Editorial

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5 pages, 211 KiB

Open AccessEditorial

Diagnosis, Characterization and Treatment of Emerging Pathogens

by Shengxi Chen

Microorganisms 2023, 11(8), 2032; https://doi.org/10.3390/microorganisms11082032 - 08 Aug 2023

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Abstract

Emerging infectious diseases are perhaps the most rapidly spreading diseases [...] Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

Research

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14 pages, 1471 KiB

Open AccessArticle

The Role of Aspartate Aminotransferase-to-Lymphocyte Ratio Index (ALRI) in Predicting Mortality in SARS-CoV-2 Infection

by José Manuel Reyes-Ruiz, Omar García-Hernández, Gustavo Martínez-Mier, Juan Fidel Osuna-Ramos, Luis Adrián De Jesús-González, Carlos Noe Farfan-Morales, Selvin Noé Palacios-Rápalo, Carlos Daniel Cordero-Rivera, Tatiana Ordoñez-Rodríguez and Rosa María del Ángel

Microorganisms 2023, 11(12), 2894; https://doi.org/10.3390/microorganisms11122894 - 30 Nov 2023

Cited by 1 | Viewed by 779

Abstract

COVID-19 has a mortality rate exceeding 5.4 million worldwide. The early identification of patients at a high risk of mortality is essential to save their lives. The AST-to-lymphocyte ratio index (ALRI) is a novel biomarker of survival in patients with hepatocellular carcinoma, an [...] Read more.

COVID-19 has a mortality rate exceeding 5.4 million worldwide. The early identification of patients at a high risk of mortality is essential to save their lives. The AST-to-lymphocyte ratio index (ALRI) is a novel biomarker of survival in patients with hepatocellular carcinoma, an organ susceptible to SARS-CoV-2 infection. For this study, the prognostic value of ALRI as a marker of COVID-19 mortality was evaluated. For this purpose, ALRI was compared with the main biomarkers for COVID-19 mortality (neutrophil-to-lymphocyte ratio [NLR], systemic immune-inflammation index [SII], platelet-to-lymphocyte ratio [PLR], lactate dehydrogenase (LDH)/lymphocyte ratio [LDH/LR]). A retrospective cohort of 225 patients with SARS-CoV-2 infection and without chronic liver disease was evaluated. In the non-survival group, the ALRI, NLR, SII, and LDH/LR were significantly higher than in the survival group (p_corrected < 0.05). ALRI had an area under the curve (AUC) of 0.81, a sensitivity of 70.37%, and a specificity of 75%, with a best cut-off value >42.42. COVID-19 patients with high ALRI levels had a mean survival time of 7.8 days. Multivariate Cox regression revealed that ALRI > 42.42 (HR = 2.32, 95% CI: 1.35–3.97; p_corrected = 0.01) was a prognostic factor of COVID-19 mortality. These findings prove that ALRI is an independent predictor of COVID-19 mortality and that it may help identify high-risk subjects with SARS-CoV-2 infection upon admission. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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12 pages, 1246 KiB

Open AccessArticle

Analysis of the Frequency of Mutations at Diagnostic Oligonucleotide Sites and Their Impact on the Efficiency of PCR for HIV-1

by Elena V. Bogoslovskaya, Galina M. Tsyganova, Anastasiia O. Nosova and German A. Shipulin

Microorganisms 2023, 11(12), 2838; https://doi.org/10.3390/microorganisms11122838 - 22 Nov 2023

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Abstract

The development of effective diagnostic kits for HIV-1 remains a pressing concern. We designed diagnostic oligonucleotides for HIV-1 real-time PCR to target the most conserved region of the HIV-1 genome and assessed the mutation frequency at annealing sites. Two databases of nucleotide sequences, [...] Read more.

