25 μg/23.75 μg). PFGE-RFLP (Pulsed-Field Gel Electrophoresis – RFLP) Genomic DNA was prepared in agarose plugs as previously described  and digested at 37°C with 40 U of SpeI (New England Biolabs). SpeI fragments were
separated by PFGE using www.selleckchem.com/products/4egi-1.html a CHEF-DRII apparatus (Bio-Rad, Laboratories) in a 1% agarose gel in 0.5× Tris-Borate-EDTA buffer (TBE) at 150 V and at 10°C. Pulse ramps were 5 to 35 s for 35 h followed by 2 to 10 s for 10 h. Molecular weight marker was a concatemer of phage l (New England Biolabs). The strains were randomly distributed among the SRT2104 nmr different gels. SpeI-digested DNAs from strains ADV48 and ADV90 were respectively loaded in the first and the last well on each gel in order to standardize the migration patterns. Fingerprinting profiles generated by PFGE were standardized with PhotoCapt® software (Vilbert Lourmat). The automated band detection was visually checked. The profiles were scored for the AZD8931 supplier presence or absence of DNA
bands. Restriction fragment variability was determined by the Nei and Li distance method modified by using the RESTDIST program in the Phylip package v.3.66 . Clustering was predicated by the unweighted pair group average method (UPGMA) using the SplitsTree v4.0 [30, 31]. Gene amplification and sequencing Genomic DNA was obtained using the Aquapure DNA extraction kit (EpiCentre). Seven genes (dnaK, recA, rpoB, trpE, aroC, omp25 and gap) were amplified using the PI-1840 primers shown in Table 3. PCR was carried out in 50 μL of reaction mixture containing 200 nM (each) primer (Sigma Genosys), 200 μM (each) desoxy-nucleoside triphosphates (dNTP) (Euromedex), 2.5 U of Taq DNA polymerase (Promega) in the appropriate reaction buffer and 50 ng of genomic DNA as the template. Amplification conditions were as follows: initial denaturation of 3 min at 95°C followed by 35-cycles with 1 min at
94°C, 1 min at 60°C (for dnaK, rpoB recA and gap fragments) or 1 min at 65°C (for trpE, aroC and omp25 fragments) and 2 min 30 s at 72°C. The final extension was carried out at 72°C during 10 min. PCR products and molecular weight marker (phage phiX DNA digested with HaeIII, New England Biolabs) were separated in 1.5% (w/v) agarose gel in 0.5× TBE buffer. Amplification products were sequenced in both direction using forward and reverse sequencing primers (Table 3) on an ABI 3730xl automatic sequencer (Cogenics, France). The sequences were deposited to GenBank database with accession numbers: GQ429327 to GQ429816. Table 3 Primers used for genes amplification and sequencing.