By comparison with the available genome sequences of the other K. pneumoniae strains, MGH 78578 (GenBank: CP000647), and 342 (GenBank: buy Adriamycin CP000964) [14], we discovered that the entire 13-kb chromosomal region carrying the aforementioned citrate fermentation genes in MGH 78578 and 342 was missing in NTUH-K2044. We postulated that the 13-kb genomic region containing genes for citrate fermentation might facilitate the use of urine citrate in oxygen-limited or anaerobic conditions, and thus, permit the growth of K. pneumoniae in the urinary tract. To test this hypothesis, an artificial urine medium (AUM) designed to provide controlled composition of the human

urine [15] was used in this study to ensure reproducibility. The correlation between presence/absence of the citrate fermentation genes and anaerobic PU-H71 nmr growth in this system was investigated. The distribution of the citrate fermentation genes among different K. pneumoniae clinical isolates was also analyzed. Results and Discussion The citrate fermentation genes in a 13-kb genomic region Located at 27916-40906 bp in the genomic sequence of K. pneumoniae strain MGH 78578, the 13-kb citrate fermentation gene locus contains 11 orfs, which constitute two divergently transcribed

operons citC2D2E2F2G2 and citS-oadGAB(dcoCAB)-citAB (Figure 1). The organization of these genes is the same as in the recently VX-680 ic50 published K. pneumoniae check 342 genome [14]. The dihydrodipicolinate reductase gene dapB and the hypothetical orfs located at the two ends of the 13-kb region in the MGH 78578 and 342 genomes are next to each other in the NTUH-K2044 genome. Missing in the corresponding location, the citrate genes are nowhere found in the NTUH-K2044 genome, and the region is replaced by a 155-bp

non-coding sequence. Since many genomic or pathogenicity islands found in bacteria genomes were associated with tRNA genes, we also tried to look for tRNA genes at the edge of this region. However, it appeared that the 13-kb genomic region carrying the citrate fermentation genes is not located within or near any tRNA gene, nor does it contain any direct repeat or known mobility sequence. This is in agreement with a recent study of bacterial genome flux, which indicated that, among twenty Escherichia coli genomes, many of the integration hotspots are not necessarily recombinogenic [16]. Figure 1 Comparative analysis of citrate fermentation gene locus. The 13-kb genomic region is present in K. pneumoniae MGH 78578 but absent in NTUH-K2044 (a). The location of the 13-kb genomic region for citrate fermentation, which includes two divergently transcribed operons, citS-oadGAB-citAB and citC2D2E2F2G2, are marked. The adjacent hypothetical orfs are shown in gray, among which the ltrA encodes a putative transcriptional regulator.