Pathogens

15 pages, 580 KB

Open AccessReview

Nocardia Osteomyelitis in Humans—A Narrative Review of Reported Cases, Microbiology, and Management

by Afroditi Ziogou, Alexios Giannakodimos, Ilias Giannakodimos, Stella Baliou, Andreas G. Tsantes and Petros Ioannou

Pathogens 2025, 14(10), 1032; https://doi.org/10.3390/pathogens14101032 (registering DOI) - 12 Oct 2025

Abstract

Nocardiosis is an infection caused by Gram-positive, saprophytic bacteria most often affecting immunocompromised hosts. The lungs, central nervous system, and skin are the sites most typically involved, although any organ may be affected. Skeletal involvement, particularly osteomyelitis, remains uncommon. This study is a [...] Read more.

Nocardiosis is an infection caused by Gram-positive, saprophytic bacteria most often affecting immunocompromised hosts. The lungs, central nervous system, and skin are the sites most typically involved, although any organ may be affected. Skeletal involvement, particularly osteomyelitis, remains uncommon. This study is a review of all published cases of Nocardia osteomyelitis in humans, emphasizing epidemiology, microbiology, clinical features, management, and patient outcomes. A narrative review was performed using data from the PubMed/MedLine and Scopus databases. Fifty studies describing 55 patients were included. The median age was 54 years, and 65.5% were male. The main risk factors were immunosuppression (21.8%) and trauma (18.2%). The vertebrae constituted the most commonly affected site (25.5%), followed by the lower limb bones (20%); 23.6% had multifocal disease. Nocardia asteroides accounted for the majority of cases (34.8%). Trimethoprim-sulfamethoxazole was the most frequently administered agent (81.5%), followed by cephalosporins (29.6%) and carbapenems (27.8%). Overall mortality was 9.3%, with 5.6% of reported deaths directly attributed to the infection. Although uncommon, osteomyelitis due to Nocardia spp. should be considered when Gram-positive, filamentous microorganisms are detected in bone specimens, particularly in immunocompromised or post-trauma patients, as early suspicion and targeted therapy may improve survival. Full article

(This article belongs to the Special Issue Infections and Bone Damage)

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20 pages, 1732 KB

Open AccessArticle

The Impact of Bacterial–Fungal Interactions on Childhood Caries Pathogenesis

by Shiyan Huang, Haojie Wang, Jing Tian, Man Qin, Ruixiang Gao, Bingqian Zhao, Jingyan Wang, Huajun Wu and He Xu

Pathogens 2025, 14(10), 1033; https://doi.org/10.3390/pathogens14101033 (registering DOI) - 11 Oct 2025

Abstract

Caries is the most prevalent chronic disease affecting oral health in preschool children. In this 12-month prospective cohort study of 3–4-year-olds, we investigated the community-level bacterial–fungal interkingdom interactome and its role in cariogenic microenvironments, using 16S rRNA gene (bacterial) sequencing and ITS2 gene [...] Read more.

Caries is the most prevalent chronic disease affecting oral health in preschool children. In this 12-month prospective cohort study of 3–4-year-olds, we investigated the community-level bacterial–fungal interkingdom interactome and its role in cariogenic microenvironments, using 16S rRNA gene (bacterial) sequencing and ITS2 gene (fungal) sequencing of unstimulated saliva. Longitudinal analysis identified 19 key bacterial and fungal species that were associated with both caries progression and clinical features. Salivary bacteria Desulfovibrio, Bacteroides heparinolyticus, Alloprevotella, Anaerobiospirillum, and fungus Candida tropicalis not only showed altered abundances during caries development but also correlated with severity of caries, establishing diagnostic microbial signatures for caries prediction. The salivary mycobiome exhibited highly active and complex intra-network interactions in the caries-active state, suggesting that fungal networks may drive the broader community-wide microbiota interaction network in the caries state. Metabolic profiling further revealed distinct pathway shifts before and after caries onset. The findings demonstrate that caries progression follows ecological succession governed by cross-domain interactions. This study highlighted the fungal network’s important role in driving dysbiosis, advancing the current understanding of early childhood caries beyond bacterial-centric models, and also highlighted fungi not only as modulators but as active contributors to cariogenesis, which could guide future antimicrobial strategies. Full article

17 pages, 510 KB

Open AccessReview

Optimizing Surgical Antibiotic Prophylaxis in the Era of Antimicrobial Resistance: A Position Paper from the Italian Multidisciplinary Society for the Prevention of Healthcare-Associated Infections (SIMPIOS)

by Massimo Sartelli, Francesco M. Labricciosa, Beatrice Casini, Francesco Cortese, Monica Cricca, Alessio Facciolà, Domitilla Foghetti, Matteo Moro, Angelo Pan, Daniela Pasero, Giuseppe Pipitone and Giancarlo Ripabelli

Pathogens 2025, 14(10), 1031; https://doi.org/10.3390/pathogens14101031 (registering DOI) - 11 Oct 2025

Abstract

Background: Although surgical antibiotic prophylaxis (SAP) is considered a standard of care for preventing surgical site infections, the rising incidence of antimicrobial resistance (AMR) increases the likelihood of infections caused by multidrug-resistant organisms (MDROs), which may be associated with worse surgical outcomes. Methods: [...] Read more.

