Microbiome/Nature Jiangxi Agricultural University Huang Lusheng/Chen Congying/Gao Jun detailing the intestinal antibiotic resistance profile of pigs

iNature Antimicrobial Resistance (AMR) has been recognized as a major threat to global health
.

Pigs are considered to be an important source of antimicrobial resistance genes (ARGs)
.

However, large-scale quantitative data on the distribution of ARGs in the pig industry are currently lacking
.

The bacterial species that integrate ARGs in the gut microbiome have not been identified
.

On March 4, 2022, Jiangxi Agricultural University Huang Lusheng, Chen Congying and Gao Jun jointly published a research paper titled "Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance" in Microbiome (IF=15).
The study used deep metagenomic sequencing data from 451 samples from 425 pigs, including wild boars, Tibetan pigs, commercial or hybrid experimental pigs under different feeding patterns, and detected bacteria integrated in these ARGs
.

The study identified a total of 1295 open reading frames (ORFs), which are believed to encode genes for antimicrobial resistance proteins
.

The ORFs clustered into 349 unique ARGs, which could be further classified into 69 resistance classes
.

Tetracycline resistance was most abundant in pig manure
.

Pigs raised on commercial farms had significantly higher AMR levels than pigs or wild boars in semi-free-range conditions
.

The study tracked changes in the composition of ARGs at different growth stages and gut locations
.

Thirty resistance classes showed markedly different abundances in pigs aged 25 to 240 days
.

The abundance of ARGs and the 41 resistance classes differed significantly in the caecal cavity and feces of pigs on commercial farms, but not in wild boars
.

The study identified 24 bacterial species present in almost all tested samples (core bacteria) and integrated 128 ARGs in their genomes
.

However, only 9 of these 128 ARGs were core ARGs, suggesting that the majority of ARGs in these bacterial species may be acquired rather than constitutive
.

This study selected three subsets of ARGs as indicators to assess the contamination level of ARGs in the samples with high accuracy (r = 0.
73~0.
89)
.

In conclusion, this study provides a preliminary overview of the ARGs profiles of various farms under different feeding patterns, and these data can provide a reference for optimizing the use of antimicrobials and assessing the risk of ARGs contamination on pig farms
.

In addition, on April 27, 2022, Jiangxi Agricultural University Huang Lusheng, Chen Congying and Michel Georges co-corresponded (Yang Hui and Wu Jinyuan are the co-first authors) in a Nature online publication entitled "ABO genotype alters the gut microbiota by regulating GalNAc levels in pigs" "Research paper, which explores the effect of host genotype on the composition of the swine gut microbiota
.

The findings provide very strong evidence for the influence of host genotype on the abundance of specific bacteria in the gut, combined with insights into the molecular mechanisms supporting this association
.

They paved the way for the same effects to be found in human rural populations (click to read)
.

Antimicrobials are widely used in livestock raising to treat disease, improve health and promote growth
.

It is estimated that food animals consume about 73% of the world's antimicrobial drugs
.

The widespread availability of antimicrobial agents has contributed to the emergence of antimicrobial resistance (AMR) in microorganisms under selective pressure
.

Studies have shown that long-term antimicrobial use can lead to changes in the composition and diversity of gut commensal microbes, which can adversely affect host health
.

Resistance genes can be transferred between humans and animals, so the animal microbiota can serve as a repository for clinically important antimicrobial resistance genes (ARGs)
.

Therefore, AMR is a potential risk to both animals and humans
.

ARGs are now recognized as an emerging environmental pollutant that has attracted worldwide attention
.

The World Health Organization has identified the antimicrobial resistance crisis as one of the most pressing threats to modern healthcare
.

However, the origin, distribution, diversity, and metastasis of AMRs have not been elucidated, and large-scale quantitative data on ARGs in the animal gut are still lacking
.

Characterization of the resistance group and quantification of current levels of ARGs are critical for assessing the risk of AMR to public health
.

In addition, different bacteria exhibit different responses to antimicrobials, and different antimicrobials have different effects on microbial activity, composition, and metabolism
.

