Clinical Case Study

You are a pathologist working in the lab at Daigger Memorial Hospital (located in central Oregon). The emergency room is sending you cultures collected from patients. Your job is to determine:

  1. The pathogenic bacteria causing the disease
  2. What disease is being presented
  3. What is the best treatment given the patient’s unique symptoms and history

Review the patient assessment form provided. Consider the type of sample taken and determine the relevant primary and secondary symptoms. Generally, samples taken in a clinical setting contain multiple organisms. In this case study, the sample will contain one contaminant organism and one causative agent.

Note: Watch for allergies. These may affect the appropriate treatment you will prescribe for the patient.

For some diseases, an irregularity in pulse or respiration, for example, may be indicative of the seriousness of the illness or may even be a direct indicator of the disease presented. Therefore, it is important that you understand what is considered “Within Normal Limits” for all assessment areas on the patient assessment form. Familiarize yourself with the acceptable normal ranges for pulse, respiration, oxygen saturation, blood pressure, and temperature for the age group your patient falls within.

Clinical Case Study Flowchart »

Patient Assessment Form »

Normal Flora According to Body System

Adapted from: Strohl, W.A. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001 and Forbes, B.A. Bailey and Scott's Diagnostic Microbiology. Eleventh Edition. Mosby. St. Louis, MO. 2002

System Common Normal
(Resident) Flora
Rare Normal Flora
& Comments
Ear Coagulase neg. Staphylococci (most prevalent)
Corynebacteria spp. (most prevalent)
Aspergillis, Alternaria, Penicillium, Candida
Bacillus, Micrococcus, Neisseria, Mycobacteria
Eye Staphylococcus epidermidis (most prevalent)
Lactobacillus spp. (most prevalent)
Proprionibacterium acnes
Staphylococcus aureus < 30% of population 
Haemophilus influenzae, Moraxella catarrhalis, Enterobacteriaceae, S. pyogenes, S. pneumoniae, other alpha and gamma hemolytic Streptococcus spp., Corynebacterium spp., Neisseria spp.
The bacteria inhibiting enzyme lysozyme is present in tears.  
Genitourinary tract Lactobacillus spp., Actinomyces, Micrococcus spp.
Coagulase negative Staphylococcus spp.
Microaerophilic & anaerobic Streptococcus spp.
Corynebacterium spp., Klebsiella spp., Proteus spp.
Pseudomonas spp., Bacteroides spp., Enterococcus faecalis, Mycoplasma spp., yeasts  
Candida albicans 
Intestinal tract Over 98% of species in intestine are strict anaerobes.
Bacteroides spp., Bifidobacterium, Actinomyces,
S. aureus, S. viridans, Enterococcus spp.
Enterobacter spp., E. coli (< 0.1%), Klebsiella spp.
Proteus spp., Pseudomonas spp.
Clostridium spp., Lactobacillus spp. 
Candida albicans  
Mouth and Nose Streptococcus spp. (30-60% of bacterial flora of the mouth), S. mutans, S. pneumoniae, S. viridans
Staph. aureus, Staph. epidermidis
Actinomyces, Bacteriodes spp., Neisseria spp., Corynebacterium spp., Lactobacillus spp.,
Proprionibacterium spp., Haemophilus spp., Prevotella spp., Fusobacterium spp. 
Candida albicans
Vionela spp.
Skin Staphylococcus epidermidis & coagulase negative Staphylococcus account for 90% of resident flora.
Hemolytic Streptococci, Bacillus spp.
Proprionibacterium acnes, Micrococcus luteus,
Mycobacterium spp.
Yeasts: Malassezia spp., Candida spp. 
Transient flora either die or are removed by washing.
Many organisms prefer specific sites. 
Stomach Generally low concentration of acid resistant species: Helicobacter, Streptococci, Staphylococci, Lactobacilli, fungi  Peptostreptococci
Bacteroides spp. 

