Bacteria have been present from the beginning. These unicellular organisms exist in water, soil, and all phases of our environment. The existence of nonvisible matter was considered early on and this reality was confirmed after van Leeuwenhoek observed “animalcules” through a microscope (see Chapter 1, Scope of Microbiology). Van Leeuwenhoek’s descriptions of his microscopic observations of dental scrapings suggest he was observing what are currently called bacteria. The term “bacteria” comes from the Greek word meaning little rod or stick, which is one of the shapes (bacillus) that aids in the morphological description of bacteria. Pasteur, in his eloquent discourses on extensions of the germ theory, refers to “bacteridium,” a term that we have shortened to bacteria (plural) or bacterium (singular).

IMPACT

Pure and simple, pathogenic bacteria and the germ theory are founded on the association of certain bacteria, that is, pathogens, with disease. Antibiotics, drug and chemical treatments for disease, the foundations of health and hygiene practice, the potential causes of bacterial disease outbreaks, and the steps necessary to keep them under control are all based on the growth of knowledge about bacteria, which has led to its development as the scientific discipline of bacteriology. In addition, Pasteur’s studies on fermentation led to the demise of spontaneous generation (see Chapter 1) as a source for bacteria. Useful roles for bacteria have emerged as well, such as nitrogen fixation and the role of bacteria in food preparation.

FUTURE

There are three areas for concern regarding bacteria that need to be addressed: emerging bacterial infectious diseases, reemerging pathogenic diseases that may or may not be resistant to current antibacterial drugs, and bacteria with bioterrorism potential (see Chapter 18, Emerging Infectious Diseases, and Chapter 24, Microorganisms in the Environment and Environmental Safety). Some examples of emerging bacterial infectious diseases include, but are not limited to, Staphylococcus aureus inducing toxic shock syndrome, Escherichia coli O157:H7 hemorrhagic colitis and hemolytic uremic syndrome, and Vibrio cholerae O139, a new strain of cholera. Some reemerging bacterial diseases such as plague (Yersinia pestis) also will be a problem to deal with by healthcare professionals. In addition, the threat of bioterrorism by intentional release or contamination of areas, food, water, and other environments by biological agents including bacteria, viruses, or their toxins represents a real threat for the future of humankind (see Chapter 24).

On the other hand, bacteria are also being used in a variety of industries and research continues to explore the use of bacteria as a food source, in food production, in the production of a variety of pharmaceutical agents, in agriculture, and as microbial fuel cells, to just name a few (see Chapter 1).

Bacterial Structure

Bacteria are prokaryotic unicellular (single-celled) independent organisms that can live as an individual cell or attached to others, forming colonies or groupings, such as biofilms. Each of the cells in such a colony is capable of carrying out all essential activities for survival, such as regular cellular metabolism and reproduction.

Shapes

Bacterial cell morphology displays a variety of different shapes and sizes (Figure 6.1), and the cells are generally much smaller than eukaryotic cells. According to their morphological characteristics most bacteria are classified into different basic shapes: coccus, bacillus, spirochetes (spiral or helical), and pleomorphic (see Chapter 4, Microbiological Laboratory Techniques).

• Cocci (singular, coccus) are bacteria whose overall shape is spherical or nearly spherical (Figure 6.2). Several cocci are human pathogens causing, for example, urinary tract infections, food poisoning, toxic shock syndrome, gonorrhea, some forms of meningitis, throat infections, pneumonias, and sinusitis.

FIGURE 6.2 *Staphylococcus aureus.*
This gram-positive coccus, appearing as grapelike clusters, is one of the most common causes of staph infections.

• Bacilli (singular, bacillus) are rod-shaped bacteria, some of which are endospore forming (Figure 6.3). Diseases caused by bacilli include anthrax, botulism, and tetanus, and gastrointestinal infections caused by bacilli such as Escherichia coli and Salmonella.

FIGURE 6.3 *Escherichia coli.*
This micrograph shows a Gram stain of *E. coli,* a typical gram-negative bacillus.

• Pleomorphic bacteria are bacterial species that are morphologically indistinct, depending on environmental conditions. This group includes Coccobacillus (coccobacilli), which are bacilli that are elongated as well as spherical in shape (Figure 6.4).

FIGURE 6.4 Coccobacilli.
This micrograph illustrates a Gram stain of an organism from the genus *Corynebacterium*. The cells are variable in shape, from spheres to short rods, and therefore are considered pleomorphic (cells with a variable or indistinct shape).

• Spirals occur as vibrios, spirilla, or spirochetes.

• Vibrios are curved or comma-shaped rods (Figure 6.5) and several species are human pathogens associated with gastroenteritis, cholera, food poisoning, and septicemia. Vibrio fischeri and V. harveyi are symbiotes of marine organisms such as jellyfish and produce light via bioluminescence.

FIGURE 6.5 Vibrio.
The micrograph shows a Gram stain of *Vibrio natriegens,* demonstrating the vibrioid shape, a simple curved rod. Note that not all cells appear curved, due to the viewing of the cells on the side with the convex/concave faces of the cell pointing directly at or away from the viewer.

• A spirillum (plural, spirilla) is a thick, rigid, spiral organism (Figure 6.6) that can cause rat bite fever, an uncommon but worldwide condition caused by rodent bites. These bacteria are present in the oropharyngeal flora of approximately 50% of healthy wild and laboratory rats, as well as in other rodents.

FIGURE 6.6 Spirillum.
This micrograph is taken from a Gram stain of the genus *Campylobacter,* showing the corkscrew or “snakelike” shape referred to as *spirilla.* Although a spirilla and a spirochete may appear very similar in overall shape, the spirilla often have flagella as a means of locomotion, whereas the spirochetes have a structure called an *axial filament* that facilitates movement and lack flagella.

• Spirochetes are thin, flexible spirals (Figure 6.7) and can cause leptospirosis, Lyme disease, and syphilis.

FIGURE 6.7 Spirochete.
This micrograph shows *Treponema pallidum*, the causative agent of syphilis. From Murray PR, Rosenthal KS, Pfaller MA: *Medical Microbiology,* ed 5, St. Louis, Mosby, 2005.

HEALTHCARE APPLICATION
Examples of Pathogens and Opportunistic Pathogens by Shape

Organism	Shape	Reservoir	Disease(s)
Staphylococcus aureus	Coccus	Common on skin, nose, gastrointestinal and urogenital tracts of humans	Toxin mediated: Food poisoning, scaled skin syndrome, toxic shock syndrome, folliculitis, carbuncles, impetigo, wound infections, bacteremia, and more
Staphylococcus epidermidis	Coccus	Common on human skin	Bacteremia, endocarditis, urinary tract infections, opportunistic infections of catheters, shunts, prosthetic devises, and more
Enterococcus faecalis	Coccus	Common in human gastrointestinal tract	Bacteremia, endocarditis, urinary tract infections, wound infections
Bacillus anthracis	Bacillus	Soil organism	Anthrax
Bacillus cereus	Bacillus	Soil organism	Toxin mediated: Gastroenteritis (emetic, diarrheal), ocular infections, opportunistic infections
Bacillus thuringiensis	Bacillus	None (soil, gut of caterpillars, butterflies, moths)	Gastroenteritis, opportunistic infections
Haemophilus influenzae	Pleomorphic	Mucous membranes of humans	Meningitis, epiglottitis, pneumonia, bacteremia, opportunistic infections
Chlamydia trachomatis	Pleomorphic	Obligate intracellular human pathogen	Sexually transmitted: Prostatitis, epididymitis, cervicitis, pelvic inflammatory disease, urethritis, and more
Vibrio cholerae	Spiral (vibrio)	Estuarine and marine environments	Toxin mediated: Acute diarrheal illness
Spirillum minus	Spiral (spirillum)	Rodents	Rat bite fever
Borrelia burgdorferi	Spiral (spirochete)	Vector-borne, transmitted by ticks	Lyme disease

Arrangements

In addition to their shape, bacteria can also be categorized according to their arrangement or their style of grouping after cell division.

