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

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.本补充数据对应Shilov等人发表的题为《哈萨克斯坦四地区猪鼻咽微生物组与耐药组的牛津纳米孔（Oxford Nanopore）宏基因组数据集》的手稿。本研究针对猪鼻咽部细菌菌群中鉴定出的抗生素耐药基因相关数据展开评估。样本源自哈萨克斯坦四个地区私人农场饲养生猪的鼻咽拭子。带有相同区域编码但数字后缀不同的样本，代表在不同时间或不同农场开展的独立采样活动（例如_1与_2）。每个采样点均采集三头生猪的鼻咽拭子，因此每个采样点设置三份独立生物学重复。从每份生物学重复中单独提取细菌基因组DNA。使用搭载R10.4.1流通池（flow cell）的MinION Mk1B测序平台对提取的细菌DNA进行测序。使用耐药基因标识符bwt流程（Resistance Gene Identifier bwt，版本6.0.5）对每份宏基因组样本的分子耐药特征进行表征。研究采用从综合抗生素耐药数据库（Comprehensive Antibiotic Resistance Database，CARD，版本4.0.1）与WildCARD（版本4.0.2）中精心筛选的检测模型来鉴定抗菌药物耐药（Antimicrobial resistance，AMR）基因，以此实现对分子耐药组的全面表征，涵盖耐药基因变异体及其流行情况。