Food Microbiology 

12/10/2018 

Fundamental Food Microbiology 

Objectives 

1. Identify the basic types of microbes. 

2. Describe the typical bacterial growth pattern, and explain important factors 

affecting microbial growth. 

3. Describe basic mechanisms and indications of microbial food spoilage. 

4. Describe how certain microbes are used in food preservation. 

5. List important pathogens of concern in meat and poultry products. 

6. Describe sources of microbes in meat and poultry products. 

7. Explain fundamental methods of controlling microbial contamination of meat 

and poultry. 

Introduction 

Microbiology is a specialized area of biology dealing with organisms too small to be 

seen without sufficient magnification. Microbiologists study bacteria, fungi, parasites, 

and viruses, including their interactions with humans, animals, plants, and the 

environment. While viruses are not a living organisms like bacteria, fungi, and parasites, 

they are studied by microbiologists; therefore, we will use the term microbe (any 

microscopic entity that exhibits the properties of life) to collectively refer to any of these 

biologically active and microscopic entities. In addition, there is an infectious agent 

responsible for numerous neurodegenerative diseases found in animals and humans 

known as “prions”, which will be covered in this module. 

Food microbiology is specifically concerned with the desirable and undesirable effects 

microbes can have on the quality and safety of food products. In this section, we will 

briefly survey the importance of microbes in food, as well as prions. We will have an 

overview of some the fundamental microbiological concepts and consider how microbes 

are involved in food spoilage, food preservation, and foodborne illness We will conclude 

by considering the sources of microbes and prions and the l ways in which both may be 

controlled in food processing environments. 

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Types of Microbes 

Bacteria 

Bacteria are small, single-celled organisms that occur in almost any natural 

environment. Common bacteria are too small to be seen individually without the aid of a 

microscope. Bacteria can multiply to form groups or colonies on a food source. After a 

sufficient number of replication cycles a colony of bacteria can be seen with the naked 

eye. 

Viewed under a microscope, different kinds of bacteria will have different shapes or 

forms. Many bacteria have either a spherical shape or an elongated rod shape. A 

spherical shaped bacterium (singular) is called a coccus, and a group of sphericalshaped bacteria (plural) are called cocci. A rod shaped bacterium is called a bacillus, 

and a group of rod-shaped bacteria are called bacilli. 

Some species of bacteria appear as individual cells microscopically. Other bacterial 

species may combine to form pairs (e.g., diplococci), groups of four (tetrads), grape-like 

clusters (e.g., staphylococci), and chains (e.g., streptococci or streptobacilli). 

Many bacteria have projections from their cell walls called fimbriae (or attachment pili). 

These structures assist those bacteria in attaching to one another as well as to other 

surfaces. Some types of bacteria possess flagella that allow those bacteria to be motile. 

Certain bacteria (e.g., Clostridia spp.) have the capacity to sporulate or form spores 

(also called endospores). Simply put, a spore-forming bacterium encapsulates its vital 

structures in a tough outer coat when environmental conditions become harsh. Spores 

are resistant to heat, chemicals, and other environmental conditions. Bacterial spores 

are unable to reproduce; however, once conditions again become favorable for growth 

the spores reactivate and become vegetative (reproducing) cells again. 

Some bacteria can produce toxins that in sufficient doses cause foodborne illness (e.g., 

botulism). Toxins can be produced by spore-forming bacteria, but only in the vegetative 

state. Suppressing reactivation to the vegetative state, then, is important in ensuring 

food safety in many processes. Some non-spore forming bacteria, like Staphylococcus 

aureus, can also produce toxins. 

Fungi 

The fungi consist of two major groups of microbes, molds and yeasts. Molds are multicellular organisms. Yeasts are single-celled organisms. Molds and yeasts tend to be 

significantly larger than bacteria. Both molds and yeasts are widely distributed in nature, 

both in the soil and in dust carried by air. 

Molds have a branching filamentous structure, and can develop into colonies visible as 

a colorful, furry or downy coating on food or surfaces. They reproduce by producing 

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small spores, which are not related to bacterial spores mentioned above. Mold spores 

can be picked up and spread by air currents. If mold spores settle on suitable surfaces, 

they will begin to germinate and produce new mold growth. 

Yeasts are usually egg-shaped, and tend to be smaller than molds. Like molds, yeasts 

can be spread via air currents. They reproduce by a process known as budding. Visible 

colonies of yeast are generally slimy in appearance and creamy white. 

Parasites 

Parasites are living organisms that derive nourishment and protection from other living 

organisms called hosts. These organisms live and reproduce within the tissues and 

organs of infected human and animal hosts. There are different types of parasites, and 

they range in size from single-celled protozoa to multi-cellular worms. Protozoan 

parasites are visible only through a microscope. Many adult parasitic worms are visible 

without a microscope; however, a microscope is necessary for detecting eggs and preadult forms of some worms. Identification of the adult forms of certain parasitic worms 

can also require microscopy. 

The respective lifecycle of different parasites also varies. While some parasites use a 

permanent host, others go through a series of developmental phases using different 

animals or human hosts. They may be transmitted from host to host through 

consumption of contaminated food and water. Several parasites have emerged as 

significant causes of foodborne and waterborne illness. 

Viruses 

Viruses are much smaller than bacteria. They are too small to be seen with a standard 

light microscope. An electron microscope is necessary to see viruses. These microbes 

are not true living organisms. They are composed of genetic material—either 

deoxyribonucleic acid (DNA) or ribonucleic acid (RNA)—enclosed in a protein coat. A 

virus must invade a living host cell in order to replicate. Once inside the host cell, the 

viral genetic material directs the host cell’s “machinery” to make more virus particles, 

which interferes with normal host cell function and may result in destruction of the host 

cell. 

Infectious Agent – Prions 

Prions are not true living organisms; they are proteinaceous infectious particle with no 

nucleic acid genome. The prion protein exists in every mammal in a healthy state and is 

called cellular prion protein (PrPc). When misfolded they become a proteinaceous 

infected particle (PrPSc). 

Protein molecules fold into a three-dimensional (3-D) form. The 3-D form of a particular 

protein is related to its particular biological function. Folding into its normal form, then, 

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allows a protein to be functionally active. Failure of a protein molecule to fold into its 3-D 

normal form renders it dysfunctional and harmful to tissue or organs. As mentioned 

earlier, prions are misfolded proteins (aberrant or abnormal form – PrPSc) that appear to 

be infectious causing disease within the animal itself or when transferred from one 

animal to another. The mechanism by which this change occurs is not clear. To 

understand the structure of prion proteins, scientist use different techniques including 

magnetic resonance imaging and X-ray crystallography. 

