PDF(Pubmed)
Abstract：
Antimicrobial resistance (AMR) is an ever-present threat to the treatment of infectious diseases. However, the potential relevance of this phenomenon in environmental reservoirs still raises many questions. Detection of antimicrobial-resistant bacteria in the environment is a critical aspect for understanding the prevalence of resistance outside of clinical settings, as detection in the environment indicates that resistance is likely already widespread. We isolated antimicrobial-resistant Escherichia coli from three urban waterbodies over a 15-month time series, determined their antimicrobial susceptibilities, investigated their population structure, and identified genetic determinants of resistance. We found that E. coli populations at each site were composed of different dominant phylotypes and showed distinct patterns of antimicrobial and multidrug resistance, despite close geographic proximity. Many strains that were genome-sequenced belonged to sequence types of international concern, particularly the ST131 clonal complex. We found widespread resistance to clinically important antimicrobials such as amoxicillin, cefotaxime, and ciprofloxacin, but found that all strains were susceptible to amikacin and the last-line antimicrobials meropenem and fosfomycin. Resistance was most often due to acquirable antimicrobial resistance genes, while chromosomal mutations in gyrA, parC, and parE conferred resistance to quinolones. Whole-genome analysis of a subset of strains further revealed the diversity of the population of E. coli present, with a wide array of AMR and virulence genes identified, many of which were present on the chromosome, including blaCTX-M. Finally, we determined that environmental persistence, transmission between sites, most likely mediated by wild birds, and transfer of mobile genetic elements likely contributed significantly to the patterns observed.IMPORTANCEA One Health perspective is crucial to understand the extent of antimicrobial resistance (AMR) globally, and investigation of AMR in the environment has been increasing in recent years. However, most studies have focused on waterways that are directly polluted by sewage, industrial manufacturing, or agricultural activities. Therefore, there remains a lack of knowledge about more natural, less overtly impacted environments. Through phenotypic and genotypic investigation of AMR in Escherichia coli, this study adds to our understanding of the extent and patterns of resistance in these types of environments, including over a time series, and showed that complex biotic and abiotic factors contribute to the patterns observed. Our study further emphasizes the importance of incorporating the surveillance of microbes in freshwater environments in order to better comprehend potential risks for both human and animal health and how the environment may serve as a sentinel for potential future clinical infections.
摘要：
抗菌素耐药性（AMR）是对传染病治疗的持续威胁。然而,这种现象在环境水库中的潜在相关性仍然提出了许多问题。检测环境中的抗微生物细菌是了解临床环境之外的耐药性流行的关键方面。因为在环境中的检测表明耐药性可能已经普遍存在。我们在15个月的时间序列中从三个城市水体中分离出了耐药性大肠杆菌，确定了它们的抗菌敏感性，调查了他们的人口结构，并确定了抗性的遗传决定因素。我们发现，每个地点的大肠杆菌种群由不同的显性基因型组成，并显示出不同的抗菌和多药耐药性模式。尽管地理上很接近。许多基因组测序的菌株属于国际关注的序列类型，特别是ST131克隆复合物。我们发现对临床上重要的抗菌药物如阿莫西林有广泛的耐药性，头孢噻肟,还有环丙沙星,但发现所有菌株都对阿米卡星和最后一线抗生素美罗培南和磷霉素敏感。耐药性通常是由于可获得的抗菌素耐药性基因，而gyrA的染色体突变，ParC,并赋予了对喹诺酮类药物的耐药性。对菌株子集的全基因组分析进一步揭示了存在的大肠杆菌种群的多样性，鉴定了一系列AMR和毒力基因，其中许多存在于染色体上，包括blaCTX-M.最后,我们确定环境的持久性，站点之间的传输，很可能是由野生鸟类介导的，移动遗传元件的转移可能对观察到的模式有重要贡献。IMPORTANCEA一种健康观点对于了解全球抗菌素耐药性（AMR）的程度至关重要，近年来，对环境中AMR的调查越来越多。然而,大多数研究都集中在被污水直接污染的水道上，工业制造,或农业活动。因此,仍然缺乏关于更自然的知识，对环境的影响较小。通过对大肠杆菌AMR的表型和基因型调查,这项研究增加了我们对这些类型环境中抵抗的程度和模式的理解，包括时间序列，并表明复杂的生物和非生物因素有助于观察到的模式。我们的研究进一步强调了在淡水环境中纳入微生物监测的重要性，以便更好地理解人类和动物健康的潜在风险，以及环境如何作为未来潜在临床感染的前哨。
