safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	4	16.88

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.
CDKELIEP_1	2735378	2736232	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
CDKELIEP_1	2716669	2717871	blt	ARO:3003006	blt	100.00	100.00	L32599.1
CDKELIEP_1	2494350	2495519	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
CDKELIEP_1	1376553	1376870	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
CDKELIEP_1	1376215	1376553	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
CDKELIEP_1	916471	919041	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
CDKELIEP_1	604428	606071	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
CDKELIEP_1	338849	339442	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
CDKELIEP_1	288346	289779	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
CDKELIEP_1	275531	276451	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.
CDKELIEP_1	2735378	2736232	aadK	Streptomycin	100.00	100.00	M26879
CDKELIEP_1	275531	276451	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
CDKELIEP_1	4187390	4188766	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.
CDKELIEP_1	2735381	2736232	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
CDKELIEP_1	275531	276448	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
CDKELIEP_1	4184872	4185390	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
CDKELIEP_1	4187393	4188766	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
CDKELIEP_1	604431	606071	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
CDKELIEP_1	2051035	2053629	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.
CDKELIEP_1	3697529	3698671	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
CDKELIEP_1	3699154	3700335	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
CDKELIEP_1	3698690	3699139	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
CDKELIEP_1	2004377	2006140	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
CDKELIEP_1	3291206	3291991	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
CDKELIEP_1	3287370	3288308	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
CDKELIEP_1	3289984	3291180	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
CDKELIEP_1	3288336	3289955	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
CDKELIEP_1	3280214	3287350	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
CDKELIEP_1	2295003	2295644	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
CDKELIEP_1	132567	133703	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
CDKELIEP_1	18758	19627	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
CDKELIEP_1	1689817	1690593	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
CDKELIEP_1	3545917	3546486	ClpP	2.54e-98	part of proteolytic complex	81.05	97.44	BAB94595

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
CDKELIEP_1	0.0	1.0	0.0
CDKELIEP_2	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
CDKELIEP_1	1320268	1346376	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
CDKELIEP_1	2666740	2696984	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
CDKELIEP_2	39232	91551	False	Myoviridae	VOG11016, VOG4714, VOG0703, VOG9091, VOG4615, VOG7230, VOG0647, VOG5173, VOG3432, VOG9244, VOG5242, VOG3389, VOG0275, VOG8609, VOG8610, VOG5534, VOG6940, VOG7628, VOG7629, VOG6472, VOG6036, VOG6941, VOG6246, VOG6524, VOG6031, VOG5721, VOG7724, VOG5722, VOG4570, VOG0048, VOG0678, VOG7814, VOG5216, VOG0058, VOG9245, VOG10598, VOG8611, VOG7848
CDKELIEP_2	113383	139030	False	Unknown	VOG8610, VOG5534, VOG6940, VOG7628, VOG7629, VOG6472, VOG6036, VOG6941, VOG6246, VOG6524, VOG6031, VOG5721, VOG7724, VOG5722, VOG4570, VOG0048, VOG0678, VOG7814, VOG5216, VOG0058, VOG9245, VOG10598, VOG8611, VOG7848
CDKELIEP_2	188608	197601	False	Myoviridae / Siphoviridae	VOG9220, VOG7627, VOG0025, VOG4551, VOG5263, VOG0918, VOG0677, VOG0982

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