Meta-genomic analysis of toilet waste from long distance flights

Human populations worldwide are increasingly confronted with infectious diseases and antimicrobial resistance spreading faster and appearing more frequently. Knowledge regarding their occurrence and worldwide transmission is important to control outbreaks and prevent epidemics. Here, we performed shotgun sequencing of toilet waste from 18 international airplanes arriving in Copenhagen, Denmark, from nine cities in three world regions. An average of 18.6?Gb (14.8 to 25.7?Gb) of raw Illumina paired end sequence data was generated, cleaned, trimmed and mapped against reference sequence databases for bacteria and antimicrobial resistance genes. An average of 106,839 (0.06%) reads were assigned to resistance genes with genes encoding resistance to tetracycline, macrolide and beta-lactam resistance genes as the most abundant in all samples. We found significantly higher abundance and diversity of genes encoding antimicrobial resistance, including critical important resistance (e.g. blaCTX-M) carried on airplanes from South Asia compared to North America. Presence of Salmonella enterica and norovirus were also detected in higher amounts from South Asia, whereas Clostridium difficile was most abundant in samples from North America. Our study provides a first step towards a potential novel strategy for global surveillance enabling simultaneous detection of multiple human health threatening genetic elements, infectious agents and resistance genes.

全球范围内的人类群体正日益面临传染病与抗菌药物耐药性（antimicrobial resistance）传播速度加快、出现频次攀升的双重挑战。针对其发生与全球传播的相关认知，对控制疫情暴发、防范流行病扩散具有至关重要的意义。本研究对来自全球三大区域9座城市、抵达丹麦哥本哈根的18架国际航班的马桶废弃物开展了鸟枪法测序（shotgun sequencing）。研究共生成平均18.6 Gb（14.8至25.7 Gb）的原始Illumina双端测序数据，经质量清洗、序列修剪后，与针对细菌及抗菌药物耐药基因的参考序列数据库进行比对分析。平均有106,839条测序读段（reads），占总测序读段数的0.06%，被比对至耐药基因，其中编码四环素类、大环内酯类及β-内酰胺类抗菌药物耐药性的基因在所有样本中丰度最高。研究发现，相较于北美航班样本，南亚航班样本中的抗菌药物耐药基因丰度与多样性均显著更高，其中包含blaCTX-M等极重要的耐药基因。此外，南亚航班样本中还检测到丰度更高的肠炎沙门氏菌（Salmonella enterica）与诺如病毒（norovirus）；而艰难梭菌（Clostridium difficile）则在北美样本中丰度居首。本研究为构建可同时检测多种威胁人类健康的遗传元件、病原体及耐药基因的新型全球监测策略迈出了关键第一步。