Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach

Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

媒介物（fomites）是微生物感染的常见传染源，既往研究已对不同来源媒介物的暂居微生物组开展了相关解析。纸币作为最常流通的物品之一，其传播病原微生物的潜力早已得到广泛认可。此前用于鉴定纸币关联微生物组的方法，大多局限于依赖培养的技术。后续研究则采用了基于16S核糖体RNA（16S rRNA）的方法，实现了微生物组分类学分布的解析。然而，包括鸟枪测序法在内的新兴技术，可实现基因层面的分辨率，并能估算其在宏基因组中的拷贝数。本研究采用鸟枪宏基因组测序方法，对印度纸币的微生物组展开了调查。研究人员从高频流通面额的印度纸币样本中分离宏基因组DNA，并通过Illumina Hiseq测序仪完成测序。数据分析显示，样本中存在隶属于真核与原核生物属的物种。界水平的分类学分布结果显示，可比对至真核生物的重叠群占比70%、细菌占9%，病毒与古菌约占1%。本研究共鉴定出78种病原菌，包括金黄色葡萄球菌（Staphylococcus aureus）、谷氨酸棒杆菌（Corynebacterium glutamicum）、粪肠球菌（Enterococcus faecalis）；同时鉴定出75种纤维素降解生物，包括解纤维热酸菌（Acidothermus cellulolyticus）、产黄纤维单胞菌（Cellulomonas flavigena）与白色瘤胃球菌（Ruminococcus albus）。此外，本研究共鉴定出78个抗生素抗性基因，其中18个在所有样本中均被检出。78种病原菌中有6种至少携带上述18个常见抗生素抗性基因中的1个。据我们所知，本数据集为首个纸币鸟枪宏基因组测序数据集，可应用于包括可流通媒介物传染病原体生物监测在内的未来研究场景。