# Detection of Klebsiella pneumoniae in healthy poultry: Insights and perspectives from culturing and metagenomics

## TL;DR

This study finds that Klebsiella pneumoniae is more abundant in turkey flocks than in broiler flocks, but metagenomic methods may not reliably detect low-abundance bacteria.

## Contribution

The study compares culturing, qPCR, and metagenomics to detect K. pneumoniae in poultry and highlights the limitations of metagenomic methods for low-abundance taxa.

## Key findings

- Culturing showed significantly higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks.
- Metagenomic analysis found no difference in Klebsiella spp. abundance between turkey and broiler flocks.
- Shotgun metagenomics has poor sensitivity for low-abundance taxa like Klebsiella, suggesting caution in relying solely on these results.

## Abstract

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.

This study investigates the abundance of Klebsiella pneumoniae in healthy poultry flocks in Norway, using culturing, qPCR and metagenomics. The results indicate a higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks, although at an overall low level. The results also suggest that shotgun metagenomic studies targeting low abundant taxa such as Klebsiella have a poor sensitivity when comparing groups, indicating that care should be taken to only rely on results from metagenomic analysis without experimental validation.