The antibiotics tested were amikacin, aztreonam, cefepime, ceftazidime, ciprofloxacin, colistin, gentamicin, fosfomycin, imipenem, levofloxacin, meropenem, piperacillin-tazobactam and tobramycin. For the isolates resistant to imipenem and/or meropenem, the determination of metallo-β-lactamases (MBLs) using E-test strips with Imipenem-EDTA was performed (bioMérieux, Marcy d’Etoile, France). The classification of multiresistance was performed according to Magiorakos et al. [11].
The isolates were classified according to the resistance pattern as multidrug resistant (MDR, non-susceptible to at least one agent in three or more antimicrobial categories), extensively drug resistant (XDR, non-susceptible to at least one agent in all but two or fewer antimicrobial categories; i.e. bacterial isolates remain susceptible to only one or two categories), pandrug-resistant (PDR, non-susceptible NF-��B inhibitor to all agents in all antimicrobial
categories), and non-multidrug resistant (non-MDR). DNA extraction: PCR amplification and DNA sequencing Bacterial genomic DNA for PCR amplification was obtained as previously described [12]. The housekeeping genes acsA, aroE, guaA, mutL, nuoD, ppsA and trpE were amplified and sequenced for the 56 isolates using the primers described previously [8]. The PCR conditions have been slightly modified. The reactions were performed using an Eppendorf thermocycler, with an initial denaturation step at 96°C 2 min, followed by 35 cycles of denaturation at 96°C for 1 min for all of selleck kinase inhibitor the genes, a primer annealing temperature, depending on the gene (55–58°C for aroE and nuoD; 58°C for acsA and guaA; and 58–60°C for mutL, ppsA and trpE), for 1 min and a primer extension at 72°C for 1 min for all of the genes, with
the exception of aroE (1.5 min). A final elongation step was performed Etofibrate at 72°C for 10 min. The PCR amplification reactions were performed as previously described [12]. The amplified products were purified with Multiscreen HTS PCR 96-well filter plates (Millipore). Sequence reactions were carried out using the ABI Prism BigDye Terminator BAY 1895344 in vivo version 3.1 and the sequences were read with an automatic sequence analyser (3130 genetic analyzer; Applied Biosystems). Sequence analysis and allele and nucleotide diversity Sequence analysis was performed as described previously [12]. Individual phylogenetic trees and concatenated analyses of the sequenced gene fragments were constructed [12]. The allelic and nucleotide diversities were calculated from the gene sequences using the DnaSP package, version 3.51 [13]. For each isolate, the combination of alleles obtained at each locus defined its allelic profile or sequence type (ST). The ST and allele assignment were performed at the P. aeruginosa MLST website (http://pubmlst.org/paeruginosa/). If a sequence did not match with an existing locus in the database, it was designated as a “new” allele.