Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones

Typing carbapenem-resistant Klebsiella pneumoniae (CR-KPN) is crucial in controlling their dissemination and solving outbreaks. In this context, we searched for an effective, faster, and cheaper alternative technique to type KPN by analyzing the fosA KP sequence. We analyzed the nucleotide sequences of chromosomal fosA KP gene in 350 KPN genomes (70 per sequence type [ST] or clonal complex [CC]). Assembly genomes were randomly downloaded from NCBI and annotated using RAST in PATRIC platform. The isolate STs were verified using multilocus sequence typing 2.0 by the Center for Genomic Epidemiology. Chromosomally encoded fosA KP was confirmed in MLplasmid, and the sequence alignments were performed in Clustal Omega. The amino acid sequences were analyzed using SNAP2 and SMART platforms. Out of the 70 genomes analyzed for each ST/CC, we observed 100% fosA sequence identity for CC258/11, ST15, ST307, and ST101. For ST16, only two fosA sequences were different from each other. We observed differences in amino acid sequences at positions 25 and 79 (ST16) and 86 (ST16, ST101). The C-terminal (amino acid 138, 139, 140) was different for each cluster. None of these polymorphisms is related to the protein active site. Moreover, L25Q (ST16) polymorphism was predicted to probably affect the protein function. We observed that chromosomal fosA KP sequences from KPN are highly conserved in ST15, ST307, ST16, ST101, and CC258/11, suggesting fosA KP sequencing as an alternative, easier, faster, and less expensive technique in identifying epidemiological STs for KPN, and discriminating them from CC258/11.