2.6. Comparative Genomic Analysis

Sequences containing resistance genes were obtained from the NCBI nucleotide database by the BLASTN program using the resistance gene sequences of K. pneumoniae R46 as the query. The resulting sequences were filtered, and only sequences containing resistance genes were retained. CD-HIT was used to cluster the retained sequences using the genome sequence of K. pneumoniae R46 as the reference with identity of 90% and coverage of 85% [26]. The sequence sharing the greatest similarity to the other sequences in each cluster was chosen as the candidate for ortholog analysis. Orthologous groups of the genes from the candidate sequences were identified using BLASTP [22]. Sequence retrieval, statistical analysis, and other bioinformatic tools used in this study were applied with Perl and Bioperl scripts (http://www.perl.org/).