摘要
出身背景
详细了解所有人类相关环境中的抗微生物耐药性趋势是应对全球健康威胁的关键。然而，在食品科学中，抵抗力仍然很少被考虑。在这里，我们通过宏基因组方法、基因组重建和分离测序，研究了不同品种（Royal Gala和Braeburn）和来源（在南非新鲜收获和在奥地利超市出口的苹果）的苹果微生物组和抗性。
后果
所有的水果都含有一个本土的、多功能的耐药组，由132个编码19种不同抗生素类别的抗微生物耐药性基因（ARGs）组成。ARGs部分具有临床相关性并且是质粒编码的；然而，它们在宏基因组中的丰度非常低（≤ 0.03%）。收获后，经过洲际运输，苹果的微生物组和抗性组发生了显著变化，与品种无关。与新鲜苹果相比，收获后的微生物组的特征是肠杆菌类丰度更高，ARGs库更多样化，尤其与多药耐药性以及喹诺酮类、利福平、磷霉素和氨基糖苷类耐药性有关。ARGs与宏基因组组装基因组（MAGs）的关联表明微生物组内的抗性相互联系。γ-变形菌门、α-变形菌和放线菌门的细菌分离株是积极具有多药耐药性的代表，基因组测序证实了ARGs。
结论
我们的研究结果揭示了苹果内在的和潜在的获得性抗微生物耐药性，并加强了所有植物微生物群都具有不同耐药性特征的论点。尽管苹果抗性似乎相对不明显，但我们将储存和运输确定为在全球分布AMR的潜在风险参数，并强调需要监测复杂食物链中抗性的出现。
Abstract
Background
A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing.

Results
All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing.

Conclusion
Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.

https://environmentalmicrobiome.biomedcentral.com/articles/10.1186/s40793-022-00402-8