Genetic background of Cambodian pneumococcal carriage isolates following pneumococcal conjugate vaccine 13

Abstract

Streptococcus pneumoniae (the pneumococcus) is a leading cause of childhood mortality globally and in Cambodia. It is commensal in the human nasopharynx, occasionally resulting in invasive disease. Monitoring population genetic shifts, characterized by lineage and serotype expansions, as well as antimicrobial-resistance (AMR) patterns is crucial for assessing and predicting the impact of vaccination campaigns. We sought to elucidate the genetic background (global pneumococcal sequence clusters; GPSCs) of pneumococci carried by Cambodian children following perturbation by pneumococcal conjugate vaccine (PCV) 13. We sequenced pre-PCV13 (01/2013-12/2015, N=258) and post-PCV13 carriage isolates (01/2016-02/2017, N=428) and used PopPUNK and SeroBA to determine lineage prevalence and serotype composition. Following PCV13 implementation in Cambodia, we saw expansions of non-vaccine type (NVT) serotypes 23A (GPSC626), 34 (GPSC45) and 6D (GPSC16). We predicted antimicrobial susceptibility using the CDC-AMR pipeline and determined concordance with phenotypic data. The CDC-AMR pipeline had >90 % concordance with the phenotypic antimicrobial-susceptibility testing. We detected a high prevalence of AMR in both expanding non-vaccine serotypes and residual vaccine serotype 6B. Persistently high levels of AMR, specifically persisting multidrug-resistant lineages, warrant concern. The implementation of PCV13 in Cambodia has resulted in NVT serotype expansion reflected in the carriage population and driven by specific genetic backgrounds. Continued monitoring of these GPSCs during the ongoing collection of additional carriage isolates in this population is necessary.

Keywords: AMR; Cambodia; PCV; Streptococcus pneumoniae; carriage; genomics.

Fig. 1.

Phylogenetic tree of 686 carriage isolates from healthy children in Cambodia, isolated between 2013 and 2017. GPSCs with N>20 in the population are highlighted. The tree was built from a nucleotide alignment in FastTree using a generalized time reversible model. Branches are coloured by GPSC corresponding with the first colour strip. ermB and mefA are macrolide (e.g. erythromycin) resistance genes, cat causes resistance to chloramphenicol, tet results in resistance to tetracycline and refers to presence of either tet(M) or tet(O), and folA I20L and folP cause resistance to trimethoprim and sulfamethoxazole (the components of co-trimoxazole), respectively. Antimicrobials are coloured as follows: resistant, red; susceptible, blue; and in the case of co-trimoxazole – intermediate, pink. This figure can be visualized interactively using webtool Microreact at: https://microreact.org/project/mvgn3EvNgmxAcPjPBnyFMj/a32e0dc6.

Fig. 2.

Prevalence of dominant GPSCs (N>20) in pre- and post-PCV13 periods. The bars are coloured by in silico serotype. GPSCs in descending order by count, each with pre-PCV (left) and post-PCV13 (right), are along the x-axis. The prevalence of each GPSC in each vaccine period is along the y-axis. Prevalence changes in GPSC (increasing, except for GPSC 1) notably occurred for 1, 626, 45 and 16. Notable changes in serotype prevalence between pre- and post-PCV13 were observed in serotypes 19F, 23A, 34, 6D and 18C.

Fig. 3.

The prevalence of AMR among the 11 dominant pneumococcal lineages or GPSCs in Cambodia. GPSCs are ordered by their overall prevalence in the population (rows) and colours indicate the prevalence of AMR and resistance determinants (columns) for each dominant GPSC in Cambodia. Coloured by AMR prevalence from 0 (light purple) to 100 % (dark purple). ermB and mefA are macrolide (e.g. erythromycin) resistance genes, cat causes resistance to chloramphenicol, tet results in resistance to tetracycline and refers to presence of either tet(M) or tet(O), and folA I20L and folP cause resistance to trimethoprim and sulfamethoxazole (the components of co-trimoxazole), respectively.