A collection of processes whereby bacteria and other microorganisms hydrolyse (break down) biodegradable material in an oxygen free environment. The processes commonly generate gas such as methane that can be burned as an energy source.
A biofilm is a collection of microorganisms, frequently of different species, growing on top of a surface within a mesh of exopolysaccharide. Biofilms are resistant to a variety of environmental stresses such as desiccation and cleaning and sanitation chemicals.
Brucella is the causative agent of brucellosis an illness characterised by abdominal pain, diarrhoea, vomiting, rapid weight loss and impaired liver function. Brucellosis is a zoonosis transmitted by ingesting contaminated food, direct contact with infected wildlife or domesticated animals or the inhalation of contaminated aerosol. Brucellosis is difficult to treat because Brucella is an intracellular pathogen which can enter human cells to hide from the immune responses sent to tackle an infection.
A soil cap is a crust of hard soil that forms on or near the soil surface. Caps form in response to low rainfall, hot temperatures or strong winds. Some crops, such as baby carrots, can be damaged if they are harvested whilst the soil is capped. For that reason caps are softened by an application of water prior to the harvest of damage-susceptible crops.
The movement of an organism in response to a chemical stimulus. For example a bacterium that detects a diffusing nutrient may swim towards the source by following an increasing concentration of nutrient.
Citrobacter are a subgroup of the Enterobacteriaceae. The majority of strains are not pathogenic, and they rarely cause human illness. Citrobacter are widely dispersed in soils, waters and the waste from mammalian gastrointestinal tracts. The Enterobacteriaceae are an indicator of general hygiene of the environment used to grow and process crops.
Coxpox is a zoonotic disease spread from animals to humans. The causative agent is the cowpox virus. Human cases are very rare, although the UK has a higher incidence than continental Europe. Domestic cats and cattle udders are common sources of human infections. Cowpox is generally self-limiting, but can be fatal in immunocompromised patients.
A protozoa that can cause gastroenteritis, diarrhoea and severe cramping of the gastrointestinal tract in humans. A common route of infection for C. parvum is via contaminated drinking water. C. parvum is largely unaffected by common water treatments such as chlorination used to render water potable. Consequently, outbreaks can be quite large. In Milwaukee in 1993, more than 400,000 people became infected from drinking contaminated mains water. Commonly, C. parvum is isolated from water in the form of oocysts, which are stress-resistant, thick-walled spores; designed to survive for extended periods outside of a host. Ruminants such as cattle and sheep are common sources for the contamination of surface waters.
Escherichia coli is ubiquitous inhabitant of the gastro intestinal tract of a wide variety of mammalian, reptile and avian hosts. The majority of E. coli strains are harmless; however some acquire virulence genes that allow them to cause serious illness in humans. Human pathogenic strains of E. coli appear to be zoonotic agents because animal infection does not appear to cause much distress, although human infection can cause serious illness.
Although the majority of E. coli are harmless, some acquire virulence genes such as the abilities to attach to intestine walls and the manufacture of toxins that allow them to cause illness in humans. Not all strains of E. coli O157 and E. coli O157:H7 generate the toxins that help cause human illness. However, infection of E. coli with a type of virus called an stx-harbouring coliphage can confer an ability to manufacture a toxin that is closely related to one exported by Shigella called shiga-toxin. The reception required for coliphage infection is the H7 antigen, which is part of a whip-like flagella used by E. coli to propel itself though aqueous environments. Thus it is common for E. coli O157:H7 to contain toxin genes, although not all E. coli O157:H7 have the toxin genes.
Enterobacter are a subgroup of the Enterobacteriaceae. There are some strains that are pathogenic, although food is rarely a vector of infection. Commonly the Enterobacter cause infections of respiratory equipment, human airways and human urinary tracts. The Enterobacter are a member of the indicator group of bacteria known as coliforms, but tend not to grow at the elevated incubation temperatures required for faecal coliforms. The Enterobacter are also a member of the Enterobacteriaceae, a general hygiene indicator of the environment used to grow and process crops.
The Enterobacteriaceae are a large and diverse collection of more than 30 different species of bacteria. Despite the name, some members of the Enterobacteriaceae group can be isolated from surface waters and soil, although the majority are composed of bacteria associated with human and animal digestive tracts. The numbers of Enterobacteriaceae present in a test sample can be thought of as a general indicator of the degree of contamination acquired by fresh produce from contaminated water, insects, faecal material, wildlife, soil and other plants (including some plant pathogens).
Coliforms are a subgroup of the Enterobacteriaceae. They comprise mostly of the Escherichia, Klebsiella, Citrobacter, Enterobacter, and Serratia species; although some other species can grow on the selective growth media that is used to determine coliform numbers. Some members of the coliform group can also be isolated from the environment although they are more closely correlated with faecal material than the true Enterobacteriaceae. Faecal coliforms are a sub group of the coliforms. A higher incubation temperature used to isolate faecal coliforms. The underlying strategy of the increased temperature for faecal coliform isolation is that when coliforms have been present in the environment for a while, they begin to lose the ability to grow at the sorts of temperatures found in mammalian and other digestive tracts. The use of a higher incubation temperature selects for bacteria that have been recently deposited into the environment. It is worth noting that a very high percentage (more than 80%) of a faecal coliform count is typically made up of E. coli.
