Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children

Riaz, Muhammad; Ahmad, Shabir; Sattar, Fazal; Li, Ganwu; Din, Zia Ud; Ahmad, Sajjad; Azra,; Waheed, Aiman; Ul Haq, Ihtisham; Phelan, Jody E.; Rani, Gulab Fatima; Cabral-Marques, Otavio; Campino, Susana; Khan, Taj Ali; Clark, Taane G.

doi:10.3390/pathogens14100967

Open AccessArticle

Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children

by

Muhammad Riaz

^1,†,

Shabir Ahmad

^1,†,

Fazal Sattar

^2,3

,

Ganwu Li

³,

Zia Ud Din

⁴,

Sajjad Ahmad

⁵,

Azra

⁵,

Aiman Waheed

⁶,

Ihtisham Ul Haq

⁷

,

Jody E. Phelan

⁸,

Gulab Fatima Rani

⁵

,

Otavio Cabral-Marques

^9,10,11,12

,

Susana Campino

⁸,

Taj Ali Khan

^5,13,* and

Taane G. Clark

^8,14,*

¹

Department of Allied Health Sciences, Sarhad University of Science and Information Technology, Peshawar 25000, Pakistan

²

National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad 38000, Punjab, Pakistan

³

Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA

⁴

Department of Pharmacy, Kohat University of Science and Technology, Kohat 26000, Pakistan

⁵

Institute of Pathology and Diagnostic Medicines, Khyber Medical University, Peshawar 25100, Pakistan

⁶

Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar 25120, Pakistan

⁷

Post-Graduate Programme in Innovation in Technology, Federal University of Minas Gerais, Belo Horizonte 30150-240, MG, Brazil

⁸

Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK

⁹

Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil

¹⁰

Laboratory of Medical Investigation 29, Division of Molecular Medicine, Department of Medicine, School of Medicine, University of São Paulo, São Paulo 05508-220, SP, Brazil

¹¹

Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508-220, SP, Brazil

¹²

D’Or Institute for Research and Education (IDOR), São Paulo 01401-002, SP, Brazil

¹³

Public Health Reference Laboratory, Khyber Medical University, Peshawar 25100, Pakistan

¹⁴

Faculty of Epidemiology and Population Health, School of Hygiene and Tropical Medicine, London WC1E 7HT, UK

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^*

Authors to whom correspondence should be addressed.

^†

These authors equally contributed to this work.

Pathogens 2025, 14(10), 967; https://doi.org/10.3390/pathogens14100967

Submission received: 29 August 2025 / Revised: 15 September 2025 / Accepted: 18 September 2025 / Published: 24 September 2025

(This article belongs to the Special Issue Advances in Salmonella Epidemiology and Pathogenesis)

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Abstract

Typhoid fever, caused by Salmonella enterica subsp. enterica serovar Typhi (S. typhi), remains a major public health concern, particularly in low-resource settings with poor sanitation. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains have significantly complicated treatment, especially in vulnerable pediatric populations. This study aimed to characterize the genetic profiles of drug resistance in MDR and XDR S. typhi isolates from pediatric patients. Methods: A cross-sectional study was conducted on 800 blood samples from pediatric typhoid patients. S. typhi isolates were identified using the BacT/ALERT 3D system, followed by culture on MacConkey and blood agar. Antimicrobial susceptibility was assessed using the disk diffusion method according to CLSI 2022 guidelines. Whole-genome sequencing (WGS) was performed on 29 isolates using Illumina MiSeq technology, and resistance genes and mutations were analyzed. Results: Antimicrobial susceptibility testing revealed that 68 (48.57%) of S. typhi isolates were XDR and 61 (43.57%) were MDR, exhibiting widespread resistance to ciprofloxacin, ampicillin, chloramphenicol, ceftriaxone, and co-trimoxazole. WGS identified key resistance genes across all 29 isolates, including bla_CTX-M-15, bla_TEM-1B, qnrS1, aac(6′)-Iaa, catA1, dfraA7, sul1, qacEΔ1, and the gyrA-S83F mutation. Notably, gyrA-S83F and qnrS1 were detected in all isolates and strongly correlated with ciprofloxacin resistance. Virulence genes were consistently present in all isolates, indicating a high pathogenic potential. The IncY plasmid, found in four (14%) isolates, was linked to resistance against third-generation cephalosporins, including ceftriaxone. Conclusion: This study underscores the alarming prevalence of MDR and XDR S. typhi isolates among pediatric patients, driven by resistance genes such as bla_CTX-M-15, bla_TEM-1B, and gyrA-S83F. These findings highlight the urgent need for targeted therapeutic strategies and robust surveillance systems to combat the growing threat of drug-resistant typhoid fever.

Keywords: Salmonella Typhi; antimicrobial resistance; whole-genome sequencing; beta-lactamase genes (blaCTX-M-15; blaTEM-1B); gyrA-S83F mutation; genetic resistome; plasmid-mediated resistance

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MDPI and ACS Style

Riaz, M.; Ahmad, S.; Sattar, F.; Li, G.; Din, Z.U.; Ahmad, S.; Azra; Waheed, A.; Ul Haq, I.; Phelan, J.E.; et al. Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children. Pathogens 2025, 14, 967. https://doi.org/10.3390/pathogens14100967

AMA Style

Riaz M, Ahmad S, Sattar F, Li G, Din ZU, Ahmad S, Azra, Waheed A, Ul Haq I, Phelan JE, et al. Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children. Pathogens. 2025; 14(10):967. https://doi.org/10.3390/pathogens14100967

Chicago/Turabian Style

Riaz, Muhammad, Shabir Ahmad, Fazal Sattar, Ganwu Li, Zia Ud Din, Sajjad Ahmad, Azra, Aiman Waheed, Ihtisham Ul Haq, Jody E. Phelan, and et al. 2025. "Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children" Pathogens 14, no. 10: 967. https://doi.org/10.3390/pathogens14100967

APA Style

Riaz, M., Ahmad, S., Sattar, F., Li, G., Din, Z. U., Ahmad, S., Azra, Waheed, A., Ul Haq, I., Phelan, J. E., Rani, G. F., Cabral-Marques, O., Campino, S., Khan, T. A., & Clark, T. G. (2025). Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children. Pathogens, 14(10), 967. https://doi.org/10.3390/pathogens14100967

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Whole-Genome Sequencing Analysis of Drug-Resistant Salmonella Typhi in Children

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