Genomic perspectives on NDM Salmonella Typhi, and a case report from India

Carbapenem resistance in Enterobacterales is a growing public health concern, primarily driven by carbapenemase enzymes such as OXA-48, VIM, NDM, and IMP. Among these, New Delhi Metallo-β-lactamase (NDM) has disseminated widely across various Enterobacterales species, including Salmonella Typhi, though reports remain rare.

We report an 11-year-old boy from Bangalore with a 10-day history of high-grade fever, chills, rigors, and cough. Laboratory investigations revealed elevated CRP, normal CBC, and microcytic hypochromic anemia. A respiratory panel detected Human Rhinovirus/ Enterovirus. Blood cultures grew non-lactose fermenting gram-negative bacilli, identified as Salmonella spp. via Vitek ID/AST. The isolate exhibited resistance to ampicillin, ciprofloxacin, ceftriaxone, tetracycline, and meropenem but remained susceptible to azithromycin, chloramphenicol, and Co-trimoxazole. Serotyping confirmed the serotype as Salmonella Typhi. Whole-genome sequencing (Illumina) revealed blaNDM-5 and aac(6')-Ia, InCX3 plasmid, and the fluoroquinolone resistance-associated gyrAS83Y mutation. Phylogenetic analysis placed the isolate (IOB-SWH-01) within a cluster of recently sequenced S. Typhi strains from India belonging to the H58 haplotype.

To date, NDM-producing S. Typhi has been reported only once, from Pakistan. This is the first documented case in India. The presence of blaNDM-5 in S. Typhi poses a serious clinical and public health threat, given its multidrug-resistant nature and potential for interspecies transmission. Continued genomic surveillance is crucial to monitor its spread and guide treatment strategies.