Pathogens

12 pages, 1678 KiB

Open AccessArticle

Molecular Surveillance of Plasmodium spp. Infection in Neotropical Primates from Bahia and Minas Gerais, Brazil

by Luana Karla N. S. S. Santos, Sandy M. Aquino-Teixeira, Sofía Bernal-Valle, Beatriz S. Daltro, Marina Noetzold, Aloma Roberta C. Silva, Denise Anete M. Alvarenga, Luisa B. Silva, Ramon S. Oliveira, Cirilo H. Oliveira, Iago A. Celestino, Maria E. Gonçalves-dos-Santos, Thaynara J. Teixeira, Anaiá P. Sevá, Fabrício S. Campos, Bergmann M. Ribeiro, Paulo M. Roehe, Danilo Simonini-Teixeira, Filipe V. S. Abreu, Cristiana F. A. Brito and George R. Albuquerque Show full author list Hide full author list

Pathogens 2025, 14(8), 757; https://doi.org/10.3390/pathogens14080757 (registering DOI) - 31 Jul 2025

Abstract

In Brazil, Plasmodium infections in non-human primates (NHPs) have been associated with P. simium and P. brasilianum, which are morphologically and genetically similar to the human-infecting species P. vivax and P. malariae, respectively. Surveillance and monitoring of wild NHPs are crucial [...] Read more.

In Brazil, Plasmodium infections in non-human primates (NHPs) have been associated with P. simium and P. brasilianum, which are morphologically and genetically similar to the human-infecting species P. vivax and P. malariae, respectively. Surveillance and monitoring of wild NHPs are crucial for understanding the distribution of these parasites and assessing the risk of zoonotic transmission. This study aimed to detect the presence of Plasmodium spp. genetic material in Platyrrhini primates from 47 municipalities in the states of Bahia and Minas Gerais. The animals were captured using Tomahawk-type live traps baited with fruit or immobilized with tranquilizer darts. Free-ranging individuals were chemically restrained via inhalation anesthesia using VetBag^® or intramuscular anesthesia injection. Blood samples were collected from the femoral vein. A total of 298 blood and tissue samples were collected from 10 primate species across five genera: Alouatta caraya (25), Alouatta guariba clamitans (1), Callicebus melanochir (1), Callithrix geoffroyi (28), Callithrix jacchus (4), Callithrix kuhlii (31), Callithrix penicillata (175), Callithrix spp. hybrids (15), Leontopithecus chrysomelas (16), Sapajus robustus (1), and Sapajus xanthosthernos (1). Molecular diagnosis was performed using a nested PCR targeting the 18S small subunit ribosomal RNA (18S SSU rRNA) gene, followed by sequencing. Of the 298 samples analyzed, only one (0.3%) from Bahia tested positive for Plasmodium brasilianum/P. malariae. This represents the first detection of this parasite in a free-living C. geoffroyi in Brazil. These findings highlight the importance of continued surveillance of Plasmodium infections in NHPs to identify regions at risk for zoonotic transmission. Full article

(This article belongs to the Section Parasitic Pathogens)

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18 pages, 3030 KiB

Open AccessArticle

Morphometric and Molecular Insights into Hepatozoon spp. in Wild and Synanthropic Rodents from Southern and Southeastern Brazil

by Tatiana Pádua Tavares de Freitas, Bernardo Rodrigues Teixeira, Eduarda de Oliveira Silva Lima Machado, Isaac Leandro Lira Pinto, Laís da Silva de Oliveira, Karina Varella, Huarrisson Azevedo Santos, Fernando de Oliveira Santos, Liliani Marilia Tiepolo, Carlos Luiz Massard and Maristela Peckle

Pathogens 2025, 14(8), 756; https://doi.org/10.3390/pathogens14080756 (registering DOI) - 31 Jul 2025

Abstract

Small rodents are known hosts of various pathogens, including Hepatozoon, but until now, in Brazil, only Hepatozoon milleri has been described in these animals. In this study, liver samples and blood smears were obtained from 289 rodents belonging to 14 Cricetidae and [...] Read more.

Small rodents are known hosts of various pathogens, including Hepatozoon, but until now, in Brazil, only Hepatozoon milleri has been described in these animals. In this study, liver samples and blood smears were obtained from 289 rodents belonging to 14 Cricetidae and two Muridae species that had been captured in municipalities of the states of Paraná and Rio de Janeiro. Smears were stained with Giemsa, and gametocytes were detected via microscopy in 10.72% (n = 31/289) of samples, with these individuals representing three rodent species. Significant morphometric differences were observed in gametocyte measurements in Akodon rodents. Using conventional PCR, Hepatozoon spp. 18S rDNA fragments were amplified in 24.91% (n = 72/289) of samples, with those individuals representing seven rodent species. Phylogenetic analyses clustered 41 sequences from this study into a subclade with other sequences from small mammals in Brazil, identifying four distinct haplotypes, and, for the first time, a relationship between Hepatozoon haplotype and gametocyte length was observed. Based on phylogenetic analysis, this study reinforces the trophic relationship between rodents and reptiles as a possible link in the Hepatozoon transmission cycle in South America. Furthermore, our findings expand knowledge on Hepatozoon spp. hosts, describing Oxymycterus nasutus and Oxymycterus quaestor as new host species and identifying two novel circulating haplotypes in rodents from Paraná State, southern Brazil. Full article

