Phenotypic Characterization of Carbapenem-Resistant Enterobacteriaceae in Presumptive Tuberculosis Patient across One Health Interface
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Introduction Globally, Nigeria remains one of the 30 countries highly burdened with tuberculosis (TB), TB/Human immunodeficiency virus and multidrug-resistant TB (MDR-TB). Objective This study aimed to characterize carbapenem-resistant Enterobacteriaceae (CRE) in presumptive tuberculosis patients across one health interface. Methods Sixty-six sputum samples from presumptive tuberculosis patients, fecal samples of animals loitering the hospital and environmental soil samples were collected and characterized. Isolated Enterobacteriaceae were screened for multidrug resistance and characterized for carbapenemase production. Result Fifty-seven enterobacteriaceae were isolated from 66 samples of sputum, fecal and soil samples. The frequency of occurrence of Klebsiella pneumoniae was 66.7% and 100% in sputum and fecal samples, respectively, while 60% of the soil sample was Proteus mirabilis. Multidrug resistance was exhibited, with ceftizidime showing the highest resistance of 100%, augumentin (95.7%), and nitrofurantoin (59.6%) in sputum samples. Animal and fecal samples showed similar resistance patterns to antibiotics with gentamicin, cefixime augementin and nitrofurantin. Majority (70.2%) were carbapenemase-producing Enterobacteriaceae, while only 34% were producing metallo-beta lactamase from sputum samples. Conclusions: The interconnectivity and frequency of CRE occurrence was found to be high in this study across the three pillars of One Health.
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Your methods are robust, but the reviewers raise several concerns that need to be addressed. Please focus particularly on the suggestions concerning presentation and readability. The aims should also be clear, and the title should accurately reflect the study.
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Comments to Author
The manuscript and its main objectives focuses heavily on presumptive tuberculosis which does not feature in the rest of the manuscript. Result section majorly focuses on the frequency of occurrence of CRE in different samples, Showing it more of prevalence study rather then research on presumptive TB and its relation with CRE. How does this article corelates its objectives with the results and conclusions? Th article still looks delinked between its objectives and findings. Why the researchers sampled soil and animal loitering for presumptive TB studies. The relatedness mentioned in comment 4 by the authors still seems insufficient as the study do not focuses on Mycobacterium Tuberculosis rather it is on other Enterobacteriaceae. Does they try to show that CRE can cure the TB ? (Still unclear)
Comments to Author
The manuscript and its main objectives focuses heavily on presumptive tuberculosis which does not feature in the rest of the manuscript. Result section majorly focuses on the frequency of occurrence of CRE in different samples, Showing it more of prevalence study rather then research on presumptive TB and its relation with CRE. How does this article corelates its objectives with the results and conclusions? Th article still looks delinked between its objectives and findings. Why the researchers sampled soil and animal loitering for presumptive TB studies. The relatedness mentioned in comment 4 by the authors still seems insufficient as the study do not focuses on Mycobacterium Tuberculosis rather it is on other Enterobacteriaceae. Does they try to show that CRE can cure the TB ? (Still unclear) line 99, does TB suspects and patients are taken n the same criteria? line 100-101, still unclear. a mentioned in these lines, what is environmental sample (soil) of the study? what is specific site of sputum production of the TB patients in hospitals? line 108, has the ethical approval for both human and animals are taken under one process or the approval was granted by concerning committees separately? Clarify line 116-117, how about TB patients? line 158, The heading does not match with the abbreviations used throughout the paragraph. plz crosscheck. Specify the class of antibiotics along with the individual antibiotics belonging to that particular class under study . TABLE 3: How does these methods are compared in terms of their efficacy. The table numerals does not show the comparison criteria ? The discussion section should be in line with the title and objectives of the study. plz improve.
