PONE-D-20-10479

Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

PLOS ONE

Dear Dr. Olsen,

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The manuscript has been reviewed by two reviewers and both found interest in it. There are some issues to solve though as the materials and methods should be more complete. Also, further analysis on the WGS data should be performed. It should include more analysis, as the antimicrobial resistance, virulence, plasmids,... make a complete analysis of the WGS data you have.

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Reviewers' comments:

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: This study was designed to quantify the prevalence of Salmonella in poultry production in Nigeria. In order to understand the Salmonella serotypes most often associated with poultry production, whole genome sequencing was used to serotype isolates collected from shoe sock and dust samples from 165 poultry farms in northwest Nigeria. The data show that Salmonella is commonly found on poultry farms in Nigeria and that Salmonella Kentucky is ubiquitous. In general, this paper is well-written and represents important data that is timely and relevant.

General Comments

1. Some minor typos and grammatical issues throughout. Suggest a thorough edit during revisions.

2. The methods are lacking sufficient detail for the study to be repeatable. Specific comments are included below.

3. Why was serotype PCR and WGS done for serotyping?

4. The terminology used in this manuscript needs attention, specifically as it refers to strains. More details below.

Specific Comments

Study design and sample collection

1. if a farm raised broilers OR layers, then 2 samples were collected per farm. However, if a farm raised BOTH, then 4 samples were collected per type, for a total of 8 samples on the farm? If this is true, then why were double the number of samples collected on farms that had both types of birds? If this is not true, then suggest rewording this to be less confusing. Also, is this only referring to the number of dust samples collected? Or does it also include shoe socks? In general, the sampling scheme is not clear. How did the authors end up with 558 total samples?

2. Species should not be italicized.

3. What are composed materials?

4. How were the dust samples collected? From one spot in the pen? Multiple spots in the pen? Was there a strategy to ensure consistency and representative sampling?

5. How were the shoe sock samples handled? Placed into a sterile sample bag?

Farm Description

1. It seems like the sampling strategy should have been developed to also consider farm size. More samples taken from larger farms. Was this considered?

Isolation and Characterization of Salmonella

1. How was the shoe sock sampled? The methods state 1 gram was added to BPW, but how was 1 gram obtained from the shoe sock?

Risk Factor Analysis

1. Why were only 65 farmers surveyed when a total of 165 farms were sampled?

Results

1. Several instances where Salmonella is not italicized in the tables.

2. Above table 2, sample types are referred to as (faeces, dust). Why is faeces now being mentioned when shoe socks have been the focus and are what is mentioned in the table?

3. Age has not been mentioned previously as a variable of interest. What was the sampling strategy for this? Or, how was this included in the study?

4. In reference to serotyping, the authors are using the term "strains". Shouldn't this be isolates? For example: "Seventy-four strains were sequenced, and a total of 23 serotypes..." In this instance, shouldn't it be that 74 isolates were sequenced?

5. How were isolates pulled from the plates? Were isolated colonies picked and re-streaked to ensure purity? At one point, it is stated the "Multiple serotype predictions were observed for four strains..." It is assumed that the authors mean that multiple serotypes were predicted for four different isolates. Is this true? If so, this goes back to the initial question asking about re-streaking and purity. Could it be possible that the isolates were not pure and could have represented multiple serotypes?

6. It's not clear if 1 isolate was pulled per sample or if multiple. These types of details are lacking and should be included.

7. When referring to multiple isolates within a single serotype, it would be more appropriate to refer to these as strains; however, it is difficult to know if different strains exist within a single serotype without further characterization, such as WGS.

8. It is difficult to interpret the results section with the term strain being used to mean isolate.

Discussion

1. Salmonella Kentucky has also been found in cattle.

2. Once again, the authors need to pay particular attention to the use of isolate, strain, and serotype. For example, on page 20, the authors state that "S. Virchow is a strain associated with poultry..." However, the term serotype would be most appropriate here.

Reviewer #2: Hello!

I liked this. I think you can do additional analyses with the WGS and look at things like antibiotic resistance and virulence as well, but that is up to you (it would be a stronger paper). The written language is a bit rough and could use a good revision as tense and subject/verb disagreement is common place.

Usually, data like this comes out from various parts of the world and it is not complete, this is good.

A quick question though, socks? Do you mean boot covers or did someone actually step on socks? Were their feet washed between barns? Why not fresh dropping collections and how did you control for human to sock contamination?

Flush out your methods a bit. Tell me more about the sequencing. If you have a media or reagent, include the company name and city (with state or country) of origin. Be sure to spell out any acronym.

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Reviewer #1: No

Reviewer #2: No

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Prevalence and risk factors of Salmonella in commercial poultry farms in Nigeria

PONE-D-20-10479R1

Dear Dr. Olsen,

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Kind regards,

Patrick Butaye, DVM, PhD

Academic Editor

PLOS ONE

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