Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach

• Published in: PloS one 2015-06, Vol.10 (6), p.e0128711-e0128711
• Main Authors: Jalali, Saakshi, Kohli, Samantha, Latka, Chitra, Bhatia, Sugandha, Vellarikal, Shamsudheen Karuthedath, Sivasubbu, Sridhar, Scaria, Vinod, Ramachandran, Srinivasan
• Format: Article
• Language: English
• Subjects: Acids; Antibiotic resistance; Antibiotics; Bacillus; Bacteriology; Biology; Cell culture; Cellulose; Corynebacterium glutamicum; Data processing; Deoxyribonucleic acid; Disease; DNA; DNA sequencing; Drug resistance; Drug Resistance, Microbial - genetics; Fomites; Fomites - microbiology; Food contamination & poisoning; Gene mapping; Gene sequencing; Genera; Genes; Genetic aspects; Genomes; Genomics; Health aspects; India; Informatics; Medical screening; Metagenomics - methods; Methods; Microbial drug resistance; Microbiomes; Microbiota - genetics; Microorganisms; Money; Object recognition; Pathogenic microorganisms; Pathogens; Physiological aspects; Ribonucleic acid; RNA; rRNA 16S; Sequence Analysis, DNA; Staphylococcus aureus; Staphylococcus infections; Vibrio cholerae; Viruses
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0128711

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.