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Pathogens
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Molecular Epidemiology of Pathogenic Agents
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Molecular Epidemiology of Pathogenic Agents

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

Deadline for manuscript submissions: 31 March 2025 | Viewed by 9914

Special Issue Editor

Dr. Maria Antonia De Francesco

E-Mail Website
Guest Editor
Department of Molecular and Translational Medicine, Institute of Microbiology, Università degli Studi di Brescia, 25123 Brescia, Italy
Interests: antibiotic resistance; antiviral resistance; molecular epidemiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Pathogenic agents can cause various infectious diseases when they enter the bodies of humans and animals, and can spread through water, air, soil, and physical contact. These infectious diseases are major public health problems. The molecular epidemiology of pathogenic agents enables us to observe and analyze the frequency of infectious diseases from the perspectives of pathogens, transmission routes, susceptible hosts, etc. This knowledge is important for revealing the mechanisms and control of pathogenic infectious diseases.

This Special Issue aims to provide the latest findings on various aspects of pathogenic agents’ epidemiology. We invite experts from around the world to submit research articles or review articles related to this important topic.

Dr. Maria Antonia De Francesco
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 2200 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

  • pathogenic agent
  • pathogens
  • viruses
  • bacteria
  • fungi
  • parasites
  • molecular epidemiology
  • surveillance
  • prevalence
  • risk factors
  • public health

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Published Papers (6 papers)

