Easter College Microbiology – Parasitology Module 1 2024-25 PDF

1 Easter College Microbiology – Parasitology Module 1 MICROBES IN OUR LIVES For many people, the words germ and microbe...

1 Easter College Microbiology – Parasitology Module 1 MICROBES IN OUR LIVES For many people, the words germ and microbe bring to mind a group of tiny creatures that do not quite fit into any of the categories in that old question, “Is it animal, vegetable, or mineral?” Microbes, also called microorganisms, are minute living things that individually are usually too small to be seen with the unaided eye. The group includes bacteria, fungi (yeasts and molds), protozoa, and microscopic algae. It also includes viruses, those noncellular entities sometimes regarded as straddling the border between life and nonlife. You will be introduced to each of these groups of microbes shortly. We tend to associate these small organisms only with major diseases such as AIDS, uncomfortable infections, or such common inconveniences as spoiled food. However, the majority of microorganisms actually help maintain the balance of living organisms and chemicals in our environment. Marine and freshwater microorganisms form the basis of the food chain in oceans, lakes, and rivers. Soil microbes help break down wastes and incorporate nitrogen gas from the air into organic compounds, thereby recycling chemical elements between the soil, water, life, and air. Certain microbes play important roles in photosynthesis, a food- and oxygen-generating process that is critical to life on Earth. Humans and many other animals depend on the microbes in their intestines for digestion and the synthesis of some vitamins that their bodies require, including some B vitamins for metabolism and vitamin K for blood clotting. Microorganisms also have many commercial applications. They are used in the synthesis of such chemical products as vitamins, organic acids, enzymes, alcohols, and many drugs. For example, microbes are used to produce acetone and butanol, and the vitamins B 2 (riboflavin) and B12 (cobalamin) are made biochemically. The process by which microbes produce acetone and butanol was discovered in 1914 by Chaim Weizmann, a Russian-born chemist working in England. With the outbreak of World War I in August of that year, the production of acetone became very important for making cordite (a smokeless form of gunpowder used in munitions). Weizmann’s discovery played a significant role in determining the outcome of the war. The food industry also uses microbes in producing, for example, vinegar, sauerkraut, pickles, soy sauce, cheese, yogurt, bread, and alcoholic beverages. In addition, enzymes from microbes can now be manipulated to cause the microbes to produce substances they normally do not synthesize, including cellulose, digestive aids, and drain cleaner, plus important therapeutic substances such as insulin. Microbial enzymes may even have helped produce your favorite pair of jeans (see the box on the next page).  2 Though only a minority of microorganisms are pathogenic (disease-producing), practical knowledge of microbes is necessary for medicine and the related health sciences. For example, hospital workers must be able to protect patients from common microbes that are normally harmless but pose a threat to the sick and injured. Today we understand that microorganisms are found almost everywhere. Yet not long ago, before the invention of the microscope, microbes were unknown to scientists. Thousands of people died in devastating epidemics, the causes of which were not understood. Entire families died because vaccinations and antibiotics were not available to fight infections. We can get an idea of how our current concepts of microbiology developed by looking at a few historic milestones in microbiology that have changed our lives. First, however, we will look at the major groups of microbes and how they are named and classified. Clinical Case: A Simple Mosquito Bite? Zendaya is a normally healthy 20-year-old college student who lives at home with her mother and younger sister, a high school gymnast. She is trying to work on a paper for her Microbiology class but is having a hard time because a red, swollen sore on her right wrist is making typing difficult. “Why won’t this mosquito bite heal?” she wonders. “It’s been there for days!” She makes an appointment with her doctor so she can show him the painful lesion. Although Zendaya does not have a fever, she does have an elevated white blood cell count that indicates a bacterial infection. Zendaya’s doctor suspects that this isn’t a mosquito bite at all, but a staph infection. He prescribes a β-lactam antibiotic, cephalosporin. Learn more about the development of Andrea’s illness on the following pages. NOMENCLATURE The system of nomenclature (naming) for organisms in use today was established in 1735 by Carolus Linnaeus. Scientific names are latinized because Latin was the language traditionally used by scholars. Scientific nomenclature assigns each organism two names—the genus (plural: genera) is the first name and is always capitalized; the specific epithet (species name) follows and is not capitalized. The organism is referred to by both the genus and the specific epithet, and both names are underlined or italicized. By custom, after a scientific name has been mentioned once, it can be abbreviated with the initial of the genus followed by the specific epithet. Scientific names can, among other things, describe an organism, honor a researcher, or identify the habitat of a species. For example, consider Staphylococcus aureus (staf-i-lō-kok’kus ô’rē-us), a bacterium commonly found on human skin. Staphylo- describes the clustered arrangement of the cells; coccus indicates that they are shaped like spheres. The specific epithet, aureus, is Latin for golden, the color of many colonies of this bacterium. The genus of the bacterium Escherichia coli (esh-ë-rik’-ē-ä kō’lī or kō’lē) is named for a scientist, Theodor Escherich, whereas its specific epithet, coli, reminds us that E. coli live in the colon, or large intestine. Table 1.1 contains more examples. TYPES OF MICROORGANISMS The classification and identification of microorganisms will be discussed soon. Here is an overview of the major groups. Bacteria Bacteria (singular: bacterium) are relatively simple, single-celled (unicellular) organisms. Because their genetic material is not enclosed in a special nuclear membrane, bacterial cells are called prokaryotes (prō-kare-ōts), from Greek words meaning prenucleus. Prokaryotes include both bacteria and archaea. Bacterial cells generally appear in one of several shapes. Bacillus (bä-sillus) (rodlike), illustrated in Figure 1.1a, coccus (kok- kus) (spherical or ovoid), and spiral (corkscrew or curved) are among the most common shapes, but some bacteria are star-shaped or square. Individual bacteria may form pairs, chains, clusters, or other groupings; such formations are usually characteristic of a particular genus or species of bacteria. Bacteria are enclosed in cell walls that are largely composed of a carbohydrate and protein complex called peptidoglycan. (By contrast, cellulose is the main substance of plant and algal cell walls.) Bacteria generally reproduce by dividing into two equal cells; this process is called binary fission. For nutrition, most bacteria use organic chemicals, which in nature can be derived from either dead or living organisms. Some bacteria can manufacture their own food by photosynthesis, and some can derive nutrition from inorganic substances. Many bacteria can “swim” by using moving appendages called flagella.  3 Archaea Like bacteria, archaea (ärkē-ä) consist of prokaryotic cells, but if they have cell walls, the walls lack peptidoglycan. Archaea, often found in extreme environments, are divided into three main groups. The methanogens produce methane as a waste product from respiration. The extreme halophiles (halo = salt; philic = loving) live in extremely salty environments such as the Great Salt Lake and the Dead Sea. The extreme thermophiles (therm = heat) live in hot sulfurous water, such as hot springs at Yellowstone National Park. Archaea are not known to cause disease in humans. Fungi Fungi (singular: fungus) are eukaryotes (yū-karē-ōts), organisms whose cells have a distinct nucleus containing the cell’s genetic material (DNA), surrounded by a special envelope called the nuclear membrane. Organisms in the Kingdom Fungi may be unicellular or multicellular. Large multicellular fungi, such as mushrooms, may look somewhat like plants, but unlike most plants, fungi cannot carry out photosynthesis. True fungi have cell walls composed primarily of a substance called chitin. The unicellular forms of fungi, yeasts, are oval microorganisms that are larger than bacteria. The most typical fungi are molds (Figure 1.1b). Molds form visible masses called mycelia, which are composed of long filaments (hyphae) that branch and intertwine. The cottony growths sometimes found on bread and fruit are mold mycelia. Fungi can reproduce sexually or asexually. They obtain nourishment by absorbing solutions of organic material from their environment—whether soil, seawater, freshwater, or an animal or plant host. Organisms called slime molds have characteristics of both fungi and amoebas. Protozoa Protozoa (singular: protozoan) are unicellular eukaryotic microbes. Protozoa move by pseudopods, flagella, or cilia. Amebae (Figure 1.1c) move by using extensions of their cytoplasm called pseudopods (false feet). Other protozoa have long flagella or numerous shorter appendages for locomotion called cilia. Protozoa have a variety of shapes and live either as free entities or as parasites (organisms that derive nutrients from living hosts) that absorb or ingest organic compounds from their environment. Some protozoa, such as Euglena, are photosynthetic. They use light as a source of energy and carbon dioxide as their chief source of carbon to produce sugars. Protozoa can reproduce sexually or asexually.  