A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes
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Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.
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The work presented is clear and the arguments well formed.
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Comments to Author
Thank you for allowing me to review the manuscript entitled: A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes. The paper is well written and the objectives are correctly evaluated throughout the manuscript. I only have a few minor notes that could improve the quality of the manuscript. 1. Probably the most important detail that I found was that the introduction talks about the large samples needed for culture-based methods to determine the causative agent in an infection, in this case, endophthalmitis. However, the authors encounter that the volumen that was extracted from the patients (100 µl) was insufficient in some cases (10 cases out of 19 with endophthalmitis). Also, the …
Comments to Author
Thank you for allowing me to review the manuscript entitled: A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes. The paper is well written and the objectives are correctly evaluated throughout the manuscript. I only have a few minor notes that could improve the quality of the manuscript. 1. Probably the most important detail that I found was that the introduction talks about the large samples needed for culture-based methods to determine the causative agent in an infection, in this case, endophthalmitis. However, the authors encounter that the volumen that was extracted from the patients (100 µl) was insufficient in some cases (10 cases out of 19 with endophthalmitis). Also, the introduction mentions that a caveat regarding culture-based diagnosis is the time. Again, this issue is raised at Results/Discussion with metagenomics. Even if the purpose of the study is to describe only the results from the metagenomics analysis, these two issues should be discussed, since it raises obvios questions about the test per se: How much volumen is needed for a proper analysis? How fast can these test be performed to impact eventually the treatment decision of the patients? How could a metagenomics and culture-based approach improve the quality of care in these cases? There is no mention of results from a culture-based approach, that should have been done as standard of care for patients with endophthalmitis. How did these results differ from the actual metagenomics analysis? 2. Similar to Point #1, there is no discussion on the strengths and, more importantly, the weaknesses of the study. What could be improved? Minor points 3. The Introduction-Purpose describes the use of Vanco/Ceftazidime, but Methods only comment on the application of Moxifloxacin. Then Results metion that some patients were treated with one or the other. While the study is not related to the actual treatment of the patients, this is confusing and should be clarified. 4. Figure 1 has no abscissa indicating the labels for each bar. There is a description at the Figure Legend, but the Figure could be better with th information embedded within. 5. Lines 311-313 reads: "In our shotgun sequencing study, many bacterial species were identified in all confirmed endophthalmitis patients..." This is not true, since all 19 patients had confirmed clinical endophtahlmitis and were treated as so. The shotgun sequencing was only performed in a few of the 19 patients. Please correct and elaborate. 6. Lines 229 - 234: The paragraph "Effect of moxifloxacin treatment" does not add any information for the study, and there is no actual analysis on the "effect of moxifloxacin (or Vanco/Ceftazidime for that matter) on the patients. It only mentions that "the patients responded well", but two had to be eviscerated. And in the end the authors metion that these results are not within the scope of the article. Then it should be eliminated. Please consider either eliminating the paragraph of elaborating the actual results on visual acuity and clinical effect of the antibiotic used.
Please rate the manuscript for methodological rigour
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?
Yes
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The work presented is clear and the arguments well formed. This is a study that would be of interest to the field and community.
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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data 2. Presentation of results 3. How the style and organization of the paper communicates and represents key findings 4. Literature analysis or discussion 5. Any other relevant comments This study presents the identification of microorganisms in biopsies of Mexican endophthalmitis patients by metagenomic next-generation sequencing means and also determine autibiotic resistance genes. Authors found a wide variety of bacteria species in the samples and in the resistome analysis they showed that several genes were present in several biopsy samples. The results are very interesting in this study and showed a bacterial, fungal and viral profile species present in these kind of samples, that can be used to explain the …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data 2. Presentation of results 3. How the style and organization of the paper communicates and represents key findings 4. Literature analysis or discussion 5. Any other relevant comments This study presents the identification of microorganisms in biopsies of Mexican endophthalmitis patients by metagenomic next-generation sequencing means and also determine autibiotic resistance genes. Authors found a wide variety of bacteria species in the samples and in the resistome analysis they showed that several genes were present in several biopsy samples. The results are very interesting in this study and showed a bacterial, fungal and viral profile species present in these kind of samples, that can be used to explain the complexity of endophthalmitis, taken also an antibiotic resistance genes profiles. However, there are some point that must be clarified: 1. The author mention that some samples not present enough DNA concentration to done sequence analysis, and after also mention that some of them showed a depth sequencing analysis (meta) and others that not showed a good depth sequencing (C), and in results and discussion the authors mentioned this point, However, they do not discuss in depth the importance of the DNA concentration difference in the diversity and abundance of microorganisms, and also in the resistome analysis. 2. The demographic data from patients is not discussed in the presentation of the results, as age, etiology and visual acuity. 3. Patients of this study received gold standard diagnosis and treatment? 4.
Please rate the manuscript for methodological rigour
Satisfactory
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?
Yes
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