Final answer:
The pathogen likely disrupted the phosphodiester bonds present within the sugar-phosphate backbone of DNA, not the hydrogen bonds which stabilize base pairs.
Step-by-step explanation:
If a rare pathogen has compromised the structural backbone of DNA, it must have disrupted the phosphodiester bonds. These bonds are present within the sugar-phosphate backbone and are covalent in nature. They are crucial for maintaining the integrity and continuity of the DNA structure. Unlike hydrogen bonds which stabilize the base pairing between complementary nitrogenous bases and can be broken under conditions like high temperature, the covalent phosphodiester bonds provide a much stronger link within the backbone itself. Therefore, the correct answer to which type of bond the pathogen most likely disrupted is (B) Phosphodiester bonds.