4 Algae Algae (singular: alga) are photosynthetic eukaryotes with a wide variety of shapes and both sexual and asexual reproductive forms (Figure 1.1d). The algae of interest to microbiologists are usually unicellular. The cell walls of many algae, are composed of a carbohydrate called cellulose. Algae are abundant in freshwater and salt water, in soil, and in association with plants. As photosynthesizers, algae need light, water, and carbon dioxide for food production and growth, but they do not generally require organic compounds from the environment. As a result of photosynthesis, algae produce oxygen and carbohydrates that are then utilized by other organisms, including animals. Thus, they play an important role in the balance of nature. Viruses Viruses (Figure 1.1e) are very different from the other microbial groups mentioned here. They are so small that most can be seen only with an electron microscope, and they are acellular (not cellular). Structurally very simple, a virus particle contains a core made of only one type of nucleic acid, either DNA or RNA. This core is surrounded by a protein coat, which is sometimes encased by a lipid membrane called an envelope. All living cells have RNA and DNA, can carry out chemical reactions, and can reproduce as self-sufficient units. Viruses can reproduce only by using the cellular machinery of other organisms. Thus, on the one hand, viruses are considered to be living only when they multiply within host cells they infect. In this sense, viruses are parasites of other forms of life. On the other hand, viruses are not considered to be living because they are inert outside living hosts. Multicellular Animal Parasites Although multicellular animal parasites are not strictly microorganisms, they are of medical importance and therefore will be discussed in this text. Animal parasites are eukaryotes. The two major groups of parasitic worms are the flatworms and the roundworms, collectively called helminths. During some stages of their life cycle, helminths are microscopic in size. Laboratory identification of these organisms includes many of the same techniques used for identifying microbes. Classification of Microorganisms Before the existence of microbes was known, all organisms were grouped into either the animal kingdom or the plant kingdom. When microscopic organisms with characteristics of animals and plants were discovered late in the seventeenth century, a new system of classification was needed. Still, biologists could not agree on the criteria for classifying these new organisms until the late 1970s. In 1978, Carl Woese devised a system of classification based on the cellular organization of organisms. It groups all organisms in three domains as follows: 1. Bacteria (cell walls contain a protein–carbohydrate complex called peptidoglycan) 2. Archaea (cell walls, if present, lack peptidoglycan) 3. Eukarya, which includes the following: Protists (slime molds, protozoa, and algae) Fungi (unicellular yeasts, multicellular molds, and mushrooms) Plants (mosses, ferns, conifers, and flowering plants) Animals (sponges, worms, insects, and vertebrates)  5 A BRIEF HISTORY OF MICROBIOLOGY The science of microbiology dates back only 200 years, yet the recent discovery of Mycobacterium tuberculosis (mī-kō-bak-tirē-um tü-bėr-ku-lōsis) DNA in 3000-year-old Egyptian mummies reminds us that microorganisms have been around for much longer. In fact, bacterial ancestors were the first living cells to appear on Earth. Although we know relatively little about what earlier people thought about the causes, transmission, and treatment of disease, we know more about the history of the past few hundred years. Let’s look now at some key developments in microbiology that have spurred the field to its current technological state. The First Observations One of the most important discoveries in biology occurred in 1665. After observing a thin slice of cork through a relatively crude microscope, an Englishman, Robert Hooke, reported to the world that life’s smallest structural units were “little boxes,” or “cells,” as he called them. Using his improved version of a compound microscope (one that uses two sets of lenses), Hooke was able to see individual cells. Hooke’s discovery marked the beginning of the cell theory—the theory that all living things are composed of cells. Subsequent investigations into the structure and function of cells were based on this theory. Though Hooke’s microscope was capable of showing large cells, it lacked the resolution that would have allowed him to see microbes clearly. The Dutch merchant and amateur scientist Anton van Leeuwenhoek was probably the first actually to observe live microorganisms through the magnifying lenses of more than 400 microscopes he constructed. Between 1673 and 1723, he wrote a series of letters to the Royal Society of London describing the “animalcules” he saw through his simple, single lens microscope. Van Leeuwenhoek made detailed drawings of “animalcules” he found in rainwater, in his own feces, and in material scraped from his teeth. These drawings have since been identified as representations of bacteria and protozoa (Figure 1.2).  6 The Debate over Spontaneous Generation After van Leeuwenhoek discovered the previously “invisible” world of microorganisms, the scientific community of the time became interested in the origins of these tiny living things. Until the second half of the nineteenth century, many scientists and philosophers believed that some forms of life could arise spontaneously from nonliving matter; they called this hypothetical process spontaneous generation. Not much more than 100 years ago, people commonly believed that toads, snakes, and mice could be born of moist soil; that flies could emerge from manure; and that maggots (which we now know are the larvae of flies) could arise from decaying corpses. Evidence Pro and Con A strong opponent of spontaneous generation, the Italian physician Francesco Redi set out in 1668 to demonstrate that maggots did not arise spontaneously from decaying meat. Redi filled two jars with decaying meat. The first was left unsealed; the flies laid their eggs on the meat, and the eggs developed into larvae. The second jar was sealed, and because the flies could not lay their eggs on the meat, no maggots appeared. Still, Redi’s antagonists were not convinced; they claimed that fresh air was needed for spontaneous generation. So Redi set up a second experiment, in which he covered a jar with a fine net instead of sealing it. No larvae appeared in the gauze-covered jar, even though air was present. Maggots appeared only when flies were allowed to leave their eggs on the meat. Redi’s results were a serious blow to the long-held belief that large forms of life could arise from nonlife. However, many scientists still believed that small organisms, such as van Leeuwenhoek’s “animalcules,” were simple enough to be generated from nonliving materials. The case for spontaneous generation of microorganisms seemed to be strengthened in 1745, when John Needham, an Englishman, found that even after he heated nutrient fluids (chicken broth and corn broth) before pouring them into covered flasks, the cooled solutions were soon teeming with microorganisms. Needham claimed that microbes developed spontaneously from the fluids. Twenty years later, Lazzaro Spallanzani, an Italian scientist, suggested that microorganisms from the air probably had entered Needham’s solutions after they were boiled. Spallanzani showed that nutrient fluids heated after being sealed in a flask did not develop microbial growth. Needham responded by claiming the “vital force” necessary for spontaneous generation had been destroyed by the heat and was kept out of the flasks by the seals. This intangible “vital force” was given all the more credence shortly after Spallanzani’s experiment, when Anton Laurent Lavoisier showed the importance of oxygen to life. Spallanzani’s observations were criticized on the grounds that there was not enough oxygen in the sealed flasks to support microbial life. The Theory of Biogenesis The issue was still unresolved in 1858, when the German scientist Rudolf Virchow challenged the case for spontaneous generation with the concept of biogenesis, the claim that living cells can arise only from  7 preexisting living cells. Because he could offer no scientific proof, arguments about spontaneous generation continued until 1861, when the issue was finally resolved by the French scientist Louis Pasteur. With a series of ingenious and persuasive experiments, Pasteur demonstrated that microorganisms are present in the air and can contaminate sterile solutions, but that air itself does not create microbes. He filled several short-necked flasks with beef broth and then boiled their contents. Some were