The dataset on the resistome of the swine nasopharyngeal microbiome from different regions of Kazakhstan

Description

Supplementary data for the manuscript by Shilov et al. “Oxford Nanopore Metagenomic Dataset of Swine Nasopharyngeal Microbiomes and Resistomes From Four Regions of Kazakhstan”. In this study, we assessed data on antibiotic resistance genes identified in the bacterial microbiota of the swine nasopharynx. The samples consisted of nasopharyngeal swabs collected from pigs reared on private farms in four regions of Kazakhstan. Samples with the same regional code, but different numerical suffixes represented separate sampling events conducted at different times and/or on different farms (e.g., _1 and _2). At each sampling site, nasopharyngeal swabs were taken from three individual pigs, resulting in three independent biological replicates at each sampling site. Bacterial genomic DNA was extracted separately from each biological replicate. The isolated bacterial DNA was sequenced using a MinION Mk1B platform equipped with an R10.4.1 flow cell. The molecular resistance of each metagenomic sample was characterized using the Resistance Gene Identifier bwt pipeline (RGI bwt, version 6.0.5). Antimicrobial resistance (AMR) genes were identified using carefully selected detection models from the Comprehensive Antibiotic Resistance Database (CARD, version 4.0.1) and WildCARD (version 4.0.2), which enabled a comprehensive characterisation of the molecular resistome, including resistance gene variants and their prevalence.

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Funders

• Ministry of Science and Higher Education of the Republic of Kazakhstan

  Grant ID: AP26194599

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