(This article belongs to the Special Issue Vector Control and Parasitic Infection in Animals)

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16 pages, 4439 KiB

Open AccessArticle

Baseline Assessment of Taeniasis and Cysticercosis Infections in a High-Priority Region for Taenia solium Control in Colombia

by Carlos Franco-Muñoz, María Camila Jurado Guacaneme, Sonia Dayanni Castillo Ayala, Sofia Duque-Beltrán, Adriana Arévalo, Marcela Pilar Rojas Díaz, Julián Trujillo Trujillo, Luz Elena Borras Reyes, Luis Reinel Vásquez Arteaga, Julio César Giraldo Forero and Mario J. Olivera

Pathogens 2025, 14(8), 755; https://doi.org/10.3390/pathogens14080755 (registering DOI) - 31 Jul 2025

Abstract

Coyaima is a town in the department of Tolima, Colombia, that was prioritized in a pilot program under Colombia’s National Plan for the Control of the Taeniasis/Cysticercosis Complex, focusing on this neglected health issue. The project engaged local indigenous communities, promoting education and [...] Read more.

Coyaima is a town in the department of Tolima, Colombia, that was prioritized in a pilot program under Colombia’s National Plan for the Control of the Taeniasis/Cysticercosis Complex, focusing on this neglected health issue. The project engaged local indigenous communities, promoting education and outreach within the One Health framework. The study included 444 randomly selected volunteers, who filled a Knowledge, Attitudes, and Practices (KAP) survey on the taeniasis/cysticercosis complex. The baseline study found no Taenia spp. eggs via microscopy on 383 stool samples examined, and no T. solium DNA was detected on human stool and soil samples by Copro-qPCR. However, seroprevalence was 8.5% for human cysticercosis and 14% for porcine cysticercosis, as detected by in-house ELISA testing for T. solium. Moreover, 57.9% of participants who provided a stool sample were positive for at least one parasite. Following the sampling and characterization activities, local health workers implemented mass treatment with Niclosamide, based on evidence of ongoing transmission, high porcine seroprevalence, poor basic sanitation, and the presence of free-roaming pigs reported in the KAP survey. These findings provide scientific evidence to apply national public health policies for controlling taeniasis/cysticercosis complex in Coyaima. Full article

(This article belongs to the Special Issue Recent Advances in Taeniasis and Cysticercosis)

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14 pages, 3364 KiB

Open AccessArticle

Microbial Load and Diversity of Bacteria in Wild Animal Carcasses Sold as Bushmeat in Ghana

by Daniel Oduro, Winnifred Offih-Kyei, Joanita Asirifi Yeboah, Rhoda Yeboah, Caleb Danso-Coffie, Emmanuel Boafo, Vida Yirenkyiwaa Adjei, Isaac Frimpong Aboagye and Gloria Ivy Mensah

Pathogens 2025, 14(8), 754; https://doi.org/10.3390/pathogens14080754 (registering DOI) - 31 Jul 2025

Abstract

The demand for wild animal meat, popularly called “bushmeat”, serves as a driving force behind the emergence of infectious diseases, potentially transmitting a variety of pathogenic bacteria to humans through handling and consumption. This study investigated the microbial load and bacterial diversity in [...] Read more.

The demand for wild animal meat, popularly called “bushmeat”, serves as a driving force behind the emergence of infectious diseases, potentially transmitting a variety of pathogenic bacteria to humans through handling and consumption. This study investigated the microbial load and bacterial diversity in bushmeat sourced from a prominent bushmeat market in Kumasi, Ghana. Carcasses of 61 wild animals, including rodents (44), antelopes (14), and African civets (3), were sampled for microbiological analysis. These samples encompassed meat, intestines, and anal and oral swabs. The total aerobic bacteria plate count (TPC), Enterobacteriaceae count (EBC), and fungal counts were determined. Bacterial identification was conducted using MALDI-TOF biotyping. Fungal counts were the highest across all animal groups, with African civets having 11.8 ± 0.3 log₁₀ CFU/g and 11.9 ± 0.2 log₁₀ CFU/g in intestinal and meat samples, respectively. The highest total plate count (TPC) was observed in rodents, both in their intestines (10.9 ± 1.0 log₁₀ CFU/g) and meat (10.9 ± 1.9 log₁₀ CFU/g). In contrast, antelopes exhibited the lowest counts across all categories, particularly in EBC from intestinal samples (6.1 ± 1.5 log₁₀ CFU/g) and meat samples (5.6 ± 1.2 log₁₀ CFU/g). A comprehensive analysis yielded 524 bacterial isolates belonging to 20 genera, with Escherichia coli (18.1%) and Klebsiella spp. (15.5%) representing the most prevalent species. Notably, the detection of substantial microbial contamination in bushmeat underscores the imperative for a holistic One Health approach to enhance product quality and mitigate risks associated with its handling and consumption. Full article

(This article belongs to the Section Bacterial Pathogens)

