Figure 1.
Tree for 108 genomes based on a 2.93-Mbp alignment, rooted at the midpoint of the outgroup (Ecl/Yre) branch. Nodes with <30% bootstrap support were combined forming the multifurcated dashed line; otherwise support values are shown only when <100%. Brackets: Kpn multilocus sequence type (ST). Inset: enlargement of the “core Kpn” phylogeny. Kpn2146 falls in a clade containing fellow ST11 strains Kpn JM45 and Kpn HS11286 and a tight clade (circled) of ST258 and ST512 strains. The ST258/ST512 clade is heavily sequenced, and represented here with only five of its most diverse members. Bold: complete genomes used for phyloblocks analysis. Species name abbreviations: Kpn, K. pneumoniae; Ksp, K. sp.; Kpl, K. cf. planticola; Kox, K. oxytoca; Kva, K. variicola; Eae, Enterobacter aerogenes; Ecl, E. cloacae; Ror, Raoultella ornithinolytica; Yre, Yokanella regensburgei.
Table 1.
Replicon copy numbers.
Table 2.
Enzymes, efflux pumps, and mutations expected to confer resistance to antibiotics of clinical relevancea.
Figure 2.
Key, color coding of genes, mobile elements, and unique regions and juxtapositions, with additional colors for non-gene features. Inner ring, representative long matches to other plasmids. abR, antibiotic resistance.
Figure 3.
Key, color coding of genes, mobile elements, and unique regions and juxtapositions, with additional colors for non-gene features. Inner ring, representative long matches to other plasmids. Innermost black arrows, recent recombination events. HR, homologous recombination; abR, antibiotic resistance.
Figure 4.
Key, color coding of genes, mobile elements, and unique regions and juxtapositions, with additional colors for non-gene features. Inner ring, representative long matches to other plasmids. Innermost black arrows, recent recombination events. HR, homologous recombination; abR, antibiotic resistance.
Figure 5.
Learned phyloblocks identify a new island and the highly variable capsular polysaccharide and lipopolysaccharide synthesis gene cluster (cps-lps).
Nonubiquity phyloblocks: those missing in at least one of the 11 reference chromosomes. Complex phyloblocks: those requiring more than one gain/loss event to reconcile the phylotype with the genome tree of Fig. 1. As a percentage of their combined 411 kbp, the learned phyloblocks mapped either to the training islands (81.9%), the two newly indicated regions (12.0%), insertion sequences (2.1%), or to small scattered regions that did not show hallmarks of islands (4.0%). Red segments: the 11 final islands (including a tandem array of Kpn21L and Kpn11L). Circles, the two newly indicated regions.
Table 3.
Genomic islands.
Figure 6.
Operon translocation and fusion at the cps-lps polysaccharide synthesis locus.
The cps P1, P2 and P3 promoters are taken from [68], while a promoter (Plps) has been mapped in K. pneumoniae MGH 78578 to the intergenic space between uge and the first lps gene [69]. A) The cps-lps region of K. pneumoniae 342, which is typical of Klebsiella. Genes of cps are in yellow (common in most strains) or blue (varying in gene identity, count, and order); genes of lps are in red. The manCB unit (orange arrows) is occasionally found in cps, and occasionally in lps, and here unusually in both. The diamond represents the JUMPstart DNA/RNA motif at whose ops sequence RfaH is loaded onto the elongating RNA polymerase in place of NusG, preventing Rho-based termination for the small number of long transcription units that are controlled by ops-RfaH, and physically coupling the elongating RNA polymerase to the trailing ribosome [70]. B) Kpn2146 cps-lps. The boxed cps P3 unit has been deleted from its usual site, and moreover translocated to a nearby position, apparently by transposition and/or homologous recombination mechanisms; note the complex pattern of surrounding IS insertions and the directly repeated flanking sequence copies (gray arrows).ΔIS, incomplete IS copy; dotted lines, gene or IS interrupted by ISs; GT, glucosyl transferase, Hyp, hypothetical.