Lelliottia amnigena recovered from the lung of a harbour porpoise, and comparative analyses with Lelliottia spp.
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Strain M1325/93/1 (herein referred to by our laboratory identifier, GFKo1) of Lelliottia amnigena was isolated from the lung of a harbour porpoise in 1993. The genome sequence and antimicrobial resistance profile (genomic, phenotypic) of the strain were generated, with the genomic data compared with those from closely related bacteria. We demonstrate that the recently described chromosomally encoded AmpC β-lactamase bla LAQ is a core gene of L. amnigena , and suggest that new variants of this class of lactamase are encoded by other members of the genus Lelliottia . Although presence of bla LAQ is ubiquitous across the currently sequenced members of L. amnigena , we highlight that strain GFKo1 is sensitive to ampicillin and cephalosporins. These data suggest that bla LAQ may act as a useful genetic marker for identification of L. amnigena strains, but its presence may not correlate with expected phenotypic resistances. Further studies are required to determine the regulatory mechanisms of bla LAQ in L. amnigena .
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Thank you for addressing the comments from the reviewers. In your point by point response, in your answer to reviewer 1 I noticed that you refer in the last sentence to a number of references, do you meant to say in silico analyses? At least reference 10 and 22 which I checked in terms of the bla gene I did not find phenotypic analysis. I quote the paragraph here: "We are unable to find additional publications which report on concordance/discordance between genotypic predictions and phenotypic drug resistances in this species. We highlight this as an issue in the discussion. References 10, 21, 22 and 38-40 all describe phenotypic resistances in Lelliottia spp." You may want to address this prior to publication to the platform.
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This study would be a valuable contribution to the existing literature. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data The authors have satisfactorily described their isolation procedures and their methodology for phenotypic characterisation such that it could be reproduced - the methodologies themselves are sound and rational. Likewise for their descriptions of library preparation and sequencing and their assembly and annotation processes. Could the authors please change "accurate identification of genomes" to more clearly illustrate that this section refers to taxonomic identification. In their AMR gene identification, could the authors please state the version of R and RStudio they carried out their BioStrings analysis work in. The paper is methodologically sound. 2. Presentation of results The authors have satisfactorily described the …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data The authors have satisfactorily described their isolation procedures and their methodology for phenotypic characterisation such that it could be reproduced - the methodologies themselves are sound and rational. Likewise for their descriptions of library preparation and sequencing and their assembly and annotation processes. Could the authors please change "accurate identification of genomes" to more clearly illustrate that this section refers to taxonomic identification. In their AMR gene identification, could the authors please state the version of R and RStudio they carried out their BioStrings analysis work in. The paper is methodologically sound. 2. Presentation of results The authors have satisfactorily described the genome of GFKo1, however I would like to see a map of the chromosome. Is there any indication of the presence of plasmids from the assembly? When referring to ANI in this section and throughout the text, could the authors be explicit at all times that they mean OrthoANI? The reason I ask is that oANI is its own metric which, whilst suitable for this study, would likely produce slightly different results if different algorithms were used. In line 174, could the authors provide the ANI as a supplementary figure? In figure one, could the authors please reorder or reletter the panels such that they read A, B, C from left to right instead of A, C, B in the figure's current format. In panel 1b, could the authors please redraw the heatmap with black borders between cells, for better readability. In figure 1c, could the authors indicate bootstrap values on their phylogenetic tree? In figure 2, bootstrap values of the blalaq locus are indicated by circle size - this is difficult to interpret as the distinction between e.g. 80 and 85% is not immediately clear. I suggest that the authors use a colour scale to represent these values instead. Presentation of the antimicrobial resistance data is adequate, although I feel this would have been complemented with data from resistant Leliotta as a comparison. When discussing the alignment of the region surrounding blalaq¬ in figure S2, could the authors comment on the ~300 bp intergenic deletion between envC and empA - has the isolate lost any terminators etc from this region? 3. How the style and organization of the paper communicates and represents key findings The paper is logically organized and presents a sensible story, which adequately and clearly communicates its findings - I have no issue with the manuscript's organisation 4. Literature analysis or discussion The introduction of the paper adequately summarises the literature surrounding Lelliottia genomics and taxonomy. They sufficiently describe the genus' ecology, what is known about AMR phenotypes of its members, and this works context within the authors' wider projects and research interests. The authors adequately discuss how the results presented fit into current understanding of literature, and correctly acknowledge the importance confirming the taxonomy of publicly available genomes. I particularly enjoyed the section describing the variable AMR phenotype of the species. 5. Any other relevant comments The manuscript is adequate for publication, pending the quick fixes to the clarity of their methodology and figures. I feel like the authors have missed a trick by not performing a qPCR of blalaq¬, to test if it is expressed under laboratory conditions, however that experiment is not key to this paper.
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
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?
No: No animal work
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Comments to Author
In this brief report the authors describe the genome analyses of a Lelliottia amnigena isolate obtained from a dolphin with the main focus on the antibiotic resistance profile, including phenotypic resistance tests. The authors compare the genome with publically available genomic data from other Lelliottia strains. In general, the manuscript is well-written and the results are adequately presented. The two tables present the necessary information of the strains included in the study. The figures are informative with all relevant information included. The main key findings of the manuscript, the characterization of the genome, the taxonomic analyses, as well as AMR analyses and the phenotypic resistance profile are well described. The discussion sums up all relevant finding, yet, it somehow misses the …
Comments to Author
In this brief report the authors describe the genome analyses of a Lelliottia amnigena isolate obtained from a dolphin with the main focus on the antibiotic resistance profile, including phenotypic resistance tests. The authors compare the genome with publically available genomic data from other Lelliottia strains. In general, the manuscript is well-written and the results are adequately presented. The two tables present the necessary information of the strains included in the study. The figures are informative with all relevant information included. The main key findings of the manuscript, the characterization of the genome, the taxonomic analyses, as well as AMR analyses and the phenotypic resistance profile are well described. The discussion sums up all relevant finding, yet, it somehow misses the discussion of the results in comparison with other studies. Here, the relevant literature (already included in the manuscript) should be also discussed. E.g. references 10 and 22 also showed the presence of the AmpC gene, although the strain(s) showed no phenotypic resistance, comparable to the results of the manuscript. Thus, these references (and possibly others) should be included into the discussion. Specific comments: Line 62: Please cite additional relevant literature reports on AMR genes in Lelliottia in addition to the two mentioned papers. Line 105: "Accurate identification of genomes". I feel, that "accurate" is not the right terminology here and suggest removing the word.
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
Very good
To what extent are the conclusions supported by the data?
Strongly support
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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