The loxP recombination sites are only 34 bp in length and Cre will recombine essentially any DNA substrates that contain these sites, with no requirements for the accessory proteins (Abremski & Hoess, 1985; Abremski et al., 1986). However, introducing loxP NVP-BKM120 cell line sites into pathogenic E. coli genomes using the common existing techniques has the disadvantage of being time-consuming (Murphy & Campellone, 2003; Lee et al., 2009). A

simple mutagenesis method without DNA cloning has been developed in E. coli. This method depends on the lambda Red gam, bet, and exo gene products, which encode an efficient homologs recombination system (Datsenko & Wanner, 2000; Yu et al., 2000). Using this method, modifications can be targeted precisely and can range from single base-pair deletions or insertions to the addition or deletion of sequences in the kilobase-pair range. Selection for the positive phenotype of the introduced

mutation has been difficult to achieve, making the use of a counter-selection approach very useful for the mutagenesis (Reyrat et al., 1998). A powerful counter-selection system for the introduction of mutations based on the wild-type rpsL gene responsible for streptomycin sensitivity has been described (Zhang et al., 2003; Rivero-Müller et al., 2007; Heermann et al., 2008). In E. coli, the rpsL gene encodes CYC202 molecular weight the S12 ribosomal protein of the 30S subunit, which is the target of streptomycin. Streptomycin inhibits protein, synthesis by binding near the interface of S12 ribosomal PAK6 protein, hence increasing the translational errors (Karimi & Ehrenberg, 1994, 1996). The prerequisite for this system to be effective is streptomycin-resistant strain. Resistance because of chromosomal mutations within rpsL is recessive in a merodiploid strain (Reyrat et al., 1998; Gill & Amyes, 2004). When both wild-type and mutant alleles of rpsL are expressed in the same strain, the strain

becomes sensitive to streptomycin (Reyrat et al., 1998). Here a method for site-directed mutagenesis of the APEC chromosome is described. Lambda Red recombination is used to introduce the loxP sites flanking the rpsL-neo marker into the APEC genome, and the Cre/lox system is used to remove the marker. Further, it is shown that rpsL counter-selection is applicable for introducing modifications into the APEC genome. Strains used and generated in this study are listed in Table 1. APEC1 strain was isolated from an infected chicken (Vandemaele et al., 2003). APEC1 strains containing plasmid pKD46 (Table 1) responsible for the homologs recombination (Datsenko & Wanner, 2000) and plasmid pSC101-BAD-Cre-tet (Anastassiadis et al., 2009) containing the cre gene responsible for the recombination of the loxP sites were incubated at 30 °C unless otherwise mentioned.