Advances in Human Pathogen Control—a 21st Century Challenge 2.0

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19 pages, 1731 KiB

Open AccessArticle

Development and Validation of the MAST ISOPLEX^® VTEC Kit for Simultaneous Detection of Shiga Toxin/Verotoxin 1 and 2 (stx1/vt1 and stx2/vt2) with Inhibition Control (IC) in a Rapid Loop-Mediated Isothermal Amplification (LAMP) Multiplex Assay

by Monika Iwona Suwara, Matthew Bennett, Ilaria Anna Pia Voto, Christopher Allan Brownlie and Elizabeth Ann Gillies

Int. J. Mol. Sci. 2024, 25(18), 10067; https://doi.org/10.3390/ijms251810067 - 19 Sep 2024

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Abstract

Loop-mediated isothermal amplification (LAMP) is a cost-effective, rapid, and highly specific method of replicating nucleic acids. Adding multiple targets into a single LAMP assay to create a multiplex format is highly desirable for clinical applications but has been challenging due to a need to develop specific detection techniques and strict primer design criteria. This study describes the evaluation of a rapid triplex LAMP assay, MAST ISOPLEX^® VTEC, for the simultaneous detection of Shiga toxin/verotoxin 1 and 2 (stx1/vt1 and stx2/vt2) genes in verotoxigenic Escherichia coli (E. coli) (VTEC) isolates with inhibition control (IC) synthetic DNA using a single fluorophore–oligonucleotide probe, MAST ISOPLEX^® Probes, integrated into the primer set of each target. MAST ISOPLEX^® Probes used in the MAST ISOPLEX^® VTEC kit produce fluorescent signals as they integrate with reaction products specific to each target, allowing tracking of multiple amplifications in real time using a real-time analyzer. Initial validation on DNA extracts from fecal cultures and synthetic DNA sequences (gBlocks) showed that the MAST ISOPLEX^® VTEC kit provides a method for sensitive simultaneous triplex detection in a single assay with a limit of detection (LOD) of less than 100 target copies/assay and 96% and 100% sensitivity and specificity, respectively. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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15 pages, 2894 KiB

Open AccessArticle

The Response of Murine Gut Microbiome in the Presence of Altered rpoS Gene of Klebsiella pneumoniae

by Muhammad Zafar Iqbal, Pengfei He, Pengbo He, Yixin Wu, Shahzad Munir and Yueqiu He

Int. J. Mol. Sci. 2024, 25(17), 9222; https://doi.org/10.3390/ijms25179222 - 25 Aug 2024

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Abstract

The murine model is invaluable for studying intricate interactions among gut microbes; hosts; and diseases. However; the impact of genetic variations in the murine microbiome; especially in disease contexts such as Klebsiella pneumoniae (Kp) infection; still needs to be explored. Kp; an opportunistic global pathogen; is becoming increasingly prevalent in regions like Asia; especially China. This study explored the role of the gut microbiota during Kp infection using mouse model; including wild-type and rpoS mutants of Kp138; KpC4; and KpE4 from human; maize; and ditch water; respectively. Under stress conditions; RpoS reconfigures global gene expression in bacteria; shifting the cells from active growth to survival mode. Our study examined notable differences in microbiome composition; finding that Lactobacillus and Klebsiella (particularly in WKp138) were the most abundant genera in mice guts at the genus level in all wild-type treated mice. In contrast; Firmicutes were predominant in the healthy control mice. Furthermore; Clostridium was the dominant genus in all mutants; mainly in ∆KpC4; and was absent in wild-type treated mice. Differential abundance analysis identified that these candidate taxa potentially influence disease progression and pathogen virulence. Functional prediction analysis showed that most bacterial groups were functionally involved in biosynthesis; precursor metabolites; degradation; energy generation; and metabolic cluster formation. These findings challenge the conventional understanding and highlight the need for nuanced interpretations in murine studies. Additionally; this study sheds light on microbiome–immune interactions in K. pneumoniae infection and proposes new potential therapeutic strategies. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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15 pages, 4963 KiB