Prions are the prevailing theory for what causes a group of neurodegenerative diseases 

called transmissible spongiform encephalopathies (diseases of the brain). Bovine 

spongiform encephalopathy (BSE), also referred to as mad cow disease, is the 

transmissible spongiform encephalopathy that affects cattle. There are several 

transmissible spongiform encephalopathies that affect humans, such as Creutzfeldt– 

Jakob disease (CJD), Gerstmann-Straussler Scheiker Syndrome, Fatal Familial 

Insomnia and Kuru, but only CJD has been associated with meat consumption. The 

prion responsible for BSE appears to be infective to humans, and the resulting disease 

is called variant Creutzfeldt–Jakob disease (vCJD). Protein molecules are incapable of 

replicating themselves; the cells that make up the organs and tissues of animals and 

humans must manufacture them. As stated previously, the process by which prions are 

produced is not clearly understood. It is likely that prions cause other protein molecules 

to misfold (amplification process) or somehow induce cells to produce more misfolded 

proteins. 

Microbial Growth 

Our discussion of microbial growth will focus primarily on bacterial growth. Similar 

concepts apply to the growth of molds, yeasts, and some protozoa. Many parasites 

have complex life cycles, a discussion of which is beyond the scope of our purposes 

here. The most important parasites (e.g., Trichinella spiralis in pork) cannot reproduce 

in meat or poultry products. Replication of viruses will also not be discussed, because 

these microorganisms can only be replicated in the live animal. 

If favorable environmental conditions exist, bacterial growth occurs. For our purposes, 

we will use the term growth to refer to an increase in microbe numbers, not an increase 

in size of an organism. Bacteria reproduce by dividing, a process called binary fission. 

When a bacterial cell is ready to divide, the material within it gradually increases until 

the cell’s volume is almost doubled. The cocci shapes become oval while rod shapes 

stretch to nearly twice their length. The cell then constricts in the middle. This 

constriction deepens until the cell contents are held in two distinct compartments 

separated by a wall. These two compartments finally separate to form two new cells, 

which are duplicates of the former cell and each other. 

Theoretical growth patterns can be represented by a graph of bacterial numbers over 

time and broken down into four different stages or phases. 

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Bacterial Growth Chart 

The first phase is called the lag phase. The lag phase occurs when a bacterial 

population first enters a nutrient rich environment. The rate of growth is very slow 

because the bacterial cells are adjusting to their new environment. In a nutrient-rich 

environment, such as on a meat or poultry product, the lag phase is generally short; 

however, the length of the lag phase is the most variable of the four phases. For 

example, it will take a bacterium longer to adapt to temperatures below the optimum 

growth range for that bacterium. Therefore, good temperature control will prolong the 

lag phase. Other environmental factors, including pH, water activity (aw), and 

competition with other microbial species for nutrients, can also impact the length of the 

lag phase for a particular microbe. 

After some hours or days, depending on environmental conditions and characteristics of 

the particular bacterial species, the bacterial cells begin to rapidly multiply. This phase is 

called the log phase because growth occurs exponentially and is depicted on a 

logarithmic scale on the vertical axis of the growth curve. A logarithmic scale basically 

allows a wide range of values to be displayed on a graph of manageable size and in a 

visually meaningful way. Such a scale is necessary because bacterial growth can occur 

at an exponential rate, i.e., 1 cell becomes 2 cells, the 2 cells become 4, then 8, then 

16, then 32, then 64, etc. With each successive replication, the total number of cells 

doubles. The time it takes for the population of bacteria to double is referred to as 

doubling time or generation time. This doubling time can vary among species of 

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bacteria, but for most is between 10 to 30 minutes under optimal conditions for growth. 

It is important to note that, while the starting bacterial count may not have an effect on 

doubling time it will have a tremendous effect on the numbers of bacteria after each 

doubling. For example, the numbers of bacteria will differ tremendously after 1 doubling 

time if the initial count is 200 cells (become 400 cells with the first doubling) vs. 2 cells 

(become 4 cells with the first doubling). Effective sanitation to reduce bacterial load will 

limit the number of cells available to contribute to proliferation during this phase. 

Exponential Growth Example: Let’s assume a particular species of bacteria doubles 

every 30 minutes. After one hour, a single bacterium of that species becomes four. At 

the end of two hours, there will be 16 bacteria. After 15 hours, there will be 

1,000,000,000 (one billion) cells. Relating this to the processing environment, consider 

a situation where there are 75,000 of those bacterial cells per square inch on a 

conveyor belt and growth conditions are ideal. By the end of one hour there could be as 

many as 300,000 bacteria per square inch of that belt. At the end of three hours, the 

bacteria count per square inch of belt surface could be 4,800,000. 

The length and slope of the log phase will depend on a variety of factors, including 

nutrient availability, buildup of bacterial waste products, and temperature. For example, 

many bacteria still grow under refrigeration temperatures, just very slowly. The slope of 

the log phase, then, would be less steep, and the log phase prolonged. Therefore, the 

rate of growth would be much slower at refrigeration temperatures than under optimal 

conditions. 

NOTE: Later we will refer to a change in bacterial numbers as a log increase 

(multiplication) or log decrease (reduction). The concept of a log change is 

mathematically different from that of exponential growth during the log phase, and the 

two should not be confused. In mathematical terms, a graph of the phases of bacterial 

growth is a plot of the natural logarithm of cell number against time. When referring to 

processes that result in a given log increase or log reduction in the numbers of bacteria, 

calculations will be based on the common logarithm (log10 or log base 10). 

The third phase is the stationary phase. In this phase the rate of bacterial growth is the 

same as the rate of bacterial death, because the population of bacteria has reached its 

maximum due to limitations in the availability of nutrients and an increase in bacterial 

waste products. 

The fourth phase is the death phase. In this phase, more bacterial cells are dying than 

those that are dividing. There is a net loss in the number of viable bacterial cells in the 

environment. This is the result of increasingly hostile environmental conditions 

associated with decreasing availability of nutrients and increasing waste products. 

