Resistance, read for what it does
A gene result is not a verdict
Some resistance comes from losing a function, some from gaining one, and some genes defeat only part of a drug. The engine reads every gene for what it actually does.
Loss of functionSome genes only matter when they break
Nitrofurantoin is switched on by the bacterium's own enzymes. Resistance comes from losing them, so finding the gene is not resistance, and a first-line bladder agent stays available.
In the sample report: nfsA detected, nitrofurantoin retained.
Loss of functionOne broken enzyme, one lost drug
Isoniazid and pyrazinamide are also switched on by the organism. A mutation that disables one of those enzymes takes out that drug alone, not the rest of the tuberculosis regimen.
Gain of functionSome resistance switches on during treatment
Organisms such as Enterobacter carry a built-in enzyme that can ramp up once therapy starts. The report ranks down the drugs it defeats, even when the panel detects no gene at all.
Half a combinationSome genes defeat only half a drug
A sulfonamide-resistance gene compromises one half of trimethoprim-sulfamethoxazole. The report says which half, and what that does and does not rule out.
In the sample report: sul1 detected, TMP-SMX kept as the cystitis option.
A blank is not a green light. When the marker that matters for a recommended drug was not detected, the report says so, rather than letting silence read as susceptible.