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.
EDIFOIPJ_1	2740279	2741133	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
EDIFOIPJ_1	2721570	2722772	blt	ARO:3003006	blt	100.00	100.00	L32599.1
EDIFOIPJ_1	2499251	2500420	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
EDIFOIPJ_1	1381454	1381771	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
EDIFOIPJ_1	1381116	1381454	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
EDIFOIPJ_1	921375	923945	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
EDIFOIPJ_1	609335	610978	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
EDIFOIPJ_1	343756	344349	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
EDIFOIPJ_1	293253	294686	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
EDIFOIPJ_1	280438	281358	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.
EDIFOIPJ_1	2740279	2741133	aadK	Streptomycin	100.00	100.00	M26879
EDIFOIPJ_1	280438	281358	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
EDIFOIPJ_1	4192304	4193680	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.
EDIFOIPJ_1	2740282	2741133	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
EDIFOIPJ_1	280438	281355	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
EDIFOIPJ_1	4189786	4190304	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
EDIFOIPJ_1	4192307	4193680	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
EDIFOIPJ_1	609338	610978	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
EDIFOIPJ_1	2055936	2058530	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.
EDIFOIPJ_1	3702443	3703585	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
EDIFOIPJ_1	3704068	3705249	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
EDIFOIPJ_1	3703604	3704053	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
EDIFOIPJ_1	2009278	2011041	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
EDIFOIPJ_1	3296108	3296893	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
EDIFOIPJ_1	3292272	3293210	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
EDIFOIPJ_1	3294886	3296082	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
EDIFOIPJ_1	3293238	3294857	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
EDIFOIPJ_1	3285116	3292252	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
EDIFOIPJ_1	2299904	2300545	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
EDIFOIPJ_1	132472	133608	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
EDIFOIPJ_1	18664	19533	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
EDIFOIPJ_1	1694718	1695494	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
EDIFOIPJ_1	3550831	3551400	ClpP	2.54e-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
EDIFOIPJ_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
EDIFOIPJ_1	1325169	1351277	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
EDIFOIPJ_1	2671641	2701885	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

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