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25 pages, 1990 KiB

Open AccessArticle

Fecal and Environmental Shedding of Influenza A Virus in Brazilian Swine: Genomic Evidence of Recent Human-to-Swine Transmission

by Nágila Rocha Aguilar, Beatriz Senra Alvares da Silva Santos, Bruno Zinato Carraro, Brenda Monique Magalhães Rocha, Jardelina de Souza Todao Bernardino, Ana Luiza Soares Fraiha, Alex Ranieri Jeronimo Lima, Gabriela Ribeiro, Alessandra Silva Dias, Renata Rezende Carvalho, Bruna Ferreira Sampaio Ribeiro, Marta Giovanetti, Luiz Carlos Júnior Alcântara, Sandra Coccuzzo Sampaio, Maria Carolina Quartim Barbosa Elias Sabbaga, Rafael Romero Nicolino, Zélia Inês Portela Lobato, Maria Isabel Maldonado Coelho Guedes, Cesar Rossas Mota Filho, Vincent Louis Viala, Bruna Coelho Lopes and Erica Azevedo Costa Show full author list Hide full author list

Pathogens 2025, 14(8), 753; https://doi.org/10.3390/pathogens14080753 (registering DOI) - 31 Jul 2025

Abstract

Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples [...] Read more.

Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples from naturally infected pigs in a commercial farm in Minas Gerais, Brazil. IAV RNA was detected in 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses from feces and effluent samples. Whole-genome sequencing revealed co-circulation of enzootic pH1N1 clade #2 (HA) and pN1 clade #4 (NA), alongside human-origin H3N2 sequences clustering within clade 3C.2a1b.2a.2a.1, and N2 segments related to pre-3C human lineages from 2001 to 2002. Phylogenetic and p-distance analyses support both recent reverse zoonosis and historical transmission events. Detection of complete HA/NA sequences from rectal swabs and treated effluent further emphasizes the surveillance value of non-respiratory matrices. The integration of respiratory and fecal/environmental sampling appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond. Full article

(This article belongs to the Special Issue Pathogenesis, Epidemiology, and Control of Animal Influenza Viruses—2nd Edition)

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9 pages, 6176 KiB

Open AccessCase Report

Concurrent Leydig and Sertoli Cell Tumors Associated with Testicular Mycosis in a Dog: A Case Report and Literature Review

by Mirosław Kuberka, Przemysław Prządka and Stanisław Dzimira

Pathogens 2025, 14(8), 752; https://doi.org/10.3390/pathogens14080752 (registering DOI) - 31 Jul 2025

Abstract

Mycosis is caused by, among other factors, filamentous fungi, ubiquitous molds belonging to Aspergillus spp. which are often opportunistic pathogens. Over 100 species of Aspergillus have been described. The most common species responsible for diseases in humans and animals are Aspergillus fumigatus and [...] Read more.

Mycosis is caused by, among other factors, filamentous fungi, ubiquitous molds belonging to Aspergillus spp. which are often opportunistic pathogens. Over 100 species of Aspergillus have been described. The most common species responsible for diseases in humans and animals are Aspergillus fumigatus and Aspergillus niger, with Aspergillus flavus and Aspergillus clavatus being somewhat rarer. Aspergillus causes a range of diseases, from localized colonization and hypersensitivity reactions, through chronic necrotizing infections, to rapidly progressing angioinvasion and dissemination, leading to death. Testicular mycosis is extremely rarely described in both humans and animals. No studies in the literature report a simultaneous occurrence of testicular tumors and fungal infection of the organ, so the aim of this paper was to describe, for the first time, a case of two independent testicular tumors coexisting with testicular mycosis. A histopathological examination was performed on the left testicle of a male dog, specifically a mixed-breed dog resembling a husky weighing 22 kg and with an age of 8 years. Bilateral orchidectomy was performed for medical reasons due to the altered outline of the left testicle, leading to scrotal deformation. The dog did not show any clinical signs of illness, and the testicles were not painful. The right testicle, according to the operating veterinarian, showed no macroscopic changes, so histopathological verification was not performed. Microscopic imaging of the changes clearly indicated the coexistence of a tumor process involving Leydig cells (Leydigoma, interstitial cell tumor, ICT), Sertoli cells (Sertolioma), and fungal infection of the testis. The case suggests the possibility of the coexistence of tumor processes, which may have impaired local immune response of the tissue, with an infectious, in this case fungal, inflammatory process. Based on the literature, this paper is the first report on the occurrence of two independent histotype testicular tumors and their associated mycosis. Full article

(This article belongs to the Special Issue Rare Fungal Infection Studies)

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23 pages, 4510 KiB

Open AccessArticle

Identification and Characterization of Biosecurity Breaches on Poultry Farms with a Recent History of Highly Pathogenic Avian Influenza Virus Infection Determined by Video Camera Monitoring in the Netherlands

by Armin R. W. Elbers and José L. Gonzales

Pathogens 2025, 14(8), 751; https://doi.org/10.3390/pathogens14080751 - 30 Jul 2025

Abstract

Biosecurity measures applied on poultry farms, with a recent history of highly pathogenic avian influenza virus infection, were monitored using 24 h/7 days-per-week video monitoring. Definition of biosecurity breaches were based on internationally acknowledged norms. Farms of four different production types (two broiler, [...] Read more.

