Reservoirs of antimicrobial resistance genes in retail raw milk

Authors: LIU, JINXIN - University Of California, Davis; ZHU, YUANTING - University Of California, Davis; JAY-RUSSELL, MICHELE - University Of California, Davis; Lemay, Danielle; MILLS, DAVID - University Of California, Davis

Submitted to: Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/10/2020
Publication Date: 6/26/2020
Citation: Liu, J., Zhu, Y., Jay-Russell, M., Lemay, D.G., Mills, D.A. 2020. Reservoirs of antimicrobial resistance genes in retail raw milk. Microbiome. 8(99). https://doi.org/10.1186/s40168-020-00861-6.
DOI: https://doi.org/10.1186/s40168-020-00861-6

Interpretive Summary: An increasing number of people in the U.S. are consuming unpasteurized (raw) milk. Consumption of raw milk is a known risk factor for foodborne illness. However, retail milk has not yet been widely screened for foodborne illnesses using modern techniques. Using established culture-based techniques as well as modern sequencing technologies, 2034 samples of retail milk, with different degrees of heat treatment, were analyzed from 5 states in the USA. Raw milk samples had the highest prevalence of viable bacteria and their microbiota was distinct from other types of milk. While it is often implied that raw milk will grow lactic acid bacteria when naturally fermented, experiments with room temperature incubation of these milk samples demonstrated that was seldom true. Furthermore, retail raw milk samples had a higher prevalence of antimicrobial resistance genes than pasteurized milk. The antimicrobial resistance genes in raw milk differed by geographic location, likely due to regionally-distinct milk microbiota. This work suggests that in addition to being a potential source of foodborne pathogens, raw milk is also a likely reservoir of antimicrobial resistance genes.

Technical Abstract: The most recent CDC survey of 2006/2007 estimated that 3% of the U.S. population consumes unpasteurized (raw) milk and the demand of raw milk has expanded by at least 357% since then. However, consumption of raw milk can cause foodborne illness, especially in those with compromised immunity due age, disability or pharmacologic treatment. This long history of microbial contamination of humans via their foods implies that raw foods such as unpasteurized milk, in particular room temperature (RT)-fermented milk, could be a source of bacteria containing potentially exchangeable antimicrobial resistance genes (ARGs). Using complementary culture-based, 16S rRNA and metagenomic sequencing techniques, we analyzed 2,034 retail milk samples (Raw, Vat, HTST and UHT) from 5 states in the USA. Raw milk samples had the highest prevalence of viable bacteria and their microbiota was distinct from other types of milk. Pseudomonadaceae dominated raw milk with limited contents of lactic acid bacteria. RT-fermentation dramatically enriched the bacterial populations that were present in raw milk samples and, in parallel, the diversity and abundance of ARGs increased significantly. The RT-enriched resistome differed in raw milk from distinct geographic locations, a difference likely associated with regionally-distinct milk microbiota. Finally, milk samples stored at 4°C remained stable with respect to their microbiota exhibiting a constant bacterial population. Hence, in addition to being a documented source of foodborne pathogens, raw milk also serves as a potential reservoir of ARGs.