Detection ofSalmonellaTyphi bacteriophages in surface waters as a scalable approach to environmental surveillance

Abstract

AbstractEnvironmental surveillance, using detection ofSalmonellaTyphi DNA, has emerged as a potentially useful tool to identify typhoid-endemic settings; however, it is relatively costly and requires molecular diagnostic capacity. We sought to determine whetherS. Typhi bacteriophages are abundant in water sources in a typhoid-endemic setting, using low-cost assays. We collected drinking and surface water samples from urban, peri-urban and rural areas in 4 regions of Nepal. We performed a double agar overlay withS. Typhi to assess the presence of bacteriophages. We isolated and tested phages against multiple strains to assess their host range. We performed whole genome sequencing of isolated phages, and generated phylogenies using conserved genes.S. Typhi-specific bacteriophages were detected in 54.9% (198/361) of river water samples and 6.3% (1/16) drinking water samples from the Kathmandu Valley and Kavrepalanchok. Water samples collected within or downstream of population-dense areas were more likely to be positive (72.6%, 193/266) than those collected upstream from population centers (5.3%, 5/95) (p=0.005). In urban Biratnagar and rural Dolakha, where typhoid incidence is low, only 6.7% (1/15, Biratnagar) and 0% (0/16, Dolakha) samples contained phages. AllS. Typhi phages were unable to infect otherSalmonellaand non-Salmonellastrains, nor a Vi-knockoutS. Typhi strain. Representative strains fromS. Typhi lineages were variably susceptible to the isolated phages. Phylogenetic analysis showed thatS. Typhi phages belonged to two different viral families (AutographiviridaeandSiphoviridae) and clustered in three distinct groups.S. Typhi bacteriophages were highly abundant in surface waters of typhoid-endemic communities but rarely detected in low typhoid burden communities. Bacteriophages recovered were specific forS. Typhi and required Vi polysaccharide for infection. Screening small volumes of water with simple, low-cost plaque assays enables detection ofS. Typhi phages and should be further evaluated as a scalable tool for typhoid environmental surveillance.HighlightsTyphoid phages are detectable in surface water using simple assays, in communities with high typhoid burden.Bacteriophages are highly specific forS. Typhi and required Vi polysaccharide for infection.S. Typhi phages have a broad lytic activity against theS. Typhi strains circulating in Nepal.Phage plaque assay can be used as a low-cost tool to identify communities where typhoid is endemic.The high abundance of phages in river water suggest that this could be an alternative to molecular methods for environmental surveillance for typhoid.