Microbiological testing of livestock manures

Further testing of livestock manures may not be necessary if the following best practice is employed:

  1. Batch storage with no further additions of fresh material
  2. Extended storage for at least six months
  3. Implementing measures which prevent scavenging of the stored waste by wildlife 

The reason for the reduced testing requirement is that the safe storage period of six months was determined experimentally in the UK using a wide range of farm year manures (FYMs) and slurries from a range of domesticated livestock species during different seasons.  Furthermore, an additional amount of time was added to the experimentally-derived safe intervals to make especially sure that a 'safety interval' for total pathogen decline was allowed.  Thus, under best practice batch storage conditions, testing is really only to ensure that a batch of waste has not become re-contaminated by scavenging wildlife or an addition of fresh manure to the waste store.  

Figure 1 A butyl plastic-lined slurry tank which has been partly secured against scavenging by wildlife such as birds by use of a coarse metal grid. 

Testing however, may be of benefit if the waste has been stored for less than the recommended interval; has been at risk from scavenging by wildlife; or has been actively managed using a treatment which reduces, but may not eliminate, human pathogenic microbes (e.g. anaerobic digestion). If testing is required, a key consideration is the distribution of microorganisms within organic wastes.  Microorganisms are not evenly distributed throughout solid waste stores; considerable differences exist within the same heap due to variable proportions of faeces to straw or litter, nutritional and aerobic variations with faecal mass, and location in FYM heaps.  Similarly, slurry microflora can vary due to the amount of water present, oxygenation levels and the settling out of solids.  Careful sampling is therefore essential for accurate determination of the microbial population of fresh and stored animal wastes.  Where samples are to be obtained from more than one heap or lagoon, care must be taken to ensure that either clean, pre-sterilised equipment (spades, buckets etc.) is available for each sample.  Alternatively, equipment may be cleaned and disinfected between sampling each separate heap or lagoon to prevent microbial transfer between heaps, lagoons and farms.  A standard method, developed from Food Standards Agency-funded research, that describes how to collect samples of livestock manure which are representative of the stored material is available by clicking here.

Appropriate laboratory tests for manures and acceptable criteria and standards

When undertaking microbiological testing of manures, it is important that a recovery phase for bacteria is allowed before any selection is applied.  The environment created inside manure and an exposure to an oxygen-based atmosphere after the anaerobic conditions of a typical gut, is stressful to bacteria.  A recovery phase is required before exposure to selective media so that bacteria are not killed by the growth media designed to selectively promote their growth.  A brief overview of an appropriate laboratory isolation method for a number of key human pathogens is here.

A large amount of the guidance that exists for treated manures (either by extended batch storage or other treatment) concentrates on monitoring the treatment process.  The rationale is that if the treatment proceeds as expected, then the final material ought to be microbiologically inert.  Statements such as "55-60oC for several days" or "turn a manure heap frequently" tend to be provided.  It is important to recognise that whilst most of the heap may achieve "55-60oC for several days" or be effectively turned and aerated, it is likely that larger masses of waste may not be completely treated.  Microbiological testing of a properly-collected sample provides growers with an assurance that the material they are using is safe.

As has been previously explained for water testing, growers have a choice when undertaking microbiological testing.  Generally speaking, testing can be undertaken for pathogens (e.g. Salmonella species or Listeria monocytogenes) or for indicator species (e.g. generic E. coli or coliforms).  When compared with water, the choice is more difficult.  In the UK, the most recent survey which undertaken around 10 years ago, concluded that there was a one in three chance that a typical fresh livestock manure contained one of Salmonella, E. coli O157, Campylobacter, Listeria monocytogenes or Crypotosporidium parvum.  Collectively, these five species are responsible for a significant percentage of all food and water borne illness in the UK.  A one in three chance of detection in fresh manure is much greater than the odds of isolating a pathogen from water, and so there is some merit in pathogen testing of manures prior to use.  However, the likelihood of pathogen detection falls as the age of the manure increases. However, as for water, material derived from manure is likely to contain E. coli, coliforms and Enterobacteriaceae in numbers high enough to count even after prolonged storage.  Thus trending historical indicator results can provide early warning of any potential food safety problems.

An important consideration for growers when deciding to test manures prior to spreading is the cost.  A simple indicator test for E. coli or faecal coliforms typically costs less than £5.  A presence-absence test for Salmonella or E. coli O157 including biochemical or immunological conformation can cost more than £20.  The most expensive test is for viable numbers of Cryptosporidium parvum which requires several hours microscope work which generally costs in excess of £50.

As has been previously stated for water, there is no correlation between indicator numbers and the presence of pathogens in either fresh manure or processed biosolids.

In the EU, as for water, there are no standards or performance criteria which claim to reliably assure the food safety risks of manures being spread to land.  However there are some schemes which apply to related materials that have relevance.  Although it has not been widely adopted, in 1992 the European Commission approved a quality standard for ‘natural soil amendments’ produced within member states.  In 1998, the Directive was modified and updated to include specific microbiological criteria for general composted material used for soil enhancement.   Named the Eco-Label standard for composts, the criteria are an absence of Salmonella in 25g of material for pathogens, and less than 100 cfu/g for E. coli (Centermero et al., 1999).

In contrast to the EU, the USA have a loose framework called ‘the EPA 503 rules’ which have been widely adopted as a de facto compost standard.  The EPA 503 framework is wide-ranging and applies to all composted material spread to land, irrespective of whether the soil conditioner contains faecal material.  EPA 503 streams compost into one of four disposal categories depending on their chemical and microbiological ‘pollutants’ content.  The 503 rules stress that the different handling (e.g. reduction of the amounts spread to land for ‘higher risk’ material) of each of the four categories results in no difference in the overall risks of using different categories of compost.  A choice of microbiological criteria for the categorization of waste into one of the four categories are included in EPA 503.  For the least risky category - called exceptional quality (EQ); these are either that the density of fecal coliforms must be less than 1000 MPN g-1 of dried biosolids, or that Salmonella numbers are less than 3 MPN per 4 g of dried biosolids.


Anonymous 2008.  A Plain English Guide to the EPA Part 503 Biosolids Rule US Environmental Protection Agency. Accessed 22nd April 2010

Centemero, M., Ragazzi, R. and Favoino, E.  1999.  Label Policies, Marketing Strategies and Technical Developments of Compost Markets in the European Countries. ORBIT-99, Wiemar.