Reviewer’ s report
Title: Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in
antibiotic use, time to optimal antibiotics, and length of stay.
Version: 0Date: 23 Feb 2020
Reviewer: Gangadeep Kang
Reviewer's report:
This is a retrospective study that addresses the differences in patient disposition when a
multiplexed molecular approach is used for patients with acute infectious diarrhea. The questioncould have been approached in more than one way—for example, in patients with viral andparasitic diarrhea, were antibiotics used differently after an early diagnosis, but this has not beendone, and in fact, patients with viruses and parasites have been excluded. Therefore, a justificationwould be useful.
The study has several of the limitations of a retrospective analysis. Of the period from July 2015 to
April 2016, there were 123 patients of whom only 41 remained analyzable, while May toDecember 2016, 129 of 177 patients could be included in the analysis. Table 1 demonstrates themany baseline differences between the groups, making interpretation of statistically significantfindings challenging.
Many of the pathogens detected by the FilmArray may not require treatment in the absence of
symptoms, but in symptomatic patients also, it is useful to have a background rate of carriage,
which may inform appropriate decision-making on treatment. If such data from the same or similar
locations are avaiable, they should be cited. Since a proportion of patients whose FilmArray testswere positive, were not given antibiotics, this speaks to clinical judgement being appropriatelyused, and it would be helpful to expand on this in the discussion.
For the reported differences in antibiotic usage, the difference in the length of stay in the pre- and
post-FilmArray periods is so large (2.5 times), that it seems unlikely that this can be attributedsolely to early, appropriate treatment. The authors may want to consider this after reviewingclinical records, and propose a plausible explanation.
The definition of the 'optimal therapy' and 'time to optimal therapy' should be reviewed and
presented in light of available guidance. The proportion of patients for whom the initial antibioticchoice was not changed is higher in the FilmArray group, but this finding would be reinforced if itwas shown that antibiotics were not started when an infection was consider viral.
For C. difficile in particular, more detail on the treatment provided with respect to PCR/toxin
testing is important.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
No
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
YesAre you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality 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 thismanuscript, 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
financially 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 organization 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 the 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 reportincluding 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 commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Reviewer’ s report
Title: Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in
antibiotic use, time to optimal antibiotics, and length of stay.
Version: 0Date: 23 Feb 2020
Reviewer: Gangadeep Kang
Reviewer's report:
This is a retrospective study that addresses the differences in patient disposition when a
multiplexed molecular approach is used for patients with acute infectious diarrhea. The questioncould have been approached in more than one way—for example, in patients with viral andparasitic diarrhea, were antibiotics used differently after an early diagnosis, but this has not beendone, and in fact, patients with viruses and parasites have been excluded. Therefore, a justificationwould be useful.
The study has several of the limitations of a retrospective analysis. Of the period from July 2015 to
April 2016, there were 123 patients of whom only 41 remained analyzable, while May toDecember 2016, 129 of 177 patients could be included in the analysis. Table 1 demonstrates themany baseline differences between the groups, making interpretation of statistically significantfindings challenging.
Many of the pathogens detected by the FilmArray may not require treatment in the absence of
symptoms, but in symptomatic patients also, it is useful to have a background rate of carriage,
which may inform appropriate decision-making on treatment. If such data from the same or similar
locations are avaiable, they should be cited. Since a proportion of patients whose FilmArray testswere positive, were not given antibiotics, this speaks to clinical judgement being appropriatelyused, and it would be helpful to expand on this in the discussion.
For the reported differences in antibiotic usage, the difference in the length of stay in the pre- and
post-FilmArray periods is so large (2.5 times), that it seems unlikely that this can be attributedsolely to early, appropriate treatment. The authors may want to consider this after reviewingclinical records, and propose a plausible explanation.
The definition of the 'optimal therapy' and 'time to optimal therapy' should be reviewed and
presented in light of available guidance. The proportion of patients for whom the initial antibioticchoice was not changed is higher in the FilmArray group, but this finding would be reinforced if itwas shown that antibiotics were not started when an infection was consider viral.
For C. difficile in particular, more detail on the treatment provided with respect to PCR/toxin
testing is important.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
No
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
YesAre you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality 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 thismanuscript, 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
financially 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 organization 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 the 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 reportincluding 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 commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Please review this paper.
user
Reviewer’ s report
Title: Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in
antibiotic use, time to optimal antibiotics, and length of stay.
Version: 0Date: 23 Feb 2020
Reviewer: Gangadeep Kang
Reviewer's report:
This is a retrospective study that addresses the differences in patient disposition when a
multiplexed molecular approach is used for patients with acute infectious diarrhea. The questioncould have been approached in more than one way—for example, in patients with viral andparasitic diarrhea, were antibiotics used differently after an early diagnosis, but this has not beendone, and in fact, patients with viruses and parasites have been excluded. Therefore, a justificationwould be useful.
The study has several of the limitations of a retrospective analysis. Of the period from July 2015 to
April 2016, there were 123 patients of whom only 41 remained analyzable, while May toDecember 2016, 129 of 177 patients could be included in the analysis. Table 1 demonstrates themany baseline differences between the groups, making interpretation of statistically significantfindings challenging.
Many of the pathogens detected by the FilmArray may not require treatment in the absence of
symptoms, but in symptomatic patients also, it is useful to have a background rate of carriage,
which may inform appropriate decision-making on treatment. If such data from the same or similar
locations are avaiable, they should be cited. Since a proportion of patients whose FilmArray testswere positive, were not given antibiotics, this speaks to clinical judgement being appropriatelyused, and it would be helpful to expand on this in the discussion.
For the reported differences in antibiotic usage, the difference in the length of stay in the pre- and
post-FilmArray periods is so large (2.5 times), that it seems unlikely that this can be attributedsolely to early, appropriate treatment. The authors may want to consider this after reviewingclinical records, and propose a plausible explanation.
The definition of the 'optimal therapy' and 'time to optimal therapy' should be reviewed and
presented in light of available guidance. The proportion of patients for whom the initial antibioticchoice was not changed is higher in the FilmArray group, but this finding would be reinforced if itwas shown that antibiotics were not started when an infection was consider viral.
For C. difficile in particular, more detail on the treatment provided with respect to PCR/toxin
testing is important.
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
No
Are the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
YesAre you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality 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 thismanuscript, 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
financially 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 organization 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 the 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 reportincluding 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 commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
assistant