Open AccessArticle

Biosynthesis of Zinc Oxide Nanoparticles Using Garlic Peel Extract and Their Antibacterial Potential

by Ali Abdelmoteleb, Benjamín Valdez-Salas, Ernesto Beltran-Partida, Vianey Mendez-Trujillo, Daniel González-Mendoza, Olivia Tzintzun-Camacho and Ahmed F. Roumia

Microbiol. Res. 2024, 15(3), 1655-1669; https://doi.org/10.3390/microbiolres15030110 - 23 Aug 2024

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Abstract

Zinc oxide nanoparticles (ZnO NPs) have gathered interest because of their unique characteristics and potential applications. In the current work, ZnO NPs underwent an eco-friendly biosynthesis process using garlic peel extract. The biosynthesized ZnO NPs were characterized using different analyses including Ultraviolet-visible (UV-vis) spectroscopy, scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), dynamic light scattering (DLS), and Fourier transform infrared spectroscopy (FTIR). The produced ZnO NPs exhibited a UV–vis spectrum absorption peak at 365 nm, thus indicating the formation of ZnO NPs. The SEM showed that the biosynthesized ZnO NPs had an irregular surface morphological shape with an average size of 17 nm, according to the DLS analysis. Based on the FTIR findings, the bioactive functional groups responsible for stabilizing and capping the ZnO-NPs were confirmed. The biosynthesized ZnO NPs exhibited 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity and antimicrobial activities against Gram-positive (Bacillus cereus) and Gram-negative bacteria (Klebsiella pneumonia). Therefore, the plant-mediated biosynthesized ZnNPs can be considered a promising candidate as an antioxidant and antimicrobial agent against pathogenic microbes found in different areas such as food safety and agriculture. Through the utilization of bioinformatics, we identified six potential targets for drug development in K. pneumonia and B. cereus, along with their corresponding interacting residues with zinc oxide nanoparticles. Additionally, our research revealed that the zinc oxide nanoparticles exhibited binding capabilities with the sulfiredoxin domain located at the specific targets of K. pneumonia, a crucial mechanism responsible for the repair of bacterial cells under oxidative stress. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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18 pages, 997 KiB

Open AccessReview

Porphyromonas gingivalis Vaccine: Antigens and Mucosal Adjuvants

by Shuo Wang, Tong Yan, Bingtao Zhang, Yixiang Chen and Zhitao Li

Vaccines 2024, 12(6), 619; https://doi.org/10.3390/vaccines12060619 - 4 Jun 2024

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Abstract

Porphyromonas gingivalis (Pg), a Gram-negative anaerobic bacterium found in dental plaque biofilm within periodontal pockets, is the primary pathogenic microorganism responsible for chronic periodontitis. Infection by Pg significantly impacts the development and progression of various diseases, underscoring the importance of eliminating this bacterium for effective clinical treatment. While antibiotics are commonly used to combat Pg, the rise of antibiotic resistance poses a challenge to complete eradication. Thus, the prevention of Pg infection is paramount. Research suggests that surface antigens of Pg, such as fimbriae, outer membrane proteins, and gingipains, can potentially be utilized as vaccine antigens to trigger protective immune responses. This article overviews these antigens, discusses advancements in mucosal adjuvants (including immunostimulant adjuvants and vaccine-delivery adjuvants), and their application in Pg vaccine development. Furthermore, the review examines the advantages and disadvantages of different immune pathways and common routes of Pg vaccine immunization. By summarizing the current landscape of Pg vaccines, addressing existing challenges, and highlighting the potential of mucosal vaccines, this review offers new insights for the advancement and clinical implementation of Pg vaccines. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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14 pages, 2790 KiB

Open AccessArticle

Closing the Diagnostic Gap in Encephalitis and Acute Disseminated Encephalomyelitis through Digital Case Classification and Viral Metagenomics

by Patrick E. Obermeier, Xiaolin Ma, Albert Heim and Barbara A. Rath

Microbiol. Res. 2024, 15(2), 900-913; https://doi.org/10.3390/microbiolres15020059 - 23 May 2024

