Identification and Characterization of Antibiotic Resistance Genes from a Multi-drug Resistant Escherichia coli C20 Isolated from Guts of Chicken
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摘要: 为揭示动物源大肠杆菌耐药性机制，追踪潜在的抗性基因传播机制及其来源，在先前公布的分离自鸡肠道的多抗耐药性菌株大肠杆菌Escherichia coli C20基因组基础上，对E.coli C20抗生素抗性基因种类、数量、来源及其耐药性机制进行分析。通过与已知的抗生素抗性基因数据库进行对比和注释，一共预测和注释了80个潜在的耐药性基因，包括与先前筛选的7种抗生素抗性对应的抗性基因。其中，喹诺酮类抗生素抗性基因位于C20基因组上，四环素、磺胺类、氯霉素、氨基糖苷类以及大环内酯类抗生素的抗性基因则位于C20环状质粒分子上。基因组聚类分析表明，菌株C20与大肠杆菌K-12菌株DH1、BW2952和MG1655亲缘关系较近，序列相似性97%~99%。3株K-12菌株基因组中没有发现与C20质粒类似的序列，表明C20菌株的抗性基因主要是通过质粒介导的水平基因转移方式从其他环境微生物中获得。Abstract: Spreading of antibiotic resistant bacteria in the environment has become a major concern for food safety and human health. Escherichia coli C20 was isolated from the gut microbiota of a domestic chicken that showed resistances to 7 out of 10 tested antibiotics. To elucidate the underlying mechanism, origin, and transmission of the resistances, published information on C20 genome were reviewed for a detailed analysis. There were 80 antibiotic resistance determinants, including the abovementioned 7 drugs, annotated in E. coli C20 genome from the databases. Among them, the fluoroquinolone-resistant genes were identified in the chromosomes, while those resistant to tetracycline, sulphonamide, chloramphenicol, and aminoglycoside found to be expressed in the plasmids of C20. A phylogenomic analysis on C20 revealed a clustering of the strain with E. coli K-12 group, especially the substrains of DH1, BW2952 and MG1655. Their genomic nucleoid sequences shared 97-99% homology. There was no plasmid pC20-like sequence found in the genomic sequences of 3 K-12 strains reported previously. It was proposed that E. coli C20 isolated from the chicken guts might have acquired the antibiotic resistance through plasmid transfer from environmental microbiome.
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Key words:
- chicken enteric bacteria /
- antibiotic resistance /
- drug resistance mechanism /
- genome /
- gene transfer
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图 1 鸡肠道大肠杆菌多抗菌株C20基因组系统进化树
Figure 1. Phylogenomic tree of C20 from chicken guts build by CVTree 3
表 1 大肠杆菌多抗菌株C20基因组中注释的抗生素抗性基因
Table 1. Antibiotic resistance genes annotated in multidrug resistant E. coli C20 genome
基因编号 基因型 抗生素抗性 不同抗性基因数据库基因相似性/% CARD ARDB Resfams ARG-ANNOT Res Finder C20_43 folP sulfonamide - 99.88 - - - C20_145 patA fluoroquinolone 99.86 - - - - C20_161 bacA bacitracin 99.76 99.76 - - - C20_183 tolC Multidrug Resistance Efflux 99.53 99.53 - - - C20_188 parE fluoroquinolones - 98.05 - - - C20_198 parC fluoroquinolones - 99.91 - - - C20_405 tuf elfamycin - 96.37 - - - C20_472 acrF Multidrug Resistance Efflux 99.55 99.55 - - - C20_473 acrE Multidrug Resistance Efflux 98.96 98.96 - - - C20_474 acrS Multidrug Resistance Efflux 99.85 99.85 - - - C20_608 mdtF Multidrug Resistance Efflux 99.87 99.87 - - - C20_609 mdtE Multidrug Resistance Efflux 100 100 - - - C20_610 mdtE Multidrug Resistance Efflux 100 100 - - - C20_756 PmrC polymyxin 99.94 99.94 - - - C20_757 pmrA polymyxin - 99.4 - - - C20_758 pmrB polymyxin 99.91 99.91 - - - C20_789 mdtN Multidrug Resistance Efflux 100 100 - - - C20_790 mdtO Multidrug Resistance Efflux 99.85 99.85 - - - C20_791 mdtP Multidrug Resistance Efflux 98.64 98.64 - - - C20_814 rpoB rifampicin - 99.93 - - - C20_901 tufB elfamycin - 96.55 - - - C20_1154 mdtL Multidrug