This prospective study demonstrates that the illumigene test is significantly more likely than culture to identify GAS in patients who do not have clinical evidence of GAS pharyngitis. The 12.5% of swabs that were culture-positive from patients without signs or symptoms of pharyngitis or other infection approximate rates of GAS carriage reported in the literature.12–16 In contrast, more than 20% of paired swabs were positive using the illumigene test, a 60% increase over culture. GAS test results were not influenced by patient sex, age or use of corticosteroids within the previous 2 weeks.
The subjects enrolled in this study constitute a convenience sample in clinic for a health supervision visit or follow-up of a noninfectious problem. Although monthly enrollment was extremely variable, there was never a month in which there were more positive cultures than positive molecular tests. This study was designed to minimize the potential for bias in patient selection and swab sampling error. Cultures were performed in standard fashion by experienced laboratory personnel and all illumigene tests were performed according to the manufacturer’s instructions. We have no data on the prevalence of acute pharyngitis in the community during the nearly 2-year course of this study, and we did not review medical records of the study subjects.
A recent report of children enrolled in a longitudinal study of pediatric autoimmune neuropsychiatric disorder associated with streptococci found that some subjects developed an antibody response to GAS after asymptomatic acquisition of pharyngeal GAS.22 Those findings imply that some asymptomatic GAS-positive children might have “subclinical” infection and are therefore potentially at risk for GAS sequelae.23 We do not know whether some of the test-positive patients in this study had subclinical GAS infection. While illumigene might be more likely than culture to identify patients with asymptomatic (subclinical) infection, this would not explain the increase in positive tests we previously identified among patients with symptomatic pharyngitis.9 Moreover, there is no evidence that failure to identify “subclinical” acquisition of pharyngeal GAS has been associated with outbreaks of suppurative or nonsuppurative GAS disease (although some ARF patients are unable to recall sore throat24) and there is no realistic way to prospectively identify subclinically infected children.
Individuals who harbor GAS in the pharynx when asymptomatic are usually considered to be colonized rather than infected with GAS.10,11 The pathophysiology of persistent pharyngeal colonization (carriage) with GAS is unknown. Carriers traditionally have not been considered to be at risk for poststreptococcal sequelae and they have not often been identified as a source for GAS disease outbreaks.11 Current guidelines do not recommend identification or treatment of carriers except in special circumstances.4,5 When patients with clinical pharyngitis test positive for GAS it is difficult to distinguish those with acute infection from those who are GAS carriers with intercurrent illnesses. Consequently, carriers with intercurrent viral illness are often treated with antibiotics if a test is positive. Unnecessary swabbing8 and overuse of antibiotics to treat nonstreptococcal pharyngitis is well-documented.25 Any test that increases identification of GAS in asymptomatic patients, as occurs with the illumigene test, will increase unnecessary antibiotic treatment of carriers when they have pharyngeal symptoms not caused by GAS, such as when they have viral pharyngitis.
Increased identification of carriers might not be the only reason that the illumigene test is positive more often than culture. In the small subset of 13 illumigene-positive lysates that we tested by PCR, 4 (31%) were negative (and the paired swabs had been culture-negative). Culture-negative/illumigene-positive/PCR-negative results have been noted in other studies.18–20 The illumigene test has very high specificity but it sometimes yields false positive results for unknown reasons. SpeB, the target gene for the illumigene test, has been identified as a highly sensitive and specific PCR target in GAS.26 It is found universally in Streptococcus pyogenes and not in other streptococci or other pharyngeal bacteria; there is no reason to suspect that false-positive illumigene tests reflect amplification of speB from other bacteria.
Both BAP culture and RADT exhibit spectrum effect, that is, test results are affected by disease presentation. Patients with signs and symptoms more consistent with GAS pharyngitis are more likely to have a positive test.27–29 Test sensitivity is therefore directly related to pretest probability. Clinicians can take advantage of this phenomenon by limiting swabs for RADT and culture to patients with findings more consistent with bona fide GAS pharyngitis,29 as recommended by the American Academy of Pediatrics and IDSA.4,5 It is not known if the illumigene test exhibits spectrum effect.
Clinical microbiology increasingly relies on molecular methods for diagnosis of infectious diseases. In 2018, IDSA and the American Society of Microbiology published a comprehensive guide to microbiology testing that includes NAATs for GAS pharyngitis.30 The American Academy of Microbiology has released a report of a 2016 colloquium on diagnostic testing focused on POC and rapid diagnostic methods, including NAATs.31 Both documents note that clinical guidelines for molecular testing for GAS pharyngitis are lacking. Nevertheless, GAS molecular tests are available to be used in microbiology laboratories and POLs and an argument has been made that NAATs should supplant BAP culture for evaluation of patients with pharyngitis.32 Our data indicate that caution is needed before NAATs fully replace culture for GAS.
