Co-occurrence of bacteria and viruses and serotype distribution of Streptococcus pneumoniae in the nasopharynx of Tanzanian children below 2 years of age following introduction of the PCV13

Abstract

Introduction: Pneumococcal conjugate vaccines have reduced severe disease attributed to vaccine-type pneumococci in children. However, the effect is dependent on serotype distribution in the population and disease development may be influenced by co-occurrence of viral and bacterial pathogens in the nasopharynx.

Methods: Following introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Tanzania we performed repeated cross-sectional surveys, including 775 children below 2 years of age attending primary healthcare centers. All children were sampled from nasopharynx and pneumococci were detected by single-target PCR. Pneumococcal serotypes/groups and presence of viruses and other bacteria were determined by two multiplex PCR assays.

Results: The prevalence of PCV13 vaccine-type pneumococci decreased by 50%, but residual vaccine-types were still detected in 21% of the children 2 years after PCV13 introduction. An increase in the non-vaccine-type 15 BC was observed. Pneumococci were often co-occurring with Haemophilus influenzae, and detection of rhino/enterovirus was associated with higher pneumococcal load.

Discussion: We conclude that presence of residual vaccine-type and emerging non-vaccine-type pneumococci in Tanzanian children demand continued pneumococcal surveillance. High co-occurrence of viral and bacterial pathogens may contribute to the disease burden and indicate the need of multiple public health interventions to improve child health in Tanzania.

Keywords: Streptococcus pneumoniae; infant; pneumococcal conjugate vaccines; sub-Saharan Africa; viruses.

Figure 1

Ratio of PCV13 vaccine-type (VT) pneumococci in relation to all detected pneumococci (142/309 in 2013, 45/131 in 2014 and 44/174 in 2015) in the nasopharynx of Tanzanian children under 2 years of age. Error bars represent 95% confidence intervals; *p-value 0.027; **p-value < 0.0001.

Figure 2

Prevalence of detected pneumococcal serotypes or groups in relation to year and inclusion in PCV13 (total number of VTs, 252 and NVTs, 152). *Between 2013 and 2015, there was a significant decrease of the detected VTs 6ABCD, 19A and 19F whilst there was a significant increase of the NVT 15BC.

Figure 3

Pneumococcal load in relation to detection of other potential respiratory pathogens. The Ct (cycle threshold) value is inversely proportional to the amount of nucleic acid; lower Ct values thus relate to higher pneumococcal load. RSV, respiratory syncytial virus; ns, non-significant.