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

## TL;DR

This study analyzes the genome of Mycobacterium avium subsp. paratuberculosis in Saudi Arabian camels, revealing genetic diversity and antimicrobial resistance genes.

## Contribution

The study provides the first comprehensive genomic analysis of MAP in camels, identifying AMR and virulence genes and phylogenetic clades.

## Key findings

- MAP sheep (S) strain was more prevalent than cattle (C) strain in camel samples.
- Whole-genome sequencing identified 34 antimicrobial resistance genes and 10 virulence genes in MAP isolates.
- Phylogenetic analysis grouped MAP strains into four clades, suggesting cross-species transmission potential.

## Abstract

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.

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.

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.

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.