赛鸽源大肠杆菌耐药性检测及多重耐药菌株的全基因组测序分析

doi:10.11843/j.issn.0366-6964.2025.05.034

Abstract

Abstract:

There is widespread misuse of antibiotics in pigeon breeding, leading to an increase in antibiotic-resistant strains and exacerbating multidrug resistance. The present study aimed to understand the prevalence of antibiotic resistance and resistance genes in Escherichia coli sourced from racing pigeons in Tongliao City, and to provide reference information for clinical treatment of E. coli infections in racing pigeons. Using E. coli selective culture media and methods such as 16S rRNA sequencing, pathogenic bacteria from diarrheic racing pigeons in Tongliao were isolated and purified. Drug susceptibility testing and PCR detection of resistance genes were conducted to assess the resistance profiles and distribution of resistance genes in the isolated strains. Whole genome sequencing analysis was performed on two highly resistant E. coli strains. Eight strains of E.coli sourced from racing pigeons were isolated, and all of them exhibiting multidrug resistance. The resistance rates to kanamycin and streptomycin were both 100%, while all strains were sensitive to ceftriaxone-sulbactam. Strains E-ge1 and E-ge2 showed severe resistance profiles. Whole genome sequencing analysis of these two strains revealed complete genome sequences, with lengths of 4 680 817 bp and 4 691 799 bp respectively. They encoded 4 888 and 5 070 genes respectively, and both strains carried three plasmids.E-ge1 carries a total of 81 antibiotic resistance genes, whereas E-ge2 harbors 74 such genes. The situation of antibiotic resistance in E.coli sourced from racing pigeons in Tongliao is severe, with strains carrying a large number of resistance genes. It is imperative to optimize treatment strategies to control the exacerbation of resistance and the spread of resistance genes.

Key words: racing pigeons, Escherichia coli, antibiotic resistance, resistance genes, whole-genome sequencing

CLC Number:

S852.612

SHI Jinchuan, SUN Miao, MENG Linghao, WANG Yongqiang, GENG Chao, QI Chaolumeng, CHEN Hengli, WANG Zi, LIU Kai. Detection of Antibiotic Resistance in Escherichia coli Strains Sourced from Racing Pigeons and Whole-genome Sequencing Analysis of Multidrug-resistant Strains[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(5): 2372-2382.

