B05003/04: Pathogens in organic wastes - their levels and survival both during storage and following application to agriculture land

Study Duration: July 1999 to March 2004

Contractor: ADAS Consulting Ltd / University of Southampton

Large quantities of organic by-products, mainly animal manures, sewage sludge, food processing (e.g. abattoir) and industrial (e.g. de-inked paper) wastes are recycled to agricultural land in the UK, as an economical and environmentally friendly means of treatment and reuse. These materials have a fertiliser (nutrient replacement) value hence reducing the costs of agricultural production, and contribute to soil quality and fertility. However, these wastes can contain enteric pathogenic micro-organisms which creates the potential for the spread of food poisoning organisms from the farm environment into the food chain. Routes of transmission will vary and include: contamination of water supplies and hence either food crops by irrigation or livestock via sources of drinking water; contamination of animal feedingstuffs or direct ingestion of contaminated plants or leaves.

Over the past few years various guidance documents for farmers, waste contractors and interested parties have been produced, in particular the MAFF Codes of Good Agricultural Practice for the Protection of Water, Soil and Air and the DETR Code of Practice for Agricultural Use of Sewage Sludge. However, these have largely concentrated on measures to reduce chemical pollution and protect soil fertility. Consequently they have not addressed fully the issue of controlling the spread of pathogens. More recently UK retailers, via the British Retail Consortium, have raised concern over the microbiological risks associated with the application of sewage sludge to agricultural land. In response ADAS brokered a Safe Sludge Matrix, which gives recommended minimum time periods between the application of sludges to land and the use of that land for food production.

The Safe Sludge Matrix will help to minimise the risk of pathogens in sludge entering the food chain. However, there are 90 million tonnes of animal manures recycled to agricultural land per annum compared to only 520,000 tonnes of sludge in 1996/97. This means the agricultural use of animal manures potentially poses a far greater risk in terms of food safety.

There is scant information on the level of pathogens in animal manures or their survival during storage and after land application. This lack of data makes it difficult to assess the likelihood of pathogens in animal manures being transferred into the human food chain and therefore to determine whether current guidance such as the Safe Sludge Matrix is appropriate for manures in terms of minimising the risks to food safety.

The objectives of the project are as follows:

• To determine the levels of enteric pathogenic micro-organisms in stored and fresh animal manures produced on British farms.
• To study pathogen survival in manures both during storage and after application to agricultural land.
• To assess the risks of pathogens in animal manures transferring into the human food chain.

Technique development
Laboratory techniques to enumerate enteric pathogens in sewage sludges were developed at CAMR as part of research funded by the United Kingdom Water Industries Research (UKWIR) organisation. These methods have been validated in CAMR, ADAS, Southampton University and Thames Water laboratories for the most-commonly found animal manures produced by British farms: dairy slurry and farmyard manure; beef slurry and farmyard manure; pig slurry and farmyard manure; sheep farmyard manure; poultry broiler litter; poultry layer manure; and dirty water. Methods for the following pathogens have been validated: beta-glucuronidase negative E. coli including E. coli O157, Salmonella spp, Campylobacter spp, Listeria monocytogenes and Listeria ivanovii, Cryptosporidium parvum, Giardia intestinalis (lamblia).

Validation was undertaken by spiking the wastes with known levels of the pathogens, storage to stabilise the materials and recovery by a range of experimental procedures. The methods giving optimum recovery of the pathogens were further validated to ensure they gave satisfactory performance for sub-lethally damaged organisms.

Assessment of pathogen levels in freshly produced animal manures
To determine the levels of pathogens in fresh and stored animal manures a national study is being undertaken. A statistically-based sampling plan was developed which took into account factors such as: relative quantities of each manure produced in Great Britain, manure management practices, seasonality and animal husbandry. Based on this plan and using standardised sampling procedures, approximately 1500 samples are being collected from livestock farms throughout GB over a two year period. The samples are representative of the waste produced on the farms and are being examined for pathogens using the validated methods. 1000 of the samples will be of freshly produced manures with an additional 500 being from the same manures after on-farm storage.

Assessment of pathogen survival in manures during storage
The survival of pathogens in freshly produced animal manures is being investigated using both controlled laboratory experiments and farm-scale storage studies. Fully replicated laboratory studies are being undertaken at Southampton University. Manures seeded with pathogens were stored under different conditions and sampled regularly so that the effects of storage time, varying temperature, pH, ammonium, nitrogen concentration and dry matter content on pathogen survival could be studied.

The farm scale trials are being undertaken by ADAS. Liquid manures with high (c 10%) and low (c 4%) dry matters as well as dirty water were seeded with appropriate levels of pathogens and stored in 20,000 litre above-ground circular steel tanks. Solid manures were stored in managed (actively composted) and unmanaged 10m³ heaps. Samples of liquid wastes and litter bags for manures are withdrawn at regular intervals and pathogen levels determined. Environmental conditions are monitored throughout the storage period. At the end of this work survival curves for pathogens in all types of animal wastes will be produced and the factors which are likely to affect pathogen survival will be identified.

Assessment of pathogen survival after application of animal manures to agricultural land
Survival of pathogens in animal manures applied to agricultural land were undertaken also in controlled laboratory studies at Southampton University and in commercial-scale experiments at ADAS research centres.

