Phase variation in the glycosyltransferase genes of Pasteurella multocida associated with outbreaks of fowl cholera on free-range layer farms

Retrospective analysis of antimicrobial resistance associated with bovine respiratory disease

The administration and utility of antibiotics to control and treat bovine respiratory disease (BRD) in beef cattle feedlots is a growing concern. Antimicrobial resistance (AMR) among BRD-associated bacterial pathogens has been the subject of cultivation-dependent and cultivation-independent surveillance. Bacterial genome sequencing and metagenomic approaches facilitate the characterization of AMR in the beef industry; however, the current collection of cattle-associated AMR research programs lack connections to each other. A more integrated view of how antimicrobial use (AMU) is related to resistance at a gene level is needed. We sought to establish a catalog of commonly observed AMR genes (ARGs) in opportunistic bacterial pathogens that contribute to BRD using publicly available data sets that were generated by the scientific community with and without AMU in mind. The presence of these clinically relevant ARGs appeared to differ by geography. Greater sampling in North America facilitated the generation of a list of ARGs often encoded by Mannheimia haemolytica and Pasteurella multocida. Detection of clinically relevant ARGs in shotgun metagenomes of cattle-associated and accessible feedlot samples such as water, soil, and feces was possible but limited by relative sequence read abundance. An exception was the tylosin esterase-encoding gene estT, which is among the most frequently observed ARGs in M. haemolytica and feedlot-related metagenomic data sets. Finally, by re-evaluating studies on the impact of AMU on AMR in beef production systems, we show that conventional practices, including in-feed antibiotic use, increase the relative abundance of ARGs in animal-derived samples.IMPORTANCEThis retrospective analysis delivers a list of ARGs found in opportunistic pathogens that contribute to BRD. The high incidence of BRD in North America is linked to the origin and implementation of metaphylaxis to mitigate detrimental animal losses at feedlots. Notably, ARGs commonly observed in these pathogens isolated in North America were not conserved across the globe, underscoring the relationship between regional AMU and AMR. A positive relationship was also observed between the relative abundance of ARGs in cattle-associated metagenomes with greater exposure to antibiotics. Overall, this analysis should help to guide future surveillance efforts and experimental designs to more directly evaluate the impacts of feedlot practices on AMR.

Welfare issues and potential solutions for laying hens in free range and organic production systems: A review based on literature and interviews

In free-range and organic production systems, hens can make choices according to their needs and desires, which is in accordance with welfare definitions. Nonetheless, health and behavioral problems are also encountered in these systems. The aim of this article was to identify welfare challenges observed in these production systems in the EU and the most promising solutions to overcome these challenges. It is based on a review of published literature and research projects complemented by interviews with experts. We selected EU specific information for welfare problems, however, the selected literature regarding solutions is global. Free range use may increase the risk of infection by some bacteria, viruses and parasites. Preventive methods include avoiding contamination thanks to biosecurity measures and strengthening animals' natural defenses against these diseases which can be based on nutritional means with new diet components such as insect-derived products, probiotics and prebiotics. Phytotherapy and aromatherapy can be used as preventive and curative medicine and vaccines as alternatives to antibiotics and pesticides. Bone quality in pullets and hens prevents keel deviations and is favored by exercise in the outdoor range. Free range use also lead to higher exposure to variable weather conditions and predators, therefore shadow, fences and guard animals can be used to prevent heat stress and predation respectively. Granting a free range provides opportunities for the expression of many behaviors and yet many hens usually stay close to the house. Providing the birds with trees, shelters or attractive plants can increase range use. Small flock sizes, early experiences of enrichment and personality traits have also been found to enhance range use. Severe feather pecking can occur in free range production systems, although flocks using the outdoor area have better plumage than indoors. While many prevention strategies are facilitated in free range systems, the influence of genetics, prenatal and nutritional factors in free range hens still need to be investigated. This review provides information about practices that have been tested or still need to be explored and this information can be used by stakeholders and researchers to help them evaluate the applicability of these solutions for welfare improvement.