Pathogens

30 pages, 361 KiB

Open AccessReview

Risk of Venous Thromboembolism in Infectious Diseases: A Literature Review

by Ilaria Pati, Francesca Masiello, Vanessa Piccinini, Lucia De Fulvio, Maria Simona Massari, Vincenzo De Angelis and Mario Cruciani

Pathogens 2025, 14(8), 816; https://doi.org/10.3390/pathogens14080816 (registering DOI) - 18 Aug 2025

Abstract

Systemic or localized infections increase the risk of venous thromboembolism (VTE). All types of infection can elevate the risk of VTE thrombosis, although some appear to increase risk more than others. In the current narrative review, we seek to overview the available evidence [...] Read more.

Systemic or localized infections increase the risk of venous thromboembolism (VTE). All types of infection can elevate the risk of VTE thrombosis, although some appear to increase risk more than others. In the current narrative review, we seek to overview the available evidence related to the epidemiology of VTE caused by infections. We focused on patients with infection in community setting or hospitalized, on patients with COVID-19, HIV infection, tuberculosis, HCV infection, and CMV infection, as well as on individuals with other types of infection that might increase the risk of VTE. Moreover, we tried to evaluate how the risk of VTE in person with different types of infections could be addressed in clinical practice with the use of anticoagulants. Extended VTE prophylaxis may not be warranted for all infections, but may be very helpful for some, such as those with intra-abdominal infection, systemic bloodstream infection, lower respiratory infection, and symptomatic urinary tract infection. Full article

21 pages, 4238 KiB

Open AccessArticle

Relationship Between Cell Surface Viral Glycoprotein Expression and Resistance of Parainfluenza Virus Persistently Infected Cells to Complement-Mediated Lysis

by Nasser N. Yousef and Griffith D. Parks

Pathogens 2025, 14(8), 815; https://doi.org/10.3390/pathogens14080815 (registering DOI) - 17 Aug 2025

Abstract

Persistent RNA virus infections (PI) are often characterized by extended viral shedding and maintained cycles of inflammation. The innate immune Complement (C′) pathways can recognize acute infected (AI) cells and result in their lysis, but the relative sensitivity of PI cells to C′-directed [...] Read more.

Persistent RNA virus infections (PI) are often characterized by extended viral shedding and maintained cycles of inflammation. The innate immune Complement (C′) pathways can recognize acute infected (AI) cells and result in their lysis, but the relative sensitivity of PI cells to C′-directed killing is incompletely understood. Here, we extended our previous studies on the interactions of C′ with parainfluenza virus AI and PI A549 cells to two additional respiratory tract cell lines. AI Hep2 and H1975 cells infected with Parainfluenza virus 5 (PIV5) were found to be highly sensitive to C′ lysis. By contrast, PIV5 PI cells were highly resistant to killing by C″. Surface deposition of membrane attack complex (MAC) and C3 was also greatly reduced on the surface of PI cells compared to AI cells. PI cells had lower levels of surface viral glycoprotein expression compared to AI cells. Treatment of AI cells with ribavirin (RBV) showed a dose-dependent decrease in both viral glycoprotein expression and sensitivity to C′-mediated lysis. When surface viral glycoprotein levels were reduced in AI cells to those in PI cells, AI cells became similarly resistant to C′. While sialic acid levels on PI cell surfaces matched that of naïve cells, enzymatic removal of this sialic acid did not increase sensitivity to C′-mediated lysis. Despite their varying profiles of C′ activation and deposition, these studies indicate downregulation of viral gene expression as a common mechanism of C′ resistance across various parainfluenza virus PI cell lines. Full article

(This article belongs to the Special Issue Virus–Host Cell Interactions and Research of New Antivirals)

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10 pages, 1184 KiB

Open AccessArticle

Differential Exposure to Borrelia spp. and Spotted Fever Group Rickettsia in Serbia and North Macedonia: A Comparative Study

by Dejan Jakimovski, Sofija Mateska, Marija Najdovska, Angela Stamenkovska, Verica Pavleva, Mile Bosilkovski, Dragana Mijatović, Verica Simin, Ivana Bogdan, Jasmina Grujić, Milica Simeunović, Miodrag Vranješ, Eleftherios Meletis, Polychronis Kostoulas, Olympia Lioupi and Pavle Banović

Pathogens 2025, 14(8), 814; https://doi.org/10.3390/pathogens14080814 (registering DOI) - 17 Aug 2025

Abstract

Several diseases caused by tick-borne pathogens, including Lyme borreliosis (LB) and spotted fever group rickettsioses, are endemic in the Balkan Peninsula, positioned between Central Europe and the Middle East. This cross-sectional study aimed to assess serological exposure to Borrelia spp. and spotted fever [...] Read more.

