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Antibiotics
Special Issues
Infectious Disease Testing and Pathogenic Bacterial Virulence Identification
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Infectious Disease Testing and Pathogenic Bacterial Virulence Identification

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Genetic and Biochemical Studies of Antibiotic Activity and Resistance".

Deadline for manuscript submissions: closed (30 June 2024) | Viewed by 7354

Special Issue Editor

Dr. Michał Złoch

E-Mail Website
Guest Editor
1. Centre For Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toruń, Torun, Poland
2. Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University in Toruń, Torun, Poland
Interests: rapid microbial identification; antibiotic detection methods development; clinical and food microbiology studies; MALDI-TOF MS; lipidomics; proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, there has been a growing awareness among patients and clinicians of the importance of rapid and accurate diagnosis of the source of infection to prevent the spread of high-risk pathogenic microorganisms and counteract the development of antibiotic resistance. A major contribution to this was made by the preventive tasks undertaken to limit the spread of the COVID-19 pandemic, which showed that the current state of knowledge makes it possible to create a reliable diagnostic test against the new pathogen in a relatively short period of time. The range of techniques that are used to rapidly identify pathogens and assess their virulence is constantly expanding to include such areas as next-generation sequencing (NGS), immunoblotting, as well as immunofluorescence assays (e.g., ELISA), and more recently various laser desorption/ionization mass spectrometry techniques (MALDI-TOF MS, NALDI/SALDI-TOF MS). In addition to genomic and proteomic approaches, which are most widely used in the context of in-depth identification of microorganisms, there are increasing reports on the use of lipidomic analysis to push the boundaries of the previously mentioned methods.

To help to understand the latest developments in pathogen testing and their virulence assessment, this Special Issue presents works related to new methods of microbial identification, drug resistance detection, and virulence factor determination using genomic, proteomic, as well as lipidomic approaches.

Dr. Michał Złoch
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. Antibiotics 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 2900 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

  • whole genome sequencing
  • MALDI-TOF MS
  • NALDI-TOF MS
  • lipidomics
  • proteomics
  • genomics
  • antibiotic resistance detection
  • virulence biomarkers indication

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Published Papers (4 papers)

