• Part 1. Approach to Learning Microbiology

• Part 2. Approach to Disease

• Part 3. Approach to Reading

Part 1. Approach to Learning Microbiology

The student of microbiology should be aware of the scientific characteristics of each microbe, with a particular interest in the relevance to clinical manifestations. The following is a systematic 3-pronged approach:

1. How does one know that a person is infected?

2. Where and how is a person infected?

3. What can be done if a person is infected?

1. How does one know that a person is infected? The clinician may have a suspicion of a certain etiologic agent based on clinical clues, but this educated guess must be corroborated by laboratory confirmation. This necessitates an understanding of the basis for presumptive and definitive diagnosis. Possible laboratory tests include culture, polymerase chain reaction of DNA or RNA, antigen tests, or antibody tests.

2. Where and how is a person infected? This question translates to understanding about the mechanisms of disease transmission. For example, if a patient is infected with the hepatitis B virus, then the student should be aware that the most common methods of disease acquisition are intravenous drug use, sexual transmission, and vertical transmission. Blood transfusion at one time was a common modality, but now with screening of banked blood, the incidence is very low.

3. What can be done if a person is infected? This translates to knowing the best treatment and method of prevention of infection. In other words, once a patient is known to be infected with a certain microbe, what is the best treatment? The student is best served by learning more than 1 antimicrobial therapy and some of the advantages and disadvantages of each therapeutic choice. For example, urinary tract infection caused by Escherichia coli may be treated empirically with a variety of antibiotics; however, a quinolone antibiotic, such as ciprofloxacin, is contraindicated in pediatric patients, and gentamicin is relatively contraindicated in those with renal insufficiency.

Likewise, the student should have a systematic approach to classifying microorganisms: viruses, bacteria, protozoa, and fungi.

Virus: A noncellular organism having genetic nucleic acid that requires a host to replicate. They are usually 15 to 450 nanometers in diameter. Viruses do not have a cell membrane or cell wall, but they have a rigid protein coat called the “capsid.” The inner cavity contains DNA or RNA. Viruses come in various shapes, including spherical, tetrahedral, polygonal, rod shaped, and polyhedral. One end is usually broader (head), and one end narrower (tail). The tail often has antigenic proteins for attachment to the host. Because viruses do not reproduce without a host, they are considered obligate parasites and not living. See Table I-1 for a schematic of viruses.

Bacteria: These single-celled organisms belong in the kingdom Prokaryotae, and they usually have a cell wall as an outer covering consisting of a complex of sugar and amino acids, and often a cell membrane surrounding the cytoplasm. Being prokaryotes, bacteria do not have a membrane around their nuclei. Some bacteria have flagella, which are cytoplasmic fibrous structures for locomotion. Bacteria may be classified according to shape (cocci, bacilli, or vibrio [comma-shaped], or spirilla [corkscrew]). Bacteria may also be classified by Gram stain characteristics, metabolism requirements (anaerobic versus aerobic), and presence or absence of cell wall (Mycoplasma do not have a cell wall). See Figure I-1 for cell wall characteristics of gram-negative versus gram-positive bacteria.

Parasites: Usually consisting of the protozoa and helminths. Helminths are parasitic worms usually subdivided into flatworms or platyhelminths and roundworms or nemathelminths.

Protozoa: Parasites in humans belonging to the kingdom Protozoa are classified into 3 phyla: Sarcomastigophora (flagellates and amebas), Ciliophora (ciliates), and Apicomplexa (sporozoans).

Fungi: Eukaryotic organisms growing in two basic forms: yeasts and molds. The mold form usually consists of multicellular filamentous colonies. Branching cylinder-like tubules form, called hyphae. The yeast forms are single cells, usually spherical or ellipsoid in shape. Most yeast will reproduce by budding. When the yeast cells bud but fail to break off, they can form elongated yeast cells, called pseudohyphae. Fungi can be classified according to their ability to produce superficial versus deep invasive infection, or by their appearance or sexual reproduction characteristics.

Part 2. Approach to Disease

Physicians usually approach clinical situations by taking a history (asking questions), performing a physical examination, obtaining selective laboratory and imaging tests, and then formulating a diagnosis. The conglomeration of the history, physician examination, and laboratory tests is called the clinical database. After reaching a diagnosis, a treatment plan is usually initiated, and the patient is followed for a clinical response. Rational understanding of disease and plans for treatment are best acquired by learning about the normal human processes on a basic science level, and, likewise, being aware of how disease alters the normal physiologic processes is understood on a basic science level.

Clinicians should be aware of the laboratory methods of diagnosis, including the advantages and disadvantages, cost, time requirements, and potential morbidity to the patient. Various laboratory techniques include detecting DNA or RNA sequences, identifying certain protein components of the microorganism (antigen), or unique enzyme or toxin; microscopic examination such as Gram stain (most bacteria), acid-fast stain (Mycobacterium), and immunofluorescence techniques (used to detect difficult-to-culture organisms such as Legionella). Cultures are the traditional method of diagnosis, and they must be taken in such a way as to minimize contamination and placed on the appropriate media (or mammalian cell for viruses), with temperature and atmospheric conditions for optimal amplification. Thereafter, the correct identification process should be used to assess characteristics such as colony morphology (both grossly and under the microscope), hemolytic pattern on agar, fermentation profile, Gram stain appearance, and the like.