Many of the microorganisms that cause human illness are enteric pathogens, which means they colonise the gut of animals and humans. When they are colonised, animals shed pathogens into their faeces. The pathogens can then spread from the manure to other hosts. The faecal oral route is a common vector whereby the pathogens in faeces somehow finds it’s way from waste into the mouth of a new host. Common routes are infected people not washing their hands and touching doors and similar, leaving infectious agents behind, which are then picked up by other people.
A mixture of livestock faecal material and spent bedding. Typically, farmyard manure (FYM) has a dry matter content of greater than 13% (w/w). Unless it is properly composed or otherwise treated, FYM can be a source of microorganisms capable of causing human illness.
Heavy metal salts are a class of compounds that are composed of a heavy metal such as lead, mercury, arsenic or cadmium and a salt such as chloride, nitrite or phosphate. Heavy metal salts can pose a health risk to humans.
A pathogenic virus that causes illness and liver damage in humans. Like most viruses, the Hepatitis virus family has a very narrow range of hosts they can infect. Hepatitis A is only transmitted by the faeces of infected humans. The Hepatitis A virus and Hepatitis A infection of workers are specific indicators of quite fresh human faecal wastes.
Leptospirosis is a zoonosis, spread to humans from animals. Infection is commonly by touching soil or water contaminated with the urine of wild animals infected with the Leptospira bacteria. Typically, leptospirosis causes flu-like symptoms, including headaches and muscle pain. More severe forms of the infection are called Weil's disease, which is characterised by liver damage, bleeding and meningitis. Animals known to be carriers of Leptospira include cattle, pigs, dogs and rodents, particularly rats.
Listeria is the genus name for a range of closely-related bacteria that are widely dispersed in soils and on vegetation. Some of these bacteria such as Listeria monocytogenes can be pathogenic to vulnerable groups of humans. The vulnerable groups include pregnant women where some Listeria can cause spontaneous abortion of the unborn child. Elderly people and the immunocompromised are also susceptible to infection by some Listeria strains. General infections commonly result in Listeria multiplying in cerebrospinal fluids and symptoms similar to meningitis. Listeria monocytogenes
Listeria ivanovii is a type of Listeria that can cause infection in humans. However, L. ivanovii infection in humans is quite rare and the bacteria more commonly infects ovine hosts such as sheep. Infection with L. ivanovii can lead to sepsis (colonisation and multiplication of L. ivanovii in blood and an immune response that is damaging to the human) with enteritis (infection and inflammation of the small intestine) and the spontaneous abortion of lambs.
The best approach for food safety is to identify or create a critical control point (CCP) in a process that absolutely controls a foodborne hazard or reduces the risk from that hazard to an acceptable level. For processes where no CCP exists, a common strategy is to employ multiple stages that each reduces the hazard. Such a strategy is called a multiple hurdles approach. No individual hurdle completely controls the hazard, but each one causes a reduction and collectively they reduce the risk associated with the hazard to an acceptable level.
The Mycobacterium are a class of bacteria that are particularly robust. Their ability to survive outside a suitable host for extended periods is due to a particularly thick cell wall that is composed of waxy lipids and strongly hydrophobic. They are associated with variety of diseases in humans including Crones disease (M. paratuberculosis) and difficult to treat respiratory infections (M. tuberculosis). Common food vectors include the consumption of unpasteurised milk from an infected animal and the inhalation of air containing Mycobacterium aerosols.
Newcastle disease is a zoonotic illness that is typically spread from avian (bird) sources. The symptoms are mild conjunctivitis (inflammation of the eye) and flu-like symptoms, such as headache and muscle pain. The Newcastle disease virus is not considered to be very dangerous to human health.
Animal manures contain high concentrations of nitrogenous compounds including nitrates. If faecal wastes are disposed of by spreading to agricultural land close before a rainfall event or if too much waste material is applied to land, some of the nitrate can be washed into watercourses such as rivers and lakes. Nitrate pollution of surface water can cause rapid algal growth, which removes oxygen from the water, reduces fish numbers and has other negative impacts on aquatic populations.
Osmosis is a process that allows the movement of water across a natural or synthetic semi-permeable membrane. The process is driven by different salt or sugar concentrations on either side of the membrane. Generally, water will move from a low solute concentration to a high one in an attempt to equalise the solute concentrations on either side of the membrane.
The phyllosphere is the above ground external surfaces of plants. Phyllospheres include leaf surfaces (called phylloplanes) and the surfaces of flowers (anthoplane), seed bodies (carpoplane) and stems (cauloplane).
Protozoa are single celled eukaryotic organisms. In many ways they are considered to be an evolutionary stepping stone between bacteria and other prokaryotic organisms and simple multicellular life forms such as pond algae.
