Phenotypic antibiotic susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna State, northwest Nigeria
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Background. The increasing resistance of clinical Enterobacteriaceae isolates to commonly prescribed antibiotics has been reported around the world. Data are generally lacking on the prevalence and antibiotic susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna, northwest Nigeria. This study thus aimed to determine the diversity and antibiotic resistance profile of clinical Enterobacteriaceae isolates recovered from clinical specimens from patients admitted to two selected healthcare institutions in Kaduna.
Methods. This was a prospective cross-sectional study conducted between September and December 2021. Non-duplicate clinical bacterial isolates recovered from various specimens were collected and identified using rapid biochemical identification kits. The susceptibility of identified Enterobacteriaceae to various antibiotics and phenotypic detection of carbapenemase enzymes were thereafter determined. The data were analysed and visualized using R software version 4.3.1.
Results. Of the 500 bacterial isolates recovered from specimens collected for the purpose of clinical bacteriology diagnostics, 108 (21.6 %) were identified as Enterobacteriaceae , with Pantoea agglomerans (52, 48.1 %) and Klebsiella oxytoca (19, 17.6 %) being the most prevalent. The isolates exhibited high resistance to azithromycin (69 %) and ceftazidime (42 %), while exhibiting low resistance to amikacin (7 %) and imipenem (10 %). Among the carbapenem-resistant Enterobacteriaceae (CRE) isolates, a significant proportion (12/17, 70.6 %) tested positive for carbapenemase activity.
Conclusion. This study reports a high prevalence of multidrug-resistant Enterobacteriaceae in Kaduna, northwest Nigeria. The emergence of pathogenic P. agglomerans and an alarmingly high prevalence of carbapenemase-producing CRE were also observed. The presence of carbapenemase producers in an area with low carbapenem usage and resistance rates raises significant concerns. Continuous surveillance and robust antibiotic stewardship policies are imperative to preserve the efficacy of carbapenems in this region.
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Thank you for addressing the comments and including a clear statement regarding the limitation of the study.
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You have not sufficiently addressed the point 4 raised by reviewer 1 regarding the discussion if there is any association of the bacteria to gender, age, disease type. This is not touched on in the discussion, eg it seems from Table 2 that Pantoea spp is a lot more prevalent in females and E.coli/Klebsiella in males. Do you have any idea why this might be the case? Or can these patterns not be described due to sample size? This needs to be addressed in the discussion. Are there any patterns related to the demographics/disease types? Has this pattern been seen before in other studies for Pantoea for example? You already have a section on this pathogen in the discussion, it would benefit the manuscript to include this aspect as well since you have the data recorded and shown in your results section. There is a typo in line 267 , it …
You have not sufficiently addressed the point 4 raised by reviewer 1 regarding the discussion if there is any association of the bacteria to gender, age, disease type. This is not touched on in the discussion, eg it seems from Table 2 that Pantoea spp is a lot more prevalent in females and E.coli/Klebsiella in males. Do you have any idea why this might be the case? Or can these patterns not be described due to sample size? This needs to be addressed in the discussion. Are there any patterns related to the demographics/disease types? Has this pattern been seen before in other studies for Pantoea for example? You already have a section on this pathogen in the discussion, it would benefit the manuscript to include this aspect as well since you have the data recorded and shown in your results section. There is a typo in line 267 , it should be heatmap
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The description of your methods is still insufficient in detail, please address the concerns raised by the reviewers. Furthermore the results and discussion requires some clarification (point 7 reviewer 2) and extension (reviewer 1 point 3 and 4).
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Comments to Author
Dear author I am writing to you about your paper with Title: Phenotypic antibiotics susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna State, North-west Nigeria Access Microbiology I have some questions and notes that need your explanations and answers. 1- The introduction needs to be shorter. 2- Line 112-122 you didn't mention if you used any method to adjust your bacterial inoculum as 0.5 Mcfarland. I want to ask why did you use Linzolid on your antibiotic panel for Enterobacteriaceae isolates as it is not recommended to be used with type of bacteria. 3- Line 148- 154 you described the total bacterial isolate source and the patients age and sex, however it will be more valuable if you describe the same information about Enterobacteriaceae isolates only. 4- Line166-171 please …
Comments to Author
Dear author I am writing to you about your paper with Title: Phenotypic antibiotics susceptibility profile of clinical Enterobacteriaceae isolates from Kaduna State, North-west Nigeria Access Microbiology I have some questions and notes that need your explanations and answers. 1- The introduction needs to be shorter. 2- Line 112-122 you didn't mention if you used any method to adjust your bacterial inoculum as 0.5 Mcfarland. I want to ask why did you use Linzolid on your antibiotic panel for Enterobacteriaceae isolates as it is not recommended to be used with type of bacteria. 3- Line 148- 154 you described the total bacterial isolate source and the patients age and sex, however it will be more valuable if you describe the same information about Enterobacteriaceae isolates only. 4- Line166-171 please explain how did you categorize resistance as highly resistant and moderate resistant? 5- Line 175-176 (The modified carbapenem inactivation test indicated positive results for 12/17 (70.6%) carbapenem-resistant Enterobacteriaceae), this finding is very important, however you need to have higher number of isolate to conclude such critical information. 6- Line184 (The length of the bars represent the overall level of resistance of the isolates to various antibiotics) but in figure 1,you write on one axis word (susceptibility) not resistance. 7- Please revise the discussion part as regarding the percentage of resistant or susceptible isolates, it is confusing
Please rate the manuscript for methodological rigour
Poor
Please rate the quality of the presentation and structure of the manuscript
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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Comments to Author
This manuscript is an observational study reiterating the high prevalence of AMR in clinical settings. Over 20% clinical isolates were identified as AMR in this study, alarmingly. Albeit as an observational study, this manuscript could look deeper and identify associations of AMR with different factors, such as diseases, gender, age, etc. In addition, more details of all methods used should be described. Detailed suggestions are as below: 1. Describe details what samples were collected and how they were processed for each sample type. Sample processing procedures are key in the study and should be described in details. 2. The gut microbiota contain diverse types of microorganisms, including E. coli, etc. So is the airway. How did the authors differentiate disease-causing bacteria versus microbiota?
Comments to Author
This manuscript is an observational study reiterating the high prevalence of AMR in clinical settings. Over 20% clinical isolates were identified as AMR in this study, alarmingly. Albeit as an observational study, this manuscript could look deeper and identify associations of AMR with different factors, such as diseases, gender, age, etc. In addition, more details of all methods used should be described. Detailed suggestions are as below: 1. Describe details what samples were collected and how they were processed for each sample type. Sample processing procedures are key in the study and should be described in details. 2. The gut microbiota contain diverse types of microorganisms, including E. coli, etc. So is the airway. How did the authors differentiate disease-causing bacteria versus microbiota? 3. In data analysis, present data of what bacteria were detected in each sample type and disease type. Discuss whether certain diseases tend to have more AMR issues, and maybe certain diseases were overly prescribed with antibiotics. Are detected AMR bacteria in line with the sample type from patients undergoing the same antibiotic treatment? 4. Are any of the infections or bacteria associated with gender, disease type, or age? Discuss these. 5. Describe in details how data were analyzed in Figure 1 and 2. These details are key for readers to understand. How susceptibility and resistance were calculated and classified? Those details are needed in Methods. 6. For quantitative AMR determination, MIC assays are preferred to Kirby Bauer disk assays. If quantitative data are needed for claims in this manuscript, please conduct MIC assays.
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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This is a study that would be of interest to the field and community. Please provide more detail in the Methods section and ensure that software is consistently cited and its version and parameters included.
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