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

ABSTRACT 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 penicillin-binding protein (PBP), PBP1b, and the paralogous class B PBP, PBP3 PARA . Loss of either PBP1b or PBP3 PARA 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. IMPORTANCE Beta-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 physicochemical environments and highlight potential new therapeutic targets.