Comprehensive genome analysis of Mycobacterium avium subsp. paratuberculosis in camels from Saudi Arabia: Molecular epidemiology and antimicrobial resistance

Vet World Vol.18 April-2025 Article-12

Research Article

Veterinary World, 18(4): 859-876

https://doi.org/10.14202/vetworld.2025.859-876

M. Salem^1,2, A. Zaghawa³, F. Housawi¹, Ahmed Elsify³, Mohamed E. Hasan^4,5, Alyaa Elrashedy^3,5, Kazem AlMohammed Salem⁶, Nidhal Ben Amor⁷, and A. Al Naeem¹

1. Department of Clinical Sciences, College of Veterinary Medicine, King Faisal University, Hofuf, Kingdom of Saudi Arabia.
2. Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt.
3. Department of Animal Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Minoufiya, Egypt.
4. Department of Bioinformatics, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt.
5. Department of Health Information Technology , Faculty of Health Science Technology, Borg Al Arab Technological University (BATU), Alexandria, Egypt.
6. Animal Resources Management, Ministry of Environment, Water and Agriculture, Al-Ahsa, Saudi Arabia.
7. Department of Public Health, College of Veterinary Medicine, King Faisal University, Hofuf, Kingdom of Saudi Arabia.

Background and Aim: Paratuberculosis, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is a significant infectious disease affecting livestock, including camels in Saudi Arabia, leading to severe economic losses. Despite its impact, limited genomic studies have been conducted to characterize MAP strains in camels and their antimicrobial resistance (AMR) profiles. This study aimed to (1) characterize the clinical and pathological findings of MAP infections in camels; (2) determine the seroprevalence of MAP in the eastern region of Saudi Arabia; (3) differentiate between MAP strains using polymerase chain reaction (PCR) and bioinformatics tools; (4) conduct a comprehensive genomic analysis; and (5) identify genes associated with AMR, virulence, and immune response.

Materials and Methods: A total of 345 blood samples were collected for seroprevalence analysis using enzyme-linked immunosorbent assay (ELISA), and 68 rectal scraping samples were analyzed using Ziehl–Neelsen staining and PCR for strain differentiation. Seventeen clinical cases underwent clinical, postmortem, and histopathological examinations. Whole-genome sequencing and bioinformatics analyses were performed using the Bacterial and Viral Bioinformatics Resource Center to identify genetic variations, AMR genes, and phylogenetic relationships among MAP isolates.

Results: Clinical findings revealed progressive emaciation and chronic diarrhea in affected camels. Gross examination showed intestinal wall thickening and mesenteric lymph node congestion. Histopathological analysis indicated hyperactivation of crypts of Lieberkühn and mononuclear cell infiltration. PCR analysis identified a higher prevalence of the sheep (S) strain (162 bp) compared to the cattle (C) strain (310 bp). The overall seroprevalence of MAP was 8.11% (ELISA). Whole-genome sequencing identified 34 AMR genes and 10 virulence genes, with annotation revealing 4.7 million base pairs, coding sequences, transfer RNA, ribosomal RNA, and pseudogenes. Phylogenetic analysis grouped MAP strains into four distinct clades, indicating potential cross-species transmission.

Conclusion: This study provides critical insights into the genetic diversity and AMR mechanisms of MAP strains in camels, emphasizing the need for targeted control strategies. The findings highlight potential zoonotic risks and inform future vaccine development to mitigate MAP infections in livestock.

Keywords: antimicrobial resistance, camel health, Mycobacterium avium subsp. paratuberculosis, phylogenetics, Saudi Arabia, whole-genome sequencing.

How to cite this article: Salem M, Zaghawa A, Housawi F, Elsify A, Hasan ME, Elrashedy A, Salem KA, Amor NB, and Al Naeem A (2025) Comprehensive genome analysis of Mycobacterium avium subsp. paratuberculosis in camels from Saudi Arabia: Molecular epidemiology and antimicrobial resistance, Veterinary World, 18(4): 859-876.

Received: 27-10-2024 Accepted: 12-03-2025 Published online: 19-04-2025

Corresponding author: Ahmed Elsify E-mail: ahmedelsify@gmail.com

DOI: 10.14202/vetworld.2025.859-876

Copyright: Salem, et al. This article is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http:// creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.