Pathogens

19 pages, 6927 KB

Open AccessArticle

Serum Proteomics Reveals Systemic Responses in Didelphis aurita Naturally Infected with Hepatozoon sp.

by Andrés Mauricio Ortega Orozco, Camilo Jose Ramirez-Lopez, Lucas Drumond Bento, Pollyanna Cordeiro Souto, Fabrícia Modolo Girardi, Veronica Rodrigues Castro, Edvaldo Barros, Joao Vitor Gonçalves de Oliveira, Renner Philipe Rodrigues Carvalho, Artur Kanadani Campos and Leandro Abreu da Fonseca

Pathogens 2025, 14(10), 1042; https://doi.org/10.3390/pathogens14101042 - 14 Oct 2025

Abstract

Didelphis aurita is a widely distributed neotropical marsupial frequently found in peri-urban environments and known to harbor various pathogens, including hemoparasites of the genus Hepatozoon. However, the systemic physiological responses of naturally infected individuals remain poorly understood. This study aimed to characterize the [...] Read more.

Didelphis aurita is a widely distributed neotropical marsupial frequently found in peri-urban environments and known to harbor various pathogens, including hemoparasites of the genus Hepatozoon. However, the systemic physiological responses of naturally infected individuals remain poorly understood. This study aimed to characterize the serum proteomic profile of Didelphis aurita naturally infected with Hepatozoon sp., providing insights into host–parasite interactions and potential biomarkers of infection. Serum samples were analyzed using liquid chromatography–tandem mass spectrometry (LC-MS/MS), followed by functional annotation based on Gene Ontology and KEGG pathway enrichment. A total of 67 proteins were identified, 33 of which were exclusive to infected animals. The most abundant proteins included albumin, hemoglobin subunits, and venom metalloproteinase inhibitors (DM43 and DM64). Functional enrichment revealed significant involvement in complement and coagulation cascades, protease inhibition, antioxidant defense, and extracellular vesicle localization. Key proteins such as fibrinogen, plasminogen, antithrombin, SERPIN family members, vitronectin, and fibronectin suggest an integrated host response involving hemostasis, inflammation control, and tissue remodeling. This is the first report of the serum proteome of Didelphis aurita naturally infected with Hepatozoon sp. Despite the absence of protein validation, the findings provide novel insights into marsupial immunophysiology and offer a foundation for future biomarker research and ecoimmunological surveillance in synanthropic species. Full article

(This article belongs to the Special Issue Proteomic Approaches in Different Animal Pathogens)

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20 pages, 3708 KB

Open AccessArticle

Bacillus anthracis Phylogeography: Origin of the East Asian Polytomy and Impact of International Trade for Its near Global Dispersal

by Gilles Vergnaud, Markus H. Antwerpen and Gregor Grass

Pathogens 2025, 14(10), 1041; https://doi.org/10.3390/pathogens14101041 - 14 Oct 2025

Abstract

Bacillus anthracis is the etiological agent of the zoonotic disease anthrax. The pathogen has colonized many regions of all inhabited continents. Increasing evidence points to a strong contribution of anthropogenic activities (trade) in this almost global spread. This article contributes further genomic data [...] Read more.

Bacillus anthracis is the etiological agent of the zoonotic disease anthrax. The pathogen has colonized many regions of all inhabited continents. Increasing evidence points to a strong contribution of anthropogenic activities (trade) in this almost global spread. This article contributes further genomic data from 21 B. anthracis strains, including 19 isolated in Germany, aiming to support and detail the human role in anthrax dispersal. The newly sequenced genomes belong to the B. anthracis lineage predominant in China. This lineage is remarkable because of its phylogenetic structure. A polytomy with nine branches radiating from a central node was identified by whole-genome single-nucleotide polymorphism (wgSNP) analysis. Strains from Germany populate two among the nine branches. Detailed analysis of the polytomy indicates that it most likely emerged in China. We propose that the polytomy is the result of the import of contaminated animal products in a limited spatiotemporal frame, followed by the distribution of these products to different locations within China, where new B. anthracis lineages then became independently established. Currently available data point to Bengal as a likely geographic source of the original contamination, and the history of trade exchanges between Bengal and China agrees with the early fifteenth century as a likely time period. The subsequent exports to Germany would have occurred during the 19th century according to German trade history. Notably, Germany has been experiencing localized anthrax outbreaks from this trade heritage up into the 21st century. Full article

