1. REVIEW OF MEDICAL MICROBIOLOGY
Infections of
Respiratory tract
Cardiovascular system
Gastrointestinal tract
Skin and soft tissue
Central nervous system
Genitourinary tract

2. Upper Respiratory Tract
THE RESPIRATORY TRACT
Upper Respiratory Tract
Pharyngitis (mostly 2 years through adolescence)
Adenoviruses
Group A Streptococci (S. pyogenes)
Potential for rheumatic fever
Chlamydophila pneumoniae
Neisseria gonorrhoeae
Corynebacterium diphtheriae
Mycoplasma pneumoniae

3. Otitis media (infants and young children) Streptococcus pneumoniae
THE RESPIRATORY TRACT
Otitis media (infants and young children)
Streptococcus pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Group A streptococcus
Moraxella catarrhalis
Formerly “Branhamella”
Gram-negative cocci
Opportunistic pathogen

4. Staphylococcus aureus Pseudomonas aeruginosa Group A Streptococcus
THE RESPIRATORY TRACT
Otitis externa
Staphylococcus aureus
Pseudomonas aeruginosa
Group A Streptococcus
Malignant otitis externa
• In diabetics, elderly & immunocompromised
• Can lead to osteomyelitis and meningitis

5. Streptococcus pneumoniae Haemophilus influenzae Staphylococcus aureus
THE RESPIRATORY TRACT
Sinusitis
Streptococcus pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Chlamydophila pneumoniae
Moraxella catarrhalis
Group A Streptococcus
Pseudomonas aeruginosa
Viruses
Oral anaerobic bacteria

6. Streptococcus pneumoniae Group B Streptococcus Viridans Streptococcus
THE RESPIRATORY TRACT
Conjunctivitis
Streptococcus pneumoniae
Group B Streptococcus
Viridans Streptococcus
Staphylococcus aureus
Haemophilus influenzae
Moraxella catarrhalis

7. Conjunctivitis (contd) Pseudomonas aeruginosa Corynebacterium species
THE RESPIRATORY TRACT
Conjunctivitis (contd)
Pseudomonas aeruginosa
Corynebacterium species
Francisella tularensis
Adenoviruses
Chlamydia trachomatis

8. Rhinocerebral mucormycosis • Life-threatening
THE RESPIRATORY TRACT
Rhinocerebral mucormycosis
• Life-threatening
• Most common in diabetics
• The fungi Mucor and Rhizopus invade blood
vessels, resulting in necrosis of bone and
thrombosis of the cavernous sinus and internal
carotid artery

9. Bacterial epiglottitis Life-threatening Haemophilus influenzae type b
THE RESPIRATORY TRACT
Bacterial epiglottitis
Life-threatening
Haemophilus influenzae type b
Streptococcus pneumoniae
Staphylococcus aureus

10. Corynebacterium diphtheriae Whooping cough Bordetella pertussis
THE RESPIRATORY TRACT
Diphtheria
Corynebacterium diphtheriae
Whooping cough
Bordetella pertussis

11. “Common colds” Rhinoviruses Adenoviruses Influenza C Coronaviruses
THE RESPIRATORY TRACT
“Common colds”
Rhinoviruses
Adenoviruses
Influenza C
Coronaviruses
Coxsackie viruses

12. Respiratory syncytial virus Influenza virus Parainfluenza virus
THE RESPIRATORY TRACT
“Croup”
Respiratory syncytial virus
Influenza virus
Parainfluenza virus

13. Lower Respiratory Tract Community acquired infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Community acquired infections
Streptococcus pneumoniae (elderly)
Klebsiella pneumoniae (alcoholics)
Mycoplasma pneumoniae (school-age children)
Mycobacterium tuberculosis
RSV (infants and young children)
Influenza virus

14. Lower Respiratory Tract Community acquired infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Community acquired infections
Bronchitis or pneumonia secondary to viral pneumonia
Streptococcus pneumoniae
Haemophilus influenzae
Staphylococcus aureus
Moraxella cararrhalis

15. Lower Respiratory Tract Nosocomial infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Nosocomial infections
Mycobacterium tuberculosis
RSV in pediatric patients
Methicillin-resistant S. aureus (pneumonia)
Pseudomonas aeruginosa
Legionella spp.

