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.
LDAOGJCE_1	2735054	2735908	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LDAOGJCE_1	2716345	2717547	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LDAOGJCE_1	2494028	2495197	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LDAOGJCE_1	1376302	1376619	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LDAOGJCE_1	1375964	1376302	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LDAOGJCE_1	916235	918805	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LDAOGJCE_1	604195	605838	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
LDAOGJCE_1	338618	339211	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LDAOGJCE_1	288115	289548	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
LDAOGJCE_1	275300	276220	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.
LDAOGJCE_1	2735054	2735908	aadK	Streptomycin	100.00	100.00	M26879
LDAOGJCE_1	275300	276220	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LDAOGJCE_1	4186889	4188265	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.
LDAOGJCE_1	2735057	2735908	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LDAOGJCE_1	275300	276217	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LDAOGJCE_1	4184371	4184889	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LDAOGJCE_1	4186892	4188265	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LDAOGJCE_1	604198	605838	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LDAOGJCE_1	2050751	2053345	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.
LDAOGJCE_1	3697141	3698283	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LDAOGJCE_1	3698766	3699947	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LDAOGJCE_1	3698302	3698751	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LDAOGJCE_1	2004093	2005856	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LDAOGJCE_1	3290882	3291667	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LDAOGJCE_1	3287046	3287984	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LDAOGJCE_1	3289660	3290856	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LDAOGJCE_1	3288012	3289631	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LDAOGJCE_1	3279890	3287026	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
LDAOGJCE_1	2294698	2295339	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
LDAOGJCE_1	132876	134012	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LDAOGJCE_1	19074	19943	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LDAOGJCE_1	1689563	1690339	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
LDAOGJCE_1	3545593	3546162	ClpP	2.53e-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
LDAOGJCE_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LDAOGJCE_1	1320017	1346125	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
LDAOGJCE_1	2666417	2696661	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)