Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method

Abstract

The genetic diversity of Campylobacter jejuni and Campylobacter coliisolates from commercial broiler farms was examined by multilocus sequence typing (MLST), with an assessment of the impact of the sample type and laboratory method on the genotypes of Campylobacter isolated. A total of 645C. jejuniand 106C. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The Campylobacter jejuniisolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of Campylobacter population in broiler flocks at the farm level. ForC. coli, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms forC. jejuni, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for C. jejuni and 64.1% forC. coli). These results show the complexity of the population structure of Campylobacterin broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of C. jejuni isolates among broiler farms should be taken into account when designing studies to understand Campylobacter populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on C. jejuni populations even when laboratory and sampling methods are not identical.

FIG 1

Frequency distribution of C. jejuni (n = 645) and C. coli (*) (n = 106) STs from 32 broiler flocks.

FIG 2

Bar chart showing the frequency distribution of C. jejuni (n = 645) and C. coli (*) (n = 106) STs between sample types. STs identified in 10 or fewer isolates were grouped into the category “Other.”

FIG 3

Unrooted neighbor-joining tree displaying the pairwise genetic distances (F_ST values) between C. jejuni populations from different flocks (H) from different farms (F). The same color represents isolates from flocks from the same farm. The F_ST values were calculated from nucleotide polymorphisms in the concatenated sequences from seven loci in the 645 C. jejuni isolates. All differences between flocks were significant at a P value of <0.05.

FIG 4

Unrooted neighbor-joining tree displaying the pairwise genetic distances (F_ST values) between C. coli populations from different flocks from different farms. The same color represents isolates from flocks from the same farm. The F_ST values were calculated from nucleotide polymorphisms in the concatenated sequences from seven loci in the 106 C. coli isolates. All differences between flocks were significant at a P value of <0.05.