청주시 생활하수처리장 유출수에서 분리한 항생제 내성 Enterococcus faecium의 전장유전체 분석 기반 특성 연구

Abstract

Background: Municipal wastewater treatment plants (WWTPs) are designed to reduce microbial loads, including antibiotic-resistant bacteria. Nevertheless, Enterococcus faecium , a clinically relevant opportunistic pathogen, can persist in effluents and disseminate into aquatic environments, raising public health concerns. Objectives: This study aimed to assess whether WWTP effluents act as reservoirs and potential dissemination routes for antibiotic-resistant E. faecium by characterizing their phenotypic resistance, genomic features, and relatedness to clinical isolates. Methods: Six E. faecium isolates were obtained from WWTP effluents in Cheongju, South Korea. Their genomes were compared with 160 vanA-positive clinical genomes retrieved from the NCBI Pathogen database. Antibiotic susceptibility was evaluated using the disc diffusion method. Whole-genome sequencing was performed through the Illumina NovaSeq platform, followed by annotation of antibiotic resistance genes and mobile genetic elements, and by determination of their localization on chromosomes or plasmids. Phylogenetic relationships were assessed using average nucleotide identity and sequence types were determined by multi-locus sequence typing. Results: Several WWTP-derived isolates exhibited vancomycin resistance and carried the vanA operon, which is predominantly located on plasmids. Some discrepancies between resistance phenotypes and genomic profiles were observed, suggesting the possible presence of a novel antibiotic resistance gene, while in part these inconsistencies may also reflect limitations of short-read–based assemblies. Four isolates from WWTP effluents were assigned to the CC17 clonal complex, which is predominantly associated with clinical samples. Conclusions: This study demonstrates that whole-genome sequencing provides a more comprehensive assessment than does PCR- or qPCR-based monitoring, enabling analysis of resistance gene localization, identification of novel candidate genes, and evaluation of their association with mobile genetic elements. Notably, the detection of the CC17 clonal complex in WWTP effluents indicates that these strains can spread beyond hospitals and into the environment and potentially return to human settings. Strengthening environmental surveillance and implementing regular monitoring can help limit the spread of resistant strains in communities.