Infections caused by carbapenem-resistant Enterobacterales (CRE) incur unacceptable mortality. Clinical infections arise from CRE colonizing the gut. While much has been studied on clinical risk factors favoring the acquisition of CRE colonization and transition from colonization to infection, little has been studied on the microbiome features preceding such events.
Aims: To study the microbiome features and changes that precede CRE colonization acquisition among hospitalized patients. Secondarily, we aim to study the microbiome features that precede clinical infections among those colonized by CRE.
Methods: Molecular microbiome analysis and an observational cohort study. The study will include patients in the medical-surgical intensive care unit (ICU), the hemato-oncology and bone marrow transplantation departments, and the cohorting medical department at Rambam Health Care Campus. We will include 100 CRE colonized patients and a group of 30 control patients matched by department and sampling period. All rectal swabs preceding, detecting, and following CRE acquisition (or matched index date in controls) will be stored at -80ºC (~500 samples). DNA will be extracted from all samples and PCR amplified for 16S rRNA or deep-sequenced for microbiota diversity characterization. Microbiome characteristics and dynamics in samples preceding and following CRE acquisition will be associated with CRE acquisition and infection, respectively. Clinical data predating and following the CRE acquisition will be collected retrospectively, into a pre-designed data collection form.
This study will advance our understanding of the microbiome’s role in patients’ disposition to acquire CRE colonization and their risk for infection following CRE acquisition, leading possibly to preventive measures.