Initially the rate of death is exponential, but it may slow down after significant numbers 

of bacterial cells have died. Spore-forming bacteria may begin to sporulate and remain 

viable but dormant. Because the nutrient supply in meat and poultry products is almost 

unlimited, an exponential rate of death may not occur. 

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Factors Affecting Microbial Growth 

There are a variety of factors that affect the rate of microbial growth in food. Again, our 

discussion will focus on bacteria; however, much of it is applicable to yeasts and molds 

as well. It is not applicable to parasites or viruses. 

Like all other living organisms, bacteria require favorable environment to live and grow. 

There are six basic environmental factors that impact bacterial growth. An easy way to 

remember these conditions is to use the memory device FAT TOM. 

Food Composition Acidity Temperature 

Time Oxygen Moisture 

Food Composition 

Here we are using the word food to refer to nutrients available to the microbes, which 

could be a human food product, product residue on equipment, or organic debris in 

some non-product contact growth niche. A suitable supply of nutrients is the most 

important condition affecting growth of bacteria. Every living cell requires certain 

nutrients to multiply. These include solutions of sugars or other carbohydrates, proteins, 

and small amounts of other materials such as phosphates, chlorides and calcium. If the 

nutrient supply is removed, bacteria will not multiply. 

Acidity 

The degree of acidity or alkalinity of an aqueous solution is expressed on a scale 

between 0 and 14 referred to as the pH scale. As acidity increases, we move down on 

the pH scale (i.e., the pH is lower). As alkalinity increases, we move up on the pH scale 

(i.e., the pH is higher). The pH of pure water is 7.0, which is referred to as neutral pH. 

The pH of a meat or poultry product can have a profound effect on the growth and 

viability of microbial cells. Each species of microbe grows within an optimal range of pH 

values. Most microbes thrive when the pH is near neutral or slightly acidic, but there are 

exceptions. Most bacteria will not grow at pH levels below 4.6 because the environment 

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is too acidic. Many molds and yeasts can grow at a lower pH than do bacteria. On the 

basis of pH, food products are often grouped as high-acid foods (pH below 4.6) and 

low-acid foods (pH 4.6 and above). The pH of fresh meat ranges between 5.3 and 6.4 

(i.e., high pH or low-acid). Meat with a pH in the 6.0 to 6.4 range spoils faster than meat 

in the lower pH range of 5.3 to 5.7, because spoilage microbes are more active in the 

pH range of 6.0 to 6.4. We will discuss later how meat and poultry processors can 

control pH to limit microbial growth. 

Temperature 

All bacteria, molds, and yeasts have an optimum, maximum, and minimum temperature 

for growth. These temperatures can vary among different species of microbes. 

Therefore, environmental temperature not only impacts the rate of growth of microbes 

but can determine which microbial species thrive. A temperature difference of only a few 

degrees may favor the growth of an entirely different population of microbes. Below 

approximately 41°F proliferation of spoilage microbes is slow, and growth of most 

pathogenic microbes stops. Listeria monocytogenes (Lm), a bacterial pathogen of 

concern in many ready-to-eat products, is a notable exception. While Lm grows 

optimally at temperatures in the range of 86 to 98.6°F, it is capable of growing at a 

temperature as low 31.3°F. Lm’s rate of growth at that temperature may be slow, but 

can still be significant as will be discussed in a later module. At temperatures above 

140°F most microbes begin to die, although the time needed for cell destruction at a 

particular temperature will vary for different species of microbes and may depend on 

other environmental factors such as humidity. In food processing, the temperature 

range of 41 – 140°F is commonly referred to as the danger zone, because the 

optimum, maximum, and minimum temperature for growth of most microbes will fall 

somewhere within that range. However, it is important to note that time is a major factor 

associated with the rate of growth at a particular temperature. For example, depending 

on other factors, the rate of growth of many pathogens may be extremely slow in the 40 

to 50°F temperature range. 

Time 

We have already mentioned ways in which time can influence microbial growth. 

Permitting sufficient time for microbes to adapt to their environment (lag phase) is 

necessary before they can enter the rapid growth phase (log phase). The doubling time 

for most bacterial species is between 10-30 minutes under optimal conditions for 

growth. Generally doubling times in this range would only occur under ideal laboratory 

conditions. Bacteria would grow much more slowly in meat and poultry products, 

especially if those products are properly handled and stored. Allowing the temperature 

of meat and poultry products to remain in the danger zone for a sufficient period of time 

will promote significant proliferation of microbes and microbial toxins. In addition, time 

may be a factor involved in how well certain microbes adhere to the surface of a meat or 

poultry product. For example, it may be more difficult to eliminate bacteria from the 

surface of a carcass by washing or with antimicrobial sprays the longer the bacteria are 

allowed to remain on that carcass before washing or spraying. 

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Oxygen 

Similar to temperature, oxygen availability can determine which microbes will be active. 

Microbes that have an absolute requirement for oxygen are called obligate aerobes. 

Those that require the total absence of oxygen are called obligate anaerobes. Some 

microbes are called facultative anaerobes, because they can grow in the presence or 

absence of oxygen. Molds require oxygen for growth. Yeasts grow best under aerobic 

conditions, but some can grow slowly under anaerobic conditions. The kinds of bacteria 

that cause food spoilage tend to be aerobes, but those that cause foodborne illness are 

anaerobes or facultative anaerobes. 

Moisture 

The availability of water in a food (referred to as water activity, or aw) is an important 

factor for microbial growth. Nutrients for microbial growth must be in a soluble form for 

microbes to utilize them. Generally, bacteria have the highest aw requirements, molds 

have the lowest, and yeasts are intermediate. It is important to note that aw is not 

necessarily equivalent to measures of moisture content (e.g., Moisture Protein Ratio or 

MPR) in a product. Most moist food products will have greater water availability to 

support microbial growth than dryer food products, but there are exceptions. For 

example, some processing methods might incorporate certain chemical ingredients 

(e.g., salt) that bind to free water and in sufficient concentrations significantly reduce aw 

limiting the growth of some microbes. 

Interaction of Factors 

We have considered each factor individually, but it is important to recognize that the 

rate of microbial growth will be affected by complex interactions among these factors. 

The precise impact of these interactions on microbial growth is often very difficult to 

predict. The optimal range of a factor may change when another factor is not optimal. 

For example, if aw is less than optimal, the pH range at which many microbes can grow 

is more limited. When pH is less than optimal, aw necessary for growth will be higher. 

The presence of certain chemical ingredients can also affect the pH or temperature at 

which some microbes grow. 

