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Antimicrobial Resistance Genes in Pigs, Chickens Differ Between European Countries

NEW YORK (GenomeWeb) – Antimicrobial resistance genes harbored in the guts of pigs and chickens varies by country, especially among pigs, according to a new study focused on European farms.

Resistance to antimicrobials is a key threat to human health, according to the World Health Organization. While antimicrobial resistance occurs naturally, the WHO says the misuse of antibiotics in both people and livestock accelerates its development and that as resistance spreads, more infections become increasingly difficult to treat.

As part of the European Union-funded Ecology from Farm to Fork of Microbial Drug Resistance and Transmission (EFFORT) project examining the effects of antimicrobial resistance (AMR), researchers led by the Technical University of Denmark's Frank Aarestrup collected samples from more than 9,000 pigs and chickens living on farms in nine different European countries. As they reported today in Nature Microbiology, the researchers characterized the suite of resistance genes the animals' feces carried to uncover not only country-to-country differences, but also differences linked to their microbial backgrounds.

"To our knowledge, this study represents the single largest metagenomic AMR monitoring effort of livestock," Aarestrup and his colleagues wrote in their paper.

The researchers collected fresh fecal samples from animal pen floors from 359 animal herds for shotgun metagenomic analysis. By mapping the reads they generated to the ResFinder database, which is a curated database of acquired AMR genes, the researchers were able to estimate AMR gene abundance. Overall, pigs had higher AMR gene levels than poultry, with Italian pigs harboring the highest and Danish poultry the least number of AMR genes.

The most common AMR phenotype among pigs, the researchers found, was resistance to tetracycline, followed by macrolides. And while resistance among poultry varied, it included resistance to tetracycline and macrolides as well as to b-lactams and aminoglycosides.

In all, the team uncovered 407 different resistance genes across their pig and poultry samples. In a clustering analysis, they found perfect separation between the pig and poultry samples, indicating that their respective 'resistomes' are distinct. In particular, the researchers uncovered 33 core AMR genes in pigs and 49 core AMR genes in poultry, two dozen of which were shared.

After separating them by species, the researchers found that their samples also clustered by country of origin, though the effect was sharper among pig samples.

Some AMR genes were found in both species, while others were more common in one species as compared to the other. For instance, tet(W) and erm(B) were found throughout the pig and poultry samples, while cat(pC194), catP, and cat_2 were more common among Italian pig samples.

In addition, the scientists found that the colistin resistance gene mcr-1 was much more abundant at Bulgarian and Italian poultry farms than others. While Bulgarian farmers in the study didn't report any polymyxin use, Italian farmers reported high treatment levels.

Still, the researchers noted a positive association between countries' veterinary antimicrobial usage and AMR abundance among pigs and poultry. Countries with similar antimicrobial usage also exhibited similar resistomes, the researchers said. Poultry herds in Spain, Italy, Poland, and Belgium had a higher abundance of Bla genes, for example, which could be due to the increased usage of fluoroquinolones in those countries.

However, the researchers also found that functionally determined AMR genes — as gauged through the functional resistance database — were not associated with total drug use, suggesting that some genes might be functional only in certain hosts.

The resistomes of the pigs and poultry also varied with the bacterial makeup of their microbiomes, the researchers reported. Samples with similar bacterial taxonomic makeups tended to have similar resistomes.

"We found that the metagenomic resistome varied significantly between the pig and poultry reservoirs, but also within each species, in a country-dependent manner," the researchers wrote. "Within each country, we found different levels of variation, with some countries having more homogenous herds than others."