Environmental surveillance for Sabin polioviruses, Salmonella, and antimicrobial resistance genes in an urban setting in southern India

Abstract

Sewage is the easiest place to find organisms that replicate in human or animal guts. Although World Health Organization (WHO) recommends the WHO 2-phase method for environmental surveillance of polioviruses, new methods such as the Bag Mediated Filtration System (BMFS) have been used recently. The current resource intensive surveillance for polioviruses may not be sustainable in future, and should be amalgamated with other surveillance methods (such as Salmonella Typhi, antimicrobial resistance genes) for a more comprehensive approach to environmental monitoring for detection of multiple targets of interest. Sewage samples from the 10–12 main sewage channels in Vellore were collected using BMFS and the WHO 2-phase method for detection of Sabin polioviruses 1 and 3. The polio multiplex real-time PCR assay was used to detect Sabin polioviruses. In addition, public and hospital sewage samples, community drinking water and food samples were tested for Salmonella and AMR genes. Singleplex and multiplex real-time PCR (qPCR) assays were used for detection of S . Typhi and other Salmonella spp. For detection of AMR genes, 4 multiplex conventional PCRs were used. All data were analysed using Stata IC/15.1 (StataCorp, College Station, TX). A p value of ≤ 0.05 was considered as statistically significant. During February-July, 2018, 138 sewage samples were collected using the BMFS and WHO 2-phase methods. 13.8% samples (19/138) were positive for Sabin polioviruses using BMFS, compared to 8.7% (12/138) using WHO 2-phase method. Of the 342 sewage samples collected using BMFS until February 2020, S . Typhi was detected in 14.6% (50/342) samples using singleplex qPCR, compared to 8.1% (22/270) using multiplex qPCR. 16.3% (43/264) and 12.8% (23/180) hospital sewage samples were positive for S . Typhi by singleplex and multiplex qPCR respectively. S . Typhi was detected in 1.6% (2/124) of drinking water samples, and not detected in food samples. Of the 210 community sewage samples tested for AMR, > 90% samples were positive for CTX-M1, VIM, KPC and qnrS genes. This study demonstrated the simultaneous detection of Sabin polioviruses 1 and 3, Salmonella Typhi, and AMR genes from sewage samples using BMFS. Although the proportion of samples positive for Sabin polioviruses in sewage samples was higher in BMFS compared to WHO 2-phase method, the difference was not statistically significant ( p = 0.18). The study findings emphasize the effectiveness of environmental surveillance approaches for multiple pathogens.