Biosecurity measures applied on poultry farms, with a recent history of highly pathogenic avian influenza virus infection, were monitored using 24 h/7 days-per-week video monitoring. Definition of biosecurity breaches were based on internationally acknowledged norms. Farms of four different production types (two broiler, two layer, two breeder broiler, and one duck farm) were selected. Observations of entry to and exit from the anteroom revealed a high degree of biosecurity breaches in six poultry farms and good biosecurity practices in one farm in strictly maintaining the separation between clean and potentially contaminated areas in the anteroom. Hand washing with soap and water and/or using disinfectant lotion was rarely observed at entry to the anteroom and was almost absent at exit. Egg transporters did not disinfect fork-lift wheels when entering the egg-storage room nor change or properly disinfect footwear. The egg-storage room was not cleaned and disinfected after egg transport by the farmer. Similarly, footwear and trolley wheels were not disinfected when introducing young broilers or ducklings to the poultry unit. Biosecurity breaches were observed when introducing bedding material in the duck farm. This study shows a need for an engaging awareness and training campaign for poultry farmers and their co-workers as well as for transporters to promote good biosecurity practices. Full article

(This article belongs to the Special Issue Pathogenesis, Epidemiology, and Control of Animal Influenza Viruses—2nd Edition)

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12 pages, 1078 KiB

Open AccessFeature PaperArticle

Aerostability of Sin Nombre Virus Aerosol Related to Near-Field Transmission

by Elizabeth A. Klug, Danielle N. Rivera, Vicki L. Herrera, Ashley R. Ravnholdt, Daniel N. Ackerman, Yangsheng Yu, Chunyan Ye, Steven B. Bradfute, St. Patrick Reid and Joshua L. Santarpia

Pathogens 2025, 14(8), 750; https://doi.org/10.3390/pathogens14080750 - 30 Jul 2025

Abstract

Sin Nombre virus (SNV) is the main causative agent of hantavirus cardiopulmonary syndrome (HCPS) in North America. SNV is transmitted via environmental biological aerosols (bioaerosols) produced by infected deer mice (Peromyscus maniculatus). It is similar to other viruses that have environmental [...] Read more.

Sin Nombre virus (SNV) is the main causative agent of hantavirus cardiopulmonary syndrome (HCPS) in North America. SNV is transmitted via environmental biological aerosols (bioaerosols) produced by infected deer mice (Peromyscus maniculatus). It is similar to other viruses that have environmental transmission routes rather than a person-to-person transmission route, such as avian influenza (e.g., H5N1) and Lassa fever. Despite the lack of person-to-person transmission, these viruses cause a significant public health and economic burden. However, due to the lack of targeted pharmaceutical preventatives and therapeutics, the recommended approach to prevent SNV infections is to avoid locations that have a combination of low foot traffic, receive minimal natural sunlight, and where P. maniculatus may be found nesting. Consequently, gaining insight into the SNV bioaerosol decay profile is fundamental to the prevention of SNV infections. The Biological Aerosol Reaction Chamber (Bio-ARC) is a flow-through system designed to rapidly expose bioaerosols to environmental conditions (ozone, simulated solar radiation (SSR), humidity, and other gas phase species at stable temperatures) and determine the sensitivity of those particles to simulated ambient conditions. Using this system, we examined the bioaerosol stability of SNV. The virus was found to be susceptible to both simulated solar radiation and ozone under the tested conditions. Comparisons of decay between the virus aerosolized in residual media and in a mouse bedding matrix showed similar results. This study indicates that SNV aerosol particles are susceptible to inactivation by solar radiation and ozone, both of which could be implemented as effective control measures to prevent disease in locations where SNV is endemic. Full article

(This article belongs to the Special Issue Airborne Transmission of Pathogens)

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15 pages, 1843 KiB

Open AccessArticle

Genotype-Specific HPV mRNA Triage Improves CIN2+ Detection Efficiency Compared to Cytology: A Population-Based Study of HPV DNA-Positive Women

by S. Sørbye, B. M. Falang, M. Antonsen and E. Mortensen

Pathogens 2025, 14(8), 749; https://doi.org/10.3390/pathogens14080749 - 30 Jul 2025

Abstract

Background: Effective triage of women testing positive for high-risk HPV DNA is essential to reduce unnecessary colposcopies while preserving cancer prevention. Cytology, the current standard, has limited specificity and reproducibility. The genotype-specific 7-type HPV E6/E7 mRNA test (PreTect HPV-Proofer’7), targeting HPV types 16, [...] Read more.

Background: Effective triage of women testing positive for high-risk HPV DNA is essential to reduce unnecessary colposcopies while preserving cancer prevention. Cytology, the current standard, has limited specificity and reproducibility. The genotype-specific 7-type HPV E6/E7 mRNA test (PreTect HPV-Proofer’7), targeting HPV types 16, 18, 31, 33, 45, 52, and 58, detects transcriptionally active infections and may enhance risk stratification. Methods: Between 2019 and 2023, 34,721 women aged 25–69 underwent primary HPV DNA screening with the Cobas 4800 assay at the University Hospital of North Norway, within the national screening program. Of these, 1896 HPV DNA-positive women were triaged with liquid-based cytology with atypical squamous cells of undetermined significance or worse (≥ASC-US) and the 7-type HPV mRNA test. Histological outcomes were followed through October 2024. Diagnostic performance for CIN2+ was evaluated overall and by genotype. Results: CIN2+ prevalence was 13.3%. The mRNA test reduced test positivity from 50.3% to 33.4% while maintaining comparable sensitivity (70.6% vs. 72.2%) and improving specificity (72.3% vs. 53.0%) and PPV (28.1% vs. 19.1%). Genotype-specific PPVs were highest for HPV16 mRNA (47.7%), followed by HPV33 (39.2%) and HPV31 (32.2%), all exceeding corresponding DNA-based estimates. Conclusion: Genotype-specific HPV mRNA triage offers superior risk discrimination compared to cytology, supporting more targeted, efficient, and accessible cervical cancer screening. Full article

