Monitoring viruses and beta-lactam resistance genes through wastewater surveillance during a COVID-19 surge in Suwon, South Korea

Abstract

The present study reports data on a long-term campaign for monitoring SARS-CoV-2, norovirus, hepatitis A virus, and beta-lactam resistance genes in wastewater samples from a wastewater treatment plant during COVID-19 surge in Suwon, South Korea. Real-time digital PCR (RT-dPCR) assays indicated 100 % occurrence of all but hepatitis A virus and bla_NDM gene in influent wastewater samples. CDC-N1 assay detected SARS-CoV-2 in all influent samples with an average log-transformed concentration of 5.1 ± 0.39 and the highest level at 6.02 gene copies/L. All samples were also positive for norovirus throughout the study with a mean concentration 5.67 ± 0.65 log₁₀ gene copies/L. On the contrary, all treated wastewater (effluent) tested negative for both viruses' genetic materials. Furthermore, plasmid-mediated AmpC β-lactamases (PABLs) genes bla_DHA, bla_ACC, and bla_FOX, extended-spectrum β-lactamases (ESBLs) genes bla_TEM and bla_CTX, and Klebsiella pneumoniae carbapenemase (bla_KPC) gene were measured at average concentrations of 7.05 ± 0.26, 5.60 ± 0.35, 7.82 ± 0.43, 8.38 ± 0.20, 7.64 ± 0.29, and 7.62 ± 0.41 log₁₀ gene copies/L wastewater, respectively. Beta-lactam resistance genes showed strong correlations (r), the highest being 0.86 for bla_KPC - bla_FOX, followed by 0.82 for bla_TEM - bla_CTX and 0.79 for bla_TEM - bla_DHA. SARS-CoV-2 RNA occurrence in the wastewater was strongly associated (r = 0.796) with COVID-19 cases in the catchment during the initial study period of six months. A positive association of the SARS-CoV-2 RNA with the prevalence of COVID-19 cases showed a promising role of community-scale monitoring of pathogens to provide considerable early signals of infection dynamics. High concentrations of beta-lactam resistance genes in wastewater indicated a high concern for one of the biggest global health threats in South Korea and the need to find control measures. Moreover, antibiotic-resistance genes in treated wastewater flowing through water bodies and agricultural environments indicate further dissemination of antibiotic resistance traits and increasing microbial antibiotic resistance.

Keywords: Antibiotic resistance gene; Beta-lactam resistance gene; Virus; Wastewater surveillance.