Fig 1.
Nanopore sequencing workflow to rapidly identify bacteria in ambulances.
(A) Samples are acquired from three locations in three vehicles over a three-week period, followed by DNA isolation, 16S rRNA gene amplification and sample preparation. The prepared library is then sequenced using the MinION and analyzed to identify bacterial species present. Taxonomic identification is possible within 24 hours from initial sample acquisition. (B) Bioinformatics analysis pipeline for generating taxonomic data.
Table 1.
Raw Nanopore sequencing read statistics.
Table 2.
Filtered Nanopore sequencing read statistics.
Table 3.
Opportunistic pathogenic bacteria identified in EMS vehicles at the genus level.
Fig 2.
Diversity of bacterial genera detected in ambulances.
(A) Phylogenetic analysis of ambulance microbiota with confidence to the genus level. Colored segments correspond to unique phyla of bacteria. Organisms are unique to the EMS vehicles and were not identified in the control samples. Pathogenic genera are indicated by a red asterisk. (B) Relative abundance of bacterial genera with pathogenic species, represented as the average normalized sequencing reads detected over a three-week period from all ambulances for each sampling location and (C) from all sampling locations for each ambulance.
Fig 3.
A comparison of fold-change of taxa found in ambulances relative to first sampling event.
Heatmap illustrating the log2-fold change of organisms sequenced using ONT MinION relative to the first week of sampling. Yellow squares correspond to an increase in a given taxa at a corresponding week relative to Week 1, while blue squares indicate a decrease in abundance of a taxa relative to Week 1. Asterisks indicate a significant change relative to Week 1 (p<0.05). All changes from week 2 are significant relative to week 1 as indicated by the red asterisk.