Table 3. Coding sequences related to virulence factors present in the outbreak clone.
| Virulence factor | Gene(s) detected | Best hit*(coverage, identity) | Genetic context |
|---|---|---|---|
| Adhesin | |||
| Type 1 fimbriae | fimBEAICDFGHK | PMK1 (100%, 99%) | Chromosome |
| Type 3 fimbriae | mrkABCDF | PMK1 (100%, 100%) | Chromosome |
| Kpa fimbriae | kpaABCDE | PMK1 (100%, 100%) | Chromosome |
| Kpb-like fimbriae± | kpbRABCD2 | PMK1 (100%, 100%) | Chromosome |
| Kpe fimbriae# | ΔkpeA, kpeBCD | PMK1 (100%, 100%) | Chromosome |
| Kpf fimbriae | kpfRABCD | PMK1 (100%, 100%) | Chromosome |
| Kpg fimbriae | kpgABCD | pittNDM01 (100%, 99%) | Chromosome |
| Fim2ǂ | fim2AIC, fim2D::tnpA, fimF-K | PMK1 (100%, 100%) | Chromosome |
| ECP (Mat) fimbriae | ecpRABCDE | PMK1 (100%, 100%) | Chromosome |
| polysaccharide adhesin | pgaABCD | PMK1 (100%, 100%) | Chromosome |
| Capsule | |||
| wzi24/K24 | galF-wzc, wcaJ-ugd† (Fig. 3) | ATCC 43816 KPPR1 (50%, 95%) | Chromosome |
| Iron uptake system | |||
| Fep-ent (Enterobactin) | fepA-entD, fes-entF, fepDGC, ybdA, fepB, entCEBA | PMK1 (100%, 100%) | Chromosome |
| Iuc (Aerobactin) | iutA | PMK1 (100%, 100%) | Chromosome |
| IroA (Salmochelin) | iroN | PMK1 (100%, 100%) | Chromosome |
| Fhu (Ferrichrome) | fhuACDB | PMK1 (100%, 100%) | Chromosome |
| ABC transporter Sit (Ferrous iron) | sitABCD | PMK1 (100%, 100%) | Chromosome |
| ABC transporter Eit (Iron/B12/siderophore/hemin) | eitABCD | PMK1 (100%, 100%) | Chromosome |
| ABC transporter Kfu (Ferric iron) | kfuABC | PMK1 (100%, 100%) | Chromosome |
| High-pathogenicity island (Yersiniabactin) | ybtPQXS, ybtA-irp2-irp1-ybtUTE-fyuA | E. coli ED 1a (100%, 99%) | Chromosome |
| Feo (Ferrous iron) | feoABC | PMK1 (100%, 100%) | Chromosome |
| Hmu (Hemin/hemoprotein) | hmuRSTUV | PMK1 (100%, 100%) | Chromosome |
| Nitrogen source utilization | |||
| Urease | ureDCBAEFG | PMK1 (100%, 100%) | Chromosome |
| Secretion system | |||
| F-type T4SS | traALEKBVCGFHNUW, trbC† | JM45 plasmid p1 (100%, 99%) | Plasmid |
| T4SS (type IVA) | virB1-2, virB4-6, virB8-11, virD4 | E. coli ED 1a (100%, 99%) | Chromosome |
| T6SS | impH-G, imcF, vgrG, ompA, impJ, clpV† | PMK1 (100%, 100%) | Chromosome |
*The best hit is defined by Blastn on http://blast.ncbi.nlm.nih.gov/Blast.cgi. The species name is not shown if the matches are from K. pneumoniae. ±The adhesin gene kpbD was replaced by a different adhesin gene kpdD2 (the gene was named in this study).
#The subunit gene kpeA was replaced by a gene encoding Tn903 transposase.
ǂThe intact gene cluster of this fimbriae was identified on a genomic island KpGI-5 (JN181158) of K. pneumoniae KR116.
†Only conserved/hallmark genes are shown here.