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Pathogens
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Foodborne Pathogens—Genome Sequencing Collection
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Foodborne Pathogens—Genome Sequencing Collection

A special issue of Pathogens (ISSN 2076-0817).

Deadline for manuscript submissions: closed (30 April 2021) | Viewed by 11513

Special Issue Editors

Dr. Shabarinath Srikumar

E-Mail Website
Guest Editor
United Arab Emirates University, UAE
Interests: functional genomics of foodborne bacteria; antimicrobial resistance in the food environment
Dr. Ben D. Tall

E-Mail Website
Guest Editor
Senior Research Microbiologist
U.S. Food and Drug Administration, 5001, Campus Drive, College Park, MD 20740, USA
Interests: study of the pathogenic mechanisms of foodborne enteric bacteria; characterization and expression of adherence factors; fimbriae ultrastructure, effects of environmental influences on bacterial attachment/invasion mechanisms associated with foodborne enteric pathogens
Dr. Gopal. R. Gopinath

E-Mail Website
Guest Editor
Center of Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, MD 20708, USA
Interests: microbial genomics; bioinformatics; food-safety; biological ontologies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

It is my pleasure to invite your participation in the upcoming issue on ‘Application of Next- or Third-Generation Sequencing Technologies for the Detection, Identification, and Characterization of Foodborne Pathogens’.

It is well known that next/third-generation sequencing technologies along with bioinformatic applications are currently revolutionizing food microbiology. DNA deep sequencing technologies are being used either in the characterization of ‘single’ isolates (wherein Single Nucleotide Polymorphisms (SNPs) and genomic multilocus sequence typing (gMLST) are used to type the strain to identify similarities by generating a phylogenetic trese) or in the identification of microbial population associated with a particular food or food process environment.

  The focus of this Special Issue is to address the most recent trends in the application of deep sequencing technologies in characterizing foodborne pathogens, therefore ensuring food safety. The scope of this Special Issue will be broad so as to encompass well-known foodborne pathogens in addition to emerging foodborne pathogens. Reports on the utilization of next/third-generation sequencing technologies in characterization of the microbiome associated with food/food process environments are also very welcome.

The main goal of this issue is to enlighten and promote the broad application of DNA deep sequencing technologies within the food industry. In addition, we also endeavor to address the novel applications highlighting the research gaps with an aim to increase food safety by driving further research into this theme.

Dr. Shabarinath Srikumar
Dr. Ben. D. Tall
Dr. Gopal. R. Gopinath
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Pathogens is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • next-generation sequencing
  • third generation sequencing
  • DNA deep sequencing
  • microbiome
  • phylogenetic tree

Published Papers (4 papers)