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Research

Jump to: Review

10 pages, 972 KiB  
Article
Genotypic Characterization of Human Parvovirus B19 Circulating in the 2024 Outbreak in Tuscany, Italy
by Giada Beligni, Giulia Alessandri and Maria Grazia Cusi
Pathogens 2025, 14(2), 121; https://doi.org/10.3390/pathogens14020121 - 28 Jan 2025
Viewed by 442
Abstract
Human Parvovirus B19 (hB19V) is a widespread virus, causing erythema infectiosum in children and several clinical manifestations from acute to persistent infections in adults. In early 2024, ECDC reported an increased human Parvovirus B19 circulation in 14 European countries. A hB19V outbreak was [...] Read more.
Human Parvovirus B19 (hB19V) is a widespread virus, causing erythema infectiosum in children and several clinical manifestations from acute to persistent infections in adults. In early 2024, ECDC reported an increased human Parvovirus B19 circulation in 14 European countries. A hB19V outbreak was also reported in Tuscany, Italy, prompting a detailed investigation of its genetic characteristics. In this context, through strict monitoring of circulating strains via next-generation sequencing (NGS), we carried out a phylogenetic analysis based on the whole of hB19V genomes. Phylogenetic clustering assigned all isolates to the G1a genotype, although with some mutations in NS1, VP1, and VP2, compared to the reference strains. Further characterization of these variants is necessary to fully assess their potential implications for public health. This study provides valuable insights into the spread of Parvovirus B19 and underlines the importance of continuous genomic surveillance to monitor and respond to possible hB19V epidemics that could impact public health. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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15 pages, 3279 KiB  
Article
Genomic Analysis of Aeromonas salmonicida ssp. salmonicida Isolates Collected During Multiple Clinical Outbreaks Supports Association with a Single Epidemiological Unit
by Konrad Wojnarowski, Paulina Cholewińska, Peter Steinbauer, Tobias Lautwein, Wanvisa Hussein, Lisa-Marie Streb and Dušan Palić
Pathogens 2024, 13(10), 908; https://doi.org/10.3390/pathogens13100908 - 17 Oct 2024
Viewed by 1414
Abstract
Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease [...] Read more.
Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease in production facilities. In such a regulatory environment, the utility of autogenous vaccines to assist with disease prevention and control as a veterinary-guided prophylactic measure is of high interest to the producers and veterinary services alike. However, evolving concepts of epidemiological units and epidemiological links need to be considered during approval and acceptance procedures for the application of autogenous vaccines in multiple aquaculture facilities. Here, we present the results of solid-state nanopore sequencing (Oxford Nanopore Technologies, ONT) performed on 54 isolates of Aeromonas salmonicida ssp. salmonicida sampled during clinical outbreaks of furunculosis in different aquaculture facilities from Bavaria, Germany, from 2017 to 2020. All of the performed analyses (phylogeny, single nucleotide polymorphism and 3D protein modeling for major immunogenic proteins) support a high probability that all studied isolates belong to the same epidemiological unit. Simultaneously, we describe a cost/effective method of whole genome analysis with the usage of ONT as a viable strategy to study outbreaks of other pathogens in the field of aquatic veterinary medicine for the purpose of developing the best autogenous vaccine candidates applicable to multiple aquaculture establishments. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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11 pages, 4232 KiB  
Article
The Recombinase Polymerase Amplification Test for Strongyloides stercoralis Is More Sensitive than Microscopy and Real-Time PCR in High-Risk Communities of Cusco, Peru
by Jose L. Malaga, Martha V. Fernandez-Baca, Alejandro Castellanos-Gonzalez, Melinda B. Tanabe, Clara Tift, Maria Luisa Morales, Martha Lopez, Angela Valdivia-Rodriguez, Frecia Mamani-Licona and Miguel M. Cabada
Pathogens 2024, 13(10), 869; https://doi.org/10.3390/pathogens13100869 - 3 Oct 2024
Viewed by 1545
Abstract
Strongyloidiasis is a neglected, soil-transmitted helminth infection prevalent worldwide. The true burden of strongyloidiasis is unclear due to the lack of sensitive, field-friendly diagnostic tests. PCR tests to detect Strongyloides DNA in stool are sensitive and specific, but the need for expensive equipment [...] Read more.
Strongyloidiasis is a neglected, soil-transmitted helminth infection prevalent worldwide. The true burden of strongyloidiasis is unclear due to the lack of sensitive, field-friendly diagnostic tests. PCR tests to detect Strongyloides DNA in stool are sensitive and specific, but the need for expensive equipment limits their use in endemic regions. Isothermal PCR amplification tests are easier to deploy while maintaining sensitivity and specificity. We developed and evaluated a recombinase polymerase amplification lateral flow assay (RPA-LFA) to detect Strongyloides stercoralis in human stool samples. Three hundred stool samples were collected in three communities in the jungle of Cusco, Peru. Samples were tested for S. stercoralis larvae using microscopy (Baermann’s, agar plate culture (APC), and rapid sedimentation), real-time PCR, and RPA-LF for Strongyloides DNA. The RPA-LFA showed an analytical limit of detection of 20 pg/µL. The prevalence of S. stercoralis was 27%, 38%, 46.3%, and 46% using microscopy, PCR, microscopy/PCR, and RPA-LFA, respectively. RPA-LFA had a sensitivity and specificity of 59.3% and 58.9%, 66.2% and 71.4%, and 77.2% and 73.1% when microscopy, microscopy/PCR, and real-time PCR were used as the gold standards, respectively. The Strongyloides RPA-LFA is a novel, fast, highly sensitive, and specific molecular method with the potential for deployment in endemic regions. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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16 pages, 7214 KiB  
Article
Molecular Confirmation, Epidemiology, and Pathophysiology of Ehrlichia canis Prevalence in Eastern India
by Ankita Chakraborty, Prasana Kumar Rath, Susen Kumar Panda, Bidyut Prava Mishra, Manaswini Dehuri, Sangram Biswal, Manoj Kumar Jena, Basanta Pravas Sahu, Biswaranjan Paital and Dipak Kumar Sahoo
Pathogens 2024, 13(9), 803; https://doi.org/10.3390/pathogens13090803 - 16 Sep 2024
Viewed by 2247
Abstract
The present study aimed to investigate pathological epidemiology and molecular confirmation of Ehrlichia canis among pet dogs in Bhubaneswar, Odisha, a state in eastern India. A total of 178 dogs were screened for Ehrlichiosis based on history, clinical signs, blood, and buffy coat [...] Read more.
The present study aimed to investigate pathological epidemiology and molecular confirmation of Ehrlichia canis among pet dogs in Bhubaneswar, Odisha, a state in eastern India. A total of 178 dogs were screened for Ehrlichiosis based on history, clinical signs, blood, and buffy coat smear examination, resulting in only 56 dogs (31.46%) screening positive. The epidemiological study recorded a non-significant (p ≥ 0.05) increase in incidences among male dogs (68%), German Shepherds (25%), dogs more than 20 kg body weight (75%), in the summer months (55%), and dogs housed in pukka houses with exposure to the outside (59%). The majority of the infected dogs had a history of tick infestation (79%) at some point in their lives. Clinical signs showed non-typical manifestations like fever, lethargy, diarrhoea, epistaxis, hind limb edema, and corneal opacity. Haematological studies revealed anaemia and thrombocytopenia along with neutrophilia with relative lymphopenia and monocytosis. A decreasing trend was observed in the levels of total protein and albumin, with an increase in the levels of globulin, alanine aminotransferase, alanine aminotransferase, aspartate aminotransferase, blood urea nitrogen, and creatinine. The ultrasonography studies revealed hepatosplenomegaly along with hyper-echogenicity in various organs. Proteinuria and haematuria were consistent, along with the presence of bile salts in the urine of affected dogs. Molecular confirmation from n-type PCR data using Ehrlichia-specific primers targeting the p28 gene (843 bp) was done, and the identified gene sequences submitted to NCBI databases have accession numbers OQ383671-OQ383674 and OP886674-OP886677. Ticks collected from dogs were identified morphologically through microscopy and scanning electron microscopy as Rhipicephalus sanguineus. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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15 pages, 6438 KiB  
Article
Evidence for Horizontal Transmission and Recirculation of Shiga Toxin-Producing Escherichia coli in the Beef Production Chain in South Africa Using Whole Genome Sequencing
by Libby Obumneke Onyeka, Abiodun A. Adesiyun, Arshad Ismail, Mushal Allam, Karen H. Keddy and Peter N. Thompson
Pathogens 2024, 13(9), 732; https://doi.org/10.3390/pathogens13090732 - 29 Aug 2024
Viewed by 1166
Abstract
We used whole genome sequencing (WGS) as an epidemiologic surveillance tool to elucidate the transmission dynamics of Shiga toxin-producing Escherichia coli (STEC) strains along the beef production chain in South Africa. Isolates were obtained from a cattle farm, abattoirs and retail outlets. Isolates [...] Read more.
We used whole genome sequencing (WGS) as an epidemiologic surveillance tool to elucidate the transmission dynamics of Shiga toxin-producing Escherichia coli (STEC) strains along the beef production chain in South Africa. Isolates were obtained from a cattle farm, abattoirs and retail outlets. Isolates were analysed using WGS on a MiSeq platform (Illumina, San Diego, CA, USA) and phylogenetic analysis was carried out. Of the 85 isolates, 39% (33) carried the stx gene and 61% (52) had lost the stx gene. The prevalence of stx subtypes was as follows; stx1a 55% (18/33), stx1b 52% (17/33), stx2a 55% (18/33), stx2b 27% (9/33), stx2dB 30% (10/33) and stx2d1A 15% (5/33). Thirty-five different serogenotypes were detected, of which 65% (56) were flagellar H-antigens and 34% (29) were both O-antigens and flagellar H-antigens. We identified 50 different sequence types (STs), and only nine of the isolates were assigned to three different clonal complexes. Core genome phylogenetic analysis revealed genetic relatedness, and isolates clustered mainly according to their STs and serogenotypes regardless of stx subtypes. This study provides evidence of horizontal transmission and recirculation of STEC strains in Gauteng province and demonstrates that every stage of the beef production chain plays a significant role in STEC entry into the food chain. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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Review

