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.
HLKPNGBE_12	454573	455775	blt	ARO:3003006	blt	100.00	100.00	L32599.1
HLKPNGBE_12	436212	437066	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
HLKPNGBE_10	424262	424579	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
HLKPNGBE_10	423924	424262	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
HLKPNGBE_14	251998	252918	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
HLKPNGBE_14	238664	240103	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
HLKPNGBE_14	189007	189600	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
HLKPNGBE_11	35042	36211	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
HLKPNGBE_2	28877	30520	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
HLKPNGBE_15	27404	29974	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.
HLKPNGBE_12	436212	437066	aadK	Streptomycin	100.00	100.00	M26879
HLKPNGBE_14	251998	252918	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
HLKPNGBE_3	32525	33901	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.
HLKPNGBE_12	436212	437063	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
HLKPNGBE_14	252001	252918	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
HLKPNGBE_3	30007	30525	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
HLKPNGBE_3	32528	33901	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
HLKPNGBE_2	28877	30517	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
HLKPNGBE_11	476932	479526	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.
HLKPNGBE_13	157318	158460	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
HLKPNGBE_13	155654	156835	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
HLKPNGBE_13	156850	157299	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
HLKPNGBE_11	524421	526184	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
HLKPNGBE_29	112771	113556	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
HLKPNGBE_29	108935	109873	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
HLKPNGBE_29	111549	112745	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
HLKPNGBE_29	109901	111520	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
HLKPNGBE_29	101779	108915	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
HLKPNGBE_11	234917	235558	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
HLKPNGBE_4	27982	26846	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
HLKPNGBE_8	4286	5155	pdxS	1.10e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
HLKPNGBE_10	737526	738302	CodY	8.23e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
HLKPNGBE_13	310072	309503	ClpP	2.27e-99	part of proteolytic complex	81.05	97.44	BAB94595
HLKPNGBE_10	275101	275493	spxA1	2.44e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
HLKPNGBE_6	20553	20795	SpoVG	7.49e-39	RNA-binding protein	81.48	79.41	AAT02994
HLKPNGBE_2	75992	75795	CspA	3.36e-32	cold shock protein	90.91	100.00	CAA62903
HLKPNGBE_11	222955	222761	CspD	3.39e-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
HLKPNGBE_1	0.0	1.0	0.0
HLKPNGBE_2	0.0	1.0	0.0
HLKPNGBE_3	0.0	1.0	0.0
HLKPNGBE_4	0.0	1.0	0.0
HLKPNGBE_5	0.0	1.0	0.0
HLKPNGBE_6	0.0	1.0	0.0
HLKPNGBE_7	0.0	1.0	0.0
HLKPNGBE_8	0.0	1.0	0.0
HLKPNGBE_9	0.0	1.0	0.0
HLKPNGBE_10	0.0	1.0	0.0
HLKPNGBE_11	0.0	1.0	0.0
HLKPNGBE_12	0.0	1.0	0.0
HLKPNGBE_13	0.0	1.0	0.0
HLKPNGBE_14	0.0	1.0	0.0
HLKPNGBE_15	0.0	1.0	0.0
HLKPNGBE_17	0.0	1.0	0.0
HLKPNGBE_26	0.0	1.0	0.0
HLKPNGBE_29	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
HLKPNGBE_10	367977	394085	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
HLKPNGBE_26	17868	48245	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)