Comprehensive genomic characterization of extraintestinal pathogenic Escherichia coli isolated from neonates: multiple center insights into virulence, resistance, and transmission dynamics

Abstract

Neonatal extraintestinal pathogenic Escherichia coli (ExPEC), which can cause severe long-term sequelae by systemic infections, is gradually becoming the primary pathogen threatening neonatal health. The lack of large-scale genomic epidemiological investigation hinders further understanding of neonatal ExPEC. We conducted this nationwide multicenter study to support further strategies for improving neonatal ExPEC management. The neonatal ExPEC strains and clinical information, including antimicrobial resistance phenotype, were collected from nine centers within 7 provinces across China between 2018 and 2023. Whole-genome sequencing was performed. Sequence types (ST) and serotypes were acquired to characterize the strains. Phylogenetic analysis and pan-genomic analysis were conducted to identify the population structure. Bioinformatics analysis associated with virulence factors, antimicrobial resistance genes, and mobile genetic elements were conducted. To characterize the situation of horizontal gene transfer, we developed a computational tool for identifying horizontal evolutionary patterns from large-scale genomic draft assemblies. Co-occurrence and co-localization metrics were used to describe the synergistic effects and transmission mechanism of genes. A total of 411 neonatal ExPEC strains were included. ST1193 (18·0%) was the main ST, while O75 (15·8%) was the most common serotype. Virulence factors and antimicrobial resistance genes were widely distributed across various STs, provinces, years, and isolation sites. Co-occurrence analysis revealed multiple clusters of virulence factors and antimicrobial resistance genes, suggesting co-transmission or co-evolution. Multiple kinds of mobile genetic elements were widely distributed throughout the country. The predicted plasmid-derived contig, genome islands, prophages, and transposons carry different pathogenic genes, respectively. Multiple pathogenic genes exhibited co-occurrence with a specific plasmid replicon, suggesting the critical role of plasmids in the evolution of ExPEC. Our findings indicate that neonatal ExPEC had a shared phylogenetic spectrum with adult ExPEC isolates, but distinct dominant subtypes. Multiple virulence factors and drug resistance genes form a complex network that enhances pathogenicity. The formation of these gene clusters is associated with both the inherent genetic factors of ExPEC and the involvement of complex mobile genetic elements. These data accelerate the understanding of neonatal ExPEC, revealing the distribution of STs, serotypes, pathogenic genes, and transmission dynamics.