Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms

Kindle, Patrick; Zurfluh, Katrin; Nüesch-Inderbinen, Magdalena; von Ah, Sereina; Sidler, Xaver; Stephan, Roger; Kümmerlen, Dolf

doi:10.1186/s40813-019-0116-y

Table 1 Escherichia coli isolated from dust, wipes and slurry samples from pig farms

From: Phenotypic and genotypic characteristics of Escherichia coli with non-susceptibility to quinolones isolated from environmental samples on pig farms

Isolate ID	Farm ID	Farm type	FQ usage	Source	NA	CIP	QRDR gyrA	PMQR gene	PG	ST	CC	Additional resistance
19	11	F&R	+	D	R	IR	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, GM
45	12	F&R	+	D	R	R	S83L, D87N	–	B1	162	469	AM, SXT, TE, STR, K
22	13	F&R	+	D	R	R	S83L, D87N	–	B1	1642	–	AM, SXT, C, TE, STR, K, GM
28	13	F&R	+	D	R	R	S83L, D87N	–	B1	1642	–	AM, SXT, C, TE, STR, K, GM
40	17	F&R	+	D	R	R	S83L, D87N	–	A	10	10	AM, SXT, C, TE, STR
44	17	F&R	+	D	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, K, GM
8	18	F&R	+	D	R	R	S83L, D87N	–	A	2197	–	AM, SXT, AZM, C, TE, STR, K, GM
9	18	F&R	+	D	R	R	S83L, D87N	–	A	2197	–	AM, CTX, SXT, AZM, C, TE, STR, K, GM
54	21	F&R	+	D	R	R	S83L, D87N	–	A	2197	–	AM, SXT, C, TE, STR, GM
55	21	F&R	+	D	R	S	S83L	–	B1	345	–	AM, SXT, STR, K
117	22	F&R	+	D	R	S	S83L	–	C	90	23	–
126	23	F&R	+	D	R	S	S83L	–	A	898	–	TE
127	23	F&R	+	D	R	S	S83L	–	A	898	–	–
129	23	F&R	+	D	R	S	S83L	–	A	898	–	–
62	29	F&R	+	D	R	R	S83L, D87N	aac(6′)-Ib-cr	C	6332	–	AM, AMC, CZ, CTX, FEP, SXT, AZM, TE, STR, GM
149	29	F&R	+	D	IR	S	–	qnrS	A	542	–	SXT, TE, STR
66	30	F&R	+	D	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, K, GM
160	30	F&R	+	D	IR	S	–	qnrB	A	new	–	AM, SXT, TE, STR
168	30	F&R	+	D	IR	S	–	qnrB	A	34	10	TE, STR
169	30	F&R	+	D	IR	S	–	qnrB	A	43	10	–
2	71	F&R	+	D	R	R	S83L, D87N	–	B1	297	–	AM, AMC
11	71	F&R	+	D	R	S	S83L	qnrS	A	2496	–	AM, AMC, STR
145	71	F&R	+	D	IR	IR	–	qnrS	A	301	165	SXT, TE, STR
107	73	F&R	+	D	R	S	S83L	–	A	10	10	AM, C, TE, STR
109	73	F&R	+	D	R	S	S83L	–	A	898	–	TE, STR
97	69	FF	+	D	R	R	S83L, D87N	–	B1	297	–	TE
173	69	FF	+	D	IR	S	–	qnrB	E	1607	–	–
113	1	M&G	+	D	R	S	S83L	qnrS	A	10	10	AM, SXT, STR
164	1	M&G	+	D	IR	S	–	qnrS	A	new	–	AM
13	6	M&G	+	D	R	S	S83L	–	B1	737	–	SXT, TE, STR
14	6	M&G	+	D	R	S	S83L	–	B1	737	–	SXT, TE, STR
41	17	F&R	+	W	R	R	S83L, D87N	–	B1	58	155	AM, SXT, TE, STR
125	22	F&R	+	W	R	S	S83L	–	A	4691	–	STR
56	23	F&R	+	W	R	S	S83L	–	A	1684	–	SXT, STR
128	23	F&R	+	W	R	S	S83L	–	C	410	23	TE, STR, K
59	26	F&R	+	W	R	S	S83L	–	E	302	–	AM, STR
139	26	F&R	+	W	R	S	S83L	–	E	302	–	AM, STR
65	29	F&R	+	W	R	S	–	qnrB	E	1607	–	SXT, AZM, STR