• Aggregations of cocci occur after cell division and can be classified as the following (Figure 6.8):

FIGURE 6.8 Arrangements of cocci.
Cocci occur in five basic arrangements: diplo, in pairs; staph(ylo), in grapelike irregular clusters; strep(to), in chains; tetrads, in squares of four; and sarcinae, three-dimensional cubes. A, *Staphylococcus;* B, *Streptococcus;* C, *Micrococcus* in tetrads.

• Diplo– is a prefix typically describing cells that occur in pairs of two, joined in one plane only. Examples of diplococci are Streptococcus pneumoniae, Neisseria gonorrhoeae, and Neisseria meningitidis.

• Strepto– is a prefix used to indicate an arrangement of cells in beadlike chains, because cell division occurs along a single axis, in contrast to staphylococci, which divide along multiple axes. Individual species of Streptococcus are identified primarily on the basis of their hemolytic properties on blood agar. The species Streptococcus pyogenes is responsible for strep throat, many cases of meningitis, bacterial pneumonia, endocarditis, erysipelas (acute skin infection), and necrotizing fasciitis (“flesh-eating” infections).

• Tetrads are produced by division within two planes, with the cocci arranged in squares of four in irregular clusters. Micrococcus luteus, which can be found in many areas including the human skin, water, dust, and soil, shows this growth pattern. It is considered to be a harmless bacterium but some cases of Micrococcus infections have been reported in people with a compromised immune system (e.g., HIV patients).

• Sarcinae are cocci arranged in cubes of eight as a result of division in three planes. This coccal grouping occurs when any cocci fail to separate after they divide and the resultant daughter cells remain attached.

• Staphylo– is a prefix indicating arrangements in grapelike clusters formed by cell division in random planes. Most members of the genus Staphylococcus are harmless and are part of the normal flora of the skin and mucous membranes in humans. A small percentage of staphylococci are also part of the soil microbial flora. The organism can cause an array of diseases in humans and other animals by invasion and also by toxin production. The toxins of Staphylococcus are a common cause of food poisoning because the bacteria can grow in improperly stored food. Although the organism is killed by the cooking process, the enterotoxin is heat resistant and can survive boiling for several minutes.

• Bacilli divide in one plane, producing diplobacilli and streptobacilli (Figure 6.9).

FIGURE 6.9 Arrangements of bacilli.
Bacilli can be found in three basic arrangements: A, diplo, in pairs; B, strep(to), in chains; or palisades, lying next to each other along their long sides.

• Diplobacilli are paired rods that remain in pairs after division.

• Streptobacilli fail to separate after they divide and remain in chains of cells.

MEDICAL HIGHLIGHTS

Fusobacterium: Dental Freeloaders

Bacteria of the genus Fusobacterium have a distinct shape—that of a rod with pointed ends or a spindle shape. This is, however, not the only interesting feature about these organisms. Fusobacterium nucleatum is a human pathogen that is typically found in the oral cavity, part of the oral flora that is responsible for plaque formation and tooth decay. One of the unique features about this spindle-shaped bacterium is its ability to adhere to other plaque-forming gram-negative bacteria that have already established a biofilm on the surface of the teeth or mucous membranes. Once added to the existing biofilm, F. nucleatum shares the same environmental advantages that the original builders of the biofilm enjoy and their acidic metabolic by-products contribute to tooth decay and periodontal disease. Although linked primarily with the oral cavity, this pathogen has also been associated with infections in the digestive tract, lungs, and liver.

Bacterial Growth

Growth is an increase in the quantity of cellular material and depends on the ability of the cell to form new protoplasm from available nutrients. Bacterial growth requires a source of energy for protein synthesis and to maintain bacterial metabolism. Bacteria must obtain or synthesize nucleic acids, carbohydrates, and lipids that are used as building blocks of cells. The minimal requirements for growth are a source of carbon and nitrogen, an energy source, water, and a variety of ions and minerals. Oxygen is necessary for some bacteria but can be lethal for many others (see Atmospheric Conditions, later in this chapter).

Basis of Bacterial Growth: Binary Fission

Bacterial replication is a coordinated process accomplished primarily by binary fission. Binary fission results in two identical daughter cells (Figure 6.10). In order for growth to occur sufficient metabolites are necessary to support the synthesis of bacterial components. A cascade of regulatory events must occur to initiate replication. Once replication is started DNA synthesis must run to completion. Chromosome replication starts at the plasma membrane and each daughter chromosome is anchored to a different portion of the membrane. Membrane, peptidoglycan synthesis, and cell division are linked together and as the bacterial membrane grows, the daughter chromosomes are pulled apart. At the end of chromosome replication septum formation between the daughter cells starts, indicating cell division (see Chapter 3, Cell Structure and Function). New initiation may begin even before chromosome duplication and cell division are complete.

FIGURE 6.10 Binary fission.
Bacterial replication is a coordinated process accomplished primarily by binary fission. The circular DNA molecule is replicated, the bacterial cell elongates, and the cell splits into two identical cells, each containing an exact copy of the original DNA.

At the point at which metabolites are depleted or toxic by-products build up, chemical alarmones are produced, which stops synthesis. Degradative processes and DNA synthesis continue until all initiated chromosomes are completed. Ribosomes are broken down during the degradative process to provide deoxyribonucleotide precursors. Peptidoglycan and proteins are degraded for metabolites and the cell may shrink in response. Complete cell division may not occur and the cell may ultimately die. Under degradative processes sporulation may occur in species capable of this process.

Population Growth Curve

To produce a bacterial culture in a laboratory environment, the organism must be added to a medium (see Types of Culture Media in Chapter 4, Microbiological Laboratory Techniques). Under favorable conditions a growing bacterial culture doubles at regular intervals. Under ideal conditions, bacterial growth can be described by four different phases: the lag phase, the exponential or logarithmic growth phase, the stationary phase, and the death phase (Figure 6.11).

FIGURE 6.11 Bacterial growth curve.
Bacterial growth can be described by four different phases: the lag phase, the exponential or logarithmic growth phase, the stationary phase, and the death phase.

• Lag phase: Bacteria must adapt to the medium before cell division starts. This period of time is referred to as the lag phase of the bacterial growth curve. During this phase the cells are metabolically active, producing molecules necessary for cell division; the individual bacteria are maturing, yet they are not able to divide at this time.

• Logarithmic or exponential growth phase: The rate of growth increases with time in the so-called logarithmic or exponential growth phase. Each cell introduced to the medium divides by binary fission into two cells. With each subsequent binary fission a doubling of the bacterial cells occurs as long as the growth conditions are favorable. The time required for doubling of the population is called the generation time. In other words the number of new bacteria per unit of time is proportional to the present population, and the actual rate of growth depends on the growth conditions, which directly affect the frequency of cell division.

