Spontaneous Emergence of Azithromycin Resistance in Independent Lineages of Salmonella Typhi in Northern India

Megan E. Carey, Ruby Jain, Mohammad Yousuf, Mailis Maes, Zoe A. Dyson, Trang Nguyen Hoang Thu, To Nguyen Thi Nguyen, Thanh Ho Ngoc Dan, Quynh Nhu Pham Nguyen, Jaspreet Mahindroo, Duy Thanh Pham, Kawaljeet Singh Sandha, Stephen Baker, Neelam Taneja

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BACKGROUND: The emergence and spread of antimicrobial resistance (AMR) pose a major threat to the effective treatment and control of typhoid fever. The ongoing outbreak of extensively drug-resistant Salmonella Typhi (S. Typhi) in Pakistan has left azithromycin as the only remaining broadly efficacious oral antimicrobial for typhoid in South Asia. Ominously, azithromycin-resistant S. Typhi organisms have been subsequently reported in Bangladesh, Pakistan, and Nepal. METHODS: Here, we aimed to understand the molecular basis of AMR in 66 S. Typhi organisms isolated in a cross-sectional study performed in a suburb of Chandigarh in Northern India using whole-genome sequencing and phylogenetic analysis. RESULTS: We identified 7 S. Typhi organisms with the R717Q mutation in the acrB gene that was recently found to confer resistance to azithromycin in Bangladesh. Six out of the seven azithromycin-resistant S. Typhi isolates also exhibited triple mutations in gyrA (S83F and D87N) and parC (S80I) genes and were resistant to ciprofloxacin. These contemporary ciprofloxacin/azithromycin-resistant isolates were phylogenetically distinct from each other and from those reported from Bangladesh, Pakistan, and Nepal. CONCLUSIONS: The independent emergence of azithromycin-resistant typhoid in Northern India reflects an emerging broader problem across South Asia and illustrates the urgent need for the introduction of typhoid conjugate vaccines in the region.

Original languageEnglish
Pages (from-to)e120-e127
Number of pages8
JournalClinical Infectious Diseases
Issue number5
Publication statusPublished - 1 Mar 2021


  • Salmonella Typhi
  • antimicrobial resistance
  • azithromycin resistance
  • India
  • typhoid fever

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