Antibiotic resistance is a global problem affecting both human and animal health. Ensuring the strategic and effective use of antibiotics is paramount to combatting the emergence and spread of resistance. This study explored New York State (NYS) dairy farmers' perceptions regarding antibiotic use in dairy farming and antibiotic resistance. Dairy farmers' perceptions were assessed through semi-structured, in-person interviews. Twenty interviews with farm owners and/or managers of 15 conventional and five USDA certified organic dairy farms with 40 to 2,300 lactating cows were conducted. Thematic analysis was used to assess, compare and contrast transcripts for farmers' characterization of their beliefs, values, and concerns. Conventional dairy farmers had a low level of concern about the possible impacts of on-farm antibiotic resistance on human health and believed their antibiotic use was already judicious. Generally, they believed their cattle's health would suffer if antibiotic use were further curtailed. Conventional farmers expressed frustration over the possibility of more stringent governmental, milk cooperative, buyer, or marketer requirements for antibiotic use and associated animal welfare in the future. They attributed expanding regulations in part to misinformed consumer preferences, that farmers felt were influenced by the marketing of organic dairy products. Organic dairy farmers were generally more concerned about issues related to antibiotic resistance than conventional farmers. Both conventional and organic farmers placed emphasis on disease prevention through herd health management rather than treatment. In conclusion, the conventional NYS dairy farmers in this study were skeptical of the need for and benefits of reduced antibiotic use on their dairy farms. Interventions for farmers, delivered by a trusted source such as a veterinarian, that provide training about proper antibiotic use practices and information of possible financial benefits of refining antibiotic use may hold promise.

Occurrence of Listeria monocytogenes (Lm), the causative agent of listeriosis, in food processing facilities presents considerable challenges to food producers and food safety authorities. Design of an effective, risk-based environmental monitoring (EM) program is essential for finding and eliminating Lm from the processing environment to prevent product contamination. A scoping review was conducted to collate and synthesize available research and guidance materials on Listeria EM in food processing facilities. An exhaustive search was performed to identify all available research, industry and regulatory documents, and search results were screened for relevance based on eligibility criteria. After screening, 198 references were subjected to an in-depth review and categorized according to objectives for conducting Listeria sampling in food processing facilities and food sector. Mapping of the literature revealed research and guidance gaps by food sector, as fresh produce was the focus in only 10 references, compared to 72 on meat, 52 on fish and seafood, and 50 on dairy. Review of reported practices and guidance highlighted key design elements of EM, including the number, location, timing and frequency of sampling, as well as methods of detection and confirmation, and record-keeping. While utilization of molecular subtyping methods is a trend that will continue to advance understanding of Listeria contamination risks, improved study design and reporting standards by researchers will be essential to assist the food industry optimize their EM design and decision-making. The comprehensive collection of documents identified and synthesized in this review aids continued efforts to minimize the risk of Lm contaminated foods.

A canine coronavirus (CCoV) has now been reported from two independent human samples from Malaysia (respiratory, collected in 2017–2018; CCoV-HuPn-2018) and Haiti (urine, collected in 2017); these two viruses were nearly genetically identical. In an effort to identify any novel adaptations associated with this apparent shift in tropism we carried out detailed evolutionary analyses of the spike gene of this virus in the context of related Alphacoronavirus 1 species. The spike 0-domain retains homology to CCoV2b (enteric infections) and Transmissible Gastroenteritis Virus (TGEV; enteric and respiratory). This domain is subject to relaxed selection pressure and an increased rate of molecular evolution. It contains unique amino acid substitutions, including within a region important for sialic acid binding and pathogenesis in TGEV. Overall, the spike gene is extensively recombinant, with a feline coronavirus type II strain serving a prominent role in the recombinant history of the virus. Molecular divergence time for a segment of the gene where temporal signal could be determined, was estimated at around 60 years ago. We hypothesize that the virus had an enteric origin, but that it may be losing that particular tropism, possibly because of mutations in the sialic acid binding region of the spike 0-domain.

The increased accessibility of next generation sequencing has allowed enough genomes from a given bacterial species to be sequenced to describe the distribution of genes in the pangenome, without limiting analyses to genes present in reference strains. Although some taxa have thousands of whole genome sequences available on public databases, most genomes were sequenced with short read technology, resulting in incomplete assemblies. Studying pangenomes could lead to important insights into adaptation, pathogenicity, or molecular epidemiology, however given the known information loss inherent in analyzing contig-level assemblies, these inferences may be biased or inaccurate. In this study we describe the pangenome of a clonally evolving pathogen, Mycobacterium bovis , and examine the utility of gene content variation in M. bovis outbreak investigation. We constructed the M. bovis pangenome using 1463 de novo assembled genomes. We tested the assumption of strict clonal evolution by studying evidence of recombination in core genes and analyzing the distribution of accessory genes among core monophyletic groups. To determine if gene content variation could be utilized in outbreak investigation, we carefully examined accessory genes detected in a well described M. bovis outbreak in Minnesota. We found significant errors in accessory gene classification. After accounting for these errors, we show that M. bovis has a much smaller accessory genome than previously described and provide evidence supporting ongoing clonal evolution and a closed pangenome, with little gene content variation generated over outbreaks. We also identified frameshift mutations in multiple genes, including a mutation in glpK, which has recently been associated with antibiotic tolerance in Mycobacterium tuberculosis . A pangenomic approach enables a more comprehensive analysis of genome dynamics than is possible with reference-based approaches; however, without critical evaluation of accessory gene content, inferences of transmission patterns employing these loci could be misguided.