safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	7	17.83

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.
PNMJLFGI_10	1779708	1780562	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
PNMJLFGI_10	1760999	1762201	blt	ARO:3003006	blt	100.00	100.00	L32599.1
PNMJLFGI_10	1538680	1539849	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
PNMJLFGI_31	428462	430105	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
PNMJLFGI_10	425257	425574	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
PNMJLFGI_10	424919	425257	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
PNMJLFGI_47	276579	279149	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
PNMJLFGI_31	162884	163477	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
PNMJLFGI_31	112381	113820	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
PNMJLFGI_31	99566	100486	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.
PNMJLFGI_10	1779708	1780562	aadK	Streptomycin	100.00	100.00	M26879
PNMJLFGI_31	99566	100486	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
PNMJLFGI_42	331045	332421	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.
PNMJLFGI_10	1779711	1780562	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
PNMJLFGI_31	99566	100483	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
PNMJLFGI_42	328527	329045	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
PNMJLFGI_42	331048	332421	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
PNMJLFGI_31	428465	430105	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
PNMJLFGI_10	1095367	1097961	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.
PNMJLFGI_20	519108	520250	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
PNMJLFGI_20	520733	521914	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
PNMJLFGI_20	520269	520718	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
PNMJLFGI_10	1048709	1050472	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
PNMJLFGI_20	112772	113557	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
PNMJLFGI_20	108936	109874	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
PNMJLFGI_20	111550	112746	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
PNMJLFGI_20	109902	111521	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
PNMJLFGI_20	101780	108916	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
PNMJLFGI_10	1339334	1339975	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
PNMJLFGI_49	27982	26846	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
PNMJLFGI_51	4304	5173	pdxS	1.11e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
PNMJLFGI_10	738521	739297	CodY	1.80e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
PNMJLFGI_20	367496	368065	ClpP	4.07e-99	part of proteolytic complex	81.05	97.44	BAB94595
PNMJLFGI_10	276096	276488	spxA1	5.33e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
PNMJLFGI_50	20553	20795	SpoVG	7.49e-39	RNA-binding protein	81.48	79.41	AAT02994
PNMJLFGI_31	382990	383187	CspA	1.98e-31	cold shock protein	90.91	100.00	CAA62903

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
PNMJLFGI_10	0.0	1.0	0.0
PNMJLFGI_20	0.0	1.0	0.0
PNMJLFGI_31	0.0	1.0	0.0
PNMJLFGI_42	0.0	1.0	0.0
PNMJLFGI_47	0.0	1.0	0.0
PNMJLFGI_48	1.0	0.0	1.0
PNMJLFGI_49	0.0	1.0	0.0
PNMJLFGI_50	0.0	1.0	0.0
PNMJLFGI_51	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
PNMJLFGI_10	368972	395080	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
PNMJLFGI_10	1711070	1741314	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
PNMJLFGI_48	24876	37974	False	Unknown	VOG0052, VOG11080, VOG2352, VOG0397, VOG1198, VOG4561, VOG4714, VOG2352, VOG3851, VOG2725
PNMJLFGI_48	66029	82552	False	Siphoviridae	VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852

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