190. Non-pneumococcal streptococci confounding PCR serotyping of Streptococcus pneumoniae in US colonized adults.
Session: Poster Abstract Session: Diagnostics: Bacteriology, Sequencing, and Resistance
Thursday, October 27, 2016
Room: Poster Hall
  • IDweek.poster.uscolonizationstudy.FINAL.10.20.2016.pdf (559.7 kB)
  • Background:

    Carriage studies are often used to evaluate the impact of pneumococcal conjugate vaccine (PCV) on serotype-specific pneumococcal colonization rates. Although culture has been considered the gold standard laboratory test for carriage studies, molecular methods have increasingly been used despite concerns that non-pneumococcal streptococci may carry homologs to pneumococcal-serotype genes. We evaluated use of PCR-serotyping for pneumococci in upper respiratory samples. 


    We performed culture- and PCR-based tests for pneumococcal identification and serotyping on nasopharyngeal (NP) and oropharyngeal (OP) specimens collected between July 2015 and March 2016 from US adults≥ 65 years in four states. Adults were recruited from outpatient centers or residential communities. NP and OP swabs were stored and processed separately using broth culture enrichment and real-time PCR targeting the pneumococcal lytA gene. Pneumococci were serotyped by Quellung, and a subset of lytA-positive and -negative specimens were PCR-serotyped. Non-pneumococcal isolates were speciated by multilocus sequence analysis.


    Of 1241 adults enrolled, 16 (1.3%) had pneumococci isolated from either NP or OP specimens; 4 isolates were 13-valent PCV-types (19A and 19F). Of the remaining 1225 culture-negative patients, 70 were pneumococcal-positive by lytA PCR (65 from OP, 1 from NP and 4 from both), putatively increasing pneumococcal colonization prevalence to 6.9% (86/1241). PCR serotyping on 52 OP lytA-positive specimens identified 21 (40%) with PCV13-types; serotypes 1, 4, 9V/9A, uncommon pneumococcal serotypes in the US, were most prevalent. When 398 lytA-negative specimens were tested, PCV13-types were found in 25% of OP and 1.8% of NP specimens, with serotypes 1, 4, and 9V/9A again most common.  Streptococcus mitis and oralis PCR-positive for serotypes 1, 4, and 9V/9A were isolated from lytA-negative specimens


    We confirmed that PCR serotyping for pneumococci can identify homologs to pneumococcal serotype genes on other streptococci species, leading to erroneous serotyping results and biased vaccine impact estimates. The 5-fold increase in pneumococcal positivity by PCR raises concerns about specificity of lytA for pneumococci.

    Fernanda C. Lessa, MD, MPH1, Jennifer Milucky, MPH1, Nadine Rouphael, MD2, Nancy M. Bennett, MD3, H. Keipp Talbot, MD, MPH, FIDSA4, Lee Harrison, MD5, Monica Farley, MD, FIDSA6, Jeremy Walston, MD7, Diane Kober, RN8, Fabiana Pimenta, PhD1, Bernard Beall, PhD1, Cynthia G. Whitney, MD1 and Maria Da Gloria Carvalho, PhD1, (1)Division of Bacterial Diseases, CDC, Atlanta, GA, (2)Emory University, Atlanta, GA, (3)University of Rochester Medical Center, Rochester, NY, (4)Medicine, Vanderbilt University School of Medicine, Nashville, TN, (5)University of Pittsburgh, Pittsburgh, PA, (6)Department of Medicine, Emory University School of Medicine and Atlanta VA Medical Center, Atlanta, GA, (7)Medicine/Geriatrics, Johns Hopkins University School of Medicine, Baltimore, MD, (8)New York Emerging Infections Program, Rochester, NY


    F. C. Lessa, None

    J. Milucky, None

    N. Rouphael, None

    N. M. Bennett, None

    H. K. Talbot, Novartiis and Vaxlnnate: Consultant , Consulting fee
    Sanofi Pasteur: Grant Investigator , Grant recipient
    MedImmune: Grant Investigator , Grant recipient

    L. Harrison, None

    M. Farley, None

    J. Walston, None

    D. Kober, None

    F. Pimenta, None

    B. Beall, None

    C. G. Whitney, None

    M. D. G. Carvalho, None

    Findings in the abstracts are embargoed until 12:01 a.m. CDT, Wednesday Oct. 26th with the exception of research findings presented at the IDWeek press conferences.