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Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Microbiology".

Deadline for manuscript submissions: closed (31 October 2020) | Viewed by 26489

Special Issue Editors

Prof. Dr. Hans-Peter Deigner

E-Mail Website
Guest Editor
Fakult Medical and Life Sciences, Institute of Precision Medicine, Hochschule Furtwangen University, 78120 Furtwangen, Germany
Interests: diagnostic assays; new biomarker approaches; small molecule quantification; endogenous metabolites
Dr. Esra Aǧel

E-Mail Website
Guest Editor
TUBITAK Marmara Research Center, Kocaeli, Turkey
Interests: Microbiology; Moleculer microbiology; Infection diseases Loop Mediated isothermal amplification (LAMP) method; RT-PCR; Point of care (POC); Labonadisc; Aptasensor
Dr. Markus Egert

E-Mail Website
Guest Editor
Hochschule Furtwangen, Furtwangen, Germany
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The conserved nature of host responses offers new approaches for diagnostic development in infectious diseases. Routine diagnostic methods are very useful but do not provide enough sensitivity and specificity. For many decades, a diverse range of analytical targets such as metabolites, nucleic acids, proteins are established as biomarkers now also including parts of the microbiome and one objective of this special issue will be evaluation of the role of emerging host and microbial biomarkers in diagnosis of infectious diseases.

In fact, the development of universal and reliable methods to detect biomarkers for diagnostics and prognostics and the search for highly specific and sensitive biomarkers for infectious diseases and beyond have posed the biggest challenges and options now include analysis of the structure and functionality of complex microbial communities in the human microbiome.

Aptamers for instance are now providing opportunities for quantitative diagnostic assays although translation into practice remains challenging in many cases. Aptamers are highly stable, short nucleic acid sequences capable of binding to the target with high affinity and specificity; small molecules that are problematic for toxins, proteins, cells, and even antibodies can be targeted by aptamers.  The technology (applied in chip- or horizontal flow tests), the target analyte can be quickly detected of target molecules in quantitative and multiplex formats, also on-site in miniaturized portable systems requiring less reagents, energy, and no special infrastructure and laborious/long sample preparation. These systems provide a high level of integration and automation. Emerging options for quantification of large and in small molecules by additional novel approaches will also be covered by this special issue.

Prof. Dr. Hans-Peter Deigner
Dr. Esra Aǧel
Dr. Markus Egert
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Assay systems development
  • Point-of-care testing
  • Metabolomic and proteomic approaches
  • Host response diagnostics
  • Infectious diseases diagnostics
  • Small molecule biomarkers
  • Gene expression profiling

Published Papers (4 papers)

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Research

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12 pages, 1853 KiB  
Article
Epidemiological and Genomic Characterization of Campylobacter jejuni Isolates from a Foodborne Outbreak at Hangzhou, China
by Hua Yu, Mohammed Elbediwi, Xiaohong Zhou, Huiqun Shuai, Xiuqin Lou, Haoqiu Wang, Yan Li and Min Yue
Int. J. Mol. Sci. 2020, 21(8), 3001; https://doi.org/10.3390/ijms21083001 - 24 Apr 2020
Cited by 31 | Viewed by 3862
Abstract
Background: Foodborne outbreaks caused by Campylobacter jejuni have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand [...] Read more.
Background: Foodborne outbreaks caused by Campylobacter jejuni have become a significant public health problem worldwide. Applying genomic sequencing as a routine part of foodborne outbreak investigation remains in its infancy in China. We applied both traditional PFGE profiling and genomic investigation to understand the cause of a foodborne outbreak in Hangzhou in December 2018. Method: A total of 43 fecal samples, including 27 sick patients and 16 canteen employees from a high school in Hangzhou city in Zhejiang province, were recruited. Routine real-time fluorescent PCR assays were used for scanning the potential infectious agents, including viral pathogens (norovirus, rotavirus, adenovirus, and astrovirus), and bacterial pathogens (Salmonella, Shigella, Campylobacter jejuni, Vibrio parahaemolyticus and Vibrio cholerae). Bacterial selection medium was used to isolate and identify the positive bacteria identified by molecular test. Pulsed field gel electrophoresis (PFGE), and next generation sequencing (NGS) were applied to fifteen recovered C. jejuni isolates to further understand the case linkage of this particular outbreak. Additionally, we retrieved reference genomes from the NCBI database and performed a comparative genomics analysis with the examined genomes produced in this study. Results: The analyzed samples were found to be negative for the queried viruses. Additionally, Salmonella, Shigella, Vibrio parahaemolyticus and Vibrio cholera were not detected. Fifteen C. jejuni strains were identified by the real-time PCR assay and bacterial selection medium. These C. jejuni strains were classified into two genetic profiles defined by the PFGE. Out of fifteen C. jejuni strains, fourteen have a unified consistent genotype belonging to ST2988, and the other strain belongs to ST8149, with a 66.7% similarity in comparison with the rest of the strains. Moreover, all fifteen strains harbored blaOXA-61 and tet(O), in addition to a chromosomal mutation in gyrA (T86I). The examined fourteen strains of ST2988 from CC354 clone group have very minimal genetic difference (3~66 SNPs), demonstrated by the phylogenomic investigation. Conclusion: Both genomic investigation and PFGE profiling confirmed that C. jejuni ST2988, a new derivative from CC354, was responsible for the foodborne outbreak Illustrated in this study. Full article
(This article belongs to the Special Issue Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options)
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Review

