safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
16	10	8	20.49

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.
HFLGGCGD_2	676784	677953	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
HFLGGCGD_1	494334	494672	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
HFLGGCGD_1	494017	494334	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
HFLGGCGD_2	454433	455635	blt	ARO:3003006	blt	100.00	100.00	L32599.1
HFLGGCGD_2	436072	436926	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
HFLGGCGD_31	276623	279193	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
HFLGGCGD_46	50773	51693	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
HFLGGCGD_4	47454	49097	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
HFLGGCGD_7	44877	45470	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
HFLGGCGD_46	37439	38878	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
HFLGGCGD_15	3448	4308	TEM-1	ARO:3000873	TEM-1	100.00	100.00	AL513383.1
HFLGGCGD_15	1145	1879	ErmC	ARO:3000250	ErmC	97.54	100.00	M12730.1
HFLGGCGD_17	961	1713	ANT(9)-Ib	ARO:3007401	ANT(9)-Ib	99.60	98.04	M69221.1

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.
HFLGGCGD_2	436072	436926	aadK	Streptomycin	100.00	100.00	M26879
HFLGGCGD_17	946	1713	ant(9)-Ia	Spectinomycin	100.00	100.00	M69221
HFLGGCGD_15	3448	4308	blaTEM-1A	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin	100.00	100.00	HM749966
HFLGGCGD_15	1145	1879	erm(C)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S	100.00	100.00	V01278
HFLGGCGD_46	50773	51693	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
HFLGGCGD_23	330973	332349	tet(L)	Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline	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.
HFLGGCGD_2	436072	436923	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
HFLGGCGD_17	946	1710	ant(9)-Ib	aminoglycoside nucleotidyltransferase ANT(9)-Ib	EXACTX	100.00	100.00	WP_063840673.1
HFLGGCGD_15	3451	4308	blaTEM-1	broad-spectrum class A beta-lactamase TEM-1	ALLELEX	100.00	100.00	WP_000027057.1
HFLGGCGD_15	1145	1876	erm(C)	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(C)	EXACTX	100.00	100.00	WP_007410443.1
HFLGGCGD_46	50776	51693	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
HFLGGCGD_23	328455	328973	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
HFLGGCGD_23	330976	332349	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
HFLGGCGD_4	47457	49097	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
HFLGGCGD_42	54885	57479	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.
HFLGGCGD_47	157307	158449	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
HFLGGCGD_47	155643	156824	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
HFLGGCGD_47	156839	157288	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
HFLGGCGD_42	8227	9990	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
HFLGGCGD_13	112881	113666	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
HFLGGCGD_13	109045	109983	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
HFLGGCGD_13	111659	112855	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
HFLGGCGD_13	110011	111630	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
HFLGGCGD_13	101889	109025	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
HFLGGCGD_2	876664	877305	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
HFLGGCGD_5	31737	32873	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
HFLGGCGD_9	11281	10412	pdxS	1.12e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
HFLGGCGD_1	181070	180294	CodY	7.55e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
HFLGGCGD_13	367604	368173	ClpP	2.93e-99	part of proteolytic complex	81.05	97.44	BAB94595
HFLGGCGD_1	643491	643099	spxA1	5.94e-70	redox-responsive transcription factor	83.97	100.00	AAF21893
HFLGGCGD_1	643491	643099	spx	3.54e-68	essential gene which is a thiol/oxidative stress sensor	80.15	100.00	BAB57159
HFLGGCGD_6	20597	20839	SpoVG	2.73e-38	RNA-binding protein	80.25	79.41	AAT02994
HFLGGCGD_4	1982	2179	CspA	3.38e-32	cold shock protein	90.91	100.00	CAA62903
HFLGGCGD_2	864702	864508	CspD	5.69e-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.
HFLGGCGD_15	2903	3033	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
HFLGGCGD_1	0.0	1.0	0.0
HFLGGCGD_2	0.0	1.0	0.0
HFLGGCGD_3	0.0	1.0	0.0
HFLGGCGD_4	0.0	1.0	0.0
HFLGGCGD_5	0.0	1.0	0.0
HFLGGCGD_6	0.0	1.0	0.0
HFLGGCGD_7	0.0	1.0	0.0
HFLGGCGD_8	0.0	1.0	0.0
HFLGGCGD_9	0.0	1.0	0.0
HFLGGCGD_10	0.0	1.0	0.0
HFLGGCGD_11	0.0	1.0	0.0
HFLGGCGD_12	0.0	1.0	0.0
HFLGGCGD_13	0.0	1.0	0.0
HFLGGCGD_14	0.0	1.0	0.0
HFLGGCGD_15	1.0	0.0	1.0
HFLGGCGD_17	0.0	1.0	0.0
HFLGGCGD_18	0.0	1.0	0.0
HFLGGCGD_20	1.0	0.0	1.0
HFLGGCGD_23	0.0	1.0	0.0
HFLGGCGD_31	0.0	1.0	0.0
HFLGGCGD_42	0.0	1.0	0.0
HFLGGCGD_46	0.0	1.0	0.0
HFLGGCGD_47	0.0	1.0	0.0
HFLGGCGD_48	0.0	1.0	0.0
HFLGGCGD_49	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
HFLGGCGD_1	524511	550619	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667
HFLGGCGD_2	475186	505563	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)