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17 pages, 698 KiB  
Review
Gut Microbiota in Patients Receiving Dialysis: A Review
by Xintian Lim, Lijin Ooi, Uzhe Ding, Henry H. L. Wu and Rajkumar Chinnadurai
Pathogens 2024, 13(9), 801; https://doi.org/10.3390/pathogens13090801 - 15 Sep 2024
Cited by 3 | Viewed by 1952
Abstract
The human gut microbiota constitutes a complex community of microorganisms residing within the gastrointestinal tract, encompassing a vast array of species that play crucial roles in health and disease. The disease processes involved in chronic kidney disease (CKD) and end-stage kidney disease (ESKD) [...] Read more.
The human gut microbiota constitutes a complex community of microorganisms residing within the gastrointestinal tract, encompassing a vast array of species that play crucial roles in health and disease. The disease processes involved in chronic kidney disease (CKD) and end-stage kidney disease (ESKD) are now increasingly established to result in dysregulation of gut microbiota composition and function. Gut microbiota dysbiosis has been associated with poor clinical outcomes and all-cause mortality in patients with ESKD, particularly individuals receiving dialysis. Prior studies highlighted various factors that affect gut microbiota dysbiosis in CKD and ESKD. These include, but are not limited to, uraemic toxin accumulation, chronic inflammation, immune dysfunction, medications, and dietary restrictions and nutritional status. There is a lack of studies at present that focus on the evaluation of gut microbiota dysbiosis in the context of dialysis. Knowledge on gut microbiota changes in this context is important for determining their impact on dialysis-specific and overall outcomes for this patient cohort. More importantly, evaluating gut microbiota composition can provide information into potential targets for therapeutic intervention. Identification of specific microbial signatures may result in further development of personalised treatments to improve patient outcomes and mitigate complications during dialysis. Optimising gut microbiota through various therapeutic approaches, including dietary adjustments, probiotics, prebiotics, medications, and faecal transplantation, have previously demonstrated potential in multiple medical conditions. It remains to be seen whether these therapeutic approaches are effective within the dialysis setting. Our review aims to evaluate evidence relating to alterations in the gut microbiota of patients undergoing dialysis. A growing body of evidence pointing to the complex yet significant relationship which surrounds gut microbiota and kidney health emphasises the importance of gut microbial balance to improve outcomes for individuals receiving dialysis. Full article
(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)
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