A new study details the genetic diversity of Streptococcus pneumoniae within individual infants, including hidden multidrug-resistant and virulent strains. The findings suggest that the detection of such resistant variants is only possible using a population deep sequencing (PDS) approach and that their presence may be due to individuals being treated with antibiotics. The research highlights the potential for PDS to improve our understanding of pathogens like S. pneumoniae and to inform treatment strategies when antimicrobial resistance is a concern.