Enterotoxigenic Escherichia coli in Blantyre, Malawi
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We announce the deposition of the first two enterotoxigenic Escherichia coli (ETEC) genomes from Malawi. They were isolated from the faeces of asymptomatically infected children obtained in 2014. Both genomes encode the porcine variant of the heat labile toxin and no known ETEC colonisation factors.
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Thank you very much for submitting your revised manuscript to Access Microbiology and for including the reviewers' recommendations. I am pleased to let you know that your manuscript is now accepted for publication. Congratulations to all authors!
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Comments to Author
This piece of work, as outlined in the introduction, will be important in helping the fight against childhood diarrhoea. However, I think there are some amendments that need to be made before this is ready for publication. Mainly, the details on the bioinformatic processing of the samples. I couldn't see any information in your report on how the library prep was done, how the reads were treated (trimming? etc), how long the genome was, how many genes your annotation predicted (and whether that is different to other ETEC strains), and whether there were any plasmids present. This is all information you should have already so should not require any new analysis. I understand that the main finding from this paper is the toxin sequences and the analysis is focused on that, but the other information I have …
Comments to Author
This piece of work, as outlined in the introduction, will be important in helping the fight against childhood diarrhoea. However, I think there are some amendments that need to be made before this is ready for publication. Mainly, the details on the bioinformatic processing of the samples. I couldn't see any information in your report on how the library prep was done, how the reads were treated (trimming? etc), how long the genome was, how many genes your annotation predicted (and whether that is different to other ETEC strains), and whether there were any plasmids present. This is all information you should have already so should not require any new analysis. I understand that the main finding from this paper is the toxin sequences and the analysis is focused on that, but the other information I have listed above is still important for the general reliability and transparency of the manuscript, and useful information for others should they use the sequence you have uploaded. Therefore I am currently recommending this paper go through minor revisions. Other minor points. L55 - you mention Lineage 15 - is this one of the most dangerous lineages globally for childhood diarrhoea? L68 - Table 1. I think you need to provide more information in both the title and the main text as to what is being shown here. The title does not provide enough detail for what the reader is looking at. Also, I think that the paper could benefit from moving towards the structure of other genome announcement papers, where the main text is all in one block under the heading "Announcement". This is not essential, but I feel it may help the flow of the manuscript.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Thank you very much for submitting your manuscript to Access Microbiology. It has now been reviewed by two experts in the field, whose comments are attached below. Over all, they acknowledge this is a valuable contribution, however it needs some amendments that would increase the quality of the manuscript and the value to the potential readers. Please pay special attention to recommendations in terms of methodological transparency and clarity (including the bioinformatics pipeline) and phylogeny analysis. Please provide a revised version of the manuscript (including a tracked changes version of the document) along with a point-by-point response to the reviewers' comments within four weeks.
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Comments to Author
The authors have presented a well-written manuscript detailing the deposition of the first two ETEC genomes isolated from children in Malawi. They contextualise these genomes in a broader global landscape to identify which lineage the genomes are associated with and screen the genomes for known virulence and colonisation factors. I recommend that the authors include an additional figure showing the phylogeny of the 301 von Mentzer et al. genomes with the two isolates sequenced in this study that is described in the manuscript but not shown. This would improve the work by helping the reader to understand how the genomes were assigned to lineage 15. This could be included as a separate initial figure, or as a precursory panel in the current Figure 1. Minor comments: Line 43: include details of the …
Comments to Author
The authors have presented a well-written manuscript detailing the deposition of the first two ETEC genomes isolated from children in Malawi. They contextualise these genomes in a broader global landscape to identify which lineage the genomes are associated with and screen the genomes for known virulence and colonisation factors. I recommend that the authors include an additional figure showing the phylogeny of the 301 von Mentzer et al. genomes with the two isolates sequenced in this study that is described in the manuscript but not shown. This would improve the work by helping the reader to understand how the genomes were assigned to lineage 15. This could be included as a separate initial figure, or as a precursory panel in the current Figure 1. Minor comments: Line 43: include details of the DNA extraction process prior to sequencing (extraction kit used etc.) Line 45: Include further details of chemistry (barcoding/ligation kit etc.) for MinION sequencing. Line 45: include a reference for Guppy (link to GitHub). Line 46: what settings were used to run flye? If none were specified, please state that default settings were used. Line 53: replace the numeral 2 with the word 'two' for consistency within the manuscript. Line 54: include the name of the substitution model used when running IQ-TREE. Line 54: Figure 1 is referenced here but Figure 1 does not show the 303-genome phylogeny described in this sentence (see first recommendation).
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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