Characterizing E. coli and K. pneumoniae Isolates

E. coli and K. pneumoniae isolates were characterized by multi-locus sequence typing (MLST), as previously described (Diancourt et al., 2005 (link); Wirth et al., 2006 (link)). E. coli isolates belonging to the same sequence type (ST) and recovered from child and parent isolates from the same household, were assessed for genetic relatedness by PFGE of XbaI-digested genomic DNA using a CHEF DR-III apparatus (Bio-Rad Laboratories, Hercules, CA, USA) following the standardized protocol of PulseNet (Ribot et al., 2006 (link)). XbaI-digested genomic DNA from Salmonella enterica serotype Braenderup strain H9812 was used as a molecular reference marker (Hunter et al., 2005 (link)). Cluster analysis was performed using BioNumerics, version 6.6 (Applied Maths, Sint-Martens-Latem, Belgium) as previously described (Liakopoulos et al., 2016 (link)).