Epidemiology, resistance profiles, and molecular characteristics of pediatric salmonella isolates: prevalence of a clonal blaNDM-5-bearing S. typhimurium ST34 cluster in Nanning

Abstract

Background Salmonella poses a significant threat to immunocompromised patients and is associated with high morbidity and mortality rates. Pediatric populations, owing to their immature immune systems and lack of specific protective antibodies, are particularly susceptible to Salmonella infection. This study aimed to comprehensively investigate the epidemiology, resistance profiles, and molecular characteristics of pediatric Salmonella isolates. Methods A retrospective study was conducted at Guangxi Children’s Hospital, in Nanning, China, spanning from January to December 2025. Isolates were identified by MALDI-TOF MS and serotyped via slide agglutination. Antibiotic susceptibility testing was performed using either the DL-96 II or VITEK 2 Compact system. Whole-genome sequencing (WGS) was conducted on the 11 identified carbapenem-resistant Salmonella isolates. Genomic analyses included multilocus sequence typing (MLST), serotyping, virulence and antimicrobial resistance gene profiling, and SNP-based phylogenetic analysis. Results Among 1,372 unique Salmonella isolates, S. Typhimurium was the predominant serotype (55.1%, 757/1,372), peaking in infants aged less than 1 year (n = 213) and during late spring and summer (May-June). High resistance rates were observed for ampicillin (70.1%), chloramphenicol (49.1%), sulfamethoxazole (41.0%), and minocycline (39.4%), with S. Typhimurium exhibiting significantly higher resistance to multiple antibiotics (including ceftriaxone and carbapenems) than non-Typhimurium strains (p < 0.05). Genomic analysis of the 11 carbapenem-resistant Salmonella isolates revealed that 10 (90.9%) carried blaNDM-5, while one carried blaNDM-13, typically co-existing with blaTEM-1B, blaOXA-10, and IncHI2/IncHI2A/IncQ1 replicons. All carbapenem-resistant Salmonella isolates shared 111 virulence genes (across 17 categories), showing a 100% carriage rate for 83 core virulence genes. Furthermore, S. Typhimurium ST34 carrying blaNDM-5 was identified as the predominant genetically related lineage. Conclusion Pediatric Salmonella infections, predominantly caused by S. Typhimurium, exhibit strong seasonality and primarily affect children under 2 years of age. Importantly, the detection of this genetically related, blaNDM-5-positive S. Typhimurium ST34 lineage among pediatric patients underscores the risk of potential clonal dissemination within the clinical setting. These findings underscore the urgent need for continuous genomic surveillance of carbapenem-resistant Salmonella in pediatric settings.