Background: Although surgical antibiotic prophylaxis (SAP) is considered a standard of care for preventing surgical site infections, the rising incidence of antimicrobial resistance (AMR) increases the likelihood of infections caused by multidrug-resistant organisms (MDROs), which may be associated with worse surgical outcomes. Methods: A multidisciplinary working group was convened by the Italian Multidisciplinary Society for the Prevention of Healthcare-Associated Infections (SIMPIOS) to define key measures for optimizing SAP in the era of AMR. Selecting the most appropriate SAP in patients colonized with MDROs is a complex decision that cannot be generalized, as it depends on both host factors and the specific surgical procedure. At present, there is limited evidence of SAP in these patients. Results: This position paper aims to provide practical guidance for optimizing SAP in the context of an AMR era. It is structured in three sections: (1) core principles of surgical antibiotic prophylaxis; (2) the role of screening, decolonization, and targeted prophylaxis for MDROs; and (3) barriers to changing surgeons’ prescribing behaviours. Conclusions: The working group developed 15 recommendation statements based on scientific evidence. Full article

(This article belongs to the Special Issue Classic and Emerging Pathogens as a Cause of Healthcare-Associated Infections: Current Knowledge and Future Approaches)

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12 pages, 1759 KB

Open AccessArticle

Molecular Transmission Network and Pretreatment Drug Resistance of Newly Diagnosed HIV-1 Infections in Taizhou, a Coastal City in Eastern China, from 2021–2023

by Junxiao Lin, Haijiang Lin, Guixia Li, Shanling Wang, Tingting Wang, Qiguo Meng, Tingting Hua, Yali Xie, Jiafeng Zhang and Weiwei Shen

Pathogens 2025, 14(10), 1030; https://doi.org/10.3390/pathogens14101030 (registering DOI) - 11 Oct 2025

Abstract

Objective: This study conducted a comprehensive analysis of molecular transmission networks and pretreatment drug resistance (PDR) in newly diagnosed HIV-1 infections in Taizhou, China. Methods: From 2021 to 2023, we collected 1126 plasma samples from newly diagnosed HIV patients in Taizhou. The HIV [...] Read more.

Objective: This study conducted a comprehensive analysis of molecular transmission networks and pretreatment drug resistance (PDR) in newly diagnosed HIV-1 infections in Taizhou, China. Methods: From 2021 to 2023, we collected 1126 plasma samples from newly diagnosed HIV patients in Taizhou. The HIV pol gene was amplified, and the obtained sequence was used to construct a maximum likelihood (ML) phylogenetic tree and molecular transmission network. PDR-related mutations were analyzed based on the Stanford University HIV Resistance Database. We conducted genotyping analysis and analysis of factors related to the larger clusters (≥10). Results: We successfully amplified and sequenced the pol region from 937 (83.2%, 937/1126) treatment-naïve HIV-1 patients, each with comprehensive epidemiological documentation. Phylogenetic characterization revealed significant subtype heterogeneity, with CRF07_BC (42.1%, 395/937), CRF01_AE (27.6%, 259/937) and CRF08_BC (22.1%, 209/937) being the most prevalent. Notably, 11.4% of the sequenced population (107/937) presented detectable PDR mutations. Univariate analysis revealed that larger clusters (≥10) are more inclined to be aged ≥60, divorced or widowed, have high or technical secondary school education, and have sexual contact with homosexuality. Multivariate analysis revealed that age ≥60 years and not having a PDR mutation (p < 0.05) were factors associated with larger clusters (≥10). Conclusions: Molecular transmission networks suggest that CRF08_BC is spreading rapidly among the older male population. Consequently, targeted interventions aimed at this population are crucial for halting the ongoing rapid dissemination of this subtype. Full article

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18 pages, 2155 KB

Open AccessArticle

PRV gD-Based DNA Vaccine Candidates Adjuvanted with cGAS, UniSTING, or IFN-α Enhance Protective Immunity

by Xinqi Shi, Shibo Su, Yongbo Yang, Liang Meng, Wei Yang, Xinyu Qi, Xuyan Xiang, Yandong Tang, Xuehui Cai, Haiwei Wang, Tongqing An and Fandan Meng

Pathogens 2025, 14(10), 1026; https://doi.org/10.3390/pathogens14101026 (registering DOI) - 11 Oct 2025

Abstract

Pseudorabies virus (PRV), a major swine pathogen, causes severe neurological, respiratory, and reproductive disorders, resulting in substantial economic losses to the global swine industry. Previous studies have shown that the gD glycoprotein of PRV has an effective protective effect. In this study, we [...] Read more.

