Phylotyping, Pathotyping and Phenotypic Characteristics of Escherichia coli Isolated from Various Street Foods in Bangladesh

  1. Anindita Bhowmik
  2. Sharmistha Goswami
  3. Ahmad Salman Sirajee
  4. Sunjukta Ahsan

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Abstract

The burden of street food contamination remains significantly higher among developing countries, making its consumers’ health compromised. This study aimed at identifying Escherichia coli in local street foods, track their sources and characterize their virulence properties, antimicrobial susceptibility patterns, and incidence of recent fecal contamination. Twelve E. coli isolates isolated from 28 types of street foods sold at different locations of Dhaka metropolitan city were confirmed by both culture-based and molecular methods. Phylogroup B1 of environment origin was the most predominant (58%, n=12) among the isolates, followed by commensal phylogroup A (16%), phylogroup C (8%), D (8%), and E (8%). Alarmingly, 8% of the isolates were confirmed to be Enteropathogenic E. coli (EPEC), harboring hly A gene, and 41% were due to recent fecal contamination cases confirmed by the presence of the eae gene. Isolates showed the highest resistance to ampicillin, followed by chloramphenicol. However, resistance could not be correlated to the presence of class 1 integron as isolates sensitive to these antibiotics also harbored this mobile genetic element. The findings of this study demonstrated the presence of antibiotic-resistant, potentially pathogenic E. coli in street food which emphasizes the health hazard associated with consumption of such foods.

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  1. PeerRef

    Peer review report

    Reviewer: Dr. Kilani Hajer,

    Institution: Tunisian Institute of Veterinary Research

    email: hajerkilani@yahoo.fr

    General assessment

    The article is scientifically correct, the English language is acceptable; discussion is rich and linked to their results. The article can be accepted after minor revision.

    Essential revisions that are required to verify the manuscript

    1- Abstract, you said that you found ‘Twelve E. coli’, then you wrote ‘Phylogroup B1 of environment origin was the most predominant (58%, n=12) among the isolates, followed by commensal phylogroup A (16%), phylogroup C (8%), D (8%), and E (8%)’. The number of these phylogroups do not correspond to the total isolates that you collected (n=12)?? Please verify. I realized that you mean by percentage among 12 isolates, therefore it is better for example to write ‘most predominant (n=7; 58%), also for the other phylogroups

    2- If the number of studied isolates is 12, please never use percentages, since it is not appropriate for number under at least 30.

    3- In the abstract as well in the manuscript, the occurrence of integrons do not means that these integrons contains gene cassettes that encode antimicrobial resistance. Many studies reported the occurrence of class 1 integrons with empty variable regions. Therefore, please take this in mind and modify your discussion.

    4- Introduction, you wrote ‘..are typically comprised of phylogenetic groups A, B, and D’. I believe you mean B1 phylogroup, correct this.

    5- You wrote ‘..prepared, as Mandal et al. (2014) said’. PLEASE delete the word ‘said’

    6- Write ‘Purified 16S rRNA amplicons (Figure 2) were digested with three different restriction enzymes’ correct this also in Figure 2.

    7- You wrote ‘In this research, E. coli was isolated at a rate of 8%’. Please, you investigate 60 samples and you find 12 isolates, so 12/60 X100 = 20%. So how you speak about 8%?

    8- As I mentioned above since you find only 12 isolates, please avoid to provide percentage, please provide the number of isolates when appropriate and especially in the section ‘Distribution of phylogroups of E. coli in street foods’

    9- You provide figure 4, but it is not indicated in your manuscript. If it is not necessary, you can delete it.

    10- You wrote ‘..Genes carried by integrons usually express multiple resistance mechanisms, such as resistance to beta-lactams…’ in reality beta-lactamase genes are not part of integrons, they are not gene cassette, they can be near integrons but not as gene casette.

    Other suggestions to improve the manuscript

    Try to avoid unnecessary figures, and shorten the discussion if possible

    Decision

    Verified with reservations: The content is scientifically sound but has shortcomings that could be improved by further studies and/or minor revisions.

  2. PeerRef

    Peer review report

    Reviewer: Richard L. Guerrant Institution: University of Virginia email: guerrant@vrginia.edu

    Section 1 – Serious concerns

    • Do you have any serious concerns about the manuscript such as fraud, plagiarism, unethical or unsafe practices? No

    • Have authors’ provided the necessary ethics approval (from authors’ institution or an ethics committee)? not applicable

    Section 2 – Language quality

    • How would you rate the English language quality? Low to medium quality, but I understand the content

    Section 3 – validity and reproducibility

    • Does the work cite relevant and sufficient literature? Yes
    • Is the study design appropriate and are the methods used valid? No — See comments
    • Are the methods documented and analysis provided so that the study can be replicated? No — See comments
    • Is the source data that underlies the result available so that the study can be replicated? not applicable
    • Is the statistical analysis and its interpretation appropriate? Yes
    • Is quality of the figures and tables satisfactory? Yes
    • Are the conclusions adequately supported by the results? No — See comments
    • Are there any objective errors or fundamental flaws that make the research invalid? Yes, see comments below

    Section 4 – Suggestions

    • Based on your answers in section 3 how could the author improve the study?

    Major concerns include:

    1. Quantification of coliforms is key; if done as suggested by MPN method, actual projected counts should be put into a table and discussed by food type, pathogenic potential.

    2. Were any actual pathogens detected? (ex ETEC, EPEC, EAEC, EHEC); probes are not those typically used for that. Were any Shigella, Salmonella? Are other pathogens detected? If not, why not?

    3. Many statements are expressed as causal facts, but this is far from proven. Examples include ‘foodborne infections …have accelerated … resistance’ on page 1; ‘infections … are due to fast food ingredients;’ on page 2; these points require citation of documented data.

    4. At the bottom of page 2, the objective of ‘determining the origin’ is not addressed.

    • Do you have any other feedback or comments for the Author? No

    Tighten statements, like the opening line of abstract to say more directly, ‘burden…compromises health.’

    Section 5 – Decision

    Requires revisions: The manuscript contains objective errors or fundamental flaws that must be addressed and/or major revisions are suggested.

  3. Version published to 10.1101/2022.02.07.22270615v1 on medRxiv