ARCH 2.0: AMR pathogens in critically ill ICU & NICU patients
Colonization with multidrug-resistant organisms (MDROs) significantly increases the risk of subsequent infections with resistant pathogens. Antimicrobial resistance (AMR) rates are consistently higher among ICU patients compared to non-ICU populations. In our previous study conducted in general wards of a tertiary-level hospital, colonization rates of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) and carbapenem-resistant Enterobacterales (CRE) were 82% and 37%, respectively. However, the burden of colonization and infection due to resistant organisms among critically ill patients remains poorly understood in low-resource settings.Despite substantial global evidence on MDRO dissemination and its contribution to healthcare-associated infections in high-resource settings, key gaps persist regarding ICU- and NICU-specific AMR prevalence, transmission dynamics, and the relationship between colonization and infection in resource-limited contexts. Addressing these gaps is essential to quantify disease burden, inform infection prevention strategies, and monitor the effectiveness of control measures.We aimed to determine the burden of colonization and infection with extended-spectrum cephalosporin-resistant organisms (ESCrO) and carbapenem-resistant organisms (CRO) among critically ill ICU and NICU patients. It also assessed associated risk factors, clinical outcomes, and potential transmission pathways. Whole-genome sequencing is used to evaluate the genetic relatedness between colonizing and infecting isolates, thereby estimating the risk of progression from colonization to invasive infection.Patients were enrolled within 24 hours of admission to the ICU or NICU. At enrollment, rectal swab samples were collected using sterile swab sticks containing liquid Amies transport medium. Follow-up rectal swabs were obtained on days 3, 7, and 14, and subsequently at 7-day intervals until an in-hospital outcome (death, ICU/NICU discharge, or transfer to a high-dependency unit).Sociodemographic data were collected at enrollment from patients or their primary caregivers. Clinical and laboratory data were recorded at baseline and during follow-up. Patients were monitored daily by clinical teams, and additional clinical specimens (e.g., blood, tracheal aspirates, urine) for culture were collected as clinically indicated.Blood samples were collected in BACT/ALERT FA Plus bottles by trained hospital staff. All specimens were transported to the laboratory on the same day in a temperature-controlled cool box (2-8 C) for microbiological processing.