Nasopharyngeal carriage rate, serotype distribution, and antimicrobial profiles of Streptococcus pneumoniae among patients with acute respiratory tract infection in Manado, North Sulawesi, Indonesia
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We studied the carriage rate, distribution of serotype, and antimicrobial profile of Streptococcus pneumoniae ( S. pneumoniae ) among patients with acute respiratory tract infections (ARTI) in two primary health centres and a tertiary referral hospital from 2019 to 2020 in Manado, North Sulawesi, Indonesia before 13-valent pneumococcal conjugate vaccine (PCV13) introduction. A total of 106 nasopharyngeal swab samples were collected from children and adult patients. Serotyping of S. pneumoniae strain was performed by sequential multiplex PCR and Quellung reaction. Antimicrobial profile was performed by the disc diffusion method. We identified thirty-one patients carried S. pneumoniae strains (29 %). The S. pneumoniae carriage rate was found to be higher among children aged 2–5 years (13/32; 40.6 %) than in children under 1 year (8/27; 29.6 %), children and adolescents under 18 years of age (5/20; 25.0 %) and adult patients (5/27; 18.5 %). The distribution of serotypes varied, including 14, 18C, 19A, 23F, 19F and 35B (two strains each) and 1, 3, 6B, 6C, 31, 9V, 15C, 16F, 17F, 23A, 35F (one strain each) and non-typeable (9/31; 29 %). We found S. pneumoniae isolates were susceptible to vancomycin (30/31; 97 %), chloramphenicol (29/31; 94 %), clindamycin (29/31; 94 %), erythromycin (22/31; 71 %), azithromycin (22/31; 71 %), tetracycline (14/31; 45 %), penicillin (11/31; 35 %), and sulfamethoxazole/trimethoprim (10/31; 32 %). This study provides supporting baseline data on distribution of serotype and antimicrobial profile of S. pneumoniae among patients with ARTI before PCV13 introduction in Manado, North Sulawesi, Indonesia.
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Thank you very much for submitting your revised manuscript to Access Microbiology. I am pleased to let you know that your manuscript is now accepted for publication. Congratulations to all authors!
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Thank you very much for submitting your revised manuscript to Access Microbiology and for addressing the reviewer comments and suggestions. This has undoubtedly improved the quality of the manuscript. However, there are a couple of point that need further clarification: In L173-178, there is a description of the prevalence to a number of antibiotics in the isolates tested and it is stated that "the majority of the strains were susceptible" to them. However, less than 50% were susceptible to tetracycline, penicillin and sulfamethoxazole/trimethoprim, meaning that the majority of the isolates were actually non-susceptible to those three antibiotics. Please revise this to improve the precision of the data presented in this paragraph. There are occasional grammatical errors in the manuscript. Some examples are: L42: "One hundred and six …
Thank you very much for submitting your revised manuscript to Access Microbiology and for addressing the reviewer comments and suggestions. This has undoubtedly improved the quality of the manuscript. However, there are a couple of point that need further clarification: In L173-178, there is a description of the prevalence to a number of antibiotics in the isolates tested and it is stated that "the majority of the strains were susceptible" to them. However, less than 50% were susceptible to tetracycline, penicillin and sulfamethoxazole/trimethoprim, meaning that the majority of the isolates were actually non-susceptible to those three antibiotics. Please revise this to improve the precision of the data presented in this paragraph. There are occasional grammatical errors in the manuscript. Some examples are: L42: "One hundred and six of nasopharyngeal swab samples..." should be "106 nasopharyngeal swab samples..." L79: "Pneumococcal disease have higher prevalence..." should be "Pneumococcal disease has higher prevalence..." Please carefully revise the grammar in those examples and throughout the manuscript. Otherwise, the manuscript will result in a good contribution to the field.
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This study would be a valuable contribution to the existing literature. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments.
