Comprehensive genomic and metagenomic profiling of antibiotic resistance genes in Klebsiella pneumoniae isolates from whole-genome sequencing

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   Access Microbiology

   Jan 6, 2026

   Dear Dr Kamyabi, Thank you for your submission and choosing ACMI. Unfortunately, the manuscript is no longer under consideration. This decision has been made following my review of the paper and that, in its current state, it does not fit ACMI’s standard for methodological rigor and needs substantial editing. I’ve included some notes from me below to help with rewrites. The content itself is no unreasonable (i.e. screening clinical isolates for resistance markers). However i would suggest a clearer picture is necessary for publication (a more refined genome assembly and resistance genes present) and perhaps some wet lab validation of the results (though this isn't strictly necessary). Best wishes, John. --------- Authors isolate a single K. pneumoniae strain from a clinical lung infection sample and perform whole genome …

   Dear Dr Kamyabi, Thank you for your submission and choosing ACMI. Unfortunately, the manuscript is no longer under consideration. This decision has been made following my review of the paper and that, in its current state, it does not fit ACMI’s standard for methodological rigor and needs substantial editing. I’ve included some notes from me below to help with rewrites. The content itself is no unreasonable (i.e. screening clinical isolates for resistance markers). However i would suggest a clearer picture is necessary for publication (a more refined genome assembly and resistance genes present) and perhaps some wet lab validation of the results (though this isn't strictly necessary). Best wishes, John. --------- Authors isolate a single K. pneumoniae strain from a clinical lung infection sample and perform whole genome sequencing. Reads were assembled, contigs annotated and particularly antibiotic resistance genes identified using ShortBRED. The results are reported. It is unclear if the authors have pooled multiple strains into a single sequencing library or it is indeed a single isolate. “Isolates” is used frequently throughout but I would suggest having looked at the genome assembly page this is not the case. The purpose of ShortBRED is specifically to work with shotgun metagenomic data. Not that it can’t be used as in this case but it doesn’t seem appreciate, or indeed to report results based on read count. If it is a single genome, annotated as suggested, results should be presence/absence of genes. This aside, method section lack substantial and essential information and in its current state is unacceptable. Isolates and WGS data were processed following “standard microbiological procedures”. At ACMI, our primary standard is methodological rigour and transparency. In addition, “WGS pipeline (v2.1.1)” is unreferenced as are all bioinformatics tools mentioned. It’s unclear if this a publicly available pipeline or one generated by the authors but it certainly uses standard tools. Assuming default settings on all tools, the assembled genome is in 1,126 contigs (I suggest this is very high for Klebsiella) with an N50 of 11.5kb (very short contigs) I would not consider a high-quality genome. The assembly metrics make me concerned that the genome annotation is weak. This said, ShortBRED relies on very short sequences. Either way, for a single isolate, there are other tools including RGI (https://hpc.nih.gov/apps/RGI.html) which uses the same data base that would provide more useful, single isolate data. Additional comments, the assembly metrics stated in the paper do not match the NCBI reference at all…

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   Version published to 10.1099/acmi.0.001159.v1 on Access Microbiology

   Dec 22, 2025