kleborate

Kleborate

About: |

Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:

• MLST sequence type
• species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
• ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
• virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
• antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
• K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and Kaptive

• https://github.com/klebgenomics/Kleborate/tree/main

Documentation : https://github.com/klebgenomics/Kleborate/wiki

Citation : https://www.nature.com/articles/s41467-021-24448-3

Directory tree:

kleborate/
├── sample_results.tsv
├── sample_results.txt
└── kleborate_results.tsv

Example file for an individual sample (sample_results.txt)

strain	species	species_match	contig_count	N50	largest_contig	total_size	ambiguous_bases	QC_warnings	ST	virulence_score	resistance_score	num_resistance_classes	num_resistance_genes	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	K_type	K_locus_problems	K_locus_confidence	K_locus_identity	K_locus_missing_genes	O_locus	O_type	O_locus_problems	O_locus_confidence	O_locus_identity	O_locus_missing_genes	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_inhR_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	Chr_ST	gapA	infB	mdh	pgi	phoE	rpoB	tonB	ybtS	ybtX	ybtQ	ybtP	ybtA	irp2	irp1	ybtU	ybtT	ybtE	fyuA	clbA	clbB	clbC	clbD	clbE	clbF	clbG	clbH	clbI	clbL	clbM	clbN	clbO	clbP	clbQ	iucA	iucB	iucC	iucD	iutA	iroB	iroC	iroD	iroN	rmpA	rmpD	rmpC	spurious_virulence_hits
kleb_GCF_000240185.1	Klebsiella pneumoniae	strong	7	5333942	5333942	5682322	yes (1)	ambiguous_bases	ST11	1	3	9	13	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	unknown (KL103)	*	Very high	96.69%		O1/O2v1	O2a	none	Very high	97.72%		aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%	ST11	3	3	1	1	1	1	4	14	11	14	5	9	22	19	10	5	11	11	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Example file for a run (kleborate_results.tsv)

sample	strain	species	species_match	contig_count	N50	largest_contig	total_size	ambiguous_bases	QC_warnings	ST	virulence_score	resistance_score	num_resistance_classes	num_resistance_genes	Yersiniabactin	YbST	Colibactin	CbST	Aerobactin	AbST	Salmochelin	SmST	RmpADC	RmST	rmpA2	wzi	K_locus	K_type	K_locus_problems	K_locus_confidence	K_locus_identity	K_locus_missing_genes	O_locus	O_type	O_locus_problems	O_locus_confidence	O_locus_identity	O_locus_missing_genes	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_inhR_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	Chr_ST	gapA	infB	mdh	pgi	phoE	rpoB	tonB	ybtS	ybtX	ybtQ	ybtP	ybtA	irp2	irp1	ybtU	ybtT	ybtE	fyuA	clbA	clbB	clbC	clbD	clbE	clbF	clbG	clbH	clbI	clbL	clbM	clbN	clbO	clbP	clbQ	iucA	iucB	iucC	iucD	iutA	iroB	iroC	iroD	iroN	rmpA	rmpD	rmpC	spurious_virulence_hits
kleb_GCF_000240185.1	kleb_GCF_000240185.1	Klebsiella pneumoniae	strong	7	5333942	5333942	5682322	yes (1)	ambiguous_bases	ST11	1	3	9	13	ybt 9; ICEKp3	15	-	0	-	0	-	0	-	0	-	wzi74	KL103	unknown (KL103)	*	Very high	96.69%		O1/O2v1	O2a	none	Very high	97.72%		aadA2^;rmtB;strA.v1^;strB.v1	-	-	-	-	-	-	-	sul2	tet(G).v1	-	dfrA12*	TEM-1;TEM-1;TEM-1	-	CTX-M-14;CTX-M-14	-	KPC-2	SHV-11	35Q	OmpK35-40%	PmrB-10%	GyrA-83I;ParC-80I	aac(3)-IId*?-0%	floR.v2*?;sul1?-63%	ST11	3	3	1	1	1	1	4	14	11	14	5	9	22	19	10	5	11	11	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
kleb_GCF_003812925.1	kleb_GCF_003812925.1	Klebsiella oxytoca	strong	3	5864574	5864574	5879076	no	-	NA	1	1	3	3	ybt unknown	0	-	0	-	0	-	0	-	0	-	-	unknown (KL50)	unknown (K50)	?-+*	None	80.34%	KL50_02_cpsACP,KL50_07_wcuU,KL50_09_wzx	OL104	unknown (OL104)	none	Very high	99.13%		ant(2'')-Ia*	-	-	-	-	-	-	-	-	tet(39)	-	-	-	-	OXY-2-1	-	-	-	-	-	-	-	-	-	NA	-	-	-	-	-	-	-	2*	21*	178*	148*	42*	161*	533*	39*	57*-0%	130*	262*	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
kleb_GCF_015139575.1	kleb_GCF_015139575.1	Klebsiella michiganensis	strong	2	5935402	5935402	6041841	no	-	NA	1	1	2	5	ybt unknown	0	-	0	-	0	-	0	-	0	-	-	unknown (KL131)	unknown (KL131)	-+*	None	74.30%	KL131_02_cpsACP,KL131_05_wzb,KL131_06_wzc,KL131_08_wcaA,KL131_09_rmlB,KL131_10_rmlA,KL131_11_rmlC,KL131_12_rmlD,KL131_13_wcpI,KL131_14_wzx,KL131_15_wckG,KL131_16,KL131_17_wzy,KL131_18_wclI,KL131_19	O1/O2v1	O1ab	-+*	Good	72.26%	O1/O2v1_03_wbbM,O1/O2v1_05_wbbN,O1/O2v1_07_kfoC	aph(3')-Ia*	-	-	-	-	-	-	-	-	-	-	-	-	-	CTX-M-8;CTX-M-8;CTX-M-8;OXY-1-2^	-	-	-	-	-	-	-	-	-	NA	-	-	-	-	-	-	-	117*	138*	178*	49*	100*	221*	533*	111*	102*	130*	262*	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-