Respiratory bacterial co-infections and their antibiotic resistance pattern in COVID-19 patients at a tertiary care centre in India
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Introduction. Patients with coronavirus disease-2019 (COVID-19) are prone to develop respiratory bacterial infections irrespective of their need for mechanical ventilatory support.
Hypothesis/Gap Statement. Information about the incidence of concomitant respiratory bacterial infections in COVID- 19 patients from India is limited.
Aim. This study aimed to determine the incidence of concomitant respiratory bacterial pathogens and their drug resistance in these patients.
Methodology. A prospective study was performed by including patients who were admitted to our tertiary care centre from March 2021 to May 2021 to evaluate secondary bacterial respiratory co-infections in patients via real-time PCR (RT-PCR)-confirmed cases of COVID-19 disease caused by SARS CoV-2.
Results. Sixty-nine culture-positive respiratory samples from patients with COVID-19 were incorporated into this study. The most commonly isolated bacterial microorganisms were Klebsiella pneumoniae (23 samples, 33.33 %) and Acinetobacter baumannii (15, 21.73 %), followed by Pseudomonas aeruginosa (13, 18.84 %). Among the microorganisms isolated, 41 (59.4 %) were multidrug-resistant (MDR) and nine (13 %) were extensively drug-resistant (XDR). Among the Gram-negative bacteria isolated, K. pneumoniae showed high drug resistance. Fifty carbapenem-resistant microorganisms were isolated from the patients included in our study. Concerning the hospital stay of the patients enrolled, there was an increased length of intensive care unit stay, which was 22.25±15.42 days among patients needing mechanical ventilation in comparison to 5.39±9.57 days in patients on ambient air or low/high-flow oxygen.
Conclusion. COVID-19 patients need increased length of hospitalization and have a high incidence of secondary respiratory bacterial infections and high antimicrobial drug resistance.
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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. Dear Dr Sahu, Thank you for your revised submission and efforts to bring the manuscript inline with reviewers comments. I'm happy to say that the manuscript has now been accept. Please do consider Access Microbiology for future submissions. Best wishes, John.
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This study would be a valuable contribution to the existing literature. The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments. Please include more rigour criteria and resources in your methods section, as highlighted by the SciScore reports. Including RRIDs and negative statements to explain why things were not performed should increase the rigour and reproducibility of your work. You can find tips on how to improve your article here: https://sciscore.com/reports/Core-Report.php The reviewers raise concerns regarding the scientific rigour and experimental design of the work.
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Comments to Author
In this study Kar et al have investigated the respiratory bacterial coinfections in cohorts suffering from COVID-19. The authors have reported a number of bacterial isolates including evidences of drug resistance such as resistance to carbapenem. My concern with the current version of this manuscript is the lack of details such as steps of isolation of bacteria from cohorts. Besides culture based approaches, it is absolutely essential to sequence 16S rRNA region of the bacterial isolates to completely confirm the taxonomic affiliation. While the authors talk about carbapenem resistance, it is not clear if this is plasmid mediated. I would suggest the authors to provide more details in support of these questions.
Please rate the manuscript for methodological rigour
Satisfactory
Comments to Author
In this study Kar et al have investigated the respiratory bacterial coinfections in cohorts suffering from COVID-19. The authors have reported a number of bacterial isolates including evidences of drug resistance such as resistance to carbapenem. My concern with the current version of this manuscript is the lack of details such as steps of isolation of bacteria from cohorts. Besides culture based approaches, it is absolutely essential to sequence 16S rRNA region of the bacterial isolates to completely confirm the taxonomic affiliation. While the authors talk about carbapenem resistance, it is not clear if this is plasmid mediated. I would suggest the authors to provide more details in support of these questions.
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?
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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Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Much of the data used to make meaningful claims within the manuscript are not available. Microscopy assessments and antibiotic resistance testing results. Additionally, because it is not specifically elaborated on, it is not clear how either of these experiments/tests were carried out. Please elaborate on this within the method section and make available the data for generating claims (Microscopy images for example and individual isolate assessments). As a result, none of the claims from the manuscript can currently be corroborated. 2. Presentation of results The results in general could be better represented. The complex listing in the tables is fine for reference in general. Figure two could easily be expanded to …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Much of the data used to make meaningful claims within the manuscript are not available. Microscopy assessments and antibiotic resistance testing results. Additionally, because it is not specifically elaborated on, it is not clear how either of these experiments/tests were carried out. Please elaborate on this within the method section and make available the data for generating claims (Microscopy images for example and individual isolate assessments). As a result, none of the claims from the manuscript can currently be corroborated. 2. Presentation of results The results in general could be better represented. The complex listing in the tables is fine for reference in general. Figure two could easily be expanded to reduce the amount of referencing to the main results. For example including specific isolate information and trends etc. more than 3 sub groupings of a relatively complex data set. As it stands, while well written, much of the microbiological data is only available as raw test result and not visualised, which would make interpretation of the results easier. The same could be said for much of the table data. While fine, it is not the easiest to analyse. I would suggest including a range of figures that better represent this information. There are no figure limits at ACMI (within reason). 3. How the style and organization of the paper communicates and represents key findings Well written and structured, the text in general is at a good standard. Much of the important microbiological data is buried within the text however and not easily accessible. 4. Literature analysis or discussion Literature analysis and discussion were carried out well, for future reference, ACMI accept combined Results and discussions sections when suitable and i would argue that this would be a good example. No expectation to change this, but there is a bleed through of results in the discussion section already. 5. Any other relevant comments Generally, i would appreciate an expanded methods section. Especially on microbial identification and antibiotic resistance testing. This data is hopefully available, otherwise it will be impossible to validate the results. Also, it would be useful to have an expanded criteria for how MDR and XDR were determined and what resistance resulted in this. This data would be useful as currently, almost completely absent from the manuscript. Minor notes: Line 61 - please provide a reference? Line 68 - super infection? - please provide a reference. Table 1 - Expand MV to mechanical ventialtion in the figure legend. Figure 1 (and all future figures). - Please adjust so there is no overlap in label text. The overlap makes it difficult to read. Figure 2 - please expand the information represented here. Perhaps to the species level or isolate level to represent more specifically what is being reported and observed.
Please rate the manuscript for methodological rigour
Poor
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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