Unravelling the genetic threads: Comparative genomic analysis of Salmonella from food and clinical cases in England, 2015–2019

IF 7 1区农林科学 Q1 FOOD SCIENCE & TECHNOLOGY

Food Control Pub Date : 2026-05-01 Epub Date: 2025-12-17 DOI:10.1016/j.foodcont.2025.111928

Beata Orzechowska , Jim McLauchlin , Caroline Willis , Frieda Jorgensen , Anaïs Painset , Sandra Lai , Heather Aird , Amina Ismail Ahmed , Marie Anne Chattaway

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Abstract

Despite advances in Salmonella testing, surveillance, and improved food safety practices, salmonellosis remains prevalent in the UK. The primary challenge of preventing infections is determining how to ensure that food safety management plans are effective and to prioritise food sampling activities before the outbreaks occur.

In this genomic study, we assessed the relative contribution of various foods over a five-year period to cases of human salmonellosis in England, aiming to rank the associated food risks based on genetic similarity. To achieve this, we conducted a comparative genomic analysis of Salmonella recovered from food (802) and environmental samples (131) against routinely tested Salmonella isolates from clinical cases (37,673) between 2015 and 2019.

The analysis revealed that of all Salmonella-positive food and environmental isolates, 19.7 % were genetically related to Salmonella from clinical cases. A significant portion of these isolates was collected due to reactive sampling, which occurs in response to recognised public health concerns. In terms of Salmonella from clinical cases, only 2.5 % were genetically similar to isolates from food and 2.6 % from the environment. This relatively low rate of similarity may be due to other infection pathways, such as travel-related exposure or contact with animals, as well as infection from food items that are not subject to regular microbiological testing by public health bodies in the UK.

We found that isolates from food products of animal origin, specifically eggs and poultry, were genetically linked to a higher number of isolates from clinical cases compared to non-animal origin products or composite foods, potentially indicating a greater public health risk. Meanwhile, non-animal origin foods were mostly associated with sporadic cases or clusters of fewer than five cases that had not previously been identified.

The findings from this study underscore the need to shift from primarily reactive to additional proactive, risk-based food testing to better mitigate foodborne hazards and reduce the potential for outbreaks. While our genomic approach offers a valuable method for ranking food-related risks through genetic linkages, it does not replace the need for integrated epidemiological analysis. Such data are essential for understanding exposure pathways and quantifying foodborne risks, but were beyond the scope of this study. Nevertheless, the proposed genomic framework has the potential to inform future microbiological risk assessments, guide prioritisation of food sampling activities, support outbreak investigations, and contribute to the development of genomics-based public health interventions.

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解开遗传线索：2015-2019年英国食物和临床病例中沙门氏菌的比较基因组分析

尽管在沙门氏菌检测、监测和改进食品安全措施方面取得了进展，但沙门氏菌病在英国仍然普遍存在。预防感染的主要挑战是确定如何确保食品安全管理计划有效，并在疫情发生之前确定食品抽样活动的优先次序。在这项基因组研究中，我们评估了在英国五年内各种食物对人类沙门氏菌病病例的相对贡献，旨在根据遗传相似性对相关食物风险进行排名。为了实现这一目标，我们对2015年至2019年间从食物（802）和环境样本（131）中回收的沙门氏菌与从临床病例（37,673）中常规检测的沙门氏菌分离物进行了比较基因组分析。分析显示，在所有沙门氏菌阳性的食物和环境分离株中，19.7%与临床病例中的沙门氏菌有遗传关系。这些分离物的很大一部分是由于反应性取样而收集的，这种取样是为了响应公认的公共卫生问题而进行的。在临床病例中，只有2.5%的沙门氏菌与来自食物的分离株基因相似，2.6%来自环境。这种相对较低的相似性可能是由于其他感染途径，例如与旅行有关的暴露或与动物接触，以及来自英国公共卫生机构未定期进行微生物检测的食品的感染。我们发现，与非动物源性食品或复合食品相比，来自动物源性食品（特别是蛋和家禽）的分离株与临床病例中更多的分离株存在遗传关联，这可能表明存在更大的公共卫生风险。与此同时，非动物源性食品大多与以前未发现的散发性病例或少于5例的聚集性病例有关。这项研究的结果强调，需要从主要的反应性检测转向额外的主动的、基于风险的食品检测，以更好地减轻食源性危害并减少暴发的可能性。虽然我们的基因组方法为通过遗传联系对食物相关风险进行排序提供了一种有价值的方法，但它并不能取代对综合流行病学分析的需求。这些数据对于了解暴露途径和量化食源性风险至关重要，但超出了本研究的范围。然而，拟议的基因组框架有可能为未来的微生物风险评估提供信息，指导确定食品抽样活动的优先次序，支持疫情调查，并有助于制定基于基因组学的公共卫生干预措施。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Food Control 工程技术-食品科技

CiteScore

12.20

自引率

6.70%

发文量

758

审稿时长

33 days

期刊介绍： Food Control is an international journal that provides essential information for those involved in food safety and process control. Food Control covers the below areas that relate to food process control or to food safety of human foods: • Microbial food safety and antimicrobial systems • Mycotoxins • Hazard analysis, HACCP and food safety objectives • Risk assessment, including microbial and chemical hazards • Quality assurance • Good manufacturing practices • Food process systems design and control • Food Packaging technology and materials in contact with foods • Rapid methods of analysis and detection, including sensor technology • Codes of practice, legislation and international harmonization • Consumer issues • Education, training and research needs. The scope of Food Control is comprehensive and includes original research papers, authoritative reviews, short communications, comment articles that report on new developments in food control, and position papers.