then left open and allowed to cool. In a few days, these flasks were found to be contaminated with microbes. The other flasks, sealed after boiling, were free of microorganisms. From these results, Pasteur reasoned that microbes in the air were the agents responsible for contaminating nonliving matter. Pasteur next placed broth in open-ended, long-necked flasks and bent the necks into S-shaped curves (Figure 1.3). The contents of these flasks were then boiled and cooled. The broth in the flasks did not decay and showed no signs of life, even after months. Pasteur’s unique design allowed air to pass into the flask, but the curved neck trapped any airborne microorganisms that might contaminate the broth. (Some of these original vessels are still on display at the Pasteur Institute in Paris. They have been sealed but, like the flask shown in Figure 1.3, show no sign of contamination more than 100 years later.) Pasteur showed that microorganisms can be present in nonliving matter—on solids, in liquids, and in the air. Furthermore, he demonstrated conclusively that microbial life can be destroyed by heat and that methods can be devised to block the access of airborne microorganisms to nutrient environments. These discoveries form the basis of aseptic techniques, techniques that prevent contamination by unwanted microorganisms, which are now the standard practice in laboratory and many medical procedures. Modern aseptic techniques are among the first and most important concepts that a beginning microbiologist learns. Pasteur’s work provided evidence that microorganisms cannot originate from mystical forces present in nonliving materials. Rather, any appearance of “spontaneous” life in nonliving solutions can be attributed to microorganisms that were already present in the air or in the fluids themselves. Scientists now believe that a form of spontaneous generation probably did occur on the primitive Earth when life first began, but they agree that this does not happen under today’s environmental conditions. Figure 1.3. Disproving the Theory of Spontaneous Generation. The Golden Age of Microbiology The work that began with Pasteur started an explosion of discoveries in microbiology. The period from 1857 to 1914 has been appropriately named the Golden Age of Microbiology. During this period, rapid advances, spearheaded mainly by Pasteur and Robert Koch, led to the establishment of microbiology as a science. Discoveries during these years included both the agents of many diseases and the role of immunity in preventing and curing disease. During this productive period, microbiologists studied the chemical activities of microorganisms, improved the techniques for performing microscopy and culturing microorganisms, and  8 developed vaccines and surgical techniques. Some of the major events that occurred during the Golden Age of Microbiology are listed in Figure 1.4. Fermentation and Pasteurization One of the key steps that established the relationship between microorganisms and disease occurred when a group of French merchants asked Pasteur to find out why wine and beer soured. They hoped to develop a method that would prevent spoilage when those beverages were shipped long distances. At the time, many scientists believed that air converted the sugars in these fluids into alcohol. Pasteur found instead that microorganisms called yeasts convert the sugars to alcohol in the absence of air. This process, called fermentation, is used to make wine and beer. Souring and spoilage are caused by different microorganisms called bacteria. In the presence of air, bacteria change the alcohol into vinegar (acetic acid). Pasteur’s solution to the spoilage problem was to heat the beer and wine just enough to kill most of the bacteria that caused the spoilage. The process, called pasteurization, is now commonly used to reduce spoilage and kill potentially harmful bacteria in milk as well as in some alcoholic drinks. Showing the connection between food spoilage and microorganisms was a major step toward establishing the relationship between disease and microbes. The Germ Theory of Disease As we have seen, the fact that many kinds of diseases are related to microorganisms was unknown until relatively recently. Before the time of Pasteur, effective treatments for many diseases were discovered by trial and error, but the causes of the diseases were unknown. The realization that yeasts play a crucial role in fermentation was the first link between the activity of a microorganism and physical and chemical changes in organic materials. This discovery alerted scientists to the possibility that microorganisms might have similar relationships with plants and animals—specifically, that microorganisms might cause disease. This idea was known as the germ theory of disease. The germ theory was a difficult concept for many people to accept at that time because for centuries disease was believed to be punishment for an individual’s crimes or misdeeds. When the inhabitants of an entire village became ill, people often blamed the disease on demons appearing as foul odors from sewage or on poisonous vapors from swamps. Most people born in Pasteur’s time found it inconceivable that “invisible” microbes could travel through the air to infect plants and animals or remain on clothing and bedding to be transmitted from one person to another. Despite these doubts scientists gradually accumulated the information needed to support the new germ theory. In 1865, Pasteur was called upon to help fight silkworm disease, which was ruining the silk industry throughout Europe. Years earlier, in 1835, Agostino Bassi, an amateur microscopist, had proved that another silkworm disease was caused by a fungus. Using data provided by Bassi, Pasteur found that the more recent infection was caused by a protozoan, and he developed a method for recognizing afflicted silkworm moths. In the 1860s, Joseph Lister, an English surgeon, applied the germ theory to medical procedures. Lister was aware that in the 1840s, the Hungarian physician Ignaz Semmelweis had demonstrated that physicians, who at the time did not disinfect their hands, routinely transmitted infections (puerperal, or childbirth, fever) from one obstetrical patient to another. Lister had also heard of Pasteur’s work connecting microbes to animal diseases. Disinfectants were not used at the time, but Lister knew that phenol (carbolic acid) kills bacteria, so he began treating surgical wounds with a phenol solution. The practice so reduced the incidence of infections and deaths that other surgeons quickly adopted it. Lister’s technique was one of the earliest medical attempts to control infections caused by microorganisms. In fact, his findings proved that microorganisms cause surgical wound infections. The first proof that bacteria actually cause disease came from Robert Koch in 1876. Koch, a German physician, was Pasteur’s young rival in the race to discover the cause of anthrax, a disease that was destroying cattle and sheep in Europe. Koch discovered rod-shaped bacteria now known as Bacillus anthracis (bä-sil’lus an-thrā’sis) in the blood of cattle that had died of anthrax. He cultured the bacteria on nutrients and then injected samples of the culture into healthy animals. When these animals became sick and died, Koch isolated the bacteria in their blood and compared them with the originally isolated bacteria. He found that the two sets of blood cultures contained the same bacteria. Koch thus established Koch’s postulates, a sequence of experimental steps for directly relating a specific microbe to a specific disease. During the past 100 years, these same criteria have been invaluable in investigations proving that specific microorganisms cause many diseases. Koch’s postulates, their limitations, and their application to disease will be discussed in future topics.  9 Figure 1.4 Milestones in Microbiology, highlighting those that occurred during the Golden Age of Microbiology. Vaccination Often a treatment or preventive procedure is developed before scientists know why it works. The smallpox vaccine is an example. On May 4, 1796, almost 70 years before Koch established that a specific microorganism causes anthrax, Edward Jenner, a young British physician, embarked on an experiment to find a way to protect people from smallpox. Smallpox epidemics were greatly feared. The disease periodically swept through Europe, killing thousands, and it wiped out 90% of the American Indians on the East Coast when European settlers first brought the infection to the New World. When a young milkmaid informed Jenner that she couldn’t get smallpox because she already had been sick from cowpox—a much milder disease—he decided to put the girl’s story to the test. First Jenner collected scrapings from cowpox blisters. Then he inoculated a healthy 8-year-old volunteer with the cowpox material by scratching the person’s arm with a pox-contaminated needle. The scratch turned into a raised bump. In a few days, the volunteer became mildly sick but recovered and never again contracted either cowpox or smallpox. The process was called vaccination, from the Latin word “vacca”, meaning cow.  10 Pasteur gave it this name in honor of Jenner’s work. The protection from disease provided by vaccination (or by recovery from the disease itself) is called immunity. Years after Jenner’s experiment, in about 1880, Pasteur discovered why vaccinations work. He