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.
EFDBCGOD_10	678306	679475	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
EFDBCGOD_10	455954	457156	blt	ARO:3003006	blt	100.00	100.00	L32599.1
EFDBCGOD_10	437593	438447	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
EFDBCGOD_9	425652	425969	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
EFDBCGOD_9	425314	425652	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
EFDBCGOD_11	280305	281225	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
EFDBCGOD_11	266971	268410	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
EFDBCGOD_11	217314	217907	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
EFDBCGOD_14	47482	49125	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
EFDBCGOD_12	27546	30116	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3

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.
EFDBCGOD_10	437593	438447	aadK	Streptomycin	100.00	100.00	M26879
EFDBCGOD_11	280305	281225	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
EFDBCGOD_1	36378	37754	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.
EFDBCGOD_10	437593	438444	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
EFDBCGOD_11	280308	281225	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
EFDBCGOD_1	39754	40272	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
EFDBCGOD_1	36378	37751	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
EFDBCGOD_14	47485	49125	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
EFDBCGOD_13	56316	58910	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.
EFDBCGOD_1	526355	527497	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
EFDBCGOD_1	524691	525872	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
EFDBCGOD_1	525887	526336	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
EFDBCGOD_13	9658	11421	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
EFDBCGOD_1	933047	933832	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
EFDBCGOD_1	936730	937668	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
EFDBCGOD_1	933858	935054	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
EFDBCGOD_1	935083	936702	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
EFDBCGOD_1	937688	944824	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
EFDBCGOD_10	878181	878822	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
EFDBCGOD_15	28208	27072	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
EFDBCGOD_2	4392	5261	pdxS	1.13e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
EFDBCGOD_9	738916	739692	CodY	8.25e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
EFDBCGOD_1	679109	678540	ClpP	6.29e-99	part of proteolytic complex	81.05	97.44	BAB94595
EFDBCGOD_9	276491	276883	spxA1	2.45e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
EFDBCGOD_16	20899	21141	SpoVG	7.57e-39	RNA-binding protein	81.48	79.41	AAT02994
EFDBCGOD_14	2010	2207	CspA	3.38e-32	cold shock protein	90.91	100.00	CAA62903
EFDBCGOD_10	866219	866025	CspD	5.70e-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
EFDBCGOD_1	0.0	1.0	0.0
EFDBCGOD_2	0.0	1.0	0.0
EFDBCGOD_3	0.0	1.0	0.0
EFDBCGOD_4	0.0	1.0	0.0
EFDBCGOD_9	0.0	1.0	0.0
EFDBCGOD_10	0.0	1.0	0.0
EFDBCGOD_11	0.0	1.0	0.0
EFDBCGOD_12	0.0	1.0	0.0
EFDBCGOD_13	0.0	1.0	0.0
EFDBCGOD_14	0.0	1.0	0.0
EFDBCGOD_15	0.0	1.0	0.0
EFDBCGOD_16	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
EFDBCGOD_9	369367	395475	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
EFDBCGOD_10	476708	507085	False	Myoviridae	VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718

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