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.
CNMPGEDA_12	602866	603204	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
CNMPGEDA_12	602549	602866	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
CNMPGEDA_18	488885	489739	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
CNMPGEDA_18	470176	471378	blt	ARO:3003006	blt	100.00	100.00	L32599.1
CNMPGEDA_19	276772	279342	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
CNMPGEDA_18	247857	249026	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
CNMPGEDA_21	163073	163666	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
CNMPGEDA_21	112571	114010	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
CNMPGEDA_21	99756	100676	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
CNMPGEDA_24	29374	31017	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3

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.
CNMPGEDA_18	488885	489739	aadK	Streptomycin	100.00	100.00	M26879
CNMPGEDA_21	99756	100676	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
CNMPGEDA_1	36508	37884	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.
CNMPGEDA_18	488888	489739	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
CNMPGEDA_21	99756	100673	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
CNMPGEDA_1	39884	40402	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
CNMPGEDA_1	36508	37881	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
CNMPGEDA_24	29374	31014	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
CNMPGEDA_20	55847	58441	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.
CNMPGEDA_1	526603	527745	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
CNMPGEDA_1	524939	526120	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
CNMPGEDA_1	526135	526584	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
CNMPGEDA_20	9189	10952	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
CNMPGEDA_1	933296	934081	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
CNMPGEDA_1	936979	937917	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
CNMPGEDA_1	934107	935303	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
CNMPGEDA_1	935332	936951	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
CNMPGEDA_1	937937	945073	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
CNMPGEDA_18	48511	49152	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
CNMPGEDA_2	28223	27087	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
CNMPGEDA_4	4497	5366	pdxS	1.14e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
CNMPGEDA_12	289602	288826	CodY	8.34e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
CNMPGEDA_1	679357	678788	ClpP	6.30e-99	part of proteolytic complex	81.05	97.44	BAB94595
CNMPGEDA_12	752027	751635	spxA1	2.47e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
CNMPGEDA_3	34823	34581	SpoVG	7.58e-39	RNA-binding protein	81.48	79.41	AAT02994
CNMPGEDA_24	76489	76292	CspA	3.40e-32	cold shock protein	90.91	100.00	CAA62903
CNMPGEDA_18	61114	61308	CspD	5.71e-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
CNMPGEDA_1	0.0	1.0	0.0
CNMPGEDA_2	0.0	1.0	0.0
CNMPGEDA_3	0.0	1.0	0.0
CNMPGEDA_4	0.0	1.0	0.0
CNMPGEDA_5	0.0	1.0	0.0
CNMPGEDA_12	0.0	1.0	0.0
CNMPGEDA_18	0.0	1.0	0.0
CNMPGEDA_19	0.0	1.0	0.0
CNMPGEDA_20	0.0	1.0	0.0
CNMPGEDA_21	0.0	1.0	0.0
CNMPGEDA_22	0.0	1.0	0.0
CNMPGEDA_23	1.0	0.0	1.0
CNMPGEDA_24	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
CNMPGEDA_12	633043	659151	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667
CNMPGEDA_18	420247	450491	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
CNMPGEDA_23	13545	26643	False	Unknown	VOG0052, VOG11080, VOG2352, VOG0397, VOG1198, VOG4561, VOG4714, VOG2352, VOG3851, VOG2725
CNMPGEDA_23	54698	78035	False	Siphoviridae	VOG0221, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024

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