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Population analysis of Vibrio parahaemolyticus originating from different geographical regions demonstrates a high genetic diversity

Sara Urmersbach*, Thomas Alter, Madura Sanjeevani Gonsal Koralage, Lisa Sperling, Gunnar Gerdts, Ute Messelhäusser and Stephan Huehn

BMC Microbiology 2014, 14:59  doi:10.1186/1471-2180-14-59

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Misleading information could lead to improper conclusions   Misleading information could lead to improper conclusions Misleading information could lead to improper conclusions Misleading information could lead to improper conclusions

Narjol Gonzalez-Escalona   (2014-03-18 11:41)  Center for Food Safety and Applied Nutrition, Food and Drug Administration, email

The manuscript has a lot of interesting data however it fails in several issues and shows milseading information and conclusions. I will try to summarize the some of the main issues that I have with this publication:

The entire manuscript should have focused on their actual data which are 130 V. parahaemolyticus strains. The focus of the manuscript gets lost when adding the other Vp strains on the database.

 

The pMLST should be used cautiously and restricted to what it is important to show, like the genes chosen for the MLST are in fact bona fide “house keeping” as shown by the relatively less variability at the peptide level compare to the gene sequences, evidencing purifying selection.  And this is not novel information, since it is widely accepted that house keeping genes will be under purifyng selection. The paper goes to much extent to explain this over and over again to get to the same conlcusion that pMLST is no good for geographical or typing (differentiating) Vp populations as obtained by MLST (nucleotide sequences).  

 

 

Specific comments:

 

  1. This phrase is misleading an accurate “V. parahaemolyticus strain sets, these studies have been restricted to specific areas, have focused exclusively on pathogenic or pandemic isolates or have been based on a limited strain number” There are many MLST works done on V. parahaemolyticus that analyze large number of strains (~>100) from diverse areas as well as from environmental and clinical settings.

  2. Introduction: Any reference to pandemic O3:K6 has to be stated, do not leave O3:K6 alone since many readers get confused all the time. Only “pandemic” O3:K6 has identical or very similar strains that are serovariants. There are plenty of O3:K6 Vp that are not pandemic or even related to it at all.

  3.  “…forms the distinct cluster of clonal complex 3 (CC3) founded by Sequence Type 3 (ST3)” – This is incorrect. The correct way to said is: ST3 appears to be the ancestral type and possible founder of this clonal complex.

  4. “CC3 is formed by pandemic as well as non-pathogenic strains [14].”- This is also incorrect. The CC3 of the referenced publication is composed of different strains. The CC2 of that publication is the one containing the “pandemic” strains. Please be careful citing other studies. All “pandemic” strains are considered pathogenic.

  5. “Environmental isolates can genetically be very similar to pandemic or non-pandemic

  6. “Theethakaew et al. [21] showed that strains from farmed prawns and clinical cases formed distinct clusters and the infectious strains were no random samples from the environment. For the identification of related strains the approach of clustering isolates on the basis of their amino acid sequence was applied to V. parahaemolyticus [21, 25]” – The cited paper has a lot of misinterpretation of their data. Fist, most clinical strains were the same ST, which will make them cluster (as it is expected for a strain causing a small outbreak). Second, they do cluster (clinical strains) with a lot of seafood isolates, therefore their main conclusion that there were unrelated strains is incorrect. The only conclusion that can be drawn from their data is that Vp from shrimp farm 1 and 2 were two different and independent Vp populations (Fig. 3 of that paper).

Competing interests

None declared

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