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.
PBEOOPMJ_1	2621336	2622190	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
PBEOOPMJ_1	2602627	2603829	blt	ARO:3003006	blt	100.00	100.00	L32599.1
PBEOOPMJ_1	2380308	2381477	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
PBEOOPMJ_1	1355941	1356258	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
PBEOOPMJ_1	1355603	1355941	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
PBEOOPMJ_1	895859	898429	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
PBEOOPMJ_1	583818	585461	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
PBEOOPMJ_1	338753	339346	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
PBEOOPMJ_1	288250	289683	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
PBEOOPMJ_1	275435	276355	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.
PBEOOPMJ_1	2621336	2622190	aadK	Streptomycin	100.00	100.00	M26879
PBEOOPMJ_1	275435	276355	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
PBEOOPMJ_1	4112180	4113556	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.
PBEOOPMJ_1	2621339	2622190	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
PBEOOPMJ_1	275435	276352	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
PBEOOPMJ_1	4109662	4110180	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
PBEOOPMJ_1	4112183	4113556	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
PBEOOPMJ_1	583821	585461	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
PBEOOPMJ_1	2071397	2073991	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.
PBEOOPMJ_1	3622320	3623462	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
PBEOOPMJ_1	3623945	3625126	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
PBEOOPMJ_1	3623481	3623930	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
PBEOOPMJ_1	2024739	2026502	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
PBEOOPMJ_1	3215986	3216771	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
PBEOOPMJ_1	3212150	3213088	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
PBEOOPMJ_1	3214764	3215960	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
PBEOOPMJ_1	3213116	3214735	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
PBEOOPMJ_1	3204994	3212130	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
PBEOOPMJ_1	2180963	2181604	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
PBEOOPMJ_1	132471	133607	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
PBEOOPMJ_1	18665	19534	pdxS	3.08e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
PBEOOPMJ_1	1669205	1669981	CodY	3.36e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
PBEOOPMJ_1	3470709	3471278	ClpP	2.49e-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
PBEOOPMJ_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
PBEOOPMJ_1	1299656	1325764	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
PBEOOPMJ_1	1860153	1895703	False	Siphoviridae	VOG4602, VOG9667, VOG5353, VOG0181, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG6093, VOG7462, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918
PBEOOPMJ_1	2552698	2582942	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
PBEOOPMJ_1	2751426	2781509	False	Siphoviridae	VOG4707, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0531, VOG0198, VOG6340, VOG7372, VOG2752, VOG4606

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