The development of effective diagnostic kits for HIV-1 remains a pressing concern. We designed diagnostic oligonucleotides for HIV-1 real-time PCR to target the most conserved region of the HIV-1 genome and assessed the mutation frequency at annealing sites. Two databases of nucleotide sequences, Los Alamos and NCBI, were analyzed, revealing that more than 99% of the sequences either lack mutations or contain 1–2 mutations at the binding site of the forward and reverse primers. Additionally, 98.5% of the sequences either lack mutations or contain 1–2 mutations at the binding site of the TaqMan probe. To evaluate the efficiency of primers and the probe in real-time PCR in the case of mutations at their binding sites, we constructed several plasmids containing the most common mutations and, in a model experiment, showed how different mutations affect the efficiency of PCR. Our analysis demonstrated that about 98.5% of HIV-1 strains can be efficiently detected using a single pair of selected primers. For the remaining 1.5% of strains, a more careful selection of the second target is needed. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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17 pages, 6217 KiB

Open AccessArticle

Comparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen

by José R. Aguirre-Sánchez, Beatriz Quiñones, José A. Ortiz-Muñoz, Rogelio Prieto-Alvarado, Inés F. Vega-López, Jaime Martínez-Urtaza, Bertram G. Lee and Cristóbal Chaidez

Microorganisms 2023, 11(8), 2114; https://doi.org/10.3390/microorganisms11082114 - 19 Aug 2023

Cited by 1 | Viewed by 1755

Abstract

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and [...] Read more.

Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes’ presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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12 pages, 347 KiB

Open AccessArticle

Characterization of Food Chain Clostridioides difficile Isolates in Terms of Ribotype and Antimicrobial Resistance

by Pilar Marcos, Aoife Doyle, Paul Whyte, Thomas R. Rogers, Máire McElroy, Seamus Fanning, Jesus Frias and Declan Bolton

Microorganisms 2023, 11(5), 1296; https://doi.org/10.3390/microorganisms11051296 - 16 May 2023

Cited by 1 | Viewed by 1396

Abstract

The aim of this study was to characterize C. difficile isolates from the farm, abattoir, and retail outlets in Ireland in terms of ribotype and antibiotic resistance (vancomycin, erythromycin, metronidazole, moxifloxacin, clindamycin, and rifampicin) using PCR and E-test methods, respectively. The most common [...] Read more.

The aim of this study was to characterize C. difficile isolates from the farm, abattoir, and retail outlets in Ireland in terms of ribotype and antibiotic resistance (vancomycin, erythromycin, metronidazole, moxifloxacin, clindamycin, and rifampicin) using PCR and E-test methods, respectively. The most common ribotype in all stages of the food chain (including retail foods) was 078 and a variant (RT078/4). Less commonly reported (014/0, 002/1, 049, and 205) and novel (RT530, 547, and 683) ribotypes were also detected, but at lower frequencies. Approximately 72% (26/36 tested) of the isolates tested were resistant to at least one antibiotic, with the majority of these (65%; 17/26) displaying a multi-drug (three to five antibiotics) resistant phenotype. It was concluded that ribotype 078, a hypervirulent strain commonly associated with C. difficile infection (CDI) in Ireland, was the most frequent ribotype along the food chain, resistance to clinically important antibiotics was common in C. difficile food chain isolates, and there was no relationship between ribotype and antibiotic resistance profile. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

16 pages, 5218 KiB

Open AccessArticle

Molecular Characterization of Dengue Virus Strains from the 2019–2020 Epidemic in Hanoi, Vietnam

by Juthamas Phadungsombat, Huong Thi Thu Vu, Quynh Thi Nguyen, Ha Thi Van Nguyen, Ha Thi Nhu Nguyen, Bich Thi Dang, Emi E. Nakayama, Azumi Ishizaki, Hiroshi Ichimura, Tatsuo Shioda and Thach Ngoc Pham

Microorganisms 2023, 11(5), 1267; https://doi.org/10.3390/microorganisms11051267 - 11 May 2023

Cited by 2 | Viewed by 1777

Abstract

Dengue virus (DENV), which has circulated in Vietnam for several decades, has multiple serotypes and genotypes. A 2019 dengue outbreak resulted in a larger number of cases than any other outbreak. We conducted a molecular characterization using samples collected in 2019–2020 from dengue [...] Read more.

