,House flies (Musca domestica L.) are a global pest ubiquitous in urban and agricultural settings. Their dependence on microbe-rich substrates for development, as well as ability to acquire and transmit pathogenic and antimicrobial resistant (AMR) bacteria, make house flies a risk to human and animal health. Large livestock operations, like confined cattle, are environments which are conducive to both house flies and developing AMR due to large accumulations of animal feed and waste. However, little is known about what factors influence bacterial abundances and AMR prevalence carried by house flies in confined cattle operations. Adult house flies (n=6/fly sex/location) were collected on alternating weeks mid-August through early October of 2019 from a dairy and beef feedlot cattle operation in each of three Kansas counties (Riley, Marion, and Washington). We enumerated colony forming units (CFUs) of culturable aerobic bacteria and suspected coliforms (SC) from house fly homogenates on nonselective (tryptic soy agar, TSA) and selective (violet-red bile agar, VRBA) media to investigate factors, such as fly sex, farm type, location, and climate, which may be associated with bacterial abundances carried by house flies. Further, we screened unique morphotypes of SC isolates for tetracycline (Tet) resistance, then tested for additional resistance to florfenicol (Flo), enrofloxacin (Enr) ceftiofur (Cef), and ampicillin (Amp) to identify multi-drug resistant (MDR) isolates. AMR isolates were identified via 16S rRNA Sanger sequencing or, in select cases, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).,Resources in this dataset:,Resource description: Raw CFU counts for culturable aerobic bacteria (TSA) and suspected coliforms (VRBA) cultured from replica plating of ten-fold serially diluted house fly homogenates.,Resource File: Raw_daily_avg_climate_Jul-Oct 2019.xlsx,Resource description: Raw climate data downloaded from Kansas Mesonet weather stations for sampling period.,Resource File: Metadata_bacterial_isolates.xlsx,Resource description: Spreadsheet gives information linking individual isolate (Isolate ID #) data resources with which fly they originated from and other collection information (fly sex, farm type, collection date, county).,Resource File: Raw_isolates_disk_susceptibility.xlsx,Resource description: Measured inhibition zones (in millimeters) of individual isolates which underwent disk susceptibility testing against 5 antibiotics (Tet, Flo, Enr, Cef, Amp).,Resource file: Raw_isolates_MALDI-TOF_outputs.xlsx,Resource description: Spreadsheet of best and second-best matches of Bruker MALDI Biotyper Identification Results for individual isolates (Sample ID). Each isolate was measured in duplicate.,All trimmed Sanger sequence reads of AMR isolates are publicly available at GenBank (PQ636534 - PQ636762).,The code repository for 16S sequence analysis for this project can be found here:https://github.com/vlpickens04/Sanger_Phred_Code,

,Adult house flies (Musca domestica L.) are important reservoirs and mechanical vectors of bacteria in livestock operations. House fly bacterial communities are influenced by their local environment, yet a comprehensive understanding of bacterial diversity, pathogen prevalence, and bacterial source is not fully understood. We characterized bacterial communities from adult female house flies and associated manure samples from beef and dairy cattle farms in Kansas, Oklahoma, and Texas over four months (July-October). Bacterial community composition in flies and manure reflected the local environment, and house flies shared the majority (≥99%) of bacterial taxa with manure. The variability of bacterial diversity was greater among individual fly (species richness range: 48 - 1747) samples than manure (species richness range: 345 - 1162). Temporal variability of fly bacterial diversity was observed within each farm type. Bacterial taxa of veterinary and medical importance such as Corynebacterium, Turicibacter, Staphylococcus, Streptococcus, and Acinetobacter were highly prevalent in flies, constituting core bacterial communities. The prevalence of bacterial taxa associated with bovine keratoconjunctivitis (IBK) and bovine respiratory disease (BRD) was higher in flies than in manure and prevalence varied monthly. This study underscores the crucial role house flies play as carriers of cattle pathogens, contributing to their dissemination among animals and to off-site locations, where they pose a threat to surrounding communities and agricultural operations.,The raw Illumina MiSeq sequence data for this project can be found here: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1009094,Resources in this dataset:,,

,Datasheet for the abundance of total bacteria, gram positive indicator bacteria, horizontal gene transfer indicator genes and antibiotic resistance genes in the soil measured over 3 years.,,

,Nebraska Prairie Study for Agricultural Antibiotic Resistance in Lincoln, Nebraska The inherent spatial heterogeneity and complexity of antibiotic resistant bacteria and antibiotic resistance (AR) genes in manureaffected soils makes it difficult to sort out resistance that can be attributed to human antibiotic use from resistance that occurs naturally in the soil. This study characterizes native Nebraska prairie soils that have not been affected by human or food-animal waste products to provide data on background levels of resistance in southeastern Nebraskan soils. Soil samples were collected from 20 sites enumerated on tetracycline and cefotaxime media; screened for tetracycline-, sulfonamide-, b-lactamase–, and macrolide-resistance genes; and characterized for soil physical and chemical parameters. All prairies contained tetracyclineand cefotaxime-resistant bacteria, and 48% of isolates collected were resistant to two or more antibiotics. Most (98%) of the soil samples and all 20 prairies had at least one tetracycline gene. Most frequently detected were tet(D), tet(A) tet(O), tet(L), and tet(B). Sulfonamide genes, which are considered a marker of human or animal activity, were detected in 91% of the samples, despite the lack of human inputs at these sites. No correlations were found between either phenotypic or genotypic resistance and soil physical or chemical parameters. Heterogeneity was observed in AR within and between prairies. Therefore, multiple samples are necessary to overcome heterogeneity and to accurately assess AR. Conclusions regarding AR depend on the gene target measured. To determine the impacts of food-animal antibiotic use on resistance, it is essential that background and/or baseline levels be considered, and where appropriate subtracted out, when evaluating AR in agroecosystems.,