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38 pages, 3975 KiB  
Review
Pulling the Brakes on Fast and Furious Multiple Drug-Resistant (MDR) Bacteria
by Abid Ali Khan, Khanzadi Nazneen Manzoor, Aamir Sultan, Maria Saeed, Mahrukh Rafique, Sameen Noushad, Ayesha Talib, Simone Rentschler and Hans-Peter Deigner
Int. J. Mol. Sci. 2021, 22(2), 859; https://doi.org/10.3390/ijms22020859 - 16 Jan 2021
Cited by 19 | Viewed by 4914
Abstract
Life-threatening bacterial infections have been managed by antibiotics for years and have significantly improved the wellbeing and lifetime of humans. However, bacteria have always been one step ahead by inactivating the antimicrobial agent chemically or by producing certain enzymes. The alarming universal occurrence [...] Read more.
Life-threatening bacterial infections have been managed by antibiotics for years and have significantly improved the wellbeing and lifetime of humans. However, bacteria have always been one step ahead by inactivating the antimicrobial agent chemically or by producing certain enzymes. The alarming universal occurrence of multidrug-resistant (MDR) bacteria has compelled researchers to find alternative treatments for MDR infections. This is a menace where conventional chemotherapies are no longer promising, but several novel approaches could help. Our current review article discusses the novel approaches that can combat MDR bacteria: starting off with potential nanoparticles (NPs) that efficiently interact with microorganisms causing fatal changes in the morphology and structure of these cells; nanophotothermal therapy using inorganic NPs like AuNPs to destroy pathogenic bacterial cells; bacteriophage therapy against which bacteria develop less resistance; combination drugs that act on dissimilar targets in distinctive pathways; probiotics therapy by the secretion of antibacterial chemicals; blockage of quorum sensing signals stopping bacterial colonization, and vaccination against resistant bacterial strains along with virulence factors. All these techniques show us a promising future in the fight against MDR bacteria, which remains the greatest challenge in public health care. Full article
(This article belongs to the Special Issue Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options)
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29 pages, 1356 KiB  
Review
Emerging Options for the Diagnosis of Bacterial Infections and the Characterization of Antimicrobial Resistance
by Simone Rentschler, Lars Kaiser and Hans-Peter Deigner
Int. J. Mol. Sci. 2021, 22(1), 456; https://doi.org/10.3390/ijms22010456 - 05 Jan 2021
Cited by 25 | Viewed by 8489
Abstract
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall [...] Read more.
Precise and rapid identification and characterization of pathogens and antimicrobial resistance patterns are critical for the adequate treatment of infections, which represent an increasing problem in intensive care medicine. The current situation remains far from satisfactory in terms of turnaround times and overall efficacy. Application of an ineffective antimicrobial agent or the unnecessary use of broad-spectrum antibiotics worsens the patient prognosis and further accelerates the generation of resistant mutants. Here, we provide an overview that includes an evaluation and comparison of existing tools used to diagnose bacterial infections, together with a consideration of the underlying molecular principles and technologies. Special emphasis is placed on emerging developments that may lead to significant improvements in point of care detection and diagnosis of multi-resistant pathogens, and new directions that may be used to guide antibiotic therapy. Full article
(This article belongs to the Special Issue Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options)
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18 pages, 673 KiB  
Review
Research Advances of Beneficial Microbiota Associated with Crop Plants
by Lei Tian, Xiaolong Lin, Jun Tian, Li Ji, Yalin Chen, Lam-Son Phan Tran and Chunjie Tian
Int. J. Mol. Sci. 2020, 21(5), 1792; https://doi.org/10.3390/ijms21051792 - 05 Mar 2020
Cited by 43 | Viewed by 8639
Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of [...] Read more.
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions. Full article
(This article belongs to the Special Issue Analysing Bacterial Infection, Microbiome Characterics and Small Molecules in Diagnostics: Emerging Options)
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