Pseudorabies virus (PRV), a major swine pathogen, causes severe neurological, respiratory, and reproductive disorders, resulting in substantial economic losses to the global swine industry. Previous studies have shown that the gD glycoprotein of PRV has an effective protective effect. In this study, we constructed a plasmid DNA vaccine (pVAX1-GD-Fc) encoding a gD protein fused with pig IgG Fc and evaluated the adjuvant effects of porcine cGAS, the universal STING complex mimic (UniSTING), or IFN-α in mice. The mice were immunized three times (days 0, 14, and 21) with pVAX1-GD-Fc in the presence or absence of an adjuvant, followed by lethal challenge with PRV-HLJ8 3 days after the final immunization. The results revealed that the pVAX1-GD-Fc group exhibited 20% mortality (1/5 mice) on day 7 postchallenge, and all adjuvanted groups achieved 100% survival during the 14-day observation period. Flow cytometric analysis of splenocytes one week after the second immunization revealed significantly greater CD8+ T cell proportions in the adjuvant groups than in both the mock and pVAX1-GD-Fc-only control groups (p < 0.01). Furthermore, T cell proliferation assays demonstrated a significantly increased stimulation index in the adjuvant-treated mice, confirming enhanced cellular immunity. These findings demonstrate that cGAS, UniSTING, and IFN-α can serve as effective vaccine adjuvants to rapidly enhance cellular immune responses to PRV, highlighting their potential application in veterinary vaccines. Full article

(This article belongs to the Special Issue Advancing Vaccine Strategies and Technologies for Controlling Swine Infectious Diseases)

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27 pages, 3600 KB

Open AccessArticle

TREM-1 Interacts with Rotavirus Proteins and Drives Inflammatory Responses: A Combined Experimental and Computational Approach

by Amanda de Oliveira Matos, José Rodrigues do Carmo Neto, Fernanda Craveiro Franco, Jefferson do Carmo Dietz, Pedro Henrique dos Santos Dantas, Andrei Giacchetto Felice, Adriana Luchs, Milton Adriano Pelli de Oliveira, Artur Christian Garcia da Silva, Siomar de Castro Soares, Simone Gonçalves da Fonseca, Fátima Ribeiro-Dias, Bruno Junior Neves, Carolina Horta Andrade, Marcelle Silva-Sales and Helioswilton Sales-Campos

Pathogens 2025, 14(10), 1029; https://doi.org/10.3390/pathogens14101029 - 10 Oct 2025

Abstract

Rotavirus (RV) is one of the main etiologic agents associated with diarrheal diseases (DDs), being responsible for approximately 200 thousand deaths annually. Currently, there are still many aspects regarding the virus biology, cell cycle, and pathophysiology of RV that need further elucidation. Therefore, [...] Read more.

Rotavirus (RV) is one of the main etiologic agents associated with diarrheal diseases (DDs), being responsible for approximately 200 thousand deaths annually. Currently, there are still many aspects regarding the virus biology, cell cycle, and pathophysiology of RV that need further elucidation. Therefore, the present work aimed to investigate whether the triggering receptor expressed on myeloid cells 1 (TREM-1) might be associated with RV infection. This immune receptor has been observed as an amplifier of inflammatory responses in different infectious and non-infectious diseases, including inflammatory bowel disease and celiac disease. Initially, we searched for public transcriptomic data regarding RV infection and the expression of TREM-1 and its associated genes, which were significantly upregulated in infected mice and children. Then, we infected monocytes with the virus, with or without a TREM-1 inhibitor. The inhibition of the receptor’s activity resulted in a significant decrease in IL-1β production. We also observed a reduction in cytopathic effects when MA104 cells were treated with TREM-1 inhibitors and then infected with simian RV. To further elucidate the interactions between the virus and TREM-1, in silico tools were used to simulate interactions between the receptor and RV proteins. These simulations suggested the occurrence of interactions between TREM-1 and VP5*, a protein involved in viral attachment to target cells, and also between the receptor and NSP4, a viral enterotoxin with immunostimulant properties. Hence, our results indicate that TREM-1 is involved in RV infection, both as a mediator of inflammatory responses and as a player in the host–virus relationship. Full article

(This article belongs to the Special Issue From Gastroenteritis to Emerging Threats: One Health Surveillance of Viral Infections)

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11 pages, 901 KB

Open AccessArticle

Optimizing PRRSV Detection: The Impact of Sample Processing and Testing Strategies on Tongue Tips

by Igor A. D. Paploski, Mariana Kikuti, Xiaomei Yue, Claudio Marcello Melini, Albert Canturri, Stephanie Rossow and Cesar A. Corzo

Pathogens 2025, 14(10), 1028; https://doi.org/10.3390/pathogens14101028 - 10 Oct 2025

Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant challenge, costing annually approximately USD 1.2 billion to the U.S. swine industry due to production losses associated with, but not limited to, reproductive failure, abortion, and high pre-weaning mortality among piglets. PRRSV is [...] Read more.

