Genetic characterization of Escherichia coli and Klebsiella spp. from humans and poultry in Nigeria
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The emergence of antibiotic resistance in livestock, especially food-producing animals, is of major public health importance as a result of the possibility of these bacteria entering the food chain. In this study, the genetic characteristics of antibiotic-resistant Escherichia coli and Klebsiella spp. isolates from humans and poultry in Edo state, Nigeria, were investigated. In April 2017, 45 Klebsiella spp. and 46 E. coli isolates were obtained from urine, clinical wounds, nasal and chicken faecal samples. Isolates were recovered and identified as previously described. Species identification was achieved by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and ribosomal multilocus sequence typing. Antimicrobial susceptibility testing was carried out using the Kirby–Bauer method for 12 antibiotics. A double disc synergy test was used to screen for extended-spectrum beta-lactamse (ESBL) production. Whole genome sequencing was performed for strain characterization of the isolates. Thirteen Klebsiella spp. isolates yielded positive results by the ESBL phenotypic test and harboured ESBL genes. Of the 46 E. coli isolates, 21 human and 13 poultry isolates were resistant to at least one of the tested antibiotics. Four human E. coli isolates harboured ESBL genes and revealed positive results when applying ESBL double disc synergy tests. ESBL genes in the Klebsiella spp. and E. coli isolates include bla CTX-M-15 and bla SHV-28 . Whole genome-based core gene multilocus sequence typing of the Klebsiella spp. and E. coli isolates revealed a close relatedness among the isolates. An integrated ‘One Health’ surveillance system is required to monitor transmission of antimicrobial resistance in Nigeria.
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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.
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The reviewer was positive about your revised manuscript and has suggest minor changes to approve the manuscript. There were two remaining concerns 1) clarification of the genomic analysis approaches and 2) in depth discussion of your results in the context of the literature. I would like to provide you with a further opportunity to review these sections of your manuscript in line with the reviewer's comments.
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Comments to Author
1. Whole genome sequencing was conducted on a subset of resistant isolates, and the genomic data was analyzed using various bioinformatics tools. The specific protocols and software used for sequencing and analysis are not explicitly mentioned. 2. The study primarily focuses on the methodology, results, and presentation of the key findings. It didn't provide insights into how the results are interpreted in light of existing literature or how they contribute to the current knowledge in the field. It may include comparisons with similar studies, identification of novel findings or discrepancies, exploration of underlying mechanisms, and the implications of the results for future research or clinical practice.
Please rate the manuscript for methodological rigour
Satisfactory
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Comments to Author
1. Whole genome sequencing was conducted on a subset of resistant isolates, and the genomic data was analyzed using various bioinformatics tools. The specific protocols and software used for sequencing and analysis are not explicitly mentioned. 2. The study primarily focuses on the methodology, results, and presentation of the key findings. It didn't provide insights into how the results are interpreted in light of existing literature or how they contribute to the current knowledge in the field. It may include comparisons with similar studies, identification of novel findings or discrepancies, exploration of underlying mechanisms, and the implications of the results for future research or clinical practice.
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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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
1. Methodological rigour, reproducibility and availability of underlying data Some parts need further information to allow replication studies 2. Presentation of results A very General Description of the isolates. The manuscript would benefit from a more detailed description of the isolates and extension of the in silico analysis especially for mobile genetic element, transmissible resistance and virulence factors as well as an assessment of the potential 8mpact of the isolates for human (virulence factors) 3. How the style and organization of the paper communicates and represents key findings Style is ok, but the key findings can be presented in more detail. 4. Literature analysis or discussion Ok 5. Any other relevant comments The manuscript would benefit of a general revision and additional in …
Comments to Author
1. Methodological rigour, reproducibility and availability of underlying data Some parts need further information to allow replication studies 2. Presentation of results A very General Description of the isolates. The manuscript would benefit from a more detailed description of the isolates and extension of the in silico analysis especially for mobile genetic element, transmissible resistance and virulence factors as well as an assessment of the potential 8mpact of the isolates for human (virulence factors) 3. How the style and organization of the paper communicates and represents key findings Style is ok, but the key findings can be presented in more detail. 4. Literature analysis or discussion Ok 5. Any other relevant comments The manuscript would benefit of a general revision and additional in silico analysis using the prevailing data. This reviewer suggest to conduct this as the manuscript lacks depth.
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
Overall clearly written paper. The importance of the issue of AMR is highlighted in every part of the paper with clear emphasis of combatting this issue through awareness and a "one health" approach. 1. Methodological rigour, reproducibility and availability of underlying data Clear methodology with reproducible techniques. Whole genome Illumina sequencing was used for further bioinformatic analysis, which was appropriate. Line 73: is information of the bed capacity needed? 2. Presentation of results Tables highlight the results accurately, however maybe another way to present this would be easier to follow (Table 1 and Table 2)? Perhaps via graphs using other statistical programs (R etc). More bioinformatic analyses outputs can be highlighted in figure format vs. written in the text as this makes …
Comments to Author
Overall clearly written paper. The importance of the issue of AMR is highlighted in every part of the paper with clear emphasis of combatting this issue through awareness and a "one health" approach. 1. Methodological rigour, reproducibility and availability of underlying data Clear methodology with reproducible techniques. Whole genome Illumina sequencing was used for further bioinformatic analysis, which was appropriate. Line 73: is information of the bed capacity needed? 2. Presentation of results Tables highlight the results accurately, however maybe another way to present this would be easier to follow (Table 1 and Table 2)? Perhaps via graphs using other statistical programs (R etc). More bioinformatic analyses outputs can be highlighted in figure format vs. written in the text as this makes it easier to follow and provides evidence. 3. How the style and organization of the paper communicates and represents key findings Clear organisation and style of writing. Methodological order with clear results subtitles and text, which is also reflected in the discussion. Each key finding was stated and evidence of other studies highlighting this matter were shown. 4. Literature analysis or discussion Indication of key results and limitations to own research were layed out well. Limitations of other papers and advantages of the current study were mentioned but not discussed well/enough. 5. Any other relevant comments Line 58: Refer to Nigerian studies, please show which ones and highlight these in your references. Line 113: By paired end sequencing* Line 133: Missing full stop at end of paragraph.
Please rate the manuscript for methodological rigour
Good
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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