safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	7	17.83

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.
BMEBJOBC_1	755947	756801	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
BMEBJOBC_1	737238	738440	blt	ARO:3003006	blt	100.00	100.00	L32599.1
BMEBJOBC_4	591888	592226	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
BMEBJOBC_4	591571	591888	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
BMEBJOBC_1	514920	516089	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
BMEBJOBC_2	358983	359903	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
BMEBJOBC_2	345649	347088	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
BMEBJOBC_2	295992	296585	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
BMEBJOBC_2	29362	31005	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
BMEBJOBC_3	27409	29859	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	95.33	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.
BMEBJOBC_1	755947	756801	aadK	Streptomycin	100.00	100.00	M26879
BMEBJOBC_2	358983	359903	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
BMEBJOBC_9	836617	837993	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.
BMEBJOBC_1	755950	756801	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
BMEBJOBC_2	358986	359903	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
BMEBJOBC_9	834099	834617	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
BMEBJOBC_9	836620	837993	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
BMEBJOBC_2	29362	31002	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
BMEBJOBC_1	71600	74194	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.
BMEBJOBC_9	346756	347898	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
BMEBJOBC_9	348381	349562	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
BMEBJOBC_9	347917	348366	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
BMEBJOBC_1	24942	26705	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
BMEBJOBC_6	58774	59559	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
BMEBJOBC_6	62457	63395	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
BMEBJOBC_6	59585	60781	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
BMEBJOBC_6	60810	62429	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
BMEBJOBC_6	63415	70551	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
BMEBJOBC_1	315568	316209	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
BMEBJOBC_10	31914	33050	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
BMEBJOBC_11	4286	5155	pdxS	1.11e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
BMEBJOBC_4	278624	277848	CodY	8.25e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
BMEBJOBC_9	195169	195738	ClpP	5.26e-99	part of proteolytic complex	81.05	97.44	BAB94595
BMEBJOBC_4	741049	740657	spxA1	2.45e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
BMEBJOBC_5	20813	21055	SpoVG	2.74e-38	RNA-binding protein	80.25	79.41	AAT02994
BMEBJOBC_2	76477	76280	CspA	1.99e-31	cold shock protein	90.91	100.00	CAA62903

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
BMEBJOBC_1	0.0	1.0	0.0
BMEBJOBC_2	0.0	1.0	0.0
BMEBJOBC_3	0.0	1.0	0.0
BMEBJOBC_4	0.0	1.0	0.0
BMEBJOBC_5	0.0	1.0	0.0
BMEBJOBC_6	0.0	1.0	0.0
BMEBJOBC_9	0.0	1.0	0.0
BMEBJOBC_10	0.0	1.0	0.0
BMEBJOBC_11	0.0	1.0	0.0
BMEBJOBC_12	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
BMEBJOBC_1	687310	717554	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
BMEBJOBC_4	622065	648173	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)