found that the bacterium that causes fowl cholera lost its ability to cause disease (lost its virulence, or became avirulent) after it was grown in the laboratory for long periods. However, it—and other microorganisms with decreased virulence—was able to induce immunity against subsequent infections by its virulent counterparts. The discovery of this phenomenon provided a clue to Jenner’s successful experiment with cowpox. Both cowpox and smallpox are caused by viruses. Even though cowpox virus is not a laboratory-produced derivative of smallpox virus, it is so closely related to the smallpox virus that it can induce immunity to both viruses. Pasteur used the term vaccine for cultures of avirulent microorganisms used for preventive inoculation. Jenner’s experiment marked the first time in a Western culture that a living viral agent—the cowpox virus—was used to produce immunity. Physicians in China had immunized patients from smallpox by removing scales from drying pustules of a person suffering from a mild case of smallpox, grinding the scales to a fine powder, and inserting the powder into the nose of the person to be protected. Some vaccines are still produced from avirulent microbial strains that stimulate immunity to the related virulent strain. Other vaccines are made from killed virulent microbes, from isolated components of virulent microorganisms, or by genetic engineering techniques. The Birth of Modern Chemotherapy: Dreams of a “Magic Bullet” After the relationship between microorganisms and disease was established, medical microbiologists next focused on the search for substances that could destroy pathogenic microorganisms without damaging the infected animal or human. Treatment of disease by using chemical substances is called chemotherapy. (The term also commonly refers to chemical treatment of noninfectious diseases, such as cancer.) Chemicals produced naturally by bacteria and fungi to act against other microorganisms are called antibiotics. Chemotherapeutic agents prepared from chemicals in the laboratory are called synthetic drugs. The success of chemotherapy is based on the fact that some chemicals are more poisonous to microorganisms than to the hosts infected by the microbes. Antimicrobial therapy will be discussed in further detail in the future. The First Synthetic Drugs Paul Ehrlich, a German physician, was the imaginative thinker who fired the first shot in the chemotherapy revolution. As a medical student, Ehrlich speculated about a “magic bullet” that could hunt down and destroy a pathogen without harming the infected host. He then launched a search for such a bullet. In 1910, after testing hundreds of substances, he found a chemotherapeutic agent called salvarsan, an arsenic derivative effective against syphilis. The agent was named salvarsan because it was considered to offer salvation from syphilis and it contained arsenic. Before this discovery, the only known chemical in Europe’s medical arsenal was an extract from the bark of a South American tree, quinine, which had been used by Spanish conquistadors to treat malaria. By the late 1930s, researchers had developed several other synthetic drugs that could destroy microorganisms. Most of these drugs were derivatives of dyes. This came about because the dyes synthesized and manufactured for fabrics were routinely tested for antimicrobial qualities by microbiologists looking for a “magic bullet.” In addition, sulfonamides (sulfa drugs) were synthesized at about the same time.  11 A Fortunate Accident—Antibiotics In contrast to the sulfa drugs, which were deliberately developed from a series of industrial chemicals, the first antibiotic was discovered by accident. Alexander Fleming, a Scottish physician and bacteriologist, almost tossed out some culture plates that had been contaminated by mold. Fortunately, he took a second look at the curious pattern of growth on the contaminated plates. Around the mold was a clear area where bacterial growth had been inhibited (Figure 1.5). Fleming was looking at a mold that could inhibit the growth of a bacterium. The mold was later identified as Penicillium notatum (pen-i-sil’lē-um nō-tā’tum), later renamed Penicillium chrysogenum (krĪ-so’jen-um), and in 1928 Fleming named the mold’s active inhibitor penicillin. Thus, penicillin is an antibiotic produced by a fungus. The enormous usefulness of penicillin was not apparent until the 1940s, when it was finally tested clinically and mass produced. Since these early discoveries, thousands of other antibiotics have been discovered. Unfortunately, antibiotics and other chemotherapeutic drugs are not without problems. Many antimicrobial chemicals are too toxic to humans for practical use; they kill the pathogenic microbes, but they also damage the infected host. For reasons we will discuss later, toxicity to humans is a particular problem in the development of drugs for treating viral diseases. Viral growth depends on life processes of normal host cells. Thus, there are very few successful antiviral drugs, because a drug that would interfere with viral reproduction would also likely affect uninfected cells of the body. Another major problem associated with antimicrobial drugs is the emergence and spread of new strains of microorganisms that are resistant to antibiotics. Over the years, more and more microbes have developed resistance to antibiotics that at one time were very effective against them. Drug resistance results from genetic changes in microbes that enables them to tolerate a certain amount of an antibiotic that would normally inhibit them. For example a microbe might produce chemicals (enzymes) that inactivate antibiotics, or a microbe might undergo changes to its surface that prevent an antibiotic from attaching to it or entering it. The recent appearance of vancomycin-resistant Staphylococcus aureus and Enterococcus faecalis (en-te-rō- kok’kus fe-kā’lis) has alarmed health care professionals because it indicates that some previously treatable bacterial infections may soon be impossible to treat with antibiotics. Modern Developments in Microbiology The quest to solve drug resistance, identify viruses, and develop vaccines requires sophisticated research techniques and correlated studies that were never dreamed of in the days of Koch and Pasteur. The groundwork laid during the Golden Age of Microbiology provided the basis for several monumental achievements during the twentieth century (Table 1.2). New branches of microbiology were developed, including immunology and virology. Most recently, the development of a set of new methods called recombinant DNA technology has revolutionized research and practical applications in all areas of microbiology. Bacteriology, Mycology, and Parasitology Bacteriology, the study of bacteria, began with van Leeuwenhoek’s first examination of tooth scrapings. New pathogenic bacteria are still discovered regularly. Many bacteriologists, like Pasteur, look at the roles of bacteria in food and the environment. One intriguing discovery came in 1997, when Heide Schulz discovered a bacterium large enough to be seen with the unaided eye (0.2 mm wide). This bacterium, named Thiomargarita namibiensis (thī’o-mä-gär-e-tä na’mib-ē-ėn-sis), lives in the mud on the African coast. Thiomargarita is unusual because of its size and its ecological niche. The bacterium consumes hydrogen sulfide, which would be toxic to mud-dwelling animals. Mycology, the study of fungi, includes medical, agricultural, and ecological branches. Recall that Bassi’s work leading up to the germ theory of disease focused on a fungal pathogen. Fungal infection rates have been rising during the past decade, accounting for 10% of hospital-acquired infections. Climatic and environmental changes (severe drought) are thought to account for the tenfold increase in Coccidioides immitis (kok-sid-ē- oi’dēz im’mi-tis) infections in California. New techniques for diagnosing and treating fungal infections are currently being investigated. Parasitology is the study of protozoa and parasitic worms. Because many parasitic worms are large enough to be seen with the unaided eye, they have been known for thousands of years. It has been speculated that the medical symbol, the rod of Asclepius, represents the removal of parasitic guinea worms (Figure 1.6). Asclepius was a Greek physician who practiced about 1200 B.C. and was deified as the god of medicine. The clearing of rain forests has exposed laborers to previously undiscovered parasites. Previously unknown parasitic diseases are also being found in patients whose immune systems have been suppressed by organ transplants, cancer chemotherapy, or AIDS. Bacteriology, mycology, and parasitology are currently going through a “golden age” of classification. Recent advances in genomics, the study of all of an organism’s genes, have allowed scientists to classify bacteria and fungi according to their genetic relationships with other bacteria, fungi, and protozoa. These microorganisms were originally classified according to a limited number of visible characteristics.  