16. Lower Respiratory Tract Patients with underlying lung infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Patients with underlying lung infections
Chronic obstructive pulmonary disease
P. aeruginosa
S. pneumoniae
H. influenzae
Moraxella cararrhalis
Allergic bronchopulmonary aspergillosis

17. Lower Respiratory Tract Patients with underlying lung infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Patients with underlying lung infections
Cystic fibrosis
S. aureus
P. aeruginosa
Allergic bronchopulmonary aspergillosis

18. Lower Respiratory Tract Patients with underlying lung infections
THE RESPIRATORY TRACT
Lower Respiratory Tract
Patients with underlying lung infections
Cavitary lung disease (due to prior MTB infection)
Aspergillus spp (Aspergilloma or fungus ball)

19. Lower Respiratory Tract Immunocompromised individuals
THE RESPIRATORY TRACT
Lower Respiratory Tract
Immunocompromised individuals
At risk for all recognized respiratory tract pathogens
AIDS patients
Pneumocystis carinii
S. pneumoniae
MDR M. tuberculosis

20. Lower Respiratory Tract Immunocompromised individuals
THE RESPIRATORY TRACT
Lower Respiratory Tract
Immunocompromised individuals
Neutropenic patients
Invasive aspergillosis
Mucormycosis

21. Lower Respiratory Tract Immunocompromised individuals
THE RESPIRATORY TRACT
Lower Respiratory Tract
Immunocompromised individuals
Transplant patients
Invasive fungi
CMV
HSV
Legionella spp.
Pneumocystis carinii

22. A 40-year-old male with multisystem failure secondary to bilateral pneumonia was transferred to our hospital via helicopter.
He had presented to his local physician 3 days previously complaining of fever, malaise, and vague respiratory symptoms.
He was given amantadine for suspected influenza. His condition became progressively worse, with shortness of breath and a fever to 40.5˚C.
From: “Cases in Medical Microbiology and Infectious Disease”

23. He was admitted to an outside hospital 24 h prior to transfer.
A laboratory examination revealed abnormal liver and kidney function.
Therapy with Timentin (ticarcillin-clavulanic acid) and trimethoprim-sulfamethoxazole was begun.
He underwent pronchoscopic examination which revealed mildly inflamed airways containing thin, watery secretions.

24. A Gram-stain of bronchial washings and culture results are shown in the figure.
Based on these findings, he was begun on appropriate antimicrobial therapy.

25. Which organisms are common causes of community-acquired bacterial pneumonia?

26. Streptococcus pneumoniae
Haemophilus influenzae
Mycoplasma pneumoniae
Staphylococcus aureus
(frequently following an influenza infection)
Klebsiella pneumoniae
(elderly & alcoholics)
Legionella pneumophila
Chlamydophila pneumoniae

27. On the basis of the Gram-stain of bronchial washings, and the patient’s presentation, what is the most likely cause of this patient’s catastrophic infection?
Why must the laboratory be notified if this organism is considered in the differential diagnosis?

28. The patient has Legionella pneumophila.
Renal and hepatic dysfunction and thin watery secretions are characteristic of this infection.
Patients with bacterial pneumonia due to most other bacterial agents have thick, purulent secretions.
The laboratory needs to be informed because the organism requires a specific growth medium, buffered charcoal yeast extract (BCYE) agar.

29. What techniques other than culture can be used to detect this organism within 24 h?

30. DFA

31. What is the appropriate antimicrobial agent for the treatment of this infection?
Which other Gram-negative respiratory pathogen is treated with this antibiotic?

32. Erythromycin
Can penetrate into white blood cells
Legionella multiplies in macrophages
Bordetella pertussis

33. THE CARDIOVASCULAR SYSTEM
Septicemia: Predisposing factors and agents
Abdominal sepsis
Enterobacteria
Bacteroides fragilis
Enterococcus faecalis
Enterococcus faecium
Infected wounds
Staphylococcus aureus
Streptococcus pyogenes

34. THE CARDIOVASCULAR SYSTEM
Septicemia: Predisposing factors and agents
Osteomyelitis
Staphylococcus aureus
Pneumonia
Streptococcus pyogenes
Food poisoning
Salmonella spp.
Campylobacter spp.

