Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia; Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food and Environment (CRC SAAFE), South Australia, Australia.
Australian Institute for Microbiology & Infection, University of Technology Sydney, NSW, Australia; Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, NSW, Australia.
Sci Total Environ. 2024 Nov 1;949:175079. doi: 10.1016/j.scitotenv.2024.175079. Epub 2024 Jul 31.
Extended-spectrum β-lactamases (ESBLs)-producing E. coli have been proposed as an indicator bacterium for antimicrobial resistance (AMR) surveillance within a OneHealth framework. However, it is important to understand the effects and potential biases ESBL-selection has on E. coli populations. Utilising whole genome sequencing, this study compared 80 ESBL-selected E. coli isolates with 201 non-selected isolates from Australian wastewater. The findings revealed significant variations between these cohorts in genetic diversity, AMR profiles, and carriage of virulence-associated genes (VAGs), plasmids, and the transmissible Locus of Stress Tolerance (tLST), a genomic island that imparts resistance to extreme heat and chlorination. The study highlights the predominance of certain sequence types (STs), particularly ST131 (75 % clade A), in ESBL-selected isolates (40 % vs 2 %) and overall the ESBL-selected isolates were largely multidrug-resistant (MDR), predominantly carrying genes for resistance to aminoglycosides, extended-spectrum β-lactams, fluoroquinolone, macrolides, sulphonamides/trimethoprim, and tetracyclines. The ESBLs identified were almost exclusively bla genes, most commonly bla > bla > bla. These were predominately carried on IncF plasmids or chromosomally (always ISEcp1 associated), in equal numbers. In contrast, 80 % of non-selected isolates carried no acquired ARGs, and none carried bla genes. In both cohorts, extraintestinal pathogenic E. coli (ExPEC) was the dominate pathotype (35 % total) with few (4 % total) intestinal pathogenic E. coli pathotypes identified (aEPEC > ETEC > EAEC). Nevertheless, some clinically important genes were only identified in the non-selected group, namely tigecycline-resistance gene tet(X4) and AmpC ESBL bla. Additionally, the presence of tLST, associated with higher metal resistance gene carriage (Ag, As, Cu, Hg, Ni), in a substantial portion of non-selected isolates (20 % vs 0 %), underscores environmental pressures shaping bacterial populations in wastewater ecosystems. These insights are important for developing comprehensive, less biased genomic surveillance strategies to understand and manage public health threats posed by pathogenic E. coli and AMR.
产超广谱β-内酰胺酶（ESBL）的大肠杆菌已被提议作为一个指标菌，用于在一个 OneHealth 框架内进行抗菌药物耐药性（AMR）监测。然而，了解 ESBL 选择对大肠杆菌种群的影响和潜在偏见是很重要的。本研究利用全基因组测序，比较了 80 株 ESBL 选择的大肠杆菌分离株与 201 株非选择的澳大利亚废水分离株。研究结果表明，这两组之间在遗传多样性、AMR 谱和携带毒力相关基因（VAGs）、质粒以及可传播的应激耐受基因座（tLST）方面存在显著差异，tLST 是一个赋予对极端热和氯化抗性的基因组岛。该研究强调了某些序列类型（STs）的优势，特别是 ST131（75%的 A 群），在 ESBL 选择的分离株中（40%对 2%），而总的来说，ESBL 选择的分离株主要是多药耐药（MDR），主要携带对氨基糖苷类、扩展谱β-内酰胺类、氟喹诺酮类、大环内酯类、磺胺类/甲氧嘧啶类和四环素类的耐药基因。鉴定的 ESBL 几乎完全是 bla 基因，最常见的是 bla>bla>bla。这些基因主要携带在 IncF 质粒或染色体上（总是与 ISEcp1 相关），数量相等。相比之下，80%的非选择分离株不携带获得性 ARGs，也不携带 bla 基因。在两个队列中，肠外致病性大肠杆菌（ExPEC）是主要的病原型（占 35%），只有少数（占 4%）肠道致病性大肠杆菌病原型（aEPEC>ETEC>EAEC）被识别。然而，一些临床重要的基因只在非选择组中被识别，即替加环素耐药基因 tet(X4)和 AmpC ESBL bla。此外，tLST 的存在与更高的金属耐药基因携带有关（Ag、As、Cu、Hg、Ni），在相当一部分非选择分离株中（20%对 0%），这突显了环境压力对废水生态系统中细菌种群的影响。这些见解对于制定全面、偏差较小的基因组监测策略，以了解和管理致病性大肠杆菌和 AMR 带来的公共卫生威胁非常重要。
