safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	4	16.88

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.
NLJPJGBH_1	2716506	2717360	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
NLJPJGBH_1	2697797	2698999	blt	ARO:3003006	blt	100.00	100.00	L32599.1
NLJPJGBH_1	2475478	2476647	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
NLJPJGBH_1	1355940	1356257	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
NLJPJGBH_1	1355602	1355940	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
NLJPJGBH_1	895866	898436	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
NLJPJGBH_1	583823	585466	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
NLJPJGBH_1	338755	339348	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
NLJPJGBH_1	288252	289685	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
NLJPJGBH_1	275437	276357	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1

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.
NLJPJGBH_1	2716506	2717360	aadK	Streptomycin	100.00	100.00	M26879
NLJPJGBH_1	275437	276357	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
NLJPJGBH_1	4163234	4164610	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.
NLJPJGBH_1	2716509	2717360	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
NLJPJGBH_1	275437	276354	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
NLJPJGBH_1	4160716	4161234	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
NLJPJGBH_1	4163237	4164610	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
NLJPJGBH_1	583826	585466	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
NLJPJGBH_1	2030421	2033015	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.
NLJPJGBH_1	3678663	3679805	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
NLJPJGBH_1	3680288	3681469	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
NLJPJGBH_1	3679824	3680273	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
NLJPJGBH_1	1983763	1985526	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
NLJPJGBH_1	3272337	3273122	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
NLJPJGBH_1	3268501	3269439	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
NLJPJGBH_1	3271115	3272311	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
NLJPJGBH_1	3269467	3271086	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
NLJPJGBH_1	3261345	3268481	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
NLJPJGBH_1	2276177	2276818	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
NLJPJGBH_1	132473	133609	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
NLJPJGBH_1	18665	19534	pdxS	3.11e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
NLJPJGBH_1	1669204	1669980	CodY	3.40e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
NLJPJGBH_1	3527061	3527630	ClpP	2.52e-98	part of proteolytic complex	81.05	97.44	BAB94595

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
NLJPJGBH_1	0.0	1.0	0.0
NLJPJGBH_2	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
NLJPJGBH_1	1299655	1325763	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
NLJPJGBH_1	2647868	2678112	False	Myoviridae	VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600
NLJPJGBH_2	21669	48168	False	Siphoviridae	VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581, VOG0221, VOG9096, VOG0018
NLJPJGBH_2	65294	74990	False	Siphoviridae	VOG0025, VOG4551, VOG0918, VOG1574, VOG5292, VOG4549, VOG2725, VOG3851, VOG2352

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