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ABSTRACT: Farm dust metagenomes in European poultry and pig farms

PROVIDER: PRJNA623064 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11482400_1.fastq.gz	Fastqsanger.gz
	SRR11482400_2.fastq.gz	Fastqsanger.gz
	SRR11482317_1.fastq.gz	Fastqsanger.gz
	SRR11482317_2.fastq.gz	Fastqsanger.gz
	SRR11482318_1.fastq.gz	Fastqsanger.gz

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Description and determinants of the faecal resistome and microbiome of farmers and slaughterhouse workers: a metagenome-wide cross-sectional study.

Project description:Study generating and describing the faecal metagenomes of 194 persons occupationally exposed to antimicrobial resistance in livestock (including 46 control subjects). Highlights: - DNA of faecal samples of 194 persons occupationally exposed to antimicrobial resistance (AMR) in livestock, i.e. persons living or working on pig and poultry farms and pig slaughterhouse workers and control subjects, was sequenced and metagenomically analysed. - The faecal resistomes and microbiomes of farmers and slaughterhouse workers were described and compared between occupationally exposed groups and controls. - We found an increased ARG carriage in persons working in the Dutch pork production chain as compared to poultry farmers and controls. - Significant differences were found in the resistome and bacteriome composition of pig and pork exposed workers compared to a control group, as well as within-population (farms, slaughterhouse) compositional differences. - On-farm working hours and working or living on a pig farm (versus poultry farm) are determinants for the human faecal resistome. - Direct or indirect contact with AMR in livestock may be a determinant for human ARG carriage.

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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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