Table 1.
Input DNA amounts versus sequencing yields.
Table 2.
Percentages of reads assigned at different taxonomic levels with four classification methods.
Fig 1.
Comparison of WaferGen ARG 2-ΔCT values with MinION ARG counts (hits) with reference to the 16S rRNA gene.
(A) ICU cages (B) Laundry Trolley. X axis: normalised differences in 2-ΔCT values of ARGs when compared to 16S rRNA 2-ΔCT value obtained with WaferGen; Y axis: normalised differences in counts of ARGs when compared to the 16S rRNA count obtained with program ABRicate using MinION sequence data.
Fig 2.
Abundance of bacterial reads carrying ARGs relative to their taxonomic origin in the ICU cages (ICU), Laundry Trolley (LT), Mop Bucket (MB) and Office Corridor (OC).
Table 3.
Antimicrobial resistance genes associated with mobile genetic elements in the veterinary hospital.
Table 4.
Comparison of phenotypic and genotypic detection of antimicrobial resistance in the veterinary hospital.
Fig 3.
Venn diagrams showing the distribution of shared ARGs in the ICU cages (ICU), Laundry Trolley (LT), Mop Bucket (MB) and the Office Corridor (OC) samples.
(A) Total ARG profiles; (B) High-risk ARG profiles (according to the ranking scheme from Martinez et al.).
Fig 4.
Relative abundances of high-risk genes shared between hospital sites.
Comparative abundance between (A) ICU cages and Laundry Trolley (B) ICU cages and Mop Bucket. Grey scale indicates ARG counts per mega base pairs.
Fig 5.
Microbial composition at family level in ICU cages (ICU), Laundry Trolley (LT), Mop Bucket (MB) and Office Corridor (OC) samples.
Only the families with relative abundance of >1 copy per mega base pair are represented.
Table 5.
Sequences carrying multiple antimicrobial resistance genes in the veterinary hospital.
Fig 6.
Co-occurrence of ARGs and MGEs in nanopore reads (top) and illumina contigs (bottom).
Gene organisation of representative sequences from (A) ICU cages (B) Laundry Trolley and (C) Mop Bucket. Resistance genes, light blue: trimethoprim; red: sulphonamides; purple: beta-lactams; yellow: aminoglycosides; grey: rifamycin; pink: macrolides; blue: chloramphenicol; brown: tetracycline; luminous green: fluoroquinolone; dark orange: quaternary ammonium compounds. Mobile Genetic Elements, dark blue: transposases; green: integrases; light orange: plasmid-associated. HP: Hypothetical Proteins.