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New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective
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New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Analytical Chemistry".

Deadline for manuscript submissions: closed (31 August 2020) | Viewed by 30038

Special Issue Editors

Prof. Dr. Paul Groundwater

E-Mail Website
Guest Editor
The University of Sydney School of Pharmacy, Sydney, Australia
Interests: anti-cancer agents; anti-bacterials; bacterial detection
Prof. Dr. David E. Hibbs

E-Mail Website
Guest Editor
School of Pharmacy, The University of Sydney, Sydney, Australia
Interests: molecular modelling; computational chemistry; solid state chemistry; high-resolution X-ray and neutron diffraction; experimental charge density distributions; ab initio and DFT calculations
Dr. Linda Varadi

E-Mail Website
Guest Editor
RMIT Univeristy, Melbourne, Australia
Interests: organic synthesis; trigger-responsive optical probes; active nanomaterials

Special Issue Information

Dear Colleagues,

Global initiatives, such as the Longitude Prize (https://longitudeprize.org/) for a point-of-care diagnostic bacterial test, aim to address prevalence of antimicrobial resistance (AMR), in both the community and hospital settings, as its potential impact on health is as significant as that of global warming. One approach to slowing the progression of AMR, and mitigating the lack of novel antimicrobial development, is to improve diagnostic testing in order to facilitate evidence-based prescribing and dispensing of anti-bacterials. 

In this Special Issue “New Methods for the Detection/Identification of Bacteria—The Chemistry Perspective”, we invite previously unpublished manuscripts on bacterial detection and identification techniques, with the main focus here being on the fundamental chemical challenges and developments, such as the synthesis/fabrication of novel materials responsive to specific bacterial processes/presence, the use of emerging analytical techniques, and the incorporation of novel materials and/or analytical techniques into diagnostic tests, e.g., point-of-care and lab-on-a-chip devices in combination with microfluidics, and microelectronics.

Prof. Paul Groundwater
Prof. David E. Hibbs
Dr. Linda Varadi
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. Molecules is an international peer-reviewed open access semimonthly 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 detection
  • bacterial identification
  • point-of-care diagnostics.

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Published Papers (7 papers)