• Stationary phase: A stationary phase occurs when essential nutrients are depleted or by-products of metabolism accumulate. A depletion of nutrients causes cells to decrease in size and toxic metabolic by-products limit the ability to undergo cell division. During this phase the total number of viable cells remains constant. This phase of population growth can last for a few hours to several days, depending on the environmental conditions.

• Death phase: Finally, the death phase begins when growth stops and the number of dead cells is larger than the number of viable cells.

Factors Influencing Microbial Growth

Prokaryotes exist under a wide range of physical conditions. These environmental conditions include nutritional requirements, temperature, osmotic pressure and other atmospheric conditions, all of which greatly influence the growth of microbes. The type of microbial life present reflects the physical and chemical conditions of a given environment. Some microbes can tolerate extreme temperatures, high osmotic pressure, and other extreme chemical and atmospheric conditions, whereas others can grow and reproduce only in a limited range of environmental conditions. These conditions may support the growth of one organism, while inhibiting the growth of other microbes.

Nutritional Requirements

The nutritional requirements for different microbes vary significantly from one to another. Microorganisms that acquire energy from light are called phototrophs, and those that require chemical compounds for energy are called chemotrophs. The pathways for the generation of cellular energy are photosynthesis, fermentation, and respiration (see Chapter 3, Cell Structure and Function).

Carbon atoms provide the backbone for all organic compounds and are essential for all life forms. Microorganisms called autotrophs can obtain carbon from atmospheric carbon dioxide, and heterotrophs are organisms that use carbon from organic compounds. Depending on the source of carbon and energy, bacteria are classified as photoautotrophs, chemoautotrophs, photoheterotrophs, and chemoheterotrophs.

• Photoautotrophs use sunlight as the energy source and atmospheric carbon dioxide as their carbon source. Photoautotrophs include photosynthetic bacteria, algae, and green plants. They transform carbon dioxide and water into carbohydrates and oxygen by way of photosynthesis.

• Chemoautotrophs use inorganic chemical compounds as the source of energy and carbon dioxide as the carbon source.

• Photoheterotrophs use sunlight for energy, but cannot convert carbon dioxide into energy; instead, they use organic compounds as the source for carbon.

• Chemoheterotrophs use organic compounds for both the source of energy and a carbon source. Some chemoheterotrophs such as Pseudomonas can use many different organic compounds as energy and carbon source, and therefore can grow in many different environments such as in soap dispensers. This makes this organism a particular problem in hospital environments, where Pseudomonas can also grow in respiratory equipment.

Nitrogen is another essential element for all life forms because nitrogen is an element in many organic molecules such as amino acids and nucleic acids. Many bacteria produce enzymes for the breakdown of proteins into amino acids. Some bacteria can obtain nitrogen from inorganic compounds such as nitrites, nitrates, and ammonium. Few bacteria can reduce atmospheric nitrogen independently or in association with plants. This process is known as nitrogen fixation, an important occurrence in agriculture.

Sulfur and phosphorus requirements can be met by organic compounds, inorganic salts of sulfates, sulfides, and thiosulfates. If soluble phosphate salts are not available in the environment they can be a limiting factor for microbial growth in nature.

Minerals required in trace amounts by microorganisms include potassium, magnesium, calcium, iron, trivalent iron, molybdenum, manganese, and zinc. Small organic compounds are growth factors that are either not synthesized by a bacterium or synthesized in insufficient amounts. These growth factors include vitamins, amino acids, purines, pyrimidines, and porphyrins.

Temperature

Most microorganisms can grow in a wide range of temperatures, but optimal growth occurs within a narrow range. The minimal growth temperature is the lowest temperature that supports the growth of an organism, and the maximal growth temperature is the highest temperature that allows growth. The optimal growth temperature is the range of temperature that provides ideal conditions for the growth of a particular microbe. Depending on the range of temperature in which a microbe will grow, they are classified as mesophiles, thermophiles, psychrophiles, and psychrotrophs (Table 6.1).

TABLE 6.1

Examples of Bacteria Growing at Different Temperatures

	Pathogens	Nonpathogens
Mesophiles	Salmonella typhi	Micrococcus luteus
Thermophiles	Campylobacter spp.	Bacillus thermophilus
Psychrophiles	Yersinia enterocolitica	Pseudomonas spp.
Psychrotrophs	Listeria monocytogenes	Bacillus spp.

• Mesophiles: Mesophiles are microorganisms that have optimal growth in moderate temperature, generally between 25° C and 40° C. The habitats of these organisms include soil, the human body, and animals. They also play an important role in food preparations such as the production of cheese and yogurt, as well as beer and wine production. Most medically important bacteria are mesophiles, and pathogenic organisms generally grow best at temperatures that are optimal for the cells of the host. In the laboratory environment these microbes are generally grown in incubators set at 37° C (human body temperature). Bacteria of the normal human flora are mesophiles.

• Thermophiles: These heat-loving organisms grow best at temperatures of 45° C or higher. Examples of such environments include hot springs, deep sea hydrothermal vents, tropical soil composts, and decomposing hay stacks. Some bacteria grow in water-boiling environments up to 110° C. Most photosynthetic prokaryotes are limited to environments of 70° C to 73° C, and most eukaryotic microbes cannot grow above 60° C.

• Psychrophiles (cryophiles): These bacteria are cold-loving and can grow at 0° C or lower, with an optimal growth around 15° C. They are usually found in Arctic and Antarctic regions and in streams that are fed by glaciers.

• Psychrotrophs: These organisms grow very slowly at 0° C but have an optimal growth range of 25° C to 30° C. Psychrotrophs are not considered to be psychrophiles. They are abundant in nature and can cause food spoilage at refrigerator temperatures.

Osmotic Pressure

Microorganisms with a cell wall can withstand some osmotic pressure, but most microorganisms do not tolerate environments in which the concentration of solutes is higher outside of the cell (hypertonic). Osmotolerant microorganisms can grow in the pressure of a hypertonic environment, and osmophiles are microbes that require a high solute concentration in the environment for optimal growth.

As stated previously, most microorganisms do not tolerate hypertonic concentrations of sodium chloride (NaCl), but some of them require it for optimal growth. The genera Halobacterium and Halococcus are present in saline lakes and basins where NaCl levels are close to the saturation level. Other obligate halophiles (salt lovers) found in oceans show optimal growth in about 3.5% NaCl. Facultative halophiles are salt tolerating and can live in NaCl concentrations up to 10%. Examples are Staphylococcus aureus and Enterococcus faecalis.

Hydrostatic Pressure

The hydrostatic pressure is a type of environmental pressure that a fluid exerts in a confined space. This pressure is applied to aquatic microorganisms because of the weight of water.

• Barotolerant microorganisms can survive under conditions of increased hydrostatic pressure, whereas most organisms are inhibited in growth by hydrostatic pressures of 200 to 600 atmospheres.

• Barophiles grow best under high hydrostatic pressures and occur only in the deepest parts of the oceans.

Atmospheric Conditions

Prokaryotes exist in nature under various physical conditions including different oxygen concentrations in the atmosphere (Table 6.2). It is necessary to know the atmospheric requirement of microorganisms when obtaining, transporting, and culturing microbes. Metabolic pathways or organisms often require oxygen to generate ATP molecules, but some pathways can produce energy without the presence of oxygen, and some organisms will be killed in the presence of oxygen.

