safety

PPRS ARGs VFs PGs Plasmid Prophage IS elements

ARGs	VFs	PGs	PPRS
13	10	7	17.83

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.
HCNLPJCL_56	1690973	1691827	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
HCNLPJCL_56	1672268	1673470	blt	ARO:3003006	blt	100.00	100.00	L32599.1
HCNLPJCL_56	1449949	1451118	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
HCNLPJCL_56	425602	425919	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
HCNLPJCL_56	425264	425602	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
HCNLPJCL_77	337917	338837	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
HCNLPJCL_77	324583	326022	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
HCNLPJCL_87	278462	281032	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
HCNLPJCL_77	274926	275519	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
HCNLPJCL_77	28809	30452	vmlR	ARO:3004476	vmlR	100.00	100.00	NC_000964.3

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.
HCNLPJCL_56	1690973	1691827	aadK	Streptomycin	100.00	100.00	M26879
HCNLPJCL_77	337917	338837	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
HCNLPJCL_98	36348	37724	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.
HCNLPJCL_56	1690976	1691827	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
HCNLPJCL_77	337920	338837	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
HCNLPJCL_98	39724	40242	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
HCNLPJCL_98	36348	37721	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
HCNLPJCL_77	28809	30449	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
HCNLPJCL_56	1141036	1143630	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.
HCNLPJCL_67	398306	399448	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
HCNLPJCL_67	396642	397823	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
HCNLPJCL_67	397838	398287	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
HCNLPJCL_56	1094378	1096141	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
HCNLPJCL_67	804998	805783	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
HCNLPJCL_56	1250603	1251244	hlyIII	Hemolysin III	Exotoxin	100.00	100.00	NP_390062
HCNLPJCL_67	809639	816775	dhbF	Bacillibactin	Nutritional/Metabolic factor	99.99	100.00	NP_391076
HCNLPJCL_67	808681	809619	dhbB	Bacillibactin	Nutritional/Metabolic factor	99.89	100.00	NP_391077
HCNLPJCL_67	805809	807005	dhbC	Bacillibactin	Nutritional/Metabolic factor	99.67	100.00	NP_391079
HCNLPJCL_67	807034	808653	dhbE	Bacillibactin	Nutritional/Metabolic factor	99.57	100.00	NP_391078

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
HCNLPJCL_109	31733	32869	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
HCNLPJCL_131	11259	10390	pdxS	1.11e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
HCNLPJCL_56	738866	739642	CodY	1.73e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
HCNLPJCL_67	551060	550491	ClpP	5.52e-99	part of proteolytic complex	81.05	97.44	BAB94595
HCNLPJCL_56	276441	276833	spxA1	5.12e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
HCNLPJCL_120	20575	20817	SpoVG	7.51e-39	RNA-binding protein	81.48	79.41	AAT02994
HCNLPJCL_77	75923	75726	CspA	1.89e-31	cold shock protein	90.91	100.00	CAA62903

BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)

PlasmidFinder

Query ID	Begin	End	Plasmid	Query / Template	Identity	Accession no.
HCNLPJCL_142	4728	4921	Col(SD853)	194 / 194	97.94	NC015392

PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
HCNLPJCL_56	0.0	1.0	0.0
HCNLPJCL_67	0.0	1.0	0.0
HCNLPJCL_77	0.0	1.0	0.0
HCNLPJCL_87	0.0	1.0	0.0
HCNLPJCL_98	0.0	1.0	0.0
HCNLPJCL_109	0.0	1.0	0.0
HCNLPJCL_120	0.0	1.0	0.0
HCNLPJCL_131	0.0	1.0	0.0
HCNLPJCL_142	1.0	0.0	1.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
HCNLPJCL_56	369317	395425	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
HCNLPJCL_56	929814	965346	False	Siphoviridae	VOG4602, VOG9667, VOG5353, VOG0181, VOG4552, VOG4566, VOG9600, VOG0025, VOG1884, VOG0198, VOG6093, VOG10654, VOG7462, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918
HCNLPJCL_56	1622339	1652583	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)