Dengue virus (DENV), which has circulated in Vietnam for several decades, has multiple serotypes and genotypes. A 2019 dengue outbreak resulted in a larger number of cases than any other outbreak. We conducted a molecular characterization using samples collected in 2019–2020 from dengue patients in Hanoi and nearby cities located in northern Vietnam. The circulating serotypes were DENV-1 (25%, n = 22) and DENV-2 (73%, n = 64). Phylogenetic analyses revealed that all DENV-1 (n = 13) were genotype I and clustered to local strains circulating during the previous outbreak in the 2017, whereas DENV-2 consisted of two genotypes: Asian-I (n = 5), related to local strains from 2006–2022, and cosmopolitan (n = 18), the predominant genotype in this epidemic. The current cosmopolitan virus was identified as having an Asian-Pacific lineage. The virus was closely related to strains in other recent outbreaks in Southeast Asian countries and China. Multiple introductions occurred in 2016–2017, which were possibly from maritime Southeast Asia (Indonesia, Singapore, and Malaysia), mainland Southeast Asia (Cambodia and Thailand), or China, rather than from an expansion of localized Vietnamese cosmopolitan strains that were previously detected in the 2000s. We also analyzed the genetic relationship between Vietnam’s cosmopolitan strain and recent global strains reported from Asia, Oceania, Africa, and South America. This analysis revealed that viruses of Asian-Pacific lineage are not restricted to Asia but have spread to Peru and Brazil in South America. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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19 pages, 5381 KiB

Open AccessArticle

Multiplexed Reverse Transcription Loop-Mediated Isothermal Amplification Coupled with a Nucleic Acid-Based Lateral Flow Dipstick as a Rapid Diagnostic Method to Detect SARS-CoV-2

by Derich Shalbie Simon, Chee-Wei Yew and Vijay Subbiah Kumar

Microorganisms 2023, 11(5), 1233; https://doi.org/10.3390/microorganisms11051233 - 07 May 2023

Cited by 2 | Viewed by 2054

Abstract

Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates [...] Read more.

Due to the high reproduction rate of COVID-19, it is important to identify and isolate infected patients at the early stages of infection. The limitations of current diagnostic methods are speed, cost, and accuracy. Furthermore, new viral variants have emerged with higher rates of infectivity and mortality, many with mutations at various primer binding sites, which may evade detection via conventional PCR kits. Therefore, a rapid method that is sensitive, specific, and cost-effective is needed for a point-of-care molecular test. Accordingly, we developed a rapid molecular SARS-CoV-2 detection kit with high specificity and sensitivity, RT-PCR, taking advantage of the loop-mediated isothermal amplification (LAMP) technique. Four sets of six primers were designed based on conserved regions of the SARS-CoV-2 genome: two outer, two inner and two loop primers. Using the optimized protocol, SARS-CoV-2 genes were detected as quickly as 10 min but were most sensitive at 30 min, detecting as little as 100 copies of template DNA. We then coupled the RT-LAMP with a lateral flow dipstick (LFD) for multiplex detection. The LFD could detect two genic amplifications on a single strip, making it suitable for multiplexed detection. The development of a multiplexed RT-LAMP-LFD reaction on crude VTM samples would be suitable for the point-of-care diagnosis of COVID-19 in diagnostic laboratories as well as in private homes. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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13 pages, 1956 KiB

Open AccessArticle

Comparative Evaluation of the Activity of Various Lentiviral Vectors Containing Three Anti-HIV Genes

by Olga Vladimirovna Orlova, Dina Viktorovna Glazkova, Ramil Rafailovich Mintaev, Galina Mikhailovna Tsyganova, Felix Anatolevich Urusov, German Alexandrovich Shipulin and Elena Vladimirovna Bogoslovskaya

Microorganisms 2023, 11(4), 1053; https://doi.org/10.3390/microorganisms11041053 - 18 Apr 2023

Viewed by 1185

Abstract

A promising direction in the treatment of HIV infection is a gene therapy approach based on the insertion of antiviral genes aimed at inhibiting HIV replication into the genome of host cells. We obtained six constructs of lentiviral vectors with different arrangements of [...] Read more.

A promising direction in the treatment of HIV infection is a gene therapy approach based on the insertion of antiviral genes aimed at inhibiting HIV replication into the genome of host cells. We obtained six constructs of lentiviral vectors with different arrangements of three antiviral genes: microRNAs against the CCR5 gene, the gene encoding the C-peptide, and the gene encoding the modified human TRIM5a protein. We found that despite containing the same genes, these vectors were produced at different titers and had different effects on cell viability, transduction efficiency, and expression stability. Comparative evaluation of the antiviral activity of three of the six developed vectors that showed stable expression was carried out using the continuous SupT1 lymphocytic cell line. All of the vectors protected cells from HIV infection: the viral load was several orders of magnitude lower than in control cells, and with one vector, complete cessation of virus growth in modified cells was achieved. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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14 pages, 2247 KiB