Several diseases caused by tick-borne pathogens, including Lyme borreliosis (LB) and spotted fever group rickettsioses, are endemic in the Balkan Peninsula, positioned between Central Europe and the Middle East. This cross-sectional study aimed to assess serological exposure to Borrelia spp. and spotted fever group Rickettsiae (SFGR) among individuals with recent tick bites and healthy controls in two Balkan countries—Serbia and North Macedonia. Serum samples from 223 participants were tested for anti-Borrelia and anti-SFGR IgG antibodies. SFGR exposure was significantly higher in tick-exposed individuals from Skopje (North Macedonia) compared to those from Novi Sad (Serbia) (30.9% vs. 8.0%; p = 0.003). In contrast, anti-Borrelia IgG was more frequently detected in Novi Sad, though differences did not reach statistical significance. The findings support a north-to-south gradient in Borrelia exposure and a reverse trend for SFGR, consistent with earlier studies and regional tick infection data. Given the high SFGR exposure and limited clinical reporting in North Macedonia, the results highlight the likelihood that tick-borne rickettsioses remain under-recognized. Additionally, Borrelia exposure in North Macedonia warrants further investigation. These findings emphasize the need for enhanced tick-borne disease surveillance, identification of endemic zones, and improved diagnostic and public health infrastructure in both countries. Full article

(This article belongs to the Section Ticks)

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17 pages, 1502 KiB

Open AccessReview

Perspectives on the History and Epidemiology of the Varicella Virus Vaccine and Future Challenges

by Masayuki Nagasawa

Pathogens 2025, 14(8), 813; https://doi.org/10.3390/pathogens14080813 (registering DOI) - 16 Aug 2025

Abstract

The varicella attenuated virus vaccine, developed in Japan in the 1970s, has dramatically reduced the number of pediatric chickenpox cases over the past 30 years due to its widespread use. However, a small number of cases of chickenpox, shingles, aseptic meningitis, and acute [...] Read more.

The varicella attenuated virus vaccine, developed in Japan in the 1970s, has dramatically reduced the number of pediatric chickenpox cases over the past 30 years due to its widespread use. However, a small number of cases of chickenpox, shingles, aseptic meningitis, and acute retinal necrosis caused by vaccine strains have been reported. There are also issues that need to be addressed, such as breakthrough infections and the persistence of the preventive effect of vaccination. In addition, there is the possibility of the emergence of revertants or mutations in the vaccine strain. In recent years, subunit vaccines have been developed, their immune-stimulating effects have been demonstrated, and they are being applied clinically. In addition, development of an mRNA varicella vaccine is underway. In this review, the history and impact of the varicella vaccine are overviewed, as well as its future challenges. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Human Infectious Diseases)

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14 pages, 2032 KiB

Open AccessArticle

Pandemic Disruptions to Private Pathology Testing Uptake in Australia, 2019–2024

by Melanie Keech, Shane Kavanagh, John Crothers, Liliana Orellana and Catherine M. Bennett

Pathogens 2025, 14(8), 812; https://doi.org/10.3390/pathogens14080812 - 15 Aug 2025

Abstract

A new human pathogen triggering a pandemic can impact health directly through disease resulting from infection and indirectly through health system disruption. The COVID-19 pandemic is hypothesised to have impacted pathology testing by impacting healthcare and pathology operations and reducing healthcare attendance for [...] Read more.

A new human pathogen triggering a pandemic can impact health directly through disease resulting from infection and indirectly through health system disruption. The COVID-19 pandemic is hypothesised to have impacted pathology testing by impacting healthcare and pathology operations and reducing healthcare attendance for fear of infection. The impacts of COVID-19 incidence and pandemic control measures on non-COVID pathology testing were assessed in four Australian states/territories using pathology data (histology, prostate-specific antigen, gynaecological cytology, complete blood count, haemoglobin A1c, and human immunodeficiency virus) from a large national private pathology provider (January 2019–December 2024). Weekly testing volumes from lockdown periods were compared to the equivalent weeks in 2019. All pathology tests demonstrated a substantial decline during the initial national lockdown in March 2020. Subsequent lockdowns were also associated with disruption. For example, complete blood count testing in Victoria was −22% in March 2020 and −5% in the second wave that year. Total annual testing volumes were lower for all tests in 2020 compared to 2019, excluding haemoglobin A1c, and reduced testing persisted through to 2024. The findings indicate substantial and sustained negative pandemic impacts on pathology testing. Reductions in pathology testing signal heightened risk of delayed disease diagnosis, disrupted chronic disease management, and poorer health outcomes. Full article

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6 pages, 168 KiB

Open AccessCommunication

A Cell-Free DNA Plasma Next-Generation Sequencing Test—Is It Worth the Cost?

by Sean Jung, Francesca Torriani, Shira Abeles and Ahnika Kline

Pathogens 2025, 14(8), 811; https://doi.org/10.3390/pathogens14080811 - 15 Aug 2025

Abstract

Background: The Karius Test (KT), a microbial cell-free DNA next-generation sequencing assay, is increasingly utilized in challenging infectious syndromes. However, its real-world clinical utility and cost-effectiveness remain uncertain. Methods: We conducted a retrospective review of 88 KT results from adult patients at UC [...] Read more.

