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.
OPHIPIDH_1	1797269	1797607	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
OPHIPIDH_1	1796952	1797269	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
OPHIPIDH_1	678303	679472	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
OPHIPIDH_1	455953	457155	blt	ARO:3003006	blt	100.00	100.00	L32599.1
OPHIPIDH_1	437592	438446	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
OPHIPIDH_3	358873	359793	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
OPHIPIDH_3	345539	346978	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
OPHIPIDH_3	295882	296475	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
OPHIPIDH_3	29253	30896	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
OPHIPIDH_4	27546	30116	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.
OPHIPIDH_1	437592	438446	aadK	Streptomycin	100.00	100.00	M26879
OPHIPIDH_3	358873	359793	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
OPHIPIDH_5	36557	37933	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.
OPHIPIDH_1	437592	438443	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
OPHIPIDH_3	358876	359793	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
OPHIPIDH_5	39933	40451	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
OPHIPIDH_5	36557	37930	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
OPHIPIDH_3	29253	30893	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
OPHIPIDH_1	1120195	1122789	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.
OPHIPIDH_2	398240	399382	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
OPHIPIDH_2	396576	397757	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
OPHIPIDH_2	397772	398221	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
OPHIPIDH_1	1167684	1169447	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
OPHIPIDH_2	804907	805692	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
OPHIPIDH_2	808590	809528	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
OPHIPIDH_2	805718	806914	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
OPHIPIDH_2	806943	808562	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
OPHIPIDH_2	809548	816684	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
OPHIPIDH_1	878183	878824	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
OPHIPIDH_6	28208	27072	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
OPHIPIDH_8	4392	5261	pdxS	1.13e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
OPHIPIDH_1	1484005	1483229	CodY	1.80e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
OPHIPIDH_2	550969	550400	ClpP	5.52e-99	part of proteolytic complex	81.05	97.44	BAB94595
OPHIPIDH_1	1946430	1946038	spxA1	5.34e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
OPHIPIDH_7	20900	21142	SpoVG	2.75e-38	RNA-binding protein	80.25	79.41	AAT02994
OPHIPIDH_3	76368	76171	CspA	1.98e-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
OPHIPIDH_1	0.0	1.0	0.0
OPHIPIDH_2	0.0	1.0	0.0
OPHIPIDH_3	0.0	1.0	0.0
OPHIPIDH_4	0.0	1.0	0.0
OPHIPIDH_5	0.0	1.0	0.0
OPHIPIDH_6	0.0	1.0	0.0
OPHIPIDH_7	0.0	1.0	0.0
OPHIPIDH_8	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
OPHIPIDH_1	476706	507083	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
OPHIPIDH_1	1827446	1853554	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)