Reviewer ’s report  
 
Title: Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent 
traits and capacity to persist within the host  
 
Version: 0 Date: 14 Feb 2018  
 
Reviewer: Frédéric Dalle  
 
Reviewer's report:  
 
The authors have submitted a manuscript entitled "Intestinal Candida isolates from Rett 
syndrome subjects bear potential virulent traits and capacity to persist within the host" aimed at 
characterizing genotypic and phenotypic traits of fungal strains isol ated from the stools of RTT 
patients. The authors first reported dysbiosis of the intestinal microbiota in RTT patients as 
previously reported by the same team in another publication. Especially they confirmed the over -
abundance of Candida parapsilosis in the intestinal microbiota of patients suffering Rett 
syndrom. Additionally, they demonstrated that C. parapsilosis isolates recovered from RTT 
patients displayed specific genotypic and phenotypic traits, especially with regard to their 
capacities to form b iofilm, their resistance to azole antifungal drugs as well as their ability to 
triggering a chronic pro -inflammatory response of the host as compared to C. parapsilosis strains 
isolated from healthy people. Finally even if mostly descriptive, these observa tions highlight the 
existence of specific traits of C. parapsilosis that could explain the persistence of this Candida 
species in RTT patients and contribute to pathophysiology of the intestinal disorders observed in 
such patients.  
For these reasons, the m anuscript deserves to be published in BMC gastroenterology. Indeed, 
when the association between intestinal dysbiosis and human disorders and/or diseases is widely 
reported, knowledge about the phenotypic features of some bacterial or fungal resident of th e 
intestinal microbiota that could explain their over -abundance in the gut is still lacking. In their 
manuscript, Strati et al. report specific phenotypic traits of C. parapsilosis that could explain its 
persistence and over -abundance in the gut microbiota  of RTT patients, and suggest that these 
phenotypic traits may contribute to disorders (especially intestinal disorders) observed in RTT 
patients.  
 
However, clarification of some specific methodological points must be addressed:  
1- The condition of stool sa mpling and preservation before analysis must be specify since these 
conditions can affect the  composition of the fungal mycobiota;  
 
2- In the "Methods" section, references should be cited for Hyphal formation, Biofilm 
formation, isolation and stimulation o f PBMCs protocols.  
 
3- Antifungal susceptibility testing: I don't understand why the authors used EUCAST method 
to determine the MIC of the isolated strains when using CLSI breakpoints to interpret their 
data. Indeed, EUCAST breakpoints have been proposed t hat fit better with the technical 
specificities of the EUCAST method for determining antifungal MIC. This point needs to be 
clarified.  
 
4- In the discussion section, the authors say: "RTT C. parapsilosis isolates were characterized 
by high levels of resista nce to azoles antifungals, making them a difficult target in case of 
fungal infections in these subjects". I don't think the authors can say that since the antifungal 
drugs tested are not appropriate. Indeed, except for fluconazole, itraconazole and 5FC ar e not 
a first line treatment for Candidaemia. Testing of posaconazole, echinocandins or even 
voriconazole would have been more informative since these drugs are often used as first line 
treatment for candidaemia nowadays.  
 
5- The genotypic method used in th is study in very old and most of the recent knowledge in C. 
parapsilosis typing has been described using MLMT and MLST methods. Using these 
current tools would be more powerful for characterizing the clustering of C. parapsilosis in 
RTT patients.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
If not, please specify which contr ols are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Unable to assess  
 
Are you able to assess any statistics in the manuscript or woul d you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financi ally from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organiz ation that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of th e above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under  an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be pu blished.  
 
I agree to the open peer review policy of the journal  
Reviewer ’s report  
 
Title: Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent 
traits and capacity to persist within the host  
 
Version: 0 Date: 14 Feb 2018  
 
Reviewer: Frédéric Dalle  
 
Reviewer's report:  
 
