Al-Mustapha Ahmad Ibrahim, Tiwari Ananda, Laukkanen-Ninios Riikka, Lehto Kirsi-Maarit, Oikarinen Sami, Lipponen Anssi, Pitkänen Tarja, Heikinheimo Annamari
Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
Department of Veterinary Services, Kwara State Ministry of Agriculture and Rural Development, Kwara State, Ilorin, Nigeria.
Sci Rep. 2025 Mar 3;15(1):7400. doi: 10.1038/s41598-025-91516-9.
Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we leverage the power of whole genome sequencing (WGS) to screen AmpC- and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from 77 composite samples obtained from 10 wastewater treatment plants across Finland. We found a high abundance of multidrug-resistant AmpC/ESBL-producing E. coli and significant differences in the diversity of AMR genes between the sampled cities. The in silico analysis of 73 short-read genome sequences shows the clonally diverse isolates consisting of 30 sequence types (STs), including the globally distributed pandemic ST131 clone. The CTX-M ESBL genes were detected in 86.3% (63/73) of the isolates concurrently with the blaTEM-1 (31.5%, 23/73) and blaOXA-1 (9.6%, 7/73) genes. The most prevalent ESBL genes were blaCTX-M-15 (46.6%, 34/73), blaCTX-M-27 (16.4%, 12/73), blaCTX-M-14 (4.1%, 3/73), and blaCTX-M-55 (4.1%, 3/73). Two isolates harboured the carbapenemase resistance gene, blaKPC-2 and blaNDM-1, respectively. In addition, WGS predicted phenotypic resistance against aminoglycosides, beta-lactams, cephalosporins, quinolones, sulfonamides, carbapenems, and polymyxins. The diversity of antibiotic- and stress-resistance genes correlated with the clinical incidence reported in the Finnish AMR report. Core-genome MLST revealed two wastewater genomic clusters but no genomic clusters among human and wastewater ST131 isolates. Our findings suggest the circulation of distinct clonal lineages of AmpC/ESBL-producing E. coli across Finland, with variations in AMR gene diversity and abundance by wellbeing service county. Also, our findings underscore the fact that wastewater surveillance could be key to population-level monitoring of AmpC/ESBL-producing Escherichia coli and can serve as complementary data to guide public health decisions. We propose longitudinal WGS-based epidemiology as an economically feasible approach for global AMR surveillance, pathogen evolution, and prediction of AMR.
抗菌药物耐药性（AMR）是对全球公共卫生的严重威胁，但获取健康人群AMR的代表性数据却很困难。在此，我们利用全基因组测序（WGS）的力量，从芬兰10个污水处理厂采集的77个复合样本中筛选产AmpC和超广谱β-内酰胺酶（ESBL）的大肠杆菌。我们发现产多药耐药AmpC/ESBL的大肠杆菌丰度很高，且各采样城市间AMR基因的多样性存在显著差异。对73条短读长基因组序列的计算机分析显示，克隆多样的分离株由30种序列类型（STs）组成，包括全球分布的大流行ST131克隆。在86.3%（63/73）的分离株中检测到CTX-M ESBL基因，同时还检测到blaTEM-1（31.5%，23/73）和blaOXA-1（9.6%，7/73）基因。最常见的ESBL基因是blaCTX-M-15（46.6%，34/73）、blaCTX-M-27（16.4%，12/73）、blaCTX-M-14（4.1%，3/73）和blaCTX-M-55（4.1%，3/73）。两株分离株分别携带碳青霉烯酶耐药基因blaKPC-2和blaNDM-1。此外，WGS预测了对氨基糖苷类、β-内酰胺类、头孢菌素类、喹诺酮类、磺胺类、碳青霉烯类和多粘菌素类的表型耐药性。抗生素和应激抗性基因的多样性与芬兰AMR报告中报道的临床发病率相关。核心基因组多位点序列分型揭示了两个污水基因组簇，但人和污水ST131分离株之间没有基因组簇。我们的研究结果表明，产AmpC/ESBL的大肠杆菌不同克隆谱系在芬兰各地传播，且各福利服务县的AMR基因多样性和丰度存在差异。此外，我们的研究结果强调了污水监测可能是对产AmpC/ESBL的大肠杆菌进行人群水平监测的关键，并且可以作为补充数据来指导公共卫生决策。我们提出基于WGS的纵向流行病学作为一种经济可行的方法，用于全球AMR监测、病原体进化和AMR预测。