35. THE CARDIOVASCULAR SYSTEM
Septicemia: Predisposing factors and agents
Intravascular devices
Staphylococcus aureus
Staphylococcus epidermidis
Enterobacteria
Meningitis
Streptococcus pneumoniae
Neisseria meningitidis
Haemophilus influenzae

36. THE CARDIOVASCULAR SYSTEM
Septicemia: Predisposing factors and agents
Immunocompromised patients
Staphylococcus aureus
Enterobacteria

37. THE CARDIOVASCULAR SYSTEM
Infective endocarditis
> 80% of cases caused by streptococci
or staphylococci
Total streptococci 60%
Viridans group 35%
anginosus group
mitis group
mutans group
salivarius group

38. THE CARDIOVASCULAR SYSTEM
Infective endocarditis
Total streptococci 60%
Total staphylococci 25%
S. aureus 20%
S. epidermidis 5%

39. THE CARDIOVASCULAR SYSTEM
Myocarditis
Corynebacterium diphtheriae
Clostridium perfringens
Group A Streptococcus
Borrelia burgdorferi
Neisseria meningitidis
Staphylocccus aureus

40. Five days prior to admission she had developed a cough and rhinitis.
The patient was a 4-month-old female who was admitted to the hospital in March with sever respiratory distress.
Five days prior to admission she had developed a cough and rhinitis.
Two days later she began wheezing and was noted to have a fever.
She was brought to the emergency room when she became lethargic.
From: “Cases in Medical Microbiology and Infectious Disease”

41. One sibling was reported to be coughing, and her father had a “cold”.
On examination she had
a fever of 38.9˚C
tachycardia with a pulse of 220/min
tachypnea with respirations of 80/min
Her throat was clear.

42. A chest X-ray revealed interstitial infiltrates.
She was put in respiratory isolation in the pediatric intensive care unit, and was subsequently intubated.
Blood and nasopharyngeal cultures were sent to the bacteriology and virology laboratories.
A rapid diagnostic test was positive and specific antiviral therapy was begun.

43. She was also given a bronchodilator (aminophylline) to treat the bronchospasm which was resulting in her wheezing.
She was extubated 5 days later and discharged home on day 8.
1. What are the possible causes for this patient’s pneumonia?

44. Parainfluenza virus
Influenza A and B
Respiratory syncytial virus
Mycoplasma pneumoniae
Bordetella pertussis

45. Membrane-enzyme immunoassay

46. 2. What other techniques could one use to identify this microorganism?

47. Direct Fluorescence Antibody
“Shell Vial Assay”
Fibroblasts grown on coverslips in a shell vial
Clinical specimens a centrifuged onto the cell monolayer
Incubation for 1-2 days
The monolayer is stained with a fluorescent monoclonal antibody specific for an RSV antigen

48. 2. What is the epidemiology of the disease?

49. RSV is spread by large droplets and on fomites
Can be spread via contaminated hands
Occurs primarily in winter months

50. 3. What is the pathophysiologic basis for wheezing?

51. RSV is tropic for bronchial epithelium
Edema and necrosis can lead to collapse and obstruction of a child’s small bronchioles

52. 4. What specific therapy should be given after the antigen test gives the diagnosis?

53. Only one antiviral agent is available for treatment of RSV in infants
Aerosolized ribavirin
(oral administration can result in hepatic or bone marrow toxicity)
The American Academy of Pediatrics recommends its use in children with congenital heart disease, cystic fibrosis, immunodeficiency or severe illness.

54. 5. What infection control measures should be taken?

55. Patients should be put on respiratory isolation
Gowns and gloves should be used during contact

56. 6. What can be done to prevent the disease?

