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.