Human urine and Pathogens – examples from Sweden and India with spinach

Posted: November 23, 2012 in Uncategorized

There have been some major developments in urine separation at the source. The image on the left is a urine diverting toilet. The urine is directed into a storage tank  on site and transported to fields to be spread as a fertilizer – much like how liquid animal manure is utilized. Urine contains higher concentrations of macronutrients nutrients (nitrogen, phosphate and potassium) by mass than faeces and urine is sterile from a healthy person (Höglund 2001). Treating urine and faeces separately decreases the required sterilization storage period and maintains the level of nitrogen in the urine by limiting evaporation.  There are legitimate concerns about the safety for the people handling the waste and those consuming the crops grown from the excrement. To decrease this risk some institutes are focusing on just the use of human urine as a fertilizer. A healthy person will excrete sterile urine, while the same person can still excrete potentially harmful pathogens in their faeces. Still, the use of the human urine as a fertilizer has risks due to cross-contamination from the faeces. The study by Dr. Hoglund concluded that the use of human urine as a fertilizer in temperate climates is low risk (Höglund 2001).


The following table has recommended storage periods for urine depending on the crop to be fertilizer  and temperature.



Calculations were based on statistics in Sweden where the procedure of collection, transportation, and application of urine is mechanized (Höglund 2001) and in a country with few cases of mortality from to diarrhoeal diseases.

My question is: is human urine safe to use as a fertilizer in a developing country, such as India, with higher diarrheal outbreaks?

People’s health is potentially at risk for the six stages in the process of using the urine as a fertilizer (see the figure bellow): collection, storage, transportation, application, harvest and consumption. There is a risk of accidental ingestion of urine (urine-oral pathway of transmission) during the first four stages. And there is risk of harmful pathogens present on crops during the last two stages.


For my project, I did my own rough Quantitative Microbial Risk Assessment (QMRA) to assess the risk of using human urine as fertilizer for spinach in Northern India. The QMRA is used to calculate the potential disease burden from exposure to pathogens at each stage and is based on several wide-range factors, such as the distribution and the occurrence of indicator pathogens (Howard, Pedley et al. 2006). This method is not yet widely used in developing countries due to limited available data and its complexity (Howard, Pedley et al. 2006). MatLab was used to model the QMRA and the acceptable disease burden was set to the recommend < 10-3 (Höglund, Stenstrom et al. 2002).  I don’t want bore you with all the details so below is summary of the information I used.

Pathogen excreted in urine

The urine of a healthy individual is sterile in the bladder (Höglund 2001), but from an unhealthy person microorganisms can be transmitted to the environment and potentially cause infectious diseases. There are four commonly known pathogens excreted in urine: Leptospira interrogans, Salmonella typhi, Salmonella paratyphi and Schistosoma haematobium (Feachem, Bradley et al. 1983). Leptospira is a higher risk for sewage and farm workers in developing countries and is deemed an occupational hazard (Höglund 2001). The occurrence of infection is low and urine-oral transmission is not a key route (Feachem, Bradley et al. 1983). The S. typhi and S. paratyphi are more prevalent in developing countries with 16 million reported cases per year, but the probability of urine-oral transmission is low to that of faecal-oral transmission (Feachem, Bradley et al. 1983). For Schistosoma, the eggs are excreted in the urine and are then dependent on snails to continue their life cycle; thus again urine-oral transmission is low risk.

There are other examples of pathogens being excreted in urine, such as E. Coli (cause of more than 80% of urinary tract infections), Mycobacterium tuberculosis, Mycobacterium bovis and Microsporidia (protozoa implicated in HIV-positive individuals), but there is little evidence of urine-oral transmission (Höglund 2001).  Venereal diseases caused by pathogens have in some cases been reported to be excreted in urine but their potential survival outside of the body is low (Feachem, Bradley et al. 1983).