TABLE 6.2

Examples of Bacteria Growing Under Different Atmospheric Conditions

	Pathogens	Nonpathogens
Obligate aerobes	Mycobacterium leprae	Pseudomonas fluorescens
Obligate anaerobes	Clostridium botulinum	Clostridium sporogenes
Aerotolerant anaerobes	Fusobacterium spp.	Bifidobacterium spp.
Facultative anaerobes	Escherichia coli	Staphylococcus epidermidis
Microaerophiles	Campylobacter jejunae	Thiovuhlum majus
Capnophiles	Neisseria gonorrhoeae	Mannheimia succiniciproducens

• Obligate aerobes are organisms that grow only in the presence of oxygen and therefore they obtain their energy through aerobic respiration.

• Obligate anaerobes grow only in the absence of oxygen and are often inhibited or killed by the presence of oxygen. They obtain their energy through anaerobic respiration or fermentation.

• Aerotolerant anaerobes cannot use oxygen for energy requirements but can grow in the presence of oxygen. They can transform energy by fermentation only and are also called obligate fermenters.

• Facultative anaerobes can grow either in the absence or presence of oxygen. They use aerobic respiration in the presence of oxygen, and anaerobic respiration or fermentation in the absence of oxygen.

• Microaerophiles are organisms that require a low concentration of oxygen, about 2% to 10% (much less than atmospheric oxygen at 21%); a higher oxygen concentration will inhibit their growth. They acquire their energy through aerobic cellular respiration.

• Capneic bacteria (capnophiles) require more carbon dioxide than is present in earth’s surface atmosphere.

pH

The pH of the natural environments ranges from about 0.5 in acidic soils to approximately 10.5 in alkaline lakes. The pH range of bacteria ranges from the minimal pH at which they can grow to the maximal pH above which the organism cannot grow. Microorganisms can be placed into groups based on their optimal pH requirements: neutrophiles (pH range of 5 to 8), acidophiles (grow best at pH below 5.5), and alkaliphiles (grow best at pH above 8.5). Most microorganisms tolerate alkaline environments, but grow best around pH 7. Some species, however, prefer an acidic environment for optimal growth. For example, Helicobacter pylori grows in the epithelial lining of the stomach despite the high acidity present in the lumen. Thermoacidophiles grow at high temperatures and low pH. Several groups of archaea belong in this category. Some bacteria such as Vibrio cholerae grow at pH 8.5 or higher. Fungi are generally more tolerant of acidic environments and grow best at pH 5 or 6.

MEDICAL HIGHLIGHTS

Peptic Ulcers: Helicobacter pylori

Peptic ulcers are open sores that develop in the lining of the stomach or duodenum. Peptic ulcers are common and for a long time have been believed to be caused by stress or by the eating of spicy food. Although these can make the ulcers worse, the real cause of the majority of peptic ulcers is Helicobacter pylori. H. pylori infections are common in the United States; however, most infected people do not develop ulcers. The bacterium potentially weakens the mucosa of the stomach and duodenum, allowing acids to penetrate the tissue and together with the bacterium causing a sore or ulcer. H. pylori infections are diagnosed by blood, stool, and tissue samples as well as urea breath tests. Treatment of these ulcers usually involves a combination of antibiotics, acid suppressors, and stomach protectors.

Genetics

The genome of an organism is the sum of the genetic material of a cell and generally exists in the form of chromosomes but also can occur in nonchromosomal sites, such as in plasmids of bacteria and mitochondria and chloroplasts in eukaryotic cells. Characteristics of bacteria such as morphology, metabolism, antibiotic resistance, and other characteristics are determined by inherited information, which is encoded by genes in the DNA molecules.

• A gene is a unit that codes for particular information located on a DNA molecule. The total number of genes in an organism is called the genome. Bacteria and archaea have a smaller genome compared with eukaryotes.

• A chromosome is a single DNA molecule that includes proteins called histones in eukaryotes, but prokaryotic cells do not have a nucleus and their DNA is not associated with histones. In general, bacteria and archaea store their genomes in a single large circular chromosomal DNA molecule to be found in an area that is non-membrane bound and called the nucleoid area. In addition, many bacteria contain small extrachromosomal (nonchromosomal) DNA molecules called plasmids. Linear chromosomes and plasmids previously unknown have now been found in some species of gram-positive and gram-negative bacteria.

• A plasmid is independent from the chromosomal DNA of the organism; it is generally circular, self-replicating, and usually carries between 5 and 100 genes. Plasmids are not essential for normal bacterial growth and therefore bacteria may lose or gain plasmids without causing harm. However, plasmids often contain genes that provide a selective advantage to a bacterium under certain environmental conditions such as the presence of antibiotics, when an antibiotic resistance gene in a plasmid can code for an enzyme capable of denaturing the antibiotic. These types of plasmids provide antibiotic resistance to an increasing number of bacteria, causing serious problems in hospitals and other healthcare environments.

• An episome is a unit of genetic material composed of a series of genes, such as a plasmid, that is capable of integrating itself into the chromosomal DNA of the organism and therefore can stay intact and is duplicated with every cell division. It becomes a basic part of the genetic makeup of the organism and therefore is no longer considered a plasmid or separate unit, because it became part of the chromosomal DNA.

Genotype and Phenotype

Genes located on the DNA molecule can be grouped into structural genes that code for proteins, genes that code for RNA, and regulatory genes that control gene expression.

• The genotype of an organism represents its exact genetic makeup and, in the case of bacteria, a specific species such as E. coli can have various strains, each strain with its specific and often only slightly altered genotype.

• The phenotype of an individual organism represents the observable characteristics of that organism. While an organism’s genotype has the greatest influence on the phenotype, environmental factors can somewhat alter the appearance. This phenomenon is referred to as phenotypic plasticity, describing the degree to which an organism’s phenotype is determined by its genotype. In the case of bacteria, high levels of plasticity indicate that environmental factors such as pH or temperature, or the type of medium they grow on, have a strong influence on the appearance of the bacterial culture.

• The relationship between genotype and phenotype can be simply expressed as: genotype + environment = phenotype.

Mutations

Mutations are changes to the base pair sequence of DNA or RNA, passed on by cell division. Mutations are random events that are unpredictable. The rate of mutation is a measure of the rate of genetic change and is often referred to as mutant frequency. The types of mutations can be classified as spontaneous and induced mutations.

• Spontaneous mutations occur naturally with no known cause.

• Induced mutations can occur in nature through exposure to radiation or chemicals affecting the DNA. Genetic changes can also be produced in the laboratory. Physical, chemical, or biological agents that alter the DNA are called mutagens or mutagenic agents.

A microlesion is an injury to the DNA that involves only one base pair. When more than one base pair or several genes are affected the damage is called a macrolesion. Mutations can be classified according to the type of change occurring in a gene; these include point mutations, frameshift mutations, inversions, transposons, and reversions.

