Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis. [Dataset]

Abstract

Cryptosporidium parvum is an apicomplexan, protozoan parasite that invades the small intestinal epithelium of neonatal calves. It causes an acute diarrhoeal disease known as cryptosporidiosis, which is characterised by watery diarrhoea, dehydration, weight loss and even death in severe cases. Cryptosporidiosis leads to approximately 37% of all diarrhoea events and 20% of co-infections in calves in the UK, culminating in production losses of approximately £130 per calf affected and poorer overall animal welfare. Consequently, it is a serious veterinary issue which requires effective therapies to combat infection. With no vaccine available against bovine cryptosporidiosis at this time, the current therapeutic options in cattle are limited to the antibiotic, paromomycin, and the anti-cryptosporidial, FDA-approved drug, halofuginone, which is believed to target the merozoite and sporozoite stages. Unfortunately, both halofuginone and paromomycin have been found to have variable efficacy against cryptosporidiosis in calves. While the cryptosporidiostatic effect can both reduce oocyst shedding and severity of diarrhoea, these treatments are not lethal to Cryptosporidium and oocyst shedding and diarrhoea will often commence on drug withdrawal. In addition, halofuginone has high toxicity at twice the recommended dose, leading to adverse side effects, therefore calves must be weighed in order to administer an effective, non-lethal dose. In light of this, the development of new effective therapies against cryptosporidiosis in calves is crucial, not only from an animal welfare point of view but also from an economic perspective.

Citation

HARES, M.F., GRIFFITHS, B.E., JOHNSON, F., NELSON, C., HALDENBY, S., STEWART, C.J., DUNCAN, J.S., OIKONOMOU, G. and COOMBES, J.L. 2023. Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis. [Dataset]. Animal microbiome [online], 5, article number 43. Available from: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-023-00265-5#Sec20

• Acceptance Date: Sep 3, 2023
• Online Publication Date: Sep 12, 2023
• Publication Date: Dec 31, 2023
• Deposit Date: Sep 22, 2023
• Publicly Available Date: Sep 22, 2023
• Publisher: Springer
• DOI: https://doi.org/10.1186/s42523-023-00265-5
• Keywords: Bovine; Functional profiling; Cryptosporidium parvum; Cryptosporidiosis; Faecal microbiome; Pathway abundances; Metagenome
• Public URL: https://rgu-repository.worktribe.com/output/2086362
• Publisher URL: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-023-00265-5#Sec20
• Related Public URLs: https://rgu-repository.worktribe.com/output/2083464 (Journal article)
• Type of Data: PPTX, PDF and TXT files.
• Collection Date: Apr 21, 2023
• Collection Method: The study was conducted following ethical approval by the University of Liverpool Research Ethics Committee (VREC927) and procedures regulated by the Animals (Scientific Procedures) Act were conducted under a UK Home Office License (P191F589B). 346 female Holstein dairy calves were enrolled on this study from three farms (Farm 1, 2, and 3) based in North Wales and Cheshire, UK. Calves that had received routine antibiotic and/or anti-cryptosporidial prophylactic treatment were included as this is common practice on UK farms. All calves received a similar dietary regime of cow colostrum in the first 24 h of life, followed by milk replacer, and were then weaned onto a standard cereal and hay-based diet. One faecal sample was collected from each of the 346 ≤ 1-week-old calves by rectal swab (Sterilin Regular Nylon Flocked Swabs 552C, Scientific Laboratory Supplies), prior to the development of any clinical signs of cryptosporidiosis, and stored on dry ice immediately after the collection. Faecal swab samples were placed directly into bead beating tubes provided in the DNA extraction kit (DNeasy PowerLyzer PowerSoil Kit, QIAGEN). Excess plastic applicator was removed using scissors, sterilised with 100% ethanol and a Bunsen burner between samples, to allow swabs to fit into the tubes. DNA extraction was performed on all samples following the manufacturers protocol with the following adjustments; 500 µL of Powerbead solution was added to each tube along with 60 µL of solution C1. Swabs were bead beaten for 15 min in a tube adaptor on the Vortex Genie 2 at 7.5 speed. C2 and C3 were mixed 1:1 and 300 µL of this solution was added to the sample supernatant and placed at 4 °C for 5 min. 50 µL of C6 Elution Buffer was added to the spin column membrane and incubated at room temperature for 5 min to elute the gDNA. Negative extraction controls were provided in the form of empty bead beating tubes and were processed alongside the samples. 60 gDNA samples and three negative extraction control samples underwent shotgun metagenomic sequencing and analysis at the CGR, University of Liverpool. The Illumina fragment library was prepared from the gDNA samples using the Illumina NEBNext Ultra II FS kit on the Mosquito platform using the 1/10 reduced volume protocol. 50 ng of DNA was used as input material where available, followed by size selection of Adaptor-ligated DNA.