(This article belongs to the Special Issue Current Research on Bacillus anthracis Infection)

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16 pages, 2782 KB

Open AccessArticle

Genetic Diversity and Antibiotic Resistance Paradigm of Enterobacterales in Animal-Derived Food Sources: A One Health Disquiet

by Ayesha Sarwar, Bilal Aslam, Muhammad Hidayat Rasool, Muhammad Shafique, Mohsin Khurshid, James Jacob Sasanya and Sulaiman F. Aljasir

Pathogens 2025, 14(10), 1040; https://doi.org/10.3390/pathogens14101040 - 13 Oct 2025

Abstract

The indiscriminate use of antibiotics in food-producing animals serves as a major catalyst for the emergence of antibiotic-resistant infections. This study aimed to assess the genetic diversity and antibiotic resistance of Enterobacterales in animal-derived foods. A total of 905 animal-derived food samples, including [...] Read more.

The indiscriminate use of antibiotics in food-producing animals serves as a major catalyst for the emergence of antibiotic-resistant infections. This study aimed to assess the genetic diversity and antibiotic resistance of Enterobacterales in animal-derived foods. A total of 905 animal-derived food samples, including meat, dairy, poultry, fish, and environmental sources, were collected from various locations in Pakistan. Isolates were confirmed through selective subculturing, morphological, biochemical, and MALDI-TOF analysis, followed by antibiotic susceptibility testing. Subsequently, PCR-based detection of antibiotic resistance genes and virulence-associated genes. Overall, a total of 263 (29.06%) Enterobacterales were identified, as follows: 58.55% (154/263) E. coli, 6.84% (18/263) K. pneumoniae, 21.29% (56/263) P. mirabilis, and 13.30% (35/263) Salmonella spp. Isolates showed a varying resistance pattern against different studied antibiotics, e.g., beta-lactams and inhibitors, ciprofloxacin, and tetracycline, while colistin and tigecycline remained most effective. All the isolates displayed an array of antibiotic resistance and virulence-associated genes. Particularly significant (<0.05) co-existence of bla_NDM and mcr-1 was observed among the Enterobacterales isolated from various animal-derived foods. This study underscores the need to monitor Enterobacterales in animal-derived foods, especially in developing countries, to curb the spread of resistant pathogens and ensure effective food safety measures. Full article

(This article belongs to the Special Issue Epidemiology and Molecular Pathogenesis of Antimicrobial Resistance and Virulence for Foodborne Pathogens: 2nd Edition)

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14 pages, 1301 KB

Open AccessArticle

Deciphering Escherichia coli ESBL/pAmpC Plasmids Through High-Throughput Third-Generation Sequencing and Hybrid Assembly

by Andrea Laconi, Enea Ovedani, Roberta Tolosi, Ilias Apostolakos and Alessandra Piccirillo

Pathogens 2025, 14(10), 1039; https://doi.org/10.3390/pathogens14101039 - 13 Oct 2025

Abstract

Extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases represent a threat for public health. Their dissemination is often mediated by mobile genetic elements (MGEs), but plasmid identification and characterization could be hindered by sequencing limitations. Hybrid assembly may overcome these barriers. Eight ESBL/pAmpC-producing [...] Read more.

