Modules

Kleborate v3 includes a range of modules for typing bacterial genomes, most of which are specific to a particular species or complex (currently Klebsiella pneumoniae species complex, Klebsiella oxytoca species complex, Escherichia coli/Shigella). We therefore recommend specifying --preset (kpsc, kosc, escherichia) or --modules (list of modules to run based on the organism). This will run the species detection module first, and if the species matches the expected preset or module, the modules will be run (if a different species is called, Kleborate will report the species but no further typing will be conducted and the remaining fields will be blank).

Kleborate modules are divided into:

1. General Modules

2. Modules for Klebsiella pneumoniae species complex

3. Modules for Klebsiella oxytoca species complex

4. Modules for Escherichia coli/Shigella

Summary of availabe modules and their output columns

Module Name	Columns
enterobacterales__species	species, species_match
general__contig_stats	contig_count, N50, largest_contig, total_size, ambiguous_bases, QC_warnings
kpsc__mlst	ST, gapA, infB, mdh, pgi, phoE, rpoB, tonB
klebsiella__ybst	YbST, Yersiniabactin, ybtS, ybtX, ybtQ, ybtP, ybtA, irp2, irp1, ybtU, ybtT, ybtE, fyuA
klebsiella__cbst	CbST, Colibactin, clbA, clbB, clbC, clbD, clbE, clbF, clbG, clbH, clbI, clbL, clbM, clbN, clbO, clbP, clbQ
klebsiella__abst	AbST, Aerobactin, iucA, iucB, iucC, iucD, iutA
klebsiella__smst	Salmochelin, SmST, iroB, iroC, iroD, iroN
klebsiella__rmst	RmST, RmpADC, rmpA, rmpD, rmpC
klebsiella__rmpa2	rmpA2
kpsc__virulence_score	virulence_score (Score of 0-5)
kpsc__amr	AGly_acquired, Col_acquired, Fcyn_acquired, Flq_acquired, Gly_acquired, MLS_acquired, Phe_acquired, Rif_acquired, Sul_acquired, Tet_acquired, Tgc_acquired, Tmt_acquired, Bla_acquired, Bla_ESBL_acquired, Bla_ESBL_inhR_acquired, Bla_Carb_acquired, Bla_chr, SHV_mutations, Omp_mutations, Col_mutations, Flq_mutations, truncated_resistance_hits, spurious_resistance_hits
kpsc__resistance_score	resistance_score (Score of 0-3)
kpsc__resistance_gene_count	num_resistance_genes
kpsc__resistance_class_count	num_resistance_classes
kpsc__cipro_prediction	Ciprofloxacin_prediction, Ciprofloxacin_profile, Ciprofloxacin_profile_support, Ciprofloxacin_MIC_prediction
kpsc__wzi	wzi allele
kpsc__kaptive	K_locus, K_type, K_locus_confidence, K_locus_problems, K_locus_identity, K_Missing_expected_genes,O_locus, O_type, O_locus_confidence, O_locus_problems, O_locus_identity, O_Missing_expected_genes
kpsc__cgmlst	cgST, LIN code, Sublineage, Clonal group
kpsc__mrk	mrkST, mrkA, mrkB, mrkC, mrkD, mrkF, mrkH, mrkI, mrkJ
kosc__mlst	ST, gapA, infB, mdh, pgi, phoE, rpoB, tonB
kosc__kaptive	K_locus, K_type, K_locus_confidence, K_locus_problems, K_locus_identity, K_Missing_expected_genes, O_locus, O_type, O_locus_confidence, O_locus_problems, O_locus_identity, O_Missing_expected_genes
escherichia__mlst_pasteur	ST, dinB, icdA, pabB, polB, putP, trpA, trpB, uidA
escherichia__mlst_achtman	ST, adk, fumC, gyrB, icd, mdh, purA, recA
escherichia__pathovar	Pathotype, Stx1, Stx2, ST, LT, eae, ipaH
escherichia__mlst_lee	LEE_ST, LEE_lineage, LEE_eae, LEE_tir, LEE_espA, LEE_espB, LEE_espD, LEE_espH, LEE_espZ
escherichia__stxtyper	Stx_type, operon, identity, target_start, target_stop, target_strand, A_reference ‘A_identity, A_reference_subtype, A_coverage,B_reference, B_reference_subtype, B_identity, B_coverage
escherichia__ectyper	O-type, H-type, Serotype, QC, Evidence, GeneScores, AllelesKeys, GeneIdentities(%), GeneCoverages(%), GeneLengths, Warnings
escherichia__ezclermont	Clermont_type, Clermont_profile
escherichia__amr	Aminoglycoside, Fluoroquinolone, Fosfomycin, Sulfonamide, Tetracycline, Glycopeptide, Colistin, Phenicol, Macrolide, Rifamycin, Trimethoprim, BetaLactam, Carbapenem, Cephalosporin, Methicillin, Other Classes
escherichia__cgMLST	cgST, LIN code, Sublineage, Clonal group
escherichia__kaptive	K_locus, K_type, K_locus_confidence, K_locus_problems, K_locus_identity, K_Missing_expected_genes