In this exciting proposal the research team tackled questions on how Enterococcus cecorum evolved from a commensal to an emergent pathogen, by performing whole genome sequencing (WGS). Bioinformatic analysis was performed on the WGS data to identify potential virulence and antimicrobial resistant (AMR) genes. Evolutionary relationship of the isolates was performed through phylogenetic analysis to detect lineages from diseased poultry. A quantitative real-time (q)PCR, previously published, was validated for sensitive and specific detection of E. cecorum and used for its detection in samples collected from environmental swabbing the on four farms that were recruited to the study. Video cameras and sensors associated with analytical behaviour software such as EyeNamic and Noldus EthoVision, that uses machine learning algorithms to translate video images into indices of behaviour, were used for monitoring changes in poultry behaviour in houses throughout the production cycle on all farms. Behaviour changes that may be attributed to E. cecorum infection was verified by veterinary examinations; veterinary examinations were also performed on culled or naturally dead birds.
The results from this study showed that E. cecorum was present on all four GB poultry farms sampled. The level of detection by qPCR varied and it could only be isolated by culture from caeca of culled birds on farm B, where a “sporadic” infection occurred. Veterinary inspection confirmed septic arthritis in two birds from farm B where E. cecorum was isolated from joint fluids. Phylogenetic analysis clustered the majority of GB isolates, which had been retrieved from APHA archives harbouring isolates from their disease surveillance program, into three groups. The GB isolates were mostly genomically distinct from other non-UK isolates from worldwide collections present in genomic databases, included in the phylogenetic analysis. Presence of AMR and virulence genes was variable in these isolates. Also, the data from behavioural monitoring cameras were mostly inconclusive.
The poultry industry will benefit from the findings of this project as it suggested that although E. cecorum may be present on poultry farms it does not lead to large disease outbreaks. However, it is not yet clear what changes occur either in the pathogen or the poultry or farm environment that result in large outbreaks.
Contact details:
Professor Muna Anjum
Molecular Lead in Antimicrobial Resistance and Enteric Pathogens
Animal and Plant Health Agency (APHA)