Interaction of Different Microbes 

A variety of microbes, including different species of bacteria, yeasts, and molds, can 

exist on meat and poultry products. Rarely will there be only a single species from one 

of these three classes of microbes on product or product contact surfaces. Competition 

among microbial species for vital nutrients can impact the rate of growth of microbes. 

Different bacterial species multiply more rapidly than others, and bacteria generally 

multiply more rapidly than most yeasts and molds. A rapid increase in numbers of a 

particular bacterial species may have a limiting effect on the growth of other bacteria, 

yeasts, and molds. In addition, some microbial species can produce chemical changes 

within the growth environment that have an inhibitory effect on other microbes. 

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Microbes and Food Spoilage 

Spoilage is caused by physical and chemical changes in food products that result in 

undesirable odors, flavors, textures, or colors. Spoilage costs the food industry millions 

of dollars each year. There are three primary mechanisms that can result in spoilage of 

meat and poultry products after slaughter and during processing and storage. One is 

called autolytic enzymatic spoilage, and is simply due to the normal post-mortem 

breakdown of cellular membranes and the release of enzymes that result in 

deterioration of product quality. Another mechanism is called lipid oxidation, which 

involves reactions between oxygen and fat molecules in the product, resulting in 

rancidity. The third mechanism is microbial spoilage. All raw foods and even certain 

processed foods can contain microbes that will eventually cause spoilage unless they 

are controlled or destroyed. 

Microbes can cause food spoilage by two basic mechanisms. The most important 

mechanism is related to the growth of spoilage microbes and their active metabolism of 

food components. The other mechanism of microbial spoilage can occur even in the 

absence of live microbes. As microbes die, they can release various enzymes that react 

with and change properties of food components, leading to spoilage. 

Indications of microbial food spoilage vary with the microbe(s) involved and the time 

course of spoilage. Bacteria and yeasts typically result in slime formation, bad odors, 

rancid flavors, and discoloration (grey, brown, or green). Anaerobic spoilage bacteria, 

which can be an important in vacuum packaged products, can produce a distinctive 

souring due to the production of organic acids and gases. Molds that cause food 

spoilage often result in a stickiness of the product surface and eventually the formation 

of creamy, black, or green colonies with a fuzzy or whisker-like appearance. 

Microbial food spoilage does not necessarily equate with food safety. Foods can contain 

dangerous microbes but still have a normal appearance, odor, flavor, and texture. Food 

with obvious indications of spoilage may or may not contain harmful levels of dangerous 

microbes. A variety of bacteria, yeasts, and molds are involved in food spoilage, but 

most are not pathogenic. Pathogenic microbes cause illness but generally do not affect 

the taste, smell, or appearance of food. Spoilage microbes may be better able to 

reproduce under conditions that may be less favorable to the growth of pathogens. 

However, some of the same conditions that accelerate spoilage, such as inadequate 

control of temperature and moisture, also encourage the growth of pathogenic 

microbes. Therefore, food spoilage is not just an issue of product quality; it represents 

unwholesomeness and calls into question the safety of the product. 

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Microbes and Food Preservation 

We are generally concerned with the undesirable effects of microbes on food, including 

spoilage and foodborne illness. However, many microbes are beneficial to preserving 

certain foods, controlling pathogenic microbes, and producing certain other desirable 

characteristics in some products. 

The primary mechanism through which certain microbes are used in food preservation 

is the process of fermentation. Simply put fermentation results in the conversion of 

sugars to simpler compounds by microbes under anaerobic conditions. The 

fermentative microbes gain energy through the process of fermentation, and produce 

substances, including organic acids, peroxides, and bacteriocins, that have an inhibitory 

effect on the growth and survival of other microbial species. Microbial fermentation 

processes are used in the production of a variety of common foods, including beer, 

wine, some breads, chocolate, and yogurt. Fermented meat and poultry products 

include many salamis, summer sausage, Lebanon bologna, Cervelat, and Thuringer. 

These fermented sausage products typically have a tangy flavor resulting from the 

process of fermentation. 

The process of fermentation primarily exerts a preservation effect by increasing the 

acidity of products. During this process, the pH level of the product is reduced by starter 

culture activity and by appropriate time/temperature factors. A starter culture will 

generally include bacteria that produce lactic acid (e.g., Lactobacillus spp.) along with 

certain other bacteria, yeasts, or molds used to impart certain flavor and color 

characteristics to the product. The starter culture is added to the meat or poultry 

mixture, and held in an environment optimum for the growth of the microbes in the 

culture. The temperature and humidity are carefully monitored to promote growth of the 

culture. The starter culture microbes actively reproduce. As they do, they compete with 

other microbes that might result in spoilage of the product or that might be pathogenic. 

The lactic acid produced by starter culture bacteria, like Lactobacillus, lowers the pH of 

the product. It is important that lactic acid is produced quickly, because it inhibits 

undesirable bacteria, like the toxin-producing Staphylococcus aureus. The pH is 

monitored over time to determine when the process is complete. Generally, the goal is 

to achieve a pH of 5.0 or less within a certain timeframe. 

Microbes and Food Safety 

Certain microbes associated with food can also be harmful. We refer to these as 

foodborne pathogens (see Attachment 1). There are millions of cases of foodborne 

illness in the U.S. each year. The cost of foodborne illness is staggering. According to 

the USDA’s Economic Research Service (ERS), the estimated annual cost of foodborne 

illness caused by Campylobacter, Salmonella, Listeria monocytogenes, Escherichia coli 

O157:H7 and other pathogenic serotypes of E. coli is approximately $6.9 billion. This 

figure includes the cost associated with medical expenses, lost productivity, and death. 

There are other significant costs to both industry and government. 

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In meat and poultry products, pathogenic bacteria probably account for the largest 

proportion of all foodborne illnesses. The most important bacterial pathogens include 

Salmonella, Campylobacter, Listeria monocytogenes (Lm), Clostridium botulinum, 

Clostridium perfringens, Bacillus cereus, Staphylococcus aureus, and the Shiga toxinproducing E. coli (STEC; includes E. coli O157:H7, O26, O45, O103, O111, O121, and 

O145 serogroups). Of these, Salmonella and STEC are two of the most common 

causes of large outbreaks. We will discuss more details about most of these pathogens 

in other training modules together with process familiarization and sampling programs. 