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Research

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12 pages, 1417 KiB  
Article
New Real-Time PCRs to Differentiate Rickettsia spp. and Rickettsia conorii
by Valeria Blanda, Rosalia D’Agostino, Elisabetta Giudice, Kety Randazzo, Francesco La Russa, Sara Villari, Stefano Vullo and Alessandra Torina
Molecules 2020, 25(19), 4431; https://doi.org/10.3390/molecules25194431 - 27 Sep 2020
Cited by 16 | Viewed by 3406
Abstract
Rickettsia species are an important cause of emerging infectious diseases in people and animals, and rickettsiosis is one of the oldest known vector-borne diseases. Laboratory diagnosis of Rickettsia is complex and time-consuming. This study was aimed at developing two quantitative real-time PCRs targeting [...] Read more.
Rickettsia species are an important cause of emerging infectious diseases in people and animals, and rickettsiosis is one of the oldest known vector-borne diseases. Laboratory diagnosis of Rickettsia is complex and time-consuming. This study was aimed at developing two quantitative real-time PCRs targeting ompB and ompA genes for the detection, respectively, of Rickettsia spp. and R. conorii DNA. Primers were designed following an analysis of Rickettsia gene sequences. The assays were optimized using SYBR Green and TaqMan methods and tested for sensitivity and specificity. This study allowed the development of powerful diagnostic methods, able to detect and quantify Rickettsia spp. DNA and differentiate R. conorii species. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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25 pages, 10982 KiB  
Article
Synthesis and Antimicrobial Activity of Phosphonopeptide Derivatives Incorporating Single and Dual Inhibitors
by Keng Tiong Ng, John D. Perry, Emma C.L. Marrs, Sylvain Orenga, Rosaleen J. Anderson and Mark Gray
Molecules 2020, 25(7), 1557; https://doi.org/10.3390/molecules25071557 - 28 Mar 2020
Cited by 2 | Viewed by 2821
Abstract
In diagnostic microbiology, culture media are widely used for detection of pathogenic bacteria. Such media employ various ingredients to optimize detection of specific pathogens such as chromogenic enzyme substrates and selective inhibitors to reduce the presence of commensal bacteria. Despite this, it is [...] Read more.
In diagnostic microbiology, culture media are widely used for detection of pathogenic bacteria. Such media employ various ingredients to optimize detection of specific pathogens such as chromogenic enzyme substrates and selective inhibitors to reduce the presence of commensal bacteria. Despite this, it is rarely possible to inhibit the growth of all commensal bacteria, and thus pathogens can be overgrown and remain undetected. One approach to attempt to remedy this is the use of “suicide substrates” that can target specific bacterial enzymes and selectively inhibit unwanted bacterial species. With the purpose of identifying novel selective inhibitors, six novel phosphonopeptide derivatives based on d/l-fosfalin and β-chloro-l-alanine were synthesized and tested on 19 different strains of clinically relevant bacteria. Several compounds show potential as useful selective agents that could be exploited in the recovery of several bacterial pathogens including Salmonella, Pseudomonas aeruginosa, and Listeria. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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10 pages, 344 KiB  
Article
Phosphonopeptides Revisited, in an Era of Increasing Antimicrobial Resistance
by Emma C.L. Marrs, Linda Varadi, Alexandre F. Bedernjak, Kathryn M. Day, Mark Gray, Amanda L. Jones, Stephen P. Cummings, Rosaleen J. Anderson and John D. Perry
Molecules 2020, 25(6), 1445; https://doi.org/10.3390/molecules25061445 - 23 Mar 2020
Cited by 11 | Viewed by 2913
Abstract
Given the increase in resistance to antibacterial agents, there is an urgent need for the development of new agents with novel modes of action. As an interim solution, it is also prudent to reinvestigate old or abandoned antibacterial compounds to assess their efficacy [...] Read more.
Given the increase in resistance to antibacterial agents, there is an urgent need for the development of new agents with novel modes of action. As an interim solution, it is also prudent to reinvestigate old or abandoned antibacterial compounds to assess their efficacy in the context of widespread resistance to conventional agents. In the 1970s, much work was performed on the development of peptide mimetics, exemplified by the phosphonopeptide, alafosfalin. We investigated the activity of alafosfalin, di-alanyl fosfalin and β-chloro-L-alanyl-β-chloro-L-alanine against 297 bacterial isolates, including carbapenemase-producing Enterobacterales (CPE) (n = 128), methicillin-resistant Staphylococcus aureus (MRSA) (n = 37) and glycopeptide-resistant enterococci (GRE) (n = 43). The interaction of alafosfalin with meropenem was also examined against 20 isolates of CPE. The MIC50 and MIC90 of alafosfalin for CPE were 1 mg/L and 4 mg/L, respectively and alafosfalin acted synergistically when combined with meropenem against 16 of 20 isolates of CPE. Di-alanyl fosfalin showed potent activity against glycopeptide-resistant isolates of Enterococcus faecalis (MIC90; 0.5 mg/L) and Enterococcus faecium (MIC90; 2 mg/L). Alafosfalin was only moderately active against MRSA (MIC90; 8 mg/L), whereas β-chloro-L-alanyl-β-chloro-L-alanine was slightly more active (MIC90; 4 mg/L). This study shows that phosphonopeptides, including alafosfalin, may have a therapeutic role to play in an era of increasing antibacterial resistance. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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25 pages, 1235 KiB  
Article
C-Terminal 1-Aminoethyltetrazole-Containing Oligopeptides as Novel Alanine Racemase Inhibitors
by Laszlo A. Kondacs, Sylvain Orenga, Rosaleen J. Anderson, Emma C.L. Marrs, John D. Perry and Mark Gray
Molecules 2020, 25(6), 1315; https://doi.org/10.3390/molecules25061315 - 13 Mar 2020
Cited by 4 | Viewed by 3956
Abstract
In clinical culture media inoculated with patient samples, selective inhibition of commensal bacteria is essential for accurate diagnosis and effective treatment, as they can mask the presence of pathogenic bacteria. The alanine analogue, 1-aminoethyltetrazole was investigated as a potential alanine racemase inhibitor. For [...] Read more.
In clinical culture media inoculated with patient samples, selective inhibition of commensal bacteria is essential for accurate diagnosis and effective treatment, as they can mask the presence of pathogenic bacteria. The alanine analogue, 1-aminoethyltetrazole was investigated as a potential alanine racemase inhibitor. For effective uptake and enhanced and selective antibacterial activity, a library of C-terminal 1-aminoethyltetrazole containing di- and oligopeptides were synthesized by solid phase peptide coupling techniques. The investigation of the antimicrobial activity of the synthesised compounds identified several clinically applicable selective inhibitors. These enabled differentiation between the closely related bacteria, Salmonella and Escherichia coli, which can be difficult to discriminate between in a clinical setting. In addition, differentiation between enterococci and other Gram-positive cocci was also seen. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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12 pages, 1864 KiB  
Article
A Selective, Dual Emission β-Alanine Aminopeptidase Activated Fluorescent Probe for the Detection of Pseudomonas aeruginosa, Burkholderia cepacia, and Serratia marcescens
by Linda Váradi, Elias Y. Najib, David E. Hibbs, John D. Perry and Paul W. Groundwater
Molecules 2019, 24(19), 3550; https://doi.org/10.3390/molecules24193550 - 30 Sep 2019
Cited by 5 | Viewed by 3357
Abstract
Selective detection of β-alanyl aminopeptidase (BAP)-producing Pseudomonas aeruginosa, Serratia marcescens, and Burkholderia cepacia was achieved by employing the blue-to-yellow fluorescent transition of a BAP-specific enzyme substrate, 3-hydroxy-2-(p-dimethylaminophenyl)flavone derivative, incorporating a self-immolative linker to β-alanine. Upon cellular uptake and accumulation [...] Read more.
Selective detection of β-alanyl aminopeptidase (BAP)-producing Pseudomonas aeruginosa, Serratia marcescens, and Burkholderia cepacia was achieved by employing the blue-to-yellow fluorescent transition of a BAP-specific enzyme substrate, 3-hydroxy-2-(p-dimethylaminophenyl)flavone derivative, incorporating a self-immolative linker to β-alanine. Upon cellular uptake and accumulation of the substrate by viable bacterial colonies, blue fluorescence was generated, while hydrolysis of the N-terminal peptide bond by BAP resulted in the elimination of the self-immolative linker and the restoration of the original fluorescence of the flavone derivative. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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Review

