Table 2. Bacterial WGS sequencing.
Microorganisms isolated in the hospital microbiology laboratory in parallel to the project development (Aug-2018 to July-2019) and the subsequent additional identifications using 16S rRNA V3/V4 amplicon sequencing and whole genome sequencing (WGS) by the molecular biology laboratory.
| Month | Unit | Microbiology Lab identification | 16S rRNA -V3/V4 identity | 16S rRNA oligotype | WGS identity | MLST identity | Clonal group identity |
|---|---|---|---|---|---|---|---|
| N/A | N/A | Staphylococcus aureus | Staphylococcus aureus | oligotype_4 | Staphylococcus aureus | ST1435 | N/D |
| Oct-18 | NICU | Staphylococcus aureus | Staphylococcus aureus | oligotype_4 | Staphylococcus aureus | ST2383 | S. aureus Group 1 |
| Oct-18 | NICU | Staphylococcus aureus | Staphylococcus aureus | oligotype_4 | Staphylococcus aureus | ST398 | S. aureus Group 2 |
| Oct-18 | NICU | Staphylococcus aureus | Staphylococcus aureus | oligotype_4 | Staphylococcus aureus | ST2383 | S. aureus Group 1 |
| Jan-19 | NICU | Staphylococcus aureus | Staphylococcus aureus | oligotype_4 | Staphylococcus aureus | ST398 | S. aureus Group 2 |
| Nov-18 | ICU | Staphylococcus epidermidis | Staphylococcus epidermidis | oligotype_1 | Staphylococcus epidermidis | ST2 | N/D |
| Sep-18 | ICU | Enterococcus faecalis | Enterococcus faecalis | oligotype_5 | Enterococcus faecalis | ST21 | N/D |
| Feb-19 | NICU | Enterococcus faecalis | Enterococcus faecalis | oligotype_5 | Enterococcus faecalis | ST21 | N/D |
| Dec-18 | ICU | Pseudomonas aeruginosa | Pseudomonas aeruginosa | oligotype_12 | Pseudomonas aeruginosa | ST245 | N/D |
| Feb-19 | NICU | Pseudomonas aeruginosa | Pseudomonas aeruginosa | oligotype_12 | Pseudomonas aeruginosa | ST18161 | N/D |
| Oct-18 | ICU | Klebsiella | Klebsiella pneumoniae | N/D | Klebsiella pneumoniae | ST307 | N/D |
| Oct-18 | NICU | Klebsiella oxytoca | Enterobacteriaceae | N/D | Klebsiella michiganensis | N/A | N/D |
| Nov-18 | ICU | Escherichia coli | Escherichia coli | oligotype_2 | Escherichia coli | ST131 | N/D |
| Jan-19 | NICU | Escherichia coli | Escherichia coli | N/D | Escherichia coli | ST69 | E. coli Group 1 |
| Jan-19 | NICU | Escherichia coli | Escherichia coli | N/D | Escherichia coli | ST69 | E. coli Group 1 |
| Oct-18 | ICU | Escherichia coli | Escherichia coli | oligotype_2 | Escherichia coli | ST410 | N/D |
| Sep-18 | ICU | Escherichia coli | Escherichia coli | oligotype_2 | Escherichia coli | ST10 | N/D |
1 Has one allele with less than 100% identity (99.7992%).
N/D–Not identified.
N/A–Not applicable. Sample was collected before the actual project starts.