Viral and Bacterial Respiratory Pathogens during the COVID-19 Pandemic in Israel

Round 1

Reviewer 1 Report

Thank you very much to the Editor of Microorganisms for allowing me to review the paper entitled “Viral and bacterial respiratory pathogens during the COVID-19 pandemic In Israel”.

In this short communication the authors evaluate the incidence of major respiratory infections by both viral and bacterial pathogens from January 2017 to June 2022 in Israel.

This epidemiological study described by the authors is well designed, the figures are easy to understand for the reader and the results and discussions are clear.

 

Some comments to be addressed by the authors:

 

1.     It’s my opinion that the references are too few for the paper. Please increase and update the bibliografy.

 

2.     please review paper to correct numerous punctuation and character errors. For example:

 

·       Comment figure 2: font size is different

 

·       References number 1 and 7: correct the format and follow the MDPI’s guidelines for quoting websites Author (if available). Title of the webpage (if available). Available online: http://... (accessed on date).

 

·       Line 101: please correct the sentence

 

·       In the paper are present more spaces between words: line 42,48,93,103 etc.

Author Response

Dear Reviewer

Thank you for the opportunity to revise our manuscript and for your suggestions.

According to your suggestions, we added references- currently # 5,6,10,11,12,13,14,19, and 20.

I corrected the punctuation and character errors with the help of the Mac editor tool.

The font size of figure 2 was corrected.

The accessed date for references  1 and 7 was added.

According to another reviewer's request, we used a  binary segmentation procedure  for locating multiple change-points

Sentence 101 was changed according to our new analysis

The adenovirus positivity rate decreased between April to October 2020, but ever since returned to its pre-COVID-19 pandemic pattern being monthly identified in 4.57 % (range 0-8.8%) out of the viral respiratory samples. No change in trend was identified by binary segmentation analysis of parainfluenza from April 2017 until February 2021 indicating a non-significant effect during this period.

 

 

Sincerely

Dr. Elinav the corresponding author

 

Reviewer 2 Report

The paper addresses the epidemiological change of respiratory infections during COVID-19 pandemic in a tertiary center in Jerusalem.

Minor points: SARS-COV-2 is the cause, it is not "associated" with COVID-19 (line 31); line 49, influenza not in capital letter (the I).

Major issues: the statement in line 43 ("... we observed..") comes out of the blue and it is not connected with the context.

About the methods: the viral panel is used all over the year, even in the summer for influenza? Which are the criteria for sputum testing? 

Eventually, the greatest issue and limitation, not reported by the authors, is that a proper statistical analysis is lacking: for instance, a "difference-in-difference" regression model.

Author Response

Dear reviewer,

 Thank you for the opportunity to revise our manuscript and for your fruitful suggestions. We believe that your suggestions improved the manuscript substantially. 

According to your suggestions:

 Line 39 was corrected to "SARS-CoV-2 the pathogen causing  COVID-19 disease,"

In line 49 we corrected "Influenza" to influenza (non-capitalized)

Line 43 was changed to "Previously, we reported  a trend of 46% to 100% "

 The same respiratory panel is used in our hospital since 2014 and it is used around the year. The only variation is the frequency of performing the test-from May to September it is performed twice weekly while in the winter it is performed on a daily basis.

Sputum testing is performed in any case of suspected pneumonia accompanied by productive cough- the culture is performed only when the initial gram stain indicated less than 10 squamous cells per field and  25 or higher PMNs per field.

We added statistical analysis using a binary segmentation procedure for locating multiple change points and we added the results of this analysis in the results section.

Sincerely  

Dr. Hila Elinav, the corresponding author.

 

Reviewer 3 Report

The manuscript submitted by Oster et al. and entitled “Viral and bacterial respiratory pathogens during the COVID-19 pandemic in Israel” describes a retrospective analysis of infections between 2017-2022 in a tertiary hospital in Jerusalem.  Similar to other studies there was an overall decline in respiratory testing and positivity.  Viral infections were more delayed to come back to normal distribution than bacterial infections and M. pneumoniae was significantly reduced in prevalence.  Overall, the data is well written and described.  Data is a bit confirmatory to other publications, but this is unique to Israel and goes past initial outbreak to look at additional respiratory seasons.  There are some aspects should be addressed:

 

Major Comments

The data and presentation graphing out prevalence over time is great, but it would be intriguing to create historical lines to indicate government policy changes that may have effect the results.  I.e. a vertical line in each graph when vaccination role out started or when masking policies changed.

In the materials and methods section was there any changes in PCR or culture testing that could have affected results?  For example, would a new PCR assay be implemented that had a different sensitivity and specificity that could skew the results post implementation.

Author Response

Dear reviewer,

 Thank you for your fruitful suggestions and the opportunity to revise our manuscript.

According to your suggestions, I added in each panel in the upper right corner the lockdown periods ( red vertical, the vaccination dates ( blue horizontal), the loosening of mask policy( green horizontal), and the tightening of mask policy. I added the major time point as the policy was changed very frequently...

There was no change in the policy or kits used for respiratory viruses since 2014. Every sample submitted to the virology lab is being processed. The frequency is of processing is different around the years (daily in the winter and twice weekly in the other seasons )

 Sputum is submitted to the microbiology lab in cases of pneumonia accompanied by productive cough. It is cultured only when the initial gram stain indicates less than 10 squamous cells per field and 25 or higher PMNs per field.

 

Sincerely 

 

Dr. Hila Elinav the corresponding author.

 

Round 2

Reviewer 2 Report

The authors replied sufficiently to reviewers.