受污染的湖水和鱼类可能是公共卫生关注的细菌病原体的来源,包括致病性大肠杆菌。在埃塞俄比亚境内,具体来说,奥罗米亚中部,生鱼消费是一种常见的做法。尽管很少有关于供人类食用的鱼类和五岁以下儿童中大肠杆菌O157的报道,关于大肠杆菌O157和其他山梨糖醇非发酵(SN-F)大肠杆菌从水到鱼到人的传播途径的信息,和他们的毒力因子和抗生素耐药性决定因素沿着鱼类供应链是缺乏。该研究旨在调查发生情况,分子特征,和大肠杆菌O157和其他SN-F大肠杆菌菌株在鱼类中的抗菌敏感性,奥罗米亚中部的湖水和人类,埃塞俄比亚。共750个样本(450个鱼类样本,150个水样,从五个湖泊和三个卫生设施收集了150个人类粪便样本)。按照欧洲食品安全局推荐的标准方案和用于检测细菌的Kirby-Bauer圆盘扩散方法处理样品。和抗菌药物敏感性试验,分别。使用全基因组测序(WGS)进行血清分型,毒力因子的测定,抗菌素抗性性状,和分离物的遗传连锁。总的来说,3.9%(29/750)的样品有SN-F大肠杆菌;其中6.7%(n=10),从水中提取1.8%(n=8)和7.3%(n=11),鱼,和腹泻的人类患者,分别。WGS证实所有的分离物是SN-F非O157:H7大肠杆菌菌株。我们报道了来自鱼和人样品的两种新的具有未知O-抗原的大肠杆菌菌株。所有菌株都具有多个毒力因子和编码它们的一个或多个基因。在来自相同来源的菌株中观察到遗传相关性(水,鱼,和人类)。大多数分离株对氨苄青霉素耐药(100%),四环素(100%),头孢噻肟(100%),头孢他啶(100%),美罗培南(100%),萘啶酸(93.1%)和磺胺甲恶唑/甲氧苄啶(79.3%)。大多数菌株对氯霉素(58.6%)和环丙沙星(48.3%)耐药,而一小部分对阿奇霉素表现出耐药性(3.45%)。分离物具有87.5%的总体MDR谱。多数,(62.1%;n=18)的菌株获得了MDR性状。还检测到编码突变抗性和超广谱β-内酰胺酶(ESBL)的基因。总之,我们的研究揭示了水中毒性和MDRSN-F大肠杆菌菌株的发生,鱼,和人类。尽管在各种来源的菌株中没有观察到遗传相关性,来自相同来源的菌株之间的基因组聚类强烈表明,如果没有严格的卫生鱼类生产,则在人-鱼-环境界面沿供应链传播的潜在风险。对具有未知O抗原的新菌株的进一步强大的遗传研究,和SN-F大肠杆菌的流行病学需要阐明病原体的分子谱和公共卫生影响。
Contaminated lake water and fish can be sources of bacterial pathogens of public health concern, including pathogenic E. coli. Within Ethiopia, specifically, Central Oromia, raw fish consumption is a common practice. Although there are few reports on occurrence of E. coli O157 in fish destined for human consumption and children under five years, information on the transmission pathways of E. coli O157 and other sorbitol non-fermenting (SN-F) E. coli from water-to-fish-to-human, and their virulence factors and antimicrobial resistant determinants along the fish supply chain is lacking. The study aimed to investigate the occurrence, molecular characteristics, and antimicrobial susceptibility of E. coli O157 and other SN-F E. coli strains in fish, lake water and humans in central Oromia, Ethiopia. A total of 750 samples (450 fish samples, 150 water samples, 150 human stool samples) were collected from five lakes and three health facilities. The samples were processed following the standard protocol recommended by European Food Safety Authority and Kirby-Bauer disc diffusion method for detection of the bacteria, and antimicrobial susceptibility tests, respectively. Molecular characterization of presumptive isolates was performed using Whole-Genome Sequencing (WGS) for serotyping, determination of virulence factors, antimicrobial resistance traits, and genetic linkage of the isolates. Overall, 3.9% (29/750) of the samples had SN-F E. coli; of which 6.7% (n = 10), 1.8% (n = 8) and 7.3% (n = 11) were retrieved from water, fish, and diarrheic human patients, respectively. The WGS confirmed that all the isolates were SN-F non-O157: H7 E. coli strains. We reported two new E. coli strains with unknown O-antigen from fish and human samples. All the strains have multiple virulence factors and one or more genes encoding for them. Genetic relatedness was observed among strains from the same sources (water, fish, and humans). Most isolates were resistant to ampicillin (100%), tetracycline (100%), cefotaxime (100%), ceftazidime (100%), meropenem (100%), nalidixic acid (93.1%) and sulfamethoxazole/trimethoprim (79.3%). Majority of the strains were resistant to chloramphenicol (58.6%) and ciprofloxacin (48.3%), while small fraction showed resistance to azithromycin (3.45%). Isolates had an overall MDR profile of 87.5%. Majority, (62.1%; n = 18) of the strains had acquired MDR traits. Genes encoding for mutational resistance and Extended-spectrum beta-lactamases (ESBL) were also detected. In conclusion, our study revealed the occurrence of virulent and MDR SN-F E. coli strains in water, fish, and humans. Although no genetic relatedness was observed among strains from various sources, the genomic clustering among strains from the same sources strongly suggests the potential risk of transmission along the supply chain at the human-fish-environment interface if strict hygienic fish production is not in place. Further robust genetic study of the new strains with unknown O-antigens, and the epidemiology of SN-F E. coli is required to elucidate the molecular profile and public health implications of the pathogens.