Porcine reproductive and respiratory syndrome virus (PRRSV) poses a significant challenge, costing annually approximately USD 1.2 billion to the U.S. swine industry due to production losses associated with, but not limited to, reproductive failure, abortion, and high pre-weaning mortality among piglets. PRRSV is endemic, with thirty percent of the U.S. breeding herd experiencing outbreaks annually. The shedding status of animals on a farm is typically assessed using serum or processing fluids from piglets, but tongue tips from deceased animals are emerging as a potential alternative specimen to support farm stability assessment. This study explored the impact of various processing and testing strategies on tongue tips to enhance the sensitivity and specificity of PRRSV detection in sow herds. We collected tongue tips from 20 dead piglets across seven sow farms, testing different pooling strategies (individual testing, and pools of n = 5 or n = 20) and laboratory processing methods (tongue tip fluid—TTF, versus tongue tissue homogenate—TTH). Additionally, we simulated storage and shipping conditions, comparing frozen samples to refrigerated ones tested at intervals of 1, 4, and 7 days post collection. RT-PCR testing revealed higher sensitivity and lower cycle threshold (Ct) values for TTF compared to TTH, suggesting that tongue tips are better tested as TTF rather than TTH for PRRSV detection. Pooling samples reduced diagnostic accuracy. Frozen samples had lower absolute Ct values, and Ct values increased by 0.2 Ct values each day post collection when the sample was kept refrigerated, emphasizing the importance of minimizing shipping delays. Tongue tips are a practical, easy-to-collect specimen that target potentially infected animals (dead piglets), offering valuable insights into swine herd health, but sample processing approaches significantly influence diagnostic outcomes. If tongue tips are used by veterinarians to assess viral presence on a farm, testing the TTF instead of TTH should be prioritized. Storage and shipment conditions should be considered to optimize laboratory results. Full article

(This article belongs to the Section Viral Pathogens)

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22 pages, 782 KB

Open AccessReview

Deep Mutational Scanning in Immunology: Techniques and Applications

by Chengwei Shao, Siyue Jia, Yue Li and Jingxin Li

Pathogens 2025, 14(10), 1027; https://doi.org/10.3390/pathogens14101027 - 10 Oct 2025

Abstract

Mutations may cause changes in the structure and function of immune-related proteins, thereby affecting the operation of the immune system. Deep mutational scanning combines saturation mutagenesis, functional selection, and high-throughput sequencing to evaluate the effects of mutations on a large scale and with [...] Read more.

Mutations may cause changes in the structure and function of immune-related proteins, thereby affecting the operation of the immune system. Deep mutational scanning combines saturation mutagenesis, functional selection, and high-throughput sequencing to evaluate the effects of mutations on a large scale and with high resolution. By systematically and comprehensively analyzing the impact of mutations on the functions of immune-related proteins, the immune response mechanism can be better understood. However, each stage in deep mutation scanning has its limits, and the approach remains constrained in several ways. These include data and selection biases that affect the robustness of effect estimates, insufficient library coverage and editability leading to uneven representation of sites and alleles, system-induced biased signals that deviate phenotypes from their true physiological state, and imperfect models and statistical processing that limit extrapolation capabilities. Therefore, this technology still needs further development. Herein, we summarize the principles and methods of deep mutational scanning and discuss its application in immunological research. The aim is to provide insights into the broader application prospects of deep mutational scanning technology in immunology. Full article

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15 pages, 4169 KB

Open AccessArticle

Climate and the Parasite Paradox: Tick–Host Networks Depend on Gradients of Environmental Overlap

by Agustín Estrada-Peña

Pathogens 2025, 14(10), 1025; https://doi.org/10.3390/pathogens14101025 - 10 Oct 2025

Abstract

This study investigates how climate gradients shape tick–host associations, testing the hypothesis that variations in climate leverage some associations, which can be ecosystem-specific. To test this hypothesis, we modelled tick–host associations across the Western Palearctic using climatic variables and a large dataset of [...] Read more.

This study investigates how climate gradients shape tick–host associations, testing the hypothesis that variations in climate leverage some associations, which can be ecosystem-specific. To test this hypothesis, we modelled tick–host associations across the Western Palearctic using climatic variables and a large dataset of georeferenced tick (seven species, n = 23,462) and vertebrate host records (n = 6.5 million across 162 species aggregated into 50 genera). Niche overlap with hosts is highly variable but consistently significant (p < 0.05) in every tested ecosystem of the target territory. Montane grasslands exhibit the lowest values of tick–host niche overlap, meaning that they support the smallest but still resilient set of available hosts. Host phylogenetic diversity (PD) depends on the ecosystem rather than tick species; PD is lowest in montane grasslands (supporting previous results) and in the case of D. reticulatus in savannas and scrubland. Nestedness of tick–host networks, known to be related to the resilience of parasite–host networks, is highest in climatically extreme ecosystems, reflecting adaptability of tick–host networks, as measured by niche overlap on modelled distribution. Multidimensional scaling confirms that host community composition and niche overlap vary significantly across ecosystems, supporting the hypothesis of host rewiring under diverse climatic conditions. These findings may have important implications for the concept of community composition and the circulation of tick-borne pathogens. Full article

(This article belongs to the Section Ticks)

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14 pages, 1829 KB

Open AccessArticle

Management of Odontogenic Infections in Pregnant Patients: Case-Based Approach and Literature Review

by Andrei Hramyka, Agata Wieczorkiewicz, Jakub Bargiel, Krzysztof Śliwiński, Krzysztof Gąsiorowski, Tomasz Marecik, Paweł Szczurowski, Grażyna Wyszyńska-Pawelec, Jan Zapała and Michał Gontarz

Pathogens 2025, 14(10), 1024; https://doi.org/10.3390/pathogens14101024 - 9 Oct 2025

Abstract

Background: Odontogenic abscesses may significantly affect maternal health during pregnancy. Aim: This study analyzes three cases of pregnant patients with odontogenic infections, comparing them to a control group of non-pregnant women, and reviews recent literature. Materials and Methods: Between January 2020 and April [...] Read more.

