Genomic perspectives on NDM Salmonella Typhi, and a case report from India
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Updated: May 13, 2025
Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples
Published on: October 25, 2018
Shruthi Vasanthaiah1,2, Pritibala Takey3, Prasanna Kumar Selvam4,5
1Manipal Academy of Higher Education (MAHE), Manipal, India. shruthi_vasanthaiah@ibioinformatics.org.
Background:
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.
Case Presentation:
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.
Discussion And Conclusion:
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.
Insights
This study reports the first case of New Delhi Metallo-β-lactamase (NDM)-producing Salmonella Typhi in India. This multidrug-resistant strain highlights the urgent need for genomic surveillance to track its spread and inform treatment strategies.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- Carbapenem resistance in Enterobacterales is a significant global health threat.
- New Delhi Metallo-β-lactamase (NDM) is a key carbapenemase enzyme driving resistance.
- NDM-producing Salmonella Typhi infections are rare but concerning.
Purpose of the Study:
- To report the first case of NDM-producing Salmonella Typhi in India.
- To characterize the genetic basis of resistance in the identified strain.
- To emphasize the public health implications of this multidrug-resistant pathogen.
Main Methods:
- Clinical case presentation of an 11-year-old boy with febrile illness.
- Bacterial identification and antimicrobial susceptibility testing (Vitek ID/AST).
- Whole-genome sequencing (Illumina) for resistance gene identification and phylogenetic analysis.
Main Results:
- An isolate of Salmonella Typhi identified with resistance to multiple antibiotics, including meropenem.
- Whole-genome sequencing revealed the presence of blaNDM-5 and a fluoroquinolone resistance mutation (gyrAS83Y).
- Phylogenetic analysis placed the isolate within the H58 haplotype, common in India.
Conclusions:
- This is the first documented case of NDM-producing Salmonella Typhi in India.
- The multidrug-resistant NDM-5-producing S. Typhi poses a significant clinical and public health risk.
- Ongoing genomic surveillance is essential for monitoring and controlling the spread of such resistant strains.
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