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
The methods in this paper appear to be robust and suitable for the study. There is comprehensive phenotypic analysis of the isolated Enterobacteriaceae, I feel confident reading the methods that CPE have been identified. The Sampling of soil, faeces and sputum within the same setting is relevant for a one health approach and is important and interesting. The results need to be organised and better presented for the paper to be able to be properly reviewed for publication. Some of the figures do not make sense, specifics are mentioned below. The Background and introduction need to re written to represent the results presented. Background Line 65-77, the discussion around TB is distracting as this is not relevant for the paper aside from the recruitment of individuals to provide samples. This could …
Comments to Author
The methods in this paper appear to be robust and suitable for the study. There is comprehensive phenotypic analysis of the isolated Enterobacteriaceae, I feel confident reading the methods that CPE have been identified. The Sampling of soil, faeces and sputum within the same setting is relevant for a one health approach and is important and interesting. The results need to be organised and better presented for the paper to be able to be properly reviewed for publication. Some of the figures do not make sense, specifics are mentioned below. The Background and introduction need to re written to represent the results presented. Background Line 65-77, the discussion around TB is distracting as this is not relevant for the paper aside from the recruitment of individuals to provide samples. This could be omitted. A more specific point made that if zoonotic transmission of CPE is occurring then it could be inferred that zoonotic transmission of TB could also be occurring. Line 90, there is no data presented that supports the statement that this study is considering Mycobacterium tuberculosis. This is incorrect. The Background would benefit from more information on the zoonotic transmission of CPE and the relevance of that in a one health study. Line 62, 'some b-lactams'? Methods Line 107, I would like to see clearer description of the number of samples obtained from each site/patient (Study population line 107) and the number of isolates from each site/patient. Line 116, this number is different to a previous number. Line 161, the eCIM and mCIM, It needs to be made clear what this test is for and how to perform it, it would also be nice to know what it adds, how it is different to the previous tests - this is important as you present results on the different tests in the results. Throughout the paper "presumptive Tuberculosis patient" is used interchangeably with "TB patient" It would be clearer to define the population as patients attending TB clinic? This is also a relevant comment to the title. The results presented The results need to be clarified and further reviewed to establish that the paper is suitable for publication. The tables and figures need clearer legends so that it can be understood what each figure table means as a standalone. Throughout the results and discussion it is not clear what % relates to, please could this be clearer. Line 180, is this 66.7% percent of sputum samples had Klebsiella pneumonia isolated although it could read as Klebsiella pneumonia comprised of 66.7% of all organisms found? I have noted as well line 277 in the discussion but this is an issue throughout the paper. I would like to see the actual numbers next to the percentage to help with context eg 90% (9/10) This is a comment for the whole text. Be consistent about the description of the sputum in Line 183 you have said "human sputum", Table 1 it is "TB suspect's sputum" and Table 2 "TB patients sputum". Is the sputum in Table 1 and 3 the same? If it is not this needs to be made clearer in the methods, if it is this needs to be clearer in the presentation. As you have said where the sputum is from in the methods sputum would be acceptable. I am uncertain as to what table 2 (sceptibility Pattern of Isolated Organisms in Relation to Source) shows, I can not find it referred to in the test and I can't see any indication on the table that links it to the title. Figure 1 and 2 could be combined to show environmental and human isolates together. Figure 3 and 4 could also be combined, there is no need to show % resistant and % not resistant. Line 182 does not make sense. Table 3 and 4 could be combined and require further explanation. There also needs to be a discussion as to why the different methods showed different results and if that changes the number of CPE organisms. Discussion Lines 280-290. I do not feel that this paragraph is relevant to the data presented. The results presented do not demonstrate a close relation between soil, sputum or faeces isolates, other than the same organisms being found. This should not be linked to TB transmission. To infer a closer relationship antibiogram's could be presented on sputum and soil isolates, this would add to the paper and the one health impact. The discussion needs to be expanded to discuss the results presented. Line 295 a reference should be provided Line 301, The conclusion is fair and appropriate for the data presented. General The whole paper could benefit from a 'sense check' ensuring that every sentence makes sense. There is occasionally some unusual word usage a couple, but not all are highlighted below. Line 280 "Hammering", Line 79 "arduous", Line 160 needs a reference inserted
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Very poor
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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In its current form, this manuscript is not suitable for publication in Access Microbiology. The Methods are not adequately detailed, including for species identification, antimicrobial susceptibility, and statistical analysis. There is minimal text describing the results. This section would benefit from absolute numbers of all species isolated from the different locations, and the authors should consider looking at and reporting susceptibility phenotypes in individual strains. The Introduction also focuses heavily on Mycobacterium tuberculosis which does not feature in the rest of the manuscript. I am also not clear on why the authors sampled soil (or from exactly where the soil samples were taken) or animals. There is no evidence presented of transfer between soil/animals/humans in this study. Please consider making these suggested …
In its current form, this manuscript is not suitable for publication in Access Microbiology. The Methods are not adequately detailed, including for species identification, antimicrobial susceptibility, and statistical analysis. There is minimal text describing the results. This section would benefit from absolute numbers of all species isolated from the different locations, and the authors should consider looking at and reporting susceptibility phenotypes in individual strains. The Introduction also focuses heavily on Mycobacterium tuberculosis which does not feature in the rest of the manuscript. I am also not clear on why the authors sampled soil (or from exactly where the soil samples were taken) or animals. There is no evidence presented of transfer between soil/animals/humans in this study. Please consider making these suggested improvements in a resubmission.
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