Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study

Nosocomial infections pose a significant risk to patients, especially in intensive care units where hospital-associated bacteria are endemic. During the first wave of the COVID-19 pandemic, the surge of patients presented a significant obstacle to infection control measures. A study in northern Italy assessed the risks and extent of nosocomial pathogen transmission using a novel bacterial pan-pathogen deep-sequencing approach. Inpatients were sampled to identify bacterial pathogens from respiratory, nasal, and rectal samples. DNA from each plate with positive growth was deep sequenced en masse, and antimicrobial resistance genes were detected. The study found that hospital transmission was likely a significant mode of acquisition for each pathogen species. The study suggests that a culture-based deep-sequencing approach could improve future pathogen surveillance and infection control at hospitals.