safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	8	18.25

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.
LIPNICOO_1	590811	591149	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LIPNICOO_1	590494	590811	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LIPNICOO_21	488170	489024	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LIPNICOO_21	469461	470663	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LIPNICOO_21	247144	248313	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LIPNICOO_23	228783	231353	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LIPNICOO_22	162826	163419	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LIPNICOO_22	112323	113762	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
LIPNICOO_22	99508	100428	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
LIPNICOO_27	29126	30769	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3

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.
LIPNICOO_21	488170	489024	aadK	Streptomycin	100.00	100.00	M26879
LIPNICOO_22	99508	100428	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LIPNICOO_26	36260	37636	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.
LIPNICOO_21	488173	489024	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LIPNICOO_22	99508	100425	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LIPNICOO_26	39636	40154	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LIPNICOO_26	36260	37633	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LIPNICOO_27	29126	30766	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LIPNICOO_25	192792	195386	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.
LIPNICOO_12	398122	399264	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LIPNICOO_12	396458	397639	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LIPNICOO_12	397654	398103	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LIPNICOO_25	240281	242044	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LIPNICOO_12	804789	805574	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LIPNICOO_12	808472	809410	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LIPNICOO_12	805600	806796	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LIPNICOO_12	806825	808444	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LIPNICOO_12	809430	816566	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
LIPNICOO_21	47792	48433	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
LIPNICOO_3	31638	32774	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LIPNICOO_6	11182	10313	pdxS	1.10e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LIPNICOO_1	277547	276771	CodY	8.24e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
LIPNICOO_12	550851	550282	ClpP	5.52e-99	part of proteolytic complex	81.05	97.44	BAB94595
LIPNICOO_1	739972	739580	spxA1	2.44e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
LIPNICOO_4	20512	20754	SpoVG	2.72e-38	RNA-binding protein	80.25	79.41	AAT02994
LIPNICOO_27	76241	76044	CspA	3.37e-32	cold shock protein	90.91	100.00	CAA62903
LIPNICOO_21	60395	60589	CspD	3.97e-28	cold shock protein	81.54	98.48	CAC99957

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
LIPNICOO_1	0.0	1.0	0.0
LIPNICOO_2	0.0	1.0	0.0
LIPNICOO_3	0.0	1.0	0.0
LIPNICOO_4	0.0	1.0	0.0
LIPNICOO_5	0.0	1.0	0.0
LIPNICOO_6	0.0	1.0	0.0
LIPNICOO_7	0.0	1.0	0.0
LIPNICOO_8	0.0	1.0	0.0
LIPNICOO_12	0.0	1.0	0.0
LIPNICOO_21	0.0	1.0	0.0
LIPNICOO_22	0.0	1.0	0.0
LIPNICOO_23	0.0	1.0	0.0
LIPNICOO_24	0.0	1.0	0.0
LIPNICOO_25	0.0	1.0	0.0
LIPNICOO_26	0.0	1.0	0.0
LIPNICOO_27	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LIPNICOO_1	620988	647096	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667
LIPNICOO_21	419533	449777	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
LIPNICOO_21	618138	643822	False	Siphoviridae	VOG4707, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG2545, VOG0376, VOG0198, VOG6340

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