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Pathogens
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Genomic Epidemiology of Foodborne Pathogens 2.0
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Genomic Epidemiology of Foodborne Pathogens 2.0

A special issue of Pathogens (ISSN 2076-0817). This special issue belongs to the section "Epidemiology of Infectious Diseases".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 8175

Special Issue Editor

Dr. Patrick Njage

E-Mail Website
Guest Editor
Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
Interests: whole genome sequencing; foodborne pathogens; food safety; machine learning; risk assessment; source attribution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The ability to track the spatial and temporal distribution of pathogen genomes and their genetic variations by genomic epidemiologists has revolutionized the capability to predict and prevent infectious diseases in humans and animals, as well as the speed and resolution of their global detection and control. This has been supported by the phenomenal pace of technical advancement in microbial genomics since 1995, which was when the first complete genome sequence of a free-living organism, Haemophilus influenzae, was published. A possible outcome of this is that we can gain a more complete and deeper understanding of how pathogens cause disease, emerge, adapt to the host, and spread in human populations.

This Special Issue aims to provide a channel for the dissemination of the current developments in genomic epidemiology, to provide the best evidence of the health impact and relative contribution of different genetic variants to foodborne infections. We invite the submission of manuscripts reporting research in topics such as the following:

  • Genomics tools to track the spread of foodborne pathogens;
  • Spread of foodborne pathogenic genetic variants in local and international communities;
  • Sharing and dissemination of foodborne pathogen genetic information in databases;
  • Programs and technologies for foodborne pathogen genomic data generation, analysis, visualization and data sharing;
  • Relative contribution of different foodborne pathogen sources to occurrence data from food, animals and the environment;
  • Linkage between microbial genotypes and foodborne disease phenotypes;
  • Application of novel and existing molecular microbiology tools, such as PCR and RT-PCR, to type or study the relative contribution of different genetic variants to foodborne infections.

Submissions reporting the use of existing protocols in new and interesting settings are welcome.

Dr. Patrick Njage
Guest Editor

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

  • foodborne pathogen genomics
  • foodborne pathogen tracking and source attribution
  • whole-genome sequencing
  • genetic variation
  • phylogenetics
  • genomic data sharing
  • genomic data visualization
  • genomic analysis pipelines

Published Papers (4 papers)