161	29	F&R	+	W	IR	S	–	qnrB	E	1607	–	–
67	30	F&R	+	W	R	S	S83L	–	A	746	–	SXT, TE, STR
141	30	F&R	+	W	R	S	S83L	–	E	302	–	–
143	30	F&R	+	W	IR	S	–	–	E	302	–	–
150	30	F&R	+	W	IR	S	–	qnrB	A	10	10	SXT, FM, STR
3	71	F&R	+	W	R	S	S83L	–	A	542	–	–
12	71	F&R	+	W	R	IR	S83L	qnrS	A	2496	–	AM, CZ, STR
137	71	F&R	+	W	R	S	D87G	–	A	3630	–	–
144	71	F&R	+	W	IR	IR	–	qnrS	E	new	–	AM, SXT, TE, STR
99	73	F&R	+	W	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR
101	73	F&R	+	W	R	S	S83L	–	A	898	–	SXT, TE, STR
102	73	F&R	+	W	R	S	S83L	–	A	1684	–	SXT, TE, STR
106	73	F&R	+	W	R	S	–	qnrS	A	871	–	SXT, TE, STR
123	73	F&R	+	W	R	S	S83L	–	B1	3695	–	–
155	74	F&R	+	W	IR	S	–	–	C	23	23	TE, STR, K
119	38	FF	+	W	R	S	S83L	–	A	100	165	SXT, TE, STR
152	53	FF	+	W	IR	S	–	qnrB + qnrS	E	new	–	AM10, SXT, TE, STR
146	59	FF	+	W	IR	S	–	qnrB + qnrS	A	10	10	AM, SXT, TE, STR, K, GM
132	69	FF	+	W	R	S	S83L, D87N	–	B1	297	–	SXT, TE, STR
163	1	M&G	+	W	IR	S	–	qnrB	A	34	10	TE, STR
157	4	M&G	+	W	IR	S	–	qnrB	A	1602	–	STR
158	4	M&G	+	W	IR	S	–	qnrB	A	new	–	STR
115	6	M&G	+	W	R	S	S83L	–	D	362	–	AM, SXT, C, TE, STR, K
124	6	M&G	+	W	R	S	S83L	–	A	93	168	AM, SXT, FOS, STR
20	12	F&R	+	SL	R	IR	S83L, D87N	–	B1	297	–	TE
21	12	F&R	+	SL	R	IR	S83L, D87N	–	B1	297	–	TE
27	12	F&R	+	SL	R	IR	S83L, D87Y	–	A	10	10	–
23	13	F&R	+	SL	R	S	D87Y	–	A	34	10	STR
24	13	F&R	+	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, K, GM
29	13	F&R	+	SL	R	S	D87Y	–	A	34	10	STR
30	13	F&R	+	SL	R	S	S83L	–	A	301	165	SXT, STR
31	13	F&R	+	SL	R	S	S83L	–	A	301	165	SXT, AZM, STR
25	16	F&R	+	SL	R	S	S83L	–	A	10	10	–
26	16	F&R	+	SL	R	R	S83L, D87N	–	B1	297	–	FOS, TE
42	16	F&R	+	SL	R	R	S83L, D87N	–	B1	297	–	TE
116	16	F&R	+	SL	R	S	S83L	–	A	10	10	–
165	16	F&R	+	SL	R	R	S83L, D87N	–	B1	297	–	TE
38	17	F&R	+	SL	R	R	S83L, D87N	–	B1	297	–	–
39	17	F&R	+	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, GM
43	17	F&R	+	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR, K, GM
156	18	F&R	+	SL	IR	S	–	qnrB	A	77	206	AM, SXT, C, STR
166	21	F&R	+	SL	IR	S	–	qnrB	A	10	10	SXT, STR
118	26	F&R	+	SL	R	S	S83L	–	A	6593	165	STR
130	28	F&R	+	SL	R	S	S83L	–	A	93	168	–
136	28	F&R	+	SL	R	S	S83L	–	A	93	168	–
167	28	F&R	+	SL	IR	S	–	qnrS	A	48	10	AM, TE, STR
63	29	F&R	+	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR
64	29	F&R	+	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR
4	71	F&R	+	SL	R	R	S83L, D87N	–	A	3902	–	AM, SXT, TE, STR
5	71	F&R	+	SL	R	IR	S83L	qnrS	A	2496	–	AM, CTX, FOS, AZM, STR
6	71	F&R	+	SL	R	IR	S83L, D87N	–	B1	162	469	AM, SXT, TE, STR, K
7	71	F&R	+	SL	R	R	S83L, D87N	–	B1	162	469	AM, SXT, TE, STR, K
