Prevalence, antimicrobial resistance and genomic comparison of non-typhoidal salmonella isolated from pig farms with different levels of intensification in Yangon Region, Myanmar

• Published in: PloS one Vol. 19; no. 9; p. e0307868
• Main Authors: Trung, Nguyen Vinh, Zaw Moe, Aung, May Than, Hlaing, Bich Chieu, Tran Thi, Mukarram Hossain, A S Md, Trung Thanh, Nguyen, Yen, Huynh Xuan, Yen, Phung Le Kim, Nghia, Nguyen Huu, Murray, Gemma G R, Su Wai, Thiri, Thein Maw, Min, Myint, Hnin Thidar, Win, Ye Tun, Wood, James, Thwaites, Guy, Maskell, Duncan J, Tucker, Alexander W, Hoa, Ngo Thi
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 19.09.2024
• Subjects: Agricultural practices; Analysis; Animal production; Animals; Anti-Bacterial Agents - pharmacology; Antimicrobial agents; Antimicrobial resistance; Biology and Life Sciences; Care and treatment; Developing countries; Diagnosis; Diseases; Drug resistance; Drug resistance in microorganisms; Drug Resistance, Multiple, Bacterial - genetics; Farming; Farms; Gene sequencing; Genes; Genome, Bacterial; Genomes; Genomics; Infections; Intensive farming; Laboratories; LDCs; Medicine and Health Sciences; Microbial Sensitivity Tests; Multidrug resistance; Myanmar - epidemiology; People and Places; Prevalence; Prevention; Risk factors; Salmonella; Salmonella - drug effects; Salmonella - genetics; Salmonella - isolation & purification; Salmonella Infections, Animal - epidemiology; Salmonella Infections, Animal - microbiology; Salmonellosis; Sus scrofa domesticus; Swine; Swine - microbiology; Swine Diseases - epidemiology; Swine Diseases - microbiology; Toxins; Typhoid; Virulence; Virulence (Microbiology); Whole Genome Sequencing; Zoonoses; Myanmar; Vietnam; United Kingdom > UK; United States > US; Myanmar (Burma)
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0307868

In Myanmar, where backyard, semi-intensive, and intensive pig (Sus scrofa domesticus) farming coexist, there is limited understanding of the zoonotic risks and antimicrobial resistance (AMR) associated with these farming practices. This study was conducted to investigate the prevalence, AMR and genomic features of Salmonella in pig farms in the Yangon region and the impact of farm intensification to provide evidence to support risk-based future management approaches. Twenty-three farms with different production scales were sampled for two periods with three sampling-visit each. Antimicrobial susceptibility tests and whole-genome sequencing were performed on the isolates. The prevalence of Salmonella was 44.5% in samples collected from backyard farms, followed by intensive (39.5%) and semi-intensive farms (19.5%). The prevalence of multi-drug resistant isolates from intensive farms (45/84, 53.6%) was higher than those from backyard (32/171, 18.7%) and semi-intensive farms (25/161, 15.5%). Among 28 different serovars identified, S. Weltevreden (40; 14.5%), S. Kentucky (38; 13.8%), S. Stanley (35, 12.7%), S. Typhimurium (22; 8.0%) and S. Brancaster (20; 7.3%) were the most prevalent serovars and accounted for 56.3% of the genome sequenced strains. The diversity of Salmonella serovars was highest in semi-intensive and backyard farms (21 and 19 different serovars, respectively). The high prevalence of globally emerging S. Kentucky ST198 was detected on backyard farms. The invasive-infection linked typhoid-toxin gene (cdtB) was found in the backyard farm isolated S. Typhimurium, relatively enriched in virulence and AMR genes, presented an important target for future surveillance. While intensification, in terms of semi-intensive versus backyard production, maybe a mitigator for zoonotic risk through a lower prevalence of Salmonella, intensive production appears to enhance AMR-associated risks. Therefore, it remains crucial to closely monitor the AMR and virulence potential of this pathogen at all scales of production. The results underscored the complex relationship between intensification of animal production and the prevalence, diversity and AMR of Salmonella from pig farms in Myanmar.