Norwegian Veterinary Institute, Ås, Norway.
Environ Microbiol Rep. 2024 Feb;16(1):e13240. doi: 10.1111/1758-2229.13240.
Previously, Klebsiella pneumoniae was found to occur more frequently in healthy turkey flocks than in healthy broiler flocks in Norway. This study aimed to investigate whether this higher occurrence could be attributed to a greater abundance of K. pneumoniae in turkey flocks. We compared culturing, qPCR, and shotgun metagenomic sequencing for the detection and quantification of K. pneumoniae. Using qPCR, we found that 20.7% of broiler flock samples and 63.9% of turkey flock samples were positive for K. pneumoniae. Culturing revealed a significantly higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks. However, metagenomic analysis showed no difference in the relative abundance of Klebsiella spp. between broiler and turkey flocks, and no correlation between the results of culturing and metagenomic quantification. Interestingly, the differential abundance of K. quasipneumoniae was significantly different between the two hosts. Our results indicate that Klebsiella spp. are present in both turkey and broiler flocks at relatively low levels but with a higher abundance in turkey flocks. Our findings also suggest that shotgun metagenomic studies targeting low-abundance taxa such as Klebsiella have poor sensitivity when comparing groups, indicating that reliance on results from metagenomic analysis without experimental validation should be done with caution.
先前，在挪威，与健康的肉鸡群相比，健康火鸡群中更常发现肺炎克雷伯菌。本研究旨在调查这种更高的发生率是否归因于火鸡群中肺炎克雷伯菌的丰度更高。我们比较了培养、qPCR 和 shotgun 宏基因组测序检测和定量肺炎克雷伯菌的方法。使用 qPCR，我们发现 20.7%的肉鸡群样本和 63.9%的火鸡群样本对肺炎克雷伯菌呈阳性。培养结果显示，火鸡群中肺炎克雷伯菌的丰度明显高于肉鸡群。然而，宏基因组分析显示，肉鸡和火鸡群中克雷伯菌属的相对丰度没有差异，培养和宏基因组定量的结果之间也没有相关性。有趣的是，两种宿主之间肺炎克雷伯菌的差异丰度有显著差异。我们的结果表明，克雷伯菌属在火鸡和肉鸡群中均以相对较低的水平存在，但在火鸡群中丰度更高。我们的研究结果还表明，当比较组时，针对低丰度分类群（如克雷伯菌）的 shotgun 宏基因组研究的灵敏度较差，这表明在没有实验验证的情况下依赖宏基因组分析的结果应谨慎进行。
