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.

中文翻译：

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健康家禽中肺炎克雷伯菌的检测：来自培养和宏基因组学的见解和观点

之前，肺炎克雷伯菌在挪威，健康的火鸡群中发现该病的发生率高于健康的肉鸡群。本研究旨在调查这种较高的发生率是否可以归因于更多的肺炎克雷伯菌在火鸡群中。我们比较了培养、qPCR 和鸟枪法宏基因组测序来检测和定量肺炎克雷伯菌。使用 qPCR，我们发现 20.7% 的肉鸡群样本和 63.9% 的火鸡群样本呈阳性肺炎克雷伯菌。培养显示显着更高的丰度肺炎克雷伯菌火鸡群与肉鸡群相比。然而，宏基因组分析显示，相对丰度没有差异。克雷伯菌属种。肉鸡和火鸡群之间存在差异，并且培养结果和宏基因组定量之间没有相关性。有趣的是，丰度差异准肺炎克雷伯菌两个主机之间存在显着差异。我们的结果表明克雷伯菌属。火鸡和肉鸡群中的含量相对较低，但火鸡群中的丰度较高。我们的研究结果还表明，针对低丰度类群的鸟枪法宏基因组研究，例如克雷伯菌属比较组时敏感性较差，这表明应谨慎依赖未经实验验证的宏基因组分析结果。