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.
PIOGMCEJ_1	2735445	2736299	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
PIOGMCEJ_1	2716736	2717938	blt	ARO:3003006	blt	100.00	100.00	L32599.1
PIOGMCEJ_1	2494437	2495606	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
PIOGMCEJ_1	1376617	1376934	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
PIOGMCEJ_1	1376279	1376617	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
PIOGMCEJ_1	916539	919109	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
PIOGMCEJ_1	604495	606138	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
PIOGMCEJ_1	339166	339759	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
PIOGMCEJ_1	288663	290096	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
PIOGMCEJ_1	275848	276768	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.
PIOGMCEJ_1	2735445	2736299	aadK	Streptomycin	100.00	100.00	M26879
PIOGMCEJ_1	275848	276768	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
PIOGMCEJ_1	4187442	4188818	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.
PIOGMCEJ_1	2735448	2736299	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
PIOGMCEJ_1	275848	276765	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
PIOGMCEJ_1	4184924	4185442	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
PIOGMCEJ_1	4187445	4188818	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
PIOGMCEJ_1	604498	606138	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
PIOGMCEJ_1	2051095	2053689	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.
PIOGMCEJ_1	3697586	3698728	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
PIOGMCEJ_1	3699211	3700392	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
PIOGMCEJ_1	3698747	3699196	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
PIOGMCEJ_1	2004437	2006200	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
PIOGMCEJ_1	3291277	3292062	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
PIOGMCEJ_1	3287441	3288379	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
PIOGMCEJ_1	3290055	3291251	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
PIOGMCEJ_1	3288407	3290026	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
PIOGMCEJ_1	2295062	2295703	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
PIOGMCEJ_1	3280285	3287421	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.97	100.00	NP_391076

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
PIOGMCEJ_1	132881	134017	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
PIOGMCEJ_1	19073	19942	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
PIOGMCEJ_1	1689879	1690655	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
PIOGMCEJ_1	3546000	3546569	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
PIOGMCEJ_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
PIOGMCEJ_1	1320332	1346440	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
PIOGMCEJ_1	2666808	2697052	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)