Extended-spectrum β-lactamases (ESBLs) and plasmid-mediated AmpC (pAmpC) β-lactamases represent a threat for public health. Their dissemination is often mediated by mobile genetic elements (MGEs), but plasmid identification and characterization could be hindered by sequencing limitations. Hybrid assembly may overcome these barriers. Eight ESBL/pAmpC-producing E. coli isolates from broilers were sequenced using Illumina (short-read) and Oxford Nanopore MinION (long-read). Assemblies were generated individually and using a hybrid approach. Plasmids were typed, annotated, and screened for antimicrobial resistance genes (ARGs), MGEs, and virulence factors. Short-read assemblies were highly fragmented, while long reads improved contiguity but showed typing errors. Hybrid assemblies produced the most accurate and complete plasmids, including more circularized plasmids. Long and hybrid assemblies detected IS26 associated with ESBL genes and additional virulence genes not identified by short reads. ARG profiles were consistent across methods, but structural resolution and contextualization of resistance loci were superior in hybrid assembly. Hybrid assembly integrates the strengths of short- and long-read sequencing, enabling accurate plasmid reconstruction and improved detection of resistance-associated MGEs. This approach may enhance genomic surveillance of ESBL/pAmpC plasmids and support strategies to mitigate antimicrobial resistance. Full article

(This article belongs to the Special Issue One Health Perspectives on Foodborne Pathogens: Evolution, Resistance, and Prevention)

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13 pages, 2230 KB

Open AccessArticle

Therapeutic Efficacy of an Anti-P116-661 Polyclonal Antibody Against Mycoplasma pneumoniae Infection

by Yiting Zhang, Xinqi Geng, Yan Liu, Wenli Li, Feng Shao, Mengmeng Jin, Jinzhi Wang and Linding Wang

Pathogens 2025, 14(10), 1038; https://doi.org/10.3390/pathogens14101038 - 13 Oct 2025

Abstract

The aim of this study was to investigate the therapeutic potential of a polyclonal antibody against the Mycoplasma pneumoniae (MP) P116-661 protein. A polyclonal antibody against the P116-661 protein was obtained by immunizing New Zealand white rabbits, and its therapeutic effects were systematically [...] Read more.

The aim of this study was to investigate the therapeutic potential of a polyclonal antibody against the Mycoplasma pneumoniae (MP) P116-661 protein. A polyclonal antibody against the P116-661 protein was obtained by immunizing New Zealand white rabbits, and its therapeutic effects were systematically evaluated by various experimental methods. An immunofluorescence assay was used to detect the inhibitory effect of the P116-661 polyclonal antibody on the adhesion of MP cells to A549 cells. ELISAs and Western blotting were used to analyze the expression levels of inflammatory factors, such as IL-6 and TNF-α, in Beas-2b cells and model mice after MP infection. HE staining was used to observe pathological changes in the lung tissue of the infected mice. The results showed that the P116-661 polyclonal antibody effectively inhibited the adhesion of MP cells to A549 cells. It significantly reduced the secretion levels of inflammatory factors, such as IL-6 and TNF-α, in Beas-2b cells and mice after MP infection. Moreover, the antibody significantly improved the pathological damage to the lungs that was caused by MP infection in mice. This study confirms that the P116-661 polyclonal antibody has good therapeutic effects in vitro and in vivo, providing a new experimental basis for immunotherapy against MP infection. Full article

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11 pages, 4918 KB

Open AccessArticle

Genomic Characterization of a Carbapenem-Resistant Acinetobacter pittii Strain Harboring Chromosome-Borne bla_NDM-1 from China

by Wenjuan Liu, Haixia Wang, Weijian Zhu, Xiaobin Li, Ying He and Wen Su

Pathogens 2025, 14(10), 1037; https://doi.org/10.3390/pathogens14101037 - 13 Oct 2025

Abstract

New Delhi metallo-beta-lactamase (NDM)-producing Acinetobacter spp. have been reported worldwide and become a global threat to clinics. This study aimed to characterize the genomic features of the carbapenem-resistant Acinetobacter pittii strain AP8900 harboring chromosome-borne bla_NDM-1. The genome of strain AP8900 was [...] Read more.