Background: The Karius Test (KT), a microbial cell-free DNA next-generation sequencing assay, is increasingly utilized in challenging infectious syndromes. However, its real-world clinical utility and cost-effectiveness remain uncertain. Methods: We conducted a retrospective review of 88 KT results from adult patients at UC San Diego Health between July 2017 and April 2024. Each case was evaluated for clinical impact using standardized criteria. We analyzed diagnostic yield, turnaround time, number needed to test (NNT), and institutional billing data for reimbursement and cost implications. Results: Of 88 unique tests, forty-nine (55.7%) identified at least one pathogen. Eleven (12.5%) had a positive clinical impact—eight provided the only microbiologic diagnosis, and three were faster than conventional methods. Vascular/graft infections showed the highest yield. Twenty-one tests had a neutral impact; fifty-six showed no clinical benefit. The Median turnaround time was 3 days. The NNT was 6.1 or 2.75 including neutral cases. Cost analysis revealed a substantial financial burden without transparent reimbursement mechanisms in inpatient settings. Conclusion: The KT demonstrates modest clinical utility with noteworthy benefits in select scenarios. Given its high cost and variable impact, we advocate for diagnostic stewardship led by infectious disease specialists to optimize test use and minimize unnecessary expense. Full article

10 pages, 2586 KiB

Open AccessCase Report

Comprehensive Laboratory Analysis of a Scrub Typhus and H1N1 Influenza Co-Infection: A Case Report from Hainan, China

by Siqi Chen, Fahui Wang, Shannan Wu, Yuanze Chen, Yi Niu, Yijia Guo, Dachuan Lin, Xiuji Cui, Ruoyan Peng, Zhao Xu, Biao Wu, Min Liao, Yongguo Du, Liyuan Zhang and Feifei Yin

Pathogens 2025, 14(8), 810; https://doi.org/10.3390/pathogens14080810 - 15 Aug 2025

Abstract

Co-infection of Orientia tsutsugamushi and influenza A virus complicates diagnosis and treatment in endemic regions because of overlapping clinical features and potential synergistic inflammation. We describe a 68-year-old woman from Hainan, China, who presented with five days of high fever (39.2 °C), nonproductive [...] Read more.

Co-infection of Orientia tsutsugamushi and influenza A virus complicates diagnosis and treatment in endemic regions because of overlapping clinical features and potential synergistic inflammation. We describe a 68-year-old woman from Hainan, China, who presented with five days of high fever (39.2 °C), nonproductive cough, eschar formation, lymphadenopathy, cytopenias, elevated liver enzymes, and raised inflammatory markers. On the day of admission, influenza A was confirmed by rapid antigen test and Orientia tsutsugamushi IgM/IgG was detected via colloidal-gold immunochromatography, prompting concurrent oseltamivir and doxycycline therapy. Quantitative PCR on day 2 measured an Orientia tsutsugamushi load of 2.85 × 10⁴ copies/mL (Cq 28.86), and targeted next-generation sequencing on day 3 revealed a high H1N1pdm09 viral burden (>1 × 10⁶ copies/mL) with low-level human herpesvirus 1 co-detection. Nested PCR and Sanger sequencing assigned Orientia tsutsugamushi to the Karp_A lineage and influenza A to clade 6B.1A.5a.2a. The patient defervesced by hospital day 2, laboratory indices normalized by day 3, and radiographic abnormalities resolved by day 6. This first documented Orientia tsutsugamushi–influenza A co-infection in China highlights the value of integrating rapid serology, qPCR quantification, nested PCR genotyping, and tNGS for early, precise dual-pathogen identification. Systematic multi-pathogen screening during overlapping transmission seasons is recommended to guide timely combination therapy and enhance epidemiological surveillance. Full article

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13 pages, 3546 KiB

Open AccessArticle

Ticks of the Genus Amblyomma and Lice of the Genus Eutrichophilus: Potential Vectors of Brazilian Porcupinepox Virus

by Nathana Beatriz Martins, Matias Pablo Juan Szabó, Julio Cesar de Souza Junior, Mario Henrique Alves, Marcio de Barros Bandarra, Paulo Eduardo Brandão and Aline Santana da Hora

Pathogens 2025, 14(8), 809; https://doi.org/10.3390/pathogens14080809 - 15 Aug 2025

Abstract

Brazilian porcupinepox virus (BPoPV) is a recently described pathogen associated with severe cutaneous and systemic disease in Coendou spp. porcupines, posing potential conservation and zoonotic risks. Given the solitary behavior of porcupines and the unclear mechanisms of BPoPV transmission, this study investigated the [...] Read more.

Brazilian porcupinepox virus (BPoPV) is a recently described pathogen associated with severe cutaneous and systemic disease in Coendou spp. porcupines, posing potential conservation and zoonotic risks. Given the solitary behavior of porcupines and the unclear mechanisms of BPoPV transmission, this study investigated the presence of BPoPV DNA in porcupines and their associated ectoparasites (ticks and lice). We analyzed ticks and lice collected from 17 porcupines (C. longicaudatus and C. spinosus), with or without clinical signs of BPoPV infection. Ectoparasites were identified morphologically, separated into distinct pools for ticks and lice by host, and screened by PCR. BPoPV DNA was detected in all symptomatic porcupines and their ectoparasites—including Amblyomma longirostre, A. sculptum ticks, and Eutrichophilus spp. lice—except for one tick pool. Notably, an asymptomatic, BPoPV-negative porcupine harbored A. longirostre ticks that tested positive for the virus. Sequencing confirmed 100% identity with the BPoPV reference strain. These findings suggest that Eutrichophilus lice, A. sculptum, and particularly A. longirostre ticks may play a role in BPoPV transmission. Further studies are needed to elucidate whether these ectoparasites act as biological or mechanical vectors and to assess the zoonotic potential of BPoPV in contact with humans and domestic animals. Full article

(This article belongs to the Special Issue Current Challenges in Veterinary Virology)

