Table 2.
Characterization of index isolate 4A serial passaging experiments
| Sample | ETP MIC (mg/L) | ompC | ompF | bla OXA-1 copy #a | bla CTX-M-15 copy #a |
|---|---|---|---|---|---|
| 4A | <0.5 | WT | WT | 1 | 1 |
| 4A_1 | >32 | c.208T>C; p. Q70X | c.17_18insIS1A | 6 | 7 |
| 4A_2 | >32 | c.208T>C; p. Q70X | WT | 8 | 9 |
| 4A_3 | >32 | c.208T>C; p. Q70X | insIS1Ab | 6 | 7 |
| 4A_4 | >32 | c.208T>C; p. Q70X | insIS1Ab | 6 | 7 |
| 4A_H1 | >32 | IS1A-mediated insertion 96 bp upstream of +1 ompC start site | WT | 1 | 9 |
| 4A_H2 | >32 | IS1A-mediated insertion 96 bp upstream of +1 ompC start site | WT | 1 | 17 |
ETP, ertapenem.
a
See Materials and methods for normalized coverage depth calculations.
b
Large IS1A-mediated deletion event (as described in Lee et al.)51 at ompF insertion locus precludes the ability to note correct genomic context. This is due in part to multiple variable-sized deletions detected in the long-read data. This may reflect population heterogeneity or technical difficulties in resolving a single genomic deletion size.