Open AccessArticle

Capture ELISA for KPC Detection in Gram-Negative Bacilli: Development and Standardisation

by André Valencio, Miriam Aparecida da Silva, Fernanda Fernandes Santos, Juliana Moutinho Polatto, Marcelo Marcondes Ferreira Machado, Roxane Maria Fontes Piazza and Ana Cristina Gales

Microorganisms 2023, 11(4), 1052; https://doi.org/10.3390/microorganisms11041052 - 18 Apr 2023

Cited by 2 | Viewed by 1057

Abstract

The detection of KPC-type carbapenemases is necessary for guiding appropriate antibiotic therapy and the implementation of antimicrobial stewardship and infection control measures. Currently, few tests are capable of differentiating carbapenemase types, restricting the lab reports to their presence or not. The aim of [...] Read more.

The detection of KPC-type carbapenemases is necessary for guiding appropriate antibiotic therapy and the implementation of antimicrobial stewardship and infection control measures. Currently, few tests are capable of differentiating carbapenemase types, restricting the lab reports to their presence or not. The aim of this work was to raise antibodies and develop an ELISA test to detect KPC-2 and its D179 mutants. The ELISA-KPC test was designed using rabbit and mouse polyclonal antibodies. Four different protocols were tested to select the bacterial inoculum with the highest sensitivity and specificity rates. The standardisation procedure was performed using 109 previously characterised clinical isolates, showing 100% of sensitivity and 89% of specificity. The ELISA-KPC detected all isolates producing carbapenemases, including KPC variants displaying the ESBL phenotype such as KPC-33 and -66. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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17 pages, 6447 KiB

Open AccessArticle

PreS1 Containing HBc VLPs for the Development of a Combined Therapeutic/Prophylactic Hepatitis B Vaccine

by Andris Dishlers, Ivars Petrovskis, Dace Skrastina, Ieva Zarina, Ilva Lieknina, Juris Jansons, Inara Akopjana, Jelena Zakova, Velta Ose and Irina Sominskaya

Microorganisms 2023, 11(4), 972; https://doi.org/10.3390/microorganisms11040972 - 08 Apr 2023

Cited by 3 | Viewed by 1524

Abstract

The available HBV vaccines based on the HBV surface protein are manufactured in yeasts and demonstrate excellent prophylactic but no therapeutic activity and are thus ineffective against chronic HBV infection. Five different HBV core proteins (HBc)—full length and C-terminally truncated—were used for the [...] Read more.

The available HBV vaccines based on the HBV surface protein are manufactured in yeasts and demonstrate excellent prophylactic but no therapeutic activity and are thus ineffective against chronic HBV infection. Five different HBV core proteins (HBc)—full length and C-terminally truncated—were used for the insertion of the short, preS1,aa 20–47 and long, preS1phil, aa 12–60 + 89–119 fragments. Modified virus-like particles (VLPs) were compared for their biotechnological and immunological properties. The expression level of HBc-preS1 proteins was high for all investigated proteins, allowing us to obtain 10–20 mg of purified VLPs from a gram of biomass with the combination of gel filtration and ion-exchange chromatography to reach approximately 90% purity of target proteins. The immunogenicity of chimeric VLPs was tested in BALB/c mice, showing a high anti-preS1 response and substantial T-cell proliferation after stimulation with HBc protein. Targeted incorporation of oligonucleotide ODN 1668 in modified HBc-preS1 VLPs was demonstrated. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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11 pages, 778 KiB

Open AccessArticle

Assessment of New and Genome-Reduced Pseudomonas Strains Regarding Their Robustness as Chassis in Biotechnological Applications

by María José Cárdenas Espinosa, Tabea Schmidgall, Jessica Pohl, Georg Wagner, Benedikt Wynands, Nick Wierckx, Hermann J. Heipieper and Christian Eberlein

Microorganisms 2023, 11(4), 837; https://doi.org/10.3390/microorganisms11040837 - 25 Mar 2023

Cited by 3 | Viewed by 1687

Abstract

Organic olvent-tolerant strains of the Gram-negative bacterial genus Pseudomonas are discussed as potential biocatalysts for the biotechnological production of various chemicals. However, many current strains with the highest tolerance are belonging to the species P. putida and are classified as biosafety level 2 [...] Read more.

