Draft Genome Sequence of Fusobacterium necrophorum subsp. funduliforme Bovine Liver Abscess Isolate B35

Development and validation of a multiple locus variable number tandem repeat analysis (MLVA) scheme for Fusobacterium necrophorum

Fusobacterium necrophorum is associated with various diseases in humans and animals. Reservoirs (sites where the pathogen persists in the absence of disease) of F. necrophorum are believed to be present in healthy individuals e.g. tonsillar epithelium, or their environment e.g. soil, but for most diseases the reservoir sites are unknown. Strain typing of F. necrophorum would facilitate linking specific reservoirs with a specific disease. The aim of this study was to develop multiple locus variable number tandem repeat analysis (MLVA) as a strain typing technique for F. necrophorum, and to test the use of this scheme to analyse both isolates and mixed communities of bacteria. Seventy-three tandem repeat regions were identified in the F. necrophorum genome; three of these loci were suitable and developed as a MLVA scheme. The MLVA scheme was sensitive, specific, and discriminatory for both isolates and communities of F. necrophorum. The MLVA scheme strain typed 46/52F. necrophorum isolates including isolates of both subspecies and from different countries, host species and sample sites within host. There were 12 unique MLVA strain types that clustered by subspecies. The MLVA scheme characterised the F. necrophorum community in DNA from 32/49 foot- and 28/33 mouth swabs from sheep. There were 17 community types in total. In 31/32 foot swabs, single strains of F. necrophorum were detected while in the 28 mouth swabs there were up to a maximum of 8 strains of F. necrophorum detected. The results demonstrate the potential for this method to elucidate reservoirs of F. necrophorum.

Antimicrobial usage and resistance in beef production

Antimicrobials are critical to contemporary high-intensity beef production. Many different antimicrobials are approved for beef cattle, and are used judiciously for animal welfare, and controversially, to promote growth and feed efficiency. Antimicrobial administration provides a powerful selective pressure that acts on the microbial community, selecting for resistance gene determinants and antimicrobial-resistant bacteria resident in the bovine flora. The bovine microbiota includes many harmless bacteria, but also opportunistic pathogens that may acquire and propagate resistance genes within the microbial community via horizontal gene transfer. Antimicrobial-resistant bovine pathogens can also complicate the prevention and treatment of infectious diseases in beef feedlots, threatening the efficiency of the beef production system. Likewise, the transmission of antimicrobial resistance genes to bovine-associated human pathogens is a potential public health concern. This review outlines current antimicrobial use practices pertaining to beef production, and explores the frequency of antimicrobial resistance in major bovine pathogens. The effect of antimicrobials on the composition of the bovine microbiota is examined, as are the effects on the beef production resistome. Antimicrobial resistance is further explored within the context of the wider beef production continuum, with emphasis on antimicrobial resistance genes in the food chain, and risk to the human population.

Use of Genomic Tools to Improve Cattle Health in the Context of Infectious Diseases

Although infectious diseases impose a heavy economic burden on the cattle industry, the etiology of many disorders that affect livestock is not fully elucidated, and effective countermeasures are often lacking. The main tools available until now have been vaccines, antibiotics and antiparasitic drugs. Although these have been very successful in some cases, the appearance of parasite and microbial resistance to these treatments is a cause of concern. Next-generation sequencing provides important opportunities to tackle problems associated with pathogenic illnesses. This review describes the rapid gains achieved to track disease progression, identify the pathogens involved, and map pathogen interactions with the host. Use of novel genomic tools subsequently aids in treatment development, as well as successful creation of breeding programs aimed toward less susceptible livestock. These may be important tools for mitigating the long term effects of combating infection and helping reduce the reliance on antibiotic treatment.