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

dataset
posted on 2025-05-06, 19:32 authored by Victoria PickensVictoria Pickens, Brandon Hall, Kathleen M. Yeater, Tanya Purvis, Edward Bird, Grant Brooke, Cassandra Olds, Dana NayduchDana Nayduch

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 File: Raw_fly_CFU_counts.xlsx

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

Funding

Central Life Sciences

USDA-ARS: 3020-32000-018-000D

History

Data contact name

Nayduch, Dana

Data contact email

dana.nayduch@usda.gov

Publisher

Ag Data Commons

Intended use

These data can be used for better understanding of bacterial abundance and prevalence of antimicrobial resistance in house flies associated with confined beef and dairy cattle operations.

Use limitations

These data are limited to only culturable, aerobic bacteria from house flies and should not be used to make inferences for the entire microbiome or AMR prevalence in house flies or livestock operations. Climate data may misrepresent actual climate conditions on each site for collection dates, as these variables were not measured onsite each collection date but rather collected from historical data of county Kansas Mesonet stations. These data were collected on alternating weeks from mid-August through early October, and so do not represent bacterial abundances or AMR prevalence in house flies for other months. Some bacterial isolates from this study are not species for which zone diameter interpretations are available according to the Clinical and Laboratory Standards Institute guidelines, and are therefore purely for research purposes.

Temporal Extent Start Date

2019-08-13

Temporal Extent End Date

2019-10-08

Theme

  • Not specified

Geographic location - description

Riley, Marion, and Washington counties, Kansas.

ISO Topic Category

  • farming
  • health

National Agricultural Library Thesaurus terms

antibiotic resistance; imagos; Musca domestica; Kansas; beef cattle; pests; disease transmission; risk; animal and human health; beef; coliform bacteria; agar; farms; morphs; tetracycline; florfenicol; enrofloxacin; ceftiofur; ampicillin; multiple drug resistance; ribosomal RNA; matrix-assisted laser desorption-ionization mass spectrometry; dairy cattle

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

ARS National Program Number

  • 104

ARIS Log Number

420454

Pending citation

  • No

Public Access Level

  • Public