A Case of Yellow Nail Syndrome Complicated with Pulmonary Infection Due to Nocardia cyriacigeorgica

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The paper of Li Qiuyu and collaborators  describes a very interesting case of a Yellow Nail Syndrome (YNS), a rare clinical syndrome characterized by nail bed changes, pulmonary involvement, and lymphatic drainage disorders. As far as I know, the prevalence and incidence of this disease are not known, but there have been only 400 cases reported in the literature.

This case report is very well detailed and well written. However, there is only one major issue that the authors must solve.

The microbiology aspects of the case are poorly discussed and contain relevant inaccuracies. Nocardia gelsenkirchenii is not accepted as a bacteriological name according to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), which is currently the most updated bacterial taxonomy register (Parte AC, et al., List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; https://doi.org/10.1099/ijsem.0.004332.

It is possible that this name comes from microbial identification software related to NGS methodology, but it cannot be accepted. It is maybe possible that the isolate in question is, or is very close to, Nocardia cyriacigeorgica, thus belonging to the Nocardia cyriacigeorgica complex. This microorganism was related to St. George's Church, referring to the origin of the name of the German town Gelsenkirchen, where the type strain was isolated.

As previously stated, it is important to provide more details on the microbiological aspects of this case. Was NGS applied to the isolate grown in culture or to the clinical sample? Which identification methods were used to identify the clinical isolate?  Which methods were used to determine antimicrobial susceptibilities? Was the microorganism isolated from a single respiratory sample or was it present in multiple samples?

To confirm the identification, I strongly suggest analyzing specific genetic regions that can provide reliable taxonomic resolution. The sequences of the 16S rRNA provide good resolution for distinguishing Nocardia species due to their highly conserved and variable regions, especially if used in combination with other genes such as the hsp65 gene (Heat Shock Protein 65), the rpoB (RNA Polymerase Beta-Subunit), the secA1 (encoding for a protein involved in the translocase system, an highly conserved gene among Nocardia species), the sod gene (involved in oxidative stress response) and the gyrB (DNA Gyrase Subunit B), another valuable marker that, along with rpoB, provides high-resolution identification of Nocardia species.

The most accurate identification can often be achieved by using a combination of these genetic markers, as different regions provide complementary information and help to resolve any ambiguities that may arise from relying on just one genetic marker.

To make the molecular information available to other scientists, I strongly recommend submitting the sequences of the above genes (which can be obtained easily from the sequences of NGS) to public databases (such as GenBank) and citing the reference number assigned to them.

Finally I would suggest to change the manuscript title from “Nocardia gelsenkirchenii Infection Complicated with Yellow Nail Syndrome: A Case Report and Literature Review” to “A case of Yellow Nail Syndrome complicated with pulmonary infection due to Nocardia [correct name]: A Case Report and Literature Review Infection”.

Comments on the Quality of English Language

Minor editing of English language required. Please check italic (e.g. line 35, mycobacterium tuberculosis) or spp. (not in italic).

Author Response

Thank you for your insightful feedback regarding the microbiology aspects of our case report. We appreciate your attention to detail and your recommendations for improvement.

Comment 1：

The microbiology aspects of the case are poorly discussed and contain relevant inaccuracies. Nocardia gelsenkirchenii is not accepted as a bacteriological name according to the List of Prokaryotic Names with Standing in Nomenclature (LPSN), which is currently the most updated bacterial taxonomy register (Parte AC, et al., List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; https://doi.org/10.1099/ijsem.0.004332.

It is possible that this name comes from microbial identification software related to NGS methodology, but it cannot be accepted. It is maybe possible that the isolate in question is, or is very close to, Nocardia cyriacigeorgica, thus belonging to the Nocardia cyriacigeorgica complex. This microorganism was related to St. George's Church, referring to the origin of the name of the German town Gelsenkirchen, where the type strain was isolated.

Response:

We appreciate your reference to the List of Prokaryotic Names with Standing in Nomenclature (LPSN) and the clarification regarding Nocardia gelsenkirchenii.