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11 pages, 1158 KiB

Open AccessArticle

Can Oral Fluids Replace Nasal Swabs in Swine Influenza A Virus (swIAV) PCR Diagnostics?

by Aleksandra Woźniak, Piotr Cybulski, Pia Ryt-Hansen, Lars Erik Larsen, Kinga Biernacka, Dagmara Miłek and Tomasz Stadejek

Pathogens 2025, 14(8), 808; https://doi.org/10.3390/pathogens14080808 - 14 Aug 2025

Abstract

The diagnosis of swine influenza A virus (swIAV) has to involve laboratory detection, as the clinical signs are not pathognomonic. Nasal swabs (NSs) have been the preferred sample material for swIAV PCR diagnostics, but oral fluid (OF) is a convenient alternative material. In [...] Read more.

The diagnosis of swine influenza A virus (swIAV) has to involve laboratory detection, as the clinical signs are not pathognomonic. Nasal swabs (NSs) have been the preferred sample material for swIAV PCR diagnostics, but oral fluid (OF) is a convenient alternative material. In this study, NSs and OFs from 35 Polish swine herds were collected and tested with real-time RT-PCR in order to assess swIAV circulation patterns in Poland and improve protocols for efficient, non-invasive and cost-effective swIAV surveillance in pig farms. The study showed that the swIAV RNA was detected in 65.7% of the tested farms. In total, 21.2% of NS pools and 48.6% of OF samples were positive for swIAV. The Ct values in NS pools and OFs were similar (p > 0.05), but a significant reduction (p < 0.05) in swIAV prevalence in NSs was observed in nursery pigs from farms applying swIAV vaccinations. Successful subtyping was achieved more effectively with OFs compared to NSs, and the H1avN2 was most prevalent subtype detected. The results emphasized that OF can be useful for monitoring swIAV and subtyping. However, OFs cannot replace NSs, which were more useful in the assessment of the effect of swIAV vaccinations in nursery pigs. Full article

(This article belongs to the Special Issue Emergence and Re-Emergence of Animal Viral Diseases)

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17 pages, 2415 KiB

Open AccessArticle

Dancing with the Dust Devil: Examining the Lung Mycobiome of Sonoran Desert Wild Mammals and the Effect of Coccidioides Presence

by Ana Fabio-Braga, Jaida Salois, Mitchell L. Bryant, Daniel R. Kollath and Bridget Barker

Pathogens 2025, 14(8), 807; https://doi.org/10.3390/pathogens14080807 - 14 Aug 2025

Abstract

Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, Coccidioides can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of Coccidioides-positive and -negative samples obtained from wildlife. If [...] Read more.

Microbiome studies report a decrease in diversity associated with active infections. Under the endozoan hypothesis, Coccidioides can inhabit a host without causing disease. In this study, we describe and compare the lung mycobiome of Coccidioides-positive and -negative samples obtained from wildlife. If Coccidioides is not causing infection, we predict there will be no differences in the mycobiome between positive and negative samples. Lung samples were obtained from mammals previously trapped in Tucson, Arizona, USA (n = 26), and Mesa, Arizona, USA (n = 14). Samples were screened for Coccidioides with CocciDx, and mycobiome was characterized through Illumina-based amplicon sequencing of the internal transcribed spacer 2 (ITS2). We compared alpha and beta diversity of the mycobiome to assess the effects of Coccidioides’ presence and host taxonomy. A greater number of reads were captured from Tucson samples (114,706.4 ± 57,945.8) than from Mesa (384.9 ± 953.5); however, Mesa (16.8 ± 8.8) and Tucson (12 ± 7.8) had a similar number of fungal genera per sample. CocciDx detected Coccidioides in more samples than the ITS2 amplicon sequencing. All samples from Mesa and five from Tucson tested positive for Coccidioides. Therefore, Mesa samples were excluded from statistical analysis. No difference in alpha and beta diversity was associated with Coccidioides presence, which is consistent with the endozoan hypothesis. Host taxonomy had a significant effect on beta diversity. This effect is likely driven by host behavioral and physiological differences. Full article

(This article belongs to the Special Issue Epidemiology and Molecular Detection of Emerging Fungal Pathogens)

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35 pages, 1649 KiB

Open AccessReview

Candidemia: An Update on Epidemiology, Risk Factors, Diagnosis, Susceptibility, and Treatment

by Juan Pablo Cabrera-Guerrero, Eduardo García-Salazar, Graciela Hernandez Silva, Alberto Chinney Herrera, Erick Martínez-Herrera, Rodolfo Pinto-Almazán, María Guadalupe Frías-De-León and Carlos Alberto Castro-Fuentes

Pathogens 2025, 14(8), 806; https://doi.org/10.3390/pathogens14080806 - 14 Aug 2025

Abstract

Candidemia is a highly prevalent invasive fungal infection caused primarily by C. albicans, C. parapsilosis, C. glabrata (currently Nakaseomyces glabratus), C. tropicalis, and C. krusei (currently Pichia kudriavzevii). Risk factors for the development of candidemia include steroid-induced immunosuppression [...] Read more.

