Data from: Bacterial Abundance and Antimicrobial Resistance Prevalence Carried by Adult House Flies (Diptera: Muscidae) at Kansas Dairy and Beef Cattle Operations

<p dir="ltr">House flies (<i>Musca domestica </i>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).</p><p dir="ltr">Resources in this dataset:</p><h4><b>Resource File: Raw_fly_CFU_counts.xlsx</b></h4><p dir="ltr">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.</p><p dir="ltr"><b>Resource File: </b><b>Raw_daily_avg_climate_Jul-Oct 2019.xlsx</b></p><p dir="ltr">Resource description: Raw climate data downloaded from Kansas Mesonet weather stations for sampling period.</p><p dir="ltr"><b>Resource File: Metadata_bacterial_isolates.xlsx</b></p><p dir="ltr">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).</p><p dir="ltr"><b>Resource File: </b><b>Raw_isolates_disk_susceptibility</b><b>.xlsx</b></p><p dir="ltr">Resource description: Measured inhibition zones (in millimeters) of individual isolates which underwent disk susceptibility testing against 5 antibiotics (Tet, Flo, Enr, Cef, Amp).</p><p dir="ltr"><b>Resource file: </b><b>Raw_isolates_MALDI-TOF_outputs.xlsx</b></p><p dir="ltr">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.</p><p dir="ltr">All trimmed Sanger sequence reads of AMR isolates are publicly available at GenBank (<a href="https://www.ncbi.nlm.nih.gov/nuccore/PQ636534 - PQ636762" target="_blank">PQ636534 - PQ636762</a>).</p><p dir="ltr">The code repository for 16S sequence analysis for this project can be found here:<a href="https://github.com/vlpickens04/Sanger_Phred_Code" rel="noreferrer" target="_blank">https://github.com/vlpickens04/Sanger_Phred_Code</a></p>

Tags: amr, antibiotic-resistance, antibiotic-susceptibility-testing, antimicrobial-resistance, bacteria-abundance, beef-cattle, dairy-cattle, house-fly
Organization: Department of Agriculture