Analysis of the gut microbiota of Campylobacter colonized and free flocks on (mixed) broiler farms

It is estimated that 50 to 80% of the human Campylobacter infections originate from poultry. So far, biosecurity seems to be the main field of interest with regard to Campylobacter control on poultry farms. Farms with different livestock species, which are common in Belgium, may be at higher risk for Campylobacter introduction in broiler flocks and are the focus in this study. This study was performed by means of a longitudinal molecular epidemiological study, in which both the broilers and surrounding environment of ten (mixed) broiler farms were monitored on a weekly base, for a period of two production cycles. Both cecal droppings and environmental samples were screened for the presence of Campylobacter. Cecal droppings from the second production cycle were also used for 16S metabarcoding, to study the differences in the microbiota of flocks from colonized and non-colonized farms. Isolates were further molecular typed (PFGE) in order to identify possible contamination sources. Results show a Campylobacter prevalence of 30% in the first production cycle, and 40% in the second. Broilers became colonized at the earliest when they are 4 weeks old. The majority of the flocks (57%) became positive after partial depopulation at week 5 to 6. At this time, two Campylobacter free flocks were seen to carry high numbers of Megamonas spp. in their ceca, suggesting its potential in competing with Campylobacter spp. Before colonization of the flocks, Campylobacter in the environment was rarely detected, but was frequently found in cattle and swine. Although they appeared to be consistent carriers of Campylobacter, molecular typing revealed that they were not the contamination source for the broilers. As already demonstrated for other countries, this study suggests that also in Belgium, partial depopulation appears to be an important risk factor for Campylobacter introduction into the broiler house and will be the onset for consecutive research in this area.