Streptococcus pneumoniae

  • Diagnosis
  • Background
  • Lab Tests
  • References
  • Related Topics

Indications for Testing

Laboratory Testing

  • CDC testing recommendations
  • Initial testing
    • CBC, arterial blood gas, chemistry profile
  • Antigen-based testing – urine and cerebrospinal fluid (CSF)
    • Immunochromatographic urinary antigen testing in symptomatic adults – 70-80% sensitivity, >90% specificity
      • Most sensitive with bacteremia
      • Prior antibiotic use does not affect antigen test
      • Urine antigen test may stay positive for up to one month; not useful for recurrences or for assessing therapy success
    • Caution – children may asymptomatically shed S. pneumoniae antigen in urine, decreasing clinical specificity of test
  • Culture
    • Gold standard – defined as isolation from blood or normally sterile site
    • Blood, CSF, respiratory sources
  • Nucleic amplification tests and polymerase chain reaction (PCR)
    • Under investigation
  • Meningitis
    • Gram stain and CSF culture detect most cases of meningitis
  • Bacteremia and pneumonia
    • Blood cultures are positive in a minority of cases of invasive disease
    • High-quality sputum with gram stain and culture may yield results
  • Other testing for community-acquired pneumonia

Differential Diagnosis

Streptococcus pneumoniae causes pneumonia, otitis media (OM), sinusitis, and meningitis.


  • Incidence (CDC, 2015)
    • Invasive pneumococcal disease – 12,000 cases/year in U.S.
    • Meningitis – 3-6,000 cases/year in U.S.
    • Pneumonia – >400,000 hospitalization cases/year in U.S.
  • Transmission – humans are the natural reservoir for S. pneumoniae; organism colonizes in nasopharynx
    • Most common in winter and early spring


  • S. pneumoniae are gram-positive, typically lancet-shaped diplococci
  • More than 80 serotypes
  • S. pneumoniae serotypes that are pathogenic in humans are not always heavily encapsulated
    • Virulence determined by composition of capsular polysaccharide
    • Antibodies to capsular polysaccharides confer type-specific immunity

Risk for Invasive Disease

Clinical Presentation

  • Pneumonia
    • 50% of community-acquired pneumonia cases are S. pneumoniae
      • Often develops as a secondary pneumonia during upper respiratory tract infections
      • Abrupt onset of fever, shaking chills, cough, dyspnea, tachypnea, and fatigue
  • OM
    • 30-50% of OM cases are S. pneumoniae
      • ~90% of children in U.S. have ≥1 episode by age 3
      • 50% have >6 episodes/year
      • Penicillin-resistant pneumococcus is the most common cause of recurrent or persistent OM
  • Sinusitis
    • Up to 40% of nonviral sinusitis cases are S. pneumoniae
  • Invasive disease
    • Meningitis
      • Neurologic sequelae common in survivors
    • Bacteremia in 25-40% of pneumonia
      • Causes 85% of all cases of bacteremia in pediatric population
      • Mortality rate for bacteremia is 20%, up to 60% in elderly
    • Endocarditis
    • Other – pericarditis, abdominal infections (eg, peritonitis), osteomyelitis, septic arthritis
Tests generally appear in the order most useful for common clinical situations. Click on number for test-specific information in the ARUP Laboratory Test Directory.

Streptococcus pneumoniae Antigen, Urine 0060228
Method: Qualitative Immunochromatography


False positives may occur because of cross-reactivity with other members of S. mitis group

Clinical correlation is recommended

Patients who have received the S. pneumoniae vaccines may test positive in the 48 hours following vaccination; avoid testing within 5 days of receiving vaccination

Streptococcus pneumoniae Antigen, CSF 0061162
Method: Qualitative Immunochromatography


False positives may occur because of cross-reactivity with other members of S. mitis group

Clinical correlation is recommended

Patients who have received the S. pneumoniae vaccines may test positive in the 48 hours following vaccination; avoid testing within 5 days of receiving vaccination

Respiratory Culture and Gram Stain 0060122
Method: Stain/Culture/Identification

Blood Culture 0060102
Method: Continuous Monitoring Blood Culture/Identification


Testing is limited to the University of Utah Health Sciences Center only

Low volume will result in decreased recovery of pathogens

Cerebrospinal Fluid (CSF) Culture and Gram Stain 0060106
Method: Stain/Culture/Identification

Aerobic Organism Identification with Reflex to Susceptibility 0065070
Method: Identification. Methods may include biochemical, mass spectrometry, or sequencing.


