Genomic investigation and nationwide tracking of pediatric invasive nontyphoidal Salmonella in China

Abstract

Invasive nontyphoidal Salmonella (iNTS) causes significant concern with ~15% morbidity, affecting populations mainly in African countries. However, iNTS infections among the Chinese pediatric population remain largely unknown. Here, we conducted a genomic investigation to study pediatric iNTS infections in a Chinese hospital. iNTS isolates accounted for 15.2% (18/119) of all nontyphoidal Salmonella (NTS) strains. Compared to non-iNTS isolates, iNTS isolates harbored a lower prevalence of antimicrobial-resistant genes of fluoroquinolones and β-lactams, as well as disinfectant determinants and plasmids, but carried a significantly higher prevalence of cdtB, faeCDE, and tcpC genes. Importantly, we detected an emerging serovar Goldcoast as the predominant iNTS serovar locally. By integrating 320 global Goldcoast genomes based on the One Health samplings, we conducted nationwide phylogenomic tracking and detected repeated human-to-human transmission events among iNTS cases caused by an underestimated serovar Goldcoast. Together, our exploratory genomic approach highlights a new trend in pediatric iNTS infections.

Figure 1

Phenotypic and genotypic AMR between invasive non‐typhoidal Salmonella (iNTS) and non‐iNTS groups. (A) Percentage of isolates with phenotypic resistance to distinct antimicrobials. (B) Percentage of isolates with AMR determinants. (C) Distribution of isolates with phenotypic resistance towards different antimicrobial classes. (D) Distribution of isolates with different classes of AMR determinants. (E) Prevalence of disinfectant resistance genes between the iNTS and NTS groups. RND efflux pump and SMR efflux pump were found. A chi‐squared test was conducted. *p < 0.05; ns, no significant difference. AMR, antimicrobial resistance; RND, reresistance‐nodulation‐division; SMR, small multidrug resistance; TMP‐SMX, Trimethoprim‐sulfamethoxazole.