Pathogens excreted in faeces

The pathogens from faeces are the principal concern of microbial activity when setting safety standards (WHO 2011). Examples of parasites with the ability to cause disease in humans and are transmitted in human faeces  are Campylobacter, Salmonella, Giardia, Yersinia, Shigella, Balantidum coli and helminths ( Fasciola, Fasiolopsis, Echinococcus) – the list goes on, but the typical route of transmission is food-oral and soil-oral (Höglund 2001; WHO 2011). Helminths have higher rates of infection in developing countries, causing morbidity and mortality (Höglund 2001). The viruses excreted by faeces are estimated to cause 80% of the gastrointestinal infections in humans in the United States (Höglund 2001). One of the most commonly identified viral pathogens is the rotavirus which can be transmitted in waterborne outbreaks (Höglund 2001). Their reported cases are typically underestimated as not everyone goes to the hospital each time they are sick, and the aetiological agent is also typically not known (Höglund 2001). Some diseases are zoonoses making them difficult to track and control, but also increasing the complexity of transmission to humans (Höglund 2001). It should be noted that human faeces do not always contain harmful pathogens, but for a risk assessment their presence should be assumed.

Survival of Microorganisms

After excretion, the enteric pathogens decline due to death or loss of reproductive ability (viability), but their process of life and death is complex and difficult to approximate (Höglund 2001). For urine separated at the source, the main factors affecting the pathogens survival are temperature, pH and ammonia (Höglund 2001). After a few days, the stored human urine pH rises to 9.0, creating a noxious environment for pathogens, increasing decay rate sterilizing of the urine over time (Höglund 2001). The survival of the pathogens once the urine is applied as a fertilizer is assumed to be marginal (Höglund 2001). The risk of pathogens contaminating a water source downstream was also assumed to be low risk due to the high dilution from the rain fall (Höglund 2001).

QMRA Results for use of human urine as a fertilizer for spinach in Northern India*

The disease burden will change depending on the local conditions (temperature, mortality rates, disease outbreaks, etc.) and it is impossible to have exact data for every variable, but what this roughly calculated QMRA was able to demonstrate how important the risks are when using human urine as a fertilizer in countries with greater overall risks of diseases from cross-contamination of faeces. Knowing such facts should impact how organizations promote and manage the projects.

The acceptable disease burden was set to the recommended < 10-3 (Höglund, Stenstrom et al. 2002). For the worse-case scenario (low decay rates), the disease burden for each indicator was high above the set target = not safe. For the better-case scenario (typical decay rates), the disease burden was < 10-3 except for the rotavirus, which was above the target.

Based my assumptions from literature, the QMRA demonstrates that human urine as a fertilizer for SPINACH would be a high risk in developing countries. FOR OTHER CROPS, such as rice, THE RISK WOULD BE MUCH LOWER. The high risks could be decreased with proper communication and management, personal protective equipment (PPE, such as wearing a mask while collecting the urine) and with the use of better designed models which decrease people’s interaction with the urine. 

*These results are based on the frequency of diarrhea in India and for fertilizing spinach. The risk would be very different crops used to feed animals or crops where the edible parts are higher off the ground or are cooked before consumption. If you are interested in the methodology, let me know.


Feachem, R., D. Bradley, et al. (1983). Sanitation and disease – health aspects of excreta and wastewater management. Chichester, UK, John Wiley and Sons.

Höglund, C. (2001). Evaluation of microbial health risks associated with the reuse of source-separated human urine. Department of Biotechnology. Stockholm, Royal Institute of Technology. Doctoral.

WHO (2011). Evaluating household water treatment options: Health-based targets and microbiological performance specifications. Geneva, Switzerland, World Health Organization.


  1. m3macdou says:

    This may seem like a rather simplistic approach, but can we remove pathogens at the source by installing either a microfiltration or UV unit on the urine section of the toilet? I don’t imagine this would greatly increase the cost as it would be a similar system to those used for personal drinking water, just adapted to the toilet.

    • Thanks Mark – I have to look into using a filter for the pathogens. The issue I see arising are the salt precipitating out of solution and blocking the filter regularly. I will look into it!

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