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References 28

1	LAXMINARAYAN R , SRIDHAR D , BLASER M , et al. Achieving global targets for antimicrobial resistance[J]. Science, 2016, 353 (6302): 874- 875. doi: 10.1126/science.aaf9286
2	陈霞. 猪源大肠杆菌五种毒力因子单重及多重荧光定量PCR方法的建立及初步应用[D]. 武汉: 华中农业大学, 2022.
	CHEN Xia. Establishment and preliminary application of single and multiplex qPCR methods for detection of five virulence factors of porcine E. coli[D]. Wuhan: Huazhong Agricultural University, 2022. (in Chinese)
3	WANG A Q , HU C M . Antimicrobial resistance analysis of Escherichia coli isolated from pigeons in Qingdao, Shandong Province, China[J]. Genes (Basel), 2022, 13 (9): 1510. doi: 10.3390/genes13091510
4	VON TÖNNEMANN PILATI G , CADAMURO R D , FILHO V B , et al. Bacteriophage-associated antimicrobial resistance genes in avian pathogenic Escherichia coli isolated from Brazilian poultry[J]. Viruses, 2023, 15 (7): 1485. doi: 10.3390/v15071485
5	ABERKANE C , MESSAÏ A , MESSAÏ C R , et al. Antimicrobial resistance pattern of avian pathogenic Escherichia coli with detection of extended-spectrum β-lactamase-producing isolates in broilers in east Algeria[J]. Vet World, 2023, 16 (3): 449- 454.
6	GHANBARPOUR R , AFLATOONIAN M R , ASKARI A , et al. Domestic and game pigeons as reservoirs for Escherichia coli harbouring antimicrobial resistance genes[J]. J Glob Antimicrob Resist, 2020, 22, 571- 577. doi: 10.1016/j.jgar.2020.02.015
7	CHROBAK-CHMIEL D , KWIECIE? E , GOLKE A , et al. Pigeons as carriers of clinically relevant multidrug-resistant pathogens-a clinical case report and literature review[J]. Front Vet Sci, 2021, 8, 664226. doi: 10.3389/fvets.2021.664226
8	LUO S S , LIAO C Y , PENG J J , et al. Resistance and virulence gene analysis and molecular typing of Escherichia coli from duck farms in Zhanjiang, China[J]. Front Cell Infect Microbiol, 2023, 13, 1202013. doi: 10.3389/fcimb.2023.1202013
9	王梓, 孙淼, 王永强, 等. 通辽部分地区鸭源大肠杆菌耐药性检测及多重耐药菌株YA-1全基因组测序分析[J]. 中国畜牧兽医, 2024, 51 (6): 2585- 2596.
	WANG Z , SUN M , WANG Y Q , et al. Detection of drug resistance of Escherichia coli from ducks in some areas of Tongliao and whole genome sequencing analysis of multi-drug resistant strain YA-1[J]. China Animal Husbandry & Veterinary Medicine, 2024, 51 (6): 2585- 2596.
10	王永强, 李偲, 耿超, 等. 通辽地区犊牛腹泻大肠杆菌耐药性检测及一株多重耐药菌全基因组测序分析[J]. 微生物学通报, 2022, 49 (12): 4964- 4977.
	WANG Y Q , LI C , GENG C , et al. Drug resistance of Escherichia coli strains causing calf diarrhea in Tongliao and whole-genome sequencing of a multi-drug resistant strain[J]. Microbiology China, 2022, 49 (12): 4964- 4977.
11	HUMPHRIES R , BOBENCHIK A M , HINDLER J A , et al. Overview of changes to the clinical and laboratory standards institute performance standards for antimicrobial susceptibility testing, M100, 31st edition[J]. J Clin Microbiol, 2021, 59 (12): e0021321. doi: 10.1128/JCM.00213-21
12	郭双. 通辽地区犊牛腹泻大肠杆菌耐药性检测及一株多重耐药菌株全基因组测序分析[D]. 通辽: 内蒙古民族大学, 2022.
	GUO S. Detection of drug resistance of Escherichia coli in calves with diarrhea in Tongliao region and whole genome sequencing analysis of a multi-drug resistant strain[D]. Tongliao: Inner Mongolia Minzu University, 2022. (in Chinese)
13	KOREN S , WALENZ B P , BERLIN K , et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation[J]. Genome Res, 2017, 27 (5): 722- 736. doi: 10.1101/gr.215087.116
14	HYATT D , CHEN G L , LOCASCIO P F , et al. Prodigal: prokaryotic gene recognition and translation initiation site identification[J]. BMC Bioinf, 2010, 11 (1): 119. doi: 10.1186/1471-2105-11-119
15	BERTELLI C, BRINKMAN F S L. Improved genomic island predictions with IslandPath-DIMOB[J]. Bioinformatics, 34(13): 2161-2167.
16	FU L M , NIU B F , ZHU Z W , et al. CD-HIT: accelerated for clustering the next-generation sequencing data[J]. Bioinformatics, 2012, 28 (23): 3150- 3152. doi: 10.1093/bioinformatics/bts565
17	ASHBURNER M , BALL C A , BLAKE J A , et al. Gene ontology: tool for the unification of biology[J]. Nat Genet, 2000, 25 (1): 25- 29. doi: 10.1038/75556
18	KANEHISA M , GOTO S , KAWASHIMA S , et al. The KEGG resource for deciphering the genome[J]. Nucleic Acids Res, 2004, 32 (S1): D277- D280.
19	JIA B F , RAPHENYA A R , ALCOCK B , et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database[J]. Nucleic Acids Res, 2017, 45 (D1): D566- D573. doi: 10.1093/nar/gkw1004
20	AFAYIBO D J A , ZHU H , ZHANG B B , et al. Isolation, molecular characterization, and antibiotic resistance of avian pathogenic Escherichia coli in eastern China[J]. Vet Sci, 2022, 9 (7): 319. doi: 10.3390/vetsci9070319
21	ALCOCK B P , RAPHENYA A R , LAU T T Y , et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database[J]. Nucleic Acids Res, 2020, 48 (D1): D517- D525.
22	刘安娜. 成都赛鸽源大肠埃希菌和肠球菌分离鉴定及对常用抗生素的耐药性分析[D]. 成都: 西南民族大学, 2022.
	LIU A N. Isolation and identification of Escherichia coli and enterococcus faecalis from pigeons in Chengdu and analysis of their resistance to common antibiotics[D]. Chengdu: Southwest Minzu University, 2022. (in Chinese)
23	杨文仪, 肖家伟, 雷连成, 等. 鸽源大肠杆菌O157: 非H7菌株的致病性和耐药性分析[J]. 中国农业大学学报, 2023, 28 (6): 169- 182.
	YANG W Y , XIAO J W , LEI L C , et al. Pathogenicity and drug resistance isolation, identification and biological characteristics of pigeon derived Escherichia coli O157: non H7 strain[J]. Journal of China Agricultural University, 2023, 28 (6): 169- 182.
24	吕敏娜, 孙铭飞, 沈浩铎. 2011~2018年广东鸽源大肠杆菌、沙门氏菌耐药性分析[J]. 畜牧兽医科技信息, 2019 (12): 46- 48.
	LÜ M N , SUN M F , SHEN H D . Analysis of drug resistance of Escherichia coli and Salmonella from pigeon in Guangdong Province from 2011 to 2018[J]. Chinese Journal of Animal Husbandry and Veterinary Medicine, 2019 (12): 46- 48.
25	CAPITA R , CORDERO J , MOLINA-GONZÁLEZ D , et al. Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of Escherichia coli isolates from pigeon meat[J]. Antibiotics (Basel), 2019, 8 (4): 259. doi: 10.3390/antibiotics8040259
26	GAUBA A , RAHMAN K M . Evaluation of antibiotic resistance mechanisms in gram-negative bacteria[J]. Antibiotics (Basel), 2023, 12 (11): 1590. doi: 10.3390/antibiotics12111590
27	MUKERJI S , GUNASEKERA S , DUNLOP J N , et al. Implications of foraging and interspecies interactions of birds for carriage of Escherichia coli strains resistant to critically important antimicrobials[J]. Appl Environ Microbiol, 2020, 86 (20): e01610- 20.
28	BUJŇÁKOVÁ D , KOCÚREKOVÁ T , KARAHUTOVÁ L . Distribution of virulence-associated genes, antibiotic resistance and phylogenetic groups in Escherichia coli isolated from domestic and racing pigeons[J]. Vet Res Commun, 2023, 47 (3): 1697- 1705. doi: 10.1007/s11259-023-10126-w

