Environmental sampling for typhoidal Salmonellas in household and surface waters in Nepal identifies potential transmission pathways

Abstract

Introduction

Salmonella Typhi and Salmonella Paratyphi, fecal-oral transmitted bacterium, have temporally and geographically heterogeneous pathways of transmission. Previous work in Kathmandu, Nepal implicated stone waterspouts as a dominant transmission pathway after 77% of samples tested positive for Salmonella Typhi and 70% for Salmonella Paratyphi. Due to a falling water table, these spouts no longer provide drinking water, but typhoid fever persists, and the question of the disease’s dominant pathway of transmission remains unanswered.

Methods

We used environmental surveillance to detect Salmonella Typhi and Salmonella Paratyphi A DNA from potential sources of transmission. We collected 370, 1L drinking water samples from a population-based random sample of households in the Kathmandu and Kavre Districts of Nepal between February and October 2019. Between November 2019 and July 2021, we collected 380, 50mL river water samples from 19 sentinel sites on a monthly interval along the rivers leading through the Kathmandu and Kavre Districts. We processed drinking water samples using a single qPCR and processed river water samples using differential centrifugation and qPCR at 0 and after 16 hours of liquid culture enrichment. A 3-cycle threshold (Ct) decrease of Salmonella Typhi or Salmonella Paratyphi, pre- and post-enrichment, was used as evidence of growth. We also performed structured observations of human-environment interactions to understand pathways of potential exposure.

Results

Among 370 drinking water samples, Salmonella Typhi was detected in 7 samples (1.8%) and Salmonella Paratyphi A was detected in 4 (1.0%) samples. Among 380 river water samples, Salmonella Typhi was detected in 171 (45%) and Salmonella Paratyphi A was detected in 152 (42%) samples. Samples located upstream of the Kathmandu city center were positive for Salmonella Typhi 12% of the time while samples from locations in and downstream were positive 58% and 67% of the time respectively. Individuals were observed bathing, washing clothes, and washing vegetables in the rivers.

Implications

These results suggest that drinking water was not the dominant pathway of transmission of Salmonella Typhi and Salmonella Paratyphi A in the Kathmandu Valley in 2019. The high degree of river water contamination and its use for washing vegetables raises the possibility that river systems represent an important source of typhoid exposure in Kathmandu.

Author summary

Understanding the dominant route of transmission of a pathogen is important for designing and implementing effective control strategies. Salmonella Typhi and Paratyphi A, which cause enteric fever, infect approximately 10 million people and cause over 100,000 deaths annually. In the Kathmandu Valley, prior work suggested ancient stone spouts used for drinking water were often contaminated and driving transmission of the diseases. However, many of these spouts no longer function, and people are still getting sick, suggesting other possible dominant pathways for enteric fever transmission. We tested drinking water from households in this area as well as local river water and found that only 7 drinking water samples were positive for Salmonella Typhi and 4 were positive for Salmonella Paratyphi A. We also tested river water and found many samples (>40%) tested positive for these bacteria. River water samples were not often positive upstream of Kathmandu city center (12% positive for Salmonella Typhi) but were often positive within the city center (58% positive for Salmonella Typhi) and in rural areas up to 10 km downstream of the city (67% positive for Salmonella Typhi). During sample collection, individuals were observed interacting with rivers by walking in them, washing clothes and washing vegetables for sale in markets. This study shows that drinking water may not be a primary driver of enteric fever transmission in the Kathmandu Valley, but that sewage contaminated river water may be a way disease transmits into the wider population.