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2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi
,2014 Swine CAFO Study SE for Agricultural Antibiotic Resistance in Mississippi State, Mississippi The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future “downstream” implications from both an environmental and public health perspective.,
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농림축산식품부 농림축산검역본부 가축 및 반려동물 항생제 내성 모니터링 결과
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2020년도 국가 항생제 사용 및 내성 모니터링 리포트<동물, 축산물> - 축수산용 항생제 판매량, 가축 및 도체 유래 세균의 항생제 내성, 반려동물 유래 세균의 항생제 내성, 유통 축산물 유래 세균의 항생제 내성
2014 Naive Broiler CAFO Study for Agricultural Antibiotic Resistance in Mississippi State, Mississippi
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,2014 Naive Broiler CAFO Study for Agricultural Antibiotic Resistance in Mississippi State, Mississippi Conventional commercial broiler production involves the rearing of more than 20,000 broilers in a single confined space, atop bedding material such as pine shavings or rice hulls, for approximately 6.5 weeks. This environment is known for harboring pathogens and antibiotic resistant bacteria, but studies have focused on previously established houses. A concerted effort by the broiler industry has involved the scaling back of antibiotic use on-farm, but this has only been a recent occurrence. In the current study, a set of three naïve houses were followed from inception through 11 broiler flocks and monitored for ambient climatic conditions, bacterial pathogens, and antibiotic resistance. Within the first 3 weeks of the first flock cycle, 100% of litter samples were positive for Salmonella and Listeria while Campylobacter was culture negative. In all likelihood, given that pre flock bedding and soil levels were negative for pathogens and 4-5 orders of magnitude lower for other indicators, chicks most likely provided the colonizing bacteria. The influence of intra-house location was minor with only watering lines and side walls influencing some pathogen and indicator levels. Most bacterial groups experienced the typical cyclical pattern of litter contamination seen in other studies. This study represents a first of its kind view into the time required for bacterial pathogens and antibiotic resistance to colonize and establish in naïve broiler houses.,
Persistence of antibiotic resistance genes in beef cattle backgrounding environment after cessation of operation
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,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
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,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.,
Data from: Groundwater surveillance of endemic swine pathogens on forty Iowa swine farms via dead-end ultrafiltration
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,Groundwater samples were collected in an observational study design by dead-end ultrafiltration from private wells on 40 Iowa swine farms and analyzed by quantitative polymerase chain reaction (qPCR) to assess contamination by endemic swine pathogens and swine manure markers. These data facilitate investigation of groundwater as a biosecurity risk on swine farms. Each farm was sampled one time. Twenty farms were sampled in spring of 2024 (4/15/2024 – 5/29/2024) and twenty farms were sampled in fall of 2024 (9/16/2024 – 10/29/2024). Sample volumes were 639–853 L (mean = 759). Control samples were collected in the field for each field sample, and control samples were tested for all organisms if the corresponding field sample tested positive for any organism. Samples were shipped on ice to the laboratory where they were backflushed, underwent secondary concentration, and archived at -80 degrees Celsius. Secondary concentrates were subsampled for nucleic acid extraction using the QIAGEN QIAcube Connect system, and each nucleic acid extract was analyzed in duplicate by qPCR using a Roche LightCycler 480 II for the following microorganisms: Cryptosporidium spp., enteropathogenic Escherichia coli, porcine circovirus type 2, porcine epidemic diarrhea virus, porcine reproductive and respiratory syndrome virus, rotavirus group C, Salmonella spp., swine Bacteroidales (2 qPCR assays), and swine influenza virus. Negative and positive controls were included at lab steps for concentration, nucleic acid extraction, reverse transcription, and qPCR. PCR inhibition was assessed in each nucleic acid extract and mitigated by dilution if necessary. Data are expressed as genomic copies per liter of groundwater sampled unless otherwise indicated. Dataset consists of 1 spreadsheet file: Dataset 01102025_V4.csv. Variables in this file are described in the included data dictionary.,
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