Review for 10.1186/s12876-020-01563-x (2020)

Reviewer’s report
Title: 
Compositional and drug-resistance profiling of pathogens in patients with
severe acute pancreatitis: a retrospective study
Version: 
0 
Date: 
19 Aug 2020
Reviewer's report:
Dear Authors,
Thank you for your manuscript entitled "Compositional and drug-resistance
profiling of pathogens in patients with severe acute pancreatitis" 
Please find hereby my comments and suggestions.
ABSTRACT
Clear and mostly complete, apart for the study type definition/description. Please
add the aim of the study in the Background section. Please provide a short
description of the eligible patients in the Method section and of the enrolled
patients in the result section. The number of enrolled patients should be reported
in the Result section. Please provide a short sentence to describe the association
analysis which were performed. 
ETHICS
In the "Conflict of interest and Ethical Adherence statement" it is reported that:
This study was reviewed and approved by the Medical Ethics Committee of
Tianjin NanKai Hospital, and because this observational study did not modify
surgeons' clinical practices, no informed consent was required, and all of the
patients were anonymous". Being the study type not clearly depicted it is difficult
to understand the EC decision.
MAIN MANUSCRIPT
Please revise English editing and typos throughout the manuscript. Please revise
Table position and format according to the Journal GL.
BACKGROUND
The outline is balanced, however the editing might need to be improved.
Please provide adequate references for SAP local and systemic complications.
Concepts on Lines 87 to 100 need to be better outlined and referenced.
Lines 101-103, please add adequate references.
The aims of the study are vaguely expressed and should be better supported.
METHOD SECTION
Please add the type of study (retrospective or prospective?) which is being
presented and eligible patients' characteristics.
How were the time points chosen? Please describe the timeline procedure
adequately as at present it is quite confusing. For criteria listed on lines 115-122,
one criteria was sufficient or more than one were needed for specimen
collection?
Please add a description on the patients' division in MDR and NON MDR
groups which is described in the Result section.
Please add all the methodology applied for the choice of MDR risk factors which
are described in the Result section (3.2 and 3.3).
RESULTS
Please modify the layout of description and tables according to the Journal GL.
Please provide a diagram consort including all eligible patients and all excluded
ones.
Please provide additional data on non-MDR patients: did they present other kind
of infections, apart from fungal ones? Would it be possible to create 2 separate
subgroups (infected and non-infected)?
Table 1. Please add, if possible, the following items: comorbidities and usual
home drugs, APACHE II or SASPS score at ICU admission or another severity
score at your choice, ICU stay yes/no and length of it, complications. 
Table 2. Please change the title in accordance with what is describe in 3.2. In
addition, notes c and f are unclear, please elucidate. 
No data are reported about the time points that were described in the method
section. If data were prospectively collected, it should be possible to analyse the
various times of positivity and to correlate them with the various risk factors in a
more appropriate and adequate manner.
Table 4. Please provide percentages on total specimen and patients and add
which positivities were multiple present in varios sites and in the same patients. 
Table 5. Would it be possible to highlight those patients that had more than one
MDR strain? Would it be possible to evaluate if the illness course was different
for those patients compared to the others? Were all isolated fungi multi-
sensitive?
Please add a description on targeted therapy: in which percentage of patients was
therapy not modified after bacteria identification because already appropriate
and adequate and in which percentage was it modified after bacteria
identification? Would it be possible to evaluate if a different illness course was
present?
DISCUSSION
The discussion is vaguely superficial and not adequately supported by the
presented results.
Please support the first paragraph with adequate references. 
Lines 246 and following: the justification proposed is not previously depicted.
Most of the discussion is devoted to the prophylactic use of antibiotics. But, as
previously noted, there are no data on the infection type and rate timeline during
the study period and patients' hospitalization and this could be of great interest,
instead.
Please improve the reference support of your discussion.
Please provide a part devoted to the strengths and limitations of your study.
CONCLUSIONS
I humbly do not believe that those conclusions could be pulled from the
presented data.
My warmest regards and thanks.
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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?
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gain or lose financially from the publication of this manuscript, either now
or in the future?
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Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
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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?
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Do you have any other financial competing interests?
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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
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Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
No
Are the methods sufficiently described to allow the study to be repeated?
No
Is the use of statistics and treatment of uncertainties appropriate?
No
Is the presentation of the work clear?
No
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
No