Emergence of carbapenem-resistant XDR Salmonella enterica in paediatric patients in South China: A genomic perspective study

Abstract

Background and Aim

Carbapenem-resistant Salmonella enterica (CRSE), mostly driven by plasmids, poses a growing public health threat, especially in paediatric populations. This study investigates a cluster of paediatric CRSE infections in paediatric populations, characterizes genomic features of CRSE isolates, assesses global CRSE prevalence, and explores plasmid-mediated horizontal gene transfer.

Methods

An epidemiological investigation of 18 paediatric CRSE cases was conducted. Genomic analysis included resistome profiling, plasmid typing, and phylogenetic clustering to assess genetic diversity. A global analysis of 530 113 Salmonella genomes identified carbapenemase-carrying isolates. Plasmid transfer experiments between S. enterica and Escherichia coli were performed to evaluate horizontal gene transmission.

Results

Respiratory co-infections (67% of cases, primarily respiratory syncytial virus and human parainfluenza viruses) were associated with severe clinical outcomes. Genomic analysis revealed multiple genetically distinct CRSE clones carrying bla_NDM-5, predominantly on IncI-gamma/K1 and IncHI2A plasmids. Plasmid-mediated transfer of carbapenem resistance genes between S. enterica and E. coli was confirmed. Global surveillance identified 228 carbapenemase-positive Salmonella isolates (2000–2023) across 35 genetically diverse populations and 24 countries, demonstrating widespread dissemination.

Conclusions

Respiratory co-infections may exacerbate CRSE severity in children, while plasmid circulation drives carbapenem resistance transmission. The high genetic diversity and global distribution of CRSE highlight urgent needs for integrated surveillance, antimicrobial stewardship, and interventions targeting co-infections and environmental reservoirs.