Resistance Efflux 99.74 99.74 - - - C20_1164 gyrB fluoroquinolones - 99.92 - - - C20_1574 mdtM Multidrug Resistance Efflux 96.51 96.51 - - - C20_1674 PmrE 97.08 97.08 - - - C20_1817 mdtD Multidrug Resistance Efflux 99.93 99.93 - - - C20_1818 mdtC Multidrug Resistance Efflux 99.77 99.77 - - - C20_1819 mdtB Multidrug Resistance Efflux 99.84 99.84 - - - C20_1820 mdtA Multidrug Resistance Efflux 99.2 99.2 - - - C20_1878 emrE Multidrug Resistance Efflux 93.71 93.71 - - - C20_1954 acrA Multidrug Resistance Efflux 79.44 - - - - C20_1955 acrB 85.35 85.35 - - - C20_2316 mdtH Multidrug Resistance Efflux 99.09 - - - - C20_2329 mdtG Multidrug Resistance Efflux 99.92 - - - - C20_2316 mdtH Multiple Resistance locus - 99.09 - - C20_2329 mdtG Multiple Resistance locus - 99.92 - - C20_2454 ompF - 100 - - - C20_2469 msbA 99.94 - - - - C20_2505 MacB Multidrug Resistance Efflux - - - - - C20_2506 MacA Multidrug Resistance Efflux - - - - - C20_2543 mdfA 97.65 97.65 - - - C20_2994 marA Multiple Resistance locus 100 100 - - - C20_2995 marR Multiple Resistance locus - 98.39 - - C20_3228 mdtK Multidrug Resistance Efflux - 99.34 - - - C20_3348 omp36 - 93.83 - - - C20_3688 arnA 99.95 99.95 - - - C20_3689 PmrF 99.9 99.9 - - - C20_3714 gyrA fluoroquinolones - 99.62 - - - C20_3729 omp36 - 84.79 - - - C20_3822 emrK Multidrug Resistance Efflux 99.91 99.91 - - - C20_3823 emrY Multidrug Resistance Efflux 99.81 99.87 - - - C20_3991 acrD Multidrug Resistance Efflux 99.61 99.61 - - - C20_4298 aminocoumarin 100 - - - C20_4299 aminocoumarin 99.72 - - - C20_4305 emrB Multidrug Resistance Efflux 100 100 - - - C20_4306 emrA Multidrug Resistance Efflux 98.18 98.18 - - - C20_4307 emrA Multidrug Resistance Efflux 100 100 - - - pC20_90 tetA tetracycline - - - - - pC20_298 CatB4 Phenicol resistance - - - 98.18 - pC20_300 bleO bleomycin resistance - 100 - - - pC20_301 bleO bleomycin resistance - 100 - - - pC20_302 CatB4 Phenicol resistance - - - 100 - pC20_306 sul1 Sulphonamide resistance 100 100 - 100 100 pC20_309 CatB4 Phenicol resistance - - - 100 - pC20_311 DfrA12 Trimethoprim resistance 100 100 - 100 100 pC20_312 Aac3-Ib Spectinomycin/Streptomycin 98.68 98.68 - 100 95.36 pC20_313 aac(6')-Ib' Aminoglycoside resistance 100 100 - - 100 pC20_314 CatB4 Phenicol resistance - 100 - pC20_315 aphA1-IAB Aminoglycoside resistance 99.26 99.26 98.89 99.51 99.63 pC20_316 CatB4 Phenicol resistance - - - 98.18 - pC20_321 sul3 Sulphonamide resistance 100 100 - 100 100 pC20_323 qacH/emee Aminoglycoside resistance 91.59 - - - pC20_324 aadA1 Spectinomycin/Streptomycin 99.75 100 100 99.87 100 pC20_325 cmlA1 Phenicol resistance - 100 - 99.92 99.92 pC20_326 aadA2 Spectinomycin resistance 100 100 100 100 100 pC20_328 aadA3 Spectinomycin/Streptomycin 99.29 99.29 45.16 100 96.43 pC20_329 aadA3 Aminoglycoside resistance 100 100 - - 100 pC20_340 sul2 Sulphonamide resistance 100 100 - 100 100 pC20_347 APH(4)-Ia Aminoglycoside resistance 100 100 - 100 100 pC20_349 AAC(3)-IV Aminoglycoside resistance 100 99.87 99.61 99.87 99.87 
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表 2 E. coli C20亲缘关系较近的3个不同K-12亚种注释抗生素抗性基因家族
Table 2. Antibiotic resistance genes identified in genomes of 3 E. coli K-12 strains
E. coli K-12亚种 磺胺类 氯霉素 四环素 喹诺酮 MDR 其他 E. coli C20 1 0 0 4 30 22 pC20 plasmid 3 6 1 0 - 13 E. coli BW2952 0 0 0 2 11 8 E. coli DH1 0 0 0 3 12 11 E. coli MG1655 1 0 0 2 16 22
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