Parallel Sequencing Reveals Campylobacter spp. in Commercial Meat Chickens Less than 8 Days Old

Abstract

Campylobacter from contaminated poultry meat is a major source of human gastroenteritis worldwide. To date, attempts to control this zoonotic infection with on-farm biosecurity measures have been inconsistent in outcome. A cornerstone of these efforts has been the detection of chicken infection with microbiological culture, where Campylobacter is generally not detectable until birds are at least 21 days old. Using parallel sequence based bacterial 16S profiling analysis and targeted sequencing of the porA gene, Campylobacter was identified at very low levels in all commercial flocks at less than 8 days old that were tested from the UK, Switzerland, and France. These young chicks exhibited a much greater diversity of porA types than older birds testing positive for Campylobacter by culture or qPCR. This suggests that, as the bacteria multiply sufficiently to be detected by culture methods, one or two variants, as indicated by porA type, dominate the infection. The findings that: (i) most young chicks carry some Campylobacter and (ii) not all flocks become Campylobacter positive by culture, suggest that efforts to control infection, and therefore avoid contamination of poultry meat, should concentrate on how to limit Campylobacter to low levels by the prevention of the overgrowth of single strains. Importance: Our results demonstrate the presence of Campylobacter DNA amongst faecal samples from a range of commercially reared meat chicks that are less than 8 days of age, consistent across 3 European countries. The recently developed, sensitive detection method indicates that infection occurs on commercial farms much earlier and more widely than previously thought, which opens-up new opportunities to control Campylobacter contamination at the start of the food-chain, and reduce the unacceptably high levels of human disease.

High resolution parallel sequencing reveals multi-strain Campylobacter in broiler chicken flocks testing ‘negative’ by conventional culture methods: implications for control of Campylobacter infection

“…Rather, the pattern of overgrowth of a predominant porAf2 type coincided with flocks that would usually be determined Campylobacter qPCR/culture positive using Ct thresholds, whilst a pattern of high porAf2 diversity at low prevalence was apparent amongst Campylobacter qPCR/culture negative flocks. The findings support the strong correlation between predominant porA type amongst culture/qPCR positive birds/flocks and diverse porA types amongst culture/qPCR negative birds/flocks shown in our previous work (Colles, et al, 2021). Two of the flocks had a small proportion of samples that were positive by conventional qPCR, but Campylobacter 16S nucleotide sequence was detected at very low frequency, if at all, with the porAf2 pattern remaining diverse.…”

“…That Campylobacter DNA was not equally detected for samples tested by both 16S and porA is not surprising given they are different targets, with porA specifically amplifying Campylobacter DNA, and therefore giving a greater sensitivity of detection. In contrast, the 16S bacterial profile, amongst which Campylobacter in our studies represented <0.01% of species recovered from the broiler chicken faecal samples (Colles, et al, 2021) gives a high chance that more prevalent species will be detected ahead of Campylobacter , and may give greater variation between samples. Unlike our previous studies however, Campylobacter DNA was detected at a prevalence >1% of the bacterial profile in 14.8% (43/290) of samples in this study, and at 51-79% of the bacterial profile in 1.7% (5/290) of samples collected from the Swiss broiler flocks.…”

“…It therefore seemed logical that the key to controlling Campylobacter was to prevent infection from outside sources by stricter biosecurity. However, the combination of continuing Campylobacter infection despite the introduction of tighter biosecurity measures (Anonymous, 2017) and sensitive genetic techniques for detecting the bacteria has challenged the idea of initially pristine flocks becoming later contaminated from outside due to a breach in biosecurity (Colles, et al, 2021; Cox, et al, 2012). Using a deep sequencing approach, Colles et al .…”

“…However, the combination of continuing Campylobacter infection despite the introduction of tighter biosecurity measures (Anonymous, 2017) and sensitive genetic techniques for detecting the bacteria has challenged the idea of initially pristine flocks becoming later contaminated from outside due to a breach in biosecurity (Colles, et al, 2021; Cox, et al, 2012). Using a deep sequencing approach, Colles et al . (2021) detected Campylobacter DNA in faecal samples from all the broiler flocks they tested when birds were less than 8 days old (Colles, et al, 2021).…”

“…Using a deep sequencing approach, Colles et al . (2021) detected Campylobacter DNA in faecal samples from all the broiler flocks they tested when birds were less than 8 days old (Colles, et al, 2021). Campylobacter DNA was detected amongst a total of 87.5% of 16 broiler flocks from the UK, Switzerland and France by 16S bacterial profiling assay and amongst 100% of 34 flocks using the porAf2 assay.…”