We acknowledge that this name is not accepted in current taxonomy and understand the importance of accurately identifying the isolate. We will revise our discussion to reflect that the isolate may indeed be closely related to Nocardia cyriacigeorgica and provide the necessary context regarding its classification.

Your insights are invaluable, and we will ensure that our manuscript adheres to the most up-to-date nomenclature and accurately represents the microbiological findings.

In addition, we have revised our manuscript and provided the details on the microbiological aspects of this case. Please see in Line 69-86, including the traditional culture, MAL-DI-TOF MS analysis for the cultured colonies and gene sequences alignment in the mNGS technology.

 

Comment 2：

As previously stated, it is important to provide more details on the microbiological aspects of this case. Was NGS applied to the isolate grown in culture or to the clinical sample? Which identification methods were used to identify the clinical isolate?  Which methods were used to determine antimicrobial susceptibilities? Was the microorganism isolated from a single respiratory sample or was it present in multiple samples?

To confirm the identification, I strongly suggest analyzing specific genetic regions that can provide reliable taxonomic resolution. The sequences of the 16S rRNA provide good resolution for distinguishing Nocardia species due to their highly conserved and variable regions, especially if used in combination with other genes such as the hsp65 gene (Heat Shock Protein 65), the rpoB (RNA Polymerase Beta-Subunit), the secA1 (encoding for a protein involved in the translocase system, an highly conserved gene among Nocardia species), the sod gene (involved in oxidative stress response) and the gyrB (DNA Gyrase Subunit B), another valuable marker that, along with rpoB, provides high-resolution identification of Nocardia species.

The most accurate identification can often be achieved by using a combination of these genetic markers, as different regions provide complementary information and help to resolve any ambiguities that may arise from relying on just one genetic marker.

To make the molecular information available to other scientists, I strongly recommend submitting the sequences of the above genes (which can be obtained easily from the sequences of NGS) to public databases (such as GenBank) and citing the reference number assigned to them.

Response:

Thank you for your comment. According to your suggestion, we supplement the specific processes and results of traditional culture, mass spectrometry identification and mNGS in our manuscript. Please see in Line 69-86.

Traditional Culturing and Antimicrobial Susceptibility Testing:

Nocardia cyriacigeorgica was detected by traditional culture method in the BAL in this patient. Antimicrobial susceptibility testing was also conducted using the broth microdilution method to determine the minimum inhibitory concentrations (MICs).

MAL-DI-TOF MS:

MAL-DI-TOF MS analysis identified the colonies as Nocardia cyriacigeorgica, with a comparison score exceeding 1.5 in the top ten results (Table 1)

NGS metagenomic analysis: mNGS was performed to detected the potential pathogens in the bronchoalveolar lavage fluid. In this patient, there were 11 sequences of the genes of  Nocardia cyriacigeorgica detected, which were confirmed by submitting these sequences to BLAST  database (https://blast.ncbi.nlm.nih.gov/) (Table 2).

 

Comment 3:

Finally I would suggest to change the manuscript title from “Nocardia gelsenkirchenii Infection Complicated with Yellow Nail Syndrome: A Case Report and Literature Review” to “A case of Yellow Nail Syndrome complicated with pulmonary infection due to Nocardia [correct name]: A Case Report and Literature Review Infection”.

Response:

Additionally, we will revise the manuscript title for clarity and accuracy as you suggested.

 

Comment 4:

Minor editing of English language required. Please check italic (e.g. line 35, mycobacterium tuberculosis) or spp. (not in italic).

Response:

We will carefully review the text to address the minor editing issues you mentioned, including the proper italicization of terms such as Mycobacterium tuberculosis and the correct formatting of "spp."

Thank you once again for your valuable suggestion.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript “Nocardia gelsenkirchenii Infection Complicated with Yellow Nail Syndrome: A Case Report and Literature Review” refers to a case of nocardiosis caused by Nocardia gelsenkirchenii associated with yellow nail syndrome, to provide useful information for physicians to be aware of the association of these diseases. It is an interesting case; however, I have some comments:

 

Change “Nocardia gelsenkirchen” to “Nocardia cyriacigeorgica” according to: Yassin AF, Rainey FA, Steiner U: Nocardia cyriacigeorgici sp. nov. Int J Syst Evol Microbiol 2001, 51:1419–1423.