• Point mutations occur when a single nucleotide base is altered. A base substitution involves the replacement of one base pair with another. This type of point mutation represents the most frequent type. When a purine or a pyrimidine replaces another purine or pyrimidine base, the substitution is referred to as a transition. If a purine replaces a pyrimidine or vice versa, the substitution is called a transversion. Silent mutations occur when a codon (three-nucleotide sequence; see Chapter 2, Chemistry of Life) is changed by substitution of one base but the codon still contains the code for the same amino acid, and therefore the end product of protein synthesis is the same. However, when a base substitution codes for a different amino acid the end product is different, changing the shape and function of the protein. The consequence can be minor, harmful, or lethal.

• Frameshift mutations involve the deletion or insertion of one or more bases. This mutation results in a misreading, or shift in the reading, of the genetic code, and a different end product. For example, if the original code reads “The dog was bad” and the letter (base) “o” is deleted, the reading would end up as a nonsense message, because the codons are read in three-letter words.

The dog was bad

The dgw asb ad

Small deletions can occur spontaneously. Exposure to radiation or chemical mutagens often results in the loss of several segments of DNA. Ultraviolet radiation promotes the formation of thymine dimers, which is a bonding between two adjacent thymines on the DNA strand. This results in the functional deletion of the thymine from the base sequence on the gene, because the adjacent dimers bond to each other and distort the DNA molecule and therefore prevent transcription at that spot. In ionizing radiation (x-rays and γ rays) large molecules break and leave small, electrically charged (ionized) molecules. Nucleic acids and proteins are particularly susceptible to this type of radiation. In lethal mutation prolonged radiation will cause sufficient cell damage to kill the cell. In deletions nucleotides are removed from the DNA strand, causing a mutation. Mutagens causing deletion include hydrogen peroxide, N-methyl-N-nitrosoguanidine, and manganous chloride.

Additions of one or several bases are insertions and are caused by mutagens called intercalating agents.

• Inversions are macrolesions in which the order of bases is switched or inverted. The change in the base sequence due to inversions produces nonsense codons with a high probability of gene dysfunction.

• Transposons (jumping genes) are genes that move from one segment of DNA to another on chromosomes, on plasmids, or within viruses. They contain inverted repeat segments of bases at the ends and a transposonase gene. Transposonase is an enzyme needed to transpose the sequence. Transposons can contain other genes also, such as drug resistance genes. A transposon can insert itself into chromosomal DNA, interrupting the gene sequence, and therefore is a potential mutagen.

• Reversions are mutants that can revert back to the wild-type phenotype. This back mutation restores the original phenotype and can be due to the action of mutagens.

Genetic Transfer in Prokaryotes

Bacteria can obtain new genetic material from another organism that is closely related. This can happen through transformation, transduction, or conjugation. Donors are the cells that transfer DNA and recipients are the cells receiving the DNA .

• Transformation is the transfer of free DNA or genetic elements from one cell to another. This process occurs naturally in many bacterial species. Transformation is an important tool in the genetic manipulation of bacteria performed in the laboratory environment. This process is routinely used in genetic engineering.

• Transduction is the transfer of DNA from one bacterium to another, via a bacteriophage (virus). Bacteriophages transferring the genetic material are called transducing particles. Transfer of a limited number of specific genes is called specialized transduction and the transfer of any segment of DNA is generalized transduction.

• Conjugation is the transfer of genetic material during cell-to-cell contact. This process can take place between mating cells of the same species or between closely related species. In mating types the donor carries a sex pilus (F-pilus) whereas the recipient does not.

Classification of Bacteria and Archaea

Prokaryotes are divided into bacteria and archaea. An abundance of information is available about bacteria, but much less is known about archaea. Archaea tend to live in areas not easily accessible and therefore are not involved in everyday human life. Bacteria, on the other hand, especially pathogenic ones, have been investigated extensively.

Members of the archaea are a group of bacteria that have features differing from the other bacteria. With the exception of thermoacidophiles, which are found in hot acidic springs, the rest of the archaea have cell walls lacking peptidoglycan. Archaea are most often found in unusual or extreme habitats and, based on their habitats, they are classified as

• Methanogens: Methane producers

• Thermophiles: Heat lovers

• Halophiles: Salt lovers

Criteria

Bacteria are unicellular organisms that are structurally diverse and widely distributed. With few exceptions bacteria are capable of living independently under environmental conditions favorable to them. The assignment of a bacterium to a species is not based on the same principles that govern species placement in the plant and animal kingdoms. Because bacteria divide by binary fission, bacterial species are not the result of interbreeding groups and therefore bacteria cannot be classified by means of breeding groups. The offspring may evolve in a different direction through mutation, gene transfer, or selected environmental pressures. Gene transfer from one bacterium to another is difficult to assess because the frequency of occurrence is unknown.

A bacterial species is defined as a group of bacteria that exhibit a large number of similar characteristics. The originally described bacterium is referred to as the prototype. Any subsequent bacterium isolated that has only a few modifications from the prototype is called a strain of the original species prototype. Bacteria are named according to the binominal system of nomenclature, which was first proposed by Carolus (Carl) Linnaeus (1707–1778), a Swedish botanist, physician, and zoologist, and who is considered to be the “father of modern taxonomy.” He classified nature within a hierarchy, starting with kingdoms, which are divided into classes and then into orders, which are divided into genera, followed by division into species (Figure 6.13).

FIGURE 6.13 Binominal system of nomenclature developed by Carolus Linnaeus.

Phenotypic classifications of bacteria involve the microscopic and macroscopic morphologies and were the first used to identify bacteria. For example, bacteria can be classified by Gram-staining properties and by the shape of the individual organism, such as gram-positive cocci. The appearance of bacterial colonies (see Chapter 4, Microbiological Laboratory Techniques) also can be used for identification of the organism. More discriminating methods can then be applied for more specific identification.

Measurements of the presence or absence of specific biochemical markers such as fermentation of specific carbohydrates or the presence of specific enzymes are also used for purposes of identification. Using selected biochemical tests, a high degree of precise identification can be achieved for most isolates. These methods are also useful for subdividing groups of organisms from the same species to identify whether they originate from a common source or not. This method is referred to as biotyping and is of primary use in epidemiology.

Serotyping is a technique by which antigens of a specific cell are identified with marked or labeled antibodies. This method is used primarily to identify microbes that are inert in biochemical settings, difficult to grow, or need to be rapidly identified. As with biotyping, serotyping can also be used to divide the subspecies level for epidemiological purposes. Phage typing and susceptibility of bacteria to various antibiotics are also used for species identification. The latter method, which measures antibiotic susceptibility, is called the antibiogram pattern method and has limited discriminatory power.

Analytical characteristics of bacteria can be used to classify genus, species, or subspecies of bacteria also. This method is accurate but labor intensive and the instrumentation used is expensive. Genotypic classification is by far the most precise method for bacterial identification. Genotyping has evolved over the years and has been developed into some simplified methods that can be used in many clinical laboratories.

Classification According to Bergey’s Manual of Systematic Bacteriology

“Prokaryotes are described in 33 sections of the 4 volumes comprising the first edition of Bergey’s Manual of Systematic Bacteriology (a second edition is forthcoming).” This section of the chapter provides an overview of some major groups of bacteria important in human health and disease. A more complete outline is illustrated in Appendix A: Bergey’s Manual of Systematic Bacteriology.

