safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
18	10	4	20.98

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.
ABPBAGPB_1	2735309	2736163	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
ABPBAGPB_1	2716600	2717802	blt	ARO:3003006	blt	100.00	100.00	L32599.1
ABPBAGPB_1	2494282	2495451	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
ABPBAGPB_1	1385402	1386262	TEM-1	ARO:3000873	TEM-1	100.00	100.00	AL513383.1
ABPBAGPB_1	1383163	1383924	ANT(4')-Ia	ARO:3002623	ANT(4')-Ia	99.60	100.00	K02551.1
ABPBAGPB_1	1381066	1381995	tet(C)	ARO:3000167	tet(C)	100.00	78.03	AY043299.1
ABPBAGPB_1	1369950	1370267	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
ABPBAGPB_1	1369612	1369950	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
ABPBAGPB_1	1147460	1148485	APH(4)-Ia	ARO:3002655	APH(4)-Ia	99.71	100.00	V01499.1
ABPBAGPB_1	909506	912076	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
ABPBAGPB_1	597470	599113	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
ABPBAGPB_1	331892	332485	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
ABPBAGPB_1	281389	282822	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
ABPBAGPB_1	268574	269494	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.
ABPBAGPB_1	1383163	1383924	aadD	Amikacin, Tobramycin	100.00	100.00	M19465
ABPBAGPB_1	2735309	2736163	aadK	Streptomycin	100.00	100.00	M26879
ABPBAGPB_1	1385402	1386262	blaTEM-1A	Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin	100.00	100.00	HM749966
ABPBAGPB_1	238583	238981	bleO	Bleomycin	100.00	100.00	AF051917
ABPBAGPB_1	268574	269494	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
ABPBAGPB_1	4185840	4187216	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	100.00	100.00	X08034
ABPBAGPB_1	1147460	1148485	aph(4)-Ia	Hygromycin	99.81	100.00	V01499

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

AMRFinderPlus

Query ID	Begin	End	Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
ABPBAGPB_1	1383154	1383921	aadD1	aminoglycoside O-nucleotidyltransferase ANT(4')-Ia	EXACTX	100.00	100.00	WP_001795128.1
ABPBAGPB_1	2735312	2736163	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
ABPBAGPB_1	1385405	1386262	blaTEM-1	broad-spectrum class A beta-lactamase TEM-1	ALLELEX	100.00	100.00	WP_000027057.1
ABPBAGPB_1	238577	238978	bleO	bleomycin binding protein	EXACTX	100.00	100.00	WP_001242578.1
ABPBAGPB_1	268574	269491	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
ABPBAGPB_1	4183322	4183840	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
ABPBAGPB_1	4185843	4187216	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
ABPBAGPB_1	597473	599113	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
ABPBAGPB_1	1381096	1381992	tet(C)	tetracycline efflux MFS transporter Tet(C)	PARTIALX	100.00	75.51	WP_001297013.1
ABPBAGPB_1	1147463	1148485	aph(4)-Ia	aminoglycoside O-phosphotransferase APH(4)-Ia	BLASTX	99.71	100.00	WP_000742814.1
ABPBAGPB_1	2050967	2053561	rphC	rifamycin-inactivating phosphotransferase RphC	BLASTX	81.15	99.88	WP_087347987.1
ABPBAGPB_1	1384022	1384486	cat-TC	type A-9 chloramphenicol O-acetyltransferase Cat-TC	INTERNAL_STOP	88.46	64.71	WP_032488880.1

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.
ABPBAGPB_1	3697445	3698587	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
ABPBAGPB_1	3699070	3700251	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
ABPBAGPB_1	3698606	3699055	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
ABPBAGPB_1	2004311	2006074	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
ABPBAGPB_1	3291135	3291920	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
ABPBAGPB_1	3287299	3288237	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
ABPBAGPB_1	3289913	3291109	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
ABPBAGPB_1	3288265	3289884	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
ABPBAGPB_1	3280143	3287279	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
ABPBAGPB_1	2294931	2295572	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
ABPBAGPB_1	126616	127752	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
ABPBAGPB_1	18665	19534	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
ABPBAGPB_1	1689755	1690531	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
ABPBAGPB_1	3545858	3546427	ClpP	2.53e-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.
ABPBAGPB_1	1384857	1384987	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
ABPBAGPB_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
ABPBAGPB_1	1313665	1339773	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
ABPBAGPB_1	2666672	2696916	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)