Background: Odontogenic abscesses may significantly affect maternal health during pregnancy. Aim: This study analyzes three cases of pregnant patients with odontogenic infections, comparing them to a control group of non-pregnant women, and reviews recent literature. Materials and Methods: Between January 2020 and April 2025, 3 pregnant and 70 non-pregnant women with odontogenic abscesses were treated. Clinical presentation, pathogens, therapy, and outcomes were compared. Results: Severe sequelae, such as rapid abscess spread and systemic inflammation, were more frequent in pregnant women, though not statistically significant (p = 0.068). Pregnant patients also tended toward prolonged intubation (p = 0.194) and targeted antibiotic use (p = 0.133). Antibiotic selection was based on gestational age, with beta-lactams preferred. Surgical interventions were more extensive, often involving multiple neck spaces. Hospitalization was longer (≥4 days in most cases) due to maternal–fetal monitoring. Conclusions: Odontogenic abscesses in pregnancy require individualized management and gestation-adjusted antibiotic therapy. Full article

(This article belongs to the Special Issue Oral Microbes and Oral Diseases)

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13 pages, 1676 KB

Open AccessArticle

Detection and Impact of Staphylococcus aureus Small Colony Variants in Chronic Wounds: A Pilot Study

by Eleanna Carris, Klara C. Keim, Landrye Reynolds-Reber, Isaiah K. George, Nicholas Sanford, Rocio Navarro-Garcia, Taylor D. Lenzmeier and Allie Clinton Smith

Pathogens 2025, 14(10), 1023; https://doi.org/10.3390/pathogens14101023 - 9 Oct 2025

Abstract

A unique phenotype of S. aureus called S. aureus small-colony variants (SA-SCVs) are a consequential contributor to multiple infectious processes. SA-SCVs are distinguishable from wild-type S. aureus (WT-SA) by their small size, slowed growth rate, and altered biochemical reactions; these changes make SA-SCV [...] Read more.

A unique phenotype of S. aureus called S. aureus small-colony variants (SA-SCVs) are a consequential contributor to multiple infectious processes. SA-SCVs are distinguishable from wild-type S. aureus (WT-SA) by their small size, slowed growth rate, and altered biochemical reactions; these changes make SA-SCV more difficult to detect from clinical specimens using routine diagnostics. While the clinical environment of chronic wound infections has the potential to stimulate the production of SA-SCVs, studies investigating detection of SA-SCVs in chronic wounds have not been previously conducted. Chronic wound specimens found to harbor S. aureus via qPCR screening, and screened for recent aminoglycoside treatment and/or co-infected with Pseudomonas aeruginosa, were collected from a specialty wound care clinic in April 2019. In-house enrichment methods alongside culture-dependent and independent diagnostics were utilized to recover and identify SA-SCVs from these chronic wounds. Our investigation determined difficulties in recovering and identifying SA-SCVs during routine diagnostic procedures, and the potential clinical impact of wounds harboring SA-SCVs related to antimicrobial susceptibility. Full article

(This article belongs to the Special Issue Drug Resistant Pathogens: Diagnosis, Treatment, and Global Health Implications)

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18 pages, 324 KB

Open AccessReview

HSV-1 as a Potential Driver of Alzheimer’s Disease

by Dar-Yin Li, Eun Seok Choi and Xiaoyong Bao

Pathogens 2025, 14(10), 1022; https://doi.org/10.3390/pathogens14101022 - 8 Oct 2025

Abstract

Herpes simplex virus type 1 (HSV-1) is a continuous health challenge, and current antiviral treatments cannot cure the virus. As life expectancy continues to increase worldwide, HSV-1 should remain a focus to minimize its associated health complications within the aging population. While often [...] Read more.

Herpes simplex virus type 1 (HSV-1) is a continuous health challenge, and current antiviral treatments cannot cure the virus. As life expectancy continues to increase worldwide, HSV-1 should remain a focus to minimize its associated health complications within the aging population. While often asymptomatic, HSV-1 causes oral and cutaneous lesions and establishes latency with periodic reactivation. Antivirals reduce symptoms but do not eradicate the virus. Emerging evidence links HSV-1 to Alzheimer’s disease (AD) via chronic neuroinflammation, amyloid-beta and tau accumulation, oxidative stress, and synaptic dysfunction, with viral proteins detected in AD-affected brain regions. This review assesses the current evidence for HSV-1 in dementia pathogenesis, examines antiviral strategies as potential neuroprotective interventions, and outlines the experimental models required to establish causality. Full article

(This article belongs to the Section Viral Pathogens)

12 pages, 1231 KB

Open AccessArticle

Ticks and Associated Rickettsiae from Domestic Animals in Bhutan

by Tshokey Tshokey, Mythili Tadepalli, Stephen R. Graves and John Stenos

Pathogens 2025, 14(10), 1021; https://doi.org/10.3390/pathogens14101021 - 8 Oct 2025

Abstract

In Bhutan, information on rickettsiae is limited to a few epidemiological studies. There is no information on ticks and tick-associated rickettsiae. Ticks were collected opportunistically from domestic animals residing in eight districts where a seroprevalence study had been carried out previously. Morphological identification [...] Read more.