To provide further solidity to your results, you include a brief description of the methodology that allowed you to identify Nocardia cyriacigeorgica since the details of how it was carried out or the evidence of the results obtained are not mentioned.

 

Minor corrections:

Line 65: Aspergillus fumigatus put in italics.

Remove italics from “spp.”

Line 163: standardize bibliography

 

 

Author Response

Comment 1:

Change “Nocardia gelsenkirchen” to “Nocardia cyriacigeorgica” according to: Yassin AF, Rainey FA, Steiner U: Nocardia cyriacigeorgici sp. nov. Int J Syst Evol Microbiol 2001, 51:1419–1423.

Response:

Thank you for your careful review and the correction. We have changed “Nocardia gelsenkirchen” to “Nocardia cyriacigeorgica” as per the reference: Yassin AF, Rainey FA, Steiner U: Nocardia cyriacigeorgici sp. nov. Int J Syst Evol Microbiol 2001, 51:1419–1423.

 

Comment 2:

To provide further solidity to your results, you include a brief description of the methodology that allowed you to identify Nocardia cyriacigeorgica since the details of how it was carried out or the evidence of the results obtained are not mentioned.

Response:

Thank you for your comment. According to your suggestion, we supplement the specific processes and results of traditional culture, mass spectrometry identification and mNGS in our manuscript. Please see in Line 69-86.

Traditional Culturing and Antimicrobial Susceptibility Testing:

Nocardia cyriacigeorgica was detected by traditional culture method in the BAL in this patient. Antimicrobial susceptibility testing was also conducted using the broth microdilution method to determine the minimum inhibitory concentrations (MICs).

MAL-DI-TOF MS:

MAL-DI-TOF MS analysis identified the colonies as Nocardia cyriacigeorgica, with a comparison score exceeding 1.5 in the top ten results (Table 1)

NGS metagenomic analysis: mNGS was performed to detected the potential pathogens in the bronchoalveolar lavage fluid. In this patient, there were 11 sequences of the genes of  Nocardia cyriacigeorgica detected, which were confirmed by submitting these sequences to BLAST  database (https://blast.ncbi.nlm.nih.gov/) (Table 2).

 

Comment 3:

Minor corrections:

Line 65: Aspergillus fumigatus put in italics.

Remove italics from “spp.”

Line 163: standardize bibliography

 

Response:

Thank you for your careful review and for pointing out these minor corrections. We have made the following changes:

• Italicized "Aspergillus fumigatus" in line 65.
• Removed italics from “spp.”
• Standardized the bibliography as requested.

We appreciate your attention to detail and have implemented these corrections in the manuscript.

Reviewer 3 Report

Comments and Suggestions for Authors

There are a few minor revisions needed:

• Please include a timeline diagram in the case report.
• Indicate the observation times for the CT scans shown in Figures 1 and 2.
• In the paragraph beginning on line 63, provide the timeline for when the tests were performed.
• Supply a higher-resolution image for Figure 4.
• Add details to Figure 5 regarding the timing of the scan.

Author Response

There are a few minor revisions needed:

• Please include a timeline diagram in the case report.
• Indicate the observation times for the CT scans shown in Figures 1 and 2.
• In the paragraph beginning on line 63, provide the timeline for when the tests were performed.
• Supply a higher-resolution image for Figure 4.
• Add details to Figure 5 regarding the timing of the scan.

 

Response:

Thank you for your thoughtful suggestions. We have made the following revisions in response to your feedback:

• A timeline diagram has been included in the case report to provide a clear chronological overview. Please see in Figure 7.
• The observation times for the CT scans in Figures 1,2 and 5 have been indicated.
• In this paragraph, the tests were performed during his hospitalization from January to February 2022.
• We understand the importance of image clarity, and we have tried out best to provide a high-resolution image. Unfortunately, due to the limitations of the original data or imaging technology, we are unable to further improve the resolution of this image.
• The timing of the scan of Figure 5 (Figure 6 now) has been added in the manuscript.