New work on Nosema suggests that the use of fumagillin is not justified: 


The colonies treated with fumagillin in July showed less spore load at the end of applications ...

However, 2 month after the treatment applications, the colonies
treated with fumagillin were the same size as the untreated colonies. In September, the colonies treated and not
treated with fumagillin did not differ in colony strength (adult bee population and brood area) or spores abundance.

Our study demonstrates that fumagillin treatment temporarily decreased the spore load of N. ceranae,
but this was not reflected in either the size of the colonies or the probability of surviving the winter regardless of
the dose or the administration strategy applied. Given the results obtained, we suggest to not perform the
pharmacological treatment under the conditions described in the experiment.

The most important conclusion of this study is that the use of
fumagillin in colonies heavily infected with N. ceranae in autumn–winter ...
does not improve survival or size of the colonies during the winter, 
regardless of the dose or the administration strategy applied.

Mendoza, Y., et al. "Nosema ceranae Winter Control: Study of the Effectiveness of Different Fumagillin Treatments and Consequences on the Strength of Honey Bee (Hymenoptera: Apidae) Colonies." Journal of Economic Entomology Advance Access published December 26, 2016

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