Spirochetes

Spirochetes are a group of helical, motile bacteria with a length from 5 to 500 micrometers (µm). They are flexible and motile with twisting motions of their axial fibrils. These fibrils are a type of endocellular flagella that are wound around their cell body. Free-living spirochetes can be found in various aqueous environments and in association with human or animal hosts. Pathogenic spirochetes include Treponema pallidum, Borrelia burgdorferi, and Leptospira interrogans (Figure 6.14). Treponema is the causative agent of syphilis (see Chapter 17, Sexually Transmitted Infections/Diseases), Borrelia burgdorferi is the causative agent of Lyme disease, and Leptospira interrogans is the causative agent of leptospirosis.

FIGURE 6.14 Leptospira.
Silver staining shows the tightly coiled body with hooked ends. From Murray PR, Rosenthal KS, Pfaller MA: *Medical Microbiology,* ed 5, St. Louis, Mosby, 2005.

HEALTHCARE APPLICATION
Pathogenic Spirochetes

Disease	Cause	Symptoms	Treatment
Lyme disease	Borrelia burgdorferi	Acute: Skin rash, including “bull’s-eye” rash; fever, fatigue, headache, muscle and joint aches. Not all symptoms occur in every case of the disease Chronic: Fatigue; myalgia; neuropathy, meningitis, and more	Antibiotics: Early stages: Doxycycline (except in children) and amoxicillin. Refractile or late stages: Prolonged treatment with ceftriaxone
Syphilis	Treponema pallidum	Primary, secondary, tertiary, and latent*	Antibiotics in primary and secondary stages: Penicillin, doxycycline, ceftriaxone, or azithromycin
Leptospirosis	Leptospira interrogans	Influenza-like symptoms; complications of hepatitis, jaundice, hemorrhage in the liver, uremia bacteriuria, aseptic meningitis; conjunctival hemorrhages	Antibiotics: Doxycycline or penicillin

^*See Chapter 17 (Sexually Transmitted Infections/Diseases).

Aerobic/Microaerophilic Helical Vibroid Gram-negative Bacteria

The helical/vibroid gram-negative bacteria are either slightly curved or have multiple helical turns. They are motile with the help of their flagella. These bacteria can live in fresh or coastal waters and some may cause disease in humans or animals. This group of bacteria includes Campylobacter, Helicobacter, Bdellovibrio, and Vampirovibrio (Table 6.3). Bdellovibrio and Vampirovibrio prey on other gram-negative bacteria and on algae.

TABLE 6.3

Medically Important Aerobic/Microaerophilic Helical Vibroid Gram-negative Bacteria

Organism	Disease(s)
Campylobacter	Gastrointestinal tract infections: diarrhea, fever, and cramps
Helicobacter pylori	Peptic ulcers, gastritis, duodenitis

Gram-negative Aerobic Rods and Cocci

Gram-negative aerobic rods and cocci are a diverse group of bacteria that have been extensively investigated. They are widely distributed in nature and many are human and animal pathogens. Their metabolism is respiratory in nature and not based on fermentation. Bacteria in this category include Rhizobium, Legionella, Bordetella, and Francisella. Rhizobia are soil bacteria that fix nitrogen after they are established inside the roots of legumes (Figure 6.15). They cannot fix nitrogen independently, require a plant host, and play a major role in agriculture. Medically important bacteria are shown in Table 6.4.

TABLE 6.4

Medically Important Gram-negative Aerobic Rods and Cocci

Organism	Disease(s)
Legionella pneumophila	Legionellosis: Pontiac fever, Legionnaires’ disease
Neisseria gonorrhoeae	Gonorrhea
Neisseria meningitidis	Meningitis
Bordetella pertussis	Whooping cough
Francisella tularensis	Tularemia
Pseudomonas aeruginosa	Infections in burn victims

FIGURE 6.15 Gram-negative aerobic rods and cocci.
A, Gram stain of *Pseudomonas aeruginosa,* a gram-negative aerobic bacillus. B, Gram stain of *Neisseria sicca,* a gram-negative aerobic coccus.

LIFE APPLICATION

Rhizobia in Agriculture

Harvesting of protein-rich grain removes much of the nitrogen in the soil, but sufficient amounts are generally left for future crops. Inoculation of legumes with rhizobia is a common practice in agriculture to ensure maximal biological nitrogen fixation to enhance yield potentials without the use of exogenous nitrogen fertilizers. Such inoculants are commercially available in powder, liquid, and granular form.

This inoculation of the roots of leguminous plants with the appropriate species of Rhizobium leads to the formation of root nodules that are capable of converting gaseous nitrogen to combined nitrogen through the process of nitrogen fixation. Legumes include economically important plants such as soybeans, clover, alfalfa, peas, and beans. The legume–rhizobia symbiosis is an example of mutualism, in which the bacterium supplies ammonia or amino acids to the plant and receives organic acids as carbon and energy source in return.

Facultatively Anaerobic Gram-negative Rods

Facultatively anaerobic gram-negative rods are a large group of bacteria with simple nutritional requirements. With the exception of the genus Tatumella, all motile bacteria in this group have peritrichous flagella. Bacilli are present in soil, water, and in the intestinal tract of animals and humans. Bacteria found in the intestinal tracts of humans and animals are referred to as enteric bacteria and include the genera Escherichia, Salmonella, Shigella, Enterobacter, Proteus, and Providencia (Table 6.5). The best known enteric bacterium is E. coli (Figure 6.16), which is an extremely valuable tool used in genetic engineering and recombinant DNA technology. It is often referred to as the “workhorse” in molecular biology.

TABLE 6.5

Medically Important Facultative Anaerobic Gram-negative Rods

Organism	Disease(s)
Escherichia	Urinary tract infections, peritonitis, meningitis, pneumonia, septicemia
Salmonella	Foodborne illnesses; typhoid fever
Shigella	Bacillary dysentery
Klebsiella	Pneumonia
Enterobacter	Opportunistic infections, most commonly of the urinary and respiratory tracts
Proteus	Urinary tract infections; hospital-acquired wound infection, septicemia, pneumonia in the compromised host
Providenciaz	Urinary tract infections

FIGURE 6.16 Facultative anaerobic gram-negative rods.
A, Gram stain of *Escherichia coli*. B, Gram stain of *Proteus vulgaris*.

MEDICAL HIGHLIGHTS

E. coli O157:H7: The Bad Seed

Escherichia coli is a ubiquitous gram-negative, facultatively anaerobic bacillus that can be found in the intestinal tract of many animals, including humans. Most of the strains of this species are harmless but there are a few that can cause a variety of illnesses, usually associated with infections of the gastrointestinal tract or with nosocomial-type infections. One of the most notorious is E. coli O157:H7, also referred to as enterohemorrhagic E. coli (EHEC). The vast majority of outbreaks of E. coli reported by the media involve this particular strain. Fecal in origin, this strain of bacteria is typically spread through the ingestion of contaminated food or water. Infection can be as subtle as swallowing a mouthful of water while swimming in a lake, or eating food handled by persons who did not wash their hands after using the toilet. Outbreaks have been linked to the consumption of various contaminated food products ranging from ground beef to spinach and tomatoes. Symptoms vary but often include stomach cramps, bloody diarrhea, and vomiting. Most people will recover within 5 to 7 days; however, 5% to 10% of infected people develop a life-threatening complication known as hemolytic uremic syndrome (HUS). If not treated quickly, HUS can cause serious damage to the kidneys, which is potentially fatal. With proper treatment most persons with HUS will recover within a few weeks; however, they may suffer some permanent kidney damage. The best ways to prevent an EHEC infection are by washing hands; cooking meats thoroughly; washing raw foods before eating; washing cutting boards between uses, especially when they are used for both meat and raw food preparation; avoiding unpasteurized dairy products and juices; and avoiding water ingestion from a source that may be contaminated, such as a lake or swimming pool.

