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

PLOS ONE, Dec 2019

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.

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

June Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach Saakshi Jalali 0 1 2 Samantha Kohli 0 1 2 Chitra Latka 0 1 2 Sugandha Bhatia 0 1 2 Shamsudheen Karuthedath Vellarikal 0 1 2 Sridhar Sivasubbu 0 1 2 Vinod Scaria 0 1 2 Srinivasan Ramachandran 0 1 2 0 1 GN Ramachandran Knowledge Center for Genome Informatics, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) , Mathura Road, Delhi, 110 020 , India , 2 Functional Genomics Unit, CSIR Institute of Genomics and Integrative Biology (CSIR-IGIB) , New Delhi , India , 3 Structural Biology Unit, CSIR -Institute of Genomics and Integrative Biology , Mathura Road, New Delhi, 110 020 , India , 4 Respiratory Disease Biology Unit, CSIR- Institute of Genomics and Integrative Biology , Mall Road, Delhi, 110007 , India , 5 Genomics and Molecular Medicine Unit, CSIR Institute of Genomics and Integrative Biology , Mathura Road, Delhi , India , 6 Academy of Scientific and Innovative Research (AcSIR), CSIR IGIB South Campus , Mathura Road, Delhi, 110020 , India 1 Funding: The project was funded by The Council of Scientific and Industrial Research through grant OLP1105. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript 2 Academic Editor: Ramy K. Aziz, Cairo University , EGYPT 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. - Competing Interests: VS is an editorial board member of PLOS ONE. This does not alter the Paper currency notes are extensively used in barter and trade [1]. There is well documented evidence suggesting that currency notes could act as fomites with enormous potential to carry microbes [2]. Paper currency has rough surface that provides a good niche for microorganisms and other particulates to settle and accumulate over long term and thereby constitute a potential source of infection. The levels and diversity of microbial contamination of currency notes depend on several factors including the period of their circulation, handling and its texture. The capacity of currency notes to absorb moisture also facilitates the growth and viability of microorganisms. Recently, several attempts have been made to characterize the sojourning microbial population on currency notes in various parts of the world [3–9]. Currency notes contaminated with pathogenic bacteria can also be a potential source of infection as in the case of food poisoning caused by enteropathogens [10,11]. In addition, currency notes have also been evaluated for their potential to transmit infectious pathogens like Ascaris lumbricoides, Enterobius vermicularis, Trichuris trichiura and Taenia species [1]. Carrier micro-organisms apart from reducing the lifespan of the notes, have been documented to cause infections in the skin, eye, gastrointestinal tract [8,12], internal organs [13,14], as well as the respiratory tract [15] in humans. Microorganisms such as Micrococcus spp., Corynebacterium spp., Vibrio cholerae, Mycobacterium tuberculosis and members of the Enterobacteriacea family top the list subs (...truncated)


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Saakshi Jalali, Samantha Kohli, Chitra Latka, Sugandha Bhatia, Shamsudheen Karuthedath Vellarikal, Sridhar Sivasubbu, Vinod Scaria, Srinivasan Ramachandran. Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach, PLOS ONE, 2015, Volume 10, Issue 6, DOI: 10.1371/journal.pone.0128711