Candidemia is a highly prevalent invasive fungal infection caused primarily by C. albicans, C. parapsilosis, C. glabrata (currently Nakaseomyces glabratus), C. tropicalis, and C. krusei (currently Pichia kudriavzevii). Risk factors for the development of candidemia include steroid-induced immunosuppression used in solid organ or hematopoietic transplantation, and neutropenia secondary to infectious or tumorous processes. Alterations in the gut microbiota in people living with HIV, caused by antiretroviral therapy, increase the possibility of colonization by C. albicans. Likewise, the presence of a central venous catheter, parenteral nutrition, and abdominal surgery stand out as the main risk factors for the development of candidemia. New diagnostic tools have been developed for the diagnosis of this mycosis that allow the identification of the main species, from improvements in conventional stains such as calcofluor white, which increases sensitivity, as well as technologies such as T2 Candida, MoiM assay, biomarker panel (1,3 β-D-glucan, C-reactive protein, presepsin, and procalcitonin), and, more recently, the development of biosensors for the identification of Candida spp. Regarding treatment, the use of micafungin and anidulafungin in patients with obesity defined by a BMI > 30 kg/m² has shown higher survival rates and therapeutic success. Meanwhile, newer antifungals such as rezafungin and fosmanogepix have demonstrated excellent results in the treatment of these patients. Therefore, this review aims to update the epidemiology and risk factors of candidemia, as well as analyze the diagnostic tools and treatments currently available. Full article

(This article belongs to the Special Issue An Update on Fungal Infections)

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10 pages, 351 KiB

Open AccessArticle

Serotype Distribution of Aggregatibacter actinomycetemcomitans in Periodontitis Patients

by Nabil Khzam, Omar Kujan, Dorte Haubek and Leticia Algarves Miranda

Pathogens 2025, 14(8), 805; https://doi.org/10.3390/pathogens14080805 - 13 Aug 2025

Abstract

Aim: The aim of the current investigation was to detect serotypes of Aggregatibacter actinomycetemcomitans in a cohort of Western Australians diagnosed with periodontitis. Materials and Methods: A total of 64 subjects were selected. Intra-oral samples were taken from every subject in the present [...] Read more.

Aim: The aim of the current investigation was to detect serotypes of Aggregatibacter actinomycetemcomitans in a cohort of Western Australians diagnosed with periodontitis. Materials and Methods: A total of 64 subjects were selected. Intra-oral samples were taken from every subject in the present investigation. Periodontal, radiographical, and microbiological analyses were conducted. A polymerase chain reaction was employed to investigate the presence of Aggregatibacter actinomycetemcomitans serotypes. Results: Only twelve (18.75%) patients were tested positive for Aggregatibacter actinomycetemcomitans. The most dominant serotypes of Aggregatibacter actinomycetemcomitans in this group were serotype e (80.55%), followed by serotype c (52.77%). Both serotypes b and d were absent in the present investigation. Serotype e presented in isolation or combined with other serotypes. The other serotypes tend to be present alone, but when they were isolated together, they were always combined with serotype e. It seems that serotype e of Aggregatibacter actinomycetemcomitans is associated with those who live in rural areas (p = 0.003), and those with low education (p = 0.041), and severe forms of periodontitis in this cohort. Conclusions: In patients diagnosed with severe periodontitis, serotype e was dominant in this population. Serotypes b and d did not appear in the present study. Full article

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14 pages, 1025 KiB

Open AccessArticle

Targeted Whole Genome Sequencing of African Swine Fever Virus and Classical Swine Fever Virus on the MinION Portable Sequencing Platform

by Chester D. McDowell, Taeyong Kwon, Patricia Assato, Emily Mantlo, Jessie D. Trujillo, Natasha N. Gaudreault, Leonardo C. Caserta, Igor Morozov, Jayme A. Souza-Neto, Roman M. Pogranichniy, Diego G. Diel and Juergen A. Richt

Pathogens 2025, 14(8), 804; https://doi.org/10.3390/pathogens14080804 - 13 Aug 2025

Abstract

African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170–190+ kilobases (kB) belonging to the family Asfarviridae, genus Asfivirus. CSFV is [...] Read more.

African swine fever virus (ASFV) and classical swine fever virus (CSFV) are important transboundary animal diseases (TADs) affecting swine. ASFV is a large DNA virus with a genome size of 170–190+ kilobases (kB) belonging to the family Asfarviridae, genus Asfivirus. CSFV is a single-stranded RNA virus with a genome size of approximately 12 kB, belonging to the family Flaviviridae, genus Pestivirus. Outbreaks involving either one of these viruses result in similar disease syndromes and significant economic impacts from: (i) high morbidity and mortality events; (ii) control measures which include culling and quarantine; and (iii) export restrictions of swine and pork products. Current detection methods during an outbreak provide minimal genetic information on the circulating virus strains/genotypes that are important for tracing and vaccine considerations. The increasing availability and reduced cost of next-generation sequencing (NGS) allow for the establishment of NGS protocols for the rapid identification and complete genetic characterization of outbreak strains during an investigation. NGS data provides a better understanding of viral spread and evolution, facilitating the development of novel and effective control measures. In this study, panels of primers spanning the genomes of ASFV and CSFV were independently developed to generate approximately 10 kB and 6 kB amplicons, respectively. The primer panels consisted of 19 primer pairs for ASFV and 2 primer pairs for CSFV, providing whole genome amplification of each pathogen. These primer pools were further optimized for batch pooling and thermocycling conditions, resulting in a total of 5 primer pools/reactions used for ASFV and 2 primer pairs/reactions for CSFV. The ASFV primer panel was tested on viral DNA extracted from blood collected from pigs experimentally infected with ASFV genotype I and genotype II viruses. The CSFV primer panel was tested on 11 different strains of CSFV representing the three known CSFV genotypes, and 21 clinical samples collected from pigs experimentally infected with two different genotype 1 CSF viruses. ASFV and CSFV amplicons from optimized PCR were subsequently sequenced on the Oxford Nanopore MinION platform. The targeted protocols for these viruses resulted in an average coverage greater than 1000X for ASFV, with 99% of the genome covered, and 10,000X–20,000X for CSFV, with 97% to 99% of the genomes covered. The ASFV targeted whole genome sequencing protocol has been optimized for genotype II ASF viruses that have been responsible for the more recent outbreaks outside of Africa. The CSFV targeted whole genome sequencing protocol has universal applications for the detection of all CSFV genotypes. Protocols developed and evaluated here will be essential complementary tools for early pathogen detection and differentiation, as well as genetic characterization of these high-consequence swine viruses, globally and within the United States, should an outbreak occur. Full article

