Biology subjects

Stamp Dawkins, M.

Publications and source records attributed to Stamp Dawkins, M..

5 recordsLinked to original sources

bioRxiv2022

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

Contaminated chicken meat is a major source of human Campylobacteriosis and rates of infection remain high, despite efforts to limit the colonisation of broiler (meat) chicken flocks on farms. Using conventional testing methods of culture or qPCR, Campylobacter is typically detected amongst broiler flocks from 3 weeks of age, leading to the assumption that infection is introduced horizontally into chicken rearing houses at this time. In this study, we use parallel sequencing of a fragment of the Campylobacter outer membrane protein, encoded by the porA gene, to test for presence of Campylobacter DNA amongst fresh faecal samples collected from broiler flocks aged 23-28 days. Campylobacter DNA was detected in all of the 290 samples tested using the porA target, and in 48% of samples using 16S bacterial profiling, irrespective of whether or not Campylobacter could be detected using conventional qPCR thresholds. A single porAf2 variant was predominant amongst flocks that would be determined to be Campylobacter positive by conventional means, but a diverse pattern was seen amongst flocks that were Campylobacter negative. The ability to routinely detect low levels of Campylobacter amongst broiler flocks at a much earlier age than would conventionally be identified requires a re-examination of how and when biosecurity measures are best applied for live birds. In addition, it may be useful to investigate why single Campylobacter variants proliferate in some broiler flocks and not others.

microbiology↗

bioRxiv2021

Can good broiler flock welfare prevent colonization by Campylobacter?

Using data on rearing and welfare metrics of multiple commercial broiler flocks from the last ten years, we investigate how welfare measures such as hock burn, mortality, weight, and pododermatitis, among others, impact the likelihood of a flock becoming colonized by Campylobacter. Using both logistic regression and Bayesian networks, we show that, while some welfare metrics were weakly related to Campylobacter colonization, evidence could not be found to suggest that these metrics actively exacerbated Campylobacter colonization, rather that they were both symptoms of the same underlying cause. Instead, observed dependency on the management of the flock suggested that yet-undiscovered differences in rearing practise were the principal cause of both poor bird welfare and increased risk of Campylobacter, suggesting that action can be taken to improve both these factors simultaneously.

microbiology↗

bioRxiv2020

Deep sequencing reveals Campylobacter in commercial meat chickens less than 8 days old.

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. A cornerstone of these efforts has been the detection of chicken infection with microbiological culture, which typically does not occur until birds are at least 21 days old. Using molecular methods for detecting Campylobacter presence, 16S microbiome analysis and deep sequencing of the Campylobacter porA gene, Campylobacter can be identified at very low levels in most or all flocks fewer than 8 days old. These young chicks exhibit 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 strains, 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, suggests that efforts to control infection should concentrate on how to maintain Campylobacter at low levels by the prevention of the overgrowth of single strains, which ultimately leads to the contamination of food.

microbiology↗

bioRxiv2020

A mathematical modelling approach to uncover factors influencing the spread of Campylobacter in a flock of chickens

Despite continued efforts into improving biosecurity protocol, Campylobacter continues to be detected in the majority of commercial chicken flocks across Europe. Using an extensive data set of Campylobacter prevalence within a chicken breeder flock for over a year, multiple Bayesian models are presented to explore the dynamics of the spread of Campylobacter in response to seasonal variation, species-specificity, bird health and total infection prevalence. It was found that birds within the flock varied greatly in their response to bacterial challenge, and that this phenomena had a large impact in the overall prevalence of different species of Campylobacter. Campylobacter jejuni appeared more frequently in the summer, while Campylobacter coli persisted for a longer duration, amplified by the most susceptible birds in the flock. Our study suggests that strains of Campylobacter that appear most frequently likely possess no demographic advantage, but are instead amplified due to the health of the birds that ingest it.

microbiology↗

bioRxiv2019

A mathematical model of Campylobacter dynamics within a broiler flock

Globally, the bacterial genus Campylobacter is one of the leading causes of human gastroenteritis, with its primary route of infection being through poultry meat. Despite decades of study we appear to be no closer to preventing outbreaks within commercial chicken flocks, and the application of biosecurity measures is limited by a lack of understanding of the transmission dynamics within a flock. Our work is the first to undertake a mathematical modelling approach to Campylobacter population dynamics within a flock of broilers (chickens bred specifically for meat). A system of stochastic differential equations is used to investigate the diverse and fluctuating conditions within the gut of a broiler, and models the routes of infection between co-housed birds. The presented model provides mechanistic explanations for key infection dynamics that have been long-observed but very poorly understood. We highlight several driving mechanisms behind observed infection phenomena, simulate experimentally observed inter-strain competition, and present a promising approach to hypothesising new methods of preventing flock outbreaks.\n\nAuthor summaryThe bacteria Campylobacter is one of the most common causes of food poisoning globally. The most common route of infection is through raw chicken meat, as a result of many chicken farms across the world housing fully infected flocks. Despite the magnitude of this public health risk, little is understood of the specifics of how chickens become infected, and the ways that they then infect one another. Our work presents a mathematical model of Campylobacter transmission dynamics within a flock of chickens. We compare the results of the model to real world data sets, explore key dynamical behaviours, and present a sensitivity analysis to highlight the most important factors underpinning outbreaks.

systems biology↗