PONE-D-19-18208

Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

PLOS ONE

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Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #3: Yes

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Reviewer #1: Well written paper and asking key questions about ARG movement in food system.

Limitations of the study are addressed.

No technical issues with approach.

Conclusions are appropriate.

Reviewer #2: I think this is an excellent piece of research which is explained in great detail and written to a very high standard.

I would suggest discussing the use of host depletion methods rather than simply filtering human reads from your data. Also, rather than coupling metagenomics back with culture you could explain the advantages of using long-read sequencing. This would also give further insight into the spread of the AMR genes you have identified and give context as to whether the genes are shared among species of if the same species harbouring the AMR gene is found throughout the sampling/composting process.

With regards the figures, they need to be made to a higher quality as the text can not be read as they stand.

Reviewer #3: This manuscript describes the impact of feeding farmed animals with human food scraps on the dissemination of antimicrobial resistance within the farm products and compost materials. The authors used metagenomics to explore the bacterial resistome, microbiome and virulence markers across different sites of a layer chicken farm, as well as in the food scraps that were fed to the birds. The DNA sequence analysis relied on a commercial software suite (CosmosID) which provides an integrated pipeline for processing datasets. Conventional statistical approaches for descriptive community ecology were used.

This is an interesting investigation. The technical approaches used here may be applied to a number of small-to-medium scale operations across the world, given the growing interest in the development of sustainable practices for agriculture.

The paper is clearly written and the results are convincing, albeit restricted to one farm as a case study.

Major remarks:

The apparent presence of Salmonella in some of the food scraps given to the chicken is worrying, given the zoonotic potential of this organism. This may be of particular importance as egg products can transmit some serovars (Enteritidis, Typhimurium) to humans. Some farms have surveillance programs for the detection of environmental Salmonella sp.; could the author comment on this point?

The use of antimicrobial for treatments or prevention of infectious diseases in the farm is not described in the manuscript. Relatively few antibiotics are approved in commercial layers but the situation varies depending on local regulations. This may have an impact on the nature and abundance of ARGs detected on the flora present on the eggs. Could the author comment on this point?

Minor remarks:

L356 Actinbacteria should read Actinobacteria

L440-441 The sentence “(…) they were able to identify different bacterial of these ARGs across stages (…)” is unclear. Do you mean “different bacterial origins of these ARGs”?

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Reviewer #1: Yes: James F Lowe

Reviewer #2: No

Reviewer #3: No

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Resistome metagenomics from plate to farm: the resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm

PONE-D-19-18208R1

Dear Dr. Barlow,

We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements.

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With kind regards,

Yung-Fu Chang

Academic Editor

PLOS ONE

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