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20 pages, 732 KiB

Open AccessReview

AI Methods Tailored to Influenza, RSV, HIV, and SARS-CoV-2: A Focused Review

by Achilleas Livieratos, George C. Kagadis, Charalambos Gogos and Karolina Akinosoglou

Pathogens 2025, 14(8), 748; https://doi.org/10.3390/pathogens14080748 - 30 Jul 2025

Abstract

Artificial intelligence (AI) techniques—ranging from hybrid mechanistic–machine learning (ML) ensembles to gradient-boosted decision trees, support-vector machines, and deep neural networks—are transforming the management of seasonal influenza, respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptom-based [...] Read more.

Artificial intelligence (AI) techniques—ranging from hybrid mechanistic–machine learning (ML) ensembles to gradient-boosted decision trees, support-vector machines, and deep neural networks—are transforming the management of seasonal influenza, respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptom-based triage models using eXtreme Gradient Boosting (XGBoost) and Random Forests, as well as imaging classifiers built on convolutional neural networks (CNNs), have improved diagnostic accuracy across respiratory infections. Transformer-based architectures and social media surveillance pipelines have enabled real-time monitoring of COVID-19. In HIV research, support-vector machines (SVMs), logistic regression, and deep neural network (DNN) frameworks advance viral-protein classification and drug-resistance mapping, accelerating antiviral and vaccine discovery. Despite these successes, persistent challenges remain—data heterogeneity, limited model interpretability, hallucinations in large language models (LLMs), and infrastructure gaps in low-resource settings. We recommend standardized open-access data pipelines and integration of explainable-AI methodologies to ensure safe, equitable deployment of AI-driven interventions in future viral-outbreak responses. Full article

(This article belongs to the Section Viral Pathogens)

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28 pages, 1184 KiB

Open AccessReview

Immune Modulation by Microbiota and Its Possible Impact on Polyomavirus Infection

by Giorgia Cianci, Gloria Maini, Matteo Ferraresi, Giulia Pezzi, Daria Bortolotti, Sabrina Rizzo, Silvia Beltrami and Giovanna Schiuma

Pathogens 2025, 14(8), 747; https://doi.org/10.3390/pathogens14080747 - 30 Jul 2025

Abstract

Polyomaviruses are a family of small DNA viruses capable of establishing persistent infections, and they can pose significant pathogenic risks in immunocompromised hosts. While traditionally studied in the context of viral reactivation and immune suppression, recent evidence has highlighted the gut microbiota as [...] Read more.

Polyomaviruses are a family of small DNA viruses capable of establishing persistent infections, and they can pose significant pathogenic risks in immunocompromised hosts. While traditionally studied in the context of viral reactivation and immune suppression, recent evidence has highlighted the gut microbiota as a critical regulator of host immunity and viral pathogenesis. This review examines the complex interactions between polyomaviruses, the immune system, and intestinal microbiota, emphasizing the role of short-chain fatty acids (SCFAs) in modulating antiviral responses. We explore how dysbiosis may facilitate viral replication, reactivation, and immune escape and also consider how polyomavirus infection can, in turn, alter microbial composition. Particular attention is given to the Firmicutes/Bacteroidetes ratio as a potential biomarker of infection risk and immune status. Therapeutic strategies targeting the microbiota, including prebiotics, probiotics, and fecal microbiota transplantation (FMT), are discussed as innovative adjuncts to immune-based therapies. Understanding these tri-directional interactions may offer new avenues for mitigating disease severity and improving patient outcomes during viral reactivation. Full article

(This article belongs to the Special Issue The Interplay of Microbiota and Polyomaviruses in Human Health and Disease)

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19 pages, 10978 KiB

Open AccessArticle

Identification of Fungi Causing Root Rot in Oregano Crops in Southern Peru: Morphological and Molecular Analysis

by Rubí Adelin Quispe-Mamani, Liduvina Sulca-Quispe, Wilson Huanca-Mamani, Mirna G. Garcia-Castillo, Patricio Muñoz-Torres and German Sepúlveda-Chavera

Pathogens 2025, 14(8), 746; https://doi.org/10.3390/pathogens14080746 - 29 Jul 2025

Abstract

Oregano (Origanum vulgare) cultivation is of great economic importance in Peru. Tacna stands out as its main producer. However, the presence of phytopathogenic fungi represents a challenge for its production. This study aimed to characterize both the morphological and molecular levels [...] Read more.

