It has been estimated that at least 3% of the USA population consumes unpasteurized (raw) milk from animal sources, and the demand to legalize raw milk sales continues to increase. However, consumption of raw milk can cause foodborne illness and be a source of bacteria containing transferrable antimicrobial resistance genes (ARGs). To obtain a comprehensive understanding of the microbiome and antibiotic resistome in both raw and processed milk, we systematically analyzed 2034 retail milk samples including unpasteurized milk and pasteurized milk via vat pasteurization, high-temperature-short-time pasteurization, and ultra-pasteurization from the United States using complementary culture-based, 16S rRNA gene, and metagenomic sequencing techniques. Raw milk samples had the highest prevalence of viable bacteria which were measured as all aerobic bacteria, coliform, and Escherichia coli counts, and their microbiota was distinct from other types of milk. 16S rRNA gene sequencing revealed that Pseudomonadaceae dominated raw milk with limited levels of lactic acid bacteria. Among all milk samples, the microbiota remained stable with constant bacterial populations when stored at 4 °C. In contrast, storage at room temperature dramatically enriched the bacterial populations present in raw milk samples and, in parallel, significantly increased the richness and abundance of ARGs. Metagenomic sequencing indicated raw milk possessed dramatically more ARGs than pasteurized milk, and a conjugation assay documented the active transfer of blaCMY-2, one ceftazidime resistance gene present in raw milk-borne E. coli, across bacterial species. The room temperature-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally distinct milk microbiota. Despite advertised “probiotic” effects, our results indicate that raw milk microbiota has minimal lactic acid bacteria. In addition, retail raw milk serves as a reservoir of ARGs, populations of which are readily amplified by spontaneous fermentation. There is an increased need to understand potential food safety risks from improper transportation and storage of raw milk with regard to ARGs.

中文翻译：

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零售原奶中抗菌素耐药性基因库。


据估计，至少 3% 的美国人口食用未经高温消毒的动物源（生）奶，并且生奶销售合法化的需求持续增加。然而，食用生奶可能会导致食源性疾病，并成为含有可转移抗菌素耐药基因 (ARG) 的细菌的来源。为了全面了解原奶和加工奶中的微生物组和抗生素耐药性，我们系统分析了 2034 个零售牛奶样品，包括未经巴氏灭菌的牛奶和经过大桶巴氏灭菌、高温短时巴氏灭菌和超巴氏灭菌的巴氏灭菌奶。美国使用基于互补培养的16S rRNA基因和宏基因组测序技术。生牛奶样品中活细菌的存在率最高，以所有需氧细菌、大肠菌群和大肠杆菌计数进行测量，并且其微生物群与其他类型的牛奶不同。 16S rRNA基因测序显示，原奶中以假单胞菌科为主，乳酸菌含量有限。在所有牛奶样品中，在 4 °C 下储存时，微生物群保持稳定，细菌数量恒定。相比之下，室温储存极大地丰富了原奶样品中的细菌种群，同时显着增加了 ARG 的丰富度和丰度。宏基因组测序表明，生奶比巴氏灭菌奶拥有更多的 ARG，并且结合测定记录了 blaCMY-2（生奶传播的大肠杆菌中存在的一种头孢他啶抗性基因）跨细菌物种的主动转移。 来自不同地理位置的原奶中室温富集的抗性组有所不同，这种差异可能与区域不同的牛奶微生物群有关。尽管广告宣传有“益生菌”作用，但我们的结果表明，生奶微生物群中的乳酸菌含量极少。此外，零售原奶可作为 ARG 的储存库，其数量很容易通过自然发酵而扩增。人们越来越需要了解与 ARG 相关的原奶运输和储存不当所带来的潜在食品安全风险。