Genomic characterization and comparative analysis of multidrug-resistant Escherichia coli ST361 from urban wetland.

backgroundWetlands are severely affected by human activities like untreated sewage, overuse of antibiotics and agricultural runoff, leading to the accumulation of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Migratory birds visiting these contaminated wetlands further spread the ARB and ARGs globally. Urban lakes, with high anthropogenic impact, are increasingly showing MDR E. coli, which are responsible for global infections and AMR gene dissemination. ST361 is an emerging global threat, showing an upward trend in prevalence and resistance to major antibiotic classes. The presence of this ST in aquatic environments suggests a robust transmission cycle between animals, humans, and the environment, often via agricultural runoff and contaminated wastewater. This study reports the first instance of ST361 from wetlands in India. The aim of this study is to identify the resistance and virulence genes present in this ST361 isolate and perform comparative genomic analysis of ST361 isolates from both clinical and environmental sources globally.

methodsFresh water sample (KOTW5) was collected from a lake in chennai during monsoon season. The sample was streaked on selective agar media and maintained at 37℃ for 24 h. Antimicrobial Susceptibility test were carried out in accordance with CLSI guidelines and the sample was confirmed as E.coli using MALDI-TOF. Whole genome sequencing (WGS) was performed using Illumina NovaSeq 6000 instrument after DNA extraction and then library preparation. After processing the sequencing reads, various softwares were employed for the identification of clonal subtype, serotype, antibiotic resistance genes, virulence genes and other genomic characteristics of the isolate. The phylogenetic tree was visualized using iTOL v6.

resultsKOTW5 exhibited resistance to multiple antibiotics including ampicillin, tetracycline, and colistin. KOTW5 was revealed to be an emerging pandemic clone ST361 which has a genome size of 4,481,772 bp with 50.8% GC content. It harbors resistance genes like pmr, TolC, acr, and sul2. The serotype is O9/H30. KOTW5 also possesses 50 virulence genes, including fim, esp and gsp genes. Pangenome analysis of KOTW5 and other ST361 isolates (clinical and environmental) indicated it's close relationship with UEMH01, clinical E. coli isolate from Tanzania, and DUDV01, clinical E. coli isolate from Germany, suggesting its potential to cause human infections in the future. They were found to share the genes ampC, pmrF, acr, emr, evg, tolC, esp, fim, gsp, and ompA. In indian scenario, KOTW5 belongs to a clade containing the clinical isolates JAKMBW01 and DAZBLI01 and share the following genes: ampC, H-NS, pmrF, tolC, csg, ent, espL1, espX5, fim, gsp, and ompA.

conclusionThe study highlights the presence of E. coli ST361, a multidrug-resistant, high-risk clone, in wetlands. Wetlands may act as "hotspots" for the persistence and spread of MDR E. coli, which is concerning as antibiotics are becoming less effective as last-resort treatments. The finding of ST361 in lakes underscores the "One Health" concept, emphasizing that antibiotic resistance impacts human, animal, and environmental health. To combat rising antimicrobial resistance (AMR) in aquatic environments, comprehensive strategies such as advanced wastewater treatment, stricter regulations on antibiotic use, public awareness campaigns, and routine environmental monitoring are crucial.