Pantoea agglomerans strain:IV Genome sequencing and assembly. Pantoea agglomerans strain:IV

A detailed understanding of antimicrobial resistance trends among human-related environments is key to combat global health threats. Until now, the resistome is little considered in food science. Here we studied the apple microbiome and resistome from different cultivars and origin by metagenomics approaches, genome reconstruction and isolate sequencing. All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs). They are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low. 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. Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and highlight the need for surveillance of resistance emergence along complex food chains to ensure food quality and safety.

深入了解与人类相关环境中的抗菌素耐药性流行趋势，是应对全球健康威胁的关键所在。迄今为止，食品科学领域极少关注耐药组（resistome）研究。本研究依托宏基因组学、基因组重建以及分离株测序技术，对不同品种与产地的苹果微生物组及耐药组展开分析。所有受试苹果均携带一套本土性、多样性的耐药组，共包含132个抗菌素耐药基因（antimicrobial resistance genes, ARGs）。这些耐药基因部分与临床相关，且由质粒编码；但在宏基因组中，其丰度极低。采收后经过洲际运输，苹果微生物组与耐药组均发生显著变化，且该变化与苹果品种无关。相较于新鲜苹果，采收后的苹果微生物组以更高丰度的肠杆菌目（Enterobacteriales）以及更为多样的耐药基因库为特征。本研究揭示了苹果中固有的且可能获得性的抗菌素耐药性，同时强调需对复杂食品链中的耐药性出现情况开展监测，以保障食品质量与安全。