DOI: 10.5281/zenodo.10104829
title: The Oropharyngeal Resistome of COPD Patients and Controls in a Livestock Dense Area in the Netherlands

description: Data description: 

The phyloseq S4 object "Phyloseq_resistome_VGO_COPD.rds" contains the otu_table with ARGs detected in the samples, sam_data containing sample metadata, and tax_table holding the taxonomy details (Resistance class and ARG cluster) for the ARGs. Read pairs underwent mapping against the ResFinder database (version: February 2020) (Zankari et al., 2012) using BBMap's default global alignment algorithm (Bushnell, 2013). Read pairs in this phyloseq object are raw reads. For our analysis, read pairs were firstly rarefied according to the relative correction factors per sample ("Relative_correction_factor" in the sam_data), then corrected for gene length (see gene lengths in "ARGlengths.xlsx" spreadsheet, then normalised to total bacteria in each sample ("DNA_concentration (qPCR_16S_ngml)" in the sam_data). 
The excel sheet "Sample_data_resistome_VGO_COPD.xlsx" contains the sample metadata as a separate file.
The excel sheet "ARGlengths.xlsx" contains the list of ARGs and their corresponding gene lengths.  
Metagenomic sequencing data is deposited at NCBI-SRA under BioProject accession: PRJNA1049329. Additional metadata is available upon request.
Abstract: 
Emissions from livestock farms have been associated with respiratory morbidity among neighbouring residents. These emissions, encompassing gases, bacteria and antimicrobial resistance genes (ARGs), can potentially modify the respiratory microbiome and resistome - the complete collection of bacterial genes potentially responsible for acquired antimicrobial resistance. This poses a heightened risk of more severe and difficult-to-treat infections. We aimed to elucidate potential associations between livestock farm microbial emissions and the structural composition of the oropharyngeal (OP) resistome. We conducted our research in a matched case-control study involving 35 individuals diagnosed with COPD and 34 control participants, all residing in a rural region in the Netherlands. OP swabs were collected from all participants, and resistome profiling was performed using ResCap. Exposure to livestock farms was defined using distance-based metrics as well as modelled concentrations of livestock-emitted endotoxin, PM10 and other microbial air pollutants. Our resistome analysis revealed that individuals with COPD exhibited notably heightened alpha diversity compared to the control group (Shannon diversity, p=0.047), however there were no significant compositional differences between the two groups (PERMANOVA, p=0.179). Exposure to airborne Staphylococcus and the mecA ARG (potentially carried by Staphylococcus), both common livestock-related microbial emissions, were significantly associated with reduced resistome evenness (Simpson's Evenness, p<0.05), while no significant associations were observed with the overall composition of the resistome. Additionally, significant correlations were observed between the OP resistome and microbiome compositions. In conclusion, our study highlights that the COPD airway creates a favourable environment for a variety of ARGs, irrespective of recent antimicrobial usage. Our findings also indicate the intricate interplay between the resistome and microbiome, emphasising the need to study both to gain insights into respiratory health and effective antimicrobial resistance mitigation. This study provides insights into the complex relationships between livestock farm emissions, the resistome, and respiratory health in individuals with and without COPD.