Study Protocol for Genomic Epidemiology Investigation of Intensive Care Unit Patient Colonization by...

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• ESKAPE pathogens are a leading cause of healthcare-associated infections.
• Rapid acquisition of antimicrobial resistance (AMR) by these bacteria necessitates robust surveillance.
• Understanding colonization dynamics is crucial for preventing severe infections in intensive care units (ICUs).

Purpose of the Study:

• To present a comprehensive protocol for characterizing AMR pathogen colonization in ICU patients.
• To identify risk factors associated with resistant microflora acquisition.
• To analyze the spread and mechanisms of antibiotic resistance using whole-genome sequencing (WGS).

Main Methods:

• Collection of rectal/oropharyngeal swabs or respiratory samples from ICU patients.
• Cultivation, species identification, and antibiotic susceptibility testing.
• Whole-genome sequencing (WGS) of isolates to determine resistance genes, virulence factors, and typing profiles (MLST, cgMLST).

Main Results:

• Characterization of species distribution, phenotypic and genotypic resistance profiles, and clonal structure of AMR pathogens.
• Estimation of detection frequency and colonization patterns at different body sites.
• Identification of key risk factors, including prior exposures, associated with admission colonization.

Conclusions:

• The protocol provides a framework for detailed surveillance of AMR colonization in ICUs.
• WGS data enables comprehensive analysis of pathogen composition, resistance trends, and clonal characteristics.
• This approach aids in estimating AMR infection risk and severity in critically ill patients.