Pathogen Mapping Tool (PMT)

Produces pathogen emissions in the environment and to surface water to support decision making, and resource prioritization and allocation.

About the Tool

  • Simulates the quantity of pathogens (i.e., bacteria, viruses, protozoa and helminths) excreted into the environment based on on-site and centralized treatment data.
  • Provides pathogen emission maps and .csv files that contain spatially-explicit emission quantities at 1, 10 or 50 km2 resolution or for political entities.
  • Allows a user to run scenarios representing changes from the baseline sanitation to view changes in emissions (e.g., eradicating open defecation, or increase the number of latrines that are being emptied)

PMT’s 7-Step Process

  1. Define a geographic boundary for global, national or local areas by drawing a polygon on a map to select the desired area or by using the search bar for selecting the base maps for the area of interest*. The population size is auto-populated as well as the baseline sanitation data.
    *data base will be growing;
  2. Select pathogen type (Cryptosporidium, rotavirus*)
    *data base will be growing;
  3. Select Yes/No regarding availability of local data on centralized treatment (eg. type, capacity and location). The tool provides a template to input your own data, or available more regional data on the fraction of wastewater treated can be loaded and verified.
  4. View and verify (or modify) demographic and sanitation data. Whether you input your own data or selected from already available data, the next step is to verify the data that has been selected as model input. The demographic and sanitation model inputs can still be modified at this time. The sanitation data can also be downloaded and curated based on available local data and uploaded back into the tool (optional).
  5. Verify (or modify) treatment data or input your own. This step is used to determine the proportion of waste that reaches treatment and which type. The data can be altered or added at this time.
  6. Run and View the results page and emissions maps. On this page, you can view the emissions of the pathogen you selected at a resolution of between 1km, 10km, 50km depending on the resolution of your input data. All maps and corresponding .csv files can be downloaded.
  7. Run new scenarios with changes to inputs (eg. Population, urbanization, sanitation technology/management) to assess the impact changes on pathogen emissions. For example, an increase in the proportion of waste that reaches further treatment can be increased. A new map is created based on the details selected for the scenario. All scenario maps and corresponding .csv files can be downloaded.

Overview of Inputs for the PMT

  • The model estimates the contribution of on-site sanitation systems to pathogen emissions to environmental compartments based on the following categories:
  • Fraction of sewered (connected) sanitation systems
  • Fraction of open defecation (direct emissions)
  • Fraction of lined pit latrines
  • Fraction of unlined pit latrines
  • Fraction of septic tanks
  • Fraction of composting toilets

In the current version of the online tool the on-site sanitation categories have been combined into one category on-site sanitation systems. In the future we plan to have separate on-site sanitation categories. This is work in progress. In the case study for Kampala, a new model with the separate categories have been used and in the coming months the pathogen flow tool (PFT) will be integrated in the PMT and be used to simulate the loads.

  • Each on-site sanitation type is further broken down into three categories:
    • Fraction of which that undergoes further treatment,
    • Fraction of which that is flushed into the environment,
    • Fraction of which that remains contained in the system.
  • The model also requires the average times for pit emptying and pit flushing.
  • Centralized sanitation technologies are further proportioned by total sewered wastewater that is undergoing further treatment by type:
    • Primary treatment
    • Secondary treatment
    • Tertiary treatment
    • Pond treatment

Overview PMT Outputs

  • Provides a pathogen emission map as pictured above and a .csv file that contains spatially explicit emission quantities at a 1, 10, 50 km resolution.
  • When altering the original map using the scenario tool on the results page, difference maps are created. These maps display the change in pathogen emissions based on the scenario details selected.
  • When the user decides to save their baseline and scenario runs, the data will be converted to an interactive map available for everyone to view in the visualization tool. Here the user can look at the map, click on the individual subareas and see the contribution of the different sources on the pathogen emissions.

Model assumptions

The PMT is based on an underlying microbiological water quality model. This model is based on model assumption, like any other model. The results should be seen in the light of these assumptions. The model will be written up in detail and published open access in the scientific literature.

What PMT outputs can be used for

The utility of the maps is in the comparison of the baseline maps to the scenarios (the relative change). Decision makers should not focus on the absolute log emissions in these maps as there is uncertainty around the inputs into the models.

Upgrades in progress

  • Integration of the K2P pathogen flow tool in the PMT for internal consistency of the K2P tools and to improve the pathogen emission estimates.
  • Concentration in surface water calculation, using available hydrology.
  • Expansion of the tool to outside Uganda.


Okaali, D.A., Hofstra, N. (2018) Present and Future Human Emissions of Rotavirus and Escherichia coli to Uganda’s Surface Waters. Journal of Environmental Quality 47 (5), 1130-1138.
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