Differences in the microbial community and resistome structures of feces from pre-weaned calves and lactating dairy cows

Authors: Haley, Bradd; KIM, SEON WOO - US Department Of Agriculture (USDA); Salaheen, Serajus; HOVINGH, ERNEST - Pennsylvania State University; Van Kessel, Jo Ann

Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/29/2020
Publication Date: 3/13/2020
Citation: Haley, B.J., Kim, S., Salaheen, S., Hovingh, E., Van Kessel, J.S. 2020. Differences in the microbial community and resistome structures of feces from pre-weaned calves and lactating dairy cows. Foodborne Pathogens and Disease. https://doi.org/10.1089/fpd.2019.2768.
DOI: https://doi.org/10.1089/fpd.2019.2768

Interpretive Summary: Antibiotic resistance has become a major public health concern and food animal production systems have been implicated as a source of antibiotic-resistant bacteria, or the genetic resistance elements, that impact humans. However, the ecology of resistant bacteria in farm systems, such as dairy farms, is not completely understood. Our purpose was to study the bacterial communities in the feces of animals from two different age groups on dairy farms. Pre-weaned dairy calves and lactating dairy cows are both known reservoirs of antibiotic-resistant Escherichia coli, but the calves have been shown to have a more concentrated population of resistant bacteria with respect to the total population of Escherichia coli than the cows. To further understand the differences in the microbial communities and the resistomes (genetic elements that impart resistance) between the two animal groups, we sequenced the metagenomes (total bacterial DNA) of fecal composite samples from pre-weaned dairy calves and lactating dairy cows on 17 farms (34 samples in total). There were significant differences in the structures of the microbial communities and resistomes between the two age groups. The same bacterial phyla (groups) were the predominant members of both communities, but when the groups were compared, two phyla (Bacteroidetes and Verrumicrobia) were significantly more abundant in calf fecal composite samples, while other phyla were more abundant in lactating cow fecal composite samples. Diverse suites of antibiotic resistance genes were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance (confer resistance to commonly used antibiotics). When the two groups were compared, antibiotic resistance genes were significantly more abundant in calf fecal samples than those of lactating cow samples and at the relative abundance of six antibiotic resistance class genes was significantly greater in calf samples than cow samples. Results of this study indicate that pre-weaned calf feces harbor different bacterial community and resistome structures than do feces from lactating cows, with a greater abundance of resistance genes detected in pre-weaned calf feces, indicating that feces from pre-weaned calves and lactating cows may present different public health risks. This information will be used by researchers to develop strategies for reducing antibiotic resistance bacteria in dairy cow gut microflora.

Technical Abstract: Pre-weaned dairy calves and lactating dairy cows are known reservoirs of antibiotic resistant bacteria. To further understand the differences in the resistomes and microbial communities between the two, we sequenced the metagenomes of fecal composite samples from pre-weaned dairy calves and lactating dairy cows on 17 farms (n = 34 samples). Results of analysis indicated significant differences in the structures of the microbial communities (ANOSIM R = 0.45 to 0.81, P < 0.05) and resistomes (ANOSIM R = 0.56 to 0.98, P < 0.05) between the two age groups. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the predominant members of the communities, but when the groups were compared, Bacteroidetes and Verrumicrobia were significantly more abundant in calf fecal composite samples, while Firmicutes, Spirochaetes, Deinococcus-Thermus, Lentisphaerae, Planctomycetes, Chlorofexi, and Saccharibacteria-TM7 were more abundant in lactating cow fecal composite samples (LEfSe, Padj < 0.05). Diverse suites of antibiotic resistance genes were identified in all samples, with the most frequently detected being assigned to tetracycline and aminoglycoside resistance. When the two groups were compared, antibiotic resistance genes in calf fecal samples were significantly more abundant in calf fecal samples than those of lactating cow samples (calf median ARG abundance = 1 x 10^0 ARG / 16S rRNA, cow median ARG abundance = 1.2 x 10^-1 ARG / 16S rRNA) and at the antibiotic resistance class-level the relative abundance of Tetracycline, Trimethoprim, Aminoglycoside, MLS, ß-Lactam, and Phenicol resistance genes was significantly greater in calf samples than cow samples. Results of this study indicate that pre-weaned calf feces harbor different bacterial community and resistome structures than do feces from lactating cows, with a greater abundance of resistance genes detected in pre-weaned calf feces, indicating that feces from pre-weaned calves and lactating cows may present different public health risks.