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.
CGLIHPIH_1	2735665	2736519	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
CGLIHPIH_1	2716956	2718158	blt	ARO:3003006	blt	100.00	100.00	L32599.1
CGLIHPIH_1	2494639	2495808	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
CGLIHPIH_1	1376853	1377170	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
CGLIHPIH_1	1376515	1376853	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
CGLIHPIH_1	916775	919345	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
CGLIHPIH_1	604733	606376	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
CGLIHPIH_1	339155	339748	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
CGLIHPIH_1	288652	290085	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
CGLIHPIH_1	275837	276757	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.
CGLIHPIH_1	2735665	2736519	aadK	Streptomycin	100.00	100.00	M26879
CGLIHPIH_1	275837	276757	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
CGLIHPIH_1	4187685	4189061	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.
CGLIHPIH_1	2735668	2736519	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
CGLIHPIH_1	275837	276754	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
CGLIHPIH_1	4185167	4185685	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
CGLIHPIH_1	4187688	4189061	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
CGLIHPIH_1	604736	606376	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
CGLIHPIH_1	2051334	2053928	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.
CGLIHPIH_1	3697827	3698969	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
CGLIHPIH_1	3699452	3700633	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
CGLIHPIH_1	3698988	3699437	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
CGLIHPIH_1	2004676	2006439	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
CGLIHPIH_1	3291491	3292276	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
CGLIHPIH_1	3287655	3288593	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
CGLIHPIH_1	3290269	3291465	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
CGLIHPIH_1	3288621	3290240	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
CGLIHPIH_1	3280499	3287635	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
CGLIHPIH_1	2295301	2295942	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
CGLIHPIH_1	132882	134018	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
CGLIHPIH_1	19074	19943	pdxS	3.13e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
CGLIHPIH_1	1690117	1690893	CodY	3.42e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
CGLIHPIH_1	3546215	3546784	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
CGLIHPIH_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
CGLIHPIH_1	1320568	1346676	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
CGLIHPIH_1	2667028	2697272	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)