Organic olvent-tolerant strains of the Gram-negative bacterial genus Pseudomonas are discussed as potential biocatalysts for the biotechnological production of various chemicals. However, many current strains with the highest tolerance are belonging to the species P. putida and are classified as biosafety level 2 strains, which makes them uninteresting for the biotechnological industry. Therefore, it is necessary to identify other biosafety level 1 Pseudomonas strains with high tolerance towards solvents and other forms of stress, which are suitable for establishing production platforms of biotechnological processes. In order to exploit the native potential of Pseudomonas as a microbial cell factory, the biosafety level 1 strain P. taiwanensis VLB120 and its genome-reduced chassis (GRC) variants as well as the plastic-degrading strain P. capeferrum TDA1 were assessed regarding their tolerance towards different n-alkanols (1-butanol, 1-hexanol, 1-octanol, 1-decanol). Toxicity of the solvents was investigated by their effects on bacterial growth rates given as the EC50 concentrations. Hereby, both toxicities as well as the adaptive responses of P. taiwanensis GRC3 and P. capeferrum TDA1 showed EC50 values up to two-fold higher than those previously detected for P. putida DOT-T1E (biosafety level 2), one of the best described solvent-tolerant bacteria. Furthermore, in two-phase solvent systems, all the evaluated strains were adapted to 1-decanol as a second organic phase (i.e., OD₅₆₀ was at least 0.5 after 24 h of incubation with 1% (v/v) 1-decanol), which shows the potential use of these strains as platforms for the bio-production of a wide variety of chemicals at industrial level. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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14 pages, 6331 KiB

Open AccessArticle

Knocking Down Gm16685 Decreases Liver Granuloma in Murine Schistosomiasis Japonica

by Ruyu Zhao, Xiaoxue Tang, Huiyao Lin, Chen Xing, Na Xu, Bingxin Dai, Pingping Wang, Wei Shao, Miao Liu, Jijia Shen, Shengqun Deng and Cuiping Ren

Microorganisms 2023, 11(3), 796; https://doi.org/10.3390/microorganisms11030796 - 21 Mar 2023

Cited by 1 | Viewed by 1405

Abstract

Long noncoding RNAs (lncRNAs) can regulate key genes and pathways in liver disease development. Moreover, macrophages are speculated to play an important role in regulating granulomatous inflammation during schistosomiasis. However, the role of lncRNAs in the formation of liver granulomas by influencing the [...] Read more.

Long noncoding RNAs (lncRNAs) can regulate key genes and pathways in liver disease development. Moreover, macrophages are speculated to play an important role in regulating granulomatous inflammation during schistosomiasis. However, the role of lncRNAs in the formation of liver granulomas by influencing the polarization of macrophages in Schistosoma japonicum infection is unclear. Our study aimed to determine whether lncRNAs can play a role in S. japonicum-induced hepatic egg granulomas and elucidate their effect on macrophages. We established S. japonicum infection models and screened the target lncRNA Gm16685 highly expressed in schistosomiasis mice using high-throughput sequencing. Hematoxylin and eosin staining revealed that the knockdown of Gm16685 reduced the area of egg granulomas. Moreover, M1 macrophage factor genes were significantly downregulated in Gm16685 knockdown livers. Meanwhile, M2 macrophage factor genes were significantly upregulated, which was consistent with the protein detection results. Hepatocytes, hepatic stellate cells, and macrophages were isolated from mouse models infected with S. japonicum, with Gm16685 being significantly upregulated in macrophages. Moreover, the knockdown of Gm16685 in RAW264.7 cells revealed similar results to in liver tissue. RNA fluorescence in situ hybridization (FISH) and nucleocytoplasmic separation experiments revealed that Gm16685 was predominantly localized in the cytoplasm of cells. We found that miR-205-5p was upregulated after Gm16685 was knocked down. After overexpression of miR-205-5p, the expression of Gm16685 and inflammatory factors was significantly downregulated. These results indicate that Gm16685 can participate in the pathogenesis of hepatic disease in schistosomiasis and promote M1 macrophage polarization by regulating miR-205-5p. Thus, our study may provide a new target for schistosomiasis japonica treatment. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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14 pages, 3187 KiB

Open AccessArticle

LncRNA 8244-ssc-miR-320-CCR7 Regulates IFN-β during SVA Infecting PK-15 Cells

by Xiaoyu Tang, Ruiyu Zhang, Long Gao, Xiaocheng Lv, Yuan Sun and Jingyun Ma

Microorganisms 2023, 11(3), 688; https://doi.org/10.3390/microorganisms11030688 - 08 Mar 2023

Cited by 1 | Viewed by 1218

Abstract

Seneca Valley virus (SVV), a member of the Picornaviridae family, is an oncolytic RNA virus that can cause idiopathic vesicular disease and increase mortality in newborn piglets. Although research on the pathogenic characteristics, epidemiology, pathogenic mechanism, and clinical diagnosis of SVA has increased [...] Read more.

