4. Annotation variables

Several plot tabs include an option for users to select an annotation variable drawn from the list below. Virulence and resistance genotypes are extracted from the Kleborate output and described in detail on the Kleborate wiki pages.

Summary variables

• Clone type: indicates the globally-distributed multi-drug resistant (MDR) and hypervirulent (Hv) STs described in the literature and discussed here (MDR in red; ST11, ST258, ST512, ST14, ST15, ST17, ST20, ST29, ST37, ST101, ST147, ST307; and Hv in blue; ST23, ST86, ST65, ST25, ST66, ST380). All other STs are marked as unassigned.
• Resistance score: Kleborate resistance score ranging from 0-3 and indicating escalating levels of clinically-relevant drug-resistance predicted from the genome data as described here.
• Virulence score: Kleborate virulence score ranging from 0-5 and indicating escalating levels of virulence predicted from the genome data as described here.

Virulence genotypes

• Yersiniabactin: presence/absence of the yersiniabactin synthesis locus (ybt)
• Yersiniabactin (lineages): yersiniabactin lineage determined from nucleotide sequence analysis of the ybt locus genes. '-' indicates no locus was reported.
• Colibactin: presence/absence of the colibactin synthesis locus (clb).
• Colibactin (lineages): colibactin lineage determined from nucleotide sequence analysis of the clb locus genes. '-' indicates no locus was reported.
• Aerobactin: presence/absence of the aerobactin synthesis locus (iuc).
• Aerobactin (lineages): aerobactin lineage determined from nucleotide sequence analysis of the iuc locus genes. '-' indicates no locus was reported.
• Salmochelin: presence/absence of the salmochelin synthesis locus (iro).
• Salmochelin (lineages): salmochelin lineage determined from nucleotide sequence analysis of the iro locus genes. '-' indicates no locus was reported.
• RmpADC: presence/absence of the rmpADC hypermucoidy locus.
• RmpADC (lineages): rmpADC lineage determined from nucleotide sequence analysis of the rmpADC genes. '-' indicates no locus was reported.
• RmpADC (truncations): indicates whether an intact or truncated rmpADC locus was detected (truncated loci have one or more missing genes and/or amino acid sequence truncations). '-' indicates no locus was reported.
• RmpA2: presence/absence of the rmpA2 hypermucoidy gene.
• RmpA2 (truncations): indicates whether an intact or truncated rmpA2 locus was detected (truncated loci contain a premature STOP codon in the predicted amino acid sequence). '-' indicates no locus was reported.

Resistance genotypes

• AGly: presence/absence of acquired aminoglycoside resistance genes.
• Col (genes): presence/absence of acquired colistin resistance genes.
• Col (mutations): presence/absence of colistin resistance-conferring mutations in core chromosomal genes.
• Fcyn: presence/absence of acquired fosfomycin resistance genes.
• Flq (genes): presence/absence of acquired fluoroquinolone resistance genes.
• Flq (mutations): presence/absence of fluoroquinolone resistance-conferring mutations in core chromosomal genes.
• Gly: presence/absence of acquired glycopeptide resistance genes.
• MLS: presence/absence of acquired macrolide, lincosamide and streptogramin B resistance genes.
• Phe: presence/absence of acquired phenicol resistance genes.
• Rif: presence/absence of acquired rifampin resistance genes.
• Sul: presence/absence of acquired sulphonamide resistance genes.
• Tet: presence/absence of acquired tetracycline resistance genes.
• Tmt: presence/absence of acquired trimethoprim resistance genes.
• Tgc: presence/absence of acquired tigecycline resistance genes.
• Bla: presence/absence of acquired narrow-spectrum beta-lactamases.
• Bla inhR: presence/absence of acquired narrow-spectrum beta-lactamases with inhibitor resistance.
• Bla ESBL: presence/absence of acquired extended-spectrum beta-lactamases.
• Bla ESBL (alleles): extended-spectrum beta-lactamase alleles (the most common alleles/groups detected in K. pneumoniae are specified individually; CTX-M-15, CTX-M-14, CTX-M-65, CTX-M-other; SHV, TEM, other). 'multiple' indicates that more than one ESBL was detected irrespective of the alleles.'-' indicates no ESBLs were reported.
• Bla ESBL inhR: presence/absence of extended-spectrum beta-lactamases with inhibitor resistance.
• Bla Carb: presence/absence of carbapenemases.
• Bla Carb (alleles): carbapenemase alleles (othe most common allele groups detected in K. pneumoniae are specified individually; IMP, KPC, NDM, OXA, VIM, other). 'multiple' indicates that more than one carbapenemase was detected irrespective of the allele groups. '-' indicates no carbapenemase genes were reported.