macrogen Inc., Seoul, South Korea). The numbers of reads were between two and four for each gene of each strain. The sequence results were compared with the strain PAO1 sequence (www.pseudomonas.com) with dnasis® max version 2.