safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
14	10	7	18.57

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.
EDPHBBME_1	1784375	1785229	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
EDPHBBME_1	1765666	1766868	blt	ARO:3003006	blt	100.00	100.00	L32599.1
EDPHBBME_1	1543348	1544517	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
EDPHBBME_1	425646	425963	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
EDPHBBME_1	425308	425646	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
EDPHBBME_5	358767	359687	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
EDPHBBME_5	345433	346872	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
EDPHBBME_5	295776	296369	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
EDPHBBME_5	29146	30789	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
EDPHBBME_3	27267	29837	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
EDPHBBME_10	779	1429	Streptococcus suis chloramphenicol acetyltransferase	ARO:3004455	Ssui_ACT_CHL	94.91	100.00	AB080798.1

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.
EDPHBBME_1	1784375	1785229	aadK	Streptomycin	100.00	100.00	M26879
EDPHBBME_10	779	1429	cat(pC194)	Chloramphenicol	100.00	100.00	NC_002013
EDPHBBME_5	358767	359687	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
EDPHBBME_2	36280	37656	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.
EDPHBBME_1	1784378	1785229	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
EDPHBBME_10	779	1426	catA	type A-9 chloramphenicol O-acetyltransferase	EXACTX	100.00	100.00	WP_001010387.1
EDPHBBME_5	358770	359687	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
EDPHBBME_2	39656	40174	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
EDPHBBME_2	36280	37653	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
EDPHBBME_5	29146	30786	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
EDPHBBME_1	1100111	1102705	rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	WP_087347987.1
EDPHBBME_10	4261	4776	aadD1	aminoglycoside O-nucleotidyltransferase ANT(4')-Ia	PARTIAL_CONTIG_ENDX	100.00	67.19	WP_001795128.1

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.
EDPHBBME_2	526375	527517	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
EDPHBBME_2	524711	525892	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
EDPHBBME_2	525907	526356	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
EDPHBBME_1	1053453	1055216	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
EDPHBBME_2	933042	933827	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
EDPHBBME_2	936725	937663	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
EDPHBBME_2	933853	935049	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
EDPHBBME_2	935078	936697	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
EDPHBBME_2	937683	944819	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
EDPHBBME_1	1343996	1344637	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
EDPHBBME_11	31676	32812	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
EDPHBBME_9	11252	10383	pdxS	1.13e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
EDPHBBME_1	738902	739678	CodY	1.80e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
EDPHBBME_2	679104	678535	ClpP	6.29e-99	part of proteolytic complex	81.05	97.44	BAB94595
EDPHBBME_1	276485	276877	spxA1	5.34e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
EDPHBBME_7	34728	34486	SpoVG	2.74e-38	RNA-binding protein	80.25	79.41	AAT02994
EDPHBBME_5	76261	76064	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.
EDPHBBME_10	3097	4101	rep22	1005 / 1005	100.00	AF503772

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
EDPHBBME_1	0.0	1.0	0.0
EDPHBBME_2	0.0	1.0	0.0
EDPHBBME_3	0.0	1.0	0.0
EDPHBBME_5	0.0	1.0	0.0
EDPHBBME_7	0.0	1.0	0.0
EDPHBBME_9	0.0	1.0	0.0
EDPHBBME_10	1.0	0.0	1.0
EDPHBBME_11	0.0	1.0	0.0
EDPHBBME_12	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
EDPHBBME_1	369361	395469	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
EDPHBBME_1	1715738	1745982	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)