Indicator Organisms for Potential Pathogens: Fecal coliform or E. coli?

How do we know that our compost is free of potential pathogenic organisms? The test that we use in our British Columbia regulation (OMRR) is fecal coliform bacteria, as an indicator organism. This is in part based on the US EPA Biosolids Rule 503, which suggests that fecal coliform is a good indicator organism:

“Fecal coliforms are enteric bacteria that are used as indicators of the likelihood of the presence of bacterial pathogens. Although fecal coliforms themselves are usually not harmful to humans, their presence indicates the presence of fecal waste which may contain pathogens. These bacteria are commonly used as indicators of the potential presence of pathogens in sewage sludges. They are abundant in human feces and therefore are always present in untreated sewage sludges. They are easily and inexpensively measured, and their densities decline in about the same proportion as enteric bacterial pathogens when exposed to the adverse conditions of sludge processing.” (EPA 2003).

More recent Compost Regulations use E.coli as the indicator organism rather than fecal coliform, because of concerns with bacteria of non-fecal origin are included in the fecal coliform test.

“The microbiology literature is replete with reports of studies that correlate results of fecal coliform levels with the presence of E. coli including several recent examples that advocate the fecal coliform test as an acceptable indicator in manure composts and foods. However, the value of the fecal coliform assay as an indicator of fecal contamination is negated when bacteria of nonfecal origin are the principal microbes detected by the assay.” (Doyle and Erickson 2006).

Brinton et al. (2009) observed an excellent correlation between E.coli and fecal coliform in a composts produced in Oregon and California. More recent regulations (Ontario Ministry of the Environment 2012) and the UK PAS 100:2011 (BSI 2011) use E.coli as the indicator organism for fecal contamination. Gilbert (undated) reported that measuring E.coli “is useful to demonstrate a stable product without feacal bacteria” and measuring feacal coliforms “may be problematic due to variable species composition”.

The discussion with indicator organisms has been occurring with water for a longer time. The World Health Organization (2001) has an excellent review of the indicators of water quality, and suggested that E.coli is a more specific indicator organism:

“Many members of the total coliform group and some so-called faecal coliforms (e.g. species of Klebsiella and Enterobactero) are not specific to faeces, and even E.coli has been shown to grow in some natural environments. Hence, the primary targets representing faecal contamination in temperate waters are now considered to be E. coli and enterococci.”

The BC Approved Water Quality Guidelines also discusses the limitations of measuring only fecal coliform:

“Fecal coliforms have historically been the indicator of choice, but their presence does not always correlate well with the incidence of disease. Coliforms are therefore now being supplanted by more specific indicators. These include Escherichia coli and enterococci which are good indicators of gastrointestinal disease, and Pseudomonas aeruginosa which correlates well with ear and skin infections. Criteria are set in this report for these three other indicators as well as for fecal coliforms. Although the fecal coliform criteria are the only ones that apply now, they will be phased out in the future as the change to other organisms occurs.”

We suggest that in BC, we measure fecal coliform as required by the current regulation, but also measure E.coli as a more specific indicator of potential pathogenic organisms.


BC Ministry of Environment. 2001. Approved Water Quality Guidelines Microbiological Indicators 2001 (

BC Ministry of Environment. 2002. Organic Matter Recycling Regulation.

Brinton JR., W.F., 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.

BSI. 2011. PAS 100:2011. Specification for Composted Materials.

Doyle, M.P. and M.C. Erickson. 2006. The fecal coliform assay, the results of which have led to numerous misinterpretations over the years, and may have outlived its usefulness. Microbe April 2006 (

Gilbert, undated. Monitoring sanitisation in practice at composting sites. The Composting Association.

Ontario Ministry of Environment. 2012. Compost Quality Standards.

US EPA. Control of Pathogens and Vector Attraction Reduction in Sewage Sludge. Environmental Regulations and Technology. EPA/625/R-92/013 . Revised July 2003. (

WHO. 2001. Indicators of Water Quality. Chapter 13. In L. Fewtrell and J. Bartram, eds. Water Quality: Guidelines, Standards and Health. IWA Publishing, London, UK.

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