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Abstract

Encephalitis and acute disseminated encephalomyelitis (ADEM) are often caused or triggered by viruses—but the specific pathogen commonly remains unidentified in routine care. We explored the use of viral metagenomic next-generation sequencing (mNGS) in addition to PCR testing of non-invasive stool samples to see if unbiased testing could potentially increase diagnostic yield. To identify specific clinical cases at the point of care, we took advantage of a previously published digital app allowing instant clinical case classification based on consensus case criteria, the VACC-Tool. This hospital-based prospective digital surveillance program assessed 100 pediatric patients (mean age: 11 years, range: 0.15–17.85; 49% male) with case-confirmed encephalitis and/or ADEM. Analysis of case classification at the point of care revealed that in routine care, 96% of confirmed encephalitis/ADEM cases had been missed. Overall agreement of routine care diagnoses with digital encephalitis/ADEM case classification was <50%. Also in routine care, only 13% of cases held a virus-related diagnosis, i.e., herpesvirus (n = 8) and enterovirus infection (n = 5). Use of mNGS increased the yield of virus detection by 77% (n = 23 virus hits). Specifically, mNGS identified 10 additional virus species beyond herpes- and enteroviruses. Of the additional 23 virus hits detected with mNGS, PCR confirmation was possible post hoc in 14 cases (61%). Linking digital case classification, mNGS, and PCR testing may not be feasible in routine care at this point but may help to provide hints to the pathogenesis of encephalitis/ADEM in childhood, warranting further research and exploration. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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17 pages, 1439 KiB

Open AccessEditor’s ChoiceArticle

The Impact of Pseudomonas aeruginosa Infection in Adult Cystic Fibrosis Patients—A Single Polish Centre Study

by Sylwia Jarzynka, Oliwia Makarewicz, Daniel Weiss, Anna Minkiewicz-Zochniak, Agnieszka Iwańska, Wojciech Skorupa, Marcin Padzik, Ewa Augustynowicz-Kopeć and Gabriela Olędzka

Pathogens 2023, 12(12), 1440; https://doi.org/10.3390/pathogens12121440 - 12 Dec 2023

Cited by 1 | Viewed by 1725

Abstract

Background: Pseudomonas aeruginosa (PA) is one of the most predominant pathogens of lung infections, often causing exacerbations in adult patients with cystic fibrosis (CF). Materials and Methods: Microbiological characterization of 74 PA isolates and to evaluate the correlations between the bacterial features and 44 adult Polish CF cohort clinical parameters. Results: The most common variant in the CF transmembrane conductance regulator (CFTR) gene was F508del (76.3%), followed by 3849+10kbC>T (26.3%). A total of 39.4% of the PA isolates showed multiple resistances. In patients with parameters pointing to a decline in lung function, there was a statistically significant moderate correlation with β-lactam resistance and a weak correlation between hospital frequency and colistin resistance. The mucoidity did not correlate with the biofilm formation ability, which showed 41.9% of the isolates. Proteolytic activity, observed in 60.8% of the clinical isolates, was weakly associated with motility detected in 78.4% of the strains. The genetic profiles of the PA were highly heterogeneous, and a weak positive correlation was established between cluster group and biofilm formation. Conclusion: The findings suggest that there is a high variety in P. aeruginosa populations in adult CF patients. There is a need to monitor PA strains in groups of patients with cystic fibrosis, in particular, in terms of the occurrence of antibiotic resistance related to a decline in lung function. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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7 pages, 1599 KiB

Open AccessBrief Report

The Detection of Circulating Cell-Free DNA for the Diagnosis of Schistosoma in Immigrants from African Countries in Italy

by Valentina Dimartino, Fernanda Scopelliti, Caterina Cattani, Gianluca Nicolella and Andrea Cavani

Microbiol. Res. 2023, 14(4), 2034-2040; https://doi.org/10.3390/microbiolres14040137 - 1 Dec 2023

