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

Swine wastewater can accelerate the spread of antibiotic-resistant bacteria among animals, the environment, and humans. Therefore, the molecular epidemiological characteristics of carbapenemase-producing E. coli isolates from swine wastewater was investigated. In this study, a total of 100 no-cloning carbapenemase-producing (blaNDM-1, blaNDM-5 and blaOXA-48-like) E. coli isolates were recovered from 316 swine wastewater samples collected from 29 swine farm in Shandong, China. Of which, two isolates that co-harbored blaOXA-48-like and mcr-1, as well as five isolates that co-harbored blaNDM-5 and tet(X4). All isolates were multidrug-resistant (MDR), with a majority exhibiting resistance to meropenem, ciprofloxacin, imipenem and gentamicin. Whole genome sequencing (WGS) analysis indicated that these isolates were belonged to 12 distinct sequence types (STs), with the most prevalent STs being ST10 and ST5299. Additionally, Phylogenomic analysis revealed that clonal spread of blaNDM-positive ST10 E. coli isolates at swine wastewater in multiple cities, including Binzhou, Dezhou, Heze and Weihai. Meanwhile, a notable divergence in SNPs was observed in isolates from this study and public database, which indicates that these blaNDM-positive E. coli isolates have high genetic diversity. In addition, WGS analysis further revealed that blaNDM co-existed with other antibiotic resistance genes, conferring resistance to twelve classes of antimicrobials. This study underscores the importance of surveillance for blaNDM-harboring microbes in swine wastewater, and continuous monitoring in swine wastewater is essential for ensure human and environmental health. IMPORTANCEThe study described the NDM-positive E. coli strains isolated from swine wastewater, where it was associated with antibiotic exposure. Notably, swine wastewater was increasingly considered to be related to CRE hosts. Pathogens originating from this source can be transmitted to humans via direct and indirect contact, as well as through the ingestion or inhalation of contaminated water or aerosols. In addition, under the selective pressure of antibiotics, the co-harbored of blaOXA-48-like and mcr-1, blaNDM-5 and tet(X4) genes within the same host bacterium signifies the emergence of an extremely MDR pathogen, posing a grave threat to public health. Consequently, the monitoring of blaNDM in swine wastewater is critical for containing the transmission and persistence of carbapenem-resistant pathogens.