Therefore, to avoid the use of broad-spectrum antimicrobials as much as possible, a comprehensive understanding of ARGs in bacteria and the dynamics of gut microbiota induced by antimicrobials is required to optimize antimicrobial use
.

China is the world's largest pig producer and the world's largest consumer of veterinary antimicrobials, the biggest hotspot of antimicrobial resistance
.

China's contribution to the fight against global antimicrobial resistance is critical
.

A recent survey showed that pigs account for 52.
2% of total antimicrobial use in China
.

ARGs transferred through ecological cycles pose a growing threat to public health
.

Pork is one of the major consumer meat products, and the inappropriate use of antimicrobials in hog production is thought to cause AMR in humans
.

However, systematic studies of the swine resistance group are lacking
.

A previous study used quantitative PCR (qPCR) to analyze the ARGs of 36 fecal samples from three Chinese pig farms
.

However, qPCR has limited throughput and requires specific primers from known ARG sequences
.

Metagenome sequencing is a high-throughput method to rapidly and extensively monitor the diversity and abundance of resistance genes
.

Another study investigated ARGs in 287 pig fecal samples from France, Denmark, and China, and compared the abundance of ARGs across countries
.

Previous studies in humans and cattle have shown that the composition of ARGs changes at different ages
.

Therefore, age and gut location need to be considered when studying the composition of ARGs in humans and animals
.

In addition, most previous studies have only focused on the characterization of the resistance group, including the diversity, abundance, and resistance classes of ARGs, whereas the associations between ARGs and the major host microbial gut microbiota and risk assessment of resistance genes in pigs largely unexplored
.

In this study, fecal samples from 425 adult pigs from three provinces in China were used to characterize the composition and distribution of intestinal resistance genes in pigs on different farms under different feeding patterns
.

These experimental pigs included 6 wild boars captured from the wild, 21 Tibetan pigs raised in semi-free-range conditions on 3 high-altitude farms, and 398 commercial or crossbred experimental pigs raised on 5 high-stocking density standard farms
.

A comprehensive scan using deep metagenomic sequencing to characterize the porcine intestinal resistance profile
.

Bacterial species-integrated ARGs were identified
.

The study also compared AMR between two growth stages and between cecal lumen and stool samples
.

Furthermore, in order to establish a simple and effective method for predicting AMR environmental risk and ARGs contamination levels, this study selected three subsets of resistance genes that could be used as indicators
.

Composition, abundance, and richness of fecal resistance groups in pigs under different feeding regimes (image courtesy of Microbiome) The study used 451 samples from 425 pigs under different feeding regimes, including wild boars, Tibetan pigs, commercial or hybrid experimental pigs of deep metagenomic sequencing data and detection of bacteria integrated in these ARGs
.

The study identified a total of 1295 open reading frames (ORFs), which are thought to encode genes for antimicrobial resistance proteins
.

 The ORFs clustered into 349 unique ARGs, which could be further classified into 69 resistance classes
.

Tetracycline resistance was most abundant in pig manure
.

Pigs raised on commercial farms had significantly higher AMR levels than pigs or wild boars in semi-free-range conditions
.

The study tracked changes in the composition of ARGs at different growth stages and gut locations
.

Thirty resistance classes showed markedly different abundances in pigs aged 25 to 240 days
.

The abundance of ARGs and the 41 resistance classes differed significantly in the caecal cavity and feces of pigs on commercial farms, but not in wild boars
.

The study identified 24 bacterial species present in almost all tested samples (core bacteria) and integrated 128 ARGs in their genomes
.

However, only 9 of these 128 ARGs were core ARGs, suggesting that the majority of ARGs in these bacterial species may be acquired rather than constitutive
.

This study selected three subsets of ARGs as indicators to assess the contamination level of ARGs in the samples with high accuracy (r = 0.
73~0.
89)
.

In conclusion, this study provides a preliminary overview of the ARGs profiles of various farms under different feeding patterns, and these data can provide a reference for optimizing the use of antimicrobials and assessing the risk of ARGs contamination on pig farms
.

Reference news: https://microbiomejournal.
biomedcentral.
com/articles/10.
1186/s40168-022-01241-y