Nasopharyngeal carriage and antimicrobial susceptibility profiles of Streptococcus pneumoniae among children with pneumonia and healthy children in Padang, Indonesia
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Streptococcus pneumoniae is one of the pathogenic bacteria causing invasive pneumococcal diseases such as pneumonia, sepsis, and meningitis, which are commonly reported in children and adults. In this study, we investigated the nasopharyngeal carriage rates, serotype distribution, and antimicrobial susceptibility profiles of S. pneumoniae among children with pneumonia and healthy children under 5 years old in Padang, West Sumatra, Indonesia. Nasopharyngeal swabs were collected from 65 hospitalized children with pneumonia in a referral hospital and from 65 healthy children at two day-care centers from 2018 to 2019. S. pneumoniae was identified by conventional and molecular methods. Antibiotic susceptibility was performed with the disc diffusion method. Out of 130 children, S. pneumoniae strains were carried by 53% and 9.2 % in healthy children (35/65) and children with pneumonia (6/65), respectively. Serotype 19F was the most common serotype among the isolated strains (21%) followed by 6C (10%), 14, 34 (7 % each), and 1, 23F, 6A, 6B (5 % each). Moreover, 55 % of the strains (23/42) were covered by the 13-valent pneumococcal conjugate vaccine. Most isolates were susceptible to vancomycin (100%), chloramphenicol (93%), clindamycin (76%), erythromycin (71%), and tetracycline (69%). Serotype 19F was commonly found as a multi-drug resistant strain.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. Thank you for addressing reviewer comments, I'm happy to recommend acceptance of the manuscript. Thank you again for choosing Access Microbiology and we welcome future submissions. Best wishes, John.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. This is a study that would be of interest to the field and community. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
In this manuscript, the authors set out to address a lack of information on the carriage of Streptococcus pneumoniae, a causative agent of pneumonia, in healthy and hospitalized children in Indonesia. They also attempt to identify the serotypes circulating in these cohorts and test their susceptibility to antimicrobials. I have no major concerns about the manuscript - the methods are well articulated and the authors have done what they set out what they attempted to do, namely: describe the prevalence, serotype frequency, and antimicrobial susceptibilities of S.pneumoniae in cohorts of healthy and hospitalised children in the Padang region of Indonesia. They ultimately find that few hospitalised children actually carry S.pneumoniae in the nasopharynx, identify the most common serotype of S.pneumoniae …
Comments to Author
In this manuscript, the authors set out to address a lack of information on the carriage of Streptococcus pneumoniae, a causative agent of pneumonia, in healthy and hospitalized children in Indonesia. They also attempt to identify the serotypes circulating in these cohorts and test their susceptibility to antimicrobials. I have no major concerns about the manuscript - the methods are well articulated and the authors have done what they set out what they attempted to do, namely: describe the prevalence, serotype frequency, and antimicrobial susceptibilities of S.pneumoniae in cohorts of healthy and hospitalised children in the Padang region of Indonesia. They ultimately find that few hospitalised children actually carry S.pneumoniae in the nasopharynx, identify the most common serotype of S.pneumoniae found in the these cohorts, and provide support for a recent study suggesting that S.pneumoniae is commonly resistant to a commonly used antimicrobial (co-trimoxazole). There are significant age differences between the hospitalized and healthy cohorts that could account for differences in S.pneumoniae prevalence but the authors acknowledge and discuss this in the manuscript. They also discuss their findings in relation to other studies reporting S.pneumoniae carriage and antimicrobial susceptibility in the wider region. I only have a few minor comments, most of which concern the formatting and presentation of the manuscripts figures. While the manuscript is generally well written, there are a few sentences key to understanding the results of the study that could be made clearer grammatically - I've highlighted a few below but the journal editor may be able to provide further assistance with respect to this. Minor Comments - Figures Generally, the formatting across figures could be more consistent i.e. font size, axis size etc. Figure 1 - Remove the question marks from around Age (Months). Figure 2 - This is a percentage not a proportion. Figure 3 - The figure legend does not accurately describe what the figures are. I think figure 3c is all of the samples combined and 3a and 3b are samples from hospitalised and non-hospitalised patients respectively but this should be made clearer. Figure 3 - Is there any reason why 3b and 3c are stacked bar charts and 3a is not? The data is all of the same type and would it would be easier to compare between hospitalised and healthy strains if the data is presented in the same way. Figure 3 - Figure 3a y-axis shouldn't go above 100%. Figure 3 - Figure legend should probably provide the full names of the antibiotics abbreviations used. Figure 4 - I would advise including some axis-lines on these figures. Figure 4 - Figure legend b) and c) say the same thing. Figure 4 - Y-axis could have either number of isolates or isolates (n). Minor Comments - Manuscript Line 27 - in children and adults. Line 27-28 - the authors say "Streptococcus pneumoniae commonly causes pneumonia in children" and with the next sentence say there is a lack of reports for Streptococcus pneumoniae causing pneumonia in children. Do they mean there is a lack of information on whether particular serotypes are responsible? Line 37 - should be 9.2% not 9,2%. Line 41 - most isolates. Line 62 - as one of the. Line 95 - the company producing nylon swabs should be included. Line 176 - the majority are not susceptible to oxacillin and co-trimoxazole. Line 177-179 - I think this would be clearer if stated that all isolates were resistant to oxacillin and co-trimoxazole rather than 'less susceptible'. Line 177-179 - Not sure what "tetracycline (100%)" means here…around half of the isolates in this data appear to be susceptible to tetracycline? 