Rapid rise of the ESBL and mcr-1 genes in Escherichia coli of chicken origin in China, 2008–2014

Figures & data

No. of strains, ESBL-EC strains and ESBL-EC positive rates across different provinces from 2008 to 2014

Year	Province			Total
	Guangdong	Shanghai	Shanxi	Sichuan	Shandong
2008	22^a(4^b,18.2^c)	12(2,16.7)	–	58(15, 25.9)	13(4, 30.8)	105^d(25^e, 23.8^f)
2009	23(5, 21.7)	45(11, 24.4)	25(6, 24.0)	27(7, 25.9)	20(7,35)	140(36, 25.7)
2010	23(8, 34.8)	20(8, 40)	12(4, 33.3)	34(15, 44.1)	13(7, 53.8)	102(42, 41.2)
2011	22(9, 40.9)	18(8, 44.4)	39(15, 38.5)	28(14, 50.0)	20(11, 55.0)	127(57, 44.9)
2012	25(11,44.0)	20(9, 45.0)	25(11, 44.0)	23(12, 54.5)	22(14, 56.5)	115(57, 49.6)
2013	25(12, 48.0)	20(9, 45.0)	25(9, 36.0)	28(16, 57.1)	20(13, 65.0)	118(59, 50.0)
2014	36(19, 52.8)	30(16, 53.3)	–	28(16, 57.1)	20(14, 70.0)	114(65, 57.0)
Total	176^g	165	126	226	128	821(341)

^a Number of strains

^b Number of positive strains

^c ESBL-EC positive rate

^{d, g} Total number of strains

^e Total number of positive strains

^f Total positive rate of ESBL-EC

Fig. 1 Positive rate of ESBL and polymyxin E resistance from 2008 to 2014

Fig. 2 Positive rate of ESBL-EC in five broiler production regions of China from 2008 to 2014

Elevated multiple drug resistance rate in the E. coli of chicken origin from 2008 to 2014

Antibiotics	Species	Drug resistance rate by year (%)
		2008	2009	2010	2011	2012	2013	2014
GEN	ESBL^+	52.9	54.8	63.0	65.7	72.2	76.04	77.8
	ESBL^−	41.9	42.3	48.7	50.3	52.9	56.7	56.9
DOX	ESBL^+	100	100	100	100	100	100	100
	ESBL^−	67.6	71.4	74.1	78.9	83.3	85.3	88.9
FFC	ESBL^+	67.6	71.4	74.1	78.9	83.3	85.3	88.9
	ESBL^−	50.3	51.4	53.3	53.4	54.9	56.1	58.4
NAL	ESBL^+	100	100	100	100	100	100	100
	ESBL^−	93.9	98.6	98.7	100	100	100	100
CIP	ESBL^+	52.9	59.2	75.9	80.3	81.9	84.0	86.4
	ESBL^−	43.6	45.0	45.3	47.1	46.4	48.4	52.6
P E	ESBL^+	0.0	2.0	5.6	5.6	6.9	8.0	8.6
	ESBL^−	0.0	0.0	1.3	1.9	2.1	2.6	2.9
SXT	ESBL^+	88.2	96.0	98.1	100	100	100	100
	ESBL^−	57.0	60.5	68.0	68.3	71.2	73.2	75.9

GEN gentamicin, DOX doxycycline, FFC florfenicol, NAL nalidixic acid, CIP ciprofloxacin, PE polymyxin E, SXT compound sulfamethoxazole

Fig. 3 Multiple drug resistance rate between ESBL-EC and non-ESBL-EC

Fig. 4 The distribution of CTX-M types of ESBL-EC.

a The distribution of CTX-M types of ESBL-EC of chicken origin in China. b The distribution of CTX-M types of ESBL-EC from the NCBI whole-genome sequencing database

