safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
15	10	4	18.47

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.
PINDENIF_1	3627213	3628589	tet(L)	ARO:3000179	tet(L)	99.78	100.00	M11036.1
PINDENIF_1	2848690	2849544	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
PINDENIF_1	2829981	2831183	blt	ARO:3003006	blt	100.00	100.00	L32599.1
PINDENIF_1	2665588	2666382	APH(3')-IIIa	ARO:3002647	APH(3')-IIIa	100.00	100.00	CP004067.1
PINDENIF_1	2607017	2608186	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
PINDENIF_1	1376886	1377203	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
PINDENIF_1	1376548	1376886	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
PINDENIF_1	916795	919365	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
PINDENIF_1	604748	606391	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
PINDENIF_1	339165	339758	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
PINDENIF_1	288663	290096	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
PINDENIF_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.
PINDENIF_1	2848690	2849544	aadK	Streptomycin	100.00	100.00	M26879
PINDENIF_1	2665588	2666382	aph(3')-III	Kanamycin, Amikacin, Neomycin, Butirosin, Isepamicin, Lividomycin, Paromomycin, Ribostamycin	100.00	100.00	M26832
PINDENIF_1	275848	276768	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
PINDENIF_1	3627213	3628589	tet(L)	Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline	100.00	100.00	M29725

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
PINDENIF_1	2848693	2849544	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
PINDENIF_1	2665591	2666382	aph(3')-IIIa	aminoglycoside O-phosphotransferase APH(3')-IIIa	EXACTX	100.00	100.00	WP_001096887.1
PINDENIF_1	275848	276765	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
PINDENIF_1	4285635	4286153	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
PINDENIF_1	3627216	3628589	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_001574277.1
PINDENIF_1	4288156	4289529	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
PINDENIF_1	604751	606391	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
PINDENIF_1	2051368	2053962	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.
PINDENIF_1	3798287	3799429	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
PINDENIF_1	3799912	3801093	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
PINDENIF_1	3799448	3799897	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
PINDENIF_1	2004710	2006473	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
PINDENIF_1	3404526	3405311	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
PINDENIF_1	3400690	3401628	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
PINDENIF_1	3403304	3404500	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
PINDENIF_1	3401656	3403275	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
PINDENIF_1	3393534	3400670	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
PINDENIF_1	2407662	2408303	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
PINDENIF_1	132882	134018	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
PINDENIF_1	19074	19943	pdxS	3.21e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
PINDENIF_1	1690151	1690927	CodY	3.50e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
PINDENIF_1	3646701	3647270	ClpP	2.60e-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.
PINDENIF_1	3628840	3629226	rep34	387 / 633	100.00	M29725

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
PINDENIF_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
PINDENIF_1	1320598	1346706	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
PINDENIF_1	2165207	2176132	False	Siphoviridae	VOG1652, VOG4724, VOG1198, VOG0918, VOG4551, VOG0025, VOG7476
PINDENIF_1	2236034	2251339	True	Unknown	VOG8610, VOG0275, VOG5532, VOG0944, VOG4910, VOG3389, VOG5042
PINDENIF_1	2780053	2810297	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)