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Comments to Author
General comments - The manuscript is technically sound, and the data supports the conclusion. - The data underlying the findings have been made available by the authors. - The manuscript has been presented in an intelligent fashion and written in standard English. Specific comments - The research gap that prompted this study is not coming out clearly in the introduction section. Kindly make it stand out. - Line 127-128 "The antimicrobial susceptibility test was performed according to Clinical and Laboratory Standards Institute" - which CLSI version was used? - Kindly include a statement to point out what informed the choice of the tested antibiotics. - Please be specific on how each study objective was analyzed/ presented. - Please consider revising the entire manuscript to correct minor grammatical …
Comments to Author
General comments - The manuscript is technically sound, and the data supports the conclusion. - The data underlying the findings have been made available by the authors. - The manuscript has been presented in an intelligent fashion and written in standard English. Specific comments - The research gap that prompted this study is not coming out clearly in the introduction section. Kindly make it stand out. - Line 127-128 "The antimicrobial susceptibility test was performed according to Clinical and Laboratory Standards Institute" - which CLSI version was used? - Kindly include a statement to point out what informed the choice of the tested antibiotics. - Please be specific on how each study objective was analyzed/ presented. - Please consider revising the entire manuscript to correct minor grammatical errors. For example, "We collected NP Swab specimens from 106 of patients with ARTI in Manado…" - Line 144 - The manuscript describes a sound piece of scientific research, even though study limitations and possible recommendations based on the study findings should be spelt out.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
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
1. Methodological rigour, reproducibility and availability of underlying data On the whole this looks fine but I think more information on strain serotyping would be of benefit to readers. With reference to lines 122-23 this was done by sequential PCR and Quellung reaction. Firstly, can the author clarify the use and relationship of the two distinct methods? For instance, where both methods used on all strains or were some serotyped by PCR and others by Quellung? Secondly, and more substantially, how comprehensive was this serotyping given the large number of known serotypes and that a large proportion of isolates were non-typable (n=9)? Are such isolates genuinely non-typable or did they simply not react against a limited number of primers and antisera? This should be clarified. 2. Presentation of …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data On the whole this looks fine but I think more information on strain serotyping would be of benefit to readers. With reference to lines 122-23 this was done by sequential PCR and Quellung reaction. Firstly, can the author clarify the use and relationship of the two distinct methods? For instance, where both methods used on all strains or were some serotyped by PCR and others by Quellung? Secondly, and more substantially, how comprehensive was this serotyping given the large number of known serotypes and that a large proportion of isolates were non-typable (n=9)? Are such isolates genuinely non-typable or did they simply not react against a limited number of primers and antisera? This should be clarified. 2. Presentation of results Overall, this fine but I did have some specific comments where this could potentially be improved. In the abstract I think it would be useful to readers to provide the actual numbers in addition to the percentage e.g. (12/31, 39%). This provides full context and is particularly important where some of the numbers involved are small. Non-typable isolates are a major fraction of the study isolates and this should be presented in the abstract. There seems some inconsistency in the number of studies isolates, when serotypes are tallied up on lines 158-160 they total 32 not 31. Cross-reference to Table 2 suggests that only a single isolate belonged to 19F not two as stated on line 158. Can the authors check and correct as appropriate if needed please. Line 164 majority and non-susceptible is incorrect here when the list includes antibiotics to which the majority are actually susceptible to. 3. How the style and organization of the paper communicates and represents key findings The manuscript is clearly written and well supported by comprehensive tables and supplementary information. Excel supplementary table, I am sceptical that zones of inhibition have been measured to 0.1 mm and this is not typical or appears to be consistent in the table. Can the authors express this to the nearest mm. It would also be informative to include the diameter cut-off applies to this disc diffusion. For clarity for the reader, lines 173-176 need to include a supported reference(s) even if these provided subsequently. Correct positif in the supplementary figure. Please add supplier(s) for media and susceptibility discs. 4. Literature analysis or discussion Results are discussed adequately in the context of the most relevant literature. Line 184 I think it overstates the point based on a mere five isolates to conclude that results agree with a previous study. Perhaps the authors need to caveat that statement. 5. Any other relevant comments Gram-stain-positive would be the formal phrase to use. Line 116 Is 'furthermore' correct here, or should Thereafter or similar be more appropriate? Line 86 for those not familiar with the exact details, it would be helpful to readers to have listed the serotypes included in PCV13. Although I do appreciate these are provided in the legend to Table 2, having them also presented early in the main text here is more obvious and helpful to readers. Table 1 'Smooking' presumable smoking? Throughout and including the title, antimicrobial profile would be more accurate as the antimicrobial susceptibility profile. The study patients have ARTI but the samples are from nasal carriage. What if any relationship is there between the carriage of S. pnuemoniae and ARTI? Can the authors comment on the causative agent(s) responsible for infections? Was it S. pneumoniae? Was the same serotype carried nasally? Can the authors' also comment on the rationale for the choice of patient and sample? Typically, pneumococcal epidemiological studies present data from disease and/or from carriage in healthy patients, or disease and carriage isolates from the same patients, presumably this unusual choice represents a convenience study sample.
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?
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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