The Klebsiella pheV tRNA locus: a hotspot for integration of alien genomic islands

Klebsiella sp. cause a wide range of human infections, particularly nosocomial septicaemia, pneumonia and urinary tract infections. Like other Enterobacteriaceae, Klebsiella are likely to possess plastic genomes comprised of core regions interspersed with horizontally acquired genomic islands. As phenylalanine tRNA genes are known to be occupied by islands in other Enterobacteriaceae, we utilized PCR-based screening and chromosome walking techniques to examine the pheV locus in Klebsiella isolates from blood stream and urinary tract infections. We hypothesized that this gene was an integration hotspot that served as a repository for novel genetic material in Klebsiella. The pheV site in Klebsiella KR116 and KR164 harboured an islet encoding four genes, two with similarity to genes within an island downstream of pheR in Salmonella enterica serovar Typhi CT18. In KR173 the locus contained a larger, potentially intact version of this island and harboured an integrase gene similar to that in the S. Typhi CT18 island. However, the Klebsiella and Salmonella islands were clearly distinguishable by strain-specific segments and organizational variation. On the basis of available sequence and restriction fragment length polymorphism data, three other Klebsiella isolates were found to possess an entirely distinct entity that resembled a 12.6 kb pheV associated island in K. pneumoniae MGH78578. This island was predicted to encode a P pilus-like structure, a probable virulence factor on the basis of parallels with E. coli. A unique and intriguing feature of Klebsiella pheV loci was the presence of multiple tandem repeats of up to 163 bp immediately downstream of pheV and a truncated copy at the opposite end of the islands. The tRNA proximal repeats were variable in number and size between isolates, while the solitary downstream repeats varied in length. These elements may represent genetic debris of previous recombination events. In conclusion, the pheV locus of Klebsiella exhibited considerable variability between strains and harboured at least two distinct island types that could play important roles in adaptation and/or virulence. Functional characterization of this genetic armory will help unravel basic microbial and pathogenesis processes and may in time lead to improvements in the diagnosis, prevention and treatment of Klebsiella infections.