Cluster of Salmonella Napoli in a dairy cattle farm in Piacenza (North Italy)
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB74287 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13908657_1.fastq.gz | Fastqsanger.gz | |||
| ERR13908657_2.fastq.gz | Fastqsanger.gz | |||
| ERR13908658_1.fastq.gz | Fastqsanger.gz | |||
| ERR13908658_2.fastq.gz | Fastqsanger.gz | |||
| ERR13908659_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Farm exposures in early life reduce the risks for childhood allergic diseases and asthma. There is less information about how farm exposures relate to respiratory illnesses and mucosal immune development. Objective: We hypothesized that children raised in farm environments have a lower incidence of viral illnesses over the first two years of life than non-farm children. We also analyzed between farm exposures or respiratory illnesses were related to patterns of nasal cell gene expression. Methods: The Wisconsin Infant Study Cohort (WISC) birth cohort enrolled farm and non-farm pregnant women from central Wisconsin. Parents reported prenatal farm and other environmental exposures. Illness frequency and severity were assessed using illness diaries and periodic surveys. Nasopharyngeal cell gene expression at age two years was compared to farm exposure and respiratory illness history. Results: There was a higher rate of respiratory illnesses in the non-farm vs. farm group (rate ratio 0.82 [0.69,0.97], p=0.020), but no significant differences in wheezing illnesses. There was a stepwise reduction in rates of respiratory illnesses in children exposed at least weekly to 0, 1, or ≥2 animals (p=0.006). In analyzing nasal cell gene expression, farm exposures and preceding respiratory illnesses were positively related to gene signatures for mononuclear cells and innate and antimicrobial responses. Conclusions: Children exposed to farms and farm animals had lower rates of respiratory illnesses over the first two years of life. Both farm exposures and preceding respiratory illnesses were associated with increased innate immune responses, suggesting that these exposures stimulate mucosal immune responses to reduce subsequent illness frequency.
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Project description:Dairy farm Soil Microbiome Raw sequence reads
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Project description:Prolonging dairy cattle longevity is regarded as one of the options to contribute to a more sustainable milk production. Cattle longevity is a direct result from culling decisions, which is primarily driven by economic considerations. As a consequence, at the herd level, cattle longevity can have effects on the efficiency of dairy production. This study investigates the technical inefficiency of dairy input, and its association with cattle longevity under Dutch commercial dairy production conditions, using a two-stage data envelopment analysis (DEA) approach. First, the technical inefficiency of capital, labor, land, seed & crop protection expenses, veterinary services, livestock purchase & services, feed purchase, miscellanea, livestock units and total input on total farm revenues was computed using DEA. Secondly, a bootstrap truncated regression analysis was applied to identify the association of cattle longevity with the evaluated input-specific and total input scores for technical inefficiency. Data were compiled from performance and accountancy records of 1,037 commercial Dutch dairy herds over the period of 2007 to 2014. In general, Dutch dairy farms displayed a relatively good overall technical efficiency, represented by an average inefficiency score of 0.09. The economic benefit of extending cattle longevity was evidenced by the negative association of cattle longevity with total input inefficiency. Of the evaluated inputs, the utilization of livestock units and feed was most efficient, with inefficiency scores below 0.26. This contrasts with the poor input efficiency of capital and livestock purchase & services with inefficiency scores around 0.52. Although the strength of the evaluated associations was generally low, the regression results illustrated that, except for labor, the age of culled cows was significantly negatively associated (P < 0.05) with each of the input inefficiencies. This contrasts with the significant associations of input inefficiencies with lifetime milk production, which were mostly positive. Since lifetime milk production is driven by length of cattle lifespan in combination with production level of the cows, the reverse direction of the associations with the two longevity indices illustrates that prolonging cattle longevity can improve efficiency performance of a dairy farm as long as the milk yield per cow remains unchanged.
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Project description:Salmonella Napoli isolated from human in 2019 were completely sequenced
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Project description:Lactiplantibacillus argentoratensis strain:DSM | isolate:Songhuajiang dairy Farm Genome sequencing
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Project description:Background: Inhalation exposure to biological particulate matter (BioPM) from livestock farms may provoke exacerbations in subjects suffering from allergy and asthma. The aim of this study was to use a murine model of allergic asthma to determine the effect of BioPM derived from goat farm on airway allergic responses Methods: Fine (< 2.5 μm) BioPM was collected from an indoor goat stable. Female BALB/c mice were ovalbumin (OVA) sensitized and challenged with OVA or saline as control. The OVA and saline groups were divided in sub-groups and exposed intranasally to different concentrations (0, 0.9, 3, or 9 μg) of goat farm BioPM. Bronchoalveolar lavage fluid (BALF), blood and lung tissues were collected. Results: In saline-challenged mice, goat farm BioPM alone induced a dose-dependent increase in neutrophils in BALF and induced production of macrophage inflammatory protein-3a). In OVA-challenged mice, BioPM significantly enhanced 1) inflammatory cells in BALF, 2) OVA-specific Immunoglobulin (Ig)G1, 3) interleukin-23 production, 4) airway mucus secretion-specific gene expression. RNAseq analysis of lungs indicates that neutrophil chemotaxis and oxidation-reduction processes were the representative genomic pathways in saline and OVA-challenged mice, respectively. Conclusions: A single exposure to goat farm BioPM enhanced airway inflammation in both saline and OVA-challenged allergic mice, with neutrophilic response as Th17 disorder and eosinophilic response as Th2 disorder indicative of the severity of allergic responses. Identification of the mode of action by which farm PM interacts with airway allergic pathways will be useful to design potential therapeutic approaches.
2020-08-01 | GSE148240 | GEO