Loss of Pde1 function acts as an evolutionary gateway to penicillin resistance in <i>Streptococcus pneumoniae</i>.

Abstract

<i>Streptococcus pneumoniae</i> is a major human pathogen and rising resistance to β-lactam antibiotics, such as penicillin, is a significant threat to global public health. Mutations occurring in the penicillin-binding proteins (PBPs) can confer high-level penicillin resistance but other poorly understood genetic factors are also important. Here, we combined strictly controlled laboratory experiments and population analyses to identify a new penicillin resistance pathway that is independent of PBP modification. Initial laboratory selection experiments identified high-frequency <i>pde1</i> mutations conferring <i>S. pneumoniae</i> penicillin resistance. The importance of variation at the <i>pde1</i> locus was confirmed in natural and clinical populations in an analysis of >7,200 <i>S. pneumoniae</i> genomes. The <i>pde1</i> mutations identified by these approaches reduce the hydrolytic activity of the Pde1 enzyme in bacterial cells and thereby elevate levels of cyclic-di-adenosine monophosphate and penicillin resistance. Our results reveal rapid de novo loss of function mutations in <i>pde1</i> as an evolutionary gateway conferring low-level penicillin resistance. This relatively simple genomic change allows cells to persist in populations on an adaptive evolutionary pathway to acquire further genetic changes and high-level penicillin resistance.