Some of the bacteria found in the gastrointestinal tract of humans are often referred to as coliforms. Coliforms are a group of bacteria, not necessarily enteric, but meeting six criteria to be classified as coliform:

• Gram negative

• Rod shaped

• Facultative anaerobes

• Nonsporulating

• Utilize lactose

• Produce gas

Klebsiella pneumoniae is a coliform found in the normal flora of the mouth and skin, but also in the intestine, and can cause bacterial pneumonia (see Chapter 11, Infections of the Respiratory System). The genus Citrobacter can be found in many different environments including soil, water, and wastewater and can also be found in the human intestine. In general, Citrobacter does not cause illness but occasionally can be the source of urinary tract infections and infant meningitis.

LIFE APPLICATION

Coliform Index and Water Testing

Water is essential for life and the ecosystems. The U.S. Environmental Protection Agency (EPA) enforces federal clean water and safe drinking water laws and provides support for municipal wastewater treatment plants. Two bacterial groups, coliforms and fecal streptococci, are commonly used as indicators of possible contamination with sewage because these bacteria are found in human and animal feces. The Coliform Index is used to rate the purity of water on the basis of the count of fecal bacteria. Although coliforms are generally not harmful themselves, they are indicators of the presence of possible pathogenic organisms that also live in human and animal digestive systems.

Anaerobic Gram-negative Rods

Anaerobic gram-negative rods can be straight, curved, helical, motile, or nonmotile. These bacteria are present in the intestinal tract of humans and animals. Leptotrichia buccalis and Fusobacterium species are frequently found along the gum line and on tooth surfaces. Bacteroides are normally commensal, representing a substantial portion of the mammalian gastrointestinal flora, and preventing potential pathogens from colonizing the gut; however, some species are opportunistic pathogens.

Anaerobic Gram-negative Cocci

Anaerobic gram-negative cocci often occur in pairs and are found in the mouth, the intestines, and the vagina. Veillonella causes rare opportunistic infections and has a low virulence potential; it is often associated with long-standing gingivitis in dental patients. However, cases of osteomyelitis, bacterial endocarditis, and abscesses in internal organs have been reported in the literature.

Rickettsias and Chlamydias

Rickettsias and chlamydias are very small gram-negative bacteria. The majority of these organisms require a host for replication. In general, rickettsias and chlamydias are rod shaped but also may look coccoidal (Figure 6.17). Host-dependent organisms often cause diseases in humans and animals. Rickettsias need a vertebrate and an arthropod host, whereas chlamydias do not infect invertebrates but have a complex developmental cycle. Medically important organisms include Rickettsia rickettsii, Rickettsia prowazekii, Rickettsia typhi, Chlamydia trachomatis, Chlamydophila pneumoniae, and Chlamydophila psittaci (Table 6.6). Orientia tsutsugamushi is the agent of scrub typhus, a widely endemic disease in Asian Pacific regions that was formerly classified with Rickettsia. It is a gram-negative obligate intracellular bacterium belonging to the family Rickettsiaceae.

TABLE 6.6

Medically Important Rickettsias and Chlamydias

Organism	Disease(s)
Rickettsia rickettsii	Rocky Mountain spotted fever
Rickettsia prowazekii	Epidemic typhus; recrudescent typhus, sporadic typhus
Rickettsia typhi	Endemic or murine typhus
Chlamydia trachomatis	Trachoma, adult inclusion conjunctivitis, neonatal conjunctivitis, infant pneumonia, urogenital infections, lymphogranuloma venereum
Chlamydofilia pneumoniae	Respiratory infections, atherosclerosis
Chlamydophila psittaci	Respiratory infections

FIGURE 6.17 Rickettsia.
Gimenez stain of tissue culture cells infected with *Rickettsia*. (From Murray PR, Rosenthal KS, Pfaller MA: *Medical Microbiology,* ed. 5, St. Louis, Mosby, 2005.)

Mycoplasmas and Ureaplasmas

Mycoplasma and Ureaplasma organisms are the smallest free-living bacteria. They are unique among bacteria because they do not have cell walls, resulting in a variable or indistinct shape, and therefore are pleomorphic. They measure 0.3 to 0.8 µm in diameter and are spherical to pear shaped with branched or helical filaments. Because of the absence of the cell wall the mycoplasmas are resistant to penicillins, cephalosporins, vancomycin, and other antibiotics that interfere with cell wall synthesis. Mycoplasmas have special growth requirements and most pathogenic species are host specific. These organisms can cause disease in humans (Table 6.7), animals, and plants.

TABLE 6.7

Medically Important Mycoplasmas

Organism	Disease(s)
Mycoplasma pneumoniae	Upper respiratory infections, lower respiratory infections including tracheobronchitis and bronchopneumonia
Mycoplasma genitalium	Nongonococcal urethritis
Mycoplasma hominis	Pyelonephritis, pelvic inflammatory disease, postpartum fever

Gram-positive Cocci

Gram-positive cocci include aerobic and anaerobic spherical cells, ranging from harmless to virulent forms. These cocci include the genera Micrococcus, Staphylococcus, Streptococcus, and Peptococcus. Some medically important gram-positive cocci are shown in Table 6.8.

TABLE 6.8

Selected Medically Important Gram-positive Cocci

Organism	Disease(s)
Micrococcus	Opportunistic organisms
Staphylococcus aureus	Minor skin infections, pneumonia, meningitis, endocarditis, toxic shock syndrome, septicemia
Streptococcus pyogenes	Pharyngitis (“strep throat”), scarlet fever, pyoderma, erysipelas, cellulitis, necrotizing fascilitis, streptococcal toxic shock syndrome
Streptococcus pneumoniae	Pneumonia, meningitis, bacteremia
Peptococcus and Peptostreptococcus	Opportunistic organisms

• Micrococci are aerobic organisms not associated with disease; however; they can be opportunistic pathogens in hosts with a compromised immune system. These organisms are found in soil, water, dust, and dairy products and are part of the normal flora of the skin.

• Staphylococci are gram-positive facultative anaerobes. They can cause a wide variety of diseases in humans and other animals through their production of toxins or tissue invasion. Staphylococcus toxins are a common cause of food poisoning because of the heat resistance of the enterotoxin and the ability of staphylococci to grow in foods with relatively low water activity. Staphylococcus epidermidis (Figure 6.18) is a commensal organism of the skin, but can cause severe infections in immunosuppressed patients, in those with central venous catheters, and in patients with prosthetic limbs. The pathogenic species Staphylococcus aureus produces up to 18 extracellular products that can harm human and animal hosts. Methicillin-resistant Staphylococcus aureus (MRSA) is a specific strain that has developed resistance to all penicillins. MRSA infections occur most frequently in hospital and healthcare environments and are commonly termed as a “superbug” infections.

FIGURE 6.18 *Staphylococcus epidermidis.*
This is a gram-positive bacterium and a normal resident of the human skin; it can become an opportunistic pathogen.

