摘要
出身背景
抗微生物耐药性（AMR）已被视为对全球健康的主要威胁。猪被认为是抗微生物耐药性基因（ARGs）的重要来源。然而，关于ARGs在生猪生产行业的分布，仍然缺乏大规模的定量数据。肠道微生物组中整合ARGs的细菌种类尚未明确。
后果
在本研究中，我们使用了425头猪的451个样本的深层宏基因组测序数据，包括不同饲养模式下的野猪、藏猪和商业或杂交实验猪，来全面调查ARGs的多样性和分布，并检测这些ARGs中整合的细菌。我们共鉴定了1295个开放阅读框（ORF），这些开放阅读框被认为是抗微生物耐药性蛋白编码基因。ORF被聚类为349种独特类型的ARGs，这些ARGs可以进一步分为69个耐药性类别。四环素耐药性在猪粪便中最为富集。商业农场饲养的猪的AMR水平明显高于半自由放养条件下的猪或野猪。我们追踪了ARGs在不同生长阶段和肠道位置的组成变化。在25至240日龄的猪中，有30种耐药性类别显示出显著不同的丰度。商业养殖场猪盲肠腔和粪便中ARGs的丰富度和41个耐药性类别存在显著差异，但野猪没有。我们鉴定了几乎所有测试样本中存在的24种细菌（核心细菌），并在其基因组中整合了128个ARG。然而，在这128个ARG中，只有9个是核心ARG，这表明这些细菌物种中的大多数ARG可能是后天获得的，而不是组成的。我们选择了三个子集的ARGs作为评估样本中ARGs污染水平的指标，具有较高的准确性（r=0.73~0.89）。
结论
本研究初步概述了不同饲养模式下不同养殖场的ARG情况，这些数据可作为优化抗菌药物使用和评估养猪场ARG污染风险的参考。
Abstract
Background
Antimicrobial resistance (AMR) has been regarded as a major threat to global health. Pigs are considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of large-scale quantitative data on the distribution of ARGs in the pig production industry. The bacterial species integrated ARGs in the gut microbiome have not been clarified.

Results
In the present study, we used deep metagenomic sequencing data of 451 samples from 425 pigs including wild boars, Tibetan pigs, and commercial or cross-bred experimental pigs under different rearing modes, to comprehensively survey the diversity and distribution of ARGs and detect the bacteria integrated in these ARGs. We identified a total of 1295 open reading frames (ORFs) recognized as antimicrobial resistance protein-coding genes. The ORFs were clustered into 349 unique types of ARGs, and these could be further classified into 69 drug resistance classes. Tetracycline resistance was most enriched in pig feces. Pigs raised on commercial farms had a significantly higher AMR level than pigs under semi-free ranging conditions or wild boars. We tracked the changes in the composition of ARGs at different growth stages and gut locations. There were 30 drug resistance classes showing significantly different abundances in pigs between 25 and 240 days of age. The richness of ARGs and 41 drug resistance classes were significantly different between cecum lumen and feces in pigs from commercial farms, but not in wild boars. We identified 24 bacterial species that existed in almost all tested samples (core bacteria) and were integrated 128 ARGs in their genomes. However, only nine ARGs of these 128 ARGs were core ARGs, suggesting that most of the ARGs in these bacterial species might be acquired rather than constitutive. We selected three subsets of ARGs as indicators for evaluating the pollution level of ARGs in samples with high accuracy (r = 0.73~0.89).

Conclusions
This study provides a primary overview of ARG profiles in various farms under different rearing modes, and the data serve as a reference for optimizing the use of antimicrobials and evaluating the risk of pollution by ARGs in pig farms.

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01241-y