Detection of OXA-48 and NDM-1 genes in ESBL producing Ochrobactrum anthropi from urine samples of Out-patients.
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Background Treatment of the urinary tract infections (UTIs) is vast becoming worrisome because prominent antibiotic resistance among the bacteria involve in the infection. Species of Ochrobacterum are also involve in the infection affecting urinary tract and profusely resistance to antibiotics. Methods Urine samples were collected from out-patients of some hospitals and the bacteria were isolated and identified based on the morphological and biochemical characteristics. The most resistant isolate was selected for molecular identification by amplifying 16S rRNA gene. The bacterial isolates were subjected to antibiotic susceptibility assay and interpreted using standard of CLSI. The resistant isolate was evaluated for the presence of ESBL genes, MBL genes, biofilm gene and efflux pump gene. Results Fourteen (14) Ochrobactrum spp. were isolated from urine samples. Only 3 (21%) of the isolates were resistance to all the twenty-one (21) antibiotics while 7 (50%) were resistance to twenty (20) antibiotics. However, resistance was observed to atleastnine (9) antibiotics in all the antibiotics by the bacterial isolates. The selected isolated was identified to be Ochrobactrum anthropic strain U0145 with occurrence of blaTEM,blaSHV and blaCTX-M-9 as ESBLs genes while blaOXA-48 and blaNDM-1 genes as MBLs genes however, there was no occurrence of GES 1-9,11 gene. The bacterium possessed biofilm production gene while there was no efflux pump gene. Conclusion O. anthropiis becoming prominent among the bacteria responsible for nosocomial-associated infection especially when catheter is involved and treatment may be tasking therefore adequate infection control should be put in place.
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The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments. The language used is poor, which can cause ambiguity at times. Please carefully rewrite it. We offer a discounted translation service, Editage (https://www.editage.com/; see https://www.microbiologyresearch.org/prepare-an-article#13 for more information).
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Comments to Author
The research was well-performed and well-constructed and I really appreciate it I strongly recommend that the author to check the spelling and pay attention to articles usage (a, an and the), space and prepositions. e.x Line 17 : involve/ involved Line 18: resistance /resistant Line 29 : isolated/ isolate line 71: stain/ stained line 39-41: is it one sentence or 2? please rewrite it well comment 2: line 57: how many urine sample were collected? comment 3: Stick to one type of writing "min or minutes " throughout the text. comment 4: line 123 : TAE Abbreviation must be written full name first then start using abbreviation comment 5: line 147 is it sucrose and lactose fermenter ? table 2 state both are negative.
Please rate the manuscript for methodological rigour
Very good
Comments to Author
The research was well-performed and well-constructed and I really appreciate it I strongly recommend that the author to check the spelling and pay attention to articles usage (a, an and the), space and prepositions. e.x Line 17 : involve/ involved Line 18: resistance /resistant Line 29 : isolated/ isolate line 71: stain/ stained line 39-41: is it one sentence or 2? please rewrite it well comment 2: line 57: how many urine sample were collected? comment 3: Stick to one type of writing "min or minutes " throughout the text. comment 4: line 123 : TAE Abbreviation must be written full name first then start using abbreviation comment 5: line 147 is it sucrose and lactose fermenter ? table 2 state both are negative.
Please rate the manuscript for methodological rigour
Very 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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Comments to Author
Review comments: * English language of the manuscript is very poor. * In the results section, the authors state that Ochobacterum anthropi was observed to be Gram-negative, catalase positive, oxidase positive and able to ferment glucose, sucrose and lactose, but in Table 2, they indicated that the bacterium is sucrose negative and lactose negative. The results are contradictory. Explain * In Plates 5 & 7, gel pictures show multiple bands. Molecular testing is not performed well. * Why did the authors focus only on OXA-48, NDM-1, and GES 1-9, 11, but not on other carbapenemase genes? * Abbreviations of antibiotics listed in table 3 should be expanded under the table as a note. Table 3 is not understandable. * The molecular weight should be expressed in Da or KDa or in g/mol but the authors expressed the …
Comments to Author
Review comments: * English language of the manuscript is very poor. * In the results section, the authors state that Ochobacterum anthropi was observed to be Gram-negative, catalase positive, oxidase positive and able to ferment glucose, sucrose and lactose, but in Table 2, they indicated that the bacterium is sucrose negative and lactose negative. The results are contradictory. Explain * In Plates 5 & 7, gel pictures show multiple bands. Molecular testing is not performed well. * Why did the authors focus only on OXA-48, NDM-1, and GES 1-9, 11, but not on other carbapenemase genes? * Abbreviations of antibiotics listed in table 3 should be expanded under the table as a note. Table 3 is not understandable. * The molecular weight should be expressed in Da or KDa or in g/mol but the authors expressed the molecular weight of DNA in ng/mL. * Results are not analysed and presented well. * The manuscript in its present form is not suitable for publication.
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
General Comments * The article is of potential interest that contains genomic identification of species belong to an opportunistic bacterial genus * However, attributing the isolated organism as the cause of urinary tract infection in the patients is not based on solid evidence. The diagnosis of Urinary Tract infections (UTI) is usually confirmed by obtaining a urine culture yielding a quantitatively significant isolate of a bacterial species. The presence of a particular bacterial species is not fair enough to come to a conclusion on causative pathogen. * Especially, Ochrobactrum spp. are opportunistic pathogens which are found in variety of environments and thus confirmation of the diagnosis of UTI and/or identify the particular bacteria as the cause of UTI is impracticable without a …
Comments to Author
General Comments * The article is of potential interest that contains genomic identification of species belong to an opportunistic bacterial genus * However, attributing the isolated organism as the cause of urinary tract infection in the patients is not based on solid evidence. The diagnosis of Urinary Tract infections (UTI) is usually confirmed by obtaining a urine culture yielding a quantitatively significant isolate of a bacterial species. The presence of a particular bacterial species is not fair enough to come to a conclusion on causative pathogen. * Especially, Ochrobactrum spp. are opportunistic pathogens which are found in variety of environments and thus confirmation of the diagnosis of UTI and/or identify the particular bacteria as the cause of UTI is impracticable without a quantitative analysis * There are several typos (combined words / Spelling errors) Introduction * The objectives of this study is not mentioned in the introduction Materials an methods * The number of human participants in the study is not mentioned in the manuscript. * Some of the technical procedures may be submitted as supplementary material/annexes (Preparation of agarose gel, McFarland turbidity standard preparation) Results * Line 146-148 and Table 2 - describes the biochemical characteristics which are already known characteristics of Ochrobactrum spp. * The result section would be organized further ( Eg ; Lines 151-156 describes results of genetic analysis , lines 157-162 describes zone of inhibition exhibited by antibiotics and again in Lines 163-168 there is a description on genetic analysis * The description given with Table 3 i confusing ; Seems contradictory with the contents in the table * Figures plate 3-8 may be compiled into one single figure Discussion * The discussion and conclusion section do not contain line numbers * There are large number of typing errors in the discussion section * The discussion should be focused in-order to convey the key messages and clarify the results Conclusion * "The organism is becoming prominent among the nosocomial-associated infection" is not a conclusion drawn from this study
Please rate the manuscript for methodological rigour
Satisfactory
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