-->PONE-D-26-07266-->-->Genomic surveillance of carbapenem-resistant Acinetobacter baumannii from bloodstream infections in Thailand reveals widespread dissemination of blaNDM–harboring mobile genetic elements-->-->PLOS One

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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-->2. Has the statistical analysis been performed appropriately and rigorously? -->

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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-->5. Review Comments to the Author

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Reviewer #1: The study is good and the authors have demonstrated a good grasp of the problem they tried to address. The manuscript is well writted and technically sound. The authors should provide details of how the bacteria were subcultured prior to biochemical identification and genomic studies.

Reviewer #2:  The study was well researched and findings well presented. Apart from lack of statistical backing, every aspect of the write is impeccably written. The findings made represent the current situation and calls for a

continuation of genomic surveillance to monitor the emergence and dissemination of

blaNDM-producing CRAB and also to strengthen infection prevention and antimicrobial

resistance control efforts in hospital settings. This is a very important call as it represents a critical need in our global health system

Reviewer #3: Antibiotic resistance is a major health threat and Acinetobacter baumannii is one of the pathogens included in the critical level of the WHO priority list. Unravelling resistance determinants and distribution patterns of resistant isolates is extremely important to tackle bacterial infections due to multidrug resistant species. In this study, the authors explore the resistant genes and associated mobile genetic elements associated with carbapenem-resistant A. baumannii from bloodstream infections in Thailand. The authors have done a nationwide study, collecting isolates from multiple regions. However, only 41 isolates (+14 from other sources) were taken into consideration, which I find a little low to represent one country and see it as the main limitation of the study. Another weakness of the study as it is, is that the authors de not fully explore the information obtained by WGS (for instance, regarding detection of transposition associated with NDM-carrying mobile genetic elements).

Specific comments are presented below:

Lines 59-61 -OXA-51-like variants is only related to carbapenem resistance when associated with insertion sequences such as ISAba1 or ISAba125, which work as the promotor for the gene expression. This fact is never mentioned during the text, including during the analysis of the results of the genes carried by the studied isolates. WGS was performed and the presence or absence of such insertion sequences was not acknowledged (lines 258-262).

Lines 114-115 – “Species identification was reconfirmed…”. What was the original identification method?

Lines 176-178 – The authors chose to analyse the A. baumannii bloodstream isolates, which only account for 6.26 % of the total A. baumannii isolates they had available. Why choosing this? Nothing is written to justify this choice.

Lines 192-194 – Carbapenems, cephalosporins, aminoglycosides, fluoroquinolones are antimicrobial classes, but cotrimoxazole and colistin no.

Lines 194-195 – “All isolates were resistant to all tested carbapenems, including imipenem, meropenem, and doripenem”. What about ertapenem? Either the isolates are resistant to all tested carbepenems, which include ertapenem, or are not resistant to all.

Lines 206-208 – Complete genome assemblies were generated for seven isolates, which were chosen based on the resistance to all tested antibiotics. As there were 8 isolates that were resistant to all antimicrobials (Lines 198-9), why did the authors exclude one isolate? What was the criteria?

Lines 263-264 – NDM-5 was detected in ST2 isolates. How many isolates carried NDM-5? This information is never written in the whole text.

Lines 276-277 – How does the authors explain that the ST164 isolate carry the ant(3’’)-IIa gene, but remain susceptible to aminoglycosides, especially to gentamicin? At least a short (possible) justification should be included in the discussion.

Lines 284-300 – The authors mention that the NDM-5 gene is embedded into transposon Tn125, which has flanking ISAba125 elements. However, this is not reflected in figure 3, which has ISAba125 only represented on one side and, as I understand, only the IR of the IS is represented. The ISs are also missing from the two isolates that the authors use to compare with their isolate. Are they absent from the isolates?

A chromosomal location is identified for the Ab0003 isolate and in several parts of the text it is suggested the horizontal acquisition of the NDM-5 gene and associated MGE (for instance, line 404, 422, …). As WGS was performed, did the authors detect the target site duplication that is typical of transposition and that would strengthen this idea of dissemination?

Lines 312-328 and figure 4 – the inclusion of isolates other than the 55 CRAB was never mentioned in the methods and a bunch of results appear with comparison with isolates from a previous study. This needs to be included in the methodology section.

Line 347 – Here applies the same as before for NDM-5. Did the authors detect the typical target site duplication characteristic of transposition?

Minor comments

Line 125 – Add the brand of the nephelometer.

Line 321– is “one isolate from the current study” or two isolates?

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Reviewer #1: Yes: Ayodele Oluwaseun Ajayi

Reviewer #2: No

Reviewer #3: No

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Genomic surveillance of carbapenem-resistant Acinetobacter baumannii from bloodstream infections in Thailand reveals widespread dissemination of blaNDM–harboring mobile genetic elements

PONE-D-26-07266R1

Dear Dr. Premsuriya,

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

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Kind regards,

Mustafa Sadek

Academic Editor

PLOS One

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