Seneca Valley virus (SVV), a member of the Picornaviridae family, is an oncolytic RNA virus that can cause idiopathic vesicular disease and increase mortality in newborn piglets. Although research on the pathogenic characteristics, epidemiology, pathogenic mechanism, and clinical diagnosis of SVA has increased due to its emergence and prevalence, the interaction between SVA and its host lncRNA has not been fully studied. This study used qualcomm sequencing to analyze differentially expressed lncRNAs and found that during SVA infection, lncRNA 8244 was significantly down-regulated in both PK-15 cells and piglets. Further analysis through quantitative real-time PCR and dual luciferase experiments demonstrated that lncRNA8244 could compete with ssc-miR-320 to regulate the expression of CCR7. The lncRNA824-ssc-miR-320-CCR7 axis activated the TLR-mediated signaling pathway, which recognized viral molecules and induced the expression of IFN-β. These findings provide new insight into the interaction between lncRNA and SVA infection, which could lead to a better understanding of SVA pathogenesis and contribute to the prevention and control of SVA disease. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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16 pages, 3353 KiB

Open AccessArticle

IL-27 Signaling Promotes Th1 Response by Downregulating IL-10 Production in DCs during Chlamydial Respiratory Infection

by Jiajia Zeng, Shuaini Yang, Yuqing Tuo, Xiaoyu Zha, Ruoyuan Sun, Tingsha Lu, Hong Zhang, Lu Tan, Sai Qiao and Hong Bai

Microorganisms 2023, 11(3), 604; https://doi.org/10.3390/microorganisms11030604 - 27 Feb 2023

Cited by 2 | Viewed by 1259

Abstract

Chlamydia trachomatis usually causes mucosal infections, bringing considerable morbidity and socioeconomic burden worldwide. We previously revealed that IL-27/IL-27R mediates protection against chlamydial invasion by promoting a protective Th1 response and suppressing neutrophilic inflammation. Here, we used the mouse model of Chlamydia muridarum ( [...] Read more.

Chlamydia trachomatis usually causes mucosal infections, bringing considerable morbidity and socioeconomic burden worldwide. We previously revealed that IL-27/IL-27R mediates protection against chlamydial invasion by promoting a protective Th1 response and suppressing neutrophilic inflammation. Here, we used the mouse model of Chlamydia muridarum (C. muridarum) respiratory infections to further investigate the impact of IL-27 signaling in the DCs-regulated immune response, since an elevated IL-27/IL-27R expression in DCs was identified following chlamydial infection. An adoptive transfer of Chlamydia muridarum-stimulated DCs to wild-type mice approach was subsequently used, and the donor-DCs-promoted resistance with a higher Th1 response against chlamydial infection was attenuated when DCs lacking IL-27R were used as donor cells. Flow cytometry analysis revealed the suppression of IL-27 signaling on DCs phenotypic maturation. A further functional maturation analysis of DCs revealed that IL-27 signaling restricted the protein and mRNA expression of IL-10 from DCs following infection. Thus, these findings suggest that IL-27 signaling could support the Th1 response via inhibiting IL-10 production in DCs, thus mediating the protective host defense against chlamydial respiratory infection. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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19 pages, 20752 KiB

Open AccessArticle

Combined Analysis of the Whole Transcriptome of Piglets Infected with SADS−CoV Virulent and Avirulent Strains

by Qianniu Li, Xiaoyu Tang, Ling Zhou, Xiaocheng Lv, Long Gao, Tian Lan, Yuan Sun and Jingyun Ma

Microorganisms 2023, 11(2), 409; https://doi.org/10.3390/microorganisms11020409 - 06 Feb 2023

Viewed by 1367

Abstract

When piglets are infected by virulent and avirulent strains of swine acute diarrhea syndrome coronavirus (SADS−CoV), there are obvious differences in their clinical symptoms; however, the specific mechanisms of pathogenicity and the immune regulation of highly pathogenic and low pathogenic strains are unknown. [...] Read more.