57. Inactivated RSV vaccine did not work and exacerbated the disease
Immune globulin can be used in children at greatest risk

58. THE GASTROINTESTINAL SYSTEM
Two basic mechanisms of diarrheal disease:
Enterotoxin-induced fluid loss
Cholera toxin
Direct damage to the intestinal epithelium
Cytotoxin
Entamoeba histolytica
Invasion of epithelium
Salmonella spp.
Shigella spp.
Campylobacter spp.
Yersinia enterocolitica

59. THE GASTROINTESTINAL SYSTEM
Infectious doses
Hundreds of thousands to millions
Salmonella spp.
Vibrio cholerae
Less than 100
Shigella spp.

60. THE GASTROINTESTINAL SYSTEM
Bacteria
Invasive diarrhea
Campylobacter spp.
Salmonella spp.
Shigella spp.
Yersinia enterocolitica
Large-volume watery diarrhea
Vibrio spp.

61. THE GASTROINTESTINAL SYSTEM
Bacteria
Watery diarrhea
Enterotoxigenic E. coli
Yersinia enterocolitica
Typhoid fever
Salmonella spp.

62. THE GASTROINTESTINAL SYSTEM
Bacteria
Traveler’s diarrhea
Enterotoxigenic E. coli
Dysentery
Shigella spp.

63. THE GASTROINTESTINAL SYSTEM
Bacteria
Antibiotic-associated diarrhea
Pseudomembranous colitis
Clostridium difficile
Food poisoning
Staphylococcus aureus
Clostridium perfringens
Bacillus cereus
Salmonella spp.

64. THE GASTROINTESTINAL SYSTEM
Bacteria
Abdominal abscess
Bacteroides fragilis
Gangrenous lesions of bowel or gall bladder
Clostridium perfringens
Enterohemorrhagic colitis
Enterohemorrhagic E. coli

65. THE GASTROINTESTINAL SYSTEM
Viruses
Acute, self-limited hepatitis
Hepatitis A
Acute and chronic hepatitis
Hepatitis B
Hepatitis C

66. THE GASTROINTESTINAL SYSTEM
Viruses
Diarrhea
Enterovirus
Rotavirus
Norwalk agent (calicivirus)
Vomiting
Norwalk agent (“24-hour flu”)

67. THE GASTROINTESTINAL SYSTEM
Viruses
Infants
Rotavirus A (most common cause)
Adenovirus 40, 41
Coxsackie A24 virus
Infants, children, and adults
Norwalk agent (“24-hour flu”)
Calicivirus
Reovirus

68. Rocky Mountain spotted fever Meningococcemia Entereoviral infection
SKIN AND SOFT TISSUE
Diffuse erythematous macular rash may be a manifestation of systemic disease
Rocky Mountain spotted fever
Meningococcemia
Entereoviral infection
Toxic shock syndrome
Scarlet fever
Measles
German measles

69. Vesicular skin lesions Varicella Zoster virus
SKIN AND SOFT TISSUE
Erythema migrans
Lyme diseases
Vesicular skin lesions
Varicella Zoster virus
Macular, papular or pustular, but not vesicular, skin lesions
Secondary syphilis

70. Important to treat superficial skin infections
SKIN AND SOFT TISSUE
Important to treat superficial skin infections
Folliculitis caused by Staphylococcus aureus
Cellulitis caused by Streptococcus pyogenes
Delay in treatment may result in invasion of the deeper structures (e.g necrotizing fasciitis)

71. Cat scratch disease, bacillary angiomatosis Bartonella henselae
SKIN AND SOFT TISSUE
Cat scratch disease, bacillary angiomatosis
Bartonella henselae
Lyme disease
Borrelia burgdorferi
Gas gangrene
Clostridium perfringens
Tetanus
Clostridium tetani

72. Diphtheria and wound diphtheria Corynebacterium diphtheriae Cellulitis
SKIN AND SOFT TISSUE
Diphtheria and wound diphtheria
Corynebacterium diphtheriae
Cellulitis
Group A streptococci (S. pyogenes)
Group B streptococci (S. agalactiae)
Pasteurella multocida
Staphylococcus aureus
Cryptococcus neoformans

73. Skin infection in burn patients Pseudomonas aeruginosa Thrush
SKIN AND SOFT TISSUE
Skin infection in burn patients
Pseudomonas aeruginosa
Thrush
Candida albicans
Candida spp.
Cutaneous infection
Blastomyces dermatitidis