Viewed by 1173

Abstract

The rising migration and travel from and towards endemic areas has brought renewed concerns about many parasitic infections, including neglected tropical diseases, such as schistosomiasis. Although serology is the most widely used method for the screening of schistosomiasis in non-endemic countries, this technique lacks sensitivity, especially to distinguish between past and ongoing infections. More recently, a molecular test based on the detection of Schistosoma cell-free DNA in the serum has been proposed as a diagnostic procedure for parasitosis. To test the performance of a blood PCR assay, this work investigated 102 serum samples collected from migrants coming from endemic areas by using primers specific to genomic regions of S. mansoni and S. haematobium patients. The results were then compared with the detection of specific IgG Abs with serological tests. Molecular analysis detected Schistosoma DNA in 32 patients. Among them, we characterized nine S. haematobium, 20 S. mansoni, and three coinfections. Compared with molecular assay, serological analysis detected specific antibodies against Schistosoma antigens in 52 out of 102 patients. Concordance between the two tests was found in 76 out of 102 patients (74.51%): in particular, both diagnostic tests were positive in 29 patients (28.43%) and negative in 47 (46.08%). The specificity of the molecular test was 94%. Overall, our data suggest that serological diagnosis could be combined with the molecular approach, providing the clinician with the serotyping of the parasite and useful information about the infection as well as the required further diagnostic procedures. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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8 pages, 1649 KiB

Open AccessCase Report

Chromoblastomycosis: New Perspective on Adjuvant Treatment with Acitretin

by Walter Belda, Jr., Luiz Felipe Domingues Passero, Caroline Heleno Chagas de Carvalho, Paula Celeste Rubiano Mojica and Pablo Andrade Vale

Diseases 2023, 11(4), 162; https://doi.org/10.3390/diseases11040162 - 8 Nov 2023

Cited by 1 | Viewed by 2294

Abstract

Chromoblastomycosis (CBM) is a neglected human disease, caused by different species of pigmented dematiaceous fungi that cause granulomatous and suppurative dermatosis. This infection is difficult to treat and there are limited therapeutic options, including terbinafine, itraconazole, and tioconazole. Classic treatment is administered for a long period of time, but some patients do not respond properly, and therefore, such therapeutic approaches possess low cure rates. Therefore, it is vital to develop new strategies for the treatment of CBM. In this regard, it has been observed that the association of immunomodulatory molecules such as glucan with therapy carried out with antifungal drugs improves cutaneous lesions in comparison to treatment with antifungal drugs alone, suggesting that drug association may be an interesting and significant approach to incorporate into CBM therapy. Thus, the aim of this work was to associate classical antifungal therapy with the adjuvants imiquimod and acitretin. In the present case, we reported a patient with extensive CBM caused by Fonsaecae pedrosoi, that affected an extensive area of the right leg, that was left without treatment for 11 years. He was treated with a classical combination of itraconazole and terbinafine via the oral route plus topical imiquimod and oral acitretin, as an adjuvant therapy. After five months of treatment, a significant regression of verrucous plaques was observed, suggesting that the use of these adjuvants combined with the classical antifungal drugs, intraconazole plus terbinafine, can reduce treatment time and rapidly improve the patient’s quality of life. This result confirms that the use of coadjuvant drugs may be effective in the treatment of this infectious disease. Full article

(This article belongs to the Topic Advances in Human Pathogen Control—a 21st Century Challenge 2.0)

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Journal Name	Impact Factor	CiteScore	Launched Year	First Decision (median)	APC
Diseases diseases	2.9	0.8	2013	18.9 Days	CHF 1800
International Journal of Molecular Sciences ijms	4.9	8.1	2000	18.1 Days	CHF 2900
Microbiology Research microbiolres	2.1	1.9	2010	16.7 Days	CHF 1600
Pathogens pathogens	3.3	6.4	2012	16.3 Days	CHF 2200
Vaccines vaccines	5.2	8.9	2013	17.6 Days	CHF 2700

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