When piglets are infected by virulent and avirulent strains of swine acute diarrhea syndrome coronavirus (SADS−CoV), there are obvious differences in their clinical symptoms; however, the specific mechanisms of pathogenicity and the immune regulation of highly pathogenic and low pathogenic strains are unknown. We collected intestinal tissues from SADS−CoV−infected piglets, performed a whole transcriptome sequencing analysis, including mRNA, miRNA, lncRNA, cicrRNA, and TUCP, and performed functional and correlation analyses of differentially expressed RNAs. Our results showed that the differentially expressed RNAs in group A versus group B (AvsB), group A versus group C (AvsC), and group B versus group C (BvsC) were relevant to immune and disease−related signaling pathways that participate in the organisms’ viral infection and immune regulation. Furthermore, data obtained from the HAllA analysis suggested that there was a strong correlation between the differentially expressed RNAs. Specifically, LNC_011487 in the P set was significantly negatively correlated with ssc−miR−215, and LNC_011487 was positively correlated with PI3. Moreover, we also constructed a differentially expressed RNA association network map. This study provides a valuable resource for studying the SADS−CoV transcriptome and pathogenic mechanism from the perspective of RNA to understand the differences in and consistency of the interaction between virulent and attenuated SADS−CoV strains and hosts. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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Review

Jump to: Editorial, Research, Other

19 pages, 2206 KiB

Open AccessReview

Dynamics of Hepatitis B Virus Covalently Closed Circular DNA: A Mini-Review

by Jie-Li Hu and Ai-Long Huang

Microorganisms 2023, 11(3), 600; https://doi.org/10.3390/microorganisms11030600 - 27 Feb 2023

Cited by 2 | Viewed by 2638

Abstract

Eradication of cccDNA is an ideal goal of chronic hepatitis B (CHB) therapy. Understanding the changes in the cccDNA pool during therapy provides a basis for developing CHB treatment strategies. On the other hand, the shift in the balance of the cccDNA pool [...] Read more.

Eradication of cccDNA is an ideal goal of chronic hepatitis B (CHB) therapy. Understanding the changes in the cccDNA pool during therapy provides a basis for developing CHB treatment strategies. On the other hand, the shift in the balance of the cccDNA pool following therapies allowed researchers to investigate the dynamics of cccDNA. Central to the description of cccDNA dynamics is a parameter called cccDNA half-life. CccDNA half-life is not an intrinsic property of cccDNA molecules, but a description of an observed phenomenon characterized by cccDNA pool decline. Since cccDNA has to be in the nuclei of host cells to function, the half-life of cccDNA is determined by the state and destiny of the host cells. The major factors that drive cccDNA decay include noncytopathic effects and hepatocyte turnover (death and division). In some cases, the determining factor is not the half-life of cccDNA itself, but rather the half-life of the hepatocyte. The main purpose of this review is to analyze the major factors affecting cccDNA half-life and determine the areas requiring further study. In addition, the discrepancy in cccDNA half-life between short-term and long-term nucleot(s)ide analog (NUC) therapy was reported. Hypotheses were proposed to explain the multi-phasic decline of cccDNA during NUC therapy, and a framework based on cccDNA dynamics was suggested for the consideration of various anti-HBV strategies. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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17 pages, 3861 KiB

Open AccessReview

Current Methods for the Detection of Antibodies of Varicella-Zoster Virus: A Review

by Dequan Pan, Wei Wang and Tong Cheng

Microorganisms 2023, 11(2), 519; https://doi.org/10.3390/microorganisms11020519 - 17 Feb 2023

Cited by 3 | Viewed by 4548

Abstract

Infection with the varicella-zoster virus (VZV) causes chickenpox and shingles, which lead to significant morbidity and mortality globally. The detection of serum VZV-specific antibodies is important for the clinical diagnosis and sero-epidemiological research of VZV infection, and for assessing the effect of VZV [...] Read more.