目的基因	引物序列(5'→3')	扩增长度/bp
Target gene	Primer sequence	Amplification length
16S rRNA	F: AGAGTTTGATCCTGGCTCAG R: GGTTACCTTGTTACGACTT	1 369
strA	F: ATCGCAGATAGAAGGCAAGGC R: AACTGGCAGGAGGAACAGGA	574
qnrB	F: GATCGTGAAAGCCAGAAAGG R: ACGATGCCTGGTAGTTGTCC	469
tetA	F: GCTACATCCTGCTTGCCTTC R: CATAGATCGCCGTGAAGAGG	210
TEM-1	F: TTTTCGTGTCGCCCTTAT R: GCTCGTCGTTTGGTATGG	512
qnrS	F: ACGACATTCGTCAACTGCAA R: TAAATTGGCACCCTGTAGGC	417
strB	F: GCGTTGCTCCTCTTCTCCAT R: ACCTTTTCCAGCCTCGTTTG	723
bla-CTX	F: CGCTTTGCGATGTGCAG R: ACCGCGATATCGTTGGT	550
qnrD	F: TTTTCGCTAACTAACTCGC R: GAAAGGATAAACAGGCAAAT	984
CTXM-55	F: GCTGGGTAAAGCATTGGG R: TAGGTTGAGGCTGGGTGA	224
AAC(3)-Ⅱa	F: TCACGAACTCGGTCACGC R: CCAAGCATCGGCATCTCA	177
qnrC	F: ATTTCTCACAGGCAAACT R: CTGGAATAACAATCACCC	666
tetR	F: AACAACCCGTAAACTCGC R: GGTGCCTATCTAACATCTCAAT	116
floR	F: CTGAACACGACGCCCGCTAT R: GGACCGCTCCGCAAACAA	751

