Background
Originating from poultry, particularly chickens,
Campylobacter jejuni
is the leading foodborne pathogen worldwide and a major cause of campylobacteriosis. Isolating
C. jejuni
is difficult due to its specific growth requirements, the presence of viable but non-culturable bacteria, and because it is often masked by competing flora. Currently, there is no optimized method for isolating
C. jejuni
from chicken feces. Here, we evaluated the method for isolating
C. jejuni
from chicken feces using culture-independent sequence-based metagenomics and culture-dependent tools. Further, we assessed changes in microbial communities during microbe isolation to determine how the process can be improved.
Results
Fourteen different variations of
C. jejuni
isolation procedures were applied to all 35 chicken fecal samples. These variations included using different enrichment broths (without enrichment or enrichment in Bolton or Preston broth), different ratios of sample-to-enrichment broth (1:10
1
, 1:10
2
, and 1:10
3
), and different selective agars (modified charcoal-cefoperazone-deoxycholate agar (mCCDA) or Preston agar). Enrichment during isolation of
C. jejuni
was evaluated on the basis of microbial diversity and taxonomic composition using metagenomics tools. The effect of selective media was evaluated using a combination of metagenomics and culture-dependent tools. Microbial diversity significantly decreased during the enrichment process, regardless of the type of enrichment broth, with the most significant decrease observed at a feces-to-broth ratio of 1:10
3
. Particularly, in 10
3
-Preston broth, the relative abundance of
Campylobacter
increased, while extended-spectrum beta-lactamase-producing
Escherichia coli
, which interfere with
Campylobacter
isolation, decreased. Metagenomics results were validated by quantitative PCR and culture-dependent analysis. Additionally, selective media affected the isolation results, although microbes with high relative abundance during enrichment were also frequently isolated using culture-dependent methods. Significantly more
C. jejuni
was isolated from mCCDA than from Preston agar enriched in 10
3
Preston broth.
Conclusions
Enrichment in Preston broth at a ratio of 1:10
3
followed by spreading onto mCCDA was the most effective method for isolating
C. jejuni
. This is the first study to apply metagenomics to evaluate a method for isolating a targeted microbe,
C. jejuni
, from chicken feces, a sourc...