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<p>Unsafe food remains a major public health and economic burden, particularly in developing countries. Previous genomic studies have shown that pork industrialization in developed countries has facilitated the international spread of <i>Salmonella</i>, yet the contribution of downstream stages of pork supply chains in developing countries remains unclear. Here, we integrated 591,687 public <i>S</i>. enterica genomes, including 114,042 genomes from humans and 15,094 genomes from swine, with prospective sampling and culturing of 1114 samples along a pork supply chain in Guangdong, China, yielding 368 <i>Salmonella</i> isolates. Analyses of public genomes showed that <i>S</i>. 4,[5],12:i:- ST34 was a prominent lineage associated with both humans and swine and carried elevated burdens of antimicrobial and metal resistance genes, particularly among genomes from developing countries. Field sampling identified increasing <i>Salmonella</i> isolation rates from farms to slaughterhouses and retail markets, with <i>S</i>. 4,[5],12:i:- concentrated in slaughterhouse and market isolates and accompanied by higher resistance gene burdens and mobile resistance markers. Phylodynamic, Bayesian stochastic search variable selection (BSSVS), generalized linear model (GLM), and machine-learning analyses further associated ST34 dissemination with swine-related sources, pork production, and resistome features. Together, these findings indicate that downstream stages of pork supply chains in developing countries are important hotspots for antimicrobial resistant <i>S</i>. 4,[5],12:i:- ST34 and support targeted surveillance and intervention beyond control at the farm stage.</p>

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Developing countries’ downstream pork supply chains shape the evolution of resistance and the spread of Salmonella 4,[5],12:i:- ST34

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年7月29日

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  • Junhao Peng,
  • Zhong Peng,
  • Qiqi Hong,
  • Zixin Xu,
  • Canji Wu,
  • Jinger Chen,
  • Yudi Wu,
  • Renhang Xiao,
  • Qijie Lin,
  • Kaifeng Chen,
  • Jiayi Li,
  • Chenggang Xu,
  • Ming Liao,
  • Jianmin Zhang

摘要

Unsafe food remains a major public health and economic burden, particularly in developing countries. Previous genomic studies have shown that pork industrialization in developed countries has facilitated the international spread of Salmonella, yet the contribution of downstream stages of pork supply chains in developing countries remains unclear. Here, we integrated 591,687 public S. enterica genomes, including 114,042 genomes from humans and 15,094 genomes from swine, with prospective sampling and culturing of 1114 samples along a pork supply chain in Guangdong, China, yielding 368 Salmonella isolates. Analyses of public genomes showed that S. 4,[5],12:i:- ST34 was a prominent lineage associated with both humans and swine and carried elevated burdens of antimicrobial and metal resistance genes, particularly among genomes from developing countries. Field sampling identified increasing Salmonella isolation rates from farms to slaughterhouses and retail markets, with S. 4,[5],12:i:- concentrated in slaughterhouse and market isolates and accompanied by higher resistance gene burdens and mobile resistance markers. Phylodynamic, Bayesian stochastic search variable selection (BSSVS), generalized linear model (GLM), and machine-learning analyses further associated ST34 dissemination with swine-related sources, pork production, and resistome features. Together, these findings indicate that downstream stages of pork supply chains in developing countries are important hotspots for antimicrobial resistant S. 4,[5],12:i:- ST34 and support targeted surveillance and intervention beyond control at the farm stage.