Within-Host Resistance Evolution of ST15 Klebsiella pneumoniae in an ICU Immunosuppressed Patient Under Antibiotic Pressure of Polymyxins, Ceftazidime-Avibactam, and Meropenem.

Abstract

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major pathogen in healthcare-associated infections, posing a severe and potentially fatal threat to critically ill patients. Immunocompromised patients in intensive care units (ICUs) are subjected to selective pressure from multiple antibiotics, which can lead to further resistance evolution. In this study, we report the complex dynamic evolution of resistance in ST15 CRKP in an immunocompromised critically ill patient, driven by adjustments in antibiotic regimens involving polymyxin, ceftazidime-avibactam (CZA), and meropenem. Through antimicrobial susceptibility testing, whole-genome sequencing, and mutation analysis of longitudinal clinical isolates, we identified polymyxin resistance associated with mutations, such as in mgrB, and polymyxin heteroresistance, which was detected prior to antibiotic exposure and expanded to full resistance under selective pressure. Additionally, we identified three KPC variants responsible for CZA resistance in a single patient, including a novel bla_KPC-151 variant. The novel KPC-151 enzyme features a deletion of tyrosine (Y) at position 241 to threonine (T) at position 243, with a substitution of serine (S). Cloning experiments and enzyme kinetic measurements confirmed that KPC-151 confers resistance to ceftazidime-avibactam while restoring susceptibility to carbapenems. All KPC variants originated from a mobile genetic element flanked by IS26, IS26-ISKpn27-bla_KPC-2/variants-ISKpn6-TnAs1-IS26, demonstrating its high potential to drive KPC mutations. This study underscores the rapid and diverse evolutionary adaptability of K. pneumoniae under multiple antibiotic pressures in immunocompromised critically ill patients, emphasizing the need for dynamic monitoring of antimicrobial susceptibility testing and resistance gene mutations to guide antibiotic adjustments.