Draft genome sequences of two ciprofloxacin-resistant Salmonella enterica subsp. enterica serotype Kentucky ST198 isolated from retail chicken carcasses in Egypt

Abstract Objectives Salmonella enterica serotypes, particularly antimicrobial-resistant strains, pose a major threat to public health worldwide. This study describes the draft genome sequences of two ciprofloxacin-resistant Salmonella enterica subsp. enterica serotype Kentucky isolates (H5 and H18) recovered from chicken carcass rinsates in Mansoura, Egypt. Methods Antimicrobial susceptibility phenotypes were determined for the two Salmonella Kentucky isolates by broth microdilution using a Sensititre™ system. Genomic DNA from both isolates was sequenced using an Illumina MiSeq system. Antimicrobial resistance genes were identified using ARG-ANNOT, and multilocus sequence typing (MLST) was performed using MLST 1.8. Results The draft genome for Salmonella Kentucky H5 contained 4.84 Mbp in 54 contigs, and that for Salmonella Kentucky isolate H18 contained 4.94 Mbp in 64 contigs. Sequence analysis using ARG-ANNOT identified the presence of the resistance genes bla TEM-57 , aadA1 , aadA2 , cmlA1 , sul3 and tetA in both isolates, whereas dfrA , sul2 , floR , and aph(3)-Ia were found in isolate H18 only. The amino acid substitutions Ser83Phe and Asp87Gly in GyrA and Thr57Ser and Ser80Ile in ParC were detected in both isolates. Both isolates belonged to ST198. Conclusion The draft genome sequences allowed identification of a ciprofloxacin-resistant Salmonella Kentucky ST198 epidemic clone with multidrug resistance in poultry products produced for human consumption in Egypt. These data indicate that poultry continues to be a reservoir for this persistent clone.