The University of Southampton work is investigating pathogen survival in and on soil cores stored under a range of conditions. The effects of soil type, time, temperature, soil pH, soil moisture content and autochthonous soil microbial population are being studied. The commercial scale experiments are using fully controlled, replicated field plots. Manures seeded with pathogens are surface-applied in autumn and spring to arable stubble on sandy soil with immediate, delayed and no incorporation, as well as to grassland on medium loam with no incorporation. Pathogen survival is determined by taking and testing cores at regular intervals over a period of up to nine months. Environmental conditions are monitored over the same time period. Crops, e.g. carrots or radishes, are grown in the sandy soil and tested regularly to assess potential pathogen transfer. Grass cuttings are tested for numbers of pathogens in order to quantify the potential for pathogen transfer to grazing livestock.

Survival curves for the pathogens in different soils are being produced. Information gathered as part of these experiments will allow the identification of factors which influence pathogen survival and transfer.

Risk assessment
This project will produce information on:

• The levels of pathogens likely to be found in freshly produced animal manures in GB
• The survival of pathogens in animal manures stored under conditions similar to those used on British farms
• The survival and transfer of pathogens after application of manures to agricultural land

These data will form the basis of a quantitative risk assessment of pathogens shed in animal manures transferring into the human food chain.

Results from this study showed that British animal manures do contain measurable amounts of pathogenic microorganisms. Pathogens were isolated at incidences of 5.7% for E. coli O157, 6% for salmonella, 11.9% for listeria, 6% for campylobacter, 3% for cryptosporidium and 1.4% for giardia. There is a one in three chance that a manure sample collected from a British farm will contain at least one of the above pathogens.

Results also showed that pathogens die off very rapidly in solid manure heaps, if no fresh manure is added to the heaps. The temperature in some manure heaps rose to greater than 60°C within a few days and consequently less than one month of storage was required for total kill of all pathogens. Die off in slurries took longer. Although most pathogens had completely disappeared within four months, cryptosporidium was able to survive for at least six months in liquid manures.

Manures spiked with pathogens were spread to a loam soil and grass pasture to determine if pathogens in contaminated manures survived long enough to contaminate crops or grass subsequently grown on the land. These experiments were repeated during winter and summer to determine if the season influences pathogen survival. The results showed that pathogens survived for longer during winter, when temperatures were cooler. In addition, pathogens declined faster when manures were left unincorporated on the surface of the land rather than being ploughed under. Pathogens were no longer isolated from soil four months after manure spreading.

Experiments were carried out to determine how long E. coli - which is naturally present in faeces - could survive after being deposited directly onto land. The type of E. coli that was present was not pathogenic and occurred at higher levels than pathogens that are found in wastes. Thus the results of these experiments gave a conservative indication of how long pathogens could survive after direct deposition to land. E. coli numbers returned to their background levels six months after livestock were moved out of the fields being monitored.

In summary, this study has shown than a significant proportion of British livestock manures contain pathogenic micro-organisms. Often without storage, this waste is subsequently spread to land, which is used to grow crops or graze livestock destined for human consumption. Thus the common agricultural practice of manure spreading may be contributing to the incidence of foodborne disease in the UK. The results of the manure storage and spreading experiments have shown that pathogens die off over time. The studies determined safe batch storage time intervals for fresh solid manures as three months to ensure complete die off of any pathogenic bacteria that are present. Slurries should be stored for at least four months if the pathogens are bacterial, or eight months if the wastes contain cryptosporidium. At least six months should be left between the spreading of fresh or directly deposited manures and the harvesting of crops, as long as the manure is left unincorporated.

The results of these studies are currently being written into an easy-to-follow FSA guidance document that farmers can use to ensure that food produced on their farms is free from pathogen contamination.

Peer-reviewed publications arising from this project.

Hutchison, M.L., Walters L.D., Avery, S.M. and Moore A. (2005) Declines of zoonotic agents in livestock waste and bedding heaps. J. Appl. Microbiol. 99:354-362.

Hutchison, M.L., Walters L.D., Moore, A. and Avery S.M. (2005) Declines of zoonotic agents in liquid livestock wastes stored in batches on-farm. J. Appl. Microbiol. 99:58-65.

Hutchison, M.L., Walters, L.D., Avery, S.M., Munro, F. and Moore, A. (2005) Analyses of livestock production, waste storage and pathogen levels and prevalences in farm manures. Appl. Env. Microbiol. 71:1231-1236.

Hutchison, M.L., Walters, L.D., Moore, A., Thomas D.J.I. and Avery, S. M. (2005) Fate of pathogens present in livestock wastes spread to fescue plots. Appl. Env. Microbiol. 71:691-696.

Hutchison, M.L., Walters, L.D., Moore, A., Crookes, K.M. and Avery, S. M. (2004) Effect of length of time before incorporation on the survival of pathogenic bacteria present in livestock wastes applied to agricultural soil. . Appl. Env. Microbiol. 70:5111-5118.

Hutchison, M.L., Walters, L.D., Avery, S.M., Synge, B. and Moore, A. (2004) Levels of zoonotic agents in British livestock manures. Lett. Appl. Microbiol. 39:207-214.

Avery, S.M., Moore, A. and Hutchison, M.L. (2004) Fate of Escherichia coli originating from livestock faeces deposited directly onto pasture. Lett. Appl. Microbiol. 38:355-359.

The final report is available from the Agency's Information Centre.
To obtain a copy, please contact the Enquiry Desk, Information Services, Food Standards Agency (tel: 020 7276 8181/8182 or email: infocentre@foodstandards.gsi.gov.uk)

Contact: For any enquiries concerning this research project, please contact the relevant Programme contact or email science@foodstandards.gsi.gov.uk