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Research

8 pages, 3455 KiB  
Communication
Genomic Identification of Multidrug-Resistant Salmonella Virchow Monophasic Variant Causing Human Septic Arthritis
by Zhenyu Wang, Haiyan Xu, Chao Chu, Yuanyue Tang, Qiuchun Li and Xinan Jiao
Pathogens 2021, 10(5), 536; https://doi.org/10.3390/pathogens10050536 - 29 Apr 2021
Cited by 2 | Viewed by 1862
Abstract
The monophasic variant of Salmonella Typhimurium has emerged and increased rapidly worldwide during the past two decades. The loss of genes encoding the second-phase flagella and the acquirement of the multi-drug resistance cassette are the main genomic characteristics of the S. Typhimurium monophasic [...] Read more.
The monophasic variant of Salmonella Typhimurium has emerged and increased rapidly worldwide during the past two decades. The loss of genes encoding the second-phase flagella and the acquirement of the multi-drug resistance cassette are the main genomic characteristics of the S. Typhimurium monophasic variant. In this study, two Salmonella strains were isolated from the knee effusion and feces of a 4-year-old girl who presented with a case of septic arthritis and fever, respectively. Primary serovar identification did not detect the second-phase flagellar antigens of the strains using the classical slide agglutination test. Whole-genome sequencing analysis was performed to reveal that the replacement of the fljAB operon by a 4.8-kb cassette from E. coli caused the non-expression of phase-2 flagellar antigens of the strains, which were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) by core-genome multi-locus sequence typing (cgMLST). Compared to the 16 published S. Virchow genomes, the two strains shared a unique CRISPR type of VCT12, and showed a close genetic relationship to S. Virchow BCW_2814 and BCW_2815 strains, isolated from Denmark and China, respectively, based on cgMLST and CRISPR typing. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the strains to be multidrug-resistant to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emergence of the multidrug-resistant S. Virchow monophasic variant revealed that whole-genome sequencing and CRISPR typing could be applied to identify the serovaraints of Salmonella enterica strains in the national Salmonella surveillance system. Full article
(This article belongs to the Special Issue Foodborne Pathogens—Genome Sequencing Collection)
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13 pages, 2320 KiB  
Article
Whole Genome Sequence Analysis of Phage-Resistant Listeria monocytogenes Serotype 1/2a Strains from Turkey Processing Plants
by Phillip Brown, Yi Chen, Cameron Parsons, Eric Brown, Martin J. Loessner, Yang Shen and Sophia Kathariou
Pathogens 2021, 10(2), 199; https://doi.org/10.3390/pathogens10020199 - 13 Feb 2021
Cited by 11 | Viewed by 2423
Abstract
Listeria monocytogenes is a Gram-positive bacterial pathogen and the causative agent of listeriosis, a severe foodborne infection. L. monocytogenes is notorious for its ability to persist in food processing environments (FPEs) via a variety of adaptive traits. Even though traits such as cold [...] Read more.
Listeria monocytogenes is a Gram-positive bacterial pathogen and the causative agent of listeriosis, a severe foodborne infection. L. monocytogenes is notorious for its ability to persist in food processing environments (FPEs) via a variety of adaptive traits. Even though traits such as cold tolerance, biofilm formation and sanitizer resistance have been extensively investigated for their roles in persistence of L. monocytogenes in FPEs, much less is known about resistance to bacteriophages. Previous studies explored phage resistance mechanisms in laboratory-created mutants but it is imperative to investigate phage resistance that is naturally exhibited in FPE-derived strains. Here, we integrated the analysis of whole genome sequence data from a panel of serotype 1/2a strains of sequence types 321 and 391 from turkey processing plants, with the determination of cell surface substituents required for phage adsorption and phage infection assays with the four wide-host-range phages A511, P100, 20422-1 and 805405-1. Using a specific set of recombinant phage protein probes, we discovered that phage-resistant strains lacked one or both of the serogroup 1/2-specific wall teichoic acid carbohydrate decorations, N-acetylglucosamine and rhamnose. Furthermore, these phage-resistant strains harbored substitutions in lmo1080, lmo1081, and lmo2550, which mediate carbohydrate decoration of the wall teichoic acids. Full article
(This article belongs to the Special Issue Foodborne Pathogens—Genome Sequencing Collection)
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12 pages, 2758 KiB  
Article
Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017
by Ji-Yeon Hyeon, Shaoting Li, David A. Mann, Shaokang Zhang, Kyu-Jik Kim, Dong-Hun Lee, Xiangyu Deng and Chang-Seon Song
Pathogens 2021, 10(1), 45; https://doi.org/10.3390/pathogens10010045 - 07 Jan 2021
Cited by 16 | Viewed by 4036
Abstract
Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from [...] Read more.
Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010–2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac(6’)-Iaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea. Full article
(This article belongs to the Special Issue Foodborne Pathogens—Genome Sequencing Collection)
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12 pages, 1258 KiB  
Article
Genomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018
by Lisa Di Marcantonio, Anna Janowicz, Katiuscia Zilli, Romina Romantini, Stefano Bilei, Daniela Paganico, Tiziana Persiani, Guido Di Donato and Elisabetta Di Giannatale
Pathogens 2020, 9(5), 349; https://doi.org/10.3390/pathogens9050349 - 05 May 2020
Cited by 9 | Viewed by 2393
Abstract
Salmonellosis is a major cause of bacterial foodborne infection. Since 2016, an increased number of cases of gastroenteritis caused by Salmonella enterica serovar Enteritidis linked to eggs produced in Poland has been reported in Europe. In Italy, S. Enteritidis is one of the [...] Read more.
Salmonellosis is a major cause of bacterial foodborne infection. Since 2016, an increased number of cases of gastroenteritis caused by Salmonella enterica serovar Enteritidis linked to eggs produced in Poland has been reported in Europe. In Italy, S. Enteritidis is one of the three most commonly reported serotypes, associated mainly with the consumption of contaminated eggs and derived products. In our work, we analysed 61 strains of S. Enteritidis obtained from humans and farms in the Abruzzi region, Italy, in 2018. We used Multiple-Loci Variable-Number Tandem Repeat (VNTR) analysis (MLVA)-based typing and Whole-Genome Sequencing (WGS) tools to identify closely related strains and perform cluster analysis. We found two clusters of genetically similar strains. The first one was present in the local farms and isolated from human cases and had single-linkage distance of no more than two core genes and less than five Single-Nucleotide Polymorphisms (SNPs). The second cluster contained strains isolated from humans and from a dessert (tiramisù) sample that shared identical core genome and were assigned the same SNP address. Cluster 2 isolates were found to be genetically similar to an S. Enteritidis strain from a multi-country outbreak linked to Polish eggs. Full article
(This article belongs to the Special Issue Foodborne Pathogens—Genome Sequencing Collection)
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