Stepwise within-host evolution of a bla_CTX-M-27-positive Klebsiella pneumoniae clone under changing antimicrobial pressures leading to enhancement of β-lactam resistance.

OBJECTIVE: -positive Klebsiella pneumoniae isolates (named KE411, KE412, KE413, and KE414) from a patient with acute leukemia who underwent sequential antimicrobial therapy. These isolates exhibited a stepwise increase in β-lactam resistance alongside changes in the antibiotic treatment and ultimately acquired resistance to all β-lactams examined, including carbapenems. This study aimed to identify the genetic changes between the isolates that led to increased antimicrobial resistance. METHODS: Complete genome sequences of the four isolates were compared to identify genetic differences between them. To characterize the genetic alterations, we profiled outer membrane proteins and quantified mRNA expression. RESULTS: expression. Second, a 48-bp deletion that inactivated the porin-encoding ompK36 gene, detected in isolates KE413 and KE414 (obtained after shifting to doripenem therapy). Because the K. pneumoniae clone was deficient in OmpK35 production, this deletion led to the acquisition of carbapenem resistance due to dual deficiency of OmpK35 and OmpK36. CONCLUSION: We reveal stepwise within-host evolution of a K. pneumoniae clone enabling its survival under changing antimicrobial pressures.