New Delhi metallo-beta-lactamase (NDM)-producing Acinetobacter spp. have been reported worldwide and become a global threat to clinics. This study aimed to characterize the genomic features of the carbapenem-resistant Acinetobacter pittii strain AP8900 harboring chromosome-borne bla_NDM-1. The genome of strain AP8900 was fully sequenced using Illumina and PacBio platforms. Genome analyses revealed that the chromosome-borne bla_NDM-1 of strain AP8900 was located on the Tn125 bracketed by two copies of ISAba125 in the same orientation. So far, only five strains of A. pittii with complete genomes harboring chromosome-borne bla_NDM-1 were found (four from China and one from the USA), all carrying nearly identical Tn125 carried by the strain AP8900. Furthermore, the Tn125 of strain AP8900 in this study was also distributed in other species, mainly Acinetobacter spp. Notably, the Tn125 carried by AP8900 also found in Proteus mirabilis, Klebsiella pneumoniae, and Morganella morganii. In addition, two antibiotic resistance plasmids were found in strain AP8900, and the configuration “sul2- glmM” was found on both pAP8900-1 (ISAba1-sul2-glmM-ISVsa3-IS1006) and pAP8900-2 (∆ISAba2-sul2-glmM-IS17). This study delivers comprehensive insights into the characteristics and diversity of chromosome-borne bla_NDM-1 in A. pittii. The complete genome of A. pittii AP8900 strain from southern China provides important data for the analysis of antimicrobial resistance in this region. Full article

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

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17 pages, 2852 KB

Open AccessArticle

Cytokine Profile and Oxidative Patterns in Murine Models of Disseminated Infection by Mucorales Species

by Hiram Villanueva-Lozano, Martín García-Juárez, Adrián G. Rosas-Taraco, Rogelio de J. Treviño-Rangel and Gloria M. González

Pathogens 2025, 14(10), 1036; https://doi.org/10.3390/pathogens14101036 - 13 Oct 2025

Abstract

Mucormycosis is a life-threatening infection caused by fungi of the Mucorales order, typically associated with immunocompromised hosts, but increasingly reported in immunocompetent individuals. This study investigated fungal burden, Th1/Th17 inflammatory profiles, and organ-specific dynamics in immunocompetent BALB/c mice intravenously infected with Rhizopus oryzae [...] Read more.

Mucormycosis is a life-threatening infection caused by fungi of the Mucorales order, typically associated with immunocompromised hosts, but increasingly reported in immunocompetent individuals. This study investigated fungal burden, Th1/Th17 inflammatory profiles, and organ-specific dynamics in immunocompetent BALB/c mice intravenously infected with Rhizopus oryzae, Mucor circinelloides, or Rhizomucor pusillus. Colony-forming units were quantified in spleen, liver, and kidney at multiple time points, while serum cytokines and oxidative stress markers were analyzed. The results showed fungal persistence primarily in the spleen, accompanied by species-specific Th1/Th17 responses: R. oryzae induced the highest inflammatory response among all groups, with maximal cytokine production observed on day 7, particularly for IL-17A (352.58 pg/mL). In contrast, M. circinelloides exhibited its peak cytokine levels earlier, reaching the highest TNF-α concentration on day 3 (425.43 pg/mL). Meanwhile, R. pusillus triggered an early but moderate inflammatory response, with a maximum TNF-α value of 372.62 pg/mL detected on day 1, followed by clearance. Correlation analysis highlighted distinct immunological patterns, with IL-10 acting as a negative regulator of inflammation, while TNF-α and IL-17A reflected infection intensity depending on species and timing. The spleen emerged as a key organ coordinating immune responses during systemic infection. These findings reveal that mucormycosis in immunocompetent hosts triggers complex, species-dependent immune dynamics beyond classical immunosuppression, emphasizing the need to consider host–pathogen interactions when developing targeted antifungal strategies. Full article

(This article belongs to the Section Fungal Pathogens)

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18 pages, 2569 KB

Open AccessArticle

Characterization of the Pepper Virome in Oklahoma Reveals Emerging RNA and DNA Viruses

by Caleb Paslay and Akhtar Ali

Pathogens 2025, 14(10), 1035; https://doi.org/10.3390/pathogens14101035 - 13 Oct 2025

Abstract

Pepper (Capsicum spp.) is an economically valuable crop worldwide including in the United States due to its nutritional benefits in human health and widespread use as a spice or vegetable. Although numerous viruses have been reported infecting peppers in the USA, little [...] Read more.

