pH-dependent beta-lactam resistance in Klebsiella pneumoniae is mediated by paralogous class B PBPs and the class A PBP, PBP1b.

Klebsiella pneumoniae is a leading cause of global deaths due to antibiotic resistance. Of particular concern is the rapid expansion of resistance to beta-lactam antibiotics within K. pneumoniae lineages. The environmental factors that influence pathogen physiology and, subsequently, antibiotic resistance remain poorly understood. Here we demonstrate that physiologically-relevant reductions in pH increased K. pneumoniae beta-lactam resistance as much as 64-fold, with the most dramatic increase observed for beta-lactams that specifically inhibit cell division. We identified two genes that contribute to acid-dependent beta-lactam resistance, the class A PBP, PBP1b, and the paralogous class B PBP, PBP3PARA. Loss of either PBP1b or PBP3PARA increases K. pneumoniae susceptibility to beta-lactams at low pH. Altogether these data emphasize the importance of functional redundancy among cell wall synthesis enzymes which allows for specialization and ensures robust cell wall synthesis across a range of environmental conditions. ImportanceBeta-lactams are the most prescribed class of antibiotics, but their effectiveness is threatened by a global rise in antimicrobial resistance. How the environment within a host or infection site shapes pathogen response to antibiotics is frequently overlooked in assessments of antibiotic effectiveness. We demonstrate that growth at physiologically-relevant low pH substantially increases Klebsiella pneumoniae resistance to clinically important beta-lactams. An important finding of this study is that during growth in acidic pH K. pneumoniae has a different repertoire of cell wall synthesis genes available than during growth at neutral pH due to the presence of acid-inducible paralogous copies of essential cell wall synthesis enzymes, PBP2 and PBP3. An additional functionally-redundant enzyme, PBP1b, also contributes to acid-dependent beta-lactam resistance. Together, these findings expand our understanding of how bacteria maintain cell wall synthesis across diverse physiochemical environments and highlight potential new therapeutic targets.