Infection with the varicella-zoster virus (VZV) causes chickenpox and shingles, which lead to significant morbidity and mortality globally. The detection of serum VZV-specific antibodies is important for the clinical diagnosis and sero-epidemiological research of VZV infection, and for assessing the effect of VZV vaccine immunization. Over recent decades, a variety of methods for VZV antibody detection have been developed. This review summarizes and compares the current methods for detecting VZV antibodies, and discussed future directions for this field. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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Open AccessReview

Drug Reaction with Eosinophilia and Systemic Symptoms (DRESS): Focus on the Pathophysiological and Diagnostic Role of Viruses

by Giuseppe A. Ramirez, Marco Ripa, Samuele Burastero, Giovanni Benanti, Diego Bagnasco, Serena Nannipieri, Roberta Monardo, Giacomo Ponta, Chiara Asperti, Maria Bernadette Cilona, Antonella Castagna, Lorenzo Dagna and Mona-Rita Yacoub

Microorganisms 2023, 11(2), 346; https://doi.org/10.3390/microorganisms11020346 - 30 Jan 2023

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Abstract

Drug reaction with eosinophilia and systemic symptoms (DRESS) is a heterogeneous, multiorgan and potentially life-threatening drug-hypersensitivity reaction (DHR) that occurs several days or weeks after drug initiation or discontinuation. DHRs constitute an emerging issue for public health, due to population aging, growing multi-organ [...] Read more.

Drug reaction with eosinophilia and systemic symptoms (DRESS) is a heterogeneous, multiorgan and potentially life-threatening drug-hypersensitivity reaction (DHR) that occurs several days or weeks after drug initiation or discontinuation. DHRs constitute an emerging issue for public health, due to population aging, growing multi-organ morbidity, and subsequent enhanced drug prescriptions. DRESS has more consistently been associated with anticonvulsants, allopurinol and antibiotics, such as sulphonamides and vancomycin, although new drugs are increasingly reported as culprit agents. Reactivation of latent infectious agents such as viruses (especially Herpesviridae) plays a key role in prompting and sustaining aberrant T-cell and eosinophil responses to drugs and pathogens, ultimately causing organ damage. However, the boundaries of the impact of viral agents in the pathophysiology of DRESS are still ill-defined. Along with growing awareness of the multifaceted aspects of immune perturbation caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the ongoing SARS-CoV-2-related disease (COVID-19) pandemic, novel interest has been sparked towards DRESS and the potential interactions among antiviral and anti-drug inflammatory responses. In this review, we summarised the most recent evidence on pathophysiological mechanisms, diagnostic approaches, and clinical management of DRESS with the aim of increasing awareness on this syndrome and possibly suggesting clues for future research in this field. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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Open AccessSystematic Review

Biomarkers Correlated with Tuberculosis Preventive Treatment Response: A Systematic Review and Meta-Analysis

by Haoran Zhang, Zuyu Sun, Yi Liu, Rongrong Wei and Nanying Che

Microorganisms 2023, 11(3), 743; https://doi.org/10.3390/microorganisms11030743 - 14 Mar 2023

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Abstract

Background: There is a need to identify alternative biomarkers to predict tuberculosis (TB) preventive treatment response because observing the incidence decline renders a long follow-up period. Methods: We searched PubMed, Embase and Web of Science up to 9 February 2023. The biomarker levels [...] Read more.

Background: There is a need to identify alternative biomarkers to predict tuberculosis (TB) preventive treatment response because observing the incidence decline renders a long follow-up period. Methods: We searched PubMed, Embase and Web of Science up to 9 February 2023. The biomarker levels during preventive treatment were quantitatively summarized by means of meta-analysis using the random-effect model. Results: Eleven eligible studies, published during 2006–2022, were included in the meta-analysis, with frequently heterogeneous results. Twenty-six biomarkers or testing methods were identified regarding TB preventive treatment monitoring. The summarized standard mean differences of interferon-γ (INF-γ) were −1.44 (95% CI: −1.85, −1.03) among those who completed preventive treatment (τ² = 0.21; I² = 95.2%, p < 0.001) and −0.49 (95% CI: −1.05, 0.06) for those without preventive treatment (τ² = 0.13; I² = 82.0%, p < 0.001), respectively. Subgroup analysis showed that the INF-γ level after treatment decreased significantly from baseline among studies with high TB burden (−0.98, 95% CI: −1.21, −0.75) and among those with a history of Bacillus Calmette–Guérin vaccination (−0.87, 95% CI: −1.10, −0.63). Conclusions: Our results suggested that decreased INF-γ was observed among those who completed preventive treatment but not in those without preventive treatment. Further studies are warranted to explore its value in preventive treatment monitoring due to limited available data and extensive between-study heterogeneity. Full article

(This article belongs to the Special Issue Diagnosis, Characterization and Treatment of Emerging Pathogens)

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