Oregano (Origanum vulgare) cultivation is of great economic importance in Peru. Tacna stands out as its main producer. However, the presence of phytopathogenic fungi represents a challenge for its production. This study aimed to characterize both the morphological and molecular levels of the causal agent of crown and root rot in a crop field in the Camilaca district, Candarave, Tacna. To this end, systematic sampling was carried out using the five-gold method, collecting plants with typical symptoms. Fungi were isolated from diseased roots and characterized using macroscopic and microscopic morphological analysis as well as sequencing and multilocus phylogenetic analysis (ITS, 28S, HIS3, TEF1, TUB2). In addition, pathogenicity tests were performed on healthy plants to confirm the infectivity of the isolates. The results demonstrated that root rot was caused by a complex of phytopathogenic fungi through phylogenetic analysis of Dactylonectria torresensis, Fusarium oxysporum, F. iranicum, and F. redolens. These findings represent the first report of these species as causal agents of oregano root rot in Peru, highlighting the need for integrated management strategies that reduce the economic impact of these diseases and contribute to the sustainability of the crop in key producing regions such as Tacna. Full article

(This article belongs to the Special Issue Fungal Infections—Pathogenesis, Diagnosis, and Treatment: From Bench to Bedside and Beyond)

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14 pages, 1132 KiB

Open AccessArticle

Phylogenetic Reclassification of Metarhizium granulomatis and Metarhizium viride Species Complex

by Johanna Würf and Volker Schmidt

Pathogens 2025, 14(8), 745; https://doi.org/10.3390/pathogens14080745 - 29 Jul 2025

Abstract

Metarhizium (M.) granulomatis and M. viride have previously been described as pathogens causing hyalohyphomycosis in various species of captive chameleons and bearded dragons (Pogona vitticeps). Previous studies yielded different genotypes of M. granulomatis and M. viride based on sequencing of the [...] Read more.

Metarhizium (M.) granulomatis and M. viride have previously been described as pathogens causing hyalohyphomycosis in various species of captive chameleons and bearded dragons (Pogona vitticeps). Previous studies yielded different genotypes of M. granulomatis and M. viride based on sequencing of the internal transcribed spacer 1-5.8S rDNA (ITS-1-5.8S) and a fragment of the large subunit of the 28S rDNA (LSU). The aim of this study was to clarify the relationships between these genotypes and obtain a more accurate phylogenetic classification by sequencing two different loci of the RNA polymerase II second largest subunit (NRPB2), referred to as RPB1 and RPB2, and the translation elongation factor 1 alpha (EF1α). A total of 23 frozen isolates from 21 lizards, including the first isolates of M. granulomatis and M. viride from Parson’s chameleons (Calumma parsonii), were available for phylogenetic analysis. A total of 13 isolates belonged to the M. granulomatis complex and 10 isolates belonged to the M. viride complex. Following the amplification and sequencing of the protein-coding genes, the resulting nucleotide sequences were analyzed, trimmed and assembled. These were further analyzed with regard to differences in single-nucleotide polymorphisms (SNPs) and amino acid structure. In consideration of the results of the present analyses, a phylogenetic reclassification is recommended. Three different genotypes of M. granulomatis can be distinguished, which can be phylogenetically addressed as subspecies. Six subspecies can be distinguished regarding M. viride. Full article

(This article belongs to the Special Issue Filamentous Fungal Pathogens: 2nd Edition)

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24 pages, 2240 KiB

Open AccessArticle

Yeast Diversity on Sandy Lake Beaches Used for Recreation in Olsztyn, Poland

by Tomasz Bałabański, Anna Biedunkiewicz and Jan P. Jastrzębski

Pathogens 2025, 14(8), 744; https://doi.org/10.3390/pathogens14080744 - 29 Jul 2025

Abstract

Yeasts possess a range of environmental adaptations that allow them to colonize soil and sand. They can circulate seasonally between different components of lake ecosystems, including beach sand, water, and the coastal phyllosphere. The accumulation of people on beaches promotes the development and [...] Read more.

Yeasts possess a range of environmental adaptations that allow them to colonize soil and sand. They can circulate seasonally between different components of lake ecosystems, including beach sand, water, and the coastal phyllosphere. The accumulation of people on beaches promotes the development and transmission of yeasts, posing an increasing sanitary and epidemiological risk. The aim of this study was to determine the species and quantitative composition of potentially pathogenic and pathogenic yeasts for humans present in the sand of supervised and unsupervised beaches along the shores of lakes in the city of Olsztyn (northeastern Poland). The study material consisted of sand samples collected during two summer seasons (2019; 2020) from 12 research sites on sandy beaches of four lakes located within the administrative boundaries of Olsztyn. Standard isolation and identification methods used in diagnostic mycological laboratories were applied and are described in detail in the following sections of this study. A total of 259 yeast isolates (264, counting species in two-species isolates separately) belonging to 62 species representing 47 genera were obtained during the study. Among all the isolates, five were identified as mixed (two species from a single colony). Eight isolated species were classified into biosafety level 2 (BSL-2) and risk group 2 (RG-2). The highest average number of viable yeast cells was found in sand samples collected in July 2019 (5.56 × 10² CFU/g), August, and September 2020 (1.03 × 10³ CFU/g and 1.94 × 10³ CFU/g, respectively). The lowest concentrations were in samples collected in April, September, and October 2019, and October 2020 (1.48 × 10² CFU/g, 1.47 × 10² CFU/g, 1.40 × 10² CFU/g, and 1.40 × 10² CFU/g, respectively). The results indicate sand contamination with yeasts that may pose etiological factors for human mycoses. In light of these findings, continuous sanitary-epidemiological monitoring of beach sand and further studies on its mycological cleanliness are warranted, along with actions leading to appropriate legal regulations. Full article

