Statistical methods for predicting the presence of Salmonella Typhi in wastewater samples at Asante Akyem Agogo, Ghana
Author(s)
Twumasi-Ankrah, Sampson
Owusu, Michael
Owusu-Ansah, Michael
Amenyaglo, Seidu
Osei-Wusu Sarfo, Caleb
Type
Journal Article
Abstract
Background
Monitoring wastewater is vital for tracking typhoid fever in endemic areas. This study evaluated the performance of both spatial and non-spatial models in predicting Salmonella Typhi detection in wastewater from the Asante Akim North district in Ghana and identified key environmental risk factors.
Methods
We collected wastewater samples of Moore swabs at 40 sites across Agogo, Juansa, Hwidiem, and Domeabra over a period of 27 months. Multiplex PCR was used to detect Salmonella Typhi, focusing on the ttr, tviB, and staG genes. An Aquaprobe AP-2000 was also used to measure different physicochemical factors, such as pH, temperature, dissolved oxygen, and salinity. Three non-spatial models, namely Generalized Estimating Equations (Logistic), Mixed-Effects Models, and Random Forest, as well as four spatial models, including Bayesian Generalized Additive Models (GAM) and Spatial Generalized Linear Mixed Models (GLMM), were fitted to the wastewater dataset. Model fitting was done using 5-fold cross-validation, stratified by site. Model performance was evaluated using accuracy, sensitivity, and specificity. We also used SHapley Additive exPlanations (SHAP) analysis to find the most important predictors.
Findings
In general, 44.13% of the samples tested positive for S. Typhi. Detection was much higher during wet seasons (50.17% vs. 35.11%; p < 0.001), with fast flows (64.45%), and in channels that were 1–2 meters wide (58.70%). Positive samples had relatively higher pH (7.46 vs. 7.40; p < 0.001), dissolved oxygen (46.97% vs. 36.77%; p < 0.001), and rainfall (3.92mm vs. 3.30mm; p = 0.022). In comparing both non-spatial and spatial models, the non-spatial Random Forest model demonstrated the highest performance with an accuracy of 0.993, sensitivity of 0.997, and specificity of 0.989. In the SHAP analysis of the preferred non-spatial random forest model, it was found that pH, season, dissolved oxygen, positivity from the previous month, and channel width were identified as the best predictors.
Conclusion
S. Typhi detection is influenced by wastewater physicochemical properties, with pH, seasonal rainfall, and hydraulic conditions being the most significant. The non-spatial random forest model significantly outperforms both spatial and other non-spatial statistical methods.
Monitoring wastewater is vital for tracking typhoid fever in endemic areas. This study evaluated the performance of both spatial and non-spatial models in predicting Salmonella Typhi detection in wastewater from the Asante Akim North district in Ghana and identified key environmental risk factors.
Methods
We collected wastewater samples of Moore swabs at 40 sites across Agogo, Juansa, Hwidiem, and Domeabra over a period of 27 months. Multiplex PCR was used to detect Salmonella Typhi, focusing on the ttr, tviB, and staG genes. An Aquaprobe AP-2000 was also used to measure different physicochemical factors, such as pH, temperature, dissolved oxygen, and salinity. Three non-spatial models, namely Generalized Estimating Equations (Logistic), Mixed-Effects Models, and Random Forest, as well as four spatial models, including Bayesian Generalized Additive Models (GAM) and Spatial Generalized Linear Mixed Models (GLMM), were fitted to the wastewater dataset. Model fitting was done using 5-fold cross-validation, stratified by site. Model performance was evaluated using accuracy, sensitivity, and specificity. We also used SHapley Additive exPlanations (SHAP) analysis to find the most important predictors.
Findings
In general, 44.13% of the samples tested positive for S. Typhi. Detection was much higher during wet seasons (50.17% vs. 35.11%; p < 0.001), with fast flows (64.45%), and in channels that were 1–2 meters wide (58.70%). Positive samples had relatively higher pH (7.46 vs. 7.40; p < 0.001), dissolved oxygen (46.97% vs. 36.77%; p < 0.001), and rainfall (3.92mm vs. 3.30mm; p = 0.022). In comparing both non-spatial and spatial models, the non-spatial Random Forest model demonstrated the highest performance with an accuracy of 0.993, sensitivity of 0.997, and specificity of 0.989. In the SHAP analysis of the preferred non-spatial random forest model, it was found that pH, season, dissolved oxygen, positivity from the previous month, and channel width were identified as the best predictors.
Conclusion
S. Typhi detection is influenced by wastewater physicochemical properties, with pH, seasonal rainfall, and hydraulic conditions being the most significant. The non-spatial random forest model significantly outperforms both spatial and other non-spatial statistical methods.
Editor(s)
Bourret, Travis J
Date Issued
2026-02-17
Date Acceptance
2026-01-27
Citation
PLoS Neglected Tropical Diseases, 2026, 20 (2), pp.e001973-e001973
ISSN
1935-2727
Publisher
Public Library of Science (PLoS)
Journal / Book Title
PLoS Neglected Tropical Diseases
Volume
20
Issue
2
Copyright Statement
© 2026 Twumasi-Ankrah et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41701741
PII: PNTD-D-25-01304
Subjects
Ghana
Wastewater
Salmonella typhi
Typhoid Fever
Humans
Models, Statistical
Bayes Theorem
Multiplex Polymerase Chain Reaction
Publication Status
Published
Coverage Spatial
United States
Article Number
e0013973
Date Publish Online
2026-02-17