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Dynamic changes in otopathogens colonizing the nasopharynx and causing acute otitis media in children after 13-valent (PCV13) pneumococcal conjugate vaccination during 2015–2019


The otopathogens colonizing the nasopharynx (NP) and causing acute otitis media (AOM) have shown dynamic changes following introduction of pneumococcal conjugate vaccines. Five hundred eighty-nine children were prospectively enrolled, 2015–2019. Two thousand fifty-nine visits (1528 healthy, 393 AOM, and 138 AOM follow-up) were studied. Two thousand forty-two NP and 495 middle ear fluid (MEF) samples by tympanocentesis from 319 AOM cases were cultured for bacterial identification and antibiotic susceptibility. Streptococcus pneumoniae (Spn) isolates were serotyped by Quellung, and multi-locus sequence type (ST) determined by genomic analysis. Haemophilus influenzae (Hi) was the most common otopathogen cultured from MEF during AOM (34% in MEF) followed by Spn (24% in MEF), then Moraxella catarrhalis (Mcat) (15% in MEF). NP isolates during healthy visit were Mcat (39%), Spn (32%), Hi (12%). 48.6% of Hi isolates from MEF were beta-lactamase-producing. Spn non-susceptibility to penicillin and other antibiotics was high. The most common Spn serotypes associated with AOM (and colonizing the NP during healthy visits) were 35B, 23B, and 15B/C. ST558 and ST199 were the most common sequence types. During 2015–2019, Hi was the most common otopathogen cultured from MEF during AOM among young children. Pneumococcal AOM was most commonly caused by non-PCV13 serotypes of Spn, predominantly 35B, 23B, and 15B/C. Resistance to common antibiotics among Spn strains showed an increasing trend.

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Fig. 1

adapted from a previous publication by our group [30]

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All data generated or analyzed during this study are included in this published article (and its Supplementary Information files).

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This study was supported by Sanofi Pasteur. We thank all the nurses and staff of pediatric practices, the parents who consented, the children who participated in this, study and the lab members (Karin Pryharski, Eduardo Gonzalez) who performed the microbiology over the years. Edna Yellamaty assisted with antibiotic susceptibility testing in the clinical microbiology lab of Rochester General Hospital.


Sanofi Pasteur funded this study but had no role in study design, data analysis, or preparation of the manuscript.

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Authors and Affiliations



Dr. Kaur has collected and analyzed the data. She wrote the overall manuscript. Dr. Fuji helped in data analysis and manuscript writing. Dr. Pichichero designed the study along with manuscript writing.

Corresponding author

Correspondence to Michael E. Pichichero.

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The study was approved by the Rochester General Hospital Institutional Review Board, and the study was performed in accordance with the ethical standards as set out by such.

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Parents signed informed consent regarding publishing their data.

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The authors declare no competing interests.

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Kaur, R., Fuji, N. & Pichichero, M.E. Dynamic changes in otopathogens colonizing the nasopharynx and causing acute otitis media in children after 13-valent (PCV13) pneumococcal conjugate vaccination during 2015–2019. Eur J Clin Microbiol Infect Dis 41, 37–44 (2022).

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  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Moraxella catarrhalis
  • Serotypes
  • Antibiotic susceptibility