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Metagenomics of toilet waste from long distance flights

I just saw this paper, published a couple of days ago in Nature’s Scientific Reports. And yeah, it’s open access! While reading this post, I would suggest playing Dalai Lama by Rammstein, the in-flight version of Der Erlkönig.

Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance
Thomas Nordahl Petersen, Simon Rasmussen, Henrik Hasman, Christian Carøe, Jacob Bælum, Anna Charlotte Schultz, Lasse Bergmark, Christina A. Svendsen, Ole Lund, Thomas Sicheritz-Pontén & Frank M. Aarestrup
Scientific Reports 5, Article number: 11444 doi:10.1038/srep11444

Here is the abstract:

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.

Mmm, it sounds a bit like “Big Brother is watching you” to me. But the science is cool.

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Elisabeth Bik

After receiving my PhD at Utrecht University in The Netherlands, I worked at the Dutch National Institute for Health and the St. Antonius Hospital in Nieuwegein. In 2001, I joined the Department of Microbiology and Immunology at Stanford, where I have worked on the characterization of the microbiome of human oral, gastric, and intestinal samples, as well as samples from marine mammals. Since November 2016, I am the new Science Editor at uBiome, a microbiome genomics company enabling citizen science. But you might also find me working on the detection of science misconduct, at my blog Microbiome Digest , an almost daily compilation of scientific papers in the rapidly growing microbiome field, on Twitter at @MicrobiomDigest.

One thought on “Metagenomics of toilet waste from long distance flights

  1. Update: On August 6, 2015, Sarah Zhang at Wired wrote a piece about this paper called: Airplane Poop Could Help Track Global Disease Outbreaks. It describes the airplane toilet study, but also some other studies done on sewage. Jonathan Eisen is quoted too.

    Meanwhile, analyzing toilet waste for public health is an idea still just floating around. “I’m not surprised that microbes vary between samples and they are related to the country of origin,” says Jonathan Eisen, a microbiologist at the University of California, Davis. “It’s a nice concept, but I’m not overwhelmed by the implications yet.”

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