12 Immunology Immunology, the study of immunity, dates back in Western culture to Jenner’s first vaccine in 1796. Since then, knowledge about the immune system has accumulated steadily and expanded rapidly. Vaccines are now available for numerous diseases, including measles, rubella (German measles), mumps, chickenpox, pneumococcal pneumonia, tetanus, tuberculosis, influenza, whooping cough, polio, and hepatitis B. The smallpox vaccine was so effective that the disease has been eliminated. Public health officials estimate that polio will be eradicated within a few years because of the polio vaccine. A major advance in immunology occurred in 1933, when Rebecca Lancefield proposed that streptococci be classified according to serotypes (variants within a species) based on certain components in the cell walls of the bacteria. Streptococci are responsible for a variety of diseases, such as sore throat (strep throat), streptococcal toxic shock, and septicemia (blood poisoning). Her research permits the rapid identification of specific pathogenic streptococci based on immunological techniques. In 1960, interferons, substances generated by the body’s own immune system, were discovered. Interferons inhibit replication of viruses and have triggered considerable research related to the treatment of viral diseases and cancer. One of today’s biggest challenges for immunologists is learning how the immune system might be stimulated to ward off the virus responsible for AIDS, a disease that destroys the immune system.  13 Virology The study of viruses, virology, originated during the Golden Age of Microbiology. In 1892, Dmitri Iwanowski reported that the organism that caused mosaic disease of tobacco was so small that it passed through filters fine enough to stop all known bacteria. At the time, Iwanowski was not aware that the organism in question was a virus. In 1935, Wendell Stanley demonstrated that the organism, called tobacco mosaic virus (TMV), was fundamentally different from other microbes and so simple and homogeneous that it could be crystallized like a chemical compound. Stanley’s work facilitated the study of viral structure and chemistry. Since the development of the electron microscope in the 1940s, microbiologists have been able to observe the structure of viruses in detail, and today much is known about their structure and activity. Recombinant DNA Technology Microorganisms can now be genetically modified to manufacture large amounts of human hormones and other urgently needed medical substances. In the late 1960s, Paul Berg showed that fragments of human or animal DNA (genes) that code for important proteins can be attached to bacterial DNA. The resulting hybrid was the first example of recombinant DNA. When recombinant DNA is inserted into bacteria (or other microbes), it can be used to make large quantities of the desired protein. The technology that developed from this technique is called recombinant DNA technology. Its origins can be found in two related fields. The first, microbial genetics, studies the mechanisms by which microorganisms inherit traits. The second, molecular biology, specifically studies how genetic information is carried in molecules of DNA and how DNA directs the synthesis of proteins. Although molecular biology encompasses all organisms, much of our knowledge of how genes determine specific traits has been revealed through experiments with bacteria. Through the 1930s, all genetic research was based on the study of plant and animal cells. But in the 1940s, scientists turned to unicellular organisms, primarily bacteria, which have several advantages for genetic and biochemical research. For one thing, bacteria are less complex than plants and animals. For another, the life cycles of many bacteria last less than an hour, so scientists can cultivate very large numbers of bacteria for study in a relatively short time. Once science turned to the study of unicellular life, rapid progress was made in genetics. In 1941, George W. Beadle and Edward L. Tatum demonstrated the relationship between genes and enzymes. DNA was established as the hereditary material in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty. In 1946, Joshua Lederberg and Edward L. Tatum discovered that genetic material could be transferred from one bacterium to another by a process called conjugation. Then, in 1953, James Watson and Francis Crick proposed a model for the structure and replication of DNA. The early 1960s witnessed a further explosion of discoveries relating to the way DNA controls protein synthesis. In 1961, François Jacob and Jacques Monod discovered messenger RNA (ribonucleic acid), a chemical involved in protein synthesis, and later they made the first major discoveries about the regulation of gene function in bacteria. During the same period, scientists were able to break the genetic code and thus understand how the information for protein synthesis in messenger RNA is translated into the amino acid sequence for making proteins. Microbes and Human Welfare As mentioned earlier, only a minority of all microorganisms are pathogenic. Microbes that cause food spoilage, such as soft spots on fruits and vegetables, decomposition of meats, and rancidity of fats and oils, are also a minority. The vast majority of microbes benefit humans, other animals, and plants in many ways. For example, microbes produce methane and ethanol that can be used as alternative fuels to generate electricity and power vehicles.  14 Biotechnology companies are using bacterial enzymes to break down plant cellulose so that yeast can metabolize the resulting simple sugars and produce ethanol. The following sections outline some of these beneficial activities. Recycling Vital Elements Discoveries made by two microbiologists in the 1880s have formed the basis for today’s understanding of the biogeochemical cycles that support life on Earth. Martinus Beijerinck and Sergei Winogradsky were the first to show how bacteria help recycle vital elements between the soil and the atmosphere. Microbial ecology, the study of the relationship between microorganisms and their environment, originated with the work of these scientists. Today, microbial ecology has branched out and includes the study of how microbial populations interact with plants and animals in various environments. Among the concerns of microbial ecologists are water pollution and toxic chemicals in the environment. The chemical elements carbon, nitrogen, oxygen, sulfur, and phosphorus are essential for life and abundant, but not necessarily in forms that organisms can use. Microorganisms are primarily responsible for converting these elements into forms that plants and animals can use. Microorganisms, primarily bacteria and fungi, return carbon dioxide to the atmosphere when they decompose organic wastes and dead plants and animals. Algae, cyanobacteria, and higher plants use the carbon dioxide during photosynthesis to produce carbohydrates for animals, fungi, and bacteria. Nitrogen is abundant in the atmosphere but in that form is not usable by plants and animals. Only bacteria can naturally convert atmospheric nitrogen to a form available to plants and animals. Sewage Treatment: Using Microbes to Recycle Water Our society’s growing awareness of the need to preserve the environment has made people more conscious of the responsibility to recycle precious water and prevent the pollution of rivers and oceans. One major pollutant is sewage, which consists of human excrement, waste water, industrial wastes, and surface runoff. Sewage is about 99.9% water, with a few hundredths of 1% suspended solids. The remainder is a variety of dissolved materials. Sewage treatment plants remove the undesirable materials and harmful microorganisms. Treatments combine various physical processes with the action of beneficial microbes. Large solids such as paper, wood, glass, gravel, and plastic are removed from sewage; left behind are liquid and organic materials that bacteria convert into such by-products as carbon dioxide, nitrates, phosphates, sulfates, ammonia, hydrogen sulfide, and methane. Bioremediation: Using Microbes to Clean Up Pollutants In 1988, scientists began using microbes to clean up pollutants and toxic wastes produced by various industrial processes. For example, some bacteria can actually use pollutants as energy sources; others produce enzymes that break down toxins into less harmful substances. By using bacteria in these ways—a process known as bioremediation—toxins can be removed from underground wells, chemical spills, toxic waste sites, and oil spills, such as the massive oil spill from an offshore drilling rig in the Gulf of Mexico on April 20, 2010. In addition, bacterial enzymes are used in drain cleaners to remove clogs without adding harmful chemicals to the environment. In some cases, microorganisms indigenous to the environment are used; in others, genetically modified microbes are used. Among the most commonly used microbes are certain species of bacteria of the genera Pseudomonas (sū-dō-mō'nas) and Bacillus (bä-sil'lus). Bacillus enzymes are also used in household detergents to remove spots from clothing. Insect Pest Control by Microorganisms Besides spreading diseases, insects can cause devastating crop damage. Insect pest control is therefore important for both agriculture and the prevention of human disease. The bacterium Bacillus thuringiensis (thur- in-jē-en'sis) has been used extensively in the United States to control such pests as alfalfa caterpillars, bollworms, corn borers, cabbageworms, tobacco budworms, and fruit tree leaf rollers. It is incorporated into a dusting powder that is applied to the crops these insects eat. The bacteria produce protein crystals that are toxic to the digestive