Once the organism has been identified, susceptibility testing is generally performed to assess the likelihood that certain antimicrobial agents will be effective against the particular strain of pathogen. For example, isolates of Staphylococcus aureus should be tested against β-lactam antibiotics such as methicillin to aid the clinician in treating with methicillin versus vancomycin. Susceptibility is generally performed in a qualitative manner (susceptible, intermediate, resistant), or quantitative with minimum inhibitory concentrations or minimum bactericidal concentrations as determined by successive dilutions of the isolate bathed in antimicrobial mixtures.

Part 3. Approach to Reading

There are 7 key questions that help to stimulate the application of basic science information to the clinical setting.

1. Given a particular microorganism, what is the most likely clinical manifestation?

2. Given a particular microorganism, what is the mechanism whereby clinical or subclinical findings arise?

3. Given clinical symptoms of infection, what is the most likely causative microorganism?

4. Given clinical findings, what are the most likely associated features of the microorganism (such as cell wall characteristics or viral genome)?

5. Given the clinical findings, what is the most likely vector of transmission?

6. Given the clinical findings, what is the most likely laboratory culture findings?

7. Given a particular microorganism, what is the most likely mechanism of resistance acquisition?

1. Given a particular microorganism, what is the most likely clinical manifestation? This is the fundamental knowledge that the student must learn in the broad scope of microbiology, that is, the most likely presentation of clinical disease. Each organism has certain typical patterns of clinical manifestations, based on its characteristics. The interaction between microbe and host, including replication cycle, enzymes released, and host immune response all play roles in the overt symptoms and signs. The student should have an understanding of the common presentations of disease. Likewise, the student should be aware of the mechanisms of the clinical manifestations.

2. Given a particular microorganism, what is the mechanism whereby clinical or subclinical findings arise? The student of microbiology is often tempted to memorize the extensive list of microorganisms and clinical disease. Unfortunately, this haphazard approach leads to quick forgetfulness and lack of understanding of the basic science underlying this discipline. Instead, the student should approach the field of microbiology by linking the microorganism, and its particular characteristics, to the mechanisms of disease, such as the interaction with host physiological state, cellular abnormalities that develop, and even cell death. It is the ability of the student to understand the mechanisms that allows for rational approaches to diagnosis and treatment.

3. Given clinical symptoms of infection, what is the most likely causative microorganism? The student of microbiology first learns antegrade from microbe toward disease, but patients present instead with disease symptoms and signs. Thus, the student must be able to work backward from clinical presentation to a differential diagnosis (a list of the most likely etiologies) to the probable causative organism. Again, rather than memorization, the student should incorporate mechanisms in the learning process. Thus, the student would best be served to give a reason why the suspected microorganism causes a certain clinical presentation.

   • Microorganism → Host defenses/response to invading organism → Clinical signs

   • Clinical signs → Most likely microbe(s)

4. Given clinical findings, what are the most likely associated features of the microorganism (such as cell wall characteristics or viral genome)? This is similar to question 3, but it goes back to the underlying basic science peculiarities of the microbe. First, the student must use the clinical information to discern the likely microorganism, and then the student must relate the characteristics of the microbe. Because a common and effective method of classifying viruses includes the viral genome, this is an important differentiating point. Likewise, bacteria are often subdivided by their cell wall characteristics, which lead to their Gram stain findings. For example, the clinical information may be: “A 66-year-old man complains of blisters erupting on the right chest wall region associated with pain and tingling.” The student should remember that a vesicular rash that is unilaterally associated with pain and tingling is characteristic for herpes zoster virus. The etiologic agent is varicella-zoster virus, which causes chickenpox. The virus can lay dormant in the dorsal root ganglia and, then during times of stress or immunocompromised states, travel down the nerve and cause local eruption on the dermatome distribution. The pain and tingling are caused by the stimulation of the nerve. The student may recall that varicella is a herpesvirus, and, thus, is a double-stranded DNA virus.

5. Given the clinical findings, what is the most likely vector of transmission? Again, the student must first discern the most likely etiologic agent based on the clinical findings. Then, an understanding of how the microbe causes disease, such as vector of transmission, is important. A related topic is preventive or treatment related, such as how to sterilize equipment exposed to the patient, or the best antibiotic therapy for the described patient.

6. Given the clinical findings, what are the most likely laboratory findings? Based on the clinical presentation, the student should discern the most likely microbe and then its laboratory characteristics. These laboratory findings should be correlated to its mechanisms of disease. For example, the clinical findings are: “A 10-year-old boy presents with sore throat and fever. On examination, there is exudate in the oropharynx. A Gram stain reveals gram-positive cocci in chains.” The student should be aware that a culture would reveal β-hemolytic pattern on blood agar media. Furthermore, the mechanism should be learned, that is, that the group A Streptococcus gives off hemolysin,which leads to hemolysis of the red blood cells.

7. Given a particular microorganism, what is the most likely mechanism of resistance acquisition? Patterns of antimicrobial resistance are enormous concerns for all involved in medical sciences. Bacteria and viruses are increasingly acquiring mechanisms of resistance, which spurs scientists to design new antibiotics or chemicals that disable the microbial method of resistance. For example, if the mechanism of resistance is a β-lactamase enzyme, then the addition of a β-lactamase inhibitor such as sulbactam may lead to increased efficacy of a β-lactam such as ampicillin.

References