Submit to Microorganisms Review for Microorganisms Propose a Special Issue

Journal Menu

Journal Browser

Rapid and Novel Diagnostics for Infectious Diseases

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Published Papers

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 29956

Share This Special Issue

Special Issue Editors

Prof. Jacob Moran-Gilad

E-Mail Website
Guest Editor

MAGICAL Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
Interests: genomics; metagenomics; clinical diagnostics; medical epidemiology; antimicrobial resistance; public health policy

Dr. Hillary A. Craddock

E-Mail Website
Guest Editor

MAGICAL Group, Department of Health Systems Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
Interests: genomics; antimicrobial resistance; resistomes; One Health; environmental surveillance; environmental and health justice

Special Issue Information

Dear Colleagues,

A key aspect of responding to infectious disease threats, whether from novel pathogens like SARS-CoV-2 or known threats like antimicrobial resistance, is by continuously improving and developing diagnostic methods, including developing rapid detection methods. Such rapid and novel laboratory methods are critical for appropriate treatment, as well as disease control and prevention, and include point-of-care diagnostics, PCR-based techniques, proteomics- and genomics-based (next-generation-sequencing) diagnostics, and other approaches. In this Special Issue of Microorganisms, we invite you to send contributions concerning novel and/or rapid diagnostics for infectious diseases, spanning bacteriology, virology, mycology, and parasitology.

We welcome submissions highlighting emerging infections (including SARS-CoV-2); antimicrobial resistance in humans, animals, and the environment; pathogen detection and characterization (including low resource settings); and rapid typing, among others. In addition to original studies reporting new developments, assay validation, and testing experience, articles focusing on research and development, decision-making, laboratory service provision, quality control, and management will also be considered.

Prof. Jacob Moran-Gilad
Dr. Hillary A. Craddock
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

genomics
point-of-care
diagnostics
pandemic
surveillance
antimicrobial resistance
laboratory management
clinical testing
detection techniques
field diagnostics

Published Papers (10 papers)

Download All Papers

Research

Jump to: Other

12 pages, 2137 KiB

Open AccessArticle

Long-Read Sequencing and Hybrid Assembly for Genomic Analysis of Clinical Brucella melitensis Isolates

by Hillary A. Craddock, Yair Motro, Bar Zilberman, Boris Khalfin, Svetlana Bardenstein and Jacob Moran-Gilad

Microorganisms 2022, 10(3), 619; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030619 - 14 Mar 2022

Cited by 7 | Viewed by 2410

Abstract

Brucella melitensis is a key etiological agent of brucellosis and has been increasingly subject to characterization using sequencing methodologies. This study aimed to investigate and compare short-read, long-read, and hybrid assemblies of B. melitensis. Eighteen B. melitensis isolates from Southern Israel were sequenced using Illumina and the Oxford Nanopore (ONP) MinION, and hybrid assemblies were generated with ONP long reads scaffolded on Illumina short reads. Short reads were assembled with INNUca with SPADes, long reads and hybrid with dragonflye. Abricate with the virulence factor database (VFDB) and in silico PCR (for the genes BetB, BPE275, BSPB, manA, mviN, omp19, perA, PrpA, VceC, and ureI) were used for identifying virulence genes, and a total of 61 virulence genes were identified in short-read, long-read, and hybrid assemblies of all 18 isolates. The phylogenetic analysis using long-read assemblies revealed several inconsistencies in cluster assignment as compared to using hybrid and short-read assemblies. Overall, hybrid assembly provided the most comprehensive data, and stand-alone short-read sequencing provided comparable data to stand-alone long-read sequencing regarding virulence genes. For genomic epidemiology studies, stand-alone ONP sequencing may require further refinement in order to be useful in endemic settings. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

13 pages, 1488 KiB

Open AccessArticle

Development of Real-Time Molecular Assays for the Detection of Wesselsbron Virus in Africa

by Martin Faye, Thiané Seye, Pranav Patel, Cheikh Tidiane Diagne, Moussa Moise Diagne, Moussa Dia, Fatou Diène Thiaw, Amadou Alpha Sall and Ousmane Faye

Microorganisms 2022, 10(3), 550; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10030550 - 03 Mar 2022

