Methods are disclosed for distinguishing whether an animal is experiencing a bacterial infection or a viral infection. One monitors breath taken from the animal over time to measure the relative amount of a first breath stable isotope to a second breath stable isotope therein over time. A quick change in the isotope ratios within several hours from the likely infection is indicative of a bacterial infection. A delayed change in the isotope ratios, followed by periodic repeated alterations in the ratios, is indicative of viral infection. The methods are particularly efficient when using cavity ringdown spectroscopy for the monitoring. They may be used for monitoring a patient already admitted to a hospital, or for monitoring a patient initially complaining of adverse symptoms, or for triage, or for collectively monitoring a population of animals.