PONE-D-19-32138

Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

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Reviewer #1: Partly

Reviewer #2: Yes

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Reviewer #1: N/A

Reviewer #2: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: In the present study, the authors describe the characterization of carbapenemase-producing Enterobacterales isolates recovered during two outbreaks in Slovenia (2014-2017) using whole genome sequencing. The introduction and Materials sections are well organized and presented, but the results section is very summarized and the discussion includes important results not previously mentioned in the results section. Moreover, a more rigorous analysis of plasmids must be done.

I have some major questions:

Line 120- Quality control and filtering of sequences have been performed?? Authors should make ensure that the sequences have enough quality to do the subsequent bioinformatics analysis. In the same way, they should include a quality assembly report (QUAST report or similar with N50, L50, number of contigs, length of genomes, etc.) that allows readers to know the quality of the draft genomes obtained after the assembly.

Line 208-210- A reference plasmid has not been represented along with plasmids identified during this study. To understand the epidemiological relevance of these OXA-48-encoding plasmids and their transmission in this country, they should be compared with the reference plasmids more closely related (for example the worldwide disseminated pOXA-48a described by Poirel in 2012). Alike, plasmid representation should be annotated (the genetic environment of carbapenemase genes plays an important role in the dissemination of these genes and should be represented in the figure 2).

Line 211- Plasmids with OXA-48 and NDM-1 were different? Information about this strain and both plasmids is not included in the study. Has the OXA-48-encoding plasmid been compared with the other 5 sequenced plasmids? These data must be included in the study.

Line 236- In the discussion, authors say that the combination blaOXA-48, blaNDM-1 and blaCTX-M-15 of genes is firstly detected in the ST437 clone. CTX-M enzymes has not been previously mentioned in the results section. If authors consider that this is an important finding, they should be included the result in the paragraph “Detection of beta-lactamase genes in WGS data” (not only in the table of supplementary material). The same in lines 238-240.

Line 262- Alike, blaLEN results have been firstly commented in the discussion and non-mention has been previously made in the Results.

Lines 295-301- These results should be better explained in the results section and then express a more general idea in the discussion.

Minor questions:

Line 58 and 224 - Authors comment that most frequent clones in Europe are ST11, ST15, ST101 and…ST285. With the latter the author must refer to clone ST258.

Line 59 - Authors should use “present simple” form throughout all the sentence (…ST101 are associated with carbapenemase….ST17 usually carry extended spectrum…)

Line 108 – Which are the breakpoints used for the antimicrobial susceptibility study? (EUCAST-2019 or 2018 or 2017??).

Lines 116-118 – Kits for library preparations are indicated in this section, but not the sequencing platform used (Illumina HiSeq? NovaSeq?)

Reviewer #2: This is a very interesting article presenting an outbreak caused by carbapenem resistant Klebsiella pneumoniae in Slovenia using WGS. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined with this teqnique which was not so accessible and possible in such a depth. This knowledge might be very helpful in future for possible surveillance and infectious control reasons especially for highly pathogenic bacteria such as K. pneumoniae.

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Reviewer #1: No

Reviewer #2: No

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Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates

PONE-D-19-32138R1

Dear Dr. Benulic,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Rosa del Campo

Academic Editor

PLOS ONE

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