Effect of pneumococcal conjugate vaccine availability on Streptococcus pneumoniae infections and genetic recombination in Zhejiang, China from 2009 to 2019

Abstract

Pneumococcal pneumonia is one of the main reasons for child death worldwide. Pneumococcal conjugate vaccines (PCVs) are considered the most effective strategy for pneumococcal disease (PD) prevention, but how a pause in PCV vaccination affects the prevalence of PD or the genetic evolution of Streptococcus pneumoniae genetic evolution is unknown. Based on the unique PCV introduction timeline (vaccine unavailable during April 2015-April 2017) in China, we aimed to evaluate the effect of interrupted PCV availability on PD and pneumococcal genome variation. Pneumococcal isolates (n = 386) were collected retrospectively from eight sites in Zhejiang, China from 2009 to 2019 in which 184 pathogenic (isolates from sterile and infection sites) strains were identified. An interrupted time series analysis was conducted to estimate changes in PD and the recombination frequency of whole genome-sequenced strains was estimated via SNP calling. We found that both PD and pneumococcal genome variation were affected by interrupted PCV availability. The proportion (∼70%) of vaccine-type pneumococcal LRTI (VT-LRTI) in all LRTI cases decreased to ∼30% in the later PCV7 period and rebounded to ∼70% in children once PCV7 became unavailable in April 2015 (p = 0.0007). The major clone CC271 strains showed slowed (p = 0.0293) recombination frequency (decreased from 2.82 ± 1.16-0.72 ± 0.21) upon PCV removal. Our study illustrated for the first time that VT-LRTI fluctuated upon interrupted vaccine availability in China and causing a decreased of recombination frequency of vaccine types. Promoting a nationwide continuous vaccination programme and strengthening S. pneumoniae molecular epidemiology surveillance are essential for PD prevention.

Keywords: PCV availability; Streptococcus pneumoniae; genetic variation; pneumonia; recombination.

Figure 1.

Serotype distribution of pathogenic pneumococcal isolates in different age groups. All pathogenic pneumococcal isolates were serotyped by latex and quellung reactions, where young children (<5 years old) related strains were also analyzed in silico by whole genome sequencing via SeroAB and PneumoCAT. The proportion of each PCV serotype, NVT (Non-Vaccine Type), and NT (Non Typeable) strains in all pathogenic pneumococcus were calculated in different age groups: 0–5 (red), 6–64 (pink), and, ≥65 (pink dots) years old.

Figure 2.

The ratio of vaccine type pneumococcus related lower respiratory tract infection (VT-LRTI) and its correlation with PCV coverage. A. The ratio VT-LRTI in children under 5 years old were calculated in all LRTI cases from 2009 to 2019. For the interrupted time serious analysis, two time-units in a year of 2010, 2013 2014, and 2015 were drawn for the first half and the latter half of each year. For those years have less than 3 months data or pathogenic isolates number less than 10 (2009, 2011, 2012, 2016, 2017, 2018, and 2019), only one time-unit was used for each year. The light red shaded time period (01/2013-04/2015) is the effective PCV7 intervention time. Statistically significate was determined when p < 0.05; B. The correlation of VT-LRTI rate (line) and PCV7 coverage (column) from 2009 to 2014; C. The correlation of VT-LRTI rate (line) and PCV7 coverage (column) from 2005 to 2019. A strong correlation was detected when R²> 0.6.

Figure 3.

The phylogenetic tree and recombination events in all pneumococcal isolates from children under 5 years old. A. the phylogenetic tree of all pneumococcal isolates from children under 5 years old that was constructed in PopPUNK, where the four major clone complexes (CC) were shaded in light and dark pink; B. The metadata including isolation year, CC type, ST type, and serotype of all sequenced pneumococcal isolates; C. An annotated chromosome of the reference pneumococcal strain EF3030 with red marks of cps and eps locus (top of panel C). The main part of panel C shows the recombination events in all sequenced pneumococcal strains which were detected by Snippy and Gubbins. Red blocks represent the recombination blocks in each clone complex on an internal branch, which are therefore shared by multiple isolates, while blue blocks represent the recombination that occurred on terminal branches, which are unique to individual isolates. The whole data set was visualized in Phandango (https://jameshadfield.github.io/phandango/#/).

Figure 4.

Recombination frequency (r/m) and numbers (re) of pneumococcal isolates collected from children under 5 years old. The ratio of SNP caused by recombination and mutation (r/m) (A) and recombination block numbers (re) (B) were determined in all pathogenic pneumococcal strains in children under 5 years old from 2009 to 2019. The data were presented as log (r/m) and log (re) for each isolate and a liner curve with 95%Cl was added for both. C. A two-dimensional Fig. of r/m and re of all pneumococcal isolates from children, where the blue dots represent colonized pneumococcal strains and red dots represent the pathogenic ones. D. The proportion of isolates with r/m > 1 and re > 5 in pathogenic and colonized pneumococcal strains.

Figure 5.

Recombination frequency (r/m) and numbers (re) of CC271, 19F, and 19A in different PCV time period. A. The normalized (log) r/m value of CC271 in PCV7-I (2009-2011), PCV7-II (2012-2014), PCV-pause (2015-2016), and PCV13 (2017-2019), “*” indicate a significant difference between PCV7-I, and PCV pause groups (p = 0.0293); B and C. The r/m and re value of serotype 19F (dark blue dots) and 19A (light blue dots) strain in the above four time periods.