抗生素 Antibiotic	菌株编号Strain No.								耐药率/% Resistance rate
抗生素 Antibiotic	E-ge1	E-ge2	E-ge3	E-ge4	E-ge5	E-ge6	E-ge7	E-ge8	耐药率/% Resistance rate
恩诺沙星	R(0)	R(0)	R(8)	R(9)	I(13)	I(10)	S(18)	S(26)	50(4/8)
氧氟沙星	R(0)	R(0)	R(0)	R(0)	I(11)	I(12)	I(12)	S(29)	50(4/8)
环丙沙星	R(0)	R(0)	I(11)	I(12)	I(12)	I(12)	I(13)	S(21)	25(2/8)
多黏菌素B	S(16)	R(0)	S(13)	S(12)	S(11)	S(10)	S(11)	S(11)	12.5(1/8)
卡那霉素	R(0)	R(0)	R(0)	R(0)	R(7)	R(0)	R(9)	R(7)	100(8/8)
庆大霉素	R(0)	R(0)	R(0)	R(0)	I(10)	I(10)	I(10)	R(8)	62.5(5/8)
大观霉素	R(0)	R(0)	R(0)	R(9)	I(11)	I(11)	R(7)	I(12)	62.5(5/8)
强力霉素	I(12)	R(0)	I(10)	I(13)	I(10)	R(9)	I(10)	S(18)	25(2/8)
链霉素	R(0)	R(0)	R(9)	R(7)	R(9)	R(8)	R(7)	R(9)	100(8/8)
氯霉素	R(0)	R(0)	R(0)	R(0)	R(0)	R(0)	S(18)	S(20)	75(6/8)
氟苯尼考	R(8)	R(0)	R(0)	R(0)	R(0)	R(0)	S(21)	S(21)	75(6/8)
头孢哌酮/舒巴坦	S(20)	S(17)	S(16)	S(15)	S(23)	S(21)	S(17)	S(19)	0(0/8)
头孢噻肟	R(8)	R(0)	R(0)	R(8)	S(24)	S(22)	S(23)	S(23)	50(4/8)

耐药基因种类	耐药基因	检出率/%
Types of resistance genes	Drug resistance gene	Detection rate
喹诺酮类Quinolones	qnrS	100(8/8)
	qnrB	0(0/8)
	qnrC	0(0/8)
	qnrD	0(0/8)
氯霉素类Chloramphenicols	floR	75(6/8)
四环素类Tetracyclines	tetA	100(8/8)
	tetR	100(8/8)
氨基糖苷类Aminoglycosides	strA	100(8/8)
	strB	100(8/8)
	AAC(3)-Ⅱa	0(0/8)
β-内酰胺类Beta-lactams	Bla-CTX	100(8/8)
	TEM-1	100(8/8)
	CTX-M-55	62.5(5/8)

菌株	基因岛	位置	基因位点	长度/bp
Strains	Genomic-island	Location	Position	Length
E-ge1	Genomic-island-1	染色体(Chromosome)	125575-129913	4 339
E-ge1	Genomic-island-2	染色体(Chromosome)	243652-260821	17 170
E-ge1	Genomic-island-3	染色体(Chromosome)	1138400-1160866	22 467
E-ge1	Genomic-island-4	染色体(Chromosome)	1184477-1189130	4 654
E-ge2	Genomic-island-1	染色体(Chromosome)	408991-427656	18 666
E-ge2	Genomic-island-2	染色体(Chromosome)	908091-929910	21 820
E-ge2	Genomic-island-3	染色体(Chromosome)	1135002-1143203	8 202
E-ge2	Genomic-island-4	染色体(Chromosome)	1857146-1877628	20 483

菌株	质粒	耐药基因
Strains	plasmids	Drug resistance genes
E-ge1	pE-ge1-1	floR、tet(C)、APH(6)-Id、APH(3″)-Ib、sul2、APH(3')-Ⅱa、vgaC、TEM-1、rmtB、TEM-2、 CTX-M-55、APH(3″)-Ib、sul2、APH(3')-Ⅱa、vgaC、TEM-1、rmtB、TEM-2、CTX-M-55
	pE-ge1-2	aadA23、aadA23
	pE-ge1-3	TEM-1、AAC(3)-Ⅱa、tet(C)
E-ge2	pE-ge2-1	aadA23
	pE-ge2-2	TLA-2
	pE-ge2-3	floR、tet(C)、APH(6)-Id、APH(3″)-Ib、sul2、APH(3')-Ⅱa、vgaC、TEM-1、rmtB、TEM-2、 CTX-M-55

Detection of Antibiotic Resistance in Escherichia coli Strains Sourced from Racing Pigeons and Whole-genome Sequencing Analysis of Multidrug-resistant Strains

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