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
SN - 2045-2322
VL - 5
SP - 11444
JO - Scientific Reports
JF - Scientific Reports
ER -
