Managing Potential Pathogenic Bacteria in Our Composts

Managing potential human, plant and animal pathogens during composting is important to reduce the risk of spreading disease. It is now even more important with the increasing concern regarding antibiotic resistant microorganisms (WHO 2016) and the role of the microbes in our environment (Fletcher 2015). The World Health Organization published a list of bacteria for which new antibiotics are urgently needed (WHO 2017). Many of these bacteria may be present in the organic material that we are composting,  which means we must be diligent in managing potential pathogens, but also potential pathogens that may be antibiotic resistant.

Many of us understand that there is a time temperature relationship for potential pathogen kill, where maintaining temperatures greater than 55-60 C in our composting material for a number of days will kill potential pathogenic organisms. Most fecal coliforms or potentially pathogenic organisms in our compost may not actually be pathogenic, however, we are not always able to easily distinguish them. Some of us are surprised and bewildered when, in spite of our best efforts at maintaining temperatures required for potential pathogen kill, the fecal coliform bacteria in our curing or finished compost are still high!

We are not alone. There have been some excellent research reviews on the survival of potentially pathogenic organisms in our compost. Jones and Martin (2003) observed that bacteria such as E. coli and Salmonella “may grow in the final compost if the process has been inefficient and the organic matter remains poorly stabilized.” Wichuk and McCartney (2007) reviewed the literature on time – temperature relationships for pathogen kill during composting and concluded that regrowth does occur. Brinton et al. (2009) found that 33% of 94 marketed composts in the US contained E. coli. 41. Isobaev (2014) provided an excellent literature review and research on potential pathogen survival during composting.

In our compost facility operator training courses, we have stressed that inactivation of potential pathogens during composting is a two step process. The first step is to ensure that all of the material being composted reaches temperatures required for potential pathogen kill. The second step is to allow the composting process to degrade the readily available carbon compounds on which the potential pathogenic feed. When we consider the science and what actually happens at compost facilities, it may not even be as simple as this!

In the next few blogs, we will review the following topics as they relate to managing potential pathogenic bacteria, including:

  1. Fecal coliform and E. coli as indicator organisms
  2. ensuring that all of the composting material reaches temperatures required for potential pathogen kill
  3. potential regrowth and the role of viable but not culturable microorganisms
  4. MPN and CFU, are they the same thing?
  5. Conditions during curing which may feed E.coli and other potentially pathogenic microorganisms.

Our goal is to be as diligent as we can in reducing the potential spread of potentially pathogenic microorganisms, particularly of antibiotic resistant microbes.


Brinton, W.F. Jr., P. Storms and T.C. Blewett. 2009. Occurrence and Levels of Fecal Indicators and Pathogenic Bacteria in Market-Ready Recycled Organic Matter Composts. Journal of Food Protection 72: 332–339.

Fletcher, S. 2015. Understanding the contribution of environmental factors in the spread of antimicrobial resistance. Environ Health Prev Med 20:243–252 DOI 10.1007/s12199-015-0468-0.

Isobaev. P. 2014. Developing and Testing a Framework to Measure the Sanitation Efficacy on a Random Particle Level in the Composting Industry. PhD Thesis. Department of Civil and Environmental Engineering, University of Alberta.

Jones, P. and M. Martin. 2003. A review of the literature on the occurrence and survival of pathogens of animals and humans in green compost.  Waste and Resources Action Programme.

WHO 2016. Antibiotic resistance. Factsheet October 2016. World Health Organization

WHO 2017. WHO publishes list of bacteria for which new antibiotics are urgently needed. February 27, 2017. World Health Organization.

Wickuk, K.M and D.M. McCartney. 2007. A review of the effectiveness of current time-temperature regulations on pathogen inactivation during composting. J. Environ. Eng. Sci. 6: 573-586

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