Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis

Silva, Nathália Cristina Cirone; Yang, Yongqiang; Rodrigues, Marjory Xavier; Tomazi, Tiago; Bicalho, Rodrigo Carvalho

doi:10.1186/s12917-021-03031-4

BMC Veterinary Research

Table 1 Distribution of virulence factors genes of 159 Streptococcus uberis isolated from clinical mastitis according to clinical outcomes recorded during the follow-up period

From: Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis

Virulence factor	Product	Mortality (% of cows infected by positive strains)				Bacteriological cure				Clinical cure				Loss of mammary quarter function.				Reoccurrence of CM				Total strains
		Dead		Alive		No		Yes		No		Yes		No		Yes		No		Yes		Total strains
		n	%	n	%	n	%	n	%	n	%	n	%	n	%	n	%	n	%	n	%
hasC	UTP–glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	31	19	128	81	88	55	71	45	20	13	139	87	142	89	17	11	121	76	38	24	159
leuS	Leucyl-tRNA synthetase (EC 6.1.1.4)	31	19	128	81	88	55	71	45	20	13	139	87	142	89	17	11	121	76	38	24	159
perR	Peroxide stress regulator PerR, FUR family	31	19	128	81	88	55	71	45	0	00	159	100	142	89	17	11	121	76	38	24	159
purH	IMP cyclohydrolase (EC 3.5.4.10) / Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3)	31	19	128	81	88	55	71	45	20	13	139	87	142	89	17	11	121	76	38	24	159
purN	Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2)	31	19	128	81	88	55	71	45	20	13	139	87	142	89	17	11	121	76	38	24	159
cydA	Cytochrome d ubiquinol oxidase subunit I (EC 1.10.3.-)	31	20	127	80	87	55	71	45	20	13	138	87	141	89	17	11	120	76	38	24	158
gidA	tRNA-5-carboxymethylaminomethyl-2-thiouridine(34) synthesis protein MnmG	31	20	127	80	88	56	70	44	20	13	138	87	141	89	17	11	120	76	38	24	158
purB	Adenylosuccinate lyase (EC 4.3.2.2) @ SAICAR lyase (EC 4.3.2.2)	30	19	127	81	86	55	71	45	20	13	137	87	140	89	17	11	119	76	38	24	157
SP_0121	Ribonuclease J1 (endonuclease and 5’ exonuclease)	31	20	125	80	87	56	69	44	20	13	136	87	139	89	17	11	118	76	38	24	156
SP_0494	CTP synthase (EC 6.3.4.2)	31	20	125	80	86	55	70	45	20	13	136	87	139	89	17	11	118	76	38	24	156
fba	Fructose-bisphosphate aldolase class II (EC 4.1.2.13)	31	20	124	80	85	55	70	45	20	13	135	87	138	89	17	11	117	75	38	25	155
glnA	Glutamine synthetase type I (EC 6.3.1.2)	30	19	125	81	86	55	69	45	20	13	135	87	138	89	17	11	117	75	38	25	155
rpoE	DNA-directed RNA polymerase delta subunit (EC 2.7.7.6)	31	20	124	80	85	55	70	45	20	13	135	87	138	89	17	11	117	75	38	25	155
atmB	Methionine ABC transporter substrate-binding protein	29	19	123	81	83	55	69	45	20	13	132	87	135	89	17	11	114	75	38	25	152
ccpA	Catabolite control protein A	30	20	122	80	82	54	70	46	20	13	132	87	135	89	17	11	114	75	38	25	152
luxS	S-ribosylhomocysteine lyase (EC 4.4.1.21) @ Autoinducer-2 production protein LuxS	30	20	122	80	84	55	68	45	20	13	132	87	135	89	17	11	114	75	38	25	152
SP_0320	2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase (EC 1.1.1.127) @ 2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.125)	29	19	123	81	85	56	67	44	10	07	142	93	135	89	17	11	114	75	38	25	152
clpP	ATP-dependent Clp protease proteolytic subunit ClpP (EC 3.4.21.92)	30	20	121	80	83	55	68	45	20	13	131	87	134	89	17	11	113	75	38	25	151
Spy_1633		29	19	122	81	83	55	68	45	20	13	131	87	134	89	17	11	113	75	38	25	151
vick	Histidine kinase	29	19	120	81	81	54	68	46	20	13	129	87	132	89	17	11	111	74	38	26	149
SP_2086	Phosphate ABC transporter, permease protein PstA (TC 3.A.1.7.1)	29	20	119	80	81	55	67	45	20	14	128	86	131	89	17	11	110	74	38	26	148
