safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
19	10	8	22.91

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.
ADNMNOJM_3	813823	814473	Streptococcus suis chloramphenicol acetyltransferase	ARO:3004455	Ssui_ACT_CHL	94.91	100.00	AB080798.1
ADNMNOJM_1	678025	679194	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
ADNMNOJM_1	455707	456909	blt	ARO:3003006	blt	100.00	100.00	L32599.1
ADNMNOJM_1	437346	438200	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
ADNMNOJM_3	425549	425866	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
ADNMNOJM_3	425211	425549	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
ADNMNOJM_4	276580	279150	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
ADNMNOJM_6	162573	163166	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
ADNMNOJM_6	112070	113509	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
ADNMNOJM_6	99255	100175	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
ADNMNOJM_8	29097	30740	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
ADNMNOJM_27	749	2125	tet(L)	ARO:3000179	tet(L)	99.78	100.00	M11036.1
ADNMNOJM_29	616	1353	ErmB	ARO:3000375	ErmB	97.96	98.79	AF242872.1
ADNMNOJM_25	605	1465	TEM-116	ARO:3000979	TEM-116	100.00	100.00	U36911.1
ADNMNOJM_28	574	1344	ANT(4')-Ia	ARO:3002623	ANT(4')-Ia	99.21	101.19	K02551.1

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.
ADNMNOJM_28	583	1344	aadD	Amikacin, Tobramycin	100.00	100.00	M19465
ADNMNOJM_1	437346	438200	aadK	Streptomycin	100.00	100.00	M26879
ADNMNOJM_25	605	1465	blaTEM-116	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin	100.00	100.00	AY425988
ADNMNOJM_3	813823	814473	cat(pC194)	Chloramphenicol	100.00	100.00	NC_002013
ADNMNOJM_29	616	1353	erm(B)	Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S	100.00	100.00	U86375
ADNMNOJM_6	99255	100175	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
ADNMNOJM_27	749	2125	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	100.00	100.00	M29725
ADNMNOJM_28	1567	1885	bleO	Bleomycin	100.00	79.95	AF051917

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

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
ADNMNOJM_28	574	1341	aadD1	aminoglycoside O-nucleotidyltransferase ANT(4')-Ia	EXACTX	100.00	100.00	WP_001795128.1
ADNMNOJM_1	437346	438197	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
ADNMNOJM_25	605	1462	blaTEM-116	broad-spectrum class A beta-lactamase TEM-116	ALLELEX	100.00	100.00	WP_000027050.1
ADNMNOJM_3	813823	814470	catA	type A-9 chloramphenicol O-acetyltransferase	EXACTX	100.00	100.00	WP_001010387.1
ADNMNOJM_29	616	1350	erm(B)	23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B)	EXACTX	100.00	100.00	WP_001038790.1
ADNMNOJM_6	99255	100172	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
ADNMNOJM_9	301074	301592	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
ADNMNOJM_27	749	2122	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_001574277.1
ADNMNOJM_9	303595	304968	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
ADNMNOJM_8	29097	30737	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
ADNMNOJM_28	1561	1884	bleO	bleomycin binding protein	PARTIALX	100.00	80.60	WP_001242578.1
ADNMNOJM_10	134749	137343	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.
ADNMNOJM_2	282496	283638	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
ADNMNOJM_2	284121	285302	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
ADNMNOJM_2	283657	284106	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
ADNMNOJM_10	182146	183909	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
ADNMNOJM_5	112633	113418	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
ADNMNOJM_5	108797	109735	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
ADNMNOJM_5	111411	112607	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
ADNMNOJM_5	109763	111382	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
ADNMNOJM_5	101641	108777	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
ADNMNOJM_7	48321	48962	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
ADNMNOJM_11	31696	32832	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
ADNMNOJM_18	11231	10362	pdxS	1.11e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
ADNMNOJM_3	738766	739542	CodY	8.26e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
ADNMNOJM_2	131032	131601	ClpP	2.65e-99	part of proteolytic complex	81.05	97.44	BAB94595
ADNMNOJM_3	276424	276816	spxA1	2.45e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
ADNMNOJM_13	20556	20798	SpoVG	2.80e-38	RNA-binding protein	80.25	79.41	AAT02994
ADNMNOJM_8	76212	76015	CspA	9.41e-32	cold shock protein	90.91	100.00	CAA62903
ADNMNOJM_7	60924	61118	CspD	1.10e-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.
ADNMNOJM_27	62	498	rep34	437 / 633	100.00	M29725
ADNMNOJM_19	4573	6063	rep1	1491 / 1491	99.93	AY357120
ADNMNOJM_25	1880	2010	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
ADNMNOJM_1	0.0	1.0	0.0
ADNMNOJM_2	0.0	1.0	0.0
ADNMNOJM_3	0.0	1.0	0.0
ADNMNOJM_4	0.0	1.0	0.0
ADNMNOJM_5	0.0	1.0	0.0
ADNMNOJM_6	0.0	1.0	0.0
ADNMNOJM_7	0.0	1.0	0.0
ADNMNOJM_8	0.0	1.0	0.0
ADNMNOJM_9	0.0	1.0	0.0
ADNMNOJM_10	0.0	1.0	0.0
ADNMNOJM_11	0.0	1.0	0.0
ADNMNOJM_12	0.0	1.0	0.0
ADNMNOJM_13	0.0	1.0	0.0
ADNMNOJM_14	0.0	1.0	0.0
ADNMNOJM_15	0.0	1.0	0.0
ADNMNOJM_16	0.0	1.0	0.0
ADNMNOJM_17	0.0	1.0	0.0
ADNMNOJM_18	0.0	1.0	0.0
ADNMNOJM_19	1.0	0.0	1.0
ADNMNOJM_20	0.0	1.0	0.0
ADNMNOJM_21	1.0	0.0	1.0
ADNMNOJM_22	0.0	1.0	0.0
ADNMNOJM_23	0.0	1.0	0.0
ADNMNOJM_25	1.0	0.0	1.0
ADNMNOJM_26	0.0	1.0	0.0
ADNMNOJM_27	1.0	0.0	1.0
ADNMNOJM_28	1.0	0.0	1.0
ADNMNOJM_29	1.0	0.0	1.0
ADNMNOJM_31	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
ADNMNOJM_1	476460	506804	False	Myoviridae	VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG6005, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718
ADNMNOJM_3	369300	395408	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

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