Bacterial Species and Antimicrobial Resistance of Clinical Isolates from Pediatric Patients in Yangon, Myanmar, 2020

Round 1

Reviewer 1 Report

This study presents the analysis of 1019 clinical isolates from pediatric patients, from Myanmar, collected between January and December 2020. Bacterial species were isolated from the samples and their susceptibility towards a broad spectrum of antibiotics, including cephalosporins, carbapenems and fluoroquinolones, was analyzed. The data collected and discussed in this work is highly relevant in the context of AMR investigation. However, the manuscript, especially the structure of the text and the language and grammar, should be improved to increase the clarity of the message.

Major comments:

• The manuscript needs revision for language and grammar. Some sentences are too long and difficult to read (g. line 32 - “Southeast Asia has been regarded as a global hotspot of the emergence and spread of AMR because of increased antimicrobial demand and usage via population and economic growth, suboptimal knowledge and prescribing practice of antimicrobials, and also agriculture and aquaculture dependent on antimicrobials”); some sentences are not well structured (e.g. In this report, prevalence of bacterial species and their susceptibility to antimicrobials were investigated for 1019 clinical isolates from pediatric patients in a tertiary care hospital in Myanmar for one-year period)
• The results presented in the abstract should be more carefully chosen, in order to clearly summarize the most important findings from the work. MDR, for example, is not discussed.
• Improve the clarity of the results section by re-organizing it. Discuss it either by bacterial species or by antibiotic group.
• In the methods section, the authors describe how MDR was defined in this work but the MDR data was never presented and only briefly discussed for some species. The rate of MDR for all the species tested should be listed and discussed, as it is one of the most important findings of this work, in the context of AMR.

 

Minor comments :

Table 1 – add a column, listing the sum of the results obtained for all the specimens (as the antibiotic-resistance data is not divided by type of sample)

Line 39 – “comprehensive data of AMR are limited, due to the limit…”

Line 44 – “part of the “priority pathogen list”, presented by WHO in 2017.”

Line 55 – “was studied mostly for adult patients”

Clarify the meaning of CSF

Author Response

1. The manuscript needs revision for language and grammar. Some sentences are too long and difficult to read (g. line 32 - “Southeast Asia has been regarded as a global hotspot of the emergence and spread of AMR because of increased antimicrobial demand and usage via population and economic growth, suboptimal knowledge and prescribing practice of antimicrobials, and also agriculture and aquaculture dependent on antimicrobials”); some sentences are not well structured (e.g. In this report, prevalence of bacterial species and their susceptibility to antimicrobials were investigated for 1019 clinical isolates from pediatric patients in a tertiary care hospital in Myanmar for one-year period)

Answer: Thank you for suggestions. The indicated sentences were revised to separate into two sentences or to be reconstructed. Other parts of text were checked and revised, if necessary.　

2. The results presented in the abstract should be more carefully chosen, in order to clearly summarize the most important findings from the work. MDR, for example, is not discussed.

Answer: According to the comment, abstract was revised. MDR rates of E. coli, K. pneumoniae, Acinetobacter were added, and structure of sentences were modified.

3. Improve the clarity of the results section by re-organizing it. Discuss it either by bacterial species or by antibiotic group.

Answer: Thank you for the comment. This manuscript is written as a format of “communication” and includes AMR of all the bacterial species and all the antimicrobials. Therefore, Results section was described as following order. 1) general results of isolationof bacteria, 2) bacterial species in specimens and wards, 3) AMR in Gram-negative rods (ESBL, carbapenem-resistance), 4) S. aureus (MRSA) and Enterococcus. Text was mostly described according to bacterial species (group).

4. In the methods section, the authors describe how MDR was defined in this work but the MDR data was never presented and only briefly discussed for some species. The rate of MDR for all the species tested should be listed and discussed, as it is one of the most important findings of this work, in the context of AMR.

Answer: According to the suggestion, MDR rates of E. coli, K. pneumoniae, Acinetobacter, P. aeruginosa, were added to Figure1 (a~d) and also described in Result section (line 118-123). In the text, MDR rate of Enterobacter sp. was also added.

5. Table 1 – add a column, listing the sum of the results obtained for all the specimens (as the antibiotic-resistance data is not divided by type of sample)

Answer: According to the advice, the sum of all specimen types was added on the rightmost column in Table 1.

6. Line 39 – “comprehensive data of AMR are limited, due to the limit…”

Answer: It was corrected as indicated.

7. Line 44 – “part of the “priority pathogen list”, presented by WHO in 2017.”

Answer: It was corrected as indicated.

8. Line 55 – “was studied mostly for adult patients”

Answer: It was corrected as indicated.

9. Clarify the meaning of CSF

Answer: word with full spelling, “cerebrospinal fluid” was added to text. (line 72)

Reviewer 2 Report

It would have been advisable to look at other drugs of last resort as well, provided they are used in these hospitals (e.g. colistin).

