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Microorganisms
Special Issues
Characterization, Identification, and Systematics of Clinically Relevant Bacteria
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Characterization, Identification, and Systematics 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 December 2021) | Viewed by 9056

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 Systematics, Characterizations and identification of bacteria isolated from human clinical samples. These bacteria are of utmost importance to identify and characterize to understand infection mechanisms and the underlying potential pathogenicity of the bacteria. The 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 the infection mechanisms. A thorough characterization and deeper understanding of bacteria isolated from human clinical samples may provide novel treatments of these infections.

We invite you to submit papers describing or questioning the systematics of species or genera of bacteria isolated from clinical samples, as well as the characterization of these bacteria, including 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-based methods, including MALDI TOF MS.


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 (3 papers)

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Research

10 pages, 2236 KiB  
Article
Parotid Space, a Different Space from Other Deep Neck Infection Spaces
by Shih-Lung Chen, Chi-Kuang Young, Chun-Ta Liao, Tsung-You Tsai, Chung-Jan Kang and Shiang-Fu Huang
Microorganisms 2021, 9(11), 2361; https://doi.org/10.3390/microorganisms9112361 - 15 Nov 2021
Cited by 7 | Viewed by 1729
Abstract
Deep neck infections (DNIs) such as parotid abscesses are medical emergencies with a seemingly different etiology and treatment course from other DNIs. We sought to confirm this in the present retrospective population-based cohort study. Between August 2016 and January 2020, 412 patients with [...] Read more.
Deep neck infections (DNIs) such as parotid abscesses are medical emergencies with a seemingly different etiology and treatment course from other DNIs. We sought to confirm this in the present retrospective population-based cohort study. Between August 2016 and January 2020, 412 patients with DNIs seen at a tertiary medical center were enrolled in this study. Infections of the parotid space were compared with those of other deep neck spaces, according to patient characteristics. All patients were divided into parotid space (PS; n = 91, 22.08%) and non-parotid space (NPS; n = 321, 77.92%) subgroups. We further divided the patients into single parotid space (PS-single; n = 50, 12.13%), single non-parotid space (NPS-single; n = 149, 36.16%), multiple parotid space (PS-multiple; n = 41, 9.95%), and multiple non-parotid space (NPS-multiple; n = 172, 41.76%) DNI subgroups. In the PS-single and PS-multiple subgroups, a longer duration of symptoms (p = 0.001), lower white blood cell count (p = 0.001), lower C-reactive protein level (p = 0.010), higher rate of ultrasonography-guided drainage (p < 0.001), and lower rates of surgical incision and drainage (p < 0.001) were observed compared with the NPS-single and NPS-multiple subgroups. The PS group had a higher positive Klebsiella pneumoniae culture rate (p < 0.001), and lower positive Streptococcus constellatus (p = 0.002), and Streptococcus anginosus (p = 0.025) culture rates than the NPS group. In a multivariate analysis, K. pneumoniae was independently associated with parotoid space involvement in comparisons of the PS and NPS groups, PS-single and NPS-single subgroups, and PS-multiple and NPS-multiple subgroups. The clinical presentation of a parotid space infection differs from that of other deep neck space infections. Full article
(This article belongs to the Special Issue Characterization, Identification, and Systematics of Clinically Relevant Bacteria)
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10 pages, 487 KiB  
Article
MALDI-TOF Mass Spectrometry-Based Optochin Susceptibility Testing for Differentiation of Streptococcus pneumoniae from other Streptococcus mitis Group Streptococci
by Ilka D. Nix, Evgeny A. Idelevich, Andreas Schlattmann, Katrin Sparbier, Markus Kostrzewa and Karsten Becker
Microorganisms 2021, 9(10), 2010; https://doi.org/10.3390/microorganisms9102010 - 23 Sep 2021
Cited by 2 | Viewed by 2188
Abstract
Discrimination of Streptococcus pneumoniae from other Streptococcus mitis group (SMG) species is still challenging but very important due to their different pathogenic potential. In this study, we aimed to develop a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based optochin susceptibility test with [...] Read more.
Discrimination of Streptococcus pneumoniae from other Streptococcus mitis group (SMG) species is still challenging but very important due to their different pathogenic potential. In this study, we aimed to develop a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based optochin susceptibility test with an objective read-out. Optimal test performance was established and evaluated by testing consecutively collected respiratory isolates. Optochin in different concentrations as a potential breakpoint concentration was added to a standardized inoculum. Droplets of 6 µL with optochin and, as growth control, without optochin were spotted onto a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard. Spectra were acquired, and results were interpreted as S. pneumoniae in the case of optochin susceptibility (no growth), or as non-S. pneumoniae in the case of optochin non-susceptibility (growth). Highest test accuracy was achieved after 20 h incubation time (95.7%). Rapid testing after 12 h incubation time (optochin breakpoint 2 µg/mL; correct classification 100%, validity 62.5%) requires improvement by optimization of assay conditions. The feasibility of the MALDI-TOF MS-based optochin susceptibility test was demonstrated in this proof-of-principle study; however, confirmation and further improvements are warranted. Full article
(This article belongs to the Special Issue Characterization, Identification, and Systematics of Clinically Relevant Bacteria)
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11 pages, 742 KiB  
Article
Changes in Skin and Nasal Microbiome and Staphylococcal Species Following Treatment of Atopic Dermatitis with Dupilumab
by Caroline Meyer Olesen, Anna Cäcilia Ingham, Simon Francis Thomsen, Maja-Lisa Clausen, Paal Skytt Andersen, Sofie Marie Edslev, Yasemin Topal Yüksel, Emma Guttman-Yassky and Tove Agner
Microorganisms 2021, 9(7), 1487; https://doi.org/10.3390/microorganisms9071487 - 13 Jul 2021
Cited by 29 | Viewed by 4303
Abstract
Investigation of changes in the skin microbiome following treatment of atopic dermatitis (AD) with dupilumab may provide valuable insights into the skin microbiome as a therapeutic target. The aim of this study is to assess changes in the AD skin microbiome following treatment [...] Read more.
Investigation of changes in the skin microbiome following treatment of atopic dermatitis (AD) with dupilumab may provide valuable insights into the skin microbiome as a therapeutic target. The aim of this study is to assess changes in the AD skin microbiome following treatment of AD with dupilumab (n = 27). E-swabs were collected from nose, lesional, and nonlesional skin before and after 16 weeks of dupilumab therapy, and the microbiome was analyzed by 16S rRNA and tuf gene sequencing. Data for 17 patients with milder disease receiving treatment with non-targeted therapies are also presented. The results show that both groups experienced clinical improvement (p < 0.001) following dupilumab therapy and that Shannon diversity increased and bacterial community structure changed. The relative abundance of the genus Staphylococcus (S.) and S. aureus decreased, while that of S. epidermidis and S. hominis increased. No significant changes were observed for patients receiving non-targeted treatments. The increases in S. epidermidis and S. hominis and the decrease in S. aureus correlated with clinical improvement. Furthermore, changes in S. hominis and S. epidermidis correlated inversely with S. aureus. In conclusion, treatment with dupilumab significantly changed the skin microbiome and decreased S. aureus. Our results suggest a favorable role of commensal staphylococci in AD. Full article
(This article belongs to the Special Issue Characterization, Identification, and Systematics of Clinically Relevant Bacteria)
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