Cited by 2 | Viewed by 2098

Abstract

Wesselsbron is a neglected, mosquito-borne zoonotic disease endemic to Africa. The virus is mainly transmitted by the mosquitoes of the Aedes genus and primarily affects domestic livestock species with teratogenic effects but can jump to humans. Although no major outbreak or fatal case in humans has been reported as yet worldwide, a total of 31 acute human cases of Wesselsbron infection have been previously described since its first isolation in 1955. However, most of these cases were reported from Sub-Saharan Africa where resources are limited and a lack of diagnostic means exists. We describe here two molecular diagnostic tools suitable for Wesselsbron virus detection. The newly established reverse transcription-quantitative polymerase chain reaction and reverse-transcription-recombinase polymerase amplification assays are highly specific and repeatable, and exhibit good agreement with the reference assay on the samples tested. The validation on clinical and veterinary samples shows that they can be accurately used for Wesselsbron virus detection in public health activities and the veterinary field. Considering the increasing extension of Aedes species worldwide, these new assays could be useful not only in laboratory studies for Wesselsbron virus, but also in routine surveillance activities for zoonotic arboviruses and could be applied in well-equipped central laboratories or in remote areas in Africa, regarding the reverse-transcription-recombinase polymerase amplification assay. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

12 pages, 805 KiB

Open AccessArticle

Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants

by Vanessa De Pace, Bianca Bruzzone, Andrea Orsi, Valentina Ricucci, Alexander Domnich, Giulia Guarona, Nadia Randazzo, Federica Stefanelli, Enrico Battolla, Pier Andrea Dusi, Flavia Lillo and Giancarlo Icardi

Microorganisms 2022, 10(2), 306; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020306 - 27 Jan 2022

Cited by 17 | Viewed by 3639

Abstract

The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96–100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2–3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

12 pages, 1757 KiB

Open AccessArticle

Genomic Epidemiology of Clinical Brucella melitensis Isolates from Southern Israel

by Bar Zilberman, Yair Motro, Orli Sagi, David Kornspan, Shalom Ben-Shimol, Michael Gdalevich, Yael Yagel, Nadav Davidovitch, Boris Khalfin, Peter Rabinowitz, Lior Nesher, Itamar Grotto, Svetlana Bardenstein and Jacob Moran-Gilad

Microorganisms 2022, 10(2), 238; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020238 - 22 Jan 2022

Cited by 2 | Viewed by 2170

Abstract

Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products, is endemic in Southern Israel, mainly among the Bedouin Arab population. However, the genomic epidemiology of B. melitensis in this region has not yet been elucidated. A cohort of brucellosis cases (n = 118) diagnosed between 2017–2019 was studied using whole-genome sequencing (WGS). Phylogenetic analyses utilized core genome MLST (cgMLST) for all local isolates and core genome SNPs for 347 human-associated B. melitensis genomes, including Israeli and publicly available sequences. Israeli isolates formed two main clusters, presenting a notable diversity, with no clear dominance of a specific strain. On a global scale, the Israeli genomes clustered according to their geographical location, in proximity to genomes originating from the Middle East, and formed the largest cluster in the tree, suggesting relatively high conservation. Our study unveils the genomic epidemiology of B. melitensis in Southern Israel, implicating that rather than a common source, the transmission pattern of brucellosis among Bedouin communities is complex, predominantly local, and household-based. Further, genomic surveillance of B. melitensis is expected to inform future public health and veterinary interventions and clinical care. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

16 pages, 1072 KiB

Open AccessArticle

Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance

by Alfredo Mari, Tim Roloff, Madlen Stange, Kirstine K. Søgaard, Erblin Asllanaj, Gerardo Tauriello, Leila Tamara Alexander, Michael Schweitzer, Karoline Leuzinger, Alexander Gensch, Aurélien E. Martinez, Julia Bielicki, Hans Pargger, Martin Siegemund, Christian H. Nickel, Roland Bingisser, Michael Osthoff, Stefano Bassetti, Parham Sendi, Manuel Battegay, Catia Marzolini, Helena M. B. Seth-Smith, Torsten Schwede, Hans H. Hirsch and Adrian Egli Show full author list Hide full author list

Microorganisms 2021, 9(5), 1094; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9051094 - 19 May 2021