Author Response

1. It would have been advisable to look at other drugs of last resort as well, provided they are used in these hospitals (e.g. colistin).

Answer: Colistin is not used in YCH. Tigecycline is used for sepsis with MDR Enterobacterales. In this study, we had information of resistance rates to colistin for E. coli, Klebsiella sp. and Acinetobacter sp., and those to tigecycline for E. coli, Klebsiella sp.. These data were added to Figure 1, and briefly described in Results section (line 122-123). In Discussion section, we added a brief discussion on this point, citing a previous report in Myanmar describing the isolation of coliston-resistant E. coli (line 174-179).

Reviewer 3 Report

Peer Review Report:

1. Recommendation: Minor Revision

2. Comments to authors

Overview and general recommendation:

Overall, the study is well designed, well performed and clearly presented. Although the flaws within the manuscript, I suggest its publication in case of minor revision.
Some indications for minor revisions are given below.

Define several terms and abbreviations: ESBLs, LMICs, ... for the first time through the text and then put the abbreviations in the rest of the manuscript.

Line 97: Try to write "Burkholderia cepacia" as a full name then put the abbreviation.

Line 158: Correct the name of the bacterium "K. pneumonae".

Develop the discussion section.

Try to ameliorate the quality of the tables. (S1 and S2)

Check the english language all through the text.

Check all the text in order to put commas and punctuation in right places to give the meaning to the sentences and ideas.

Check all the text for italic mode.

Author Response

1. Define several terms and abbreviations: ESBLs, LMICs, ... for the first time through the text and then put the abbreviations in the rest of the manuscript.

Answer: We checked carefully text and added full spelling of words and its abbreviation in parenthesis when it appears first in text, for AMR, MRSA, CSF, MDR, LMIC.

2. Line 97: Try to write "Burkholderia cepacia" as a full name then put the abbreviation.

Answer: It was corrected as indicated.

3. Line 158: Correct the name of the bacterium "K. pneumonae".

Answer: It was corrected as indicated.

4. Develop the discussion section.

Answer: In Discussion section, we added more descriptions about our view of last-resort antimicrobials (line 174-179), influence of covid-19 (line 206-209), guideline for antimicrobial use in Myanmar and future recommendation (line 215-219).

5. Try to ameliorate the quality of the tables. (S1 and S2)

Answer: Table S1 and S2 were modified to keep the same quality as that in main text.

6. Check the english language all through the text.

Answer: We checked English throughout the mansucript.

7. Check all the text in order to put commas and punctuation in right places to give the meaning to the sentences and ideas.

Answer: We checked comma, punctuation throughout the mansucript.

8. Check all the text for italic mode.

Answer: We checked words to be italicized throughout the mansucript.

Reviewer 4 Report

The authors examine the prevalence and antimicrobial resistance in the Yangon Children’s Hospital in 2020. They describe the pathogens present from clinical isolates, and measured the antimicrobial resistance of these isolates. The major issue with the manuscript is that the methods need to be better described. More informative figures/data would further strengthen the manuscript.

 

Major Points

1. The MIC breakpoints used to define resistance need to be listed. Furthermore, a scatterplot showing the individual isolates’ MIC for each antibiotic for the major species in Fig 1 would greatly enhance the manuscript.

 

2. The tests to identify pathogens that were performed using the Automated system need to be described.

 

3. Which antibiotics were tested?

 

4. Was identification and antibiotic susceptibility testing performed on raw isolates, or were isolates enriched first on blood agar and/or MacConkey agar? Was blood culture performed for all isolates, or only those isolated from blood?

 

5 Line 87-88, the raw number of isolates from each tissue reflects sampling bias. This statement should be removed to reduce confusion.

 

6. Line 116, the MDR data should be shown as a figure as well as described in the text.

 

7. Fig 1, does the percentage of antibiotic resistance strains vary by clinical specimen or clinical ward?

 

8. Fig S2, to what extent does sampling bias influence these numbers?

 

Minor Points

1. Line 19, Define ESBL in the abstract

 

2. Grammar editing needed throughout, especially to add articles (‘the’, ‘a’, ‘an’).

Author Response

1. The MIC breakpoints used to define resistance need to be listed. Furthermore, a scatterplot showing the individual isolates’ MIC for each antibiotic for the major species in Fig 1 would greatly enhance the manuscript.

Answer: We employed MIC breakpoints shown in CLSI guideline, for all the antimicrobials shown in this manuscript in individual bacterial species. Use of CLSI guideline was written in text, Materials and Methods section. Accordingly, readers can understand the MIC breakpoints, although all the information are not listed in the manuscript. In this study, susceptibility of antimicrobials was judged by automated system to check bacterial growth in limited range of MIC, to give results of S and R. Therefore, accurate MICs were not measured for isolates, and thus scatterplot of MIC is not able to be drawn in this study.

