Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8540, Japan.
Department of Clinical Laboratory Medicine, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan.
Water Res. 2024 Jan 1;248:120830. doi: 10.1016/j.watres.2023.120830. Epub 2023 Nov 3.
The global increase of antimicrobial resistance (AMR) is a major public health concern. An effective AMR surveillance tool is needed to track the emergence and spread of AMR. Wastewater surveillance has been proposed as a resource-efficient tool for monitoring AMR carriage in the community. Here, we performed genomic surveillance of antimicrobial-resistant Escherichia coli obtained from fecal sludge and sewage in Uganda to gain insights into E. coli epidemiology and AMR burden in the underlying population. Selective media containing different antibiotic combinations (cefotaxime, ciprofloxacin, cefotaxime + ciprofloxacin + gentamicin) were used to obtain antimicrobial-resistant E. coli from fecal sludge and sewage. Short-read sequencing was performed for the obtained isolates, and a subset of isolates (selected from predominant sequence types (STs)) was also subjected to long-read sequencing. Genomic analysis of the obtained E. coli isolates (n = 181) revealed the prevalence of clonal complex 10, including ST167 (n = 43), ST10 (n = 28), ST1284 (n = 17), and ST617 (n = 4), in both fecal sludge and sewage, irrespective of antibiotics used for selection. We also detected global high-risk clones ST1193 (n = 10) and ST131 (n = 2 clade A, n = 3 subclade C1-M27, and n = 1 subclade C2). Diverse AMR determinants, including extended-spectrum β-lactamase genes (mostly bla) and mutations in gyrA and parC, were identified. Analysis of the completed genomes revealed that diverse IncF plasmids and chromosomal integration were the major contributors to the spread of AMR genes in the predominant STs. This study showed that a combination of sewage surveillance (or fecal sludge surveillance) and whole-genome sequencing can be a powerful tool for monitoring AMR carriage in the underlying population.
全球抗菌药物耐药性（AMR）的增加是一个主要的公共卫生关注点。需要一种有效的 AMR 监测工具来跟踪 AMR 的出现和传播。废水监测已被提议作为一种资源高效的工具，用于监测社区中 AMR 携带情况。在这里，我们对从乌干达粪便污泥和污水中获得的抗药性大肠杆菌进行了基因组监测，以深入了解大肠杆菌流行病学和基础人群中的 AMR 负担。使用含有不同抗生素组合（头孢噻肟、环丙沙星、头孢噻肟+环丙沙星+庆大霉素）的选择性培养基从粪便污泥和污水中获得抗药性大肠杆菌。对获得的分离株进行短读测序，并对分离株的一部分（从主要序列类型（ST）中选择）也进行了长读测序。对获得的大肠杆菌分离株（n=181）进行基因组分析显示，克隆复合体 10 包括 ST167（n=43）、ST10（n=28）、ST1284（n=17）和 ST617（n=4），在粪便污泥和污水中均有流行，与用于选择的抗生素无关。我们还检测到全球高风险克隆 ST1193（n=10）和 ST131（n=2 个 clade A，n=3 个 subclade C1-M27，n=1 个 subclade C2）。确定了多种 AMR 决定因素，包括广谱β-内酰胺酶基因（主要是 bla）和 gyrA 和 parC 中的突变。完成基因组分析表明，多样化的 IncF 质粒和染色体整合是主要 ST 中 AMR 基因传播的主要原因。这项研究表明，污水监测（或粪便污泥监测）和全基因组测序的结合可以成为监测基础人群中 AMR 携带情况的有力工具。