Pepper (Capsicum spp.) is an economically valuable crop worldwide including in the United States due to its nutritional benefits in human health and widespread use as a spice or vegetable. Although numerous viruses have been reported infecting peppers in the USA, little is known about the diversity and distribution of pepper-infecting viruses in Oklahoma. To address this knowledge gap, we conducted a comprehensive pepper virome study to identify viruses infecting pepper and their incidence across six different counties in Oklahoma. A total of 310 plant samples including pepper and other potential hosts were collected during the 2021 and 2022 growing seasons. Samples were analyzed using high-throughput sequencing (HTS) and/or reverse transcription-polymerase chain reaction (RT-PCR) assays. Viral contigs identified via HTS were further validated through RT-PCR or PCR assays followed by Sanger sequencing. In total, 17 distinct viruses were detected, including 15 RNA and two DNA viruses, with several representing putatively novel findings. The most prevalent virus was beet curly top virus (BCTV), followed by tomato yellow leaf curl virus (TYLCV), potato yellow dwarf virus/constricta yellow dwarf virus (PYDV/CYDV), and pepper mild mottle virus (PMMoV). Virus incidence varied by season and location, with some surveys showing infection rates exceeding 80%. This study provides the first in-depth characterization of the pepper virome in Oklahoma and valuable insights into the prevalence and distribution of pepper-infecting viruses. These findings will support the development of informed, targeted strategies for virus detection and management in pepper production systems. Full article

(This article belongs to the Special Issue Advances in Molecular Characterization and Epidemiology of Plant Viruses)

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17 pages, 527 KB

Open AccessArticle

Application of Machine Learning Algorithms in Urinary Tract Infections Diagnosis Based on Non-Microbiological Parameters

by M. Mar Rodríguez del Águila, Antonio Sorlózano-Puerto, Cecilia Bernier-Rodríguez, José María Navarro-Marí and José Gutiérrez-Fernández

Pathogens 2025, 14(10), 1034; https://doi.org/10.3390/pathogens14101034 - 12 Oct 2025

Abstract

Urinary tract infections (UTIs) are among the most common pathologies, with a high incidence in women and hospitalized patients. Their diagnosis is based on the presence of clinical symptoms and signs in addition to the detection of microorganisms in urine trough urine cultures, [...] Read more.

Urinary tract infections (UTIs) are among the most common pathologies, with a high incidence in women and hospitalized patients. Their diagnosis is based on the presence of clinical symptoms and signs in addition to the detection of microorganisms in urine trough urine cultures, a time-consuming and resource-intensive test. The goal was to optimize UTI detection through artificial intelligence (machine learning) using non-microbiological laboratory parameters, thereby reducing unnecessary cultures and expediting diagnosis. A total of 4283 urine cultures from patients with suspected UTIs were analyzed in the Microbiology Laboratory of the University Hospital Virgen de las Nieves (Granada, Spain) between 2016 and 2020. Various machine learning algorithms were applied to predict positive urine cultures and the type of isolated microorganism. Random Forest demonstrated the best performance, achieving an accuracy (percentage of correct positive and negative classifications) of 82.2% and an area under the ROC curve of 87.1%. Moreover, the Tree algorithm successfully predicted the presence of Gram-negative bacilli in urine cultures with an accuracy of 79.0%. Among the most relevant predictive variables were the presence of leukocytes and nitrites in the urine dipstick test, along with elevated white cells count, monocyte count, lymphocyte percentage in blood and creatinine levels. The integration of AI algorithms and non-microbiological parameters within the diagnostic and management pathways of UTI holds considerable promise. However, further validation with clinical data is required for integration into hospital practice. Full article

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

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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 - 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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19 pages, 5650 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 - 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

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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 - 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 - 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 - 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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