• Streptococci are microaerophilic or facultatively anaerobic, organisms that produce lactic acid. The classification of Streptococcus spp. is based on the hemolytic patterns of their colonies on blood agar. Alpha hemolysis is due to the reduction of iron in hemoglobin, resulting in partial hemolysins, producing a greenish color on blood agar. Beta hemolysis is a result of complete rupture of red blood cells, resulting in clear areas around bacterial colonies on blood agar. No hemolytic action occurs with the nonhemolytic or gamma-hemolytic strains. Although a number of the Streptococcus species are pathogenic (see Table 6.8), many of the species are nonpathogenic and are part of the normal human flora of the mouth, skin, intestine, and upper respiratory tract, but can be opportunistic pathogens. Streptococcus thermophilus is not a pathogen and is used in the manufacture of Swiss cheese.

• Peptococcus and Peptostreptococcus are anaerobic gram-positive cocci and part of the normal flora in the mouth, skin, and gastrointestinal and urinary tracts. They can infect normal hosts with a compromised immune system or damaged tissues. Under these conditions the organisms can become pathogenic and can cause brain, liver, breast, and lung abscesses due to septicemia.

Endospore-forming Gram-positive Rods and Cocci

Endospore-forming rods and cocci include the genera Bacillus and Clostridium (Figure 6.19), both of which play an important role in medicine and the food industry. The spores of these genera are resistant to heat and disinfectants and both genera are widespread in the soil. Bacillus species are either obligate aerobes or facultative anaerobes; they include free-living and pathogenic species. Medically important Bacillus species include B. anthracis and B. cereus (Table 6.9). Bacillus coagulans is associated with food spoilage, B. thuringiensis is an insect pathogen, and B. subtilis is an important model organism.

TABLE 6.9

Selected Medically Important Endospore-forming Gram-positive Rods and Cocci

Organism	Disease(s)
Bacillus anthracis	Anthrax (cutaneous, gastrointestinal, inhalation)
Bacillus cereus	Gastroenteritis, ocular infections
Clostridium botulinum	Botulism
Clostridium difficile	Antibiotic-associated diarrhea, pseudomembranous colitis
Clostridium perfringens	Gas gangrene, suppurative myositis, myonecrosis, gastroenteritis, food poisoning, necrotizing enteritis
Clostridium tetani	Tetanus

FIGURE 6.19 *Bacillus.*
This micrograph shows the gram-positive, spore-forming *Bacillus cereus.*

Clostridium perfringens is widely distributed in the environment and can be found as a normal component of decaying matter, in marine sediment, and also in the intestinal tract of humans and other animals. Food poisoning by this organism is a fairly common intestinal intoxication caused by toxins produced by the bacterium. The source of this problem is usually food contaminated by soil or feces or inadequately heated or reheated food (see Chapter 12, Infections of the Gastrointestinal System). Clostridium tetani is found in soil as spores or as a parasite in the gastrointestinal tract of animals. The organism produces tetanospasmin, the causative agent of tetanus (see Chapter 13, Infections of the Nervous System and Senses). Clostridium botulinum can cause a severe type of food poisoning initiated by the ingestion of foods containing the organism’s potent neurotoxin, which is formed during the growth of the bacterium (see Chapter 13).

Regular Nonsporulating Gram-positive Rods

Regular nonsporulating gram-positive rods are obligate or facultative anaerobes with complex nutritional requirements. This group includes Carnobacterium, Lactobacillus, and Listeria. The organism Carnobacterium pleistocenium was discovered in the arctic part of Alaska. It was found in permafrost, and melting ice brought these extremophiles back to a growing vegetative state. The discovery of this organism is of interest to NASA scientists as they investigate the permafrost of Mars for bacterial life. Lactobacilli convert lactose and other sugars to lactic acid and are commonly benign. Some species are used in industry for the production of yogurt, cheese, sauerkraut, pickles, and other fermented foods. Listeria monocytogenes is the causative agent of listeriosis. Outbreaks of listeriosis have been attributed to the consumption of hot dogs, deli meats, raw milk, cheeses, raw and cooked poultry, raw meats, ice cream, raw vegetables, and smoked fish, and it has a high mortality rate compared with other food-borne diseases.

Irregular Nonsporulating Gram-positive Rods

Irregular nonsporulating gram-positive rods have unusual shapes (often cubelike), are pleomorphic, and are mostly facultative anaerobes with a few obligate aerobes. Organisms important to humans include but are not limited to the genera Actinomyces, Corynebacterium, and Propionibacterium. Propionibacterium shermanii is used in the production of Swiss cheese. Medically important organisms for this group are shown in Table 6.10.

TABLE 6.10

Selected Medically Important Irregular Nonsporulating Gram-positive Rods

Organism	Disease(s)
Actinomyces	Opportunistic pathogens, particularly in the oral cavity, formation of abscesses in mouth, lungs, or gastrointestinal tract
Corynebacterium diphtheriae	Diphtheria
Propionibacterium acnes	Acne
Actinomyces israelii	Periodontal abscesses; lung infections

Mycobacteria

The genus Mycobacterium includes gram-positive, aerobic, acid-fast rods that have the tendency to form filaments (Figure 6.20). They are widespread organisms in water, soil, and food sources, whereas some are obligate intracellular parasites (usually infecting mononuclear phagocytes) in animals and humans. Although mycobacteria have a tendency to be difficult to grow in culture, they are classified into two categories, the fast-growing type and the slow-growing type, based on laboratory growth characteristics. In general, mycobacteria can colonize in the host without showing signs and symptoms of host infection. Many people around the world are infected with M. tuberculosis and never develop symptoms, yet they are carriers of the disease. Mycobacterial infections usually are difficult to treat because of their cell wall structure, which is neither truly gram negative nor gram positive. This makes them naturally resistant to many antibiotics whose mechanism of action is the destruction of cell walls (e.g., penicillin). Some medically important mycobacteria are shown in Table 6.11.

TABLE 6.11

Selected Medically Important Mycobacteria

Organism	Disease(s)
Mycobacterium tuberculosis	Tuberculosis
Mycobacterium leprae	Leprosy
Nontuberculous mycobacteria (NTM)	Pulmonary disease resembling tuberculosis, lymphadenitis, skin disease, or dispersed disease

FIGURE 6.20 *Mycobacterium smegmatis*, an acid-fast bacillus.

Nocardioforms

Nocardioforms are aerobic, gram-positive, catalase-positive rods that form thin branching filaments. They are widespread in the environment, opportunistic, and can cause several diseases, especially in the young, the elderly, and immunocompromised patients. Although Nocardia infections are rare it is generally a chronic bacterial infection originating in the lungs and then spreading to other organ systems. The other systems most commonly affected are the brain and skin, but the kidneys, joints, heart, eyes, and bones might be involved. The symptoms of infection vary and depend on the organs involved.

Streptomycetes

Streptomycetes are gram positive, found predominantly in the soil and in decaying vegetation, and most of them are spore forming. In general they are not pathogenic, but many of the species are important sources of antibiotics (Table 6.12). Very infrequently they cause human disease, most often manifesting itself as a localized, chronic infection of the skin and underlying soft tissue. Invasive Streptomyces infections are extremely rare.

TABLE 6.12

Streptomycetes: A Source of Antibiotics

Organism	Antibiotic
Streptomyces griseus	Streptomycin
Amycolatopsis mediterranei	Rifamycin
Saccharopolyspora erythraea	Erythromycin
Streptomyces antibioticus	Oleandomycin