safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
14	10	4	17.66

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.
IGBBEFOO_1	2561691	2562545	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
IGBBEFOO_1	2542982	2544184	blt	ARO:3003006	blt	100.00	100.00	L32599.1
IGBBEFOO_1	2320663	2321832	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
IGBBEFOO_1	1202868	1203185	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
IGBBEFOO_1	1202530	1202868	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
IGBBEFOO_1	742795	745365	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
IGBBEFOO_1	430755	432398	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
IGBBEFOO_1	223786	224568	ANT(9)-Ia	ARO:3002630	ANT(9)-Ia	100.00	100.00	X02588.1
IGBBEFOO_1	162825	163418	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
IGBBEFOO_1	112323	113756	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
IGBBEFOO_1	99508	100428	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.
IGBBEFOO_1	2561691	2562545	aadK	Streptomycin	100.00	100.00	M26879
IGBBEFOO_1	223786	224568	ant(9)-Ia	Spectinomycin	100.00	100.00	X02588
IGBBEFOO_1	99508	100428	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
IGBBEFOO_1	4013718	4015094	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.
IGBBEFOO_1	2561694	2562545	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
IGBBEFOO_1	223786	224565	ant(9)-Ia	aminoglycoside nucleotidyltransferase ANT(9)-Ia	EXACTX	100.00	100.00	WP_000067268.1
IGBBEFOO_1	99508	100425	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
IGBBEFOO_1	4011200	4011718	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
IGBBEFOO_1	4013721	4015094	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
IGBBEFOO_1	430758	432398	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
IGBBEFOO_1	1877349	1879943	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.
IGBBEFOO_1	3523857	3524999	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
IGBBEFOO_1	3525482	3526663	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
IGBBEFOO_1	3525018	3525467	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
IGBBEFOO_1	1830691	1832454	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
IGBBEFOO_1	3117521	3118306	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
IGBBEFOO_1	3113685	3114623	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
IGBBEFOO_1	3116299	3117495	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
IGBBEFOO_1	3114651	3116270	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
IGBBEFOO_1	3106529	3113665	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
IGBBEFOO_1	2121317	2121958	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
IGBBEFOO_3	27975	26839	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
IGBBEFOO_1	4060717	4061586	pdxS	3.07e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
IGBBEFOO_1	1516132	1516908	CodY	3.35e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
IGBBEFOO_1	3372245	3372814	ClpP	2.49e-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.
IGBBEFOO_1	223117	223247	ColRNAI	131 / 130	87.02	DQ298019

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
IGBBEFOO_1	0.0	1.0	0.0
IGBBEFOO_2	1.0	0.0	1.0
IGBBEFOO_3	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
IGBBEFOO_1	1146583	1172691	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
IGBBEFOO_1	2493053	2523297	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
IGBBEFOO_2	27943	41041	False	Unknown	VOG0052, VOG11080, VOG2352, VOG0397, VOG1198, VOG4561, VOG4714, VOG2352, VOG3851, VOG2725
IGBBEFOO_2	69096	79933	False	Siphoviridae	VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704

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