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Approach to Microbiology 

Approach to Microbiology
Approach to Microbiology

Emily Shuman

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date: 20 May 2022

  1. A. Overview of Microbiology. The simplest way to approach microbiology is to divide the organisms into six major categories (based on Gram stain, morphology, and aerobic requirements) and consider the most important diseases each organism can cause.

    1. a. Gram-positive cocci

      1. i. Streptococcus

        1. 1. Group A streptococci cause “strep throat,” scarlet fever, rheumatic fever, erysipelas, cellulitis, and pneumonia.

        2. 2. Group B streptococci often cause perinatal infections but can lead to a variety of infections in adults (e.g., skin and soft tissue infection, urinary tract infection [UTI], sepsis).

        3. 3. Streptococcus pneumoniae causes pneumonia (usually lobar), bacteremia, and meningitis.

        4. 4. Viridans streptococci (e.g., Streptococcus milleri group) are found in the oral cavity and gastrointestinal (GI) tract and are the second most common cause of bacterial endocarditis. Viridans streptococci are also associated with central nervous system, pulmonary, and intra-abdominal abscesses.

      2. ii. Enterococcus causes UTIs, intra-abdominal infections, endocarditis, and health care–associated infections. Infections caused by Enterococcus can be difficult to treat.

      3. iii. Staphylococcus

        1. 1. Staphylococcus aureus (coagulase-positive) causes skin infections, toxic shock syndrome, endocarditis, intravascular line infections, osteomyelitis, septic arthritis, pneumonia, and health care–associated infections. S. aureus is a virulent organism that has a propensity to cause “metastatic” deposits of infection.

        2. 2. Staphylococcus epidermidis (coagulase-negative) causes intravascular line infections and prosthetic valve endocarditis.

        3. 3. Staphylococcus saprophyticus (coagulase-negative) causes UTIs.

    2. b. Gram-positive rods

      1. i. Clostridium (anaerobic) can cause tetanus, botulism, food poisoning, antibiotic-associated colitis, cellulitis and skin infections, gas gangrene, abscesses, and septicemia.

      2. ii. Bacillus can cause cutaneous and pulmonary anthrax (e.g., woolsorter’s disease, recently an agent of bioterrorism). Most cases in the United States are cutaneous; inhalation anthrax is usually fatal. Bacillus cereus is a common cause of diarrhea.

      3. iii. Nocardia usually causes pulmonary disease that may disseminate (in immunocompromised hosts), leading to brain abscesses and subcutaneous nodules. Nocardia species are weakly acid-fast and may be confused for tuberculosis.

      4. iv. Actinomyces (anaerobic) causes cervicofacial infections (following dental infection or trauma), chronic pneumonia, abdominal infections (which may be confused with Crohn’s disease), and pelvic inflammatory disease (PID) associated with the use of an intrauterine contraceptive device (IUD).

      5. v. Listeria monocytogenes causes sporadic cases of meningitis and bacteremia as well as food-borne outbreaks in older adults and in immunocompromised adults.

      6. vi. Erysipelothrix causes three types of human illness: erysipeloid (a localized skin lesion); a diffuse skin eruption accompanied by systemic illness; and bacteremia (usually associated with endocarditis). Erysipelothrix is acquired through skin abrasions following contact with infected swine, fish, turkeys, ducks, and sheep.

      7. vii. Corynebacterium

        1. 1. Corynebacterium diphtheriae causes cutaneous, nasopharyngeal, and oropharyngeal infections. Infections of the respiratory tract are characterized by a thick, gray membrane over the pharynx and tonsils.

        2. 2. Corynebacterium jeikeium (group JK) causes sepsis, primarily in hospitalized, neutropenic cancer patients who are receiving multiple antibiotics and have some type of skin disruption.

        3. 3. “Diphtheroids” are common, nonpathogenic skin contaminants.

          MNEMONIC: A handy way to remember gram-positive rods is through the mnemonic: (“CLumsy BActeria NOrmally ACt LIke ERror-prone COrnballs”)





          Listeria monocytogenes



    3. c. Gram-negative cocci

      1. i. Neisseria

        1. 1. Neisseria meningitidis causes meningitis (in children and young adults) and meningococcemia (30%–50% of patients have meningococcemia without meningitis).

        2. 2. Neisseria gonorrhoeae commonly causes urethritis (in both men and women) and endocervicitis, which may progress to PID or disseminated gonococcal infection (DGI). Neisseria gonorrhoeae also causes pharyngitis and conjunctivitis.

      2. ii. Moraxella catarrhalis causes sinusitis, bronchitis, and pneumonia; however, it is often difficult to distinguish colonization from actual infection.

