safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	8	18.25

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.
LHOOCJKP_2	677827	678996	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LHOOCJKP_4	591496	591834	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LHOOCJKP_4	591179	591496	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LHOOCJKP_2	455501	456703	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LHOOCJKP_2	437140	437994	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LHOOCJKP_1	108885	109805	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
LHOOCJKP_1	95551	96990	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
LHOOCJKP_12	47376	49019	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
LHOOCJKP_1	45894	46487	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LHOOCJKP_7	27268	29838	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3

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.
LHOOCJKP_2	437140	437994	aadK	Streptomycin	100.00	100.00	M26879
LHOOCJKP_1	108885	109805	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LHOOCJKP_6	1009133	1010509	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	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.
LHOOCJKP_2	437140	437991	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LHOOCJKP_1	108888	109805	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LHOOCJKP_6	1006615	1007133	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LHOOCJKP_6	1009136	1010509	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LHOOCJKP_12	47379	49019	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LHOOCJKP_11	55424	58018	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.
LHOOCJKP_6	519277	520419	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LHOOCJKP_6	520902	522083	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LHOOCJKP_6	520438	520887	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LHOOCJKP_11	8766	10529	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LHOOCJKP_6	112968	113753	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LHOOCJKP_6	109132	110070	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LHOOCJKP_6	111746	112942	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LHOOCJKP_6	110098	111717	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LHOOCJKP_2	877722	878363	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
LHOOCJKP_6	101976	109112	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.97	100.00	NP_391076

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
LHOOCJKP_10	31825	32961	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LHOOCJKP_13	4270	5139	pdxS	1.12e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LHOOCJKP_4	278234	277458	CodY	8.25e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
LHOOCJKP_6	367691	368260	ClpP	6.29e-99	part of proteolytic complex	81.05	97.44	BAB94595
LHOOCJKP_4	740657	740265	spxA1	2.44e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
LHOOCJKP_8	34732	34490	SpoVG	2.74e-38	RNA-binding protein	80.25	79.41	AAT02994
LHOOCJKP_12	1904	2101	CspA	3.38e-32	cold shock protein	90.91	100.00	CAA62903
LHOOCJKP_2	865760	865566	CspD	5.70e-28	cold shock protein	81.54	98.48	CAC99957

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
LHOOCJKP_1	0.0	1.0	0.0
LHOOCJKP_2	0.0	1.0	0.0
LHOOCJKP_3	0.0	1.0	0.0
LHOOCJKP_4	0.0	1.0	0.0
LHOOCJKP_5	0.0	1.0	0.0
LHOOCJKP_6	0.0	1.0	0.0
LHOOCJKP_7	0.0	1.0	0.0
LHOOCJKP_8	0.0	1.0	0.0
LHOOCJKP_10	0.0	1.0	0.0
LHOOCJKP_11	0.0	1.0	0.0
LHOOCJKP_12	0.0	1.0	0.0
LHOOCJKP_13	0.0	1.0	0.0
LHOOCJKP_14	0.0	1.0	0.0
LHOOCJKP_15	0.0	1.0	0.0
LHOOCJKP_17	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LHOOCJKP_2	476254	506631	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
LHOOCJKP_4	621673	647781	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667

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