Metagenomic insights into isolable bacterial communities and antimicrobial resistance in airborne dust from pig farms

Abstract

This study aims to investigate bacterial communities and antimicrobial resistance (AMR) in airborne dust from pig farms. Airborne dust, pig feces and feed were collected from nine pig farms in Thailand. Airborne dust samples were collected from upwind and downwind (25 meters from pig house), and inside (in the middle of the pig house) of the selected pig house. Pig feces and feed samples were individually collected from the pen floor and feed trough from the same pig house where airborne dust was collected. A direct total bacteria count on each sampling plate was conducted and averaged. The ESKAPE pathogens together with Escherichia coli, Salmonella, and Streptococcus were examined. A total of 163 bacterial isolates were collected and tested for MICs. Pooled bacteria from the inside airborne dust samples were analyzed using Metagenomic Sequencing. The highest bacterial concentration (1.9-11.2 × 10³ CFU/m³) was found inside pig houses. Staphylococcus (n = 37) and Enterococcus (n = 36) were most frequent bacterial species. Salmonella (n = 3) were exclusively isolated from feed and feces. Target bacteria showed a variety of resistance phenotypes, and the same bacterial species with the same resistance phenotype were found in airborne dust, feed and fecal from each farm. Metagenomic Sequencing analysis revealed 1,652 bacterial species across all pig farms, of which the predominant bacterial phylum was Bacillota. One hundred fifty-nine AMR genes of 12 different antibiotic classes were identified, with aminoglycoside resistance genes (24%) being the most prevalent. A total of 251 different plasmids were discovered, and the same plasmid was detected in multiple farms. In conclusion, the phenotypic and metagenomic results demonstrated that airborne dust from pig farms contained a diverse array of bacterial species and genes encoding resistance to a range of clinically important antimicrobial agents, indicating the significant role in the spread of AMR bacterial pathogens with potential hazards to human health. Policy measurements to address AMR in airborne dust from livestock farms are mandatory.

Keywords: airborne dust; antimicrobial resistance; bacterial communities; metagenomic approach; pig farm.

Figure 1

Sankey visualization from the Kraken 2 analysis of airborne bacterial communities inside pig farms (n = 7). It is shown in different taxonomy levels. The higher the portion for each phylum, the higher read counts. The number indicates the read counts. D, Domain; K, Kingdom; P, Phylum; C, Class; O, Order; F, Family; G, Genus; S, Species.

Figure 2

Metagenomic classifications of bacterial community compositions at Phylum level (A) and Genus level (B) of airborne dust inside seven pig farms by Proportion (percentage of sequencing reads that align or map to a specific phyla and genus to the total number of reads) of top 5 phyla and genus.

Figure 3

Antimicrobial resistance genes found in airborne dust inside pig farms (n = 7) by metagenomic sequencing. (A) Proportions of the number of detected genes for each antibiotic class. Proportion represents the percentage of number of detected genes for each antibiotic class to the total number of detected genes of resistance genes of different antibiotic classes from airborne dust collected inside the 7 pig farms. (B) Resistance gene profile in airborne dust inside the 7 pig farms. The stacked bar chart represents the number of detected resistance genes in each antibiotic class in each pig farm. Each colored segment within the bars corresponds to a specific resistance gene.