Microbiology Case Study: Young Girl with Community-Acquired Pneumonia

A young girl presented to the emergency department with 6 days of cough, congestion, and intermittent fever up to 102°F. Respiratory viral testing, blood cultures, and a chest x-ray were ordered. The patient was found to be RSV positive and sent home with oral steroids. Two days later she presented the emergency department once again with worsening respiratory symptoms and a positive blood culture with the following organism (Figure 1).

Figure 1. Gram stain demonstrating Gram-positive cocci in pairs and chains.

Our patient developed a Streptococcus pneumoniae superinfection and bacteremia in conjunction with RSV pneumonia.


S. pneumoniae is a Gram-positive cocci that forms “lancet” shaped pairs on Gram stain (Figure 1). Due to pretreatment with antibiotics, our Gram stain shows some pairs, but many Gram variable chains of cocci as well. S. pneumoniae grows as alpha hemolytic colonies on 5% sheep blood, chocolate, and CAN (colistin nalidixic acid) agar in 12-18 hours, where it forms umbelicated colonies with a characteristic navel-like depression in the middle due to autolysins produced by the bacterium. Some serotypes of S. pneumoniae, primarily serotype 3, have a mucoid phenotype seen in Figure 3. S. pneumoniae is a member of the Streptococcus mitis group, but due to its pathogenic potential it has always been singled out. This is accomplished using two biochemical tests: bile solubility testing with 10% deoxycholate, which dissolves colonies of S. pneumoniae but not those of other Viridans group streptococci, and optochin disc testing, to which S. pneumoniae is sensitive while other Virdians group streptococci are resistant (Figures 2 and 3). Many molecular assays have trouble differentiating S. pneumoniae from S. mitis group due to their similarities on a nucleotide and protein level, so biochemical testing is still a mainstay of organism identification.

Figure 2. Growth of α-hemolytic bacterial colonies on 5% sheep blood agar. Zone around the disc indicates the organism is optochin susceptible.


Figure 3. Growth of mucoid, α-hemolytic bacterial colonies on 5% sheep blood agar. The mucoid colony morphology suggests this isolate is likely serotype 3.

Clinical Significance

S. pneumoniae is known to cause a variety of clinical manifestations in children, from community acquired pneumonia and acute otitis media to bacteremia and meningitis. S. pneumoniae is also a colonizer of the upper respiratory tract; approximately 21% of children in developed countries and 90% of children in developing countries are asymptotically colonized. Due to the high rates of S. pneumoniae colonization in children, direct urine antigen testing is inappropriate, as it cannot distinguish asymptomatic carriage from invasive disease. S. pneumoniae direct antigen detection from CSF has been shown to have < 30% sensitivity and offers no benefit over a routine cytospin Gram stain.

Vaccination in children

Around 2000 the first S. pneumoniae vaccine became available. PCV7 was a heptavalent conjugate vaccine which provided protection from the 7 most common S. pneumoniae serotypes known to cause invasive disease (4, 6B, 9V, 14, 18C, 19F, and 23F). Routine vaccination of children was a huge success which reduced the incidence of invasive pneumococcal disease attributed to vaccine strains by 99%. An indirect benefit of the PCV7 vaccine was that adults >65 years of age saw a 92% decrease in invasive pneumococcal disease caused by PCV7 serotypes, despite not being vaccinated themselves, because of reduced transmission of S. pneumoniae from children to adults. Due to the selective pressure of the vaccine, non-vaccine serotypes of S. pneumoniae such as 19A subsequently became the predominant causes of invasive streptococcal disease. In 2010, a 13-valent pneumococcal conjugate vaccine (PCV13) was FDA approved. It includes all seven S. pneumoniae serotypes contained in PCV7, plus six additional serotypes (1, 3, 5, 6A, 7F, and 19A). PCV13 provides coverage against 2/3 of all serotypes responsible for invasive pneumococcal disease in children under 5 years of age.

Follow up

The patient had an uneventful hospital stay. All subsequent blood cultures were negative and susceptibility testing found the patient’s S. pneumoniae isolate to be susceptible to penicillin, cefotaxime, and clindamycin. The patient and was discharged home after 24 hours of observation with a 7 day course of amoxicillin.



  • Manual of Clinical Microbiology, 11th edition
  • Pediatric Red Book, 2015 Report of the Committee on Infectious Diseases, 30th edition


-Erin McElvania TeKippe, Ph.D., D(ABMM), is the Director of Clinical Microbiology at Children’s Medical Center in Dallas Texas and an Assistant Professor of Pathology and Pediatrics at University of Texas Southwestern Medical Center.

4 thoughts on “Microbiology Case Study: Young Girl with Community-Acquired Pneumonia”

    1. It’s actually very common not to wear gloves in the clinical microbiology lab when working with plates on the bench. Of course, specimen setup always requires gloves.

  1. Hi! In behalf of my study group, I would like to ask for your permission to utilize this case study as reference in one of our subject papers under Respiratory Care Management Studies. We are still students, and we hope to include this case study as it is very close to our subject. Thank you very much for your kind approval on our request!

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