safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	9	18.71

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.
IDGFLCEF_3	488285	489139	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
IDGFLCEF_3	469576	470778	blt	ARO:3003006	blt	100.00	100.00	L32599.1
IDGFLCEF_2	306516	306833	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
IDGFLCEF_2	306178	306516	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
IDGFLCEF_10	276544	279114	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
IDGFLCEF_3	247257	248426	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
IDGFLCEF_5	162917	163510	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
IDGFLCEF_5	112414	113853	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
IDGFLCEF_5	99599	100519	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
IDGFLCEF_7	29146	30789	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.
IDGFLCEF_3	488285	489139	aadK	Streptomycin	100.00	100.00	M26879
IDGFLCEF_5	99599	100519	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
IDGFLCEF_6	36280	37656	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.
IDGFLCEF_3	488288	489139	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
IDGFLCEF_5	99599	100516	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
IDGFLCEF_6	39656	40174	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
IDGFLCEF_6	36280	37653	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
IDGFLCEF_7	29146	30786	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
IDGFLCEF_2	980979	983573	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.
IDGFLCEF_1	276431	277573	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
IDGFLCEF_1	274767	275948	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
IDGFLCEF_1	275963	276412	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
IDGFLCEF_2	934321	936084	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
IDGFLCEF_1	683124	683909	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
IDGFLCEF_1	686807	687745	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
IDGFLCEF_1	683935	685131	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
IDGFLCEF_1	685160	686779	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
IDGFLCEF_1	687765	694901	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
IDGFLCEF_3	47911	48552	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
IDGFLCEF_4	31933	33069	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
IDGFLCEF_14	11331	10462	pdxS	1.11e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
IDGFLCEF_2	619779	620555	CodY	9.54e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
IDGFLCEF_1	429185	428616	ClpP	4.43e-99	part of proteolytic complex	81.05	97.44	BAB94595
IDGFLCEF_2	157355	157747	spxA1	2.83e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
IDGFLCEF_11	34595	34353	SpoVG	7.50e-39	RNA-binding protein	81.48	79.41	AAT02994
IDGFLCEF_7	76261	76064	CspA	3.38e-32	cold shock protein	90.91	100.00	CAA62903
IDGFLCEF_3	60514	60708	CspD	5.70e-28	cold shock protein	81.54	98.48	CAC99957
IDGFLCEF_9	33208	33014	CspB	1.09e-27	cold shock protein	83.08	98.48	CAD00094

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
IDGFLCEF_1	0.0	1.0	0.0
IDGFLCEF_2	0.0	1.0	0.0
IDGFLCEF_3	0.0	1.0	0.0
IDGFLCEF_4	0.0	1.0	0.0
IDGFLCEF_5	0.0	1.0	0.0
IDGFLCEF_6	0.0	1.0	0.0
IDGFLCEF_7	0.0	1.0	0.0
IDGFLCEF_8	0.0	1.0	0.0
IDGFLCEF_9	0.0	1.0	0.0
IDGFLCEF_10	0.0	1.0	0.0
IDGFLCEF_11	0.0	1.0	0.0
IDGFLCEF_13	1.0	0.0	1.0
IDGFLCEF_14	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
IDGFLCEF_2	250231	276339	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
IDGFLCEF_3	419647	449891	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
IDGFLCEF_13	1521	9437	False	Siphoviridae	VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG4544, VOG4581
IDGFLCEF_13	39332	52430	False	Unknown	VOG4549, VOG2725, VOG3851, VOG2352, VOG4714, VOG4561, VOG1198, VOG0397, VOG2352, VOG11080

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