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Microorganisms
Special Issues
Bacterial Genomics and Epidemiology
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Bacterial Genomics and Epidemiology

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Public Health Microbiology".

Deadline for manuscript submissions: closed (30 November 2022) | Viewed by 26016

Special Issue Editors

Prof. Dr. Javier Garaizar

E-Mail Website
Guest Editor
Department of Immunology, Microbiology and Parasitology, University of the Basque Country, Vitoria-Gasteiz, Spain
Interests: bacterial epidemiology
Dr. Lorena Laorden

E-Mail Website
Guest Editor
Department of Immunology, Microbiology and Parasitology, University of the Basque Country, Vitoria-Gasteiz, Spain
Interests: genomics; salmonella

Special Issue Information

Dear Colleagues,

The One Health concept makes it clear to us that apparently distant areas of study, such as the human clinical, food control, veterinary clinical or the environment, are intimately related and that there is a single health, breaking the previously set barriers. On the other hand, new genomic sequencing technologies are helping to shed new light on the understanding of the epidemiological relationship of bacteria in their different ecological niches. The practically generalized use of this technology due to its low cost and wide possibilities of use is contributing to an exponential increase in our knowledge.

This special issue of "Microorganims" collects original research articles and reviews on Bacterial genomics and epidemiology in a broad sense, covering its application to the study of bacteria present in ecosystems as diverse as human clinical, food control, veterinary clinical or environment.

Therefore, I encourage the scientific community working in the aforementioned areas of microbiology studying the epidemiology of bacteria using genomic technology to take the opportunity to publish their studies in this special issue.

Prof. Dr. Javier Garaizar
Dr. Lorena Laorden
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. Microorganisms 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

  • bacterial
  • genomics
  • epidemiology
  • sequencing
  • one health
  • clinical microbiology
  • veterinary microbiology
  • food control
  • environmental microbiology

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

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Editorial

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2 pages, 182 KiB  
Editorial
Bacterial Genomics and Epidemiology
by Javier Garaizar and Lorena Laorden
Microorganisms 2023, 11(6), 1428; https://doi.org/10.3390/microorganisms11061428 - 29 May 2023
Cited by 1 | Viewed by 1655
Abstract
Innovative technologies for Whole-Genome Sequencing (WGS) help to improve our understanding of the epidemiology and pathogenesis of bacterial infectious diseases and are becoming affordable for most microbiological laboratories [...] Full article
(This article belongs to the Special Issue Bacterial Genomics and Epidemiology)

Research

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13 pages, 1412 KiB  
Article
Molecular Epidemiology of Group B Streptococcus Colonization in Egyptian Women
by Sarah Shabayek, Verena Vogel, Dorota Jamrozy, Stephen D. Bentley and Barbara Spellerberg
Microorganisms 2023, 11(1), 38; https://doi.org/10.3390/microorganisms11010038 - 22 Dec 2022
Cited by 2 | Viewed by 3109
Abstract
(1) Background: Streptococcus agalactiae or Group B Streptococcus (GBS) causes severe neonatal infections with a high burden of disease, especially in Africa. Maternal vaginal colonization and perinatal transmissions represent the common mode of acquiring the infection. Development of an effective maternal vaccine against [...] Read more.
(1) Background: Streptococcus agalactiae or Group B Streptococcus (GBS) causes severe neonatal infections with a high burden of disease, especially in Africa. Maternal vaginal colonization and perinatal transmissions represent the common mode of acquiring the infection. Development of an effective maternal vaccine against GBS relies on molecular surveillance of the maternal GBS population to better understand the global distribution of GBS clones and serotypes. (2) Methods: Here, we present genomic data from a collection of colonizing GBS strains from Ismailia, Egypt that were sequenced and characterized within the global JUNO project. (3) Results: A large proportion of serotype VI, ST14 strains was discovered, a serotype which is rarely found in strain collections from the US and Europe and typically not included in the current vaccine formulations. (4) Conclusions: The molecular epidemiology of these strains clearly points to the African origin with the detection of several sequence types (STs) that have only been observed in Africa. Our data underline the importance of continuous molecular surveillance of the GBS population for future vaccine implementations. Full article
(This article belongs to the Special Issue Bacterial Genomics and Epidemiology)
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13 pages, 3089 KiB  
Article
A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data
by Aitor Atxaerandio-Landa, Ainhoa Arrieta-Gisasola, Lorena Laorden, Joseba Bikandi, Javier Garaizar, Irati Martinez-Malaxetxebarria and Ilargi Martinez-Ballesteros
Microorganisms 2022, 10(12), 2364; https://doi.org/10.3390/microorganisms10122364 - 29 Nov 2022
Cited by 14 | Viewed by 5996
Abstract
The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages [...] Read more.
The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogenetic clustering and sequence typing. Workflow was tested using a collection of 22 in-house sequences of Salmonella enterica isolates belonging to a local outbreak, coupled with a collection of 182 Salmonella genomes publicly available. No errors were reported during the execution period, and all genomes were analysed. The bioinformatics workflow can be tailored to other pathogens of interest and is freely available for academic and non-profit use as an uploadable file to the Galaxy platform. Full article
(This article belongs to the Special Issue Bacterial Genomics and Epidemiology)
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17 pages, 2146 KiB  
Article
Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico
by Irvin González-López, José Andrés Medrano-Félix, Nohelia Castro-del Campo, Osvaldo López-Cuevas, Jean Pierre González-Gómez, José Benigno Valdez-Torres, José Roberto Aguirre-Sánchez, Jaime Martínez-Urtaza, Bruno Gómez-Gil, Bertram G. Lee, Beatriz Quiñones and Cristóbal Chaidez
Microorganisms 2022, 10(6), 1214; https://doi.org/10.3390/microorganisms10061214 - 14 Jun 2022
Cited by 9 | Viewed by 3121
Abstract
Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. [...] Read more.
Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen. Full article
(This article belongs to the Special Issue Bacterial Genomics and Epidemiology)
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Review

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15 pages, 964 KiB  
Review
Group B Streptococcus: Virulence Factors and Pathogenic Mechanism
by Yuxin Liu and Jinhui Liu
Microorganisms 2022, 10(12), 2483; https://doi.org/10.3390/microorganisms10122483 - 15 Dec 2022
Cited by 33 | Viewed by 10662
Abstract
Group B Streptococcus (GBS) or Streptococcus agalactiae is a major cause of neonatal mortality. When colonizing the lower genital tract of pregnant women, GBS may cause premature birth and stillbirth. If transmitted to the newborn, it may result in life-threatening illnesses, including sepsis, [...] Read more.
Group B Streptococcus (GBS) or Streptococcus agalactiae is a major cause of neonatal mortality. When colonizing the lower genital tract of pregnant women, GBS may cause premature birth and stillbirth. If transmitted to the newborn, it may result in life-threatening illnesses, including sepsis, meningitis, and pneumonia. Moreover, through continuous evolution, GBS can use its original structure and unique factors to greatly improve its survival rate in the human body. This review discusses the key virulence factors that facilitate GBS invasion and colonization and their action mechanisms. A comprehensive understanding of the role of virulence factors in GBS infection is crucial to develop better treatment options and screen potential candidate molecules for the development of the vaccine. Full article
(This article belongs to the Special Issue Bacterial Genomics and Epidemiology)
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