Emergence of carbapenem-resistant Salmonella Typhi harboring blaNDM-5 in India: genomic evidence from a multicenter study

Abstract

Background: The rise of antimicrobial resistance (AMR) in Salmonella enterica serovar Typhi poses a serious threat to global enteric fever control. In particular, the emergence of resistance to third-generation cephalosporins and azithromycin critically undermines available treatment options. Sustained genomic surveillance of high-risk S. Typhi lineages and resistance determinants is essential for informing antibiotic policy and optimizing typhoid conjugate vaccine (TCV) introduction in endemic regions. In this study, we report a multicenter outbreak of carbapenem-resistant S. Typhi in India and investigate its genomic epidemiology, resistance mechanisms, and evolutionary origins. Methods: A total of 31 carbapenem-resistant S. Typhi isolates collected from multiple tertiary care hospitals were subjected to phenotypic antimicrobial susceptibility testing and whole-genome sequencing (WGS). Short-read WGS data were used to analyze core-genome SNPs, infer phylogenetic relationships, and investigate AMR determinants. Two representative isolates underwent long-read Oxford Nanopore sequencing for plasmid reconstruction and comparative genomic analysis with Enterobacterales. Results: Antimicrobial susceptibility testing of isolates revealed resistance to ampicillin, ciprofloxacin, ceftriaxone, and carbapenems while retaining susceptibility to chloramphenicol, cotrimoxazole, and azithromycin. The genomic analysis identified the presence of two plasmids: IncFIB(K) harboring blaCTX-M-15, qnrS1, tetA, and IncX3, carrying the blaNDM-5 gene. Phylogenetic analysis classified the isolates within a novel genotype, 4.3.1.1.1, belonging to genotype 4.3.1.1 (H58 lineage I). Notably, plasmid comparison revealed high similarity to resistance plasmids circulating in co-endemic Escherichia coli and Klebsiella pneumoniae, indicating recent horizontal gene transfer. Conclusion: This is the first documented outbreak of blaNDM-mediated carbapenem-resistant S. Typhi, highlighting a new stage in the evolution of drug-resistant typhoid. The acquisition of high-risk plasmids by S. Typhi and their integration into successful epidemic lineages underscores the urgent need for strengthened genomic surveillance and inter-species AMR tracking. Our findings have direct implications for treatment guidelines, TCV implementation strategies, and efforts to prevent global dissemination of carbapenem-resistant S. Typhi.