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.
MIEENMPJ_28	618365	618703	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
MIEENMPJ_28	618048	618365	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
MIEENMPJ_11	604528	605697	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
MIEENMPJ_29	428727	430370	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
MIEENMPJ_11	382176	383378	blt	ARO:3003006	blt	100.00	100.00	L32599.1
MIEENMPJ_11	363815	364669	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
MIEENMPJ_29	163152	163745	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
MIEENMPJ_29	112649	114088	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
MIEENMPJ_29	99834	100754	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
MIEENMPJ_30	27376	29946	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.
MIEENMPJ_11	363815	364669	aadK	Streptomycin	100.00	100.00	M26879
MIEENMPJ_29	99834	100754	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
MIEENMPJ_22	36397	37773	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.
MIEENMPJ_11	363815	364666	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
MIEENMPJ_29	99834	100751	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
MIEENMPJ_22	39773	40291	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
MIEENMPJ_22	36397	37770	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
MIEENMPJ_29	428730	430370	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
MIEENMPJ_11	1046417	1049011	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.
MIEENMPJ_22	526121	527263	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
MIEENMPJ_22	524457	525638	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
MIEENMPJ_22	525653	526102	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
MIEENMPJ_11	1093906	1095669	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
MIEENMPJ_22	932821	933606	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
MIEENMPJ_22	936504	937442	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
MIEENMPJ_22	933632	934828	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
MIEENMPJ_22	934857	936476	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
MIEENMPJ_22	937462	944598	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
MIEENMPJ_11	804402	805043	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
MIEENMPJ_32	28138	27002	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
MIEENMPJ_34	11309	10440	pdxS	1.12e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
MIEENMPJ_28	305101	304325	CodY	8.46e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
MIEENMPJ_22	678875	678306	ClpP	6.29e-99	part of proteolytic complex	81.05	97.44	BAB94595
MIEENMPJ_28	767525	767133	spxA1	2.51e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
MIEENMPJ_33	20625	20867	SpoVG	7.52e-39	RNA-binding protein	81.48	79.41	AAT02994
MIEENMPJ_29	383258	383455	CspA	1.99e-31	cold shock protein	90.91	100.00	CAA62903
MIEENMPJ_11	792440	792246	CspD	6.79e-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
MIEENMPJ_11	0.0	1.0	0.0
MIEENMPJ_22	0.0	1.0	0.0
MIEENMPJ_28	0.0	1.0	0.0
MIEENMPJ_29	0.0	1.0	0.0
MIEENMPJ_30	0.0	1.0	0.0
MIEENMPJ_31	0.0	1.0	0.0
MIEENMPJ_32	0.0	1.0	0.0
MIEENMPJ_33	0.0	1.0	0.0
MIEENMPJ_34	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
MIEENMPJ_11	205039	234199	False	Siphoviridae	VOG0044, VOG6517, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574
MIEENMPJ_11	402930	433307	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
MIEENMPJ_28	648542	674650	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667

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