10	71	F&R	+	SL	R	IR	S83L	qnrS	A	2496	–	AM, STR
100	73	F&R	+	SL	R	S	S83L	–	A	10	10	AM, C, TE, STR
108	73	F&R	+	SL	R	S	S83L	–	A	10	10	AM, C, TE, STR
122	73	F&R	+	SL	R	S	S83L	–	A	10	10	AM, C, TE, STR
85	53	FF	+	SL	R	R	S83L, D87N	–	B1	162	469	STR
96	69	FF	+	SL	R	R	S83L, D87N	–	B1	297	–	TE
1	1	M&G	+	SL	R	S	S83L	–	B1	156	156	SXT, STR
15	6	M&G	+	SL	R	R	S83L	–	B1	737	–	SXT, TE, STR
114	6	M&G	+	SL	R	S	S83L	–	B1	737	–	SXT, TE, STR
135	6	M&G	+	SL	R	S	S83L	–	A	93	168	–
34	14	F&R	–	D	R	R	S83L, D87N	–	E	1011	–	AM
35	14	F&R	–	D	R	R	S83L, D87N	–	E	1011	–	AM
49	20	F&R	–	D	R	R	S83L, D87N	–	A	744	–	AM, SXT, C, TE, STR, K, GM
53	20	F&R	–	D	R	IR	S83L, D87N	–	A	2197	–	AM, SXT, C, TE, STR, GM
138	20	F&R	–	D	R	S	S83L	–	B1	58	155	AM, SXT, TE, STR
50	24	F&R	–	D	R	R	S83L, D87N	–	A	10	10	AM, SXT, C, TE, STR
57	25	F&R	–	D	R	R	S83L, D87N	–	A	744	–	AM, SXT, C, TE, STR, K
60	25	F&R	–	D	R	R	S83L, D87N	–	A	744	–	AM, SXT, C, TE, STR, K
105	70	F&R	–	D	R	S	S83L	–	B1	847	–	AM, SXT, STR, K
98	72	F&R	–	D	R	R	S83L, D87N	–	B1	297	–	AM, CTX
104	72	F&R	–	D	R	R	S83 L, D87N	–	B1	new	–	SXT, TE, GM
82	52	FF	–	D	R	R	S83L, D87N	–	B1	1431	–	SXT
87	54	FF	–	D	R	S	S83L	–	C	88	23	AM, SXT, TE, STR, K
153	57	FF	–	D	IR	S	–	qnrB	B1	99	–	TE, STR
133	61	FF	–	D	R	S	S83L	–	A	93	168	–
95	67	FF	–	D	R	S	S83L	–	B1	737	–	SXT, TE, STR
112	78	M&G	–	D	R	R	S83L, D87N	–	C	90	23	AM, SXT, TE, STR, GM
32	14	F&R	–	W	R	S	S83L	–	C	88	23	AM, SXT, STR, K
33	14	F&R	–	W	R	S	S83L	–	C	88	23	AM, SXT, STR, K
48	20	F&R	–	W	R	R	S83L, D87N	–	A	2197	–	AM, SXT, C, TE, STR, GM
51	20	F&R	–	W	R	R	S83L, D87N	–	B1	297	–	TE
52	20	F&R	–	W	R	R	S83L, D87N	–	B1	297	–	TE
46	24	F&R	–	W	R	R	S83L, D87N	–	A	10	10	AM, SXT, C, TE, STR
140	70	F&R	–	W	IR	S	–	–	F	117	–	–
120	76	F&R	–	W	R	S	S83L	–	C	23	23	–
61	35	FF	–	W	R	S	S83L	–	B1	847	–	SXT, TE, STR, GM
70	35	FF	–	W	R	S	S83L	–	B1	new	–	SXT, TE, STR
162	35	FF	–	W	IR	S	–	qnrS	A	227	10	TE, STR, K
76	47	FF	–	W	R	S	S83L	–	A	898	–	TE, STR
74	50	FF	–	W	R	R	S83L, D87N	–	B1	297	–	TE
78	50	FF	–	W	R	R	S83L, D87N	–	A	2509	–	AZM, TE, STR
80	50	FF	–	W	R	R	S83L, D87N	–	B1	297	–	TE
81	52	FF	–	W	R	R	S83L, D87N	–	B1	297	–	TE
86	54	FF	–	W	R	S	S83L	–	C	88	23	AM, SXT, TE, STR, K
89	58	FF	–	W	R	S	S83L	–	B1	58	155	SXT, TE, STR
91	63	FF	–	W	R	S	S83L	–	C	88	23	AM, SXT, STR, K
90	65	FF	–	W	R	R	S83L, D87N	–	B1	297	–	TE
94	66	FF	–	W	R	R	S83L, D87N	–	B1	297	–	TE
172	68	FF	–	W	IR	S	–	qnrB	A	993	–	TE, STR
147	7	M&G	–	W	IR	IR	–	qnrB + qnrS	A	10	10	AM, SXT, TE, STR, GM
148	7	M&G	–	W	IR	S	–	qnrB + qnrS	A	10	10	AM10, SXT, TE, STR, GM
174	78	M&G	–	W	IR	S	–	qnrB	B1	3322	86	AM, STR, GM