The authors have submitted a manuscript entitled "Intestinal Candida isolates from Rett 
syndrome subjects bear potential virulent traits and capacity to persist within the host" aimed at 
characterizing genotypic and phenotypic traits of fungal strains isol ated from the stools of RTT 
patients. The authors first reported dysbiosis of the intestinal microbiota in RTT patients as 
previously reported by the same team in another publication. Especially they confirmed the over -
abundance of Candida parapsilosis in the intestinal microbiota of patients suffering Rett 
syndrom. Additionally, they demonstrated that C. parapsilosis isolates recovered from RTT 
patients displayed specific genotypic and phenotypic traits, especially with regard to their 
capacities to form b iofilm, their resistance to azole antifungal drugs as well as their ability to 
triggering a chronic pro -inflammatory response of the host as compared to C. parapsilosis strains 
isolated from healthy people. Finally even if mostly descriptive, these observa tions highlight the 
existence of specific traits of C. parapsilosis that could explain the persistence of this Candida 
species in RTT patients and contribute to pathophysiology of the intestinal disorders observed in 
such patients.  
For these reasons, the m anuscript deserves to be published in BMC gastroenterology. Indeed, 
when the association between intestinal dysbiosis and human disorders and/or diseases is widely 
reported, knowledge about the phenotypic features of some bacterial or fungal resident of th e 
intestinal microbiota that could explain their over -abundance in the gut is still lacking. In their 
manuscript, Strati et al. report specific phenotypic traits of C. parapsilosis that could explain its 
persistence and over -abundance in the gut microbiota  of RTT patients, and suggest that these 
phenotypic traits may contribute to disorders (especially intestinal disorders) observed in RTT 
patients.  
 
However, clarification of some specific methodological points must be addressed:  
1- The condition of stool sa mpling and preservation before analysis must be specify since these 
conditions can affect the  composition of the fungal mycobiota;  
 
2- In the "Methods" section, references should be cited for Hyphal formation, Biofilm 
formation, isolation and stimulation o f PBMCs protocols.  
 
3- Antifungal susceptibility testing: I don't understand why the authors used EUCAST method 
to determine the MIC of the isolated strains when using CLSI breakpoints to interpret their 
data. Indeed, EUCAST breakpoints have been proposed t hat fit better with the technical 
specificities of the EUCAST method for determining antifungal MIC. This point needs to be 
clarified.  
 
4- In the discussion section, the authors say: "RTT C. parapsilosis isolates were characterized 
by high levels of resista nce to azoles antifungals, making them a difficult target in case of 
fungal infections in these subjects". I don't think the authors can say that since the antifungal 
drugs tested are not appropriate. Indeed, except for fluconazole, itraconazole and 5FC ar e not 
a first line treatment for Candidaemia. Testing of posaconazole, echinocandins or even 
voriconazole would have been more informative since these drugs are often used as first line 
treatment for candidaemia nowadays.  
 
5- The genotypic method used in th is study in very old and most of the recent knowledge in C. 
parapsilosis typing has been described using MLMT and MLST methods. Using these 
current tools would be more powerful for characterizing the clustering of C. parapsilosis in 
RTT patients.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
If not, please specify which contr ols are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Unable to assess  
 
Are you able to assess any statistics in the manuscript or woul d you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financi ally from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organiz ation that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of th e above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under  an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be pu blished.  
 
I agree to the open peer review policy of the journal  
Please review this paper.
user
Reviewer ’s report  
 
Title: Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent 
traits and capacity to persist within the host  
 
Version: 0 Date: 14 Feb 2018  
 
Reviewer: Frédéric Dalle  
 
Reviewer's report:  
 
The authors have submitted a manuscript entitled "Intestinal Candida isolates from Rett 
syndrome subjects bear potential virulent traits and capacity to persist within the host" aimed at 
characterizing genotypic and phenotypic traits of fungal strains isol ated from the stools of RTT 
patients. The authors first reported dysbiosis of the intestinal microbiota in RTT patients as 
previously reported by the same team in another publication. Especially they confirmed the over -
abundance of Candida parapsilosis in the intestinal microbiota of patients suffering Rett 
syndrom. Additionally, they demonstrated that C. parapsilosis isolates recovered from RTT 
patients displayed specific genotypic and phenotypic traits, especially with regard to their 
capacities to form b iofilm, their resistance to azole antifungal drugs as well as their ability to 
triggering a chronic pro -inflammatory response of the host as compared to C. parapsilosis strains 
isolated from healthy people. Finally even if mostly descriptive, these observa tions highlight the 
existence of specific traits of C. parapsilosis that could explain the persistence of this Candida 
species in RTT patients and contribute to pathophysiology of the intestinal disorders observed in 
such patients.  
For these reasons, the m anuscript deserves to be published in BMC gastroenterology. Indeed, 
when the association between intestinal dysbiosis and human disorders and/or diseases is widely 
reported, knowledge about the phenotypic features of some bacterial or fungal resident of th e 
intestinal microbiota that could explain their over -abundance in the gut is still lacking. In their 
manuscript, Strati et al. report specific phenotypic traits of C. parapsilosis that could explain its 
persistence and over -abundance in the gut microbiota  of RTT patients, and suggest that these 
phenotypic traits may contribute to disorders (especially intestinal disorders) observed in RTT 
patients.  
 