(This article belongs to the Section Viral Pathogens)

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19 pages, 2245 KiB

Open AccessArticle

Biochemical Defense Mechanisms of Olive Varieties Against Pythium schmitthenneri, the Causal Agent of Root Rot Disease

by Ikram Legrifi, Mohammed Radi, Mohammed Taoussi, Mohammed Khadiri, Amal Hari, Tourya Sagouti, Jamila Al Figuigui, Zineb Belabess, Abderrahim Lazraq and Rachid Lahlali

Pathogens 2025, 14(8), 803; https://doi.org/10.3390/pathogens14080803 - 11 Aug 2025

Abstract

Pythium schmitthenneri, a soilborne pathogen responsible for root rot in olive trees, poses a significant threat to olive production. Managing this pathogen remains challenging due to its aggressive root colonization and the limited efficacy of conventional control methods. Given the concerns associated [...] Read more.

Pythium schmitthenneri, a soilborne pathogen responsible for root rot in olive trees, poses a significant threat to olive production. Managing this pathogen remains challenging due to its aggressive root colonization and the limited efficacy of conventional control methods. Given the concerns associated with chemical treatments, this study evaluated the resistance of eight olive varieties to P. schmitthenneri-induced root rot under controlled greenhouse conditions by assessing structural and biochemical defense mechanisms. Greenhouse trials revealed that Arbequina, Koroneiki, and Haouziya exhibited strong resistance, with 0% disease severity, while Picholine Marocaine and Picholine Languedoc were highly susceptible, reaching 100% disease severity. Growth parameters varied significantly, with susceptible varieties showing severe reductions in root length (RL), root fresh weight (RFW), and root dry weight (RDW), whereas resistant varieties maintained these parameters unchanged. While shoot length (SL) remained unaffected across all varieties, shoot fresh weight (SFW) and shoot dry weight (SDW) were significantly reduced in susceptible ones. Fourier-transform infrared (FTIR) spectroscopy revealed that resistant varieties maintained stable levels of lignin, cellulose, and polysaccharides, while susceptible ones exhibited extensive cell wall degradation. Additionally, total polyphenol content (TPC) and total flavonoid content (TFC) significantly increased in resistant varieties upon infection, whereas susceptible varieties experienced a substantial decline. These findings highlight the crucial role of structural and biochemical defenses in olive resistance to P. schmitthenneri and suggest that selecting resistant varieties could serve as a sustainable strategy for managing root rot in olive production. Full article

(This article belongs to the Section Fungal Pathogens)

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22 pages, 2782 KiB

Open AccessArticle

Mycobacterium tuberculosis Modulates the Expansion of Terminally Exhausted CD4⁺ and CD8⁺ T-Cells in Individuals with HIV-TB Co-Infection

by Komal Sharma, Aman Sharma and Sunil K. Arora

Pathogens 2025, 14(8), 802; https://doi.org/10.3390/pathogens14080802 - 11 Aug 2025

Abstract

Introduction: Mycobacterium tuberculosis (Mtb), the most common co-infection among people living with HIV (PLWH), aggravates the associated morbidity and mortality in these individuals; however, the immune-modulatory role of Mtb in the pathogenesis of HIV infection remains incompletely understood. Methods: We investigated the role [...] Read more.

Introduction: Mycobacterium tuberculosis (Mtb), the most common co-infection among people living with HIV (PLWH), aggravates the associated morbidity and mortality in these individuals; however, the immune-modulatory role of Mtb in the pathogenesis of HIV infection remains incompletely understood. Methods: We investigated the role of Mtb infection in regulating adaptive immune responses with reference to the expression of five immune checkpoint molecules (ICMs) in co-infected individuals in a cross-sectional study conducted on treatment-naïve human cohorts from North India, including PLWH, people with Mtb infection, people with HIV-Mtb co-infection, and healthy volunteers as controls. Results: The data revealed a significantly increased gene expression of TIM-3 (p = 0.0058), LAG-3 (p < 0.0001), PD-1 (p = 0.0090), and CTLA-4 (p = 0.0008). It also revealed a higher frequency of CD4⁺ and CD8⁺ T-cells surface-expressing TIM-3⁺, CTLA-4⁺, LAG-3⁺. Finally, it showed cells co-expressing two ICMs together (p < 0.05) in individuals with HIV–Mtb co-infection as compared to HIV mono-infected ones. Interestingly, the frequency of these cells correlated inversely with the absolute CD4⁺ T-cell count and positively with the plasma viral load (p < 0.05), indicating direct association with HIV disease progression. Conclusions: These findings suggest that Mtb co-infection exacerbates immune exhaustion in co-infected individuals. Targeting ICMs with pharmacological immune checkpoint inhibitors (ICIs) offers a promising approach for better clinical management of co-infected individuals. Full article