SP_0095	Rhodanese domain protein UPF0176, Firmicutes subgroup	30	21	115	79	82	57	63	43	20	14	125	86	128	88	17	12	107	74	38	26	145
lepA	Translation elongation factor LepA	30	21	114	79	79	55	65	45	20	14	124	86	130	90	14	10	107	74	37	26	144
sodA	Superoxide dismutase [Mn] (EC 1.15.1.1)	30	21	114	79	81	56	63	44	20	14	124	86	127	88	17	12	106	74	38	26	144
cpsY	Methionine biosynthesis and transport regulator MtaR, LysR family	30	21	110	79	79	56	61	44	20	14	120	86	126	90	14	10	103	74	37	26	140
SP_0829	Phosphopentomutase (EC 5.4.2.7)	30	21	110	79	79	56	61	44	20	14	120	86	126	90	14	10	103	74	37	26	140
ciaR	Two component system response regulator CiaR	29	21	110	79	78	56	61	44	19	14	120	86	123	88	16	12	103	74	36	26	139
SP_0916	Arginine decarboxylase (EC 4.1.1.19)	30	22	109	78	79	57	60	43	20	14	119	86	124	89	15	11	102	73	37	27	139
guaA	GMP synthase [glutamine-hydrolyzing], amidotransferase subunit (EC 6.3.5.2) / GMP synthase [glutamine-hydrolyzing], ATP pyrophosphatase subunit (EC 6.3.5.2)	28	20	110	80	77	56	61	44	19	14	119	86	123	89	15	11	102	74	36	26	138
SP_1970	Aspartate–ammonia ligase (EC 6.3.1.1)	30	22	108	78	78	57	60	43	20	14	118	86	124	90	14	10	102	74	36	26	138
SP_1396	Phosphate ABC transporter, ATP-binding protein PstB (TC 3.A.1.7.1)	28	21	108	79	76	56	60	44	19	14	117	86	120	88	16	12	101	74	35	26	136
SP_1398	Phosphate ABC transporter, permease protein PstA (TC 3.A.1.7.1)	28	21	108	79	76	56	60	44	19	14	117	86	120	88	16	12	101	74	35	26	136
SP_0856	Branched-chain amino acid aminotransferase (EC 2.6.1.42)	28	21	107	79	76	56	59	44	18	13	117	87	121	90	14	10	100	74	35	26	135
SP_1780	Oligoendopeptidase F-like protein	4	22	14	78	12	67	6	33	3	17	15	83	15	83	3	17	13	72	5	28	18
cps4L	UDP-N-acetyl-L-fucosamine synthase (EC 5.1.3.28)	3	30	7	70	4	40	6	60	1	10	9	90	9	90	1	10	8	80	2	20	10
SpyM3_0013	Cationic amino acid transporter - APC Superfamily	1	11	8	89	5	56	4	44	1	11	8	89	8	89	1	11	8	89	1	11	9
psaC	ABC transporter membrane-spanning permease-manganese transport	0	00	6	100	2	33	4	67	1	17	5	83	5	83	1	17	5	83	1	17	6
hupA	Putative DNA-binding protein HU-beta (ACLAME 290)	0	00	2	100	1	50	1	50	20	100	1	50	2	100	0	00	1	50	1	50	2
pbp1A	DD-transpeptidase	0	00	2	100	2	100	0	00	0	00	2	100	2	100	0	00	1	50	1	50	2
polC	DNA polymerase III PolC-type	1	50	1	50	2	100	0	00	0	00	2	100	2	100	0	00	2	100	0	00	2
fbp54	Fibronectin/fibrinogen-binding protein	0	00	1	100	0	00	1	100	0	00	1	100	1	100	0	00	1	100	0	00	1
glnP	Glutamine ABC transporter, substrate-binding protein GlnH / Glutamine ABC transporter, substrate-binding protein GlnH / Glutamine ABC transporter, permease protein GlnP	1	100	0	00	1	100	0	00	1	100	0	00	1	100	0	00	0	00	1	100	1
hasA	Hyaluronan synthase	0	00	1	100	1	100	0	00	0	00	1	100	1	100	0	00	1	100	0	00	1
neuB	Putative N-acetylneuraminic acid synthase	0	00	1	100	1	100	0	00	0	00	1	100	0	00	1	100	1	100	0	00	1
nox	NADH oxidase	0	00	1	100	0	00	1	100	0	00	1	100	1	100	0	00	1	100	0	00	1
pepC	Aminopeptidase C (EC 3.4.22.40)	0	00	1	100	0	00	1	100	20	200	1	100	1	100	0	00	1	100	0	00	1
purL	Phosphoribosylformylglycinamidine synthase, synthetase subunit (EC 6.3.5.3)	0	00	1	100	1	100	0	00	0	00	1	100	1	100	0	00	1	100	0	00	1
SP_0842		0	00	1	100	1	100	0	00	0	00	1	100	0	00	1	100	1	100	0	00	1
SP_1399	Phosphate ABC transporter, permease protein PstC (TC 3.A.1.7.1)	0	00	1	100	1	100	0	00	0	00	1	100	1	100	0	00	1	100	0	00	1

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