Strategies to Develop Aptamer Probes to Detect MRSA and Study of Antibacterial Activity
Round 1
Reviewer 1 Report
Kasturiarachchi report on development of aptamer probes for MRSA detection. The study has a high significance, owing to the high clinical and epidemiological significance of MRSA and the importance of its early detection. The study seems novel and enough background information has been provided on the subject being investigated. The references cited are also appropriate, the methods are also adequately described, and the conclusions are consistent with the results.
There are, however, issues that need to be resolved if the study can be published, and these are outlined as follows:
1. Abstract
a. In the first line Abstract, the authors should change “This paper investigates” to “This study investigated”. Also, “aptamer based” should be rewritten as “aptamer-based”. This should be done throughout the manuscript, such as on Line 45.
b. Line 7: “Staphylococcus aureus” needs to be italicized, as should all scientific names, such as “Staphylococcus” (Line 59), S. aureus (Lines 60, 63, 66, 68, 70, 72, 75, 95, 97, 99, 103, 111, 362, and 398), “Staphylococcus aureus” (Lines 94, 114, 120, and 121), S. epidermidis (Line 96), Streptococcus pneumoniae (Line 96), S. typhimurium (Line 103), Escherichia coli (Line 121), Pseudomonas aeruginosa (Lines 122 and 163), Pseudomonas (Line 279), Staphylococcus epidermidis (Line 122), Klebsiella pneumonia (Lines 122, 163, and 279), Burkholderia cepacian (Line 123), E. coli (Lines 123, 164, and 279), and Enterococcus (Line 362).
c. Line 9: The statement “MRSA can become resistant to methicillin” is inaccurate. MRSA is methicillin-resistant, and hence its name.
d. Lines 10 to 12 should be merged with the first sentence of the abstract, as a major part of it looks like a repetition.
e. Line 13: Please rewrite “fluorescently labelled” as “fluorescently-labelled”.
f. Line 16: Please replace “. These aptamers” with a comma.
g. Line 18: The hyphen in the word “in-vitro” should be removed, and the word needs to be italicized throughout the manuscript (Line 111).
The same thing applies to “in vivo” (Lines 113).
2. Introduction
a. The Introduction section is too long, and needs to be made concise and to the point.
b. Line 36: Please rewrite “primer binding” as “primer-binding”. This should be done throughout the manuscript, such as on Line 229.
c. Line 54: Please rewrite “FDA approved” as “FDA-approved”.
d. Line 60: As this is its first usage, “S. aureus” should be written in full, and the “S. aureus” placed in parenthesis in front of it, that is, “Staphylococcus aureus (S. aureus)”.
e. Lines 63 to 64: “hospital and community acquired infections” should be rewritten as “hospital- and community-acquired infections”.
f. Line 81: As this is its first usage, “MSSA” should be written in full, and the “MSSA” placed in parenthesis in front of it.
g. Line 83: “SCCmec” should be italicized, and this should be done throughout the manuscript.
h. Line 84: “mecA” and “PBP2A” should be italicized, and this should be done throughout the manuscript, such as on Lines 86, 88, 92, 93, 125, 128, 132, 170, 187, 188, 192, 195, 246, 253, 255 to 257, 260 to 262, 265, 267, 268, 271, 283, 304, 305, 306, 308, 309, 312, 313, 314, 321, 323, 326, 327, 330, 331, 338, 339, 344, 346, 355, 398, 400, 412, and 413.
i. Line 88: Please rewrite “possess low affinity” as “possess a low affinity”.
j. Line 96: As this is its first usage, “S. epidermidis” should be written in full, and the “S. epidermidis” placed in parenthesis in front of it.
k. Line 103: As this is its first usage, “S. typhimurium” should be written in full, and the “S. typhimurium” placed in parenthesis in front of it.
l. Line 112: “MRSA specific” should be rewritten as “MRSA-specific”.
3. Methodology
a. Line 136: The comma should be removed from the citation “Sefah et al., [47]”. This should be done for all other similar occurrences.
b. Line 142: The sentence is not clear.
c. Line 158: Please rewrite “DNase free” as “DNase-free”.
d. “Klebsiella pneumoniae” has been misspelt as “Klebsiella pneumonia” on Line 122 and as “Kebsiella pneumonia” on Lines 169 and 279:
e. Line 199: Please hyphenate “fluorescence measured”.
f. Line 208: Please rewrite “96 well” as “96-well”.
g. Line 221: Please rewrite “analysis was” as “analyses were”, and “are” as “were”.
h. Line 223: Please write the probability symbol in lowercase and italicize it.
4. Results and Discussion
a. The author may want to separate the Results from the Discussion.
b. Line 228: Please rewrite “Below table” as “The table below”.
c. Several parts of this section belong in the Methods section, for example, Lines 229 to 230, 246 to 250, 260 to 261, 282, 316 to 319, 334 to 337, 367 to 369, 378 to 385, 387 to 389, 398 to 399, and 401 to 402.
d. Line 239: Please rewrite “PCR amplified” as “PCR-amplified”.
e. Lines 349 and 350: Please italicize “in-silico” and delete its hyphen.
f. Lines 369 to 373: This belongs in the Introduction.
5. Other Comments
Although the manuscript ought to be written in reported speech, the author has mixed up reported speech with present tense.
Moderate edits are required.
Author Response
Dear sir,
Thank you very much for the comments on my paper. I have done all the correction as you have highlighted.
Thank you very much,
BW
Jagath
Author Response File: 
Author Response.pdf
Reviewer 2 Report
In this work, the author aimed to find an aptamer to bind and inhibit the function of PBP2A, the essential transpeptidase that confers beta-lactam resistance in MRSA. While the author found an aptamer that binds to PBP2A, this oligonucleotide failed to show specific binding to MRSA at the whole cell level. Despite the unsuccessful search for the ideal aptamer, the author reported a potential strategy to inhibit the pathogenesis of MRSA.
My major comment is on the process of sequencing the probe library and selecting the two aptamer probes for future studies. The methods involved in this are not clear in both the method and result sections. The author did the SELEX experiment against a spectrum of bacteria. How many probes were found specifically bound to MRSA and PBP2A but not other samples? Were the selected aptamers two of them? Were there any statistical analyses to show the significance score of these aptamers? Why were these two probes selected to be studied further?
Minor comments:
1. Lines 252-253, what do “34 sample” and “35 sample” mean?
2. Lines 398-399, is this sentence summarizing the results from a reference? It should be more clear that this is not part of the author’s story.
The author should check the grammar and spelling throughout the text as some sentences are not clear. Some examples are listed here:
1. All bacteria species, including S. aureus, should be italicized throughout.
2. Line 72, “as” to “an”.
3. Line 272, “used…” sentence is missing a subjective.
4. Figure 6, plate reader data, “trypsin” is misspelled.
5. Line 361-366, this paragraph is hard to be understood.
Author Response
Dear Sir,
Thank you very much for your comments on my paper.
I have done the corrections you have highlighted.
I have changed the title as Strategies to develop aptamer probes to detect MRSA and study of antibacterial activity.
I was focusing to develop single aptamer for MRSA. Therefore I carefully eliminated any aptamer sequences shared my other microbes and ended up with only single aptamer probe.
Thank you.
BW
Jagath
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
The authors have significantly improved the manuscript.
However, they have failed to satisfactorily address the issue concerning italicization of scientific names.
Moderate edits are needed.
Author Response
Dear Sir,
Please find the attached edited version of the manuscript for your reference.
Thank you
Jagath
Author Response File: Author Response.pdf