(This article belongs to the Special Issue New Insights into Viral Pathogenesis, Host Immune Responses and Immunotherapies)

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27 pages, 3634 KiB

Open AccessArticle

Characterising the Associated Virome and Microbiota of Asian Citrus Psyllid (Diaphorina citri) in Samoa

by Kayvan Etebari, Angelika M. Tugaga, Gayatri Divekar, Olo Aleni Uelese, Sharydia S. A. Tusa, Ellis Vaega, Helmy Sasulu, Loia Uini, Yuanhang Ren and Michael J. Furlong

Pathogens 2025, 14(8), 801; https://doi.org/10.3390/pathogens14080801 - 10 Aug 2025

Abstract

The Asian citrus psyllid (Diaphorina citri) is an economically important pest of citrus as it is a vector of the bacterium (Candidatus Liberibacter asiaticus, CLas) that causes huanglongbing disease (HLB). Understanding the virome of D. citri is important for [...] Read more.

The Asian citrus psyllid (Diaphorina citri) is an economically important pest of citrus as it is a vector of the bacterium (Candidatus Liberibacter asiaticus, CLas) that causes huanglongbing disease (HLB). Understanding the virome of D. citri is important for uncovering factors that influence vector competence, to support biosecurity surveillance, and to identify candidate agents for biological control. Previous studies have identified several D. citri-associated viruses from various geographical populations of this pest. To further investigate virus diversity in this pest, high-throughput sequencing was used to analyse D. citri populations from the Samoan islands of Upolu and Savai’i. Eleven novel viruses from the Yadokariviridae, Botourmiaviridae, Nodaviridae, Mymonaviridae, Partitiviridae, Totiviridae, and Polymycoviridae were identified as well as some that corresponded to unclassified groups. In addition, microbiome analysis revealed the presence of several endosymbiotic microorganisms, including Wolbachia, as well as some plant pathogenic fungi, including Botrytis cinerea. However, the causative agent of HLB disease (CLas) was not detected in the RNA-Seq data. These findings highlight the complex and diverse microbiota associated with D. citri and suggest potential interactions and dynamics between microorganisms and psyllid-associated viruses. Further research is needed to understand the ecological significance of these discoveries, and whether the novel viruses play a role in regulating field populations of the psyllid. Full article

(This article belongs to the Section Viral Pathogens)

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13 pages, 671 KiB

Open AccessArticle

Re-Evaluation of a Hyperendemic Focus of Metastrongyloid Lungworm Infections in Gastropod Intermediate Hosts in Southern Germany

by Alena Dusch, Lisa Segeritz, Judith Schmiedel, Anja Taubert and Carlos Hermosilla

Pathogens 2025, 14(8), 800; https://doi.org/10.3390/pathogens14080800 - 9 Aug 2025

Abstract

The metastrongyloid nematodes Angiostrongylus vasorum, Aelurostrongylus abstrusus, and Crenosoma vulpis can cause severe cardiopulmonary and respiratory symptoms in domestic dogs and cats and free-ranging canids and felids (e.g., foxes, wolves, wild cats, lynxes). Recent data on the prevalence of A. vasorum [...] Read more.

The metastrongyloid nematodes Angiostrongylus vasorum, Aelurostrongylus abstrusus, and Crenosoma vulpis can cause severe cardiopulmonary and respiratory symptoms in domestic dogs and cats and free-ranging canids and felids (e.g., foxes, wolves, wild cats, lynxes). Recent data on the prevalence of A. vasorum infections in dogs and foxes and on the prevalence of Ae. abstrusus and Troglostrongylus brevior infections in free-ranging lynxes and wild cats revealed several endemic and hyperendemic foci in Germany. Nonetheless, long-term investigations on the prevalence of metastrongyloid larvae infecting gastropod intermediate hosts are still scarce for Germany. To fill this gap, we conducted an epidemiological survey on native slugs and snails in a selected meadow close to Obrigheim, previously identified as a hyperendemic focus for canine angiostrongylosis. To re-evaluate this location as a ‘hotspot’ of canine angiostrongylosis, terrestrial slugs and snails (n = 533) were collected in all seasons, artificially digested, and microscopically and molecularly analyzed for the presence of metastrongyloid lungworm larvae. Here, the prevalence ranged greatly between seasons. In summer, 27.46% (59/215) of gastropods were infected with metastrongyloid larvae. In fall, the prevalence dropped to 10.00% (16/160) and lowest infection rates were observed in both winter (5.65%) and spring (1.47%). In total, A. vasorum was detected in 12.01% (64/533), Crenosoma sp. in 0.94% (5/533), and Ae. abstrusus in 0.38% (2/533) of gastropod samples. Even though total A. vasorum infection levels were revealed to be considerably lower than in the prior study, this epidemiological survey in principle reconfirms Obrigheim as a stable hyperendemic focus and thereby as a location with high metastrongyloid infection risk for domestic dogs, cats, and wildlife throughout the year. These results call for continuous epidemiological studies on gastropod populations to better understand metastrongyloid lungworm spread and infection dynamics over the years. Full article

