Review for "Multifactorial Chromosomal Variants Regulate Polymyxin Resistance In Extensively Drug-Resistant Klebsiella pneumoniae"

Completed on 17 May 2017 by Willem van Schaik . Sourced from http://biorxiv.org/content/early/2017/05/08/134684.

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This is an interesting whole-genome sequencing based study to identify mechanisms that contribute to colistin resistance in K. pneumoniae. Mutations in mgrB, phoPQ and pmrAB are identified and complemented to confirm their role in colistin resistance. The major weakness of this study is that the authors are limited in their choice of isolates: they do not have the susceptible counterpart of each resistant strains, so it is impossible to identify all SNPs and indels that have accumulated in the resistant strain. This limits the scope of the study as the authors now only study the ‘known knowns’ outlined above. It would be good if the authors include this limitation of their study in the discussion.
Some additional comments and suggestions are outlined below:
The abstract lacks quantitative data. l. 30 Please provide an exact number, l. 31. ‘most common’: provide number of strains.
The relevance of the ST2401 K. quasipneumoniae strain in the context of this study is unclear. It does not merit inclusion in the abstract, in my opinion.
l. 49: better to write plasmid-encoded carbapenem resistance genes
l. 54. The mortality associated with polymyxin-resistant Klebsiella infections seems awfully high. I believe the attributable mortality due to PMX-resistance is still not clear. See this interesting blog post: https://reflectionsipc.com/... for further insights on this topic.
l. 58. I apologize for being a pedant, but the disturbance of the LPS leaflet of the outer membrane will not allow PMX to act on intracellular targets. For that to happen, the inner membrane needs to be disrupted as well.
In the discussion on mgrB it may be good to refer to Kidd et al., 2017. EMBO Mol Med who were the first to systematically study the role of this gene in K. pneumoniae.
l. 67. Specify that mcr-1 confers colistin resistance. It may also be relevant to note that mcr-1 appears to be relatively rare in Klebsiella.
l. 97. ‘glycerol was added to 20% (v/v)’ may be a better way of phrasing this line
l. 107. I assume cation-adjusted Muller-Hinton broth was used? Please specify.
l. 130 – 132. I would really like to see a maximum-likelihood core genome tree here with additional reference isolates (downloadable from public databases), rather than a Neighbour-Joining tree of seven concatenated MLST alleles. It now is impossible to assess whether some of these strains (having the same ST) are truly clonally related.
l. 166. Incision should probably be replaced by introduction
l. 203. Provide exact number.
l. 225. It is not immediately obvious what is meant by (65, 66% variant allele frequency)
l. 235 – 237. Is it also not a possibility that in these strains mgrB has reverted to its wild-type state by excision of the IS element?
l. 252 – 270. This section is difficult to follow. While some mutations are proposed to act as suppressors, it appears that experimental evidence cannot confirm this, so it may be better to rewrite this paragraph to reflect this key finding.
l. 275 – 276. I am not entirely sure that it is correct to single out Brazil and Greece here.
l. 292. I am not entirely sure whether this claim of primacy is relevant. Clearly, a truncation is a loss-of-function mutation and those have been complemented previously.