Microbial Contamination and Antibiotic Resistance in Fresh Produce and Agro-Ecosystems in South Asia—A Systematic Review
, Deepak Saxena 3,4,5,* and Christiane Schreiber 7
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsWhile the article is reasonably well written, a significant improvement should be done in regards to the analysis of the data. The manuscript is much too similar to a narrative review. Clear conclusions should be evident from a systematic review.
In addition, here are some specific points that need to be addressed
Major points
- a PRISMA checklist should be added to the supplementary file (https://www.prisma-statement.org/prisma-2020-checklist)
- Line 121 - Was the protocol developed a priori? If so, was the protocol registered with Prospero? https://www.crd.york.ac.uk/prospero/
- Why was the search only conducted in three databases and between the years 2012-2022?
- Full search algorithms for each individual database should be added to a supplementary file
- How many and which authors performed the search, screening, full text eligibility for the included articles?
- When was the last search performed?
- The Prisma Flowchart should be cited as recommended on the Prisma website; Furthermore, since the grey literature was searched another flow chart should be used, as specified by PRISMA – see the section ‘systematic reviews which included searches of databases, registers and other sources’ at https://www.prisma-statement.org/prisma-2020-flow-diagram
- Reasons for exclusion in the screening step should be clearly stated on the Flowchart with the corresponding number of articles (n=)
- Reasons for exclusion in the full article eligibility step should be stated with the corresponding number of articles (n=)
- Where any automation tools or AI tools used in any of the steps of the review? If so, this should be clearly stated
- Figure 2 – the numbers for each country are not visible
- In the results section all percentages should be noted as percent and number (e.g., Line 219 – 72.7%, n= x); this provides context of the findings more than the actual percent
- Line 255 – this line specifies a supplementary table but this file is missing; was the supplementary file not uploaded?
- Due tot the relatively low number of included studies, references should be added in the text when providing an overview statement – e.g., Line 290 – Five studies etc
- Line 330 – 336 – the numbers do not match – 18 studies reported AST, 13 with disk diffusion, 2 with broth microdilution – the last 3 studies?
- The conclusions need to be completely redone and encompass a summary of the extracted data – most common examined produce types, bacterial genera, antimicrobial resistance etc
Minor points
- references should be formatted according to the journal instructions (e.g., line 57 etc)
- Table 3 – define NM – if it stands for not mentioned it should be replaced with the standard N/A – the same for all tables in the manuscript
- Table 3 – the last two columns are not clear – from the context I gather that the last column is about antibiotic resistance genes; correct this
- Table 3 – what does frequency stand for? Number of samples that were analysed?
- Figure 3 – the absolute number should be added on the graph
- Figure 4 – add percentage and absolute number in the correct format (%, n= )
- Figure 4 - Leafy and root vegetables not veg
- Line 248 – numbers and percentages for the produce
- Table 4 has no title
- Table 4 – did study 21 not evaluate any microbial counts?
- Bacterial names should be in italics throughout the manuscript – e.g., Line 275
- Line 337 – how many of the included studies used CLSI criteria? What criteria of AST interpretation did the other studies use?
- Table 5 has no title
- Table 5 – also add absolute numbers
- Line 453 – all the mentioned bacteria genera are known to be human pathogens (however, some of them are conditionally pathogenic)
- Line 488-489 – Metallo beta lactamase and AmpC beta lactamase
Comments on the Quality of English LanguageThe whole manuscript requires English revision
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThis manuscript reports on a review of the literature concerning the frequency of identification of human pathogens from agricultural soils, surface water, fruit and vegetable produce in the South Asia region. It then compares the frequency of identification of antibiotic-resistant strains of bacteria and antimicrobial-resistance genes from those same samples. The manuscript concludes that this type of systematic review is severely hampered by the lack of consistency in the approaches used in the relevant literature, and that E. coli and Salmonella spp. are the most common microbial contaminants of such samples, while tetracycline and erythromycin are the antibiotics to which resistance was most frequently identified. Circulation of antibiotic resistance genes in fresh produce that may be eaten raw is a potential public health hazard.
The final two paragraphs of the limitations section highlight the difficulties in an analysis such as this, and make clear that the review has been unable to provide the level of detail the authors intended. Significantly, these lines also serve as a warning for others who, without publication of reviews such as this, may be tempted by a similar undertaking and would encounter the same difficulties. Despite these difficulties, the message that antibiotic resistance genes and diarrhoeagenic pathogens are reasonably common on fresh produce, including those that would not be cooked prior to consumption, is clear from this study. That said, the data available within this review could be presented better - presentation of a series of numbers in text passages makes it difficult to directly compare between paragraphs and detracts from the potential significance of those values. The manuscript would also benefit from greater analysis of regional variability in antimicrobial use within agriculture and how this correlates with prevalence of antibiotic resistance genes. Without such analysis, the manuscript is rather limited in what it reveals, essentially stating that common bacteria are common.
More detail is required regarding the searches performed, as replication of the search terms in Web of Science provided 3555 articles, even when adding NOT searches in titles and abstracts to exclude animal-associated studies. Many of these would likely be excluded at a later stage, but should at least be counted in the identification stage. It is also noted that some search terms used are redundant – results for “antibiotic resistan*” will also appear under “antibiotic*”, which was combined with an OR function.
In table 4 it is unclear what the frequency is - presumably, this would be the number of times the location was sampled, though this does not explain why there are in some cases more values than there are locations or sample categories (paper 12 for example, has three frequency values but only two locations and two sample categories).
On lines 487-489 of the manuscript, it is unclear what constitutes “antibiotics of most interest”. This could be interpreted as most prescribed, most purchased over-the-counter, most used in agriculture (kg/year), most hospital cases, and maybe other possible reasons for being “of most interest”.
While most references are suitable, there is inconsistency in the approach used which will need to be rectified. Reference 5 (worldbank.org) would be better replaced with the report to which the webpage refers (World Bank. 2017. “Drug-Resistant Infections: A Threat to Our Economic Future.” Washington, DC: World Bank). References 19 and 32 provide inadequate signposting to the sources. References 20 and 26 do not appear to provide supporting evidence for the statements made. Table 3 entries 11, 12 and 18 do not have corresponding entries in the reference list.
Comments on the Quality of English LanguageThe language used is comprehensible throughout, though there are places where apparent use of a thesaurus has led to choices of words that are not ideal.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsOverall, most concerns have been addressed.
However, the conclusions might be further improved - specify the most commonly encountered bacterial isolates in the most frequent produce types along with global data on antimicrobial resistance in a concise way.
Comments on the Quality of English LanguageMinor editing of the English language is still required
Author Response
Comment 1:
Overall, most concerns have been addressed.
However, the conclusions might be further improved - specify the most commonly encountered bacterial isolates in the most frequent produce types along with global data on antimicrobial resistance in a concise way.
Response: Thank you for your review. We have accordingly modified the conclusion.
Comment 2: Minor editing of the English language is still required
Response: Thanks. We have edited the manuscript as suggested.
Reviewer 2 Report
Comments and Suggestions for AuthorsThank you for clarifying the "antibiotics of most interest", and for addressing the referencing issues.
For Table 4, it would help if a note was added beneath the table containing the explanation given in response to my previous comment.
Regarding the methods employed in the literature search: the number of articles returned from the search before removal of duplicates, is the point of most concern. The disparity between the stated number of articles returned by the search and the number returned in an attempt to replicate the search suggest that the search cannot be accurately replicated. However, given that this is a review and not an experimental protocol, this is of less concern that it otherwise might be.