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13 pages, 2021 KiB

Open AccessBrief Report

Recombinants Are the Key Drivers of Recent PRRSV-2 Evolution

by Clarissa Pellegrini Ferreira, Lucina Galina-Pantoja, Mark Wagner and Declan C. Schroeder

Pathogens 2025, 14(8), 743; https://doi.org/10.3390/pathogens14080743 - 29 Jul 2025

Abstract

Porcine reproductive and respiratory syndrome virus remains one of the most economically significant pathogens in swine production, with PRRSV-2 being the dominant variant in the United States. While lineage classification has traditionally relied on ORF5 sequencing, recent studies suggest that this single-gene approach [...] Read more.

Porcine reproductive and respiratory syndrome virus remains one of the most economically significant pathogens in swine production, with PRRSV-2 being the dominant variant in the United States. While lineage classification has traditionally relied on ORF5 sequencing, recent studies suggest that this single-gene approach may overlook key evolutionary events such as recombination. In this study, we performed whole-genome sequencing and phylogenetic analysis of seven PRRSV-2 isolates collected in the U.S. between 2006 and 2024. Using reference-guided assembly, lineage assignment, and recombination detection with RDP5 and SIMplot, we identified discordant phylogenetic placements between ORF5 and whole genomes in four of the seven isolates. These discordances were explained by multiple recombination events affecting different genomic regions, particularly ORF2–ORF7. In contrast, three isolates showed phylogenetic concordance and no strong evidence of recombination. Our findings demonstrate that recombination plays a significant role in shaping PRRSV-2 evolution and highlight the limitations of ORF5-based lineage classification. Whole-genome surveillance is therefore essential to accurately track viral diversity, detect recombinant strains, and inform control strategies. This work underscores the need for a broader adoption of full-genome analysis in routine PRRSV surveillance and research. Full article

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11 pages, 1598 KiB

Open AccessArticle

Genomic and Antimicrobial Resistance Analysis of an ST25 Streptococcus suis Strain Isolated from a Human in Zhejiang Province, China

by Shuirong Zhu, Xiaofang Wu, Wenwu Yao, Zhuoying Wu, Lingbo Wang, Zhangnv Yang, Beibei Wu and Yanjun Zhang

Pathogens 2025, 14(8), 742; https://doi.org/10.3390/pathogens14080742 - 28 Jul 2025

Abstract

A Streptococcus suis strain isolated from the blood of a patient in Zhejiang Province, China, was analysed using whole-genome sequencing and tested for antimicrobial resistance. The isolated strain was identified as S. suis serotype 2, and classified to ST25 on multilocus sequence typing [...] Read more.

A Streptococcus suis strain isolated from the blood of a patient in Zhejiang Province, China, was analysed using whole-genome sequencing and tested for antimicrobial resistance. The isolated strain was identified as S. suis serotype 2, and classified to ST25 on multilocus sequence typing (MLST). The minimum core genome group of the strain was identified as Group 4, and multilocus variable-number tandem-repeat analysis (MLVA) assigned it as type 2, 4.4, 0, 9, 3, 2, 0, 0. An antimicrobial resistance analysis showed that the strain was resistant to clindamycin, tetracycline, azithromycin, and erythromycin but sensitive to 11 other antibiotics. In a genomic evolution analysis, this isolate clustered on the same branch as North American pig isolate, Chinese pig isolates from Tianjin, and Hubei pig isolates. Full article

(This article belongs to the Special Issue Respiratory Diseases in Swine: Epidemiology, Diagnosis and Control)

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14 pages, 2266 KiB

Open AccessArticle

Advancing Extrapulmonary Tuberculosis Diagnosis: Potential of MPT64 Immunochemistry-Based Antigen Detection Test in a High-TB, Low-HIV Endemic Setting

by Ahmad Wali, Nauman Safdar, Atiqa Ambreen, Asif Loya and Tehmina Mustafa

Pathogens 2025, 14(8), 741; https://doi.org/10.3390/pathogens14080741 - 28 Jul 2025

Abstract

Extrapulmonary tuberculosis (EPTB) remains diagnostically challenging due to its paucibacillary nature and variable presentation. Xpert and culture are limited in EPTB diagnosis due to sampling challenges, low sensitivity, and long turnaround times. This study evaluated the performance of the MPT64 antigen detection test [...] Read more.

Extrapulmonary tuberculosis (EPTB) remains diagnostically challenging due to its paucibacillary nature and variable presentation. Xpert and culture are limited in EPTB diagnosis due to sampling challenges, low sensitivity, and long turnaround times. This study evaluated the performance of the MPT64 antigen detection test for diagnosing EPTB, particularly tuberculous lymphadenitis (TBLN) and tuberculous pleuritis (TBP), in a high-TB, low-HIV setting. Conducted at Gulab-Devi Hospital, Lahore, Pakistan, this study evaluated the MPT64 test’s performance against conventional diagnostic methods, including culture, histopathology, and the Xpert MTB/RIF assay. Lymph node biopsies were collected, and cell blocks were made from aspirated pleural fluid from patients clinically presumed to have EPTB. Of 338 patients, 318 (94%) were diagnosed with EPTB. For TBLN, MPT64 demonstrated higher sensitivity (84%) than Xpert (48%); for TBP, the sensitivity was 51% versus 7%, respectively. Among histopathology-confirmed TBLN cases, MPT64 outperformed both culture and Xpert (85% vs. 58% and 47%). Due to the low number of non-TB cases, specificity could not be reliably assessed. The MPT64 test shows promise as a rapid, sensitive diagnostic tool for EPTB, particularly TBLN, in routine settings. While sensitivity is notably superior to Xpert, further studies are needed to evaluate its specificity and broader diagnostic utility. Full article

