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Microorganisms
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New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens...
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New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0

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

Deadline for manuscript submissions: closed (29 February 2024) | Viewed by 12499

Special Issue Editors

Prof. Dr. Lúcia Martins Teixeira

E-Mail Website
Guest Editor
Departamento de Microbiologia Médica, Universidade Federal do Rio de Janeirodisabled, Rio de Janeiro, Brazil
Interests: molecular characterization and epidemiology of bacteria antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals
Dr. Cheryl P. Andam

E-Mail Website
Guest Editor
Department of Biological Sciences, University at Albany, Albany, NY, USA
Interests: molecular characterization; epidemiology of bactéria; antimicrobial resistance; bacterial evolution; genomic epidemiology of infectious diseases
Special Issues, Collections and Topics in MDPI journals
Dr. Stephanie S. R. Souza

E-Mail Website
Co-Guest Editor
Department of Biological Sciences, University at Albany, Albany, NY, USA
Interests: molecular characterization; epidemiology of bactéria; antimicrobial resistance; bacterial evolution; genomic epidemiology of infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our 2022 Special Issue "New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens".

Bacterial infections are a major cause of morbidity and mortality worldwide, posing considerable health, social, and economic burdens. Therefore, rapid detection and accurate identification of the causative agents play a crucial role to optimize treatment and control measures. The need for rapid and precise methods for detection and characterization is of peculiar importance in the case of highly virulent bacteria associated with severe life-threatening diseases and of multidrug-resistant agents associated with difficult to treat infections. For most cases, the gold standard for the laboratory diagnosis of bacterial infections has been based on usually time consuming phenotypic approaches that include the isolation of the etiologic agent by using growth-supporting media, identification by a variety of techniques and antimicrobial susceptibility testing.  Additionally, typing methods with high discriminatory power are needed to trace pathogens at the strain level, in order to understand the source and dissemination of bacterial strains, allowing the study of bacterial population dynamics and epidemiological surveillance of bacterial infections. The introduction and increasing improvements and applications of molecular techniques, in conjunction with advances in technologies associated with bioinformatics an artificial intelligence to handle large scale data analysis, resulted in the development of a multitude of tools that have revolutionized the diagnosis and epidemiology of infectious diseases.

In this Special Issue, we aim to address the most recent advances on the use of molecular methods based on genomic and proteomic approaches, mass spectrometry, digital microbiology, machine learning and bioinformatics applied to the detection, characterization and epidemiology of bacteria and bacterial infections.

We welcome the submission of Original Research Articles, Rewiews mainly focused on, but not limited to, the following topics:

  • Genomics and proteomics applied to the detection and characterization of bacterial agents
  • Whole-Genome Sequencing and MALDI-TOF MS as bacterial species Identification tools
  • MALDI-TOF Mass Spectrometry for detection of bacterial agents in clinical specimens
  • Bacterial molecules as diagnostic markers
  • Detection of bacterial markers by immunological, genomic and proteomic approaches
  • PCR-based techniques for detection and characterization of bacterial agents
  • Genome typing and epidemiology of bacterial pathogens
  • Bioinformatics analysis of microbial sequence data
  • Prediction of antimicrobial resistance in bacterial isolates by analysis of whole genome sequences, machine learning or MALDI-TOF MS
  • New tools to evaluate epidemiology, population structure and evolution of bacterial pathogens
  • Application and impact of Machine Learning in Bacteriology

Prof. Dr. Lúcia Martins Teixeira
Dr. Cheryl Andam
Guest Editors

Dr. Stephanie S. R. Souza
Co-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. 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 pathogens
  • bacterial infections
  • molecular detection
  • molecular identification
  • molecular epidemiology
  • strain typing
  • genomics and proteomics
  • whole-genome sequencing
  • MALDI-TOF MS
  • antimicrobial resistance
  • bacterial evolution
  • bioinformatics analysis
  • machine learning

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

Published Papers (4 papers)