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Research

13 pages, 1100 KiB  
Article
Comparison of Source Attribution Methodologies for Human Campylobacteriosis
by Maja Lykke Brinch, Tine Hald, Lynda Wainaina, Alessandra Merlotti, Daniel Remondini, Clementine Henri and Patrick Murigu Kamau Njage
Pathogens 2023, 12(6), 786; https://doi.org/10.3390/pathogens12060786 - 31 May 2023
Cited by 2 | Viewed by 1413
Abstract
Campylobacter spp. are the most common cause of bacterial gastrointestinal infection in humans both in Denmark and worldwide. Studies have found microbial subtyping to be a powerful tool for source attribution, but comparisons of different methodologies are limited. In this study, we compare [...] Read more.
Campylobacter spp. are the most common cause of bacterial gastrointestinal infection in humans both in Denmark and worldwide. Studies have found microbial subtyping to be a powerful tool for source attribution, but comparisons of different methodologies are limited. In this study, we compare three source attribution approaches (Machine Learning, Network Analysis, and Bayesian modeling) using three types of whole genome sequences (WGS) data inputs (cgMLST, 5-Mers and 7-Mers). We predicted and compared the sources of human campylobacteriosis cases in Denmark. Using 7mer as an input feature provided the best model performance. The network analysis algorithm had a CSC value of 78.99% and an F1-score value of 67%, while the machine-learning algorithm showed the highest accuracy (98%). The models attributed between 965 and all of the 1224 human cases to a source (network applying 5mer and machine learning applying 7mer, respectively). Chicken from Denmark was the primary source of human campylobacteriosis with an average percentage probability of attribution of 45.8% to 65.4%, representing Bayesian with 7mer and machine learning with cgMLST, respectively. Our results indicate that the different source attribution methodologies based on WGS have great potential for the surveillance and source tracking of Campylobacter. The results of such models may support decision makers to prioritize and target interventions. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Foodborne Pathogens 2.0)
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13 pages, 2653 KiB  
Article
The Microbial Genetic Diversity and Succession Associated with Processing Waters at Different Broiler Processing Stages in an Abattoir in Australia
by Josphat Njenga Gichure, Ranil Coorey, Patrick Murigu Kamau Njage, Gary A. Dykes, Esther K. Muema and Elna M. Buys
Pathogens 2023, 12(3), 488; https://doi.org/10.3390/pathogens12030488 - 20 Mar 2023
Viewed by 1531
Abstract
The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, [...] Read more.
The high organic content of abattoir-associated process water provides an alternative for low-cost and non-invasive sample collection. This study investigated the association of microbial diversity from an abattoir processing environment with that of chicken meat. Water samples from scalders, defeathering, evisceration, carcass-washer, chillers, and post-chill carcass rinsate were collected from a large-scale abattoir in Australia. DNA was extracted using the Wizard® Genomic DNA Purification Kit, and the 16S rRNA v3-v4 gene region was sequenced using Illumina MiSeq. The results revealed that the Firmicutes decreased from scalding to evisceration (72.55%) and increased with chilling (23.47%), with the Proteobacteria and Bacteroidota changing inversely. A diverse bacterial community with 24 phyla and 392 genera was recovered from the post-chill chicken, with Anoxybacillus (71.84%), Megamonas (4.18%), Gallibacterium (2.14%), Unclassified Lachnospiraceae (1.87%), and Lactobacillus (1.80%) being the abundant genera. The alpha diversity increased from scalding to chilling, while the beta diversity revealed a significant separation of clusters at different processing points (p = 0.01). The alpha- and beta-diversity revealed significant contamination during the defeathering, with a redistribution of the bacteria during the chilling. This study concluded that the genetic diversity during the defeathering is strongly associated with the extent of the post-chill contamination, and may be used to indicate the microbial quality of the chicken meat. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Foodborne Pathogens 2.0)
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12 pages, 8431 KiB  
Article
Campylobacter jejuni and Campylobacter coli from Houseflies in Commercial Turkey Farms Are Frequently Resistant to Multiple Antimicrobials and Exhibit Pronounced Genotypic Diversity
by Hannah Bolinger, William G. Miller, Jason A. Osborne, Jeffrey Niedermeyer and Sophia Kathariou
Pathogens 2023, 12(2), 230; https://doi.org/10.3390/pathogens12020230 - 01 Feb 2023
Cited by 1 | Viewed by 1467
Abstract
Campylobacter is a leading foodborne pathogen, and poultry are a major vehicle for infection. Houseflies play important roles in colonization of broiler flocks with Campylobacter but comparable information for turkey farms is limited. Here, we investigated houseflies as potential vectors for Campylobacter in [...] Read more.
Campylobacter is a leading foodborne pathogen, and poultry are a major vehicle for infection. Houseflies play important roles in colonization of broiler flocks with Campylobacter but comparable information for turkey farms is limited. Here, we investigated houseflies as potential vectors for Campylobacter in 28 commercial turkey flocks. We characterized species, genotypes, and the antimicrobial resistance (AMR) profiles of Campylobacter from turkey feces and houseflies in the same turkey house. Of the 28 flocks, 25 yielded Campylobacter from turkey droppings and houseflies, with an average of 6.25 and 3.11 Campylobacter log CFU/g feces and log CFU/fly, respectively. Three flocks were negative for Campylobacter both in turkey feces and in houseflies. Both C. coli and C. jejuni were detected in turkey feces and houseflies, with C. coli more likely to be recovered from houseflies than feces. Determination of Campylobacter species, genotypes, and AMR profiles revealed up to six different strains in houseflies from a single house, including multidrug-resistant strains. For the predominant strain types, presence in houseflies was predictive of presence in feces, and vice versa. These findings suggest that houseflies may serve as vehicles for dissemination of Campylobacter, including multidrug-resistant strains, within a turkey house, and potentially between different turkey houses and farms in the same region. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Foodborne Pathogens 2.0)
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20 pages, 543 KiB  
Article
Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012–2020
by Marie Anne Chattaway, Anaïs Painset, Gauri Godbole, Saheer Gharbia and Claire Jenkins
Pathogens 2023, 12(2), 223; https://doi.org/10.3390/pathogens12020223 - 31 Jan 2023
Cited by 5 | Viewed by 3339
Abstract
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. [...] Read more.
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012–2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Foodborne Pathogens 2.0)
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