Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study

Abstract

Background: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

Results: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes.

Conclusions: This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.

Figure 1:

Stacked barplots of relative abundances show the most abundant phyla (left) and species (right) within each metagenome. At the phylum-level (left), Firmicutes, Bacteroidetes, and Actinobacteria are the most abundant phyla across all samples. At the species-level (right), the 5 most abundant and prevalent species across community control and dairy worker metagenomes were F. prausnitzii, E. rectale, P. copri, and Eubacterium sp. CAG-180. Species with relative abundances less than 1% were grouped together. There was insufficient evidence to suggest major differences in the taxonomic composition of dairy worker metagenomes compared to community controls.

Figure 2:

For each metagenome, we compare the sequencing depth with the number of identified CARD genes and VFDB genes. Ages (years) of each subject have been labeled. Samples with deeper sequencing had higher numbers of identified genes from the CARD and VFDB databases and higher numbers of estimated genomes. Within the community control group, 3 samples had the highest number of identified CARD genes out of all samples studied, whereas the remaining 3 community control samples within the community control group appeared to be indistinguishable from dairy workers in the number of identified CARD genes. The number of CARD and VFDB genes identified in our study cohort appeared to be similar in range to the number of CARD and VFDB genes identified in the HMP healthy human subjects cohort despite higher sequencing depths on average per sample in the HMP study cohort.

Figure 3:

We identified ARGs from 8 antibiotic classes (rows) listed as critically important to human medicine by the WHO. log₁₀ transformed relative abundances of antibiotic resistance genes grouped by these antibiotic classes are colored from lower (light blue) to higher (darker blue) relative abundances in each metagenome. Antibiotic resistance classes (rows) have been ordered by ascending q-values. White squares denote undetected antibiotic resistance genes. Visual inspection displays patterns of increased abundance of tetracycline resistance genes and macrolide resistance genes in dairy worker metagenomes. Additionally, cephamycin resistance genes had a higher occurrence in dairy workers as these genes were identified in 90% of dairy worker samples compared to 67% of community control samples.