However, clarification of some specific methodological points must be addressed:  
1- The condition of stool sa mpling and preservation before analysis must be specify since these 
conditions can affect the  composition of the fungal mycobiota;  
 
2- In the "Methods" section, references should be cited for Hyphal formation, Biofilm 
formation, isolation and stimulation o f PBMCs protocols.  
 
3- Antifungal susceptibility testing: I don't understand why the authors used EUCAST method 
to determine the MIC of the isolated strains when using CLSI breakpoints to interpret their 
data. Indeed, EUCAST breakpoints have been proposed t hat fit better with the technical 
specificities of the EUCAST method for determining antifungal MIC. This point needs to be 
clarified.  
 
4- In the discussion section, the authors say: "RTT C. parapsilosis isolates were characterized 
by high levels of resista nce to azoles antifungals, making them a difficult target in case of 
fungal infections in these subjects". I don't think the authors can say that since the antifungal 
drugs tested are not appropriate. Indeed, except for fluconazole, itraconazole and 5FC ar e not 
a first line treatment for Candidaemia. Testing of posaconazole, echinocandins or even 
voriconazole would have been more informative since these drugs are often used as first line 
treatment for candidaemia nowadays.  
 
5- The genotypic method used in th is study in very old and most of the recent knowledge in C. 
parapsilosis typing has been described using MLMT and MLST methods. Using these 
current tools would be more powerful for characterizing the clustering of C. parapsilosis in 
RTT patients.  
Are the methods appropriate and well described?  
If not, please specify what is required in your comments to the authors.  
 
No 
 
Does the work include the necessary controls?  
If not, please specify which contr ols are required in your comments to the authors.  
 
Yes 
 
Are the conclusions drawn adequately supported by the data shown?  
If not, please explain in your comments to the authors.  
 
Unable to assess  
 
Are you able to assess any statistics in the manuscript or woul d you recommend an  
additional statistical review?  
If an additional statistical review is recommended, please specify what aspects require further  
assessment in your comments to the editors.  
 
I am able to assess the statistics  
 
Quality of written English  
Please indicate the quality of language in the manuscript:  
 
Acceptable  
 
Declaration of competing interests  
Please complete a declaration of competing interests, considering the following questions:  
 
1. Have you in the past five years received reimbursements, fees, funding, or salary from an  
organisation that may in any way gain or lose financially from the publication of this  
manuscript, either now or in the future?  
 
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose  
financi ally from the publication of this manuscript, either now or in the future?  
 
3. Do you hold or are you currently applying for any patents relating to the content of the  
manuscript?  
 
4. Have you received reimbursements, fees, funding, or salary from an organiz ation that 
holds  or has applied for patents relating to the content of the manuscript?  
 
5. Do you have any other financial competing interests?  
 
6. Do you have any non -financial competing interests in relation to this paper?  
 
If you can answer no to all of th e above, write 'I declare that I have no competing interests' 
below.  If your reply is yes to any, please give details below.  
 
I declare that I have no competing interests  
 
I agree to the open peer review policy of the journal. I understand that my name will be included  
on my report to the authors and, if the manuscript is accepted for publication, my named report  
including any attachments I upload will be posted on the website along with the authors'  
responses.  I agree for my report to be made available under  an Open Access Creative Commons 
CC-BY license ( http://creativecommons.org/licenses/by/4.0/ ). I understand that any comments 
which I do  not wish to be included in my named report can be included as confidential comments 
to the  editors, which will not be pu blished.  
 
I agree to the open peer review policy of the journal  
assistant