Genomic dynamics of antimicrobial resistance transmission between bacteria from intensive care unit surfaces and from critically ill patients

BACKGROUND: The Intensive Care Unit (ICU) is an environment where multiple factors that predispose to the transmission of Antimicrobial Resistance (AMR) coexist. Genomic sequencing is a technology that enables a better understanding of how AMR genes are transmitted within the ICU environment. OBJECTIVE: To evaluate the genomic dynamics of the transmission of antimicrobial resistance genes between bacteria from ICU surfaces and bacteria from critically ill patients. METHODS: A cross-sectional analytical study. Surface swab samples were collected from the ICU, including suction units, infusion pumps, stethoscopes, dialysis machines, monitors, ventilators and gas valves, as well as samples from critically ill patients with infections. Species were identified using microbiological microplate panels; antibiotic susceptibility testing was carried out to assess AMR; and whole-genome sequencing was performed on isolates that were multidrug-resistant (MDR). The sequencing was carried out using a nanopore long-read sequencer and the results were analysed using specialised bioinformatics tools. RESULTS: A total of 130 positive isolates were identified, of which 96 (73.85%) were from environmental samples and 34 (26.15%) from patient samples. Forty (30.76%) MDR species were identified. The most common MDR species were Klebsiella pneumoniae and Acinetobacter baumannii. The most frequently detected AMR genes were blaNDM-5 and blaOXA-23. The most common plasmids were IncFIB(K)_1_Kpn3, Col440I and IncL/M(pMU407)_1_pMU407. A clonal outbreak of Acinetobacter baumannii ST 2 was detected on the dialysis machine, stethoscopes and patient samples. Evidence of horizontal transfer of resistance genes via plasmids conjugation was found in samples taken from suction units, oxygen valves and tracheal secretion in three cases. CONCLUSION: The findings of this research show that antimicrobial resistance genes are transferred between bacteria on surfaces and bacteria in critically ill patients, and that this transfer occurs in both directions.