Molds and yeasts do not appear to be responsible for any meat- or poultry-related 

foodborne illnesses, maybe because significant mold or yeast growth is easily 

recognized and the food discarded. Some molds do produce toxins (e.g., aflatoxin 

produced by Aspergillus spp.), but food-related illness appears to be associated with 

nuts and grains not meat and poultry. Also, some molds on food products may cause 

allergic reactions and respiratory problems in sensitive individuals exposed to the mold. 

Some important foodborne parasites are Giardia duodenalis, Cryptosporidium 

parvum, Cyclospora cayetanensis, Toxoplasma gondii, Trichinella spiralis, Taenia 

saginata (beef tapeworm), and Taenia solium (pork tapeworm). It is important to note 

that, while Toxoplasma gondii is not a common cause of foodborne illness, it is among 

the top five foodborne pathogens that result in hospitalization and death. Trichinosis (or 

trichinellosis), caused by Trichinella spiralis, was historically an important foodborne 

illness resulting from the consumption of undercooked pork products. Trichinosis has 

largely been eliminated due to changes in swine production practices, consumer 

education, and prescribed treatments for destruction of trichinae in certain classes of 

pork products (9 CFR 318.10). 

Other Pathogenic Agents 

Prion-associated vCJD appears to be of relatively low incidence. BSE in cattle and 

vCJD in humans are slowly progressive diseases. Initial symptoms in humans are 

generally psychiatric, i.e., depression. As the disease progresses, neurologic signs 

appear and worsen to the extent that patients are unable to care for themselves, until 

death occurs. Cattle can initially display behavioral changes progressing to neurologic 

signs, the inability to rise, and ultimately death. There are certain cattle tissues 

considered to be of high risk for prion contamination. These tissues are referred to as 

specified risk materials (SRMs). 

The presence of viruses in food is generally associated with contaminated food 

workers in the retail or food service arena. Norovirus is recognized as the leading cause 

of foodborne-disease outbreaks in the United States. It is a highly contagious 

gastrointestinal illness. Insufficiently cooked shellfish have been direct sources of 

illness, but other foods appear to be contaminated by infected food handlers. Most 

outbreaks are likely to arise through direct contamination of food by a food handler 

immediately before the food is eaten. Hepatitis A, hepatitis E, and rotavirus are other 

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important viral diseases that may be transmitted through food, but again, their 

transmission has generally been associated with contamination by infected food service 

workers. 

Resources 

More details about foodborne pathogens can be found at the websites listed below. IPP 

are encouraged to make themselves more knowledgeable of these pathogens and the 

diseases they can cause. 

• Bad Bug Book: Handbook of Foodborne Pathogenic Microorganisms and 

Natural Toxins 

www.fda.gov/downloads/Food/FoodborneIllnessContaminants/UCM297627.pdf 

• Foodborne Illness and Disease Fact Sheets 

www.fsis.usda.gov/wps/portal/fsis/topics/food-safety-education/get-answers/foodsafety-fact-sheets/foodborne-illness-and-disease 

• Estimates of Foodborne Illness in the United States 

www.cdc.gov/foodborneburden/index.html 

• Causes of Food Poisoning

www.foodsafety.gov/poisoning/causes/index.html 

• Pathogens 101 

www.stopfoodborneillness.org/pathogens-101 

Sources of Microbes in Food 

Excluding certain areas like the gastrointestinal tract, upper respiratory tract, and lower 

urinary tract, the internal tissues (e.g., muscle tissue) of normal healthy livestock and 

poultry are generally sterile. Nevertheless, raw and many processed foods contain a 

variety of different bacteria, yeasts, molds, and viruses. Fortunately, relatively few of all 

the varieties of microbes are important with respect to food safety. Livestock and 

poultry, people, equipment, pests, water supplies, food ingredients, and air currents can 

all be important sources of microbes in the food-processing environment. A basic 

knowledge of the sources of microbes in food helps the inspector better understand 

potential vulnerable points for microbial contamination in meat and poultry processing 

and the importance of fundamental methods for controlling microbes in food. 

Healthy animals are major sources of spoilage and pathogenic microbes in raw meat 

and poultry, because they shed microbes in their feces and carry microbes on their 

hides or feathers. Large intestinal contents of normal animals may contain as many as 

10 billion bacteria per gram (a U.S. one-cent coin weighs 2.5 grams.). Soil also contains 

a variety of microbes that can also contaminate the hides and feathers of live animals. 

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While dressing animals during the slaughter process, these bacteria can easily be 

transferred from the hide, skin, feathers, and gastrointestinal tract to the carcass itself. 

Disease conditions, like mastitis, pneumonia, gastroenteritis, and uterine infections, may 

change the normal microbial flora and ecology in affected organs and tissues, and 

represent additional sources of potential contamination of the slaughter environment 

and carcass. 

People can be a major source of microbial contamination in the processing 

environment. This may result from people trafficking microbes throughout a processing 

area due to poor hygienic practices, including inadequate hand washing, wearing soiled 

clothing, and working around product while sick with an infectious disease. People are 

also responsible for the design and implementation of procedures and controls intended 

to minimize microbial contamination of products. Failure to adequately design or 

implement such procedures and controls creates insanitary conditions with the potential 

to contaminate product. For example, maintenance personnel may fail to properly 

sanitize tools or protect product from contamination when working on equipment during 

production shifts. 

A variety of different kinds of equipment may be involved in slaughtering, processing, 

storing, and transporting meat and poultry products. Many types of microbes from other 

sources can get into equipment and contaminate product. Equipment can serve as 

niches (hiding places) for the growth of certain microbes if environmental conditions are 

conducive to growth and sanitation practices inadequate. Some bacteria, including 

many pathogens, can form biofilms on equipment surfaces as multiple bacteria attach to 

the surface and produce a protective matrix. Once formed, biofilms can be difficult to 

remove with routine cleaning and sanitizing procedures. Bacteria embedded in a biofilm 

can be up to a 1,000 times more resistant to many sanitizers. During operations, 

portions of a biofilm on moving equipment can shear off, seeding the equipment with 

bacteria. Equipment contaminated by any means can lead to widespread contamination 

of product. Good sanitation and maintenance procedures are critical to preventing this. 

Just like live animals presented for slaughter, pests can carry an assortment of 

microbes on their surface and in their gastrointestinal tracts. Inadequate pest 

management may lead to the contamination of product, equipment, ingredients, and 

packaging materials. Allowing house pets (e.g., cats) to enter production related areas, 

including dry storage areas, could be a source of contamination as they can also harbor 

pathogens. 