In Bhutan, information on rickettsiae is limited to a few epidemiological studies. There is no information on ticks and tick-associated rickettsiae. Ticks were collected opportunistically from domestic animals residing in eight districts where a seroprevalence study had been carried out previously. Morphological identification of the ticks was performed in the United States National Tick Collection and testing for rickettsiae was carried out in the Australian Rickettsial Reference Laboratory. Samples positive for rickettsiae by qPCR were subjected to conventional PCR followed by DNA sequencing and phylogenetic analysis. A total of 200 ticks were sampled from 155 domestic animals including cattle, dogs, goats, horses, yaks, sheep and cats. The ticks belonged to twelve different species, the commonest being Rhipicephalus microplus, followed by Rhipicephalus haemaphysaloides, Haemaphysalis sp. near ramachandrai, Haemaphysalis tibetensis, Haemaphysalis bispinosa, Haemaphysalis sp., Haemaphysalis sp. near davisi, Rhipicephalus sanguineus, Haemaphysalis shimoga, Haemaphysalis hystricis, Ixodes ovatus, and Amblyomma testudinarium. Rickettsial DNA sequence analysis showed that the rickettsiae infesting ticks in Bhutanese domestic animals aligned with R. gravesii, R. canadensis, R. honei, R. africae, R. felis, R. akari, R. australis, R. japonica, R. africae, R. heilongjiangensis, R. conorii, R. peacockii, R. honei, R. massiliae and R. rhipicephali. However, these may not be conclusive due to low bootstrap values in the phylogenetic tree. Bhutan will benefit from larger studies on ticks and tick-borne infections, burden and damage assessment to livestock and human health, public health interventions and clinical guidelines to reduce morbidity and mortality in human and animal health. Full article

(This article belongs to the Special Issue New Insights Into Zoonotic Intracellular Pathogens)

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18 pages, 86576 KB

Open AccessArticle

Morpho-Molecular Identification and Pathogenic Characterization of Fusarium and Colletotrichum Species Associated with Intercropped Soybean Pod Decay

by Maira Munir, Muhammd Naeem, Xiaoling Wu, Weiying Zeng, Zudong Sun, Yuze Li, Taiwen Yong, Feng Yang and Xiaoli Chang

Pathogens 2025, 14(10), 1020; https://doi.org/10.3390/pathogens14101020 - 8 Oct 2025

Abstract

The fruiting stage of soybean (Glycine max L.) is critical for determining both its yield and quality, thereby influencing global production. While some studies have provided partial explanations for the occurrence of Fusarium species on soybean seeds and pods, the fungal diversity [...] Read more.

The fruiting stage of soybean (Glycine max L.) is critical for determining both its yield and quality, thereby influencing global production. While some studies have provided partial explanations for the occurrence of Fusarium species on soybean seeds and pods, the fungal diversity affecting soybean pods in Sichuan Province, a major soybean cultivation region in Southwestern China, remains inadequately understood. In this study, 182 infected pods were collected from a maize–soybean relay strip intercropping system. A total of 10 distinct pod-infecting fungal genera (132 isolates) were identified, and their pathogenic potential on soybean seeds and pods was evaluated. Using morphological characteristics and DNA barcode markers, we identified 43 Fusarium isolates belonging to 8 species, including F. verticillioides, F. incarnatum, F. equiseti, F. proliferatum, F. fujikuroi, F. oxysporum, F. chlamydosporum, and F. acutatum through the analysis of the translation elongation factor gene (EF1-α) and RNA polymerases II second largest subunit (RPB2) gene. Multi-locus phylogenetic analysis, incorporating the Internal Transcribed Spacer (rDNA ITS), β-tubulin (β-tubulin), Glyceraldehyde 3-phosphate dehydrogenase (GADPH), Chitin Synthase 1 (CHS-1), Actin (ACT), Beta-tubulin II (TUB2), and Calmodulin (CAL) genes distinguished 37 isolates as 6 Colletotrichum species, including C. truncatum, C. karstii, C. cliviicola, C. plurivorum, C. boninense, and C. fructicola. Among these, F. proliferatum and C. fructicola were the most dominant species, representing 20.93% and 21.62% of the isolation frequency, respectively. Pathogenicity assays revealed significant damage from both Fusarium and Colletotrichum isolates on soybean pods and seeds, with varying isolation frequencies. Of these, F. proliferatum, F. acutatum, and F. verticillioides caused the most severe symptoms. Similarly, within Colletotrichum genus, C. fructicola was the most pathogenic, followed by C. truncatum, C. karstii, C. cliviicola, C. plurivorum, and C. boninense. Notably, F. acutatum, C. cliviicola, C. boninense, and C. fructicola were identified for the first time as pathogens of soybean pods under the maize–soybean strip intercropping system in Southwestern China. These findings highlight emerging virulent pathogens responsible for soybean pod decay and provide a valuable foundation for understanding the pathogen population during the later growth stages of soybean. Full article

