Metagenomic analysis of the microbial communities and resistomes of feces from veal calves

Authors: Salaheen, Serajus; Kim, Seonwoo; HOVINGH, ERNEST - Pennsylvania State University; Van Kessel, Jo Ann; Haley, Bradd

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/3/2020
Publication Date: 2/9/2020
Citation: Salaheen, S., Kim, S., Hovingh, E., Van Kessel, J.S., Haley, B.J. 2020. Metagenomic analysis of the microbial communities and resistomes of feces from veal calves. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.609950.
DOI: https://doi.org/10.3389/fmicb.2020.609950

Interpretive Summary: Antimicrobial resistance (AMR) is a major public health concern, and dairy cattle, including veal calves are known reservoirs of antimicrobial-resistant (AR) bacteria. To investigate AMR in the microbial communities in feces from veal calves, we sequenced the metagenomes of feces collected from individual calves from four commercial veal farms in Pennsylvania. Three fecal samples from randomly selected calves on each farm were collected soon after the calves were brought onto the farms (younger calves, n = 12), and again, just before the calves were ready for slaughter (older calves, n = 12). Results indicated that the fecal microbial communities were significantly different between samples collected from younger and older calves. Additionally, our analyses identified a diverse array of previously known antimicrobial resistance genes in the veal calf feces. These genes (specific DNA sequences) can potentially be transferred or exchanged amongst different types of bacteria, including those that are pathogenic to humans. The resistomes (genes associated with antimicrobial resistance) consisted of genes that confer resistance to a variety of antimicrobials, including aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLS). The data presented here are useful for scientists to further identify factors that are responsible for selection and persistence of antimicrobial-resistant bacteria in the veal calf gut. Minimizing antimicrobial-resistant reservoirs in animal production will reduce the potential for human exposure to resistant bacterial pathogens.

Technical Abstract: Antimicrobial resistance (AMR) is a major public health concern, and dairy cattle, including veal calves are known reservoirs of antimicrobial resistant (AR) bacteria. To investigate AMR in the microbial communities in feces from veal calves, we sequenced the metagenomes of feces collected from individual calves from four commercial veal operations in Pennsylvania. Three fecal samples from randomly selected calves on each farm were collected soon after the calves were brought onto the farms (younger calves, n = 12), and again, just before the calves were ready for slaughter (older calves, n = 12). Results indicated that the most frequently identified phyla were Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Fecal microbial communities were significantly different between samples collected from younger and older calves at the genus level (analysis of similarities [ANOSIM] R'='0.37, p'< 0.05), but not at the phylum level. Variances among different suites of microbial communities in younger calves were significantly higher than that of older calves (betadisper F = 8.25, p < 0.05). Additionally, our analyses identified a diverse array of acquired/transferrable antimicrobial resistance genes (ARGs) in the veal calf feces. The fecal resistomes mostly consisted of ARGs that confer resistance to aminoglycosides, tetracyclines, and macrolide-lincosamide-streptogramin B (MLS), and these ARGs represented more than 70% of the veal calf fecal resistomes. Factors that are responsible for selection and persistence of AR bacteria in the veal calf gut need to be identified to discover novel control points and interrupt detrimental AMR occurrence and shedding.