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.
PNCHODLH_1	2621330	2622184	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
PNCHODLH_1	2602621	2603823	blt	ARO:3003006	blt	100.00	100.00	L32599.1
PNCHODLH_1	2380301	2381470	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
PNCHODLH_1	1355940	1356257	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
PNCHODLH_1	1355602	1355940	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
PNCHODLH_1	895859	898429	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
PNCHODLH_1	583817	585460	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3
PNCHODLH_1	338754	339347	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
PNCHODLH_1	288251	289684	lmrB	ARO:3002813	lmrB	100.00	100.00	JYFL01000006.1
PNCHODLH_1	275436	276356	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.
PNCHODLH_1	2621330	2622184	aadK	Streptomycin	100.00	100.00	M26879
PNCHODLH_1	275436	276356	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
PNCHODLH_1	4112172	4113548	tet(L)	Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline	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.
PNCHODLH_1	2621333	2622184	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
PNCHODLH_1	275436	276353	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
PNCHODLH_1	4109654	4110172	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
PNCHODLH_1	4112175	4113548	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
PNCHODLH_1	583820	585460	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
PNCHODLH_1	2071390	2073984	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.
PNCHODLH_1	3622314	3623456	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
PNCHODLH_1	3623939	3625120	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
PNCHODLH_1	3623475	3623924	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
PNCHODLH_1	2024732	2026495	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
PNCHODLH_1	3215980	3216765	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
PNCHODLH_1	3212144	3213082	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
PNCHODLH_1	3214758	3215954	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
PNCHODLH_1	3213110	3214729	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
PNCHODLH_1	3204988	3212124	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
PNCHODLH_1	2180956	2181597	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
PNCHODLH_1	132473	133609	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
PNCHODLH_1	18665	19534	pdxS	3.08e-149	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
PNCHODLH_1	1669198	1669974	CodY	3.36e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
PNCHODLH_1	3470703	3471272	ClpP	2.49e-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
PNCHODLH_1	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
PNCHODLH_1	1299656	1325764	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
PNCHODLH_1	1860146	1895696	False	Siphoviridae	VOG4602, VOG9667, VOG5353, VOG0181, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG6093, VOG7462, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918
PNCHODLH_1	2552691	2582936	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
PNCHODLH_1	2751420	2781503	False	Siphoviridae	VOG4707, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0531, VOG0198, VOG6340, VOG7372, VOG2752, VOG4606

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