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.
CCNCHJGG_1	621564	622418	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
CCNCHJGG_1	602855	604057	blt	ARO:3003006	blt	100.00	100.00	L32599.1
CCNCHJGG_12	590900	591238	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
CCNCHJGG_12	590583	590900	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
CCNCHJGG_1	380538	381707	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
CCNCHJGG_24	276585	279155	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
CCNCHJGG_25	187052	188695	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
CCNCHJGG_26	162828	163421	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
CCNCHJGG_26	112325	113764	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
CCNCHJGG_26	99510	100430	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.
CCNCHJGG_1	621564	622418	aadK	Streptomycin	100.00	100.00	M26879
CCNCHJGG_26	99510	100430	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
CCNCHJGG_27	36260	37636	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.
CCNCHJGG_1	621567	622418	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
CCNCHJGG_26	99510	100427	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
CCNCHJGG_27	39636	40154	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
CCNCHJGG_27	36260	37633	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
CCNCHJGG_25	187055	188695	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
CCNCHJGG_1	71616	74210	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.
CCNCHJGG_23	519091	520233	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
CCNCHJGG_23	520716	521897	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
CCNCHJGG_23	520252	520701	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
CCNCHJGG_1	24958	26721	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
CCNCHJGG_23	112781	113566	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
CCNCHJGG_23	108945	109883	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
CCNCHJGG_23	111559	112755	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
CCNCHJGG_23	109911	111530	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
CCNCHJGG_23	101789	108925	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
CCNCHJGG_1	181181	181822	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
CCNCHJGG_28	27975	26839	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
CCNCHJGG_2	4231	5100	pdxS	1.10e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
CCNCHJGG_12	277628	276852	CodY	8.24e-125	nutrient-responsive regulator	81.08	100.00	ACJ80679
CCNCHJGG_23	367504	368073	ClpP	5.52e-99	part of proteolytic complex	81.05	97.44	BAB94595
CCNCHJGG_12	740061	739669	spxA1	2.44e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
CCNCHJGG_29	20498	20740	SpoVG	2.72e-38	RNA-binding protein	80.25	79.41	AAT02994
CCNCHJGG_25	141580	141777	CspA	9.41e-32	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
CCNCHJGG_1	0.0	1.0	0.0
CCNCHJGG_2	0.0	1.0	0.0
CCNCHJGG_3	0.0	1.0	0.0
CCNCHJGG_4	0.0	1.0	0.0
CCNCHJGG_12	0.0	1.0	0.0
CCNCHJGG_23	0.0	1.0	0.0
CCNCHJGG_24	0.0	1.0	0.0
CCNCHJGG_25	0.0	1.0	0.0
CCNCHJGG_26	0.0	1.0	0.0
CCNCHJGG_27	0.0	1.0	0.0
CCNCHJGG_28	0.0	1.0	0.0
CCNCHJGG_29	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
CCNCHJGG_1	552927	583171	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
CCNCHJGG_12	621077	647185	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)