(This article belongs to the Section Epidemiology of Infectious Diseases)

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12 pages, 277 KiB

Open AccessArticle

Risk Factors for Latent Tuberculosis Identified Using Epidemiological Investigation in Congregate Settings of Gyeongsan City, Republic of Korea (2014–2023)

by Seonyeong Park and Kwan Lee

Pathogens 2025, 14(8), 740; https://doi.org/10.3390/pathogens14080740 - 27 Jul 2025

Abstract

Latent tuberculosis infection (LTBI) remains an important public health issue, as individuals can harbor Mycobacterium tuberculosis without symptoms and later develop active disease. This study aimed to assess the prevalence and risk factors associated with LTBI positivity among tuberculosis (TB) contacts in congregate [...] Read more.

Latent tuberculosis infection (LTBI) remains an important public health issue, as individuals can harbor Mycobacterium tuberculosis without symptoms and later develop active disease. This study aimed to assess the prevalence and risk factors associated with LTBI positivity among tuberculosis (TB) contacts in congregate settings in Gyeongsan City, the Republic of Korea (ROK), from 2014 to 2023. A total of 213 index cases and 3666 contacts were analyzed using data from the Korea Tuberculosis Infection Control System (KTB-NET). Overall, 20.7% of contacts tested positive for LTBI, with the highest rates observed among contacts aged ≥65 years (50.4%) and in healthcare facilities (34.8%). Binary logistic regression analyses revealed that age ≥65 years (OR: 2.93; 95% CI: 1.95–4.39; p < 0.001), social welfare facilities (OR: 2.75; 95% CI: 2.10–3.58; p < 0.001), workplaces (OR: 2.42; 95% CI: 1.88–3.10; p < 0.001), and healthcare facilities (OR: 3.42; 95% CI: 2.63–4.43; p < 0.001) were significantly associated with increased LTBI risk. These findings highlight the importance of targeted interventions and prevention strategies focused on older adults and high-risk groups to prevent future TB outbreaks by reducing the burden of LTBI. Full article

(This article belongs to the Special Issue Feature Papers on the Epidemiology of Infectious Diseases)

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21 pages, 471 KiB

Open AccessReview

Role and Contribution of Serological Surveillance in Animals and Exposed Humans to the Study of Zoonotic Influenza Disease Epidemiology: A Scoping Review

by Rebecca Badra, Wenqing Zhang, John S. L. Tam, Richard Webby, Sylvie van der Werf, Sergejs Nikisins, Ann Cullinane, Saad Gharaibeh, Richard Njouom, Malik Peiris, Ghazi Kayali and Jean-Michel Heraud

Pathogens 2025, 14(8), 739; https://doi.org/10.3390/pathogens14080739 - 27 Jul 2025

Abstract

Background: Zoonotic influenza viruses pose a significant and evolving public health threat. In response to the recent rise in H5N1 cross-species transmission, the World Health Organization (WHO) R&D Blueprint for Epidemics consultations have prioritized strengthening surveillance, candidate vaccines, diagnostics, and pandemic preparedness. Serological [...] Read more.

Background: Zoonotic influenza viruses pose a significant and evolving public health threat. In response to the recent rise in H5N1 cross-species transmission, the World Health Organization (WHO) R&D Blueprint for Epidemics consultations have prioritized strengthening surveillance, candidate vaccines, diagnostics, and pandemic preparedness. Serological surveillance plays a pivotal role by providing insights into the prevalence and transmission dynamics of influenza viruses. Objective: This scoping review aimed to map the global research landscape on serological surveillance of zoonotic influenza in animals and exposed humans between 2017, the date of the last WHO public health research agenda for influenza review, and 2024, as well as to identify methodological advancements. Methods: Following PRISMA-ScR guidelines, we searched PubMed for English-language peer-reviewed articles published between January 2017 and March 2024. Studies were included if they reported serological surveillance in wild or domestic animals or occupationally exposed human populations, or novel methodologies and their technical limitations and implementation challenges. Results: Out of 7490 screened records, 90 studies from 33 countries, covering 25 animal species, were included. Seroprevalence studies were in domestic poultry and swine. Surveillance in companion animals, wild mammals, and at the human–animal interface was limited. Emerging serological methods included multiplex and nanobody-based assays, though implementation barriers remain. Conclusions: The review is limited by its restriction to one database and English-language articles, lack of quality appraisal, and significant heterogeneity among the included studies. Serological surveillance is a critical but underutilized tool in zoonotic influenza monitoring. Greater integration of serological surveillance into One Health frameworks, especially in high-risk regions and populations, is needed to support early detection and pandemic preparedness. Full article

(This article belongs to the Section Emerging Pathogens)

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