Genomic analysis of the genetic background underlying Streptococcus pneumoniae beta-lactam nonsusceptibility in central Vietnam: increased beta-lactam nonsusceptibility and dynamics of the pbp2x gene

BACKGROUND: We previously reported alarmingly high carriage rates of Streptococcus pneumoniae (SP) serotype 19F and serogroup 6 isolates, which were not susceptible to multiple beta-lactams among children under five years of age in Vietnam. Multilocus sequence typing analysis revealed the predominance of two major lineages, ST320 and ST13223, among serotype 19F and serogroup 6 isolates, respectively. Investigating the association between nonsusceptible genotypes and clinical outcomes could help optimize patient care or lead to the development of new diagnostic tests. METHODS: We performed WGS on SP isolates randomly selected from the two major lineages and their related strains. FASTQ quality control and de novo assembly were performed using CLC Genomics Workbench ver. 7.5.1. Draft genome sequences were annotated using DFAST (DDBJ Fast Annotation and Submission Tool), which revealed the serogroups/serotypes and the sequences of the three major penicillin-binding protein genes and the sequence types. Draft sequences were aligned using MUMmer ver. 3.23, and putative recombination events and phylogenetic relationships excluding recombination regions were identified using Gubbins ver. 2.4.1. Finally, the association between a detected nonsusceptible genotype and the duration of hospital stay was evaluated in patients with acute respiratory infection. RESULTS: WGS analysis (serotype 19F/ST320, n = 22; serogroup 6/ST13223, n = 13; and isolates closely related to ST13223, n = 4) revealed substantial differences in genomic diversity and antimicrobial susceptibility between serogroup 6/ST13223 and serotype 19F/ST320 isolates, particularly the recombination-prone nature of serogroup 6/ST13223. Among the 23 recombination events observed in serogroup 6/ST13223, only those spanning the pbp2x region (15.5 kb and 6.4 kb) were associated with high MICs for multiple beta-lactams. A subset of ST13223 isolates and all ST320 isolates carried the identical pbp2x allele 16, which was significantly associated with a lack of susceptibility to the combination of penicillin, cefotaxime, and meropenem (p < 0.0001; odds ratio 11.5; 95% confidence interval [CI] 3.35-39.3). No significant association was demonstrated between the presence of this pbp2x allele and prolonged hospitalization (p = 0.6123). CONCLUSIONS: We revealed that the widespread nonsusceptibility to multiple beta-lactams among SP isolates circulating in central Vietnam was primarily driven by the dynamics of the pbp2x gene. However, the nonsusceptible pbp2x allele had little effect on clinical outcome.