The information regarding mcr-1 positive E. coli and mcr-1–carrying plasmids

E. coli Isolate ID	BioSample ID	Year	Area	MLST Type	Plasmid Inc type	mcr-1 contig size (bp)	No. of contigs
R02	SAMN07983251	2011	Chongqing	10	−	2943	74
R24	SAMN07983271	2011	Sichuan	10	IncI2	60,207	28
R46	SAMN07983287	2010	Shanghai	10	IncI2	61,831	21
R26	SAMN07983273	2013	Shanghai	29	IncI2	60,873	31
R37	SAMN07983280	2010	Guangzhou	29	IncI2	60,955	32
R95	SAMN07983324	2013	Shanghai	29	IncI2	60,178	34
R10	SAMN07983257	2013	Shanghai	46	IncI2	59,879	27
R12	SAMN07983261	2012	Shanghai	46	IncI2	61,943	25
R13	SAMN07983262	2013	Shanghai	46	IncI2	62,380	25
R19	SAMN07983267	2013	Shanghai	46	IncI2	61,022	27
R35	SAMN07983279	2012	Shanghai	46	–	11,027	84
R40	SAMN07983283	2012	Shanghai	46	IncI2	58,887	29
R53	SAMN07983292	2013	Shanghai	46	IncI2	63,724	26
R56	SAMN07983295	2012	Shanghai	46	IncI2	60,445	28
R64	SAMN07983303	2010	Shanghai	46	IncI2	61,022	27
R34	SAMN07983278	2011	Chongqing	48	IncI2	60,203	32
R59	SAMN07983298	2012	Guangzhou	93	–	2863	164
R61	SAMN07983300	2013	Shandong	93	IncI2	60,872	27
R14	SAMN07983263	2014	Sichuan	101	IncI2	60,872	35
R28	SAMN07983275	2011	Guangzhou	101	IncI2	60,872	34
R41	SAMN07983284	2012	Sichuan	101	IncHI2A + IncHI2 + IncI2	257,133	6
R44	SAMN07983286	2014	Shandong	156	IncI2	58,932	28
R47	SAMN07983288	2014	Sichuan	165	IncI2	62,807	26
R07	SAMN07983254	2011	Shanghai	354	IncI2	59,541	28
R48	SAMN07983289	2011	Shanghai	354	–	9910	65
R51	SAMN07983291	2011	Shanghai	354	–	20,901	46
R75	SAMN07983308	2011	Shanghai	354	IncI2	59,294	29
R09	SAMN07983256	2009	Guangzhou	533	−	11,573	43
R57	SAMN07983296	2009	Guangzhou	533	−	11,525	45
R74	SAMN07983307	2009	Guangzhou	533	−	11,022	44
R25	SAMN07983272	2013	Shanghai	542	−	2943	94
R39	SAMN07983282	2013	Shanghai	542	−	2943	90
R38	SAMN07983281	2014	Shandong	617	IncI2	61,088	25
R27	SAMN07983274	2014	Shandong	648	IncI2	60,752	24
R01	SAMN07983250	2012	Unknown	1286	IncI2	61,068	27
R134	SAMN08180604	2012	Shanghai	1286	–	11,029	49
R62	SAMN07983301	2014	Sichuan	1286	IncI2	64,482	29
R78	SAMN07983311	2012	Shanghai	1286	–	12,112	45
R86	SAMN07983317	2012	Shanghai	1286	IncI2	61,931	27
R96	SAMN07983325	2012	Shanghai	1286	–	10,915	48
R50	SAMN07983290	2010	Shanghai	1564	–	2946	82
R58	SAMN07983297	2012	Shanghai	1589	IncI2	62,044	29
R31	SAMN07983276	2012	Sichuan	3014	IncI2	60,874	27
R32	SAMN08238410	2014	Shandong	5229	–	4631	67

Fig. 5 The phylogenetic tree of ESBL-EC carrying both bla_CTX-M-55 and mcr-1. * Red, ESBL-EC from China; Green, ESBL-EC from Vietnam; Blue, ESBL-EC from Germany