Unfortunately the problem has increased tremendously since that paper was published. In IJSEM, the majority publications are one-strains species and even one-strain genera.
For different reasons we have been able to limit one-strain species and one-strain genera in the Pasteurellaceae.
Working with the Nagoya protocol
The protocol was implemented 12 October 2014. Meaning that only samples taken after this day are covered by the protocol.
The paper of Overmann & Scholz 2017 describes the implications with prokaryotic strains. A point made in this paper is that most prokaryotes are globally distributed and that many of the concepts made in the Nagoya protocol are difficult to apply to microorganisms. DSMZ maintains a website for explaining the Nagoya protocol and answering difficult questions.
DNA sequences as type material A strong opinion has been expressed against this proposal at a meeting hosted by BISMIS. Presentations can be viewed here.