Tests using methods other than loop-mediated isothermal amplification to amplify various GAS nucleic acid sequences are commercially available and some are CLIA-waived.8 While published reports of these tests include their sensitivity and specificity,31–36 we are not aware of any data (other than those we present here) that address the identification of GAS in patients who do not have GAS pharyngitis, either asymptomatic patients or GAS carriers with intercurrent illness. The performance of all GAS molecular tests in routine clinical practice, especially in POLs, will require monitoring8; their reported very high sensitivity strongly suggests that they are likely to behave much like the illumigene test. The benefit of delivering “definitive” results to patients more rapidly than possible with culture must be tempered by the reality that highly sensitive GAS molecular tests have the potential to conflict with efforts at antimicrobial stewardship, especially in areas with low rates of ARF.
Illumigene is significantly more likely than the time-honored BAP culture to identify GAS in healthy children, expanding on our observation that illumigene was significantly more likely than culture to identify GAS in RADT-negative emergency department patients with pharyngitis.9 As with multiplex respiratory viral panels, identifying the presence of a pathogen by amplifying nucleic acid found in the nonsterile upper respiratory tract may not be equivalent to diagnosing infection.8,37,38 All of the patients in this study were asymptomatic; those with positive GAS tests might have been subclinically infected but it is likely that most were asymptomatic GAS carriers. Some had false-positive illumigene results. Additional studies of GAS molecular tests and new clinical guidelines are needed to define the role of these tests in clinical care. Until we have better understanding of GAS molecular tests, clinicians in North America and most high resource countries should heed expert advice to avoid testing patients at low risk for ARF (age <3 years) or unlikely to have bona fide GAS pharyngitis because their signs and symptoms are more consistent with viral illnesses (cough, laryngitis, croup, conjunctivitis, rhinorrhea and diarrhea).4,5,8 Diagnostic testing should focus on patients who are most likely to have pharyngitis caused by GAS, placing them at risk for development of ARF: age ≥3 years with signs and symptoms such as fever, cervical adenitis, pharyngeal/tonsillar exudates and/or rash of scarlet fever. In settings with high rates of ARF, this approach may need adjustment.
The authors thank Ram Yogev, MD provided advice on study design and methodology; Sarah Gioia and Stephanie Pelligra, MPH provided essential administrative assistance.
1. Breese BB, Disney FA. The accuracy of diagnosis of beta streptococcal infections on clinical grounds. J Pediatr. 1954;44:670–673.
2. Gerber MA, Shulman ST. Rapid diagnosis of pharyngitis
caused by group A streptococci
. Clin Microbiol Rev. 2004;17:571–580, table of contents.
3. Cohen JF, Bertille N, Cohen R, et al. Rapid antigen detection test for group A streptococcus in children with pharyngitis
. Cochrane Database Syst Rev. 2016;7:CD010502.
4. Shulman ST, Bisno AL, Clegg HW, et al. Clinical practice guideline for the diagnosis and management of group A streptococcal pharyngitis
: 2012 update by the Infectious Diseases Society of America. Clin Infect Dis. 2012;55:e86–e102.
5. Kimberlin DW, Brady MT, Jackson MA; American Academy of Pediatrics. Group A streptococcal infections. In: Red Book: 2018 Report of the Committee on Infectious Diseases. 2018:31st ed. Itasca, IL: American Academy of Pediatrics; 749–762.
6. Schwartz B, Fries S, Fitzgibbon AM, et al. Pediatricians’ diagnostic approach to pharyngitis
and impact of CLIA 1988 on office diagnostic tests. JAMA. 1994;271:234–238.
7. Park SY, Gerber MA, Tanz RR, et al. Clinicians’ management of children and adolescents with acute pharyngitis
. Pediatrics. 2006;117:1871–1878.
8. Jaggi P, Leber A. Molecular testing for group A streptococcal pharyngitis
: to test or not to test, that is the question. J Pediatr Infect Dis Soc. 2018. doi: 10.1093/jpids/pix106.
9. Tanz RR, Zheng XT, Carter DM, et al. Caution needed: molecular diagnosis of pediatric group A streptococcal pharyngitis
. J Pediatric Infect Dis Soc. 2018;7:e145–e147.
10. Kaplan EL. The group A streptococcal upper respiratory tract carrier state: an enigma. J Pediatr. 1980;97:337–345.
11. Tanz RR, Shulman ST. Chronic pharyngeal carriage of group A streptococci
. Pediatr Infect Dis J. 2007;26:175–176.
12. Begovac J, Bobinac E, Benic B, et al. Asymptomatic pharyngeal carriage of beta-haemolytic streptococci and streptococcal pharyngitis
among patients at an urban hospital in Croatia. Eur J Epidemiol. 1993;9:405–410.
13. Pichichero ME, Marsocci SM, Murphy ML, et al. Incidence of streptococcal carriers
in private pediatric practice. Arch Pediatr Adolesc Med. 1999;153:624–628.
14. Ginsburg CM, McCracken GH Jr, Crow SD, et al. Seroepidemiology of the group-A streptococcal carriage state in a private pediatric practice. Am J Dis Child. 1985;139:614–617.
15. Hoffman S. The throat carrier rate of group A and other beta-hemolytic streptococci among patients in general practice. Acta Pathol Microbiol Immunol Scand. 1985; 93:347–351.