Cited by 21 | Viewed by 4117

Abstract

A variety of antiviral treatments for COVID-19 have been investigated, involving many repurposed drugs. Currently, the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp, encoded by nsp12-nsp7-nsp8) has been targeted by numerous inhibitors, e.g., remdesivir, the only provisionally approved treatment to-date, although the clinical impact of these interventions remains inconclusive. However, the potential emergence of antiviral resistance poses a threat to the efficacy of any successful therapies on a wide scale. Here, we propose a framework to monitor the emergence of antiviral resistance, and as a proof of concept, we address the interaction between RdRp and remdesivir. We show that SARS-CoV-2 RdRp is under purifying selection, that potential escape mutations are rare in circulating lineages, and that those mutations, where present, do not destabilise RdRp. In more than 56,000 viral genomes from 105 countries from the first pandemic wave, we found negative selective pressure affecting nsp12 (Tajima’s D = −2.62), with potential antiviral escape mutations in only 0.3% of sequenced genomes. Potential escape mutations included known key residues, such as Nsp12:Val473 and Nsp12:Arg555. Of the potential escape mutations involved globally, in silico structural models found that they were unlikely to be associated with loss of stability in RdRp. No potential escape mutation was found in a local cohort of remdesivir treated patients. Collectively, these findings indicate that RdRp is a suitable drug target, and that remdesivir does not seem to exert high selective pressure. We anticipate our framework to be the starting point of a larger effort for a global monitoring of drug resistance throughout the COVID-19 pandemic. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

22 pages, 3796 KiB

Open AccessArticle

Evaluation of a New Culture-Based AtbFinder Test-System Employing a Novel Nutrient Medium for the Selection of Optimal Antibiotics for Critically Ill Patients with Polymicrobial Infections within 4 h

by George Tetz and Victor Tetz

Microorganisms 2021, 9(5), 990; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050990 - 04 May 2021

Cited by 5 | Viewed by 2715

Abstract

Here, we describe the validation of a new phenotypic culture-based AtbFinder method for rapid selection of antibiotics in vitro using specimens with mono- and polybacterial infections. AtbFinder, which can be applied to any type of non-blood tissue, does not require isolation of pure bacterial cultures. The method uses a novel TGV medium that allows more rapid bacterial growth of Gram-positive and Gram-negative monoisolates compared with that achieved with conventional laboratory media, demonstrating overall sensitivity, specificity, PPV, NPV values of 99.6%, 98.1%, 98.5%, and 99.4%, respectively, after 4 h. For polymicrobial infections, AtbFinder utilized a novel paradigm of the population response to antibiotics, enabling bacterial growth in the form of a mixed microbial community and selecting antibiotics targeting not only the principal pathogen, but also those bacteria that support their growth. TGV medium allowed culturing of a more diverse set of bacteria from polymicrobial biospecimens, compared with that achieved with the standard media, and enabled, within 4 h, accurate selection of the antibiotics that completely eliminated all cultivatable bacteria from clinical samples. In conclusion, the AtbFinder system may be a valuable tool in improving antibiotic selection, and enabling targeted empirical therapy and accurate antibiotic replacement, which is especially important in high-risk patients. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

11 pages, 887 KiB

Open AccessArticle

Rapid Diagnostics of Orthopaedic-Implant-Associated Infections Using Nanopore Shotgun Metagenomic Sequencing on Tissue Biopsies

by J. Christopher Noone, Karin Helmersen, Truls Michael Leegaard, Inge Skråmm and Hege Vangstein Aamot

Microorganisms 2021, 9(1), 97; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010097 - 04 Jan 2021

Cited by 13 | Viewed by 3577

Abstract

Conventional culture-based diagnostics of orthopaedic-implant-associated infections (OIAIs) are arduous. Hence, the aim of this study was to evaluate a culture-independent, rapid nanopore-based diagnostic protocol with regard to (a) pathogen identification, (b) time to pathogen identification, and (c) identification of antimicrobial resistance (AMR). This prospective proof-of-concept study included soft tissue biopsies from 32 patients with OIAIs undergoing first revision surgery at Akershus University Hospital, Norway. The biopsies were divided into two segments. Nanopore shotgun metagenomic sequencing and pathogen and antimicrobial resistance gene identification using the EPI2ME analysis platform (Oxford Nanopore Technologies) were performed on one segment. Conventional culture-based diagnostics were performed on the other. Microbial identification matched in 23/32 OIAI patients (72%). Sequencing detected additional microbes in 9/32 patients. Pathogens detected by culturing were identified by sequencing within a median of 1 h of sequencing start [range 1–18 h]. Phenotypic AMR was explained by the detection of resistance genes in 11/23 patients (48%). Diagnostics of OIAIs using shotgun metagenomics sequencing are possible within 24 h from biopsy using nanopore technology. Sequencing outperformed culturing with respect to speed and pathogen detection where pathogens were at sufficient concentration, whereas culture-based methods had an advantage at lower pathogen concentrations. Sequencing-based AMR detection may not yet be a suitable replacement for culture-based antibiotic susceptibility testing. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

