Swine wastewater drives dissemination of high-risk blaNDM-positive Escherichia coli clones

Introduction Swine wastewater can accelerate the spread of antibiotic-resistant bacteria among animals, the environment, and humans. Therefore, the molecular epidemiological characteristics of carbapenemase-producing Escherichia coli isolates from swine wastewater was investigated. Methods Antimicrobial susceptibility testing was used to determine metallo-enzyme activity. Conjugation experiments were used to determine transmissibility of the novel carbapenemase-encoding gene. Whole-genome sequencing (WGS) with short reads and ERIC-PCR genotyping were performed to characterize the genomic features of the isolates. Single nucleotide polymorphisms (SNPs) was used to determine strain relatedness. Results A total of 100 non-duplicate carbapenemase-producing ( bla NDM-1 , bla NDM-5 , and bla OXA-48 -like) E. coli isolates were recovered from 316 swine wastewater samples. Of which, two isolates that co-harbored bla OXA-48 -like and mcr-1 , as well as five isolates that co-harbored bla NDM-5 and tet(X4) . All isolates were multidrug-resistant (MDR), with a majority exhibiting resistance to meropenem, ciprofloxacin, imipenem and gentamicin. In addition, WGS analysis further revealed that bla NDM co-existed with other antibiotic resistance genes, conferring resistance to twelve classes of antimicrobials. These isolates were assigned to 12 distinct sequence types (STs), among which ST10 and ST5299 were the most prevalent. Additionally, Phylogenomic analysis revealed that clonal spread of bla NDM -positive ST10 E. coli isolates at swine wastewater in multiple cities, including Binzhou, Dezhou, Heze and Weihai. Meanwhile, a notable divergence in single nucleotide polymorphisms (SNPs) was observed in isolates from this study and public database, which indicates that these bla NDM -positive E. coli isolates have high genetic diversity. Discussion This study underscores the importance of surveillance for bla NDM -positive microbes in swine wastewater, and continuous monitoring in swine wastewater is essential for ensure human and environmental health.