safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
17	10	4	20.12

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.
LIADFHIH_1	3350082	3350843	ANT(4')-Ia	ARO:3002623	ANT(4')-Ia	99.60	100.00	K02551.1
LIADFHIH_1	2567473	2568327	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
LIADFHIH_1	2548764	2549966	blt	ARO:3003006	blt	100.00	100.00	L32599.1
LIADFHIH_1	2326451	2327620	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
LIADFHIH_1	1358198	1359058	TEM-1	ARO:3000873	TEM-1	100.00	100.00	AL513383.1
LIADFHIH_1	1356130	1357506	tet(L)	ARO:3000179	tet(L)	99.78	100.00	M11036.1
LIADFHIH_1	1354794	1355984	tet(C)	ARO:3000167	tet(C)	100.00	100.00	AY043299.1
LIADFHIH_1	1352093	1352410	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
LIADFHIH_1	1351755	1352093	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
LIADFHIH_1	892013	894583	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
LIADFHIH_1	583970	585613	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
LIADFHIH_1	339153	339746	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
LIADFHIH_1	288650	290083	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
LIADFHIH_1	275835	276755	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.
LIADFHIH_1	3350082	3350843	aadD	Amikacin, Tobramycin	100.00	100.00	M19465
LIADFHIH_1	2567473	2568327	aadK	Streptomycin	100.00	100.00	M26879
LIADFHIH_1	1358198	1359058	blaTEM-1A	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin	100.00	100.00	HM749966
LIADFHIH_1	275835	276755	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
LIADFHIH_1	1356130	1357506	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	100.00	100.00	M29725
LIADFHIH_1	1354794	1355984	tet(C)	Doxycycline, Tetracycline	99.92	100.00	AF055345

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

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
LIADFHIH_1	3350073	3350840	aadD1	aminoglycoside O-nucleotidyltransferase ANT(4')-Ia	EXACTX	100.00	100.00	WP_001795128.1
LIADFHIH_1	2567476	2568327	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
LIADFHIH_1	1358198	1359055	blaTEM-1	broad-spectrum class A beta-lactamase TEM-1	ALLELEX	100.00	100.00	WP_000027057.1
LIADFHIH_1	275835	276752	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
LIADFHIH_1	4012599	4013117	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
LIADFHIH_1	1354797	1355984	tet(C)	tetracycline efflux MFS transporter Tet(C)	EXACTX	100.00	100.00	WP_001297013.1
LIADFHIH_1	1356133	1357506	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_001574277.1
LIADFHIH_1	4015120	4016493	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
LIADFHIH_1	583973	585613	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
LIADFHIH_1	2017529	2020123	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.
LIADFHIH_1	3525374	3526516	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
LIADFHIH_1	3526999	3528180	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
LIADFHIH_1	3526535	3526984	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
LIADFHIH_1	1970871	1972634	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
LIADFHIH_1	3123808	3124593	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
LIADFHIH_1	3119972	3120910	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
LIADFHIH_1	3122586	3123782	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
LIADFHIH_1	3120938	3122557	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
LIADFHIH_1	2127094	2127735	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
LIADFHIH_1	3112816	3119952	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.97	100.00	NP_391076

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
LIADFHIH_1	132881	134017	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
LIADFHIH_1	19073	19942	pdxS	3.00e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
LIADFHIH_1	1671720	1672496	CodY	3.28e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
LIADFHIH_1	3373761	3374330	ClpP	2.43e-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.
LIADFHIH_1	1359473	1359603	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
LIADFHIH_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
LIADFHIH_1	1295808	1321916	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
LIADFHIH_1	2498837	2529081	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)