24 pages, 12008 KiB

Open AccessArticle

Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula

by Sarah Azinheiro, Joana Carvalho, Marta Prado and Alejandro Garrido-Maestu

Microorganisms 2020, 8(9), 1359; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8091359 - 04 Sep 2020

Cited by 16 | Viewed by 3308 | Correction

Abstract

Food poisoning continue to be a threat in the food industry showing a need to improve the detection of the pathogen responsible for the hospitalization cases and death. DNA-based techniques represent a real advantage and allow the detection of several targets at the same time, reducing cost and time of analysis. The development of new methodology using SYBR Green qPCR for the detection of L. monocytogenes, Salmonella spp. and E. coli O157 simultaneously was developed and a non-competitive internal amplification control (NC-IAC) was implemented to detect reaction inhibition. The formulation and supplementation of the enrichment medium was also optimized to allow the growth of all pathogens. The limit of detection (LoD) 95% obtained was <1 CFU/25 g for E. coli O157, and 2 CFU/25 g for Salmonella spp. and L. monocytogenes and regarding the multiplex detection a LoD 95% of 1.7 CFU/25 g was observed. The specificity, relative sensitivity and accuracy of full methodology were 100% and the use of the NC-IAC allowed the reliability of the results without interfering with the sensitivity of the methodology. The described study proved to obtain results comparable to those of probe-based qPCR, and more economically than classical high resolution melting qPCR, being both important aspects for its implementation in the food industry. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures

Figure 1

Other

Jump to: Research

1 pages, 177 KiB

Open AccessCorrection

Correction: Azinheiro et al. Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula. Microorganisms 2020, 8, 1359

by Sarah Azinheiro, Joana Carvalho, Marta Prado and Alejandro Garrido-Maestu

Microorganisms 2021, 9(7), 1482; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9071482 - 12 Jul 2021

Viewed by 1933

Abstract

The authors would like to make the following correction to the published paper [...] Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

11 pages, 906 KiB

Open AccessBrief Report

Evaluation of a kDNA-Based qPCR Assay for the Detection and Quantification of Old World Leishmania Species

by Marcello Ceccarelli, Gloria Buffi, Aurora Diotallevi, Francesca Andreoni, Daniela Bencardino, Fabrizio Vitale, Germano Castelli, Federica Bruno, Mauro Magnani and Luca Galluzzi

Microorganisms 2020, 8(12), 2006; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms8122006 - 16 Dec 2020

Cited by 6 | Viewed by 2393

Abstract

The parasite protozoan Leishmania, the causative agent of leishmaniasis, includes two subgenera of medical interest: Leishmania (Leishmania) and Leishmania (Viannia). Parasite species detection and characterization is crucial to choose treatment protocols and to monitor the disease evolution. Molecular approaches can speed up and simplify the diagnostic process. In particular, several molecular assays target the mitochondrial DNA minicircle network (kDNA) that characterizes the Leishmania genus. We previously proposed a qPCR assay targeting kDNA, followed by high resolution melt (HRM) analysis (qPCR-ML) to distinguish L. (L.) infantum and L. (L.) amazonensis from L. Viannia species. Successively, this assay has been integrated with other qPCR assays, to differentiate L. (L.) infantum, L. (L.) amazonensis and L. (L.) mexicana. In this work, we tested the applicability of our qPCR-ML assay on L. (L.) donovani, L. (L.) major, L. (L.) tropica and L. (L.) aethiopica, showing that the qPCR-ML assay can also amplify Old World species, different from L. (L.) infantum, with good quantification limits (1 × 10⁻⁴–1 × 10⁻⁶ ng/pcr tube). Moreover, we evaluated 11 L. (L.) infantum strains/isolates, evidencing the variability of the kDNA minicircle target molecules among the strains/isolates of the same species, and pointing out the possibility of quantification using different strains as reference. Taken together, these data account for the consideration of qPCR-ML as a quantitative pan-Leishmania assay. Full article

(This article belongs to the Special Issue Rapid and Novel Diagnostics for Infectious Diseases)

► Show Figures