74. Infection of keratinized tissue Epidermophyton floccosum
SKIN AND SOFT TISSUE
Infection of keratinized tissue
Epidermophyton floccosum
Microsporum spp.
Trichophyton spp.
Ulcerative skin lesions
Leishmania tropica

75. Human herpesvirus type 6 Oral infections Herpes simplex virus Warts
SKIN AND SOFT TISSUE
Exanthem subitum
Human herpesvirus type 6
Oral infections
Herpes simplex virus
Warts
Human papillomavirus

76. CENTRAL NERVOUS SYSTEM
The most frequent infections are
Meningitis
Encephalitis
Abscess
Septic: caused by bacteria
CSF cloudy (>1,000 white blood cells/µl)
Aseptic: Viruses, fungi, MTB
CSF clear ( cells/µl)

77. CENTRAL NERVOUS SYSTEM
Neonatal meningitis (newborn - 2 months)
Group B streptococci (most common cause)
Listeria monocytogenes
E. coli
Klebsiella pneumoniae
Citrobacter diversus Citrobacter koseri
Treponema pallidum

78. CENTRAL NERVOUS SYSTEM
Meningitis (2 months - 5 years)
Haemophilus influenzae type b
Streptococcus pneumoniae
Neisseria meningitidis (all ages)
Meningitis (Patients with head trauma )
Coagulase-negative staphylococci
Staphylococcus aureus
Pseudomonas aeruginosa

79. CENTRAL NERVOUS SYSTEM
Aseptic meningitis
Echovirus
Coxsackievirus
Herpes simplex virus
Fungal meningitis
(primarily in the immunocompromised)
Cryptococcus neoformans (in AIDS patients)

80. CENTRAL NERVOUS SYSTEM
Viral encephalitis
Herpes simplex virus (most common)
(necrotizing; necrotizing hemorrhagic)
Eastern equine encephalitis virus
Western equine encephalitis virus
St. Louis encephalitis virus
La Crosse encephalitis virus

81. CENTRAL NERVOUS SYSTEM
Encephalitis
Toxoplasma gondii
Taenia solium (“cysticercosis”; from pork)
Meningoencephalitis
Cerebral malaria
Naegleria fowleri (an amoeba)
Citrobacter diversus

82. CENTRAL NERVOUS SYSTEM
Brain abscesses
Extension from a contiguous site
Hematogenous spread from another site (endocarditis or lung abscess)
Septic emboli (blood clots containing an infectious agent)
In immunocompetent individuals
S. aureus
viridans streptococci
Actinomyces spp.
Anaerobic bacteria

83. CENTRAL NERVOUS SYSTEM
Brain abscesses
In immunocompromised individuals
Aspergillus
Mucor
Rhizopus
Nocardia spp.
In diabetic patients
Rhinocerebral mucormycosis

84. Urinary tract infections Endogenous infections
GENITOURINARY TRACT
Urinary tract infections
Endogenous infections
Nosocomial (catheterization)
Sexually transmitted diseases
Exogenous infections

85. Urinary tract infections Enterobacter Enterococcus
GENITOURINARY TRACT
Urinary tract infections
Enterobacter
Enterococcus
Klebsiella pneumoniae
Proteus mirabilis
Pseudomonas aeruginosa
Staphylococcus saprophyticus
Candida spp.

86. Pelvic inflammatory disease Chlamydia trachomatis (PID)
GENITOURINARY TRACT
Pelvic inflammatory disease
Chlamydia trachomatis (PID)
Neisseria gonorrhoeae (PID)
Actinomyces spp. (endogenous; IUD usage)
Vaginitis
Candida spp. (endogenous)
Trichomonas vaginalis

87. Sexually transmitted diseases Chlamydia trachomatis (PID)
GENITOURINARY TRACT
Sexually transmitted diseases
Chlamydia trachomatis (PID)
Neisseria gonorrhoeae (PID)
Treponema pallidum (fetal loss or perinatal infect.)
Herpes simplex virus (fetal loss or perinatal infect.)
HIV
Human papilloma virus
Trichomonas vaginalis