36	14	F&R	–	SL	R	S	S83L	–	F	117	–	AM, SXT, C, TE, STR
37	14	F&R	–	SL	R	R	S83L, D87N	–	A	2197	–	AM, SXT, C, TE, STR, GM
47	24	F&R	–	SL	R	R	S83L, D87N	–	A	10	10	AM, SXT, C, TE, STR
58	25	F&R	–	SL	R	R	S83L, D87N	–	A	744	–	AM, SXT, C, TE, STR, K
68	33	F&R	–	SL	R	R	S83L, D87N	–	A	2509	–	AM, TE, STR
69	33	F&R	–	SL	R	R	S83L, D87N	–	A	2509	–	AM, TE, STR
103	72	F&R	–	SL	R	R	S83L, D87N	–	A	10	10	AM, AMC, SXT, C, TE, STR, K
151	35	FF	–	SL	IR	S	–	qnrB	B1	1665	–	K
71	37	FF	–	SL	R	R	S83L, D87N	–	A	2509	–	TE, STR
121	42	FF	–	SL	R	S	S83L	–	B1	1157	–	AM, SXT, TE, STR
75	45	FF	–	SL	R	S	S83L	–	C	88	23	AM, SXT, STR
73	47	FF	–	SL	R	S	S83L	–	A	898	–	TE, STR
77	47	FF	–	SL	R	S	S83L	–	A	898	–	TE, STR
79	49	FF	–	SL	R	R	S83L, D87N	–	B1	297	–	SXT, TE, STR, K, GM
72	50	FF	–	SL	R	R	S83L, D87N	–	A	2509	–	TE, STR
170	50	FF	–	SL	IR	S	–	qnrB	B1	99	–	TE, STR
83	52	FF	–	SL	R	R	S83L, D87N	–	B1	297	–	TE
154	57	FF	–	SL	IR	S	–	qnrS	A	542	–	TE, STR, K
84	58	FF	–	SL	R	S	S83L	–	C	88	23	AM, SXT, STR, K
88	58	FF	–	SL	R	S	S83L	–	C	88	23	AM, SXT, STR, K
171	63	FF	–	SL	IR	S	–	qnrB	E	524	32	–
93	64	FF	–	SL	R	R	S83L, D87N	–	B1	453	86	AM, SXT, TE, STR
92	65	FF	–	SL	R	S	S83L	–	C	88	23	AM, SXT, STR, K
131	68	FF	–	SL	R	S	S83L	–	A	93	168	–
111	77	FF	–	SL	R	R	S83L, D87N	–	B1	1196	–	AM, SXT, C, TE, STR
134	77	FF	–	SL	R	S	S83L	–	A	10	10	AM, C, STR
159	8	M&G	–	SL	IR	S	–	qnrB	A	4429	–	STR
16	9	M&G	–	SL	R	R	S83L, D87N	–	A	10	10	AM, SXT, C, TE, STR
17	9	M&G	–	SL	R	R	S83L, D87N	–	C	410	23	TE
18	10	M&G	–	SL	R	S	S83L	–	A	6593	165	STR
142	10	M&G	–	SL	IR	S	–	qnrB	A	48	10	STR
110	78	M&G	–	SL	R	R	S83L, D87N	–	C	90	23	AM, SXT, TE, STR, GM

AM ampicillin, AMC amoxicillin with clavulanic acid, AZM azithromycin, C chloramphenicol, CC clonal complex, CIP ciprofloxacin, CTX cefotaxime, CZ cefazolin, D dust sample, F&R farrowing and rearing farm, FEP cefepime, FF fattening farm, FM nitrofurantoin, FOS fosfomycin, GM gentamicin, IR intermediately resistant, K kanamycin, M&G mating and gestation farm, NA nalidixic acid, new new combination of alleles (detailed in Additional file 1: Table A1); PG phylogenetic group, PMQR plasmid-mediated quinolone resistance, QRDR quinolone resistance-determining region, R resistant, S susceptible, STR streptomycin, SL slurry sample, SXT sulfamethoxazole/trimethoprim, ST sequence type, TE tetracycline, W wipe sample; +, use of fluoroquinolone during study period 2016; −, no use of fluoroquinolone during study period 2016; −–, absence of point mutation, gene, CC, or additional resistance

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