Review of Medical Microbiology and Immunology, 13th Edition

14. Overview of the Major Pathogens & Introduction to Anaerobic Bacteria


Overview of the Major Pathogens

Introduction to Anaerobic Bacteria

Important Properties

Anaerobes of Medical Interest

Clinical Infections

Laboratory Diagnosis



Self-Assessment Questions

Practice Questions: USMLE & Course Examinations


The major bacterial pathogens are presented in Table 14–1 and described in Chapters 15 through 26. So that the reader may concentrate on the important pathogens, the bacteria that are less medically important are described in a separate chapter (see Chapter 27).

TABLE 14–1 Major Bacterial Pathogens


Table 14–1 is divided into organisms that are readily Gram stained and those that are not. The readily stained organisms fall into four categories: gram-positive cocci, gram-negative cocci, gram-positive rods, and gram-negative rods. Because there are so many kinds of gram-negative rods, they have been divided into three groups:

(1) Organisms associated with the enteric tract

(2) Organisms associated with the respiratory tract

(3) Organisms from animal sources (zoonotic bacteria)

For ease of understanding, the organisms associated with the enteric tract are further subdivided into three groups: (1) pathogens both inside and outside the enteric tract, (2) pathogens inside the enteric tract, and (3) pathogens outside the enteric tract.

As is true of any classification dealing with biologic entities, this one is not entirely precise. For example, Campylobacter causes enteric tract disease but frequently has an animal source. Nevertheless, despite some uncertainties, subdivision of the large number of gram-negative rods into these functional categories should be helpful to the reader.

The organisms that are not readily Gram stained fall into six major categories: Mycobacterium species, which are acid-fast rods; Mycoplasma species, which have no cell wall and so do not stain with Gram stain; Treponema and Leptospira species, which are spirochetes too thin to be seen when stained with Gram stain; and Chlamydia and Rickettsia species, which stain well with Giemsa stain or other special stains but poorly with Gram stain. Chlamydia and Rickettsia species are obligate intracellular parasites, whereas members of the other four genera are not.

Table 14–2 presents the 10 most common “notifiable” bacterial diseases in the United States for 2009 as compiled by the Centers for Disease Control and Prevention. Note that only notifiable diseases are included and that certain common conditions such as streptococcal pharyngitis and impetigo are not included. Two sexually transmitted diseases, chlamydial infection and gonorrhea, are by far the most common diseases listed, followed by salmonellosis, syphilis, and Lyme disease in the top five.

TABLE 14–2 The 10 Most Common Notifiable Bacterial Diseases in the United States in 20111



Important Properties

Anaerobes are characterized by their ability to grow only in an atmosphere containing less than 20% oxygen (i.e., they grow poorly if at all in room air). They are a heterogeneous group composed of a variety of bacteria, from those that can barely grow in 20% oxygen to those that can grow only in less than 0.02% oxygen. Table 14–3 describes the optimal oxygen requirements for several representative groups of organisms. The obligate aerobes, such as Pseudomonas aeruginosa, grow best in the 20% oxygen of room air and not at all under anaerobic conditions. Facultative anaerobes such as Escherichia coli can grow well under either circumstance. Aerotolerant organisms such as Clostridium histolyticum can grow to some extent in air but multiply much more rapidly in a lower oxygen concentration. Microaerophilic organisms such as Campylobacter jejuni require a reduced oxygen concentration (approximately 5%) to grow optimally. The obligate anaerobes such as Bacteroides fragilis and Clostridium perfringens require an almost total absence of oxygen. Many anaerobes use nitrogen rather than oxygen as the terminal electron acceptor.

TABLE 14–3 Optimal Oxygen Requirements of Representative Bacteria


The main reason why the growth of anaerobes is inhibited by oxygen is the reduced amount (or absence) of catalase and superoxide dismutase (SOD) in anaerobes. Catalase and SOD eliminate the toxic compounds hydrogen peroxide and superoxide, which are formed during production of energy by the organism (see Chapter 3). Another reason is the oxidation of essential sulfhydryl groups in enzymes without sufficient reducing power to regenerate them.