The rhizosphere is a narrow band of soil surrounding the roots of a plant. Rhizospheres benefit from nutrient exudates that leak from the plant roots. These exudates can support the growth of microorganisms some of which are beneficial to the plant.
Salmonella Bovismorbificans is one of the serovars of the Salmonella enterica species of human pathogens. Typical symptoms of human infections include fever, gastroenteritis including vomiting and diarrhoea; and sepsis. It has been linked in recent times with infections from chick peas and sesame seeds and products such as hummus and tahini made from these.
Salmonella enterica is a species of Salmonella that contains many serious human pathogens, including Salmonella Enteritidis and S. Typhi and S. Typhimurium. S. enterica infections are commonly traced back to contaminated foods. Typical symptoms of human infections include fever, such as typhoid fever; gastroenteritis including vomiting and diarrhoea; and sepsis.
Salmonella Typhimurium is one of the serovars of the Salmonella enterica species of human pathogens. S. Typhimurium is particularly problematic because it can infect a wide range of hosts including humans, cattle, pigs, sheep, foxes, cats and dogs, horses, rodents and chickens, geese and ducks. S. Typhimurium is an example of an invasive (the infection leaves the gut and travels in the bloodstream to other parts of the body such as the cerebrospinal fluids) Salmonella. Typical symptoms of human infections include fever, gastroenteritis including vomiting and diarrhoea; and sepsis.
The salmonellae are a complex genera of bacteria that are widely dispersed in mammalian, avian and reptile wildlife in Western countries. Some strains of Salmonella have the ability to infect humans and cause illness, although the majority of strains do not appear to significantly distress the wildlife they colonise. Thus Salmonella are classed as zoonotic agents. Typical symptoms of human infections include fever, such as typhoid fever; gastroenteritis including vomiting and diarrhoea; and sepsis.
Serratia are a subgroup of the Enterobacteriaceae. There are some strains that are pathogenic, although food is rarely a vector of infection. It is more common for Serratia to cause nosocomial (hospital-acquired) infections. A common member of the genus is S. marcescens, which is readily isolated from area that are constantly wet. The Enterobacteriaceae are a general hygiene indicator of the environment used to grow and process crops.
Slurry is a type of livestock waste which is commonly generated by cattle being fed a specific diet. Slurry has quite a watery consistency and has a dry matter content of between 4% and 9% (w/v). Some farmers favour waste generated as slurry because it can be collected in pits beneath slatted flooring in livestock sheds and readily pumped away.
A small, reproductive body that is highly resistant to environmental stresses such as desiccation, heat and the action of sanitisers and other chemicals. Fungi and some bacteria create spores as a survival mechanism in response to unfavourable, stressful environmental conditions or a shortage of nutrients. Some spores may remain viable for decades.
Streptococcus and Enterococcus are closely related bacteria that have been used as alternative indicators for faecal pollution of water. The isolation of different species of faecal Streptococcus, have been used with some success to enable differentiation between animal and human faecal pollution as a way of providing clues to the sources of water contamination. Human-derived faecal material contains a large percentage of enterococci as the dominant cocci whereas animal-derived material contains high numbers of streptococcus. Although attempting to use the ratios of enterococci to other streptococci may have a potential for use as pollution source indicators, although the strategy has at least one pitfall. The main drawback is that Enterococci and Streptococci populations decline in the environment at different rates. Enterococci, which are present at low levels in animal manures are more hardy than generic streptococci. In addition, the ratio of faecal coliforms to faecal streptococci (FC:FS) also has a potential for differentiating pollution sources. For fresh pollution, FC:FS ratios of >4 correlate well with human faeces, and <0.7 is more representative of animal faeces. However, as for the cocci discussed above, these ratios are subject to change with time because individual members of the coliform group, coliforms collectively and Enterococci decline in the environment at different rates.
Tannery wash is the waste product generated by the leather industry. Skins are tanned to make leather, which is less likely to decompose compared with untreated skin. Tannery wash is typically composed of preservatives such as dithiocarbamates, fungicides, the solutions used to dehair and degrease the skins and alkali.
Thermal and chemical water treatments involve manipulation of irrigation water to render it unfavourable for bacterial survival. Chemical treatment can be problematic and has the potential to impact irrigated crops.
Trihalomethanes are a class of chemical compounds in which three of the four hydrogen atoms of methane (CH4) are replaced by halogen atoms. The halogens include fluorine, chlorine, iodine and bromine. Trihalomethanes are environmental pollutants that spontaneously form when sanitisers such a chlorine are applied to water or surfaces with a high organic content. Many trihalomethanes are considered carcinogenic (cause cancer).
Ultraviolet light (UV) is defined as electromagnetic radiation with wavelengths between 200nm and 400nm. Exposure to UV radiation damages DNA and causes reductions in the numbers of viable bacteria. Water cloudiness has a large impact on UV effectiveness.
Yersinia are a subgroup of the Enterobacteriaceae. The majority of strains are not pathogenic, although some members of the genera can cause illness such as bubonic plague and have been linked with inflammatory bowel disease. The Enterobacteriaceae are an indicator of general hygiene of the environment used to grow and process crops.