179 - 183 - I think this needs to be more carefully worded to make it clear that "less susceptible" means fewer strains that are susceptible to the antibiotic. "vancomycin is found susceptible for all isolates is also slightly confusing - something like "All isolates from healthy children and children with pneumonia are susceptible to vancomycin" might make this clearer. Line 188 - most common. Line 204 - symptoms. Line 205 - Another explanation could be an age effect? Most children with pneumonia were under the age of 1 and most healthy children were older? Line 207 - S.pneumoniae should be italicised. Line 215 - malnourished. Line 214 - 216 - I would avoid using "this study" as readers might assume the results discussed in this sentence were produced by the authors and not in reference to another study.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
37 - Change comma to decimal point. 55 - 808,000 out of what, in what country? 60 - 12% of the 16%? Or 12% of all total deaths 60 - 9.5% of pneumonia? Or the 10.7%? 62-64 - References 95 -Cat number but no supplier ref 95- 96 - in how much media? Should be percentages. 101 - STGG abbreviation ? what is this? 102 - What is the enrichment media comprised of? what is Todd-Hewit broth comprised of? 104 - What is the blood agar comprised of? 108 - What is inoculated media comprised of? 113 - Decimal point instead of comma in percentages. 115 - Replace decimal point with comma in percentages. 116 - What is in the TE buffer? 120 - Make the rpm number the same as previous style. 130-133 - These should be concentrations rather than weights. 130 - Reference for the method. 156 - Decimal point instead of comma …
Comments to Author
37 - Change comma to decimal point. 55 - 808,000 out of what, in what country? 60 - 12% of the 16%? Or 12% of all total deaths 60 - 9.5% of pneumonia? Or the 10.7%? 62-64 - References 95 -Cat number but no supplier ref 95- 96 - in how much media? Should be percentages. 101 - STGG abbreviation ? what is this? 102 - What is the enrichment media comprised of? what is Todd-Hewit broth comprised of? 104 - What is the blood agar comprised of? 108 - What is inoculated media comprised of? 113 - Decimal point instead of comma in percentages. 115 - Replace decimal point with comma in percentages. 116 - What is in the TE buffer? 120 - Make the rpm number the same as previous style. 130-133 - These should be concentrations rather than weights. 130 - Reference for the method. 156 - Decimal point instead of comma at 12.5%. 142 -150 - 131 patients mentioned in text versus 130 in table, extra patient is unaccounted for? Table 1- Numbers don't always add up to 65 or the full cohort number, but no explanation provided. Figure 1 - Y-axis should extend to 100% and axis line is missing. Y-axis label should be clearer e.g. % of children. No stats provided on the graphs, and blue bars e.g. hospitalised patients 13-24 months looks about double that of the other two age brackets -the results text mentions that there is a difference but no statistical analysis to back it up. Figure 1 legend - S. pneumoniae Figure 2a - Y-axis should extend to 100%, no line for Y-axis, Y-axis label should be clearer. Figure 2b - No line for Y-axis Figure 3a - No line for Y-axis, units on Y-axis should have decimal point rather than comma, Y-axis needs label, different style of graph compared to figure 3b, 3c. Figure 3b, Figure 3c - Y-axis needs label to clarify what percentages are. Figure 3 legend - Explain abbreviations or include abbreviations of antimicrobials in the results text, no explanation of what figure 3c shows. 180 -182- confusing wording, state that the strains are less susceptible to these compounds rather than the compounds have been less susceptible. 186 - Explain what MDR is an abbreviation of. Figure4a - Might be helpful to state which antibiotics in figure legend, Y-axis has no line, Y-axis needs label. X-axis label could be clearer e.g. number of antibiotics resistant per strain. 188 - Change commonest to most common Figure 4b, 4c - Key should be clearer e.g. state that this is number of antibiotics in the graph, Y-axis has no line. 208 - Change comma in 54,5% to decimal point, same with 62,5% 212 - Change comma in 13,9 to decimal point 223-224 - Clarify that this is a test to diagnose pneumonia and the 90.3% was correct identification 234 - Change to "is found to vary" rather than is found vary 235 + 236 + 244- Change commonest to most common. 252- Ampicillin and gentamycin is mentioned but previous history of antibiotic administration could not be provided. clarify that this is inferred based on common treatment routine. 309-310 - Reference 4 style is not consistent with other references 248-250 - Children under 1 year of age less likely to be in day-care? Which may explain some results e.g. older children more likely to be exposed to S.pneumoniae.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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