There are numerous uses for water in food processing facilities, from clean up of 

facilities and equipment, to washing of product and product formulation. Obviously nonpotable or contaminated supplies of water could be sources of microbial contamination. 

Less obvious, though, might be water overspray from washing equipment or splashing 

of contaminated water onto product or food contact surfaces. In addition, standing water 

and damp areas of the facility could promote microbial growth and increase the 

possibility of cross contamination. 

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Non-meat and non-poultry food ingredients are possible sources of contamination. 

Spices and seasonings may be contaminated with pathogens if improperly processed or 

stored and handled under insanitary conditions. Dried herbs and spices as well as soy 

and milk protein ingredients can be a primary source of bacterial spores, since the 

spores will survive for extended times in these dry ingredients. Dried, shelf-stable nonmeat ingredients have also been identified as sources of Salmonella, Listeria and STEC 

infections in multistate outbreaks. Vegetables and vegetable products that are 

inadequately washed and sanitized can be another source of contamination in the 

processing of meat and poultry products that include these ingredients. 

Microbes, including bacterial spores, may be present in dust and moisture droplets in 

air. Obviously as air currents move dust through a processing facility, the dust can be 

deposited onto surfaces of the facility, equipment and utensils, employee clothing, and 

product. Microscopic moisture droplets traveling in air currents can condense out onto 

cooler surfaces, leading to contamination of those surfaces and forming condensate 

that potentially drips onto product or food contact surfaces. 

Controlling Microbes in Food and Food Processing Environments 

Pathogenic microbes are significant threats to public health. There are two fundamental 

ways to control microbial contamination of products and processing environments. Both 

are important. The first involves reducing opportunities for microbes to enter processing 

environments and come into contact with products. The second involves making the 

environment for microbes as inhospitable as possible to reduce their numbers and 

minimize their growth. Note that “control” is a keyword here. It is impossible to 

completely eliminate all microbes from processing environments and food products. 

However, it is possible for establishments to implement effective control strategies 

designed to protect against pathogens and the undesirable effects of spoilage 

organisms. Other portions of this training program will familiarize you with specific 

processes, including specific methods of controlling microbes in those processes. For 

now, we will broadly consider ways in which the levels of microbes in processing 

environments and on foods may be controlled. 

Prevention of Contamination 

It is important to avoid the contamination of meat and poultry whenever possible. This 

includes inadvertent contamination or cross-contamination from the live animal, 

processing procedures and equipment, employees, and the environment. 

Contamination can be minimized or avoided altogether by following appropriate 

sanitation procedures, good manufacturing procedures (GMPs), and procedures for 

employee hygiene. Good sanitary dressing process control measures in slaughter 

processes not only minimize contamination of carcasses, but also reduce the level of 

processing environment contamination. Effective pest control can help prevent the 

introduction of many microbes into the processing environment. Sound construction of 

the facility and maintaining its construction will reduce opportunities for microbial 

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contamination of the processing environment. For example, ventilation systems that 

provide fresh air in and throughout the establishment should be designed and 

constructed so as to preclude the transfer of contaminated air from the outside to the 

inside of the establishment. Ensuring appropriate hygienic standards and traffic patterns 

are followed by all employees working in and around processing areas protects against 

excessive contamination of the processing environment and product. 

NOTE: The term cross-contamination generally refers to the transfer of microbes from a 

contaminated source to a previously cleaned/sanitized surface. 

Restriction of Growth 

Recognizing that bacteria will be present on meat and poultry, it is important to keep the 

overall number of bacteria very low to minimize concern about bacterial pathogens as 

well as spoilage organisms. Making a microbe’s environment as inhospitable as 

possible can involve a variety of control measures, all of which relate to the FAT TOM 

factors impacting microbial growth. Effective procedures for cleaning and sanitizing the 

facility provide the foundation for controlling microbes. In addition, temperature, acidity, 

salting and drying, or some combination of these can be used to restrict the growth of 

pathogens. 

Sanitation – Microbes can be found in processing environments, which emphasizes the 

need for effective sanitation procedures for equipment and floors. Adequate cleaning 

and sanitizing procedures will help to ensure that little organic matter is available to 

support microbial growth. Altering the pH of a microbe’s environment may involve the 

use (and rotation) of acid and alkaline sanitizing agents. Moisture control in the 

processing environment is an important means of protecting against microbial 

proliferation. This may occur through measures designed to keep the environment dry, 

adequate ventilation, or adequate plumbing to properly convey liquid waste out of the 

processing area. Employee hygiene, airflow, and traffic flow of people and equipment 

between areas are also important to protect against cross-contamination. 

Temperature – Temperature controls are important in all classes of product. Maintaining 

products under refrigeration is one of the most important ways to inhibit microbial 

growth. Cooking product to temperatures adequate enough to eliminate pathogens of 

concern is another way to control microbes. Many pathogens are fairly easily destroyed 

with relatively mild cooking. Bacterial spores and toxins, though, can be very heat 

resistant. Inactivation of spores and some toxins requires thermal processing to high 

temperatures under pressure as in canning operations. The time it takes for products to 

reach a particular temperature is also important in inhibiting microbial growth. Chilling 

raw, heat-treated, and fully-cooked products as rapidly as possible helps to ensure 

products do not linger in the “danger zone” for too long, which could result in the 

outgrowth of bacteria, including spore-forming bacteria and toxin-producing bacteria. 

Acidity – Product pH can also be manipulated, though, to inhibit certain microbes in 

certain products. For example acidifying agents (acidulants) may be added to certain 

Inspection Methods 10-16 
 

 

 

 

 

 

 

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products to reduce pH. Similarly, some products are naturally acidified by the addition of 

fermentative microbes. Some bacteria can survive in acidic conditions, so fermentation 

alone cannot be relied upon to completely eliminate all harmful bacteria. 

Salting and Drying – Certain production processes involve steps to reduce the water 

available for microbial growth through the addition of high concentrations of salt or 

actual drying of the product. Salt and low water activity in a product can be very 

effective in controlling the growth of some harmful bacteria, but some organisms (e.g., 

Staphylococcus aureus) can survive in high salt environments. 

