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.
DOMIAKHA_8	1840592	1840930	ykkC	ARO:3003063	ykkC	100.00	100.00	AL009126.1
DOMIAKHA_8	1840275	1840592	ykkD	ARO:3003064	ykkD	100.00	100.00	AL009126.1
DOMIAKHA_8	721628	722797	bmr	ARO:3003007	bmr	99.74	100.00	M33768.1
DOMIAKHA_8	499276	500478	blt	ARO:3003006	blt	100.00	100.00	L32599.1
DOMIAKHA_8	480915	481769	aadK	ARO:3002627	aadK	100.00	100.00	AL009126.1
DOMIAKHA_20	358869	359789	mphK	ARO:3004541	mphK	100.00	100.00	CP010314.1
DOMIAKHA_20	345535	346974	lmrB	ARO:3002813	lmrB	99.79	100.42	JYFL01000006.1
DOMIAKHA_20	295878	296471	tmrB	ARO:3003059	tmrB	100.00	100.00	AL009126.3
DOMIAKHA_30	276656	279226	Bacillus subtilis mprF	ARO:3003324	Bsub_mprF	100.00	100.00	AL009126.3
DOMIAKHA_20	29253	30896	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.
DOMIAKHA_8	480915	481769	aadK	Streptomycin	100.00	100.00	M26879
DOMIAKHA_20	358869	359789	mph(K)	Spiramycin, Telithromycin	100.00	100.00	NC_000964
DOMIAKHA_13	1008995	1010371	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.
DOMIAKHA_8	480915	481766	aadK	aminoglycoside 6-adenylyltransferase AadK	EXACTX	100.00	100.00	WP_003229862.1
DOMIAKHA_20	358872	359789	mphK	macrolide 2'-phosphotransferase MphK	EXACTX	100.00	100.00	WP_003246254.1
DOMIAKHA_13	1006477	1006995	satA	streptothricin N-acetyltransferase SatA	EXACTX	100.00	100.00	WP_003242546.1
DOMIAKHA_13	1008998	1010371	tet(L)	tetracycline efflux MFS transporter Tet(L)	EXACTX	100.00	100.00	WP_003242953.1
DOMIAKHA_20	29253	30893	vmlR	ABC-F type ribosomal protection protein VmlR	EXACTX	100.00	100.00	WP_003234144.1
DOMIAKHA_8	1163517	1166111	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.
DOMIAKHA_13	519252	520394	capA	Capsule	Immune modulation	100.00	100.00	NP_391469
DOMIAKHA_13	520877	522058	capB	Capsule	Immune modulation	100.00	100.00	NP_391471
DOMIAKHA_13	520413	520862	capC	Capsule	Immune modulation	100.00	100.00	NP_391470
DOMIAKHA_8	1211006	1212769	dep/capD	Capsule	Immune modulation	100.00	100.00	NP_389723
DOMIAKHA_13	112909	113694	dhbA	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391080
DOMIAKHA_13	109073	110011	dhbB	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391077
DOMIAKHA_13	111687	112883	dhbC	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391079
DOMIAKHA_13	110039	111658	dhbE	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391078
DOMIAKHA_13	101917	109053	dhbF	Bacillibactin	Nutritional/Metabolic factor	100.00	100.00	NP_391076
DOMIAKHA_8	921502	922143	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
DOMIAKHA_36	28138	27002	tufA	0.0	elongation factor Tu	84.96	95.69	AHM69299
DOMIAKHA_38	11309	10440	pdxS	1.12e-151	encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS	83.79	98.31	ACE61268
DOMIAKHA_8	1527328	1526552	CodY	1.84e-124	nutrient-responsive regulator	81.08	100.00	ACJ80679
DOMIAKHA_13	367640	368209	ClpP	6.29e-99	part of proteolytic complex	81.05	97.44	BAB94595
DOMIAKHA_8	1989752	1989360	spxA1	5.45e-69	redox-responsive transcription factor	83.21	100.00	AAF21893
DOMIAKHA_37	20625	20867	SpoVG	7.52e-39	RNA-binding protein	81.48	79.41	AAT02994
DOMIAKHA_20	76365	76168	CspA	1.98e-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.
No hit found

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

PlasmidHunter

Query ID	Prediction	Chromosome	Plasmid
DOMIAKHA_8	0.0	1.0	0.0
DOMIAKHA_13	0.0	1.0	0.0
DOMIAKHA_20	0.0	1.0	0.0
DOMIAKHA_30	0.0	1.0	0.0
DOMIAKHA_36	0.0	1.0	0.0
DOMIAKHA_37	0.0	1.0	0.0
DOMIAKHA_38	0.0	1.0	0.0

PlasmidHunter v 1.4.5 (Database: May. 2024 release)

Phigaro

Query ID	Begin	End	Transposable	Taxonomy	pVOGs
DOMIAKHA_8	322139	351299	False	Siphoviridae	VOG0044, VOG6517, VOG0198, VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG5008, VOG0641, VOG4574
DOMIAKHA_8	520030	550407	False	Myoviridae	VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718
DOMIAKHA_8	1870769	1896877	False	Myoviridae	VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667

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