Pathogens in manure

John H. Kirk, Extension Veterinarian, UC – Davis

Many potential pathogens for livestock as well as humans can be found in manure of both livestock and poultry. These pathogens include bacteria, protozoan and viruses. The focus of this [article] will be on those pathogens commonly found in bovine manure with the greatest risk of infection for humans. When these potential pathogens move through the slaughterhouse on livestock or poultry, they may cause disease in humans.

E. coli 0157
Cattle are thought to be the primary reservoir of E. coli 0157. Poultry and birds are not felt to be important sources or reservoirs of human infections. In dairy cattle, while in most herds a fecal shedder can be found by diligent search and repeated cultures, the prevalence of fecal shedders is usually less than 1 percent of the herd. The greatest prevalence is usually found in heifers and calves under 24 months of age. Calves that have been recently weaned off milk appear to have the highest prevalence. The prevalence in milk-fed calves is very low.

While fecal shedding is sporadic, it does seem to occur at the same time in clusters of animals. Feed deprivation may cause animals to increase their shedding. The amount of E. coli 0157 shed in the manure is estimated to be between 3 and 50,000 colony-forming units (cfu) per gram of feces. Note that the E. coli 0157 infective dose for humans is about 10 cfu – the lowest of the common human food-borne pathogens.

Fortunately, E. coli 0157 does not persist for long periods in the dairy environment. This may reflect pressures from the environment itself or it may reflect the shedding patterns of animals – sporadic and short-term. Fecal shedding in cattle has not been found to reflect grazing on forages that have been fertilized with cattle manure. This may be another indication that E. coli 0157 does not survive for long periods after being spread on fields.

As illustrated by some of the foods that have been contaminated by E. coli 0157, it can grow under conditions normally considered adverse for bacteria. Outbreaks have occurred from contaminated apple cider that was kept refrigerated and has a low pH. Other times it has been found in contaminated hard salami with high nitrates, nitrites and salt content. It actually survives better in colder temperatures.

Listeria
This bacterium is found naturally living in plants and soil as well as poorly fermented silage (high pH). Cattle seem to shed more Listeria in their feces during the colder winter months. Many humans and livestock, especially sheep, are carriers. Shedding is induced by stress such as birthing or prolonged transportation. Fresh vegetables fertilized with animal manure are thought to be important sources of contamination for humans. Listeria grows well at a wide range of temperatures, wide pH range and in high salt concentrations.

Salmonella
Many types of salmonella are known to exist (2000+ species). Fortunately, only a few consistently cause disease in cattle or humans. Up to 75 percent of dairies are positive on fecal culture for Salmonella. Over 50 percent of cattle have been found to be shedding on some dairies. A small percentage of cattle are colonized carriers that continually shed Salmonella in their feces. Most shedding cattle have between 20 to 50,000 cfu of salmonella per gram of manure. There are many other sources of Salmonella on dairies such as contaminated feeds, rodents, wild animals and birds.

Salmonella has been reported to survive in detectable quantities (small quantities at the limits of detection by culture) for 286 days in slurry or lagoons. However, there is a 90 percent reduction in slurry in just 30 days. Salmonella survival in manure is highly dependent on temperature and ammonia concentration.

Mycobacterium paratuberculosis
M. paratuberculosis is the causative organism for Johne’s Disease in cattle. Infected cows may shed the pathogen in their feces for months to years before developing clinical signs. At the peak of shedding, an infected cow may shed a million bacteria per gram of manure.

Cows with clinical signs of diarrhea and weight loss tend to shed more bacteria in their feces than non-clinically infected cows. Two thimbles full of manure from an infected cow is enough to infect a calf. Consider forage crops that had fresh manure applied as fertilizer as a feed risk to young stock. The bacteria can live in the environment for up to one year.

Cryptosporidia and giardia
These protozoan are shed by wildlife, livestock and humans. The primary concern is water contamination from livestock manure. Dairy calves between 7 and 21 days old are the main shedders for Cryptosporidia on dairies. Beef calves are also the main concern for beef cattle; however, they shed at a slightly older age than dairy calves, 2 to 4 months old.

Both of these organisms survive for a long time in manure. Lagoons are usually not contaminated with Cryptosporidia unless flushing systems are used to remove the manure from beneath pens of young dairy calves.

Survival of pathogens
Survival of potentially pathogenic organisms in manure depends on many factors including: type of slurry or manure, pH, dry matter content, temperature, numbers and type of pathogens present and presence of competing organisms.

Keep in mind that manure is also made up of various elements including feces, urine, bedding materials, flush water, placenta, abortus, dead wildlife and animal secretions (nasal, blood, reproductive, mammary). There are many different organisms within what we commonly term “manure” and each of these has a preference for location. In general terms, the limiting factors are exposure to sunlight, extreme temperatures and exposure to oxygen and ammonia.

Manure management methods
Many different systems and combinations of systems for manure removal and handling can be found. Liquid manures are used for year-round irrigation, spread as a slurry, sold or transported off the dairy or seasonally irrigated. Solid manure is spread on farm land, used for bedding, sold off the farm, removed from the farm or composted.

Influence of storage methods
The method of manure storage will also impact the pathogen content of the manure. There are three common methods for handling manure – lagoon storage (slurry), deep stacking and composting. Each method may result in a decrease in the number of pathogens from the initial amount found in the manure. The rate of destruction and site of destruction may vary between methods of storage.

Stacked manure
Manure that is placed in large piles after removal from livestock housing areas is referred to as stacked manure. It is usually not turned. Heating does occur in the stack; however, it is non-homogeneous – therefore it is possible for pathogens to survive in unheated areas. Pathogens that do survive, survive near the outer crust of the stack. It has been reported that salmonella can survive for up to 200 days in stacked manure. Stacked manure is usually spread on pasture between crops.

Composting
During composting, stacked manure is turned periodically to insure that all areas of the pile reach at least 131 to 149ºF) for three days or more. Periodic turning of the pile eliminates areas within the pile and near the crust that might escape the heating process. Most composting guides suggest that the pile should be turned when the temperature exceeds 145ºF.

If the piles do not heat, they can be turned to induce heating. Often the piles need added materials if the pile dry matter is too low. Usually water is added to begin the heating process after more materials are added. After several turnings, the pile should be left undisturbed for at least a month.

Lagoon or slurry
The liquid and its contained dry matter substances taken from lagoons is slurry. The slurry is usually stored for variable time periods in the lagoon before application to pastures or field crops. During the storage time, most pathogens decline in numbers from the initial loading amounts. Storage for at least one month prior to spreading on land significantly reduces the level of salmonella contained in slurry. Colder slurry temperatures favor longer survival of salmonella.

Dry matter content and pH are other important factors. The effects of temperature, dry matter content and pH may not act directly on the salmonella. Their effect may be to favor the growth of other organisms found in the slurry that in turn affect the growth or survival of salmonella. Often there is a 90 percent reduction in the number of salmonella in the lagoon during the first two weeks.

Summary
Several potential pathogens can be found in manure. Most of these pathogens transfer by fecal contamination of feed or animals followed by ingestion. The number of pathogens is usually reduced by most storage methods used on dairies. ANM

References omitted but are available upon request at editor@progressivedairy.com

—Excerpts from UC Davis School of Veterinary Medicine website