Machine learning-based evaluation of risk factors for carbapenem-resistant Klebsiella pneumoniae dissemination in neonatal units.

Abstract

Healthcare-associated infections (HAIs), particularly in neonatal intensive care units (NICUs), pose significant challenges due to neonates' vulnerability and the rapid infection spread. However, risk factors facilitating pathogen persistence and dissemination have not been comprehensively investigated. This study aims to track HAI transmission pathways in NICUs and identify key risk factors contributing to the persistence and spread of carbapenem-resistant Klebsiella pneumoniae (CRKP). We analyzed CRKP epidemiology and population dynamics in neonatal patients at a pediatric hospital in China over 8 years. Random forest models identified primary risk factors for CRKP persistence and outbreaks, focusing on clonal spread, healthcare groups (HGs), and plasmid dynamics. Three major clonal outbreaks involving ST14 and ST433 strains were identified, highlighting the critical role of clonal dissemination in NICUs. Complex transmission patterns, characterized by periods of dormancy and resurgence, suggest the existence of underlying reservoirs. HGs were implicated in the short-term transmission of CRKP, with >80% of infection clusters involving patients from the same HG. Plasmids emerged as critical factors in the long-term persistence of CRKP, with shifts in plasmid prevalence corresponding to outbreak periods. This study advances our understanding of CRKP transmission dynamics in NICUs, highlighting the multifaceted roles of clonal dissemination, HGs, and plasmid-mediated persistence. Our findings emphasize the need for enhanced infection control measures targeting both intra- and inter-group transmissions and plasmid surveillance.IMPORTANCEThis study provides a detailed analysis of carbapenem-resistant Klebsiella pneumoniae (CRKP) transmission dynamics in neonatal intensive care units (NICUs) over eight years, utilizing 64 isolates and applying machine learning to identify risk factors associated with persistence and spread. Through phylogenetic analyses, we uncovered three clonal outbreaks and linked healthcare group (HG) interactions, bacterial genotypes, and plasmid prevalence to short- and long-term CRKP transmission. We identified that HGs are primary mediators of rapid, short-term transmission, while specific plasmids play an extended role in maintaining CRKP presence across multiple patient cohorts and bacterial strains. This finding suggests the existence of latent reservoirs or periodic reintroductions from external sources, thus reshaping the understanding of NICU-associated pathogen transmission and persistence.