16. Shaikh N, Leonard E, Martin JM. Prevalence of streptococcal pharyngitis
and streptococcal carriage in children: a meta-analysis. Pediatrics. 2010;126:e557–e564.
18. Anderson NW, Buchan BW, Mayne D, et al. Multicenter clinical evaluation of the illumigene group A streptococcus DNA amplification assay for detection of group A streptococcus from pharyngeal swabs. J Clin Microbiol. 2013;51:1474–1477.
19. Henson AM, Carter D, Todd K, et al. Detection of Streptococcus pyogenes by use of illumigene group A streptococcus assay. J Clin Microbiol. 2013;51:4207–4209.
20. Felsenstein S, Faddoul D, Sposto R, et al. Molecular and clinical diagnosis of group A streptococcal pharyngitis
in children. J Clin Microbiol. 2014;52:3884–3889.
21. Upton A, Bissessor L, Farrell E, et al. Comparison of illumigene group A streptococcus assay with culture of throat swabs from children with sore throats in the New Zealand School-based Rheumatic Fever Prevention Program. J Clin Microbiol. 2016;54:153–156.
22. Hysmith ND, Kaplan EL, Cleary PP, et al. Prospective longitudinal analysis of immune responses in pediatric subjects after pharyngeal acquisition of group A streptococci
. J Pediatric Infect Dis Soc. 2017;6:187–196.
23. Shulman ST, Tanz RR. Strep: where do we go from here? J Pediatric Infect Dis Soc. 2017;6:197–198.
24. Veasy LG, Wiedmeier SE, Orsmond GS, et al. Resurgence of acute rheumatic fever in the intermountain area of the United States. N Engl J Med. 1987;316:421–427.
25. Kronman MP, Zhou C, Mangione-Smith R. Bacterial prevalence and antimicrobial prescribing trends for acute respiratory tract infections. Pediatrics. 2014;134:e956–e965.
26. Dunne EM, Marshall JL, Baker CA, et al. Detection of group A streptococcal pharyngitis
by quantitative PCR. BMC Infect Dis. 2013;13:312.
27. DiMatteo LA, Lowenstein SR, Brimhall B, et al. The relationship between the clinical features of pharyngitis
and the sensitivity of a rapid antigen test: evidence of spectrum bias. Ann Emerg Med. 2001;38:648–652.
28. Edmonson MB, Farwell KR. Relationship between the clinical likelihood of group A streptococcal pharyngitis
and the sensitivity of a rapid antigen-detection test in a pediatric practice. Pediatrics. 2005;115:280–285.
29. Tanz RR, Gerber MA, Kabat W, et al. Performance of a rapid antigen-detection test and throat culture in community pediatric offices: implications for management of pharyngitis
. Pediatrics. 2009;123:437–444.
30. Miller JM, Binnicker MJ, Campbell S, et al. A guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2018 update by the Infectious Diseases Society of America and the American Society for Microbiology. Clin Infect Dis. 2018;67:e1–e94
31. Dolen V, Bahk K, Carroll KC, et al. Changing diagnostic paradigms for microbiology: Report on an American Academy of Microbiology colloquium held in Washington, DC, from 17 to 18 October 2016. 2017. Washington, DC: American Society for Microbiology; Available from: https://www.ncbi.nlm.nih.gov/books/NBK447255/
. Accessed March 6, 2019.
32. Pritt BS, Patel R, Kirn TJ, et al. Point-counterpoint: a nucleic acid amplification test
for Streptococcus pyogenes should replace antigen detection and culture for detection of bacterial pharyngitis
. J Clin Microbiol. 2016;54:2413–2419.
33. Uphoff TS, Buchan BW, Ledeboer NA, et al. Multicenter evaluation of the Solana Group A Streptococcus Assay: comparison with culture. J Clin Microbiol. 2016;54:2388–2390.
34. Arbefeville S, Nelson K, Thonen-Kerr E, et al. Prospective postimplementation study of Solana Group A streptococcal nucleic acid amplification test
vs conventional throat culture. Am J Clin Pathol. 2018;150:333–337.
35. Cohen DM, Russo ME, Jaggi P, et al. Multicenter clinical evaluation of the novel Alere i Strep A isothermal nucleic acid amplification test
. J Clin Microbiol. 2015;53:2258–2261.
36. Tabb MM, Batterman HJ. The Simplexa™ Group A Strep Direct Assay: a sample-to-answer molecular assay for the diagnosis of group A streptococcal pharyngitis
. Expert Rev Mol Diagn. 2016;16:269–276.
37. Byington CL, Ampofo K, Stockmann C, et al. Community surveillance of respiratory viruses among families in the Utah Better Identification of Germs-Longitudinal Viral Epidemiology (BIG-LoVE) Study. Clin Infect Dis. 2015;61:1217–1224.
38. Storch GA. Editorial commentary: plethora of respiratory viruses and respiratory virus data. Clin Infect Dis. 2015;61:1225–1227.