摘要
      缺乏关于包括尼日利亚家禽在内的大多数食品生产动物中耐药细菌基因组多样性的信息，导致危害特征不佳，缺乏保障公众健康的关键控制点。因此，本研究使用全基因组测序（WGS）来评估抗生素抗性基因、移动遗传元件、毒力基因和噬菌体在扩展谱β-内酰胺酶产生大肠杆菌（ESBL–大肠杆菌）分离株中的存在和多样性，这些分离株是通过2017年在尼日利亚伊洛林的EURL指南从家禽中获得的。家禽中ESBL–大肠杆菌的患病率为10.5%（n=37/354）。表型抗生素敏感性测试表明，所有ESBL-大肠杆菌分离株均具有多药耐药性。对11个有意选择的分离株的WGS原始读取数据的计算机分析显示，这些分离株具有广泛的ARG，这些ARG对β-内酰胺类抗生素和其他8类抗生素（氟喹诺酮类、叶理途径拮抗剂、氨基糖苷类、氯霉素、四环素、环氧化物、大环内酯类和利福霉素）产生耐药性。除了在两个分离株中检测到质粒介导的喹诺酮类耐药性（PMQR）外，所有ARG都在细菌染色体中。两个分离株携带gyrAp.S83L突变，该突变赋予对某些氟喹诺酮类药物的耐药性。移动体由几个Col质粒组成，主要的IncF质粒属于IncF64:A-：B27序列型。病毒群由具有粘附素、铁获取基因、毒素和保护素功能的基因组成。在11个分离株中的8个中发现了完整的噬菌体，噬菌体组由四个病毒家族的代表组成：肌病毒科（62.5%，n=5/8）、细胞病毒科（37.5%，n=3/8）、猪病毒科（12.5%，n=1）和足病毒科（12.5%，n=1/8）。ESBL-大肠杆菌分离株携带1-5个完整的噬菌体，在任何噬菌体上都没有发现ARG。尽管其中5个分离株属于门群A，但由于它们属于不同的血清型和序列类型，因此分离株是多样的。我们的研究结果表明，在尼日利亚伊洛林，家禽来源的ESBL-大肠杆菌具有高度的基因组多样性。这些不同的分离株携带临床相关的ARGs、移动元件、毒力基因和噬菌体，这些可能对人类健康具有有害的人畜共患潜力。
Abstract
The paucity of information on the genomic diversity of drug-resistant bacteria in most food-producing animals, including poultry in Nigeria, has led to poor hazard characterization and the lack of critical control points to safeguard public health. Hence, this study used whole genome sequencing (WGS) to assess the presence and the diversity of antibiotic resistance genes, mobile genetic elements, virulence genes, and phages in Extended Spectrum Beta Lactamase producing Escherichia coli (ESBL – E. coli) isolates obtained from poultry via the EURL guideline of 2017 in Ilorin, Nigeria. The prevalence of ESBL – E. coli in poultry was 10.5 % (n = 37/354). The phenotypic antibiotic susceptibility testing showed that all the ESBL— E. coli isolates were multi-drug resistant (MDR). The in-silico analysis of the WGS raw-read data from 11 purposively selected isolates showed that the isolates had a wide array of ARGs that conferred resistance to beta-lactam antibiotics, and 8 other classes of antibiotics (fluoroquinolones, foliate pathway antagonists, aminoglycoside, phenicol, tetracycline, epoxide, macrolides, and rifamycin). All the ARGs were in the bacterial chromosome except in two isolates where plasmid-mediated quinolone resistance (PMQR) was detected. Two isolates carried the gyrAp.S83L mutation which confers resistance to certain fluoroquinolones. The mobilome consisted of several Col-plasmids and the predominant IncF plasmids belonged to the IncF64:A-:B27 sequence type. The virulome consisted of genes that function as adhesins, iron acquisition genes, toxins, and protectins. Intact phages were found in 8 of the 11 isolates and the phageome consisted of representatives of four families of viruses: Myoviridae (62.5 %, n = 5/8), Siphoviridae (37.5 %, n = 3/8), Inoviridae (12.5 %, n = 1), and Podoviridae (12.5 %, n = 1/8). ESBL - E. coli isolates harboured 1–5 intact phages and no ARGs were identified on any of the phages. Although five of the isolates belonged to phylogroup A, the isolates were diverse as they belonged to different serotype and sequence types. Our findings demonstrate the high genomic diversity of ESBL - E. coli of poultry origin in Ilorin, Nigeria. These diverse isolates harbor clinically relevant ARGs, mobile elements, virulence genes, and phages that may have detrimental zoonotic potentials on human health.

https://www.sciencedirect.com/science/article/pii/S0168160523000028