title: Meta-genomic analysis of toilet waste from long distance flights; a step towards global surveillance of infectious diseases and antimicrobial resistance.
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.
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Nordahl Petersen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.affiliation: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Hasman
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Christian
authors.initials: C
authors.lastname: Carøe
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Jacob
authors.initials: J
authors.lastname: Bælum
authors.affiliation: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Anna Charlotte
authors.initials: AC
authors.lastname: Schultz
authors.affiliation: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Lasse
authors.initials: L
authors.lastname: Bergmark
authors.affiliation: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Christina A
authors.initials: CA
authors.lastname: Svendsen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Ole
authors.initials: O
authors.lastname: Lund
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Thomas
authors.initials: T
authors.lastname: Sicheritz-Pontén
authors.affiliation: National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark.
authors.forename: Frank M
authors.initials: FM
authors.lastname: Aarestrup
mesh_terms: D000401:Aircraft; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D016360:Clostridioides difficile / Q000235:genetics / Q000302:isolation & purification; D016000:Cluster Analysis; D003141:Communicable Diseases / Q000382:microbiology / Q000473:pathology / Q000821:virology; D004269:DNA, Bacterial / Q000737:chemistry / Q000302:isolation & purification; D024881:Drug Resistance, Bacterial / Q000187:drug effects / Q000235:genetics*; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D029322:Norovirus / Q000235:genetics / Q000302:isolation & purification; D010802:Phylogeny; D012367:RNA, Viral / Q000737:chemistry / Q000302:isolation & purification; D060888:Real-Time Polymerase Chain Reaction; D019779:Salmonella enterica / Q000235:genetics / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D062065:Wastewater / Q000382:microbiology* / Q000821:virology
chemical_list: D004269:DNA, Bacterial; D012367:RNA, Viral; D062065:Wastewater