Microbiome of Foot Lesions in Beef Cattle

Background

Foot rot is a leading reason for antibiotic treatment in feedlots, second only to bovine respiratory disease. Cuts, abrasions, and prolonged time in pens that are wet, muddy, have poor drainage and even excessively dry environments can increase likelihood of infection, but foot rot can still be prevalent in well-managed feedlots. An effective foot rot vaccine would be valuable to improve animal welfare and reduce treatment costs. Unfortunately, the commercially available foot rot vaccine has limited effectiveness. It is based on a single bacterium (F. necrophorum), but there may be more bacteria involved in foot rot infections.

Another challenge can arise when lameness is assumed to be foot rot and is treated as such when the cause is something else, like digital dermatitis (also known as hairy heel wart, strawberry foot rot, raspberry heel, or foot wart). While foot root should respond to injectable antibiotics, digital dermatitis does not. As a result, mistaking one for the other can result in the unnecessary and ineffective use of antibiotics and could result in antibiotic resistance. Although foot rot and digital dermatitis remain leading causes of lameness in cattle, we don’t fully understand all of the bacteria that are involved. Having a better understanding of the microbial populations involved in both conditions could help inform more effective prevention and treatment protocols.

Objectives

• Identify the presence and proportions of known anaerobic bacterial species (anaerobic microbiome) with anaerobic culture and 16S sequencing of all bacteria, from samples from cattle with foot rot, digital dermatitis or both, as well as determine antimicrobial resistance patterns
• Describe differences in identified bacterial species between sampling strategies (skin biopsy, swab, subcutaneous tissue sampling)
• Describe clinical characterization of cattle afflicted by foot rot, solely as well as in combination with digital dermatitis, while capturing risk factors for both diseases, and link this to laboratory diagnosis

What they Did

In the first two years, the team identified 7 feedlots from southern Alberta and assigned 100 cattle into five different categories: (1) foot rot, (2) digital dermatitis-M2 (active), (3) digital dermatitis-M4 (chronic), (4) inconclusive (not having textbook definition of lesions or having characteristics of both lesions), and (5) unaffected cattle (20 head). Samples were collected from the skin surface (swab sample), skin tissue (skin biopsy), and tissue underlying the skin (subcutaneous biopsy) of all cattle. The bacteria present in the samples were identified, and microscopic changes were examined in the skin biopsy samples. Finally, they compared antibiotic resistance and bacterial profiles (sample-wise and category-wise) between foot rot, digital dermatitis and unaffected cases. Information about breed, days on feed, leg cleanliness, and weight was collected.

What They Learned

This team determined that, although convenient, skin swabs were not useful for microbiome analysis as they collected too many skin surface bacteria that weren’t obviously related to foot rot or digital dermatitis. Further, the microscopic analysis of the tissues also did little to differentiate between the two infections. Of the sampling technics examined, skin and subcutaneous biopsy samples were much more useful in identifying bacterial differences between the categories.

Results of sampling cases of foot rot and digital dermatitis found that many of the same bacteria were often found in both, although their relative proportions varied. For example, Fusobacterium spp. and Treponema spp. were found in both infections, but while Fusobacterium spp. were more abundant in foot rot, Treponema spp. were more abundant in digital dermatitis. Additionally, Fusobacterium necrophorum was more common in foot rot compared to digital dermatitis, but the opposite was found for Fusobacterium mortiferum.

Most of the 95 anaerobic bacterial isolates carried tetracycline resistance genes but few carried genes for beta-lactam resistance (penicillin and ceftiofur).However, animal numbers were too small to determine whether these genetic differences in antibiotic resistance were related to lameness treatment outcomes.

What it means

From this analysis, it appears to foot rot and digital dermatitis are microbiologically different diseases differentiated by varying proportion of bacteria in the anaerobic microbiomes in hooves with active infections. Treatment and prevention protocols for foot rot and digital dermatitis should be approached differently as they are microbially different. Though the results suggest that the microbiome might not help to diagnose individual cases of foot rot and digital dermatitis there is potential it may help to better understand outbreaks at the herd-level.