(This article belongs to the Special Issue Fungal Pathogenicity Factors: 2nd Edition)

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21 pages, 6390 KB

Open AccessArticle

Machine Learning-Based Characterization of Bacillus anthracis Phenotypes from pXO1 Plasmid Proteins

by William Harrigan, Thi Hai Au La, Prashant Dahal, Mahdi Belcaid and Michael H. Norris

Pathogens 2025, 14(10), 1019; https://doi.org/10.3390/pathogens14101019 - 8 Oct 2025

Abstract

The Bacillus anthracis pXO1 plasmid, encoding ~143 proteins, presents a compact model for exploring protein function and evolutionary patterns using protein language models. Due to the organism’s slow evolutionary rate, its limited amino acid variation enhances detection of physiologically relevant patterns in plasmid [...] Read more.

The Bacillus anthracis pXO1 plasmid, encoding ~143 proteins, presents a compact model for exploring protein function and evolutionary patterns using protein language models. Due to the organism’s slow evolutionary rate, its limited amino acid variation enhances detection of physiologically relevant patterns in plasmid protein composition. In this study, we applied embedding-based analyses and machine learning methods to characterize pXO1 protein modules across diverse B. anthracis lineages. We generated protein sequence embeddings, constructed phylogenies, and compared plasmid content with whole genome variation. While whole genome and plasmid-based phylogenies diverge, the composition of proteins encoded along the pXO1 plasmid revealed lineage specific structure. Association rule mining combined with decision tree classification produced plasmid-encoded targets for assessing anthrax sublineage, which yielded functionally redundant protein modules that reflected geographic and phylogenetic patterns. A conserved DNA replication module exhibited both shared and B. anthracis lineage specific features. These results show that pXO1 plasmid protein modules contain biologically meaningful and evolutionarily informative signatures, exemplifying their value in phylogeographic characterizations of bacterial pathogens. This framework can be extended to study additional virulence plasmids across Bacillus and other environmental pathogens using scalable protein language model tools. Full article

(This article belongs to the Section Bacterial Pathogens)

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22 pages, 1305 KB

Open AccessReview

Neutrophil Extracellular Traps in Viral Infections

by Jiajun Chen, Rong He, Jirong Luo, Shilu Yan, Wenbo Zhu and Shuangquan Liu

Pathogens 2025, 14(10), 1018; https://doi.org/10.3390/pathogens14101018 - 8 Oct 2025

Abstract

Neutrophils are the most abundant immune cells in the human body. Neutrophil extracellular traps (NETs) have recently garnered significant attention as a novel, non-traditional mechanism for combating pathogenic microorganisms. Recent studies have shown that NETs play a crucial role in antiviral immunity, providing [...] Read more.

Neutrophils are the most abundant immune cells in the human body. Neutrophil extracellular traps (NETs) have recently garnered significant attention as a novel, non-traditional mechanism for combating pathogenic microorganisms. Recent studies have shown that NETs play a crucial role in antiviral immunity, providing new perspectives on how neutrophils defend against viral invasion. Viruses not only induce NET formation through various mechanisms but have also developed multiple escape strategies targeting NETs. It is worth noting that NETs are a double-edged sword for the host: while they possess antiviral effects that inhibit viral spread and replication, their constituent components may also exacerbate tissue damage and play important pathological roles in the progression of certain viral infections. Therefore, a thorough understanding of the regulatory mechanisms and dynamic balance of NETs in viral infections is of critical importance. Additionally, since the components of NETs may vary depending on the stimulus, NET-related markers have the potential to serve as biomarkers for the severity and prognosis of viral diseases. This article provides a systematic review of the induction mechanisms, antiviral effects, viral escape strategies, and virus-induced NET-related immunopathological damage in viral infections, offering new insights for antiviral immunotherapy. Full article

(This article belongs to the Section Viral Pathogens)

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11 pages, 436 KB

Open AccessArticle

A Novel PCR Panel for Bacterial Detection in Lower Respiratory Tract Infections: A Comparative Study with Culture Results

by Selda Kömeç, Mehmet Akif Durmuş, Ayşe Nur Ceylan and Ramazan Korkusuz

Pathogens 2025, 14(10), 1017; https://doi.org/10.3390/pathogens14101017 - 8 Oct 2025

Abstract

Lower respiratory tract (LRT) infections require rapid and accurate diagnosis. While bacterial culture remains the gold standard, multiplex PCR (mPCR) enables faster and more sensitive detection of multiple pathogens. This study evaluates the Bio-Speedy mPCR panel for 18 bacteria in comparison to conventional [...] Read more.