systems of the insects. The toxin gene also has been inserted into some plants to make them insect resistant. By using microbial rather than chemical insect control, farmers can avoid harming the environment. Many chemical insecticides, such as DDT, remain in the soil as toxic pollutants and are eventually incorporated into the food chain. Modern Biotechnology and Recombinant DNA Technology Earlier, we touched on the commercial use of microorganisms to produce some common foods and chemicals. Such practical applications of microbiology are called biotechnology. Although biotechnology has been used in some form for centuries, techniques have become much more sophisticated in the past few decades. In the last several years, biotechnology has undergone a revolution through the advent of recombinant DNA technology to expand the potential of bacteria, viruses, and yeast cells and other fungi as miniature biochemical factories. Cultured plant and animal cells, as well as intact plants and animals, are also used as recombinant cells and organisms. The applications of recombinant DNA technology are increasing with each passing year. Recombinant DNA techniques have been used thus far to produce a number of natural proteins, vaccines, and enzymes. Such  15 substances have great potential for medical use. A very exciting and important outcome of recombinant DNA techniques is gene therapy—inserting a missing gene or replacing a defective one in human cells. This technique uses a harmless virus to carry the missing or new gene into certain host cells, where the gene is picked up and inserted into the appropriate chromosome. Since 1990, gene therapy has been used to treat patients with adenosine deaminase (ADA) deficiency, a cause of severe combined immunodeficiency disease (SCID), in which cells of the immune system are inactive or missing; Duchenne’s muscular dystrophy, a muscle-destroying disease; cystic fibrosis, a disease of the secreting portions of the respiratory passages, pancreas, salivary glands, and sweat glands; and LDL-receptor deficiency, a condition in which low-density lipoprotein (LDL) receptors are defective and LDL cannot enter cells. The LDL remains in the blood in high concentrations and increases the risk of atherosclerosis and coronary artery disease because it leads to fatty plaque formation in blood vessels. Results are still being evaluated. Other genetic diseases may also be treatable by gene therapy in the future, including hemophilia, an inability of the blood to clot normally; diabetes, elevated blood sugar levels; sickle cell disease, an abnormal kind of hemoglobin; and one type of hypercholesterolemia, high blood cholesterol. Beyond medical applications, recombinant DNA techniques have also been applied to agriculture. For example, genetically altered strains of bacteria have been developed to protect fruit against frost damage, and bacteria are being modified to control insects that damage crops. Recombinant DNA has also been used to improve the appearance, flavor, and shelf life of fruits and vegetables. Potential agricultural uses of recombinant DNA include drought resistance, resistance to insects and microbial diseases, and increased temperature tolerance in crops. Microbes and Human Disease Normal Microbiota We all live from birth until death in a world filled with microbes, and we all have a variety of microorganisms on and inside our bodies. These microorganisms make up our normal microbiota, or flora* (Figure 1.7). The normal microbiota not only do us no harm, but also in some cases can actually benefit us. For example, some normal microbiota protect us against disease by preventing the overgrowth of harmful microbes, and others produce useful substances such as vitamin K and some B vitamins. Unfortunately, under some circumstances normal microbiota can make us sick or infect people we contact. For instance, when some normal microbiota leave their habitat, they can cause disease. When is a microbe a welcome part of a healthy human, and when is it a harbinger of disease? The distinction between health and disease is in large part a balance between the natural defenses of the body and the disease-producing properties of microorganisms. Whether our bodies overcome the offensive tactics of a particular microbe depends on our resistance—the ability to ward off diseases. Important resistance is provided by the barrier of the skin, mucous membranes, cilia, stomach acid, and antimicrobial chemicals such as interferons. Microbes can be destroyed by white blood cells, by the inflammatory response, by fever, and by specific responses of our immune system. Sometimes, when our natural defenses are not strong enough to overcome an invader, they have to be supplemented by antibiotics or other drugs. Clinical Case Staph is the common name for Staphylococcus aureus bacteria, which are carried on the skin of about 30% of the human population. Although Zendaya is diligent about taking her antibiotic as prescribed, she doesn’t seem to be improving. After 3 days, the lesion on her wrist is even larger than before and is now draining yellow pus. Zendaya also develops a fever. Her mother insists that she call her doctor to tell him about the latest developments. Why does Zendaya’s infection persist after treatment? Biofilms In nature, microorganisms may exist as single cells that float or swim independently in a liquid, or they may attach to each other and/or some usually solid surface. This latter mode of behavior is called a biofilm, a complex aggregation of microbes. The slime covering a rock in a lake is a biofilm. Use your tongue to feel the biofilm on your teeth. Biofilms can be beneficial. They protect your mucous membranes from harmful microbes, and biofilms in lakes are an important food for aquatic animals. Biofilms can also be harmful. They can clog water pipes, and on medical implants such as joint prostheses and catheters (Figure 1.8), they can cause such infections as endocarditis (inflammation of the heart). Bacteria in biofilms are often resistant to antibiotics because the biofilm offers a protective barrier.  16 Infectious Diseases An infectious disease is a disease in which pathogens invade a susceptible host, such as a human or an animal. In the process, the pathogen carries out at least part of its life cycle inside the host, and disease frequently results. By the end of World War II, many people believed that infectious diseases were under control. They thought malaria would be eradicated through the use of the insecticide DDT to kill mosquitoes, that a vaccine would prevent diphtheria, and that improved sanitation measures would help prevent cholera transmission. Malaria is far from eliminated. Since 1986, local outbreaks have been identified in New Jersey, California, Florida, New York, and Texas, and the disease infects 300 million people worldwide. In 1994, diphtheria appeared in the United States, brought by travelers from the newly independent states of the former Soviet Union, which were experiencing a massive diphtheria epidemic. The epidemic was brought under control in 1998. Cholera outbreaks still occur in less-developed parts of the world. Emerging Infectious Diseases These recent outbreaks point to the fact that infectious diseases are not disappearing, but rather seem to be reemerging and increasing. In addition, a number of new diseases—emerging infectious diseases (EIDs)— have cropped up in recent years. These are diseases that are new or changing and are increasing or have the potential to increase in incidence in the near future. Some of the factors that have contributed to the development of EIDs are evolutionary changes in existing organisms (e.g., Vibrio cholerae; vib’rē-ō kol’-er-ī); the spread of known diseases to new geographic regions or populations by modern transportation (e.g., West Nile virus); and increased human exposure to new, unusual infectious agents in areas that are undergoing ecologic changes such as deforestation and construction (e.g., Venezuelan hemorrhagic virus). EIDs also develop as a result of antimicrobial resistance (e.g., vancomycin- resistant S. aureus). An increasing number of incidents in recent years highlights the extent of the problem. H1N1 influenza (flu), also known as swine flu, is a type of influenza caused by a new virus called influenza H1N1. H1N1 was first detected in the United States in April 2009. In June 2009, the World Health Organization declared H1N1 flu to be a global pandemic disease (a disease that affects large numbers of individuals in a short period of time and occurs worldwide). Avian influenza A (H5N1), or bird flu, caught the attention of the public in 2003, when it killed millions of poultry and 24 people in eight countries in southeast Asia. Avian influenza viruses occur in birds worldwide. Certain wild birds, particularly waterfowl, do not get sick but carry the virus in their intestines and shed it in saliva, nasal secretions, and feces. Most often, the wild birds spread influenza to domesticated birds, in which the virus causes death. Influenza A viruses are found in many different animals, including ducks, chickens, pigs, whales, horses, and seals. Normally, each subtype of influenza A virus is specific to certain species. However, influenza A viruses normally seen in one species sometimes can cross over and cause illness in another species, and all subtypes of influenza A virus can infect pigs. Although it is unusual for people to get influenza infections directly from animals, sporadic human infections and outbreaks caused by certain avian influenza A viruses and pig influenza viruses have been reported. As of 2008, avian influenza had sickened 242 people, and about half of them died. Fortunately, the virus has not yet evolved to be transmitted successfully among humans.  