2. The tests to identify pathogens that were performed using the Automated system need to be described.

Answer: The principle of the system was briefly written in text (line 77-80) as follows. “In this system, a panel of 51 micro-wells with dried substrates is used for bacterial identification. For antimicrobial susceptibility testing, a panel of 85 micro-wells is utilized, followed by bacterial growth detection by use of a redox indicator (colorimetric oxidation-reduction).”

3. Which antibiotics were tested?

Answer: The antibiotics that were measured were fixed for individual species of bacteria, and they were shown in Figure 1 for the 6 bacterial groups (species). Because this manuscript is Communication, to list all the antibiotics for each species in the text was omitted.

4. Was identification and antibiotic susceptibility testing performed on raw isolates, or were isolates enriched first on blood agar and/or MacConkey agar? Was blood culture performed for all isolates, or only those isolated from blood?

Answer: For blood samples and CSF samples, first they were put into BACTEC™ FX40 Instrument (Becton Dickinson) to grow bacteria. Subsequently, they were cultured on blood agar plates and MacConkey agar plates. This was described briefly in the text. (line 72-74)

5. Line 87-88, the raw number of isolates from each tissue reflects sampling bias. This statement should be removed to reduce confusion.

Answer: According to the suggestion, this sentence was deleted.

6. Line 116, the MDR data should be shown as a figure as well as described in the text.

Answer: According to the comment, MDR data were added to Figure 1 and also described in text Result section, line 118-122.

7. Fig 1, does the percentage of antibiotic resistance strains vary by clinical specimen or clinical ward?

Answer: Although we have not analyzed this point, there may not be so much difference among specimens and clinical wards, because pathogenic bacterial species were derived mainly from some major symptoms/specimens, irrespective of clinical wards. (For example, E. coli was derived mostly from urine, and also from internal medicine and surgical wards.) Therefore, we did not discuss it.  

8. Fig S2, to what extent does sampling bias influence these numbers?

Answer: Although it is difficult to respond to this question, clinical doctors understand that infectious disease is primarily important for pediatric patients. Therefore, doctors in any clinical ward might have been motivated to submit clinical specimens to the clinical laboratory, to detect any pathogen. Thus, sampling bias may cause very little influence.

9. Line 19, Define ESBL in the abstract

 Answer: In Abstract, “(extended-spectrum beta-lactamases)” was added.

10. Grammar editing needed throughout, especially to add articles (‘the’, ‘a’, ‘an’).

Answer: We checked articles throughout the manusucript.

Reviewer 5 Report

This short report by San et al reported important information of bacterial species isolated from paediatric patients in a hospital in Myanmar. The authors describe and discuss results appropriately by comparing them with previous results in Myanmar and Southeast Asia. Although, it would be valuable if the authors consider the points below:

 

1) There is no reference to COVID-19 and co-infection with pneumonia/bacterial infections in the data reported. It would be interesting to see if the authors saw any important data regarding this co-infection or if this was not regarded. If not, authors should consider to add this information as well.

2) This study would require specific ethical approvals. Authors to consider adding information on this issue.

3) A final conclusion on the use of antibiotics in Myanmar should be added. Do the authors consider the current guidelines are appropriate? Do they contribute to AMR? Do they match with other existent guidelines?

 

 

Author Response

1. There is no reference to COVID-19 and co-infection with pneumonia/bacterial infections in the data reported. It would be interesting to see if the authors saw any important data regarding this co-infection or if this was not regarded. If not, authors should consider to add this information as well.

Answer: We do not have any data of bacterial co-infection with COVID-19. In 2020, the Covid-19 infected children admitted to YCH are not so many (about 50). Most have mild symptoms. Therefore, there seems to be very less influence in changes in bacterial infections and AMR, due to COVID-19. This was briefly mentioned in Discussion. (line 205-208)

2. This study would require specific ethical approvals. Authors to consider adding information on this issue.

Answer: In this study, ethic code and informed consent were not necessary, because only bacterial species and antimicrobial resistance of clinical isolates were statistically analyzed, and no patients' information were included. Thus, Institutional Review Board Statement was shown as “Not applicable”.

3. A final conclusion on the use of antibiotics in Myanmar should be added. Do the authors consider the current guidelines are appropriate? Do they contribute to AMR? Do they match with other existent guidelines?

Answer: In Myanmar, the pediatricians use the guideline prepared and distributed by Myanmar Pediatric Society. It is available as a mobile application (Firstline). Because AMR is increasing, especially for Gram-negative bacteria, some counterplan may be necessary, for example, to modify guidelines, inform the guideline efficiently to clinicians. This view was added as final para. of Discussion section.