safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
15	10	4	18.47

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.
JGNHNHCM_1	3538307	3539683	tet(L)	ARO:3000179	tet(L)	99.78	100.00	M11036.1
JGNHNHCM_1	2759793	2760647	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
JGNHNHCM_1	2741084	2742286	blt	ARO:3003006	blt	100.00	100.00	L32599.1
JGNHNHCM_1	2576692	2577486	APH(3')-IIIa	ARO:3002647	APH(3')-IIIa	100.00	100.00	CP004067.1
JGNHNHCM_1	2518122	2519291	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
JGNHNHCM_1	1408555	1408872	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
JGNHNHCM_1	1408217	1408555	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
JGNHNHCM_1	916787	919357	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
JGNHNHCM_1	604745	606388	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
JGNHNHCM_1	339163	339756	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
JGNHNHCM_1	288661	290094	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
JGNHNHCM_1	275846	276766	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.
JGNHNHCM_1	2759793	2760647	aadK	Streptomycin	100.00	100.00	M26879
JGNHNHCM_1	2576692	2577486	aph(3')-III	Kanamycin, Amikacin, Neomycin, Butirosin, Isepamicin, Lividomycin, Paromomycin, Ribostamycin	100.00	100.00	M26832
JGNHNHCM_1	275846	276766	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
JGNHNHCM_1	3538307	3539683	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	100.00	100.00	M29725

ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
JGNHNHCM_1	2759796	2760647	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
JGNHNHCM_1	2576695	2577486	aph(3')-IIIa	aminoglycoside O-phosphotransferase APH(3')-IIIa	EXACTX	100.00	100.00	WP_001096887.1
JGNHNHCM_1	275846	276763	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
JGNHNHCM_1	4196724	4197242	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
JGNHNHCM_1	3538310	3539683	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_001574277.1
JGNHNHCM_1	4199245	4200618	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
JGNHNHCM_1	604748	606388	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
JGNHNHCM_1	2083035	2085629	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.
JGNHNHCM_1	3709381	3710523	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
JGNHNHCM_1	3711006	3712187	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
JGNHNHCM_1	3710542	3710991	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
JGNHNHCM_1	2036377	2038140	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
JGNHNHCM_1	3315621	3316406	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
JGNHNHCM_1	3311785	3312723	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
JGNHNHCM_1	3314399	3315595	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
JGNHNHCM_1	3312751	3314370	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
JGNHNHCM_1	3304629	3311765	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
JGNHNHCM_1	2318770	2319411	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
JGNHNHCM_1	132882	134018	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
JGNHNHCM_1	19074	19943	pdxS	3.14e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
JGNHNHCM_1	1721819	1722595	CodY	3.43e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
JGNHNHCM_1	3557795	3558364	ClpP	2.54e-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.
JGNHNHCM_1	3539934	3540320	rep34	387 / 633	100.00	M29725

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
JGNHNHCM_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
JGNHNHCM_1	1352270	1378378	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
JGNHNHCM_1	2196871	2207796	False	Siphoviridae	VOG1652, VOG4724, VOG1198, VOG0918, VOG4551, VOG0025, VOG7476
JGNHNHCM_1	2691156	2721400	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)