Pathogenic Organisms According to Body System

Adapted from: Gilligan, P.H. Cases in Medical Microbiology and Infectious Diseases. 2nd ed. American Society for Microbiology, Washington, D.C. 1997. Murray, Patrick R. Editor. Manual of Clinical Microbiology. 8th ed. ASM Press. Washington, D.C. 2003. Strohl, W.A. Lippincott's Illustrated Reviews: Microbiology. Lippincott Williams & Wilkins. Baltimore, MD. 2001

System Disease Possible Causative Organism
[c]=community acquired infection
[n]=nosocomial infection (acquired in a hospital)
Central Nervous System Meningitis Coagulase negative Staphylococci, Staph. aureus, Strep. agalactiae, Strep. pneumoniae, Haemophilus influenzae, Listeria monocytogenes, Mycobacterium tuberculosis, Neisseria meningitidis, Pseudomonas aeruginosa, E. coli, Klebsiella spp., Gram negative bacilli, Anaerobic bacteria, Coxsackievirus
Eye Conjunctivitis Haemophilus influenzae, Strep. pneumoniae, Staph. aureus, Moraxella lacunata, Mycobacterium tuberculosis, Francisella turlarensis, Treponema pallidum, Yersinia enterocolitica, Fungi, Foreign body
Eye Blepharitis Staph. aureus, Staph. epidermidis, Herpes Simplex Virus, Phthirius pubis
Gastrointestinal tract Diarrhea Salmonella spp., Shigella spp., E. coli, B. cereus, Staph. aureus, Campylobacter spp.,
Clostridium difficile, Vibrio spp., Yersinia enterocolitica, Ascaris lumbricoides, Cryptosporidium parvum, Cyclospora spp., Entamoeba histolytica, Giardia lamblia,
Enterovirus, Norwalk agent (calicivirus), Rotavirus
Genitourinary tract Urinary tract infection (uti) and urethritis Pseudomonas aeruginosa [n], Proteus mirabilis [c,n], Staph. saprophyticus [c],
Enterococcus spp. [n], Enterobacter spp., Escherichia coli [c,n], Klebsiella pneumoniae [c,n], Chlamydia trachomatis, Candida spp., Neisseria gonorrhoeae, Morganella morganii
Respiratory tract Lung abcess K. pneumoniae, Actinomyces spp. (from aspiration)
Respiratory tract Pneumonia Chlamydia spp., Strep. pneumoniae [c], Strep. agalactiae, Strep. pyogenes,
Staph. aureus
[n], Enterobacteriaceae including E. coli [n], Pseudomonas. aeruginosa [n], Klebsiella pneumoniae [c,n],
Haemophilus influenzae, Mycoplasma pneumoniae, Neiseria meningitides, Nocardia spp., Aspergillus spp., Non-fermenting Gram negative bacilli [n], and many more including fungi, bacteria, parasites and viruses.
Respiratory tract Bronchitis Strep. pneumoniae [c], Strep. pyogenes [c], Staph. aureus [c,n], P. aeruginosa [n]
Skin and Soft Tissue Skin infections Pseudomonas aeruginosa, Staph. aureus, Strep. pyogenes, Strep. agalactiae,
Pasteurella multocida, Candida albicans (diaper rash), Cryptococcus neoformans, Mycobacterium smegmatis, Enteroviruses
Systemic Endocarditis Staph. aureus, Strep. pneumoniae, Strep. Viridans
Systemic Bacteremia Coagulase negative Staphyloccus, Staph. aureus, Strep. pyogenes, Strep. pneumoniae,
Enterococcus spp., Enterobacter spp., E. coli, Klebsiella. pneumoniae, Proteus mirabilis, Pseudomonas aeruginosa, Salmonella typhi, Acinetobacter spp., Francisella tularensis, Neiseria meningitides, Pasteurella multocida, Yersinia pestis,
Candida spp., Mycobacterium smegmatis