Gelcompar 2 5 4

Clonality of the E. coli isolates was analyzed by pulsed-field gel electrophoresis (PFGE) as described previously (http://www.cdc.gov/pulsenet/pdf/ecoli-shigella-salmonella-pfge-protocol-508c.pdf). Data were analyzed using GelCompar II v.4.6 (Applied Maths, SintMartens-Latem, Belgium). Requisites for strains to belong to the same pulsotype were to have a similarity criterion above 85%, with a position tolerance of 1% and an optimization of 1%.
Multilocus sequence typing (MLST) identification was carried out for E. coli, K. pneumoniae and E. cloacae by means of PCR and sequencing according to the protocols specified at the web sites http://mlst.ucc.ie/mlst/dbs/Ecoli, http://bigsdb.web.pasteur.fr/klebsiella/klebsiella.html and http://pubmlst.org/ecloacae, respectively.

ApaI DNA macrorestriction and PFGE of A. baumannii isolates were performed as previously reported24 (link). PFGE profiles were compared using the GelCompar II v. 4.6 software package (Applied Maths, Sint-Martens-Latem, Belgium). Clustering was based on the un-weighted pair-group method with arithmetic averages (UPGMA). The Dice correlation coefficient was used to analyze the similarities of the banding patterns with a tolerance of 1%. Interpretation of chromosomal DNA restriction patterns was based on the criteria of Tenover et al.25 (link) and also on a similarity of >85% at dendrogram analysis, to indicate strain relatedness.