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Research

21 pages, 3702 KiB  
Article
Genetic Characterization, Antibiotic Resistance, and Virulence Genes Profiling of Bacillus cereus Strains from Various Foods in Japan
by Marwa Nabil Sayed Abdelaziz, Mahmoud Gamaleldin Zayda, Aye Thida Maung, Mohamed El-Telbany, Tahir Noor Mohammadi, Su Zar Chi Lwin, Khin Zar Linn, Chen Wang, Lu Yuan, Yoshimitsu Masuda, Ken-ichi Honjoh and Takahisa Miyamoto
Antibiotics 2024, 13(8), 774; https://doi.org/10.3390/antibiotics13080774 - 16 Aug 2024
Viewed by 1378
Abstract
Bacillus cereus sensu stricto is a foodborne pathogen that causes food poisoning. Their spore and biofilm-forming abilities persist in various environments and foods. This study investigated the prevalence, virulence, antibiotic resistance, and genetic diversity of B. cereus s. s. strains isolated from various [...] Read more.
Bacillus cereus sensu stricto is a foodborne pathogen that causes food poisoning. Their spore and biofilm-forming abilities persist in various environments and foods. This study investigated the prevalence, virulence, antibiotic resistance, and genetic diversity of B. cereus s. s. strains isolated from various food samples. Of 179 samples, 22.34% were positive for B. cereus s. s., with significantly high detection rates in milk products and raw chicken meat. Forty strains were isolated from positive samples. Matrix-assisted laser desorption ionization/time of flight mass spectrometry analysis revealed nine distinct clusters and multi-locus sequence typing revealed 34 sequence types including 23 novel sequences, demonstrating high genetic diversity among the isolates. PCR analysis revealed that all the strains contained at least one toxin gene, but none contained the cytK gene. Antibiotic resistance tests revealed that all isolates were classified as multidrug-resistant, with high resistance levels, particularly to β-lactam antibiotics and vancomycin, but were susceptible to gentamicin. All isolates showed variations in biofilm formation. This study highlights the significant public health risk due to B. cereus s. s. and underscores the need for stringent monitoring and control measures in food production to manage antimicrobial resistance and ensure food safety. Full article
(This article belongs to the Special Issue Infectious Disease Testing and Pathogenic Bacterial Virulence Identification)
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8 pages, 236 KiB  
Communication
Traditional Cultures versus Next Generation Sequencing for Suspected Orthopedic Infection: Experience Gained from a Reference Centre
by Sara Giordana Rimoldi, Davide Brioschi, Daniele Curreli, Federica Salari, Cristina Pagani, Alessandro Tamoni, Concetta Longobardi, Raffaella Bosari, Alberto Rizzo, Simona Landonio, Massimo Coen, Matteo Passerini, Maria Rita Gismondo, Andrea Gori and Alfonso Manzotti
Antibiotics 2023, 12(11), 1588; https://doi.org/10.3390/antibiotics12111588 - 3 Nov 2023
Cited by 3 | Viewed by 1112
Abstract
(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, [...] Read more.
(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, data are scarce regarding the impact of molecular techniques in real-life scenarios. (Methods) We included cases of suspected orthopedic infection treated with surgery from May 2021 to September 2023. We combined traditional cultures with NGS. For NGS, we performed a metagenomic analysis of ribosomal 16s, and we queried dedicated taxonomic libraries to identify the species. To avoid false positive results, we set a cut-off of 1000 counts of the percentage of frequency of reads. (Results) We included 49 patients in our study. Our results show the presence of bacteria in 36/49 (73%) and 29/49 (59%) cases studied with NGS and traditional cultures, respectively. The concordance rate was 61%. Among the 19/49 discordant cases, in 11/19 cases, cultures were negative and NGS positive; in 4/19, cultures were positive and NGS negative; and in the remaining 4/19, different species were detected by traditional cultures and NGS. (Conclusions) Difficult-to-grow microorganisms, such as slow-growing anaerobic bacteria, were better detected by NGS compared to traditional culture in our study. However, more data to distinguish between true pathogens and contaminants are needed. NGS can be an additional tool to be used for the diagnosis of orthopedic infections and the choice of appropriate antimicrobial therapy. Full article
(This article belongs to the Special Issue Infectious Disease Testing and Pathogenic Bacterial Virulence Identification)
13 pages, 883 KiB  
Article
Identification of Vibrio metschnikovii and Vibrio injensis Isolated from Leachate Ponds: Characterization of Their Antibiotic Resistance and Virulence-Associated Genes
by Aura Falco, Miguel Ángel Villaquirán-Muriel, José David Gallo Pérez, Alejandra Mondragón-Quiguanas, Carlos Aranaga and Adriana Correa
Antibiotics 2023, 12(11), 1571; https://doi.org/10.3390/antibiotics12111571 - 28 Oct 2023
Viewed by 2139
Abstract
This study aimed to evaluate the antibiotic resistance of 22 environmental Vibrio metschnikovii isolates and 1 Vibrio injensis isolate from landfill leachates in southwestern Colombia. Isolates were identified by Matrix-Assisted Laser Desorption/Ionization–Time-Of-Flight (MALDI-TOF), and 16S ribosomal RNA gene sequencing. Analysis of the susceptibility [...] Read more.
This study aimed to evaluate the antibiotic resistance of 22 environmental Vibrio metschnikovii isolates and 1 Vibrio injensis isolate from landfill leachates in southwestern Colombia. Isolates were identified by Matrix-Assisted Laser Desorption/Ionization–Time-Of-Flight (MALDI-TOF), and 16S ribosomal RNA gene sequencing. Analysis of the susceptibility to six antibacterial agents by the Kirby–Bauer method showed susceptibility of all the isolates to ciprofloxacin and imipenem. We recorded resistance to beta-lactams and aminoglycosides, but no multidrug resistance was observed. The genome of one of the isolates was sequenced to determine the pathogenic potential of V. injensis. Genes associated with virulence were identified, including for flagellar synthesis, biofilm formation, and hemolysins, among others. These results demonstrate that landfill leachates are potential reservoirs of antibiotic-resistant and pathogenic bacteria and highlight the importance of monitoring Vibrio species in different aquatic environments. Full article
(This article belongs to the Special Issue Infectious Disease Testing and Pathogenic Bacterial Virulence Identification)
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15 pages, 2715 KiB  
Article
Silver Nanoparticle Targets Fabricated Using Chemical Vapor Deposition Method for Differentiation of Bacteria Based on Lipidomic Profiles in Laser Desorption/Ionization Mass Spectrometry
by Ewelina Maślak, Adrian Arendowski, Michał Złoch, Justyna Walczak-Skierska, Aleksandra Radtke, Piotr Piszczek and Paweł Pomastowski
Antibiotics 2023, 12(5), 874; https://doi.org/10.3390/antibiotics12050874 - 8 May 2023
Cited by 12 | Viewed by 2248
Abstract
The global threat of numerous infectious diseases creates a great need to develop new diagnostic methods to facilitate the appropriate prescription of antimicrobial therapy. More recently, the possibility of using bacterial lipidome analysis via laser desorption/ionization mass spectrometry (LDI-MS) as useful diagnostic tool [...] Read more.
The global threat of numerous infectious diseases creates a great need to develop new diagnostic methods to facilitate the appropriate prescription of antimicrobial therapy. More recently, the possibility of using bacterial lipidome analysis via laser desorption/ionization mass spectrometry (LDI-MS) as useful diagnostic tool for microbial identification and rapid drug susceptibility has received particular attention because lipids are present in large quantities and can be easily extracted similar to ribosomal proteins. Therefore, the main goal of the study was to evaluate the efficacy of two different LDI techniques—matrix-assisted (MALDI) and surface-assisted (SALDI) approaches—in the classification of the closely related Escherichia coli strains under cefotaxime addition. Bacterial lipids profiles obtained by using the MALDI technique with different matrices as well as silver nanoparticle (AgNP) targets fabricated using the chemical vapor deposition method (CVD) of different AgNP sizes were analyzed by the means of different multivariate statistical methods such as principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), sparse partial least squares discriminant analysis (sPLS-DA), and orthogonal projections to latent structures discriminant analysis (OPLS-DA). The analysis showed that the MALDI classification of strains was hampered by interference from matrix-derived ions. In contrast, the lipid profiles generated by the SALDI technique had lower background noise and more signals associated with the sample, allowing E. coli to be successfully classified into cefotaxime-resistant and cefotaxime-sensitive strains, regardless of the size of the AgNPs. AgNP substrates obtained using the CVD method were used for the first time for distinguishing closely related bacterial strains based on their lipidomic profiles and demonstrate high potential as a future diagnostic tool for the detection of antibiotic susceptibility. Full article
(This article belongs to the Special Issue Infectious Disease Testing and Pathogenic Bacterial Virulence Identification)
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