Microbiome of a cruise ship

Cruise ships are relatively small, crowded spaces where infection control is especially important. There is limited information available about the composition of the microbiome found on frequently-touched surfaces in cruise ships. This study describes the microbial composition of cruise ship surfaces and crew member skin microbiomes. Fingertips of crew members and surfaces were sampled using agar plates. After culturing, DNA was extracted and sequenced using Nanopore long-read whole metagenome sequencing. Classification was performed using Kraken2, and antibiotic resistance genes were identified using the CARD RGI Resistance Gene Identifier. In total, 10'369'710 reads were generated. In the 15 hand samples, 2'495 species were detected. 99.9% of the samples were identified as bacterial, which indicates a limitation of the extraction methods. The majority of the hand samples belonged to the Staphylococcus genus (69.38%). Significant individual differences were observed in the microbiome composition of each sample. For the surface samples, 22 species that were present in all or almost all surfaces were listed. Among them, many potentially dangerous pathogenic bacteria were identified, such as Acinetobacter baumannii, Enterobacter species, Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Their antimicrobial resistance genes were also detected in the analyzed sample.