Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France.

IF 3.7 2区 生物学 Q2 MICROBIOLOGY Microbiology spectrum Pub Date : 2024-11-08 DOI:10.1128/spectrum.00526-24
Madeleine De Sousa Violante, Carole Feurer, Valérie Michel, Karol Romero, Ludovic Mallet, Michel-Yves Mistou, Sabrina Cadel-Six
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Abstract

Salmonella Typhimurium and its monophasic variant (Salmonella 4,[5],12:i:-) are among the most prevalent serovars worldwide. Even though these serovars have been the focus of many studies, their spread has not yet been investigated in French pig herds and slaughterhouses at a regional scale. Here, we characterized the genomic diversity of 188 Salmonella strains belonging to sequence type (ST) 19 and 34. These strains were isolated from pigs in metropolitan France between 2014 and 2019. Samples were collected from 10 regions, three of which together represent 75% of French pig production in 2020. To contextualize the French Salmonella genomes at a worldwide level, 193 ST 34 genomes from three continents and 14 countries were also included. This study revealed little diversity in ST 34 strains circulating in France, suggesting that one or two clones are spreading within pig herds and slaughterhouses. In silico virulence and antimicrobial resistance genes were investigated to understand the prevalence of these strains among farmed pigs and in the slaughterhouse environment. A comparison with ST 34 isolates from other countries highlighted the genomic specificity of the ST 34 monophasic variants in France, with some exceptions concerning isolates from bordering countries. This work provides new insights into the dynamics of S. Typhimurium and its monophasic variant sampled in French pig herds and slaughterhouses.

Importance: Salmonellosis is a leading cause of bacterial infection in humans and animals around the world. This study provides a snapshot of the genomic diversity of one of the most prevalent Salmonella serovars (Salmonella Typhimurium and Salmonella 4,[5],12:i:-) circulating on French pig farms between 2013 and 2021. We investigated the link between geographical and genomic diversity. The analyses revealed little diversity of the strains, suggesting that one or two clones are spreading within French pig herds. We also in silico screened genetic elements that could explain the prevalence of these strains among farmed pigs and in the slaughterhouse environment. Finally, the comparison with isolates from other countries highlighted the genomic specificity of these two French sequence type 34 clones. This work provides new insights into the dynamics of S. Typhimurium and S. 4,[5],12:i:- sampled from pig herds and slaughterhouses in France, thus laying the foundations for future analyses.

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法国猪和猪肉生产中的鼠伤寒沙门氏菌及其单相变种的基因组多样性。
鼠伤寒沙门氏菌及其单相变种(沙门氏菌 4,[5],12:i:-)是全球最常见的血清型之一。尽管这些血清型一直是许多研究的重点,但它们在法国猪群和屠宰场中的传播尚未在区域范围内进行调查。在此,我们对属于序列类型(ST)19 和 34 的 188 株沙门氏菌进行了基因组多样性鉴定。这些菌株是在 2014 年至 2019 年期间从法国本土的猪群中分离出来的。样本采集自 10 个地区,其中三个地区的生猪产量占 2020 年法国生猪产量的 75%。为了将法国沙门氏菌基因组与全球水平联系起来,还纳入了来自三大洲和 14 个国家的 193 个 ST 34 基因组。这项研究发现,在法国流通的 ST 34 菌株几乎没有多样性,这表明有一两个克隆正在猪群和屠宰场中传播。为了了解这些菌株在养猪场和屠宰场环境中的流行情况,我们对硅毒力和抗菌药耐药性基因进行了研究。与其他国家的 ST 34 分离物进行比较后发现,法国的 ST 34 单相变异株具有基因组特异性,但来自邻国的分离物除外。这项研究为了解在法国猪群和屠宰场采样的鼠伤寒沙门氏菌及其单相变异株的动态提供了新的视角:重要意义:沙门氏菌病是全球人类和动物细菌感染的主要原因。本研究提供了 2013 年至 2021 年间在法国养猪场流行的沙门氏菌血清型之一(鼠伤寒沙门氏菌和沙门氏菌 4,[5],12:i:-)的基因组多样性快照。我们研究了地理多样性与基因组多样性之间的联系。分析结果表明,菌株的多样性很少,这表明有一两个克隆在法国猪群中传播。我们还对可解释这些菌株在养殖猪群和屠宰场环境中流行的遗传因子进行了硅筛选。最后,通过与其他国家的分离株进行比较,我们发现了这两个法国序列 34 型克隆的基因组特异性。这项工作为了解从法国猪群和屠宰场采样的鼠伤寒沙门氏菌和鼠伤寒沙门氏菌 4,[5],12:i:-的动态提供了新的视角,从而为今后的分析奠定了基础。
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来源期刊
Microbiology spectrum
Microbiology spectrum Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.20
自引率
5.40%
发文量
1800
期刊介绍: Microbiology Spectrum publishes commissioned review articles on topics in microbiology representing ten content areas: Archaea; Food Microbiology; Bacterial Genetics, Cell Biology, and Physiology; Clinical Microbiology; Environmental Microbiology and Ecology; Eukaryotic Microbes; Genomics, Computational, and Synthetic Microbiology; Immunology; Pathogenesis; and Virology. Reviews are interrelated, with each review linking to other related content. A large board of Microbiology Spectrum editors aids in the development of topics for potential reviews and in the identification of an editor, or editors, who shepherd each collection.
期刊最新文献
Analysis of Newcastle disease virus prevalence in wild birds reveals interhost transmission of genotype VI strains. Genomic diversity of Salmonella Typhimurium and its monophasic variant in pig and pork production in France. Impact of the elderly lung mucosa on Mycobacterium tuberculosis transcriptional adaptation during infection of alveolar epithelial cells. Investigating the changing taxonomy and antimicrobial resistance of bacteria isolated from door handles in a new infectious disease ward pre- and post-patient admittance. Metagenomic next-generation sequencing of osteoarticular tissue for the diagnosis of suspected osteoarticular tuberculosis.
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