TABLE 1.
WGS analysis for samples with completely discordant taxonomic assignment by Sanger, Illumina, and Nanopore 16S rRNA sequencinga
| Sample ID | Species inferred by Sanger 16S | Species inferred by resolved Illumina 16Sc | Species inferred by resolved Nanopore 16Sd | WGS results |
||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Best-matched species by WGS (reference genome accession no.) | Shasta genome assembly |
Miniasm genome assembly |
||||||||
| Query coverage (%) | Identity (%) | ANI (%)e | Query coverage (%) | Identity (%) | ANI (%)e | |||||
| Klebsiella pneumoniae BAA3079b | NA | NA | NA | Klebsiella pneumoniae (NC_016845.1) | 99.00 | 97.00 | 98.92 | 92.13 | 99.40 | 99.14 |
| Staphylococcus aureus BAA3114b | NA | NA | NA | Staphylococcus aureus (NC_007795.1) | 94.06 | 99.95 | 99.30 | 88.39 | 99.92 | 99.23 |
| R001 | Kocuria koreensis | Kocuria massiliensis | Kocuria spp. | Kocuria massiliensis (NZ_LT835161.1) | 42.21 | 87.44 | 78.29 | 42.42 | 87.41 | 78.55 |
| R006 | Kocuria koreensis | Kocuria massiliensis | Kocuria spp. | Kocuria massiliensis (NZ_LT835161.1) | 43.04 | 79.12 | 78.49 | 42.04 | 87.49 | 78.44 |
| R062 | Klebsiella grimontii | Enterobacter cloacae | Yokenella regensburgei | Klebsiella michiganensis (NZ_CP060111.1) | 92.17 | 99.17 | 98.71 | 86.30 | 98.99 | 98.69 |
| R120 | Brachybacterium conglomeratum | Brachybacterium faecium | Brachybacterium paraconglomeratum | Brachybacterium saurashtrense (NZ_CP031356.1) | 62.15 | 85.18 | 82.30 | 62.30 | 85.12 | 82.39 |
| R121 | Schaalia odontolytica | Schaalia vaccimaxillae | Sphingomonas paucimobilis | Schaalia odontolytica (NZ_CP046315.1) | 6.07 | 78.55 | 70.34 | 6.04 | 78.24 | 70.86 |
| R131 | Schaalia odontolytica | Schaalia vaccimaxillae | No reliable ID | Schaalia odontolytica (NZ_CP046315.1) | 6.19 | 82.12 | 71.21 | 6.29 | 78.25 | 71.26 |
| R158 | Microbacterium ginsengiterrae | Microbacterium assamensis | Microbacterium foliorum | Microbacterium foliorum (NZ_CP041040.1) | 65.41 | 84.52 | 82.24 | 65.21 | 84.51 | 82.15 |
| R181 | Sphingomonas yabuuchiae | Sphingomonas paucimobilis | Sphingomonas sanguinis | Sphingomonas hominis (NZ_JABULH010000007.1) | 31.48 | 89.67 | 82.09 | 30.68 | 89.59 | 81.95 |
a
ID, identification; NA, not applicable.
b
Klebsiella pneumoniae BAA3079 and Staphylococcus aureus BAA3114 served as quality control samples, which were sequenced and analyzed in parallel with the discordant samples for WGS and bioinformatics analysis.
c
Discordant samples between MSR and Illumina_BLAST+ were resolved by nf-core/ampliseq.
d
Discordant samples between Epi2me and NanoBLAST+ were resolved by NanoCLUST.
e
An average nucleotide identity (ANI) of >94% indicated that the samples belonged to the same species as the best-matched genomes.