17 Human infections with avian influenza viruses detected since 1997 have not resulted in sustained human-to- human transmission. However, because influenza viruses have the potential to change and gain the ability to spread easily between people, monitoring for human infection and person-to-person transmission is important. The U.S. Food and Drug Administration (FDA) approved a human vaccine against the avian influenza virus in April 2007. Antibiotics are critical in treating bacterial infections. However, years of overuse and misuse of these drugs have created environments in which antibiotic-resistant bacteria thrive. Random mutations in bacterial genes can make a bacterium resistant to an antibiotic. In the presence of that antibiotic, this bacterium has an advantage over other, susceptible bacteria and is able to proliferate. Antibiotic-resistant bacteria have become a global health crisis. Staphylococcus aureus causes a wide range of human infections from pimples and boils to pneumonia, food poisoning, and surgical wound infections, and it is a significant cause of hospital-associated infections. After penicillin’s initial success in treating S. aureus infection, penicillin-resistant S. aureus became a major threat in hospitals in the 1950s, requiring the use of methicillin. In the 1980s, methicillin-resistant S. aureus, called MRSA, emerged and became endemic in many hospitals, leading to increasing use of vancomycin. In the late 1990s, S. aureus infections that were less sensitive to vancomycin (vancomycin-intermediate S. aureus, or VISA) were reported. In 2002, an infection caused by vancomycin-resistant S. aureus (VRSA) in a patient in the United States was reported. In March 2010, the World Health Organization (WHO) reported that in some parts of the world (such as northwestern Russia) about 28% of all individuals with tuberculosis (TB) had the multidrug-resistant form of the disease (MDR-TB). Multidrug-resistant TB is caused by bacteria that are resistant to at least the antibiotics isoniazid and rifampicin, the most effective drugs against tuberculosis. The antibacterial substances added to various household cleaning products are similar to antibiotics in many ways. When used correctly, they inhibit bacterial growth. However, wiping every household surface with these antibacterial agents creates an environment in which the resistant bacteria survive. Unfortunately, when you really need to disinfect your homes and hands—for example, when a family member comes home from a hospital and is still vulnerable to infection—you may encounter mainly resistant bacteria. Routine housecleaning and handwashing are necessary, but standard soaps and detergents (without added antibacterials) are fine for these tasks. In addition, quickly evaporating chemicals, such as chlorine bleach, alcohol, ammonia, and hydrogen peroxide, remove potentially pathogenic bacteria but do not leave residues that encourage the growth of resistant bacteria. Clinical Case The S. aureus bacterium responsible for Zendaya’s infection is resistant to the β-lactam antibiotic prescribed by Zendaya’s doctor. Concerned about what his patient is telling him, Zendaya’s doctor calls the local hospital to let them know he is sending a patient over. In the emergency department, a nurse swabs Zendaya’s wound and sends it to the hospital lab for culturing. The culture shows that Zendaya’s infection is caused by methicillin-resistant Staphylococcus aureus (MRSA). MRSA produces β-lactamase, an enzyme that destroys β-lactam antibiotics. The attending physician surgically drains the pus from the sore on Zendaya’s wrist.  18 West Nile encephalitis (WNE) is inflammation of the brain caused by West Nile virus. WNE was first diagnosed in the West Nile region of Uganda in 1937. In 1999 the virus made its first North American appearance in humans in New York City. In 2007, West Nile virus infected over 3600 people in 43 states. West Nile virus is now established in nonmigratory birds in 48 states. The virus, which is carried by birds, is transmitted between birds—and to horses and humans—by mosquitoes. West Nile virus may have arrived in the United States in an infected traveler or in migratory birds. In 1996, countries worldwide were refusing to import beef from the United Kingdom, where hundreds of thousands of cattle born after 1988 had to be killed because of an epidemic of bovine spongiform encephalopathy (en-sef-a-lop’a-thē), also called BSE or mad cow disease. BSE first came to the attention of microbiologists in 1986 as one of a handful of diseases caused by an infectious protein called a prion. Studies suggest that the source of disease was cattle feed prepared from sheep infected with their own version of the disease. Cattle are herbivores (planteaters), but adding protein to their feed improves their growth and health. Creutzfeldt-Jakob disease (kroits’felt yä’kôb), or CJD, is a human disease also caused by a prion. The incidence of CJD in the United Kingdom is similar to the incidence in other countries. However, by 2005 the United Kingdom reported 154 human cases of CJD caused by a new variant related to the bovine disease. Escherichia coli is a normal inhabitant of the large intestine of vertebrates, including humans, and its presence is beneficial because it helps produce certain vitamins and breaks down otherwise undigestible foodstuffs. However, a strain called E. coli O157:H7 causes bloody diarrhea when it grows in the intestines. This strain was first recognized in 1982 and since then has emerged as a public health problem. It is now one of the leading causes of diarrhea worldwide. In 1996, some 9000 people in Japan became ill, and 7 died, as a result of infection by E. coli O157:H7. The recent outbreaks of E. coli O157:H7 in the United States, associated with contamination of undercooked meat and unpasteurized beverages, have led public health officials to call for the development of new methods of testing for bacteria in food. In 1995, infections of so-called flesh-eating bacteria were reported on the front pages of major newspapers. The bacteria are more correctly named invasive group A Streptococcus (strep-tō-kok’kus), or IGAS. Rates of IGAS in the United States, Scandinavia, England, and Wales have been increasing. In 1995, a hospital laboratory technician in Democratic Republic of Congo (DROC) who had fever and bloody diarrhea underwent surgery for a suspected perforated bowel. Afterward he started hemorrhaging, and his blood began clotting in his blood vessels. A few days later, health care workers in the hospital where he was staying developed similar symptoms. One of them was transferred to a hospital in a different city; personnel in the second hospital who cared for this patient also developed symptoms. By the time the epidemic was over, 315 people had contracted Ebola hemorrhagic fever (hem-ôr-raj’ik), or EHF, and over 75% of them died. The epidemic was controlled when microbiologists instituted training on the use of protective equipment and educational measures in the community. Close personal contact with infectious blood or other body fluids or tissue leads to human-to-human transmission. Microbiologists first isolated Ebola viruses from humans during earlier outbreaks in DROC in 1976. (The virus is named after Congo’s Ebola River.) In 2008, an Ebola virus outbreak occurred in Uganda with 149 cases. In 1989 and 1996, outbreaks among monkeys imported into the United States from the Philippines were caused by another Ebola virus but were not associated with human disease. Recorded cases of Marburg virus, another hemorrhagic fever virus, are rare. The first cases were laboratory workers in Europe who handled African green monkeys from Uganda. Four outbreaks were identified in Africa between 1975 and 1998, involving 2 to 154 people with 56% mortality. In 2004, an outbreak killed 227 people. Microbiologists have been studying many animals but have not yet discovered the natural reservoir (source) of EHF and Marburg viruses. In 1993, an outbreak of cryptosporidiosis (krip-tō-spô-ridē-ō’sis) transmitted through the public water supply in Milwaukee, Wisconsin, resulted in diarrheal illness in an estimated 403,000 persons. The microorganism responsible for this outbreak was the protozoan Cryptosporidium (krip-tō-spô-ri’dē-um). First reported as a cause of human disease in 1976, it is responsible for up to 30% of the diarrheal illness in developing countries. In the United States, transmission has occurred via drinking water, swimming pools, and contaminated hospital supplies. AIDS (acquired immunodeficiency syndrome) first came to public attention in 1981 with reports from Los Angeles that a few young homosexual men had died of a previously rare type of pneumonia known as Pneumocystis (nü-mō-sis’tis) pneumonia. These men had experienced a severe weakening of the immune system, which normally fights infectious diseases. Soon these cases were correlated with an unusual number of occurrences of a rare form of cancer, Kaposi’s sarcoma, among young