In a recent paper entitled Winding around non-Hermitian singularities by Zhong et al., published in Nat. Commun. 9, 4808 (2018), a formalism is proposed for calculating the permutations of eigenstates that arise upon encircling (multiple) exceptional points (EPs) in the complex parameter plane of an analytic non-Hermitian Hamiltonian. The authors suggest that upon encircling EPs one should track the eigenvalue branch cuts that are traversed, and multiply the associated permutation matrices accordingly. In this comment we point out a serious shortcoming of this approach, illustrated by an explicit example that yields the wrong result for a specific loop. A more general method that has been published earlier by us and that does not suffer from this problem, is based on using fundamental loops. We briefly explain the method and list its various advantages. In addition, we argue that this method can be verified in a three wave-guide system, which then also unambiguously establishes the noncommutativity associated with encircling multiple EPs.
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