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Prospective Whole-Genome Sequencing to Identify Bacterial Transmission and Its Modifiers in Neonates
Timmy Nguyen1, Fabian Bürkin1, Stefany Ayala-Montaño1
1Institute for Infection Prevention and Control, Medical Center-University of Freiburg, Freiburg, Germany.
JAMA Network Open
|November 21, 2025
Summary
Neonatal intensive care unit (NICU) infants are susceptible to multidrug-resistant organisms (MDROs). Whole-genome sequencing identified transmission events, revealing that increased nurse staffing and prior antibiotic use can decrease MDRO transmission risk.
Area of Science:
- Neonatalogy
- Infectious Diseases
- Genomics
Background:
- Infants in neonatal intensive care units (NICUs) face risks from multidrug-resistant organisms (MDROs), potentially leading to invasive infections.
- High-resolution analysis of MDRO transmission is crucial for targeted infection prevention.
Purpose of the Study:
- To evaluate the effectiveness of whole-genome sequencing (WGS) in identifying MDRO transmission chains in a NICU setting.
- To identify risk factors associated with MDRO cluster involvement and transmission.
Main Methods:
- A prospective monocentric cohort study included 434 infants admitted to a level III NICU.
- Whole-genome sequencing and amplified fragment length polymorphism were used to define MDRO transmission.
- Time-dependent patient and ward factors, device use, and antibiotic exposure were analyzed.
Main Results:
- Over half of the infants (51.8%) were colonized with at least one MDRO.
- Whole-genome sequencing linked 34.0% of colonizations to transmission events, identifying 37 unique transmission clusters.
- Increased full-time nurse staffing and prior antibiotic use were associated with decreased transmission risk, while vascular catheter use increased risk.
Conclusions:
- Bacterial sequencing, particularly WGS, accurately detects bacterial transmission events in NICUs.
- Multivariate analysis indicates that bacterial transmission risk within a NICU environment is modifiable through specific interventions.
