safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	9	18.71

PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).

Comprehensive Antibiotic Resistance Database (CARD)

Query ID	Begin	End	ARO name	ARO accession	CARD name	Identity	Coverage	Accession no.
LKPCHCKL_6	678009	679178	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LKPCHCKL_6	455658	456860	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LKPCHCKL_6	437297	438151	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LKPCHCKL_3	306539	306856	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LKPCHCKL_3	306201	306539	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LKPCHCKL_12	179488	182058	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LKPCHCKL_1	162862	163455	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LKPCHCKL_1	112359	113798	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
LKPCHCKL_1	99544	100464	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
LKPCHCKL_13	47375	49018	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3

RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)

ResFinder

Query ID	Begin	End	Resistance gene	Phenotype	Identity	Coverage	Accession no.
LKPCHCKL_6	437297	438151	aadK	Streptomycin	100.00	100.00	M26879
LKPCHCKL_1	99544	100464	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LKPCHCKL_2	401655	403031	tet(L)	Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline	100.00	100.00	X08034

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
LKPCHCKL_6	437297	438148	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LKPCHCKL_1	99544	100461	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LKPCHCKL_2	399137	399655	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LKPCHCKL_2	401658	403031	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LKPCHCKL_13	47378	49018	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LKPCHCKL_9	87469	90063	rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	WP_087347987.1

AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)

Virulence Factor Database (VFDB)

Query ID	qstart	qend	Gene name	VF name	VF category	Identity	Coverage	Accession no.
LKPCHCKL_8	85738	86880	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LKPCHCKL_8	84074	85255	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LKPCHCKL_8	85270	85719	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LKPCHCKL_9	134958	136721	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LKPCHCKL_8	492405	493190	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LKPCHCKL_8	496088	497026	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LKPCHCKL_8	493216	494412	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LKPCHCKL_8	494441	496060	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LKPCHCKL_8	497046	504182	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
LKPCHCKL_6	877889	878530	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062

BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)

VirulenceFinder

Query ID	Begin	End	Database	Virulence factor	Protein function	Identity	Coverage	Accession no.
No hit found

VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)

PHI-base

Query ID	qstart	qend	Gene name	e-value	Function	Identity	Coverage	Gene ID
LKPCHCKL_17	31846	32982	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LKPCHCKL_18	4416	5285	pdxS	1.12e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LKPCHCKL_3	619803	620579	CodY	6.95e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
LKPCHCKL_8	238467	237898	ClpP	3.64e-99	part of proteolytic complex	81.05	97.44	BAB94595
LKPCHCKL_3	157378	157770	spxA1	2.06e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
LKPCHCKL_10	34697	34455	SpoVG	2.74e-38	RNA-binding protein	80.25	79.41	AAT02994
LKPCHCKL_13	1903	2100	CspA	3.38e-32	cold shock protein	90.91	100.00	CAA62903
LKPCHCKL_6	865927	865733	CspD	5.70e-28	cold shock protein	81.54	98.48	CAC99957
LKPCHCKL_7	33336	33142	CspB	6.30e-28	cold shock protein	83.08	98.48	CAD00094

BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)

PlasmidFinder

Query ID	Begin	End	Plasmid	Query / Template	Identity	Accession no.
No hit found

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
LKPCHCKL_1	0.0	1.0	0.0
LKPCHCKL_2	0.0	1.0	0.0
LKPCHCKL_3	0.0	1.0	0.0
LKPCHCKL_4	0.0	1.0	0.0
LKPCHCKL_5	0.0	1.0	0.0
LKPCHCKL_6	0.0	1.0	0.0
LKPCHCKL_7	0.0	1.0	0.0
LKPCHCKL_8	0.0	1.0	0.0
LKPCHCKL_9	0.0	1.0	0.0
LKPCHCKL_10	0.0	1.0	0.0
LKPCHCKL_11	0.0	1.0	0.0
LKPCHCKL_12	0.0	1.0	0.0
LKPCHCKL_13	0.0	1.0	0.0
LKPCHCKL_15	0.0	1.0	0.0
LKPCHCKL_16	0.0	1.0	0.0
LKPCHCKL_17	0.0	1.0	0.0
LKPCHCKL_18	0.0	1.0	0.0
LKPCHCKL_21	1.0	0.0	1.0
LKPCHCKL_22	0.0	1.0	0.0
LKPCHCKL_23	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LKPCHCKL_3	250254	276362	False	Myoviridae	VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705
LKPCHCKL_6	476411	506788	False	Myoviridae	VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718

Phigaro v2.4.0 (Database: Jan. 2024 release)