homosexual men. Similar increases in such rare diseases were found among hemophiliacs and intravenous drug users. Researchers quickly discovered that the cause of AIDS was a previously unknown virus (see Figure 1.1e). The virus, now called human immunodeficiency virus (HIV), destroys CD4+ T cells, one type of white blood cell important to immune system defenses. Sickness and death result from microorganisms or cancerous cells that  19 might otherwise have been defeated by the body’s natural defenses. So far, the disease has been inevitably fatal once symptoms develop. Clinical Case Mutations develop randomly in bacteria: some mutations are lethal, some have no effect, and some may be beneficial. Once these mutations develop, the offspring of the mutated parent cells also carry the same mutation. Because they have an advantage in the presence of the antibiotic, bacteria that are resistant to antibiotics soon outnumber those that are susceptible to antibiotic therapy. The widespread use of antibiotics selectively allows the resistant bacteria to grow, whereas the susceptible bacteria are killed. Eventually, almost the entire population of bacteria is resistant to the antibiotic. The emergency department physician prescribes a different antibiotic, vancomycin, which will kill the MRSA in Zendaya’s wrist. She also explains to Zendaya what MRSA is and why it’s important they find out where Zendaya acquired the potentially lethal bacteria. What can the emergency department physician tell Andrea about MRSA? By studying disease patterns, medical researchers found that HIV could be spread through sexual intercourse, by contaminated needles, from infected mothers to their newborns via breast milk, and by blood transfusions— in short, by the transmission of body fluids from one person to another. Since 1985, blood used for transfusions has been carefully checked for the presence of HIV, and it is now quite unlikely that the virus can be spread by this means. By the end of 2010, over 1 million people in the United States are living with AIDS. Over 50,000 Americans become infected and 18,000 die each year. As of 2010, health officials estimated that 1.3 million Americans have HIV infection. In 2009, the World Health Organization (WHO) estimated that over 33 million people worldwide are living with HIV/AIDS and that 7500 new infections occur every day. Since 1994, new treatments have extended the life span of people with AIDS; however, approximately 40,000 new cases occur annually in the United States. The majority of individuals with AIDS are in the sexually active age group. Because heterosexual partners of AIDS sufferers are at high risk of infection, public health officials are concerned that even more women and minorities will contract AIDS. In 1997, HIV diagnoses began increasing among women and minorities. Among the AIDS cases reported in 2009, 26% were women, and 49% were African American. In the months and years to come, scientists will continue to apply microbiological techniques to help them learn more about the structure of the deadly HIV, how it is transmitted, how it grows in cells and causes disease, how drugs can be directed against it, and whether an effective vaccine can be developed. Public health officials have also focused on prevention through education. AIDS poses one of this century’s most formidable health threats, but it is not the first serious epidemic of a sexually transmitted disease. Syphilis was also once a fatal epidemic disease. As recently as 1941, syphilis caused an estimated 14,000 deaths per year in the United States. With few drugs available for treatment and no vaccines to prevent it, efforts to control the disease focused mainly on altering sexual behavior and on the use of condoms. The eventual development of drugs to treat syphilis contributed significantly to preventing the spread of the disease. According to the Centers for Disease Control and Prevention (CDC), reported cases of syphilis dropped from a record high of 575,000 in 1943 to an all-time low of 5979 cases in 2004. Since then, however, the number of cases has been increasing. Just as microbiological techniques helped researchers in the fight against syphilis and smallpox, they will help scientists discover the causes of new emerging infectious diseases in the twenty-first century. Undoubtedly there will be new diseases. Ebola virus and Influenza virus are examples of viruses that may be changing their abilities to infect different host species. Coronavirus disease 2019 (COVID-19) is a contagious disease caused by the virus SARS-CoV-2. The first known case was identified in Wuhan, China, in December 2019. The disease quickly spread worldwide, resulting in the COVID-19 pandemic. The symptoms of COVID‑19 are variable but often include fever, cough, headache, fatigue, breathing difficulties, loss of smell, and loss of taste. Symptoms may begin one to fourteen days after exposure to the virus. At least a third of people who are infected do not develop noticeable symptoms. Of those who develop symptoms noticeable enough to be classified as patients, most (81%) develop mild to moderate symptoms (up to mild pneumonia), while 14% develop severe symptoms (dyspnea, hypoxia, or more than 50% lung involvement on imaging), and 5% develop critical symptoms (respiratory failure, shock, or multiorgan dysfunction). Older people are at a higher risk of developing severe symptoms. Some people continue to  20 experience a range of effects (long COVID) for months or years after infection, and damage to organs has been observed. Multi-year studies are underway to further investigate the long-term effects of the disease. COVID‑19 transmits when infectious particles are breathed in or come into contact with the eyes, nose, or mouth. The risk is highest when people are in close proximity, but small airborne particles containing the virus can remain suspended in the air and travel over longer distances, particularly indoors. Transmission can also occur when people touch their eyes, nose or mouth after touching surfaces or objects that have been contaminated by the virus. People remain contagious for up to 20 days and can spread the virus even if they do not develop symptoms. Testing methods for COVID-19 to detect the virus's nucleic acid include real-time reverse transcription polymerase chain reaction (RT‑PCR), transcription-mediated amplification, and reverse transcription loop- mediated isothermal amplification (RT‑LAMP) from a nasopharyngeal swab. Several COVID-19 vaccines have been approved and distributed in various countries, which have initiated mass vaccination campaigns. Other preventive measures include physical or social distancing, quarantining, ventilation of indoor spaces, use of face masks or coverings in public, covering coughs and sneezes, hand washing, and keeping unwashed hands away from the face. While work is underway to develop drugs that inhibit the virus, the primary treatment is symptomatic. Management involves the treatment of symptoms through supportive care, isolation, and experimental measures. Infectious diseases may reemerge because of antibiotic resistance and through the use of microorganisms as weapons. The breakdown of public health measures for previously controlled infections has resulted in unexpected cases of tuberculosis, whooping cough, and diphtheria. The diseases we have mentioned are caused by viruses, bacteria, protozoa, and prions—types of microorganisms. This book introduces you to the enormous variety of microscopic organisms. It shows you how microbiologists use specific techniques and procedures to study the microbes that cause such diseases as AIDS and diarrhea—and diseases that have yet to be discovered. You will also learn how the body responds to microbial infection and how certain drugs combat microbial diseases. Finally, you will learn about the many beneficial roles that microbes play in the world around us. Clinical Case Resolved The first MRSA was health care–associated MRSA (HA-MRSA), transmitted between staff and patients in health care settings. In the 1990s, infections by a genetically different strain, community-associated MRSA (CA- MRSA), emerged as a major cause of skin disease in the United States. CA-MRSA enters skin abrasions from environmental surfaces or other people. Zendaya has never been hospitalized before now, so they are able to rule out the hospital as the source of infection. Her college courses are all online, so she didn’t contract MRSA at the university, either. The local health department sends someone to her family home to swab for the bacteria there. MRSA is isolated from Zendaya’s living room sofa, but how did it get there? After speaking with the family, the representative from the health department, knowing that clusters of CA-MRSA infections have been seen among athletes suggests swabbing the mats used by the gymnasts at the school Zendaya’s sister attends. The cultures come back positive for MRSA. Zendaya’s sister, although not infected, transferred the bacteria from her skin to the sofa, where Zendaya laid her arm. (A person can carry MRSA on the skin without becoming infected.) The bacteria entered through a scratch on Zendaya’s wrist. References: Main Book Reference: Tortora, G. et al (2013). Microbiology, An Introduction. Pearson Publication. Internet Sources: https://www.who.int/health-topics/coronavirus https://www.cdc.gov/coronavirus/2019-ncov