Vacuum Packaging – Reducing the oxygen level through vacuum packaging processes 

is a common method of enhancing the shelf life of food products. However, vacuum 

packaging reduces the growth of mainly spoilage microbes. Pathogenic bacteria, such 

as Clostridium botulinum and Listeria monocytogenes can still grow in vacuum 

packaged products. Given the enhanced shelf life, it is important for processors to 

consider other measures necessary to protect consumers from pathogens in vacuum 

packaged products. 

Ultimately there is no single method of preventing or controlling microbes in food. It 

requires a so-called multiple hurdle approach. Fundamentally, this can be represented 

by compliance with the Sanitation Performance Standards, maintaining effective 

Sanitation SOPs, and designing and implementing an effective HACCP plan. Within a 

particular process, a multiple hurdle approach may get more specific. For example, the 

use of antimicrobial agents or processes, altering the pH of the product, and 

temperature controls may together be a system of hurdles for ensuring effective 

antimicrobial control in some processes. 

Inspection Methods 10-17 
CDC Estimates of Foodborne Illness 

in the United States 

CDC 2011 Estimates 

CDC estimates that each year roughly 1 in 6 Americans (or 48 

million people) gets sick, 128,000 are hospitalized, and 3,000 

die of foodborne diseases. The 2011 estimates provide the most 

accurate picture yet of which foodborne bacteria, viruses, microbes 

("pathogens") are causing the most illnesses in the United States, 

as well as estimating the number of foodborne illnesses without a 

known cause.*The estimates show that there is still much work to be 

done-specifically in focusing efforts on the top known pathogens 

and identifying the causes of foodborne illness and death without 

a known cause. 

CDC has estimates for two major groups offoodborne illnesses: 

FINDINGS 

Reducing foodborne 

illness by 10% would 

keep about 5 million 

Americans from 

getting sick each year. 

Known foodborne pathogens- 31 pathogens known to cause foodborne illness. Many of these pathogens are 

tracked by public health systems that track diseases and outbreaks. 

*Unspecified agents- Agents with insufficient data to estimate agent-specific burden; known agents not yet 

identified as causing foodborne illness; microbes, chemicals, or other substances known to be in food whose 

ability to cause illness is unproven; and agents not yet identified. Because you can't "track" what isn't yet identified, 

estimates for this group of agents started with the health effects or symptoms that they are most likely to causeacute gastroenteritis. 

To estimate the total number offoodborne illnesses, CDC estimated the number of illnesses caused by both known 

and unspecified agents. We also estimated the number of hospitalizations and deaths caused by these illnesses. 

Table 1 provides the estimates due to known pathogens, unspecified agents, and the total burden. 

Table 1. Estimated annual number of domestically acquired foodborne illnesses, hospitalizations, 

and deaths due to 31 pathogens and unspecified agents transmitted through food, United States 

Estimated annual Estimated annual Estimated annual 

Foodborne agents 

number of % number of % number of 

Illnesses hospitalizations deaths 

(90% credible interval) (90% credible interval) (90% credible interval) 

31 known pathogens 9.4 million 20 55,961 1,351 

(6.6-12.7 million) (39,534-75,741) 44 (712-2,268) 

Unspecified agents 

38.4 million 

80 71,878 56 1,686 

(19.8-61 .2 million) (9,924-157,340) (369-3,338) 

Total 47.8 million 

100 127,839 100 3,037 

(28.7-71.1 million) (62,529-215,562) (1,492-4,983) 

National Center for Emerging & Zoonotic Infectious Diseases 

Division of Food borne, Waterborne, and Environmental Diseases 

CS218786-A 

% 

44 

56 

100 

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Attachment 1 

Inspection Methods 10-18 
Pathogens causing the most illnesses, hospitalizations, and deaths each year 

Eight known pathogens account for the vast majority of illnesses, hospitalizations, and deat hs. Tables 2-4 list the top five 

pathogens causing illness, hospitalization, and death. 

Table 2. Top five pathogens causing domestically acquired foodborne Illnesses 

Pathogen Estimated annual number of 90% Credible Interval % illnesses 

Norovirus 5,461,731 3,227,078-8,309,480 58 

Salmonella, nontyphoidal 1,027,561 644,786-1,679,667 11 

Clostridium perfringens 965,958 192,316-2,483,309 10 

Campylobacter spp. 845,024 337,031-1 ,611 ,083 9 

Staphylococcus aureus 241,148 72,341-529,417 3 

Subtotal 91 

Table 3. Top five pathogens causing domestically acquired foodborne Illnesses resulting in hospitalization 

Pathogen Estimated annual number of 90% Credible Interval % hospitalizations 

Salmonella, nontyphoidal 19,336 8,545-37,490 35 

Norovirus 14,663 8,097-23,323 26 

Campylobacter spp. 8,463 4,300-15,227 15 

Toxoplasma gondii 4,428 3,060-7,1 46 8 

E. coli (STEC) 0157 2,138 549-4,614 4 

Subtotal 88 

Table 4. Top five pathogens causing domestically acquired foodborne Illnesses resulting in death 

Pathogen Estimated annual number of 90% Credible Interval % deaths 

Salmonella, nontyphoidal 378 0-1,011 28 

Toxoplasma gondii 327 200-482 24 

Listeria monocytogenes 255 0- 733 19 

Norovirus 149 84-237 11 

Campylobacter spp. 76 0-332 6 

Subtotal 88 

February 2011 www.cdc.gov/foodborneburden 

Food Microbiology 

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Inspection Methods 10-19 
 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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Attachment 2 

A Glossary of Food Microbiology 

Aerobic - Bacteria that require oxygen to grow or will grow in the presence of oxygen. 

Anaerobic – Bacteria that do not utilize oxygen to grow, or will not grow in the presence 

of oxygen. 

Bacteriocin – A proteinaceous substance produced by specific bacteria that is toxic to 

closely related strains of the same specific bacteria and either kills or slows the growth 

of those other specific bacteria. 

Coliform – Bacteria that most often inhabit the intestine of animals, do not utilize 

oxygen, but can grow in its presence. Bacteria that are classified as coliforms have the 

same shape, and many of the same characteristics. These bacteria are used as 

indicators of sanitary quality in many food products. 

Detection limit – The lowest threshold amount of bacteria that must be present in a 

sample to be found. Detection level depends upon analytical methods used. 

Direct plating – The application of a sample, or dilution thereof, to solid media usually 

containing agar and other material used to grow and enumerate bacteria. 