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33 pages, 4101 KiB  
Review
Advances in Optical Detection of Human-Associated Pathogenic Bacteria
by Andrea Locke, Sean Fitzgerald and Anita Mahadevan-Jansen
Molecules 2020, 25(22), 5256; https://doi.org/10.3390/molecules25225256 - 11 Nov 2020
Cited by 35 | Viewed by 4725
Abstract
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native [...] Read more.
Bacterial infection is a global burden that results in numerous hospital visits and deaths annually. The rise of multi-drug resistant bacteria has dramatically increased this burden. Therefore, there is a clinical need to detect and identify bacteria rapidly and accurately in their native state or a culture-free environment. Current diagnostic techniques lack speed and effectiveness in detecting bacteria that are culture-negative, as well as options for in vivo detection. The optical detection of bacteria offers the potential to overcome these obstacles by providing various platforms that can detect bacteria rapidly, with minimum sample preparation, and, in some cases, culture-free directly from patient fluids or even in vivo. These modalities include infrared, Raman, and fluorescence spectroscopy, along with optical coherence tomography, interference, polarization, and laser speckle. However, these techniques are not without their own set of limitations. This review summarizes the strengths and weaknesses of utilizing each of these optical tools for rapid bacteria detection and identification. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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30 pages, 8060 KiB  
Review
Modified Enzyme Substrates for the Detection of Bacteria: A Review
by Laura Pala, Teja Sirec and Urs Spitz
Molecules 2020, 25(16), 3690; https://doi.org/10.3390/molecules25163690 - 13 Aug 2020
Cited by 25 | Viewed by 8220
Abstract
The ability to detect, identify and quantify bacteria is crucial in clinical diagnostics, environmental testing, food security settings and in microbiology research. Recently, the threat of multidrug-resistant bacterial pathogens pushed the global scientific community to develop fast, reliable, specific and affordable methods to [...] Read more.
The ability to detect, identify and quantify bacteria is crucial in clinical diagnostics, environmental testing, food security settings and in microbiology research. Recently, the threat of multidrug-resistant bacterial pathogens pushed the global scientific community to develop fast, reliable, specific and affordable methods to detect bacterial species. The use of synthetically modified enzyme substrates is a convenient approach to detect bacteria in a specific, economic and rapid manner. The method is based on the use of specific enzyme substrates for a given bacterial marker enzyme, conjugated to a signalogenic moiety. Following enzymatic reaction, the signalophor is released from the synthetic substrate, generating a specific and measurable signal. Several types of signalophors have been described and are defined by the type of signal they generate, such as chromogenic, fluorogenic, luminogenic, electrogenic and redox. Signalophors are further subdivided into groups based on their solubility in water, which is key in defining their application on solid or liquid media for bacterial culturing. This comprehensive review describes synthetic enzyme substrates and their applications for bacterial detection, showing their mechanism of action and their synthetic routes. Full article
(This article belongs to the Special Issue New Methods for the Detection/Identification of Bacteria–the Chemistry Perspective)
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