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20 pages, 1892 KiB

Open AccessArticle

Chemical Composition, Biocompatibility, and Anti-Candida albicans Activity of Schinus weinmanniifolia Mart. ex Engl.

by João Andrade, Adriana Almeida-Apolonio, Fabiana Dantas, Cláudio Nogueira, Luciano Pinto, Carlos Moraes, Liliana Fernandes, Maria Elisa Rodrigues, Mariana Henriques and Kelly Oliveira

Pathogens 2025, 14(8), 799; https://doi.org/10.3390/pathogens14080799 - 9 Aug 2025

Abstract

Recurrent vulvovaginal candidiasis (RVVC), predominantly caused by Candida albicans, represents a global health issue, particularly in developing regions. This study explores the antifungal potential of aqueous leaf extract of Schinus weinmanniifolia Mart. ex Engl., a native Latin American plant. The extract was [...] Read more.

Recurrent vulvovaginal candidiasis (RVVC), predominantly caused by Candida albicans, represents a global health issue, particularly in developing regions. This study explores the antifungal potential of aqueous leaf extract of Schinus weinmanniifolia Mart. ex Engl., a native Latin American plant. The extract was evaluated for phytochemical composition, antifungal efficacy, and safety profile. Phytochemical analyses identified six major compounds, including shikimic acid, gallic acid, and methyl gallate, with antioxidant and antimicrobial properties. The extract showed potent antioxidant activity, with IC₅₀ values between 1.52–5.51 µg/mL. It strongly inhibited C. albicans, with a minimum inhibitory concentration (MIC) of 1.95 µg/mL, and was active against other yeasts (MIC 0.48–62.5 µg/mL). The growth kinetics assay revealed reduced C. albicans viability after 12 h at 2 × MIC versus the positive control. Scanning electron microscopy confirmed reduced fungal counts without morphological damage. The extract impaired C. albicans virulence, reducing germ tube formation by 75.49% and hyphal transition by 84.34%, outperforming fluconazole. Biocompatibility assays showed it is non-hemolytic (IC₅₀ > 1000 µg/mL), non-mutagenic, and highly selective for fungal cells (SI = 512.82), suggesting minimal human cell toxicity. In conclusion, the extract combines strong antifungal activity and favorable safety, with cost-effective preparation suitable for traditional medicine in resource-limited regions. Full article

(This article belongs to the Special Issue Candida albicans Virulence and Therapeutic Strategies)

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12 pages, 944 KiB

Open AccessArticle

Congenital Parvovirus B19 During the 2024 European Resurgence: A Prospective Single-Centre Cohort Study

by Pasqua Betta, Roberta Leonardi, Carmine Mattia, Alessandro Saporito, Silvia Gentile, Laura Trovato, Concetta Ilenia Palermo and Guido Scalia

Pathogens 2025, 14(8), 798; https://doi.org/10.3390/pathogens14080798 - 9 Aug 2025

Abstract

Parvovirus B19 (B19V) re-emerged across Europe in 2024, raising concerns about vertical transmission and neonatal morbidity. We undertook a prospective, single-centre cohort study to characterise the early clinical course of congenitally infected neonates born between April and December 2024. Seventy-one pregnancies with serologically [...] Read more.

Parvovirus B19 (B19V) re-emerged across Europe in 2024, raising concerns about vertical transmission and neonatal morbidity. We undertook a prospective, single-centre cohort study to characterise the early clinical course of congenitally infected neonates born between April and December 2024. Seventy-one pregnancies with serologically or PCR-confirmed maternal infection were enrolled; seven neonates met laboratory criteria for congenital B19V infection and were followed with serial clinical, biochemical and imaging assessments through the first year of life. Troponin I and CK-MB were measured on days 1, 3, 7 and 15; electrocardiogram (ECG) and echocardiography were repeated in parallel, and cranial ultrasound (US), ophthalmologic and audiologic screening were scheduled prospectively. Mean troponin rose from 50.7 ng L⁻¹ on day 1 to a peak of 120.7 ng L⁻¹ on day 7 (p < 0.01), normalising by one month, while echocardiograms remained structurally normal, and only one transient arrhythmia was recorded. CK-MB exceeded the reference range in 29% of infants but showed no clinical sequelae. Multiple periventricular hyperechogenicities were identified in 8/70 neonates (11%), and moderate anaemia (Hb ≤ 9.8 g/dL) occurred in 2 cases. Serum PCR detected high-level viraemia (>10⁸ genome equivalents mL⁻¹) in 40% of those tested; saliva and urine were consistently negative. No instances of myocarditis or hydrops were observed. Our findings indicate that congenital B19V infection during the current outbreak is marked by transient biochemical myocardial stress and subtle neurosonographic changes rather than overt cardiac disease, supporting an outpatient-focused follow-up strategy incorporating serial biomarkers and targeted neuroimaging. Full article

(This article belongs to the Section Viral Pathogens)

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