TY - JOUR

T1 - Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance

AU - Nordahl Petersen, Thomas

AU - Rasmussen, Simon

AU - Hasman, Henrik

AU - Carøe, Christian

AU - Bælum, Jacob

AU - Schultz, Anna Charlotte

AU - Bergmark, Lasse

AU - Svendsen, Christina A

AU - Lund, Ole

AU - Sicheritz-Pontén, Thomas

AU - Aarestrup, Frank M.

PY - 2015/7/10

Y1 - 2015/7/10

N2 - 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.

AB - 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.

KW - Aircraft

KW - Bacteria/classification

KW - Clostridium difficile/genetics

KW - Cluster Analysis

KW - Communicable Diseases/microbiology

KW - DNA, Bacterial/chemistry

KW - Drug Resistance, Bacterial/drug effects

KW - Genomics

KW - High-Throughput Nucleotide Sequencing

KW - Humans

KW - Norovirus/genetics

KW - Phylogeny

KW - RNA, Viral/chemistry

KW - Real-Time Polymerase Chain Reaction

KW - Salmonella enterica/genetics

KW - Sequence Analysis, DNA

KW - Waste Water/microbiology

U2 - 10.1038/srep11444

DO - 10.1038/srep11444

M3 - Journal article

C2 - 26161690

VL - 5

SP - 11444

JO - Scientific Reports

JF - Scientific Reports

SN - 2045-2322

ER -