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Research

22 pages, 1768 KiB  
Article
A Photonic Immunosensor Detection Method for Viable and Non-Viable E. coli in Water Samples
by Ana Fernández Blanco, Yolanda Moreno, Jorge García-Hernández and Manuel Hernández
Microorganisms 2024, 12(7), 1328; https://doi.org/10.3390/microorganisms12071328 - 29 Jun 2024
Cited by 1 | Viewed by 2131
Abstract
Detection and enumeration of coliform bacteria using traditional methods and current molecular techniques against E. coli usually involve long processes with less sensitivity and specificity to distinguish between viable and non-viable bacteria for microbiological water analysis. This approach involves developing and validating an [...] Read more.
Detection and enumeration of coliform bacteria using traditional methods and current molecular techniques against E. coli usually involve long processes with less sensitivity and specificity to distinguish between viable and non-viable bacteria for microbiological water analysis. This approach involves developing and validating an immunosensor comprising ring resonators functionalized with specific antibodies surrounded by a network of microchannels as an alternative method for detecting and indirectly enumerating Escherichia coli in samples of water for consumption. Different ELISA assays were conducted to characterize monoclonal and polyclonal antibodies selected as detection probes for specific B-galactosidase enzymes and membrane LPS antigens of E. coli. An immobilization control study was performed on silicon nitride surfaces used in the immunosensor, immobilized with the selected antibodies from the ELISA assays. The specificity of this method was confirmed by detecting as few as 10 CFU/mL of E. coli from viable and non-viable target bacteria after applying various disinfection methods to water samples intended for human consumption. The 100% detection rate and a 100 CFU/mL Limit of Quantification of the proposed method were validated through a comprehensive assessment of the immunosensor-coupled microfluidic system, involving at least 50 replicates with a concentration range of 10 to 106 CFU/mL of the target bacteria and 50 real samples contaminated with and without disinfection treatment. The correlation coefficient of around one calculated for each calibration curve obtained from the results demonstrated sensitive and rapid detection capabilities suitable for application in water resources intended for human consumption within the food industry. The biosensor was shown to provide results in less than 4 h, allowing for rapid identification of microbial contamination crucial for ensuring water monitoring related to food safety or environmental diagnosis and allowing for timely interventions to mitigate contamination risks. Indeed, the achieved setup facilitates the in situ execution of laboratory processes, allowing for the detection of both viable and non-viable bacteria, and it implies future developments of simultaneous detection of pathogens in the same contaminated sample. Full article
(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)
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12 pages, 1819 KiB  
Article
Genetic Diversity and Expression of Intimin in Escherichia albertii Isolated from Humans, Animals, and Food
by Qian Liu, Xi Yang, Hui Sun, Hua Wang, Xinxia Sui, Peihua Zhang, Xiangning Bai and Yanwen Xiong
Microorganisms 2023, 11(12), 2843; https://doi.org/10.3390/microorganisms11122843 - 23 Nov 2023
Cited by 3 | Viewed by 1572
Abstract
Escherichia albertii (E. albertii) is an emerging diarrheagenic pathogen associated with sporadic infections and human gastroenteric outbreaks. The eae gene, which encodes intimin in the locus of enterocyte effacement (LEE) operon, contributes to the establishment of the attaching and effacing (A/E) [...] Read more.
Escherichia albertii (E. albertii) is an emerging diarrheagenic pathogen associated with sporadic infections and human gastroenteric outbreaks. The eae gene, which encodes intimin in the locus of enterocyte effacement (LEE) operon, contributes to the establishment of the attaching and effacing (A/E) lesion. Increasing collection of E. albertii strains from various sources has resulted in a rapid increase in the number of eae subtypes. This study systematically investigated the prevalence and genetic diversity of eae among E. albertii strains isolated from humans, animals, and food. The eae gene was present in 452/459 (98.5%) strains and 23 subtypes were identified including two novel subtypes, named eae-α11 and η3. The eae-σ subtype was the most predominant among humans, animals, and food-derived strains, while eae-γ3, τ, and α11 were unique in human-derived strains. Additionally, the LEE island was also analyzed at genomic, transcriptional, and functional levels through genomic analysis, quantitative reverse transcription PCR, and HEp-2 cell adherence assays, respectively. The eae transcript levels were variable and associated with eae subtypes. Three different adherence patterns, including localized adherence-like (LAL), diffuse adherence (DA), and detachment (DE), were observed among E. albertii strains. This study demonstrated a high diversity of functional intimin in E. albertii strains isolated from humans, animals, and food. Further in vivo and in vitro studies are warranted to better elucidate the role of intimin or LEE in different genetic backgrounds. Full article
(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)
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14 pages, 2184 KiB  
Article
Pangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype
by Andrea Monserrat Negrete-Paz, Gerardo Vázquez-Marrufo, Ana Gutiérrez-Moraga and Ma. Soledad Vázquez-Garcidueñas
Microorganisms 2023, 11(6), 1495; https://doi.org/10.3390/microorganisms11061495 - 4 Jun 2023
Cited by 7 | Viewed by 3214
Abstract
Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). [...] Read more.
Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype. In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene–phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene–phenotype associations in M. tuberculosis. Full article
(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)
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16 pages, 2614 KiB  
Article
Propidium Monoazide (PMAxx)-Recombinase Polymerase Amplification Exo (RPA Exo) Assay for Rapid Detection of Burkholderia cepacia Complex in Chlorhexidine Gluconate (CHX) and Benzalkonium Chloride (BZK) Solutions
by Soumana Daddy Gaoh, Ohgew Kweon and Youngbeom Ahn
Microorganisms 2023, 11(6), 1401; https://doi.org/10.3390/microorganisms11061401 - 26 May 2023
Cited by 5 | Viewed by 2385
Abstract
Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and [...] Read more.
Both sterile and non-sterile pharmaceutical products, which include antiseptics, have been recalled due to Burkholderia cepacia complex (BCC) contamination. Therefore, minimizing the frequency of outbreaks may be conducive to the development of a quick and sensitive approach that can distinguish between live and dead loads of BCC. We have assessed an exo probe-based recombinase polymerase amplification (RPA) with 10 µM propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in various concentrations of antiseptics (i.e., chlorhexidine gluconate (CHX) and benzalkonium chloride (BZK) solutions) after 24 h. The optimized assay conducted using a set of primer–probes targeting gbpT was performed at 40 °C for 20 min and shows a detection limit of 10 pg/µL of genomic DNA from B. cenocepacia J2315, equivalent to 104 colony-forming units (CFU/mL). The specificity of a newly designed primer and probe was 80% (20 negatives out of 25). The readings for total cells (i.e., without PMAxx) from 200 µg/mL CHX using PMAxx-RPA exo assay was 310 relative fluorescence units (RFU), compared to 129 RFU with PMAxx (i.e., live cells). Furthermore, in 50–500 µg/mL BZK-treated cells, a difference in the detection rate was observed between the PMAxx-RPA exo assay in live cells (130.4–459.3 RFU) and total cells (207.82–684.5 RFU). This study shows that the PMAxx-RPA exo assay appears to be a valid tool for the simple, rapid and presumptive detection of live BCC cells in antiseptics, thereby ensuring the quality and safety of pharmaceutical products. Full article
(This article belongs to the Special Issue New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens 2.0)
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