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Microorganisms
Special Issues
Identification and Characterization of Clinically Relevant Bacteria
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Identification and Characterization of Clinically Relevant Bacteria

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 6858

Special Issue Editors

Dr. Liselott Svensson Stadler

E-Mail Website
Guest Editor
1. Department of Infectious, Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
2. Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
Interests: clinical; bacteria; diagnostics; sequencing; MALDI TOF MS
Special Issues, Collections and Topics in MDPI journals
Dr. Roger Karlsson

E-Mail Website1 Website2
Guest Editor
1. Department of Infectious Diseases, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
2. Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
Interests: bacteria; mass spectrometry; proteomics; diagnostics; antimicrobial resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue covers topics regarding the identification and characterization of bacteria isolated from human clinical samples. These bacteria are of utmost importance for identifying and characterizing infection mechanisms and the underlying potential pathogenicity of the bacteria. Isolated bacteria can be represented by well-known pathogens, where a deeper understanding of the expression of virulence factors and/or antibiotic resistance genes during an infection is necessary, or so-called opportunistic pathogens, where the host-pathogen interplay can provide knowledge of infection mechanisms. A thorough characterization and deeper understanding of bacteria isolated from human clinical samples may provide novel treatments of these infections. The bacteria may also represent novel species of bacteria isolated from patient samples as the suspected cause of infection, carrying known traits of virulence and/or antimicrobial resistance.

We invite you to submit papers describing the identification and characterization of bacteria isolated from clinical samples, including the characterization of traits of antimicrobial resistance and virulence, and also how the bacteria may be identified or classified in a clinical laboratory using phenotypic, genotypic, or proteotypic methods, including WGS and Sanger, as well as mass spectrometry (MS)-based methods, including MALDI TOF MS and shotgun proteomics tandem MS-based approaches.

Dr. Liselott Svensson Stadler
Dr. Roger Karlsson
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

  • characterization
  • identification
  • systematics
  • clinically relevant bacteria
  • mass spectrometry
  • sequencing
  • sanger
  • whole-genome sequencing
  • next-generation sequencing
  • proteomics

Published Papers (2 papers)

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Research

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15 pages, 2149 KiB  
Article
Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics
by Charlotte Mappa, Béatrice Alpha-Bazin, Olivier Pible and Jean Armengaud
Microorganisms 2023, 11(5), 1170; https://doi.org/10.3390/microorganisms11051170 - 29 Apr 2023
Cited by 6 | Viewed by 2091
Abstract
Shotgun proteomics has proven to be an attractive alternative for identifying a pathogen and characterizing the antimicrobial resistance genes it produces. Because of its performance, proteotyping of microorganisms by tandem mass spectrometry is expected to become an essential tool in modern healthcare. Proteotyping [...] Read more.
Shotgun proteomics has proven to be an attractive alternative for identifying a pathogen and characterizing the antimicrobial resistance genes it produces. Because of its performance, proteotyping of microorganisms by tandem mass spectrometry is expected to become an essential tool in modern healthcare. Proteotyping microorganisms that have been isolated from the environment by culturomics is also a cornerstone for the development of new biotechnological applications. Phylopeptidomics is a new strategy that estimates the phylogenetic distances between the organisms present in the sample and calculates the ratio of their shared peptides, thus improving the quantification of their contributions to the biomass. Here, we established the limit of detection of tandem mass spectrometry proteotyping based on MS/MS data recorded for several bacteria. The limit of detection for Salmonella bongori with our experimental set-up is 4 × 104 colony-forming units from a sample volume of 1 mL. This limit of detection is directly related to the amount of protein per cell and therefore depends on the shape and size of the microorganism. We have demonstrated that identification of bacteria by phylopeptidomics is independent of their growth stage and that the limit of detection of the method is not degraded in presence of additional bacteria in the same proportion. Full article
(This article belongs to the Special Issue Identification and Characterization of Clinically Relevant Bacteria)
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Review

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37 pages, 1295 KiB  
Review
Anti-Pseudomonas aeruginosa Vaccines and Therapies: An Assessment of Clinical Trials
by Moamen M. Elmassry, Jane A. Colmer-Hamood, Jonathan Kopel, Michael J. San Francisco and Abdul N. Hamood
Microorganisms 2023, 11(4), 916; https://doi.org/10.3390/microorganisms11040916 - 31 Mar 2023
Cited by 8 | Viewed by 4127
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes high morbidity and mortality in cystic fibrosis (CF) and immunocompromised patients, including patients with ventilator-associated pneumonia (VAP), severely burned patients, and patients with surgical wounds. Due to the intrinsic and extrinsic antibiotic resistance mechanisms, [...] Read more.
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that causes high morbidity and mortality in cystic fibrosis (CF) and immunocompromised patients, including patients with ventilator-associated pneumonia (VAP), severely burned patients, and patients with surgical wounds. Due to the intrinsic and extrinsic antibiotic resistance mechanisms, the ability to produce several cell-associated and extracellular virulence factors, and the capacity to adapt to several environmental conditions, eradicating P. aeruginosa within infected patients is difficult. Pseudomonas aeruginosa is one of the six multi-drug-resistant pathogens (ESKAPE) considered by the World Health Organization (WHO) as an entire group for which the development of novel antibiotics is urgently needed. In the United States (US) and within the last several years, P. aeruginosa caused 27% of deaths and approximately USD 767 million annually in health-care costs. Several P. aeruginosa therapies, including new antimicrobial agents, derivatives of existing antibiotics, novel antimicrobial agents such as bacteriophages and their chelators, potential vaccines targeting specific virulence factors, and immunotherapies have been developed. Within the last 2–3 decades, the efficacy of these different treatments was tested in clinical and preclinical trials. Despite these trials, no P. aeruginosa treatment is currently approved or available. In this review, we examined several of these clinicals, specifically those designed to combat P. aeruginosa infections in CF patients, patients with P. aeruginosa VAP, and P. aeruginosa–infected burn patients. Full article
(This article belongs to the Special Issue Identification and Characterization of Clinically Relevant Bacteria)
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