Microwave will killed bacteria but it's hard to tell how efficient it is when there is several variable to take into account.
Sanitation, disinfection and sterilization is dependent on several variable. For example, the temperature on a surface will probably reached a killing effect much faster than in a 1L of water or any other liquid. Once the temperature is reached, it has to be maintained long enough to kill bacteria. Also, 45 sec in a microwavemight be reach 99.99% but that's only effective if you less than 10 000 bacteria per ml. If you have 100 000, 1 million, 10 million, 1 billion, then you're left with 10, 100, 1 000 and 100 000. In some cases, 10 bacteria is sufficient to cause disease. Also, bacteria can form spores that are resistant to heat and some bacteria are capable of resisting heat killing for a longer period. An 99.99% kill for one bacteria with one set of temperature and time might be a 90% kill for a different bacteria. For example, for pasteurized milk, 65c for 30 sec is sufficient to kill 99.999% of the Mycobacterium tuberculosis and Coxiella burnetii that might be present. However, there's still bacteria left in the milk and it's not consider sterile.
Killing is dependent on temperature, time and concentration of living/sporulated bacteria.