D-value – The amount of time needed to destroy one log unit of a specific bacterial 

pathogen at a specific temperature in a specific medium. 

Enrichment – Addition of nutrient rich broth so that certain bacteria or type of bacteria 

increase in number to result in a bacterial cell count that is higher than the detection 

limit. This is used to detect only the presence or absence of the bacteria, not the 

amount present. 

Enterobacteriaceae – A large group of bacteria that are closely related and are 

commonly found in fecal material of warm-blooded animals. They include coliforms and 

pathogens such as Salmonella. 

F-value – Measured in minutes, the D-value of a specific organism at 250 ̊F (121 ̊C)

multiplied by the desired log reduction. 

Germination – The process of a spore becoming a vegetative cell. 

Inhibition – The slowing or stopping of bacterial growth. 

Lag time – Time that bacteria take to become acclimated to a new environment before 

starting to multiply exponentially. 

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Lethality – The effectiveness of a treatment to destroy or kill bacteria. 

Log unit – ‘Log’ is short for logarithm, a mathematical term for a power to which a 

number can be raised (exponent of 10). A unit of 10x is typically used to count bacteria. 

Therefore, a 1-log10 change stands for a 10-fold increase (multiplication) or decrease 

(reduction) in numbers of recoverable bacteria. For example, the difference between 

106 (1,000,000) and 107 (10,000,000) is one log unit (10-fold increase); the difference 

between 106 and 104 (10,000) is two log unit (Log-2 represents 102 or 10x10 or 100; 

100-fold increase or decrease). See Attachment 3 for additional information. 

Mesophiles – Bacteria that have optimum growing temperatures between 77oF (25oC) 

and 104oF (40oC). 

Microflora – the community of microorganisms, including bacteria, molds and yeasts 

that live in or on another living organism or in a particular habitat. 

Pathogen – Organisms that cause illness. These organisms include bacteria, protozoa, 

or viruses. 

pH - Level of acidity or alkalinity in a product. The pH scale ranges from 1 to 14 with pH 

7 considered neutral; pH 1 is the most acidic and pH 14 is the most alkaline. Fresh 

meat usually has a pH near 5.6. 

Psychrotrophs - Bacteria that have optimum growing temperatures between 68oF 

(20oC) and 86oF (30oC) but can grow at temperatures as low as 32oF (0oC). 

Shocked (heat shocked) – Occurs when a product is heated but the temperature is not 

high enough to destroy the bacteria. This result in bacteria that are injured for a while 

but, in most cases, can repair themselves and are more resistant to heat the next time 

the product is heated. Heat shocked can also refer to the process by which a bacterial 

spore is induced into germination. When a product is heated thoroughly the vegetative 

cells are destroyed, but the spores are undamaged by the heat. The spores then 

germinate into vegetative cells once the temperature has decreased to an optimum 

level. 

Spore – A highly resistant, dormant structure formed in response to adverse 

environmental conditions. Bacterial spores are usually very resistant to heat, long 

periods of dryness, and other adverse conditions that normal vegetative cells cannot 

survive. When the environment becomes more favorable then the spore can reactivates 

to the vegetative state. Most of the time spore-forming bacteria have a toxin associated 

with them. When reactivation (germination) of the spore occurs metabolic activity begins 

that converts the germinated spore into a growing vegetative cell, thus producing the 

associated toxin. 

Strain – Is a genetic variant or subtype of a microorganism. For example, E. coli 

O157:H7 strain EC57: Escherichia is the genus, coli is the species, O157:H7 is the 

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serotype, and strain EC57 (assigned number or identifier) is the genotype, i.e., the 

genetic nomenclature involving specific gene variations (heat resistant). 

Thermotolerant – Bacteria that can withstand higher than normal temperatures. 

Toxin (enterotoxin, mycotoxin, neurotoxin) – A compound produced by a bacterium 

or fungi (molds and yeasts) that can cause illness in other living organisms. Specific 

examples include enterotoxins that affect the intestine, mycotoxins are those toxins 

produced by fungi, and neurotoxins attack the nervous system. 

Transdermal synergists – Compounds that work with other compounds against 

bacteria when applied to the surface of a carcass. 

Treatment – The method of processing that is being tested. A good research study will 

compare various treatments, such as levels of salt in a product, to a control; in this 

example the control maybe no salt added. All other conditions should remain the same 

for all samples tested except the specific treatment. 

Vegetative cell – The normal bacteria cell. This is in contrast to a spore. Vegetative 

cells are susceptible to destruction or damage from heat, additives, and other factors 

that can damage and destroy them relatively easily. 

Inspection Methods 10-22 
 

 

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Attachment 3 

Log Reduction & Multiplication 

"Log" stands for logarithm, which is the exponent of 10 (101 = 1-log10, 102 = 2-log10, 103 = 3-log10, etc.). A 

1-log10 change stands for a 10-fold increase (multiplication) or decrease (reduction) in numbers of 

recoverable bacteria on a food product. 

The table below indicates the percentage decrease in bacteria with each successive log reduction. 

Log Reduction Decrease in Bacteria 

1 90% 

2 99% 

3 99.9% 

4 99.99% 

5 99.999% 

6 99.9999% 

7 99.99999% 

Therefore, a 1-log reduction would reduce the number of bacteria by tenfold or 90%. This means that 100 

bacteria would be reduced to 10, or 10 bacteria would be reduced to 1. Note that the change in the 

absolute number of bacteria depends on the number of bacteria before the change. If 1,000,000 bacteria 

are reduced by 3-logs (or 99.9%) for example, then approximately 1,000 bacteria will remain. 

1,000,000 

Starting bacteria 

x 0.999 

3-log Reduction 

= 999,000 

Bacteria killed 

1,000,000 

Starting bacteria 

– 999,000 

Bacteria killed 

= 1,000 

Bacteria that remain 

The table below indicates the factor by which bacteria increase with each successive log multiplication. 

Log Multiplication Increase in Bacteria 

1 10 times 

2 100 times 

3 1,000 times 

4 10,000 times 

5 100,000 times 

6 1,000,000 times 

7 10,000,000 times 

Therefore, if 10 bacteria increase by 1-log, those 10 bacteria multiply by a factor of 10 to 100 bacteria 

(i.e., 10 x 10 = 100). If 10 bacteria increase by 2-logs, those 10 bacteria multiply by a factor of 100 to 

1,000 bacteria (i.e., 10 x 100 = 1,000). 

Inspection Methods 10-23