Probiotic potential risk score

ARGs (CARD)	VFs (VFDB)	PGs (PHI-base)	PPRS
0	6	11	12.53

PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).

Antibiotic resistance genes

Comprehensive Antibiotic Resistance Database (CARD)

ARO accession	ARO name	Identity	Coverage	CARD name	Accession no.
No hit found

RGI v6.0.0 (Database: CARD Variants v4.0.0, Jul. 2022 release)

ResFinder

Resistance gene	Identity	Coverage	Phenotype	Accession no.
msr(D)	100.00	62.77	Macrolide, Lincosamide and Streptogramin B resistance	AF274302
mef(A)	100.00	61.99	Macrolide resistance	U83667

ResFinder v4.0 (Database: resfinder_db, May 2022 release)

AMRFinderPlus

Gene symbol	Sequence name	Method	Identity	Coverage	Accession no.
msr(D)	ABC-F type ribosomal protection protein Msr(D)	PARTIAL_CONTIG_ENDX	100.00	62.83	WP_000420313.1
mef(A)	macrolide efflux MFS transporter Mef(A)	PARTIAL_CONTIG_ENDX	100.00	61.98	WP_000417519.1

AMRFinderPlus v3.10.42 (Database: Oct. 2022 release)

Virulence factors

Virulence Factor Database (VFDB)

Gene ID	Gene name	Identity	Coverage	e-value	VF name	VF category	Accession no.
VFG005556	tig/ropA	94.86	100.00	0.0	Trigger factor	Stress survival	WP_011680653
VFG019077	plr/gapA	92.79	100.00	0.0	Streptococcal plasmin receptor/GAPDH	Adherence	WP_000260685
VFG006041	rfbA	91.15	100.00	0.0	Capsule	Immune modulation	WP_011681286
VFG005579	eno	90.58	100.00	0.0	Streptococcal enolase	Exoenzyme	WP_000022815
VFG006046	STR_RS05880	90.24	100.00	0.0	Capsule	Immune modulation	WP_011226149
VFG005382	srtA	85.21	99.74	0.0	Sortase A	Exoenzyme	WP_011681303

BLASTN v2.8.1+ (Database: VFDB, Jun. 2022 release)

VirulenceFinder

Database	Virulence factor	Identity	Coverage	Protein function	Accession no.
virulence_ecoli	pet	98.73	82.95	Plasmid-encoded toxin	AF056581

VirulenceFinder v2.0.3 (Database: virulencefinder_db, Dec. 2022 release)

Pathogenic genes

PHI-base

Protein ID	Gene name	Identity	Coverage	e-value	Function	Gene ID
Q8DPC2	potA	89.84	99.48	0.0	ABC transporter ATP-binding protein - spermidine/putrescine transport	AAL00050
D5AF41	IMPDH	87.83	99.80	0.0	Inosine-5'-monophosphate dehydrogenase	ADE32434
A4VWH9	Eno	86.44	99.54	0.0	Enolase	ABP90468
Q93MY4	covR	85.53	99.58	1.52e-151	Responder protein	AAK71319
B3VA60	CovR	81.66	99.56	4.70e-138	serves to repress GAS virulence factor-encoding genes	ACE75886
U2W9V3	SpxA2	91.67	99.25	6.29e-89	Transcriptional regulator	ERL21461
Q8DQV4	spr0479	84.38	97.96	1.55e-57	essential gene	AAK99283
Q8CZ89	spr0175	85.23	98.88	1.44e-52	pathogenitcity related	AAK98979
Q8DRE1	spr0177	83.15	87.25	5.54e-51	essential gene	AAK98981
Q8DP67	spr1327	92.31	75.58	1.67e-41	essential gene	AAL00131
A0A6C7HPB2	SEN1538	87.93	95.08	2.10e-32	Conserved hypothetical protein	CAR33117
A4VYE0	gidA	85.23	69.95	0.0	tRNA uridine 5-carboxymethylaminomethyl modification enzyme	ABP91129

BLASTP v2.8.1+ (Database: PHI-base v4.14, Nov. 2022 release)

Plasmid

PlasmidFinder

Plasmid	Identity	Query / Template	Accession no.
rep35	84.47	657 / 672	AF295100

PlasmidFinder 2.0.1 (Database: plasmidfinder_db, Jan. 2023 release)

Prophage

Phigaro

Scaffold	Begin	End	Transposable	Taxonomy	pVOGs
No hit found

Phigaro v2.3.0 (Database: Aug. 2017 release)