    4. d. Gram-negative rods make up the largest category of pathogenic organisms. Infections can involve many different systems, including the genitourinary, hepatobiliary, GI, and respiratory systems. Sepsis involving gram-negative rods is a major cause of mortality, especially among neutropenic or otherwise immunocompromised patients. Although there are many bacteria in this category, a partial list of pathogens that are most often seen follows.

      1. i. Escherichia coli causes most UTIs and can cause intra-abdominal and biliary infections—all of which may lead to sepsis.

      2. ii. Klebsiella causes the same diseases as E. coli but is also a common cause of bacterial pneumonia (especially in hospitalized patients and alcoholics).

      3. iii. Pseudomonas is a destructive organism that can lead to sepsis following a variety of illnesses (e.g., skin, ear, urinary tract, or lung infections). Pseudomonas infection is often health care associated and usually occurs in the setting of local tissue damage or impaired host defenses.

      4. iv. Haemophilus influenzae causes pneumonia, bacteremia (especially in patients who have undergone splenectomy), cellulitis, otitis media, epiglottitis, sinusitis, and meningitis (although less commonly now because of the availability of an effective vaccine).

      5. v. Bordetella pertussis causes whooping cough (primarily in children) and prolonged bronchitis in adults.

      6. vi. Brucella causes an insidious febrile illness characterized by easy fatigability, headache, cervical and axillary lymphadenopathy, hepatosplenomegaly, and lymphocytosis. Acquisition of brucellosis is usually by animal contact or following ingestion of contaminated milk.

      7. vii. Francisella tularensis causes tularemia, a multisystem disorder (fever, headache, lymphadenopathy, prostration) usually acquired through rabbit or tick contact.

      8. viii. Yersinia pestis causes plague and is acquired from, flea bites.

      9. ix. Salmonella, Shigella, Campylobacter, Yersinia enterocolitica, and Vibrio species can all cause infectious diarrhea.

    5. e. Anaerobes. The anaerobes Actinomyces and Clostridium are discussed with the gram-positive rods. Bacteroides fragilis, Prevotella melaninogenicus, Peptostreptococcus, and Fusobacterium are also anaerobes.

      1. i. In general, anaerobes are implicated (either alone or in combination) in gingivitis, sinusitis, otitis, abscesses (dental, brain, lung, intra-abdominal), aspiration pneumonia, empyema, skin and soft tissue infections, and pelvic infections.

      2. ii. As a rule of thumb, treatment of an abscess primarily depends on drainage, with antibiotics being secondary to this treatment.

    6. f. Miscellaneous organisms

      1. i. Rickettsia. Infections include Rocky Mountain spotted fever, murine (endemic) typhus, and louse-borne (epidemic) typhus.

      2. ii. Mycoplasma pneumoniae is a common cause of pneumonia (“walking pneumonia”) in young adults.

      3. iii. Chlamydiae. Infections include chlamydia (the most common sexually transmitted infection in the United States), lymphogranuloma venereum (LGV), trachoma, conjunctivitis, psittacosis, and pneumonia (in young adults).

  2. B. Antimicrobial Therapy. The best way to learn about antibiotics is to know the organisms that each antibiotic (or class of antibiotics) covers and which organisms are not covered. This information can be found in many antimicrobial guides.

  3. C. Approach to the Patient

    1. a. List approximately three of the most common or potentially lethal organisms that can cause the illness with which you are confronted.

    2. b. Select an antibiotic that covers the organisms that are most likely responsible for the infection, making sure to consider cost, convenience, and coverage of potentially life-threatening pathogens.

Hot Key

Rembember, if a patient is very ill, elegant antibiotic combinations are less important than broad coverage to protect against a potentially lethal organism.

Suggested Further Readings

Caliendo AM, Hodinka RL. A CRISPR way to diagnose infectious diseases. N Engl J Med 2017;377:1685–7.Find this resource:

Catterall JR. Streptococcus pneumoniae. Thorax 1999;54:929. (Classic Article.)Find this resource:

Lowy FD. Staphylococcus aureus infections. N Engl J Med 1998;339:520–32. (Classic Article.)Find this resource:

Moore LSP, Cunningham J, Donaldson H. A clinical approach to managing Pseudomonas aeruginosa infections. Br J Hosp Med 2016;77:C50–C4.Find this resource:

Walker MJ, Barnett TC, McArthur JD, et al. Disease manifestations and pathogenic mechanisms of group A Streptococcus. Clin Microbiol Rev 2014;27:264–301.Find this resource: