Surveillance of Gram-Negative Bacteria in Pediatric Patients Requiring Mechanical Ventilation Using Whole-Genome Sequencing

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ID: 327312
2026
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Abstract
Abstract Background Despite extensive infection control measures, hospital-acquired infections remain a major challenge within hospital systems, with ventilator-associated infections (VAI) being the most intractable. This is particularly true for pediatric patients who often require mechanical ventilation for extended periods, thereby increasing the risk of infection. Gram-negative bacteria, primarily Pseudomonas aeruginosa, are the leading causes of VAI. Traditional infection prevention (IP) strategies are often reactive and may miss potential transmissions within the hospital, particularly for pathogens that are endemic to the hospital environment. Whole-genome sequencing (WGS) has demonstrated value in identifying such events in adult hospitals, but its application in pediatric facilities remains limited. Here, we conduct a retrospective analysis to determine how this technology could be utilized in a pediatric facility. Methods We performed a retrospective genomic surveillance study of Gram-negative isolates collected between 2020 and 2024 at a pediatric tertiary hospital. Clones were selected by colony morphology, cultured, and DNA was extracted. DNA libraries were prepared and sequenced on the Illumina NextSeq 1000 platform. Phylogenetic clustering was performed using core-genome alignment pipelines. Likely transmission events were defined as bacterial clones differing by fewer than 10 single-nucleotide polymorphisms based on previously described literature. Genetically related clones were evaluated with hospital metadata to determine likely transmission events. Results We sequenced 687 clones from roughly 500 clinical samples, resulting in the identification of over 50 clusters of isolates from genetically related Gram-negative species. P. aeruginosa accounted for most of the clusters, with over 40 clusters being discovered. Other pathogens found to have suspected clusters based on genetic relatedness include Serratia marcescens, Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Achromobacter xylosoxidans. These clusters range in size from 2 to 15 patients. Pairwise genome analysis confirmed at least 2 S. marcescens, 1 A. xylosoxidans, and 15 P. aeruginosa likely transmission clusters that were not detected through conventional IP strategies. Conclusion Our study demonstrates transmission events that were missed by traditional IP methods, highlighting the added value of WGS for hospital surveillance. This is especially true in the case of pathogens that are commonly found in hospitals. Integrating whole-genome sequencing with hospital epidemiology and electronic medical record data can enhance patient safety and reduce healthcare costs. These findings indicate that reliance on traditional surveillance alone may underestimate the true burden of hospital outbreaks, particularly those caused by common Gram-negative respiratory pathogens in pediatric populations.
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Authors Jacob J Scioli, Erin M Nawrocki, Luke Kiesendahl, Lindsay Montoya, Vaughn S Cooper, Glenn J. Rapsinski
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Journal journal of the pediatric infectious diseases society
Year 2026
DOI
10.1093/jpids/piag070/piag070.032
URL
https://academic.oup.com/jpids/article-pdf/15/Supplement_2/S14/70833149/piag070.032.pdf
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