We investigated the use of whole genome sequencing (WGS) to predict antibiotic resistance of circulating S. pneumoniae (pneumococcus) carriage isolates collected among PCV7 and PCV10-vaccinated toddlers in the Netherlands.
All Pneumococcal strains (n=737) isolated between 2009-2018 from 24-months old carriers were subjected to WGS. Genome assembly of short reads into contigs was performed using SPAdes, which were subsequently assigned a taxonomic origin with Kraken2. All DNA sequences identified as pneumococcus were used for resistance gene identification with RGI. Predicted resistance genes with ≥50 bitscore and ≥80% sequence identity were further analyzed and compared against phenotypical antibiotic resistance data. Susceptibility testing was performed according to EUCAST guidelines.
Based on WGS data 9.8% (72/737) of pneumococcal isolates were predicted to harbor resistance genes. Genetic markers of antibiotic resistance predicted by WGS were in concordance with resistotypes determined using the EUCAST-recommended method. Lack of susceptibility to penicillins was primarily observed for serotypes 19A (13% of 128) and 23B (19% of 63), respectively.
We have observed good congruence between antibiotic resistance prediction with WGS and standard phenotypical antibiotic sensitivity testing. Antibiotic resistance among pneumococcal carriage isolates in the Netherlands is relatively rare and is characterized by circulation of resistant serotype 19A and 23B strains.