Genome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence

  1. Deisy G. Carneiro
  2. Pedro Marcus P. Vidigal
  3. Túlio Morgan
  4. Maria Cristina D. Vanetti

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Abstract

Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2 . The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins. Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.

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  1. Version published to 10.1099/acmi.0.000828.v3 on Access Microbiology
  2. Access Microbiology

    I am pleased to tell you that your article has now been accepted for publication in Access Microbiology. The work presented is clear and the arguments well formed. The manuscript is well written and contributes to the literature. Thank you for addressing all reviewers comments satisfactorily and in a timely manner.

  3. Version published to 10.1099/acmi.0.000828.v2 on Access Microbiology
  5. Access Microbiology

    Comments to Author

    Dear author, 1- References 4, 11, 18, 23, 24, 32, 41-45, 50, 52, 56-59, 61, 64, 68, 70, 73-75, and 79-81 are old, please use new references. Kind regards

    Please rate the manuscript for methodological rigour

    Good

    Please rate the quality of the presentation and structure of the manuscript

    Satisfactory

    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

  6. Access Microbiology

    Comments to Author

    In summary, the results of this study expand the understanding of the diversity and pathogenicity of Salmonella Enteritidis PT4 578. This study is important because the expansion of knowledge about the accessory genome of Salmonella is essential to contribute to developing detection and control strategies for this pathogen. Title: Line 1: Correct the term ''enterica'' after subsp. The term must be in italics. The study basically addresses pathogenicity and virulence. Therefore, I believe that the title should add a term that mentions the pathogenicity and virulence studied. As it is, it's very generic. Abstract: Line 30-36: The introduction should briefly address virulence and pathogenicity in Salmonella, as this is the main focus of the study. Line 44-45: ''Comparative genome analysis with three other serotypes of Salmonella demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins'' Which serotypes? I recommend mentioning this in the text. Impact Statement: Important and well described. The text gives the reader the ability to understand the importance of the study, the issues addressed. Introduction Line 84: It is described that the enteric species is divided into 7 subspecies, in fact, there are 6 subspecies. Line 119-129: The objective of the work must be described in a more general way, addressing the general context of what will be accomplished. Details should be described in the material and methods. Material and methods Line 147-148: Nanodrop is a brand of spectrophotometer equipment. Therefore, it must contain ®. Enter which nanodrop was used. Ex: NanodropOne or others... Line 148: The term ''agarose gels'' was used. We know that when agarose gel is used, it is because the electrophoresis technique was used. Therefore, I suggest switching to ''agarose gel electrophoresis'' Line 149: Qubit is a brand of fluorimeter. Therefore, it must contain ®. Line 171-173: You must enter % coverage and % identity used to search for resistance genes using the Resfinder tool. Line 172-173: You must enter reference or link of CARD database. Line 200: Swimming motility analysis used the methodology described previously by (41). Even referencing the Vancouver standard, it would be interesting to write, for example: the protocol was carried out in accordance with published literature (41). As it stands, it appears to be incomplete. Line 250: SP-2: you need to replace with SPI-2. Line 257: The title: Pathogenicity islands (SPIs), virulence factors, and resistance genes. I recommend add antimicrobial term  antimicrobial resistance genes. Line 259: SP-: you need to replace with SPI. Line 263: Of these, 37 genes are in Salmonella Enteritidis PT4 578, but the figure 2A shows 36 genes. Discussion Nothing to declare. Well written and well contextualized about the topic. Conclusion The beginning of the conclusion looks like a description of the results. Furthermore, the conclusion must be objective, short and aim to "close" the study.

    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

  7. Version published to 10.1099/acmi.0.000828.v1 on Access Microbiology