In addition to oxygen concentration, the oxidation–reduction potential (Eh) of a tissue is an important determinant of the growth of anaerobes. Areas with low Eh, such as the periodontal pocket, dental plaque, and colon, support the growth of anaerobes well. Crushing injuries that result in devitalized tissue caused by impaired blood supply produce a low Eh, allowing anaerobes to grow and cause disease.

Anaerobes of Medical Interest

The anaerobes of medical interest are presented in Table 14–4. It can be seen that they include both rods and cocci and both gram-positive and gram-negative organisms. The rods are divided into the spore formers (e.g., Clostridium) and the nonspore formers (e.g., Bacteroides). In this book, three genera of anaerobes are described as major bacterial pathogens, namely, Clostridium, Actinomyces, and BacteroidesStreptococcus is a genus of major pathogens consisting of both anaerobic and facultative organisms. The remaining anaerobes are less important and are discussed in Chapter 27.

TABLE 14–4 Anaerobic Bacteria of Medical Interest


Clinical Infections

Many of the medically important anaerobes are part of the normal human flora. As such, they are nonpathogens in their normal habitat and cause disease only when they leave those sites. The two prominent exceptions to this are Clostridium botulinum and Clostridium tetani, the agents of botulism and tetanus, respectively, which are soil organisms. C. perfringens, another important human pathogen, is found in the colon and in the soil.

Diseases caused by members of the anaerobic normal flora are characterized by abscesses, which are most frequently located in the brain, lungs, female genital tract, biliary tract, and other intra-abdominal sites. Most abscesses contain more than one organism, either multiple anaerobes or a mixture of anaerobes plus facultative anaerobes. It is thought that the facultative anaerobes consume sufficient oxygen to allow the anaerobes to flourish.

Three important findings on physical examination that arouse suspicion of an anaerobic infection are a foul-smelling discharge, gas in the tissue, and necrotic tissue. In addition, infections in the setting of pulmonary aspiration, bowel surgery, abortion, cancer, or human and animal bites frequently involve anaerobes.

Laboratory Diagnosis

Two aspects of microbiologic diagnosis of an anaerobic infection are important even before the specimen is cultured: (1) obtaining the appropriate specimen and (2) rapidly transporting the specimen under anaerobic conditions to the laboratory. An appropriate specimen is one that does not contain members of the normal flora to confuse the interpretation. For example, such specimens as blood, pleural fluid, pus, and transtracheal aspirates are appropriate, but sputum and feces are not.

In the laboratory, the cultures are handled and incubated under anaerobic conditions. In addition to the usual diagnostic criteria of Gram stain, morphology, and biochemical reactions, the special technique of gas chromatography is important. In this procedure, organic acids such as formic, acetic, and propionic acids are measured.


In general, surgical drainage of the abscess plus administration of antimicrobial drugs are indicated. Drugs commonly used to treat anaerobic infections are penicillin G, cefoxitin, chloramphenicol, clindamycin, and metronidazole. Note, however, that many isolates of the important pathogen B. fragilis produce α-lactamase and are thus resistant to penicillin.


1. The main reason why some bacteria are anaerobes (i.e., they cannot grow in the presence of oxygen) is because:

(A) they do not have sufficient catalase and superoxide dismutase.

(B) they have too much ferrous ion that is oxidized to ferric ion in the presence of oxygen.

(C) they have unusual mitochondria that cannot function in the presence of oxygen.

(D) transcription of the gene for the pilus protein is repressed in the presence of oxygen.

2. Which one of the following sets consists of bacteria that are both anaerobes?

(A) Actinomyces israeli and Serratia marcescens

(B) Campylobacter jejuni and Vibrio cholerae

(C) Clostridium perfringens and Bacteroides fragilis

(D) Mycobacterium tuberculosis and Pseudomonas aeruginosa

(E) Mycoplasma pneumoniae and Corynebacterium diphtheriae


1. (A)

2. (C)


Questions on the topics discussed in this chapter can be found in the Clinical Bacteriology section of PART XIII: USMLE (National Board) Practice Questions starting on page 693. Also see PART XIV: USMLE (National Board) Practice Examination starting on page 731.