Old tools, new applications: Use of environmental bacteriophages for typhoid surveillance and evaluating vaccine impact

Typhoid-conjugate vaccines (TCVs) provide an opportunity to reduce the burden of typhoid fever, caused by Salmonella Typhi, in endemic areas. As policymakers design vaccination strategies, accurate and high-resolution data on disease burden is crucial. However, traditional blood culture-based surveillance is resource-extensive, prohibiting its large-scale and sustainable implementation. Salmonella Typhi is a water-borne pathogen, and here, we tested the potential of Typhi-specific bacteriophage surveillance in surface water bodies as a low-cost tool to identify where Salmonella Typhi circulates in the environment. In 2021, water samples were collected and tested for the presence of Salmonella Typhi bacteriophages at two sites in Bangladesh: urban capital city, Dhaka, and a rural district, Mirzapur. Salmonella Typhi-specific bacteriophages were detected in 66 of 211 (31%) environmental samples in Dhaka, in comparison to 3 of 92 (3%) environmental samples from Mirzapur. In the same year, 4,620 blood cultures at the two largest pediatric hospitals of Dhaka yielded 215 (5%) culture-confirmed typhoid cases, and 3,788 blood cultures in the largest hospital of Mirzapur yielded 2 (0.05%) cases. 75% (52/69) of positive phage samples were collected from sewage. All isolated phages were tested against a panel of isolates from different Salmonella Typhi genotypes circulating in Bangladesh and were found to exhibit a diverse killing spectrum, indicating that diverse bacteriophages were isolated. These results suggest an association between the presence of Typhi-specific phages in the environment and the burden of typhoid fever, and the potential of utilizing environmental phage surveillance as a low-cost tool to assist policy decisions on typhoid control. The WHO prequalified two typhoid conjugate vaccines for use to reduce the burden of typhoid fever. As policymakers design vaccination strategies, accurate, high-resolution estimates of typhoid burden are crucial for efficient use of the vaccines. Typhoid burden can vary widely; for example, in Bangladesh, burden is high in the urban capital city Dhaka, but is 100-fold lower in the rural site, Mirzapur. Optimal local data rely on traditional blood-culture-based surveillance, which is expensive and often unavailable. With the knowledge that Salmonella Typhi, cause of typhoid fever, is a water-borne pathogen, we tested an environmental surveillance tool that detects bacteriophages (viruses) against Salmonella Typhi in environmental water bodies using simple assays. Testing of 303 water samples from Dhaka and Mirzapur showed a 10-fold lower abundance of bacteriophages in Mirzapur, depicting a correlation with typhoid burden in the community. This low-cost surveillance can be employed in different regions to generate rapid data on typhoid burden for evidence-based introduction of vaccines and tracking their impact upon rollout.