Lower respiratory tract (LRT) infections require rapid and accurate diagnosis. While bacterial culture remains the gold standard, multiplex PCR (mPCR) enables faster and more sensitive detection of multiple pathogens. This study evaluates the Bio-Speedy mPCR panel for 18 bacteria in comparison to conventional culture. A total of 100 LRT samples were analyzed. Complete concordance between the methods was observed in 85% of samples, with mPCR detecting pathogens slightly more frequently (62% vs. 53%). Discrepancies were primarily due to prior antibiotic therapy, low bacterial loads, colonization, or pathogens not included in the PCR panel. The sensitivity and specificity of mPCR were 79.3% and 96.8%, respectively, with negative agreement at 98.9% and positive agreement at 57.0%. Considering culture-negative but clinically relevant PCR-positive results, the sensitivity improved to 98.1% and the positive agreement to 86.7%. mPCR offers early pathogen detection, enabling timely therapy and potentially improving outcomes, particularly in intensive care settings. While culture remains indispensable for viable pathogen identification, combining mPCR with conventional methods provides complementary information, particularly when prior antibiotic use or the presence of fastidious pathogens may compromise culture results. Careful consideration of cost, patient population, and clinical context is recommended for optimal implementation of mPCR panels. Full article

(This article belongs to the Section Bacterial Pathogens)

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12 pages, 2573 KB

Open AccessCase Report

An Unusual Case of Anterior Mediastinal Cystic Echinococcosis Successfully Resolved with Multidisciplinary Approach

by Katarzyna Rodak, Magdalena Mnichowska-Polanowska, Arkadiusz Waloryszak, Konrad Ptaszyński, Janusz Wójcik and Małgorzata Edyta Wojtyś

Pathogens 2025, 14(10), 1016; https://doi.org/10.3390/pathogens14101016 - 7 Oct 2025

Abstract

Human echinococcosis is a zoonotic disease caused by accidental ingestion of tapeworm eggs of the genus Echinococcus, shed in the feces of animal definitive host. In the human duodenum, these eggs release oncospheres, which penetrate the intestinal wall and via the bloodstream [...] Read more.

Human echinococcosis is a zoonotic disease caused by accidental ingestion of tapeworm eggs of the genus Echinococcus, shed in the feces of animal definitive host. In the human duodenum, these eggs release oncospheres, which penetrate the intestinal wall and via the bloodstream reach the liver—the most common site for development of cysts. However, it is important to remember that any other organ can be affected via the bloodstream, due to larvae size. In Europe, the most diagnostically relevant species are Echinococcus granulosus, with a median incidence of 0.6 cases per 100,000 inhabitants, and Echinococcus multilocularis, with 0.1 cases per 100,000 inhabitants. This article aims to describe an exceptionally unusual location of human cystic echinococcosis in the anterior mediastinum. We describe the role of multidisciplinary diagnostics in establishing the definitive diagnosis. The pathomorphological examination, radiological imaging and serological testing for diagnosing cystic echinococcosis are hereby described. It is particularly important to avoid reporting unspecified Echinococcus (NOS) if possible, as the management and treatment of patients with echinococcosis varies depending on the species. Full article

(This article belongs to the Special Issue Parasitic Diseases in the Contemporary World)

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11 pages, 5304 KB

Open AccessCase Report

Early Detection and Identification of Methylobacterium radiotolerans Bacteremia in an Early T-Cell Precursor Acute Lymphoblastic Leukemia Patient: A Rare Infection and Literature Review

by Jiayu Xiao, Lingli Liu, Xuzhen Qin and Yingchun Xu

Pathogens 2025, 14(10), 1015; https://doi.org/10.3390/pathogens14101015 - 7 Oct 2025

Abstract

(1) Background: Methylobacterium radiotolerans (M. radiotolerans) is a fastidious, aerobic, Gram-negative bacillus primarily found in environmental sources such as soil and sewage, with rare clinical isolation. Its identification remains challenging due to poor growth with conventional culture methods. (2) Case presentation: [...] Read more.

(1) Background: Methylobacterium radiotolerans (M. radiotolerans) is a fastidious, aerobic, Gram-negative bacillus primarily found in environmental sources such as soil and sewage, with rare clinical isolation. Its identification remains challenging due to poor growth with conventional culture methods. (2) Case presentation: A 42-year-old male patient with early T-cell precursor acute lymphoblastic leukemia (ETP-ALL) presented with M. radiotolerans bacteremia during hospitalization. The organism was successfully isolated from peripheral blood using the Myco/F Lytic culture vial (Becton, Dickinson and Company, Lincoln, MT, USA). Comparative analysis demonstrated markedly superior growth of M. radiotolerans in Myco/F Lytic culture vials compared with Plus Aerobic/F Lytic and Lytic/10 Anaerobic/F culture vials (Becton, Dickinson and Company, Lincoln, MT, USA). Antimicrobial susceptibility testing, performed with the epsilometer test (E-test) and Bauer–Kirby disk diffusion (BK) method, guided the selection of an appropriate therapeutic regimen. The patient’s infection was ultimately controlled following targeted antimicrobial therapy. (3) Conclusions: M. radiotolerans demonstrates a distinct growth preference for the Myco/F Lytic culture medium. This observation highlights the importance of considering alternative culture media in cases of rare or fastidious bacterial infections that cannot be reliably detected using conventional Plus Aerobic/F Lytic or Lytic/10 Anaerobic/F culture vials, which are typically employed for clinical isolation of aerobic and anaerobic bacteria. Full article

(This article belongs to the Section Bacterial Pathogens)

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