For suspected agents of bioterrorism, Salmonella or Shigella, notify your state department of health and refer isolates to your state laboratory for identification; susceptibilities on agents of bioterrorism are not performed at ARUP

Explify Respiratory Pathogens by Next Generation Sequencing 2013694
Method: Massively Parallel Sequencing


U.S. Department of Health and Human Services, Centers for Disease Control and Prevention. Manual for the Surveillance of Vaccine-Preventable Diseases. Centers for Disease Control and Prevention. Atlanta, GA [Last updated Apr 2016; Accessed: Aug 2017]

General References

Anjay MA, Anoop P. Diagnostic utility of rapid immunochromatographic urine antigen testing in suspected pneumococcal infections. Arch Dis Child. 2008; 93(7): 628-31. PubMed

Avni T, Mansur N, Leibovici L, Paul M. PCR using blood for diagnosis of invasive pneumococcal disease: systematic review and meta-analysis. J Clin Microbiol. 2010; 48(2): 489-96. PubMed

Centers for Disease Control and Prevention (CDC). Streptococcus pneumoniae. CDC. [Last updated Jun 2015; Accessed: Dec 2016]

Charles PG. Early diagnosis of lower respiratory tract infections (point-of-care tests). Curr Opin Pulm Med. 2008; 14(3): 176-82. PubMed

Couturier MR, Graf EH, Griffin AT. Urine antigen tests for the diagnosis of respiratory infections: legionellosis, histoplasmosis, pneumococcal pneumonia. Clin Lab Med. 2014; 34(2): 219-36. PubMed

Lynch JP, Zhanel GG. Streptococcus pneumoniae: epidemiology, risk factors, and strategies for prevention. Semin Respir Crit Care Med. 2009; 30(2): 189-209. PubMed

Madeddu G, Fois AG, Pirina P, Mura MS. Pneumococcal pneumonia: clinical features, diagnosis and management in HIV-infected and HIV noninfected patients. Curr Opin Pulm Med. 2009; 15(3): 236-42. PubMed

Niederman MS. Community-acquired pneumonia: the U.S. perspective. Semin Respir Crit Care Med. 2009; 30(2): 179-88. PubMed

van der Poll T, Opal SM. Pathogenesis, treatment, and prevention of pneumococcal pneumonia. Lancet. 2009; 374(9700): 1543-56. PubMed

References from the ARUP Institute for Clinical and Experimental Pathology®

Daly TM, Hill HR. Use and clinical interpretation of pneumococcal antibody measurements in the evaluation of humoral immune function Clin Vaccine Immunol. 2015; 22(2): 148-52. PubMed

Petti CA, Woods CW, Reller B. Streptococcus pneumoniae antigen test using positive blood culture bottles as an alternative method to diagnose pneumococcal bacteremia. J Clin Microbiol. 2005; 43(5): 2510-2. PubMed

Pickering JW, Hill HR. Measurement of antibodies to pneumococcal polysaccharides with Luminex xMAP microsphere-based liquid arrays. Methods Mol Biol. 2012; 808: 361-75. PubMed

Pickering JW, Hoopes JD, Groll MC, Romero HK, Wall D, Sant H, Astill ME, Hill HR. A 22-plex chemiluminescent microarray for pneumococcal antibodies. Am J Clin Pathol. 2007; 128(1): 23-31. PubMed

Pickering JW, Martins TB, Greer RW, Schroder C, Astill ME, Litwin CM, Hildreth SW, Hill HR. A multiplexed fluorescent microsphere immunoassay for antibodies to pneumococcal capsular polysaccharides. Am J Clin Pathol. 2002; 117(4): 589-96. PubMed

Waddle EA, Hanson KE, Jhaveri R. Follow-up analysis of serious bacterial infections in children with fever without localising signs: how do the National Institute for Clinical Excellence guidelines perform with the emergence of non-vaccine pneumococcal serotypes? Arch Dis Child. 2009; 94(3): 247. PubMed

Medical Reviewers

Last Update: August 2017