Phenotypic and genomic changes in enteric Klebsiella populations during long-term ICU patient hospitalization: The role of RamR regulation
Acquired antimicrobial resistance and metabolic changes are central for bacterial host adaptation during the long-term hospitalization of patients. We aimed to analyze the genomic and phenotypic evolution of enteric Klebsiella populations in long-term intensive care unit (ICU) patients. Weekly rectal swabs were prospectively collected from all patients admitted to the ICU in a teaching hospital from December 2018 to February 2019. The inclusion criterion for patients was hospitalization for more than 15 days in the ICU without any history of hospitalization or antibiotic treatment for the three months prior to admission. Among them, enteric Klebsiella pneumoniae species complex (KpSC) populations were detected. For each isolate, extensive antimicrobial resistance profiles were determined using the disk diffusion method, and the whole genome was sequenced using an Illumina platform. In silico typing methods, such as multilocus sequence typing (MLST), core-genome MLST, SNP typing, resist