Pathogens

15 pages, 538 KiB

Open AccessEditor’s ChoiceReview

Comprehensive Insights into Highly Pathogenic Avian Influenza H5N1 in Dairy Cattle: Transmission Dynamics, Milk-Borne Risks, Public Health Implications, Biosecurity Recommendations, and One Health Strategies for Outbreak Control

by Henrietta Owusu and Yasser M. Sanad

Pathogens 2025, 14(3), 278; https://doi.org/10.3390/pathogens14030278 - 13 Mar 2025

Cited by 4 | Viewed by 3598

Abstract

Highly pathogenic avian influenza (HPAI) H5N1 has been traditionally linked to poultry and wild birds, which has recently become a serious concern for dairy cattle, causing outbreaks all over the United States. The need for improved surveillance, biosecurity protocols, and interagency collaboration is [...] Read more.

Highly pathogenic avian influenza (HPAI) H5N1 has been traditionally linked to poultry and wild birds, which has recently become a serious concern for dairy cattle, causing outbreaks all over the United States. The need for improved surveillance, biosecurity protocols, and interagency collaboration is highlighted by the discovery of H5N1 in dairy herds in several states and its human transmission. The epidemiology, transmission dynamics, and wide-ranging effects of H5N1 in cattle are reviewed in this paper, with particular attention paid to the disease’s effects on agricultural systems, public health, and animal health. Nonspecific clinical symptoms, such as decreased milk production and irregular milk consistency, are indicative of infection in dairy cows. Alarmingly, significant virus loads have been discovered in raw milk, raising worries about potential zoonotic transmission. The dangers of viral spillover between species are further highlighted by cases of domestic cats experiencing severe neurological symptoms after ingesting raw colostrum and milk from infected cows. Even though human cases remain rare, and they are mostly related to occupational exposure, constant attention is required due to the possibility of viral adaptability. The necessity of a One Health approach that integrates environmental, animal, and human health efforts is further supported by the broad occurrence of H5N1 across multiple species. For early detection, containment, and mitigation, cooperation between veterinary clinics, public health organizations, and agricultural stakeholders is crucial. Controlling the outbreak requires stringent movement restrictions, regular testing of dairy cows in reference labs, and adherence to biosecurity procedures. This review highlights the importance of thorough and coordinated efforts to manage H5N1 in dairy cattle by combining existing knowledge and pointing out gaps in surveillance and response strategies. Additionally, it sheds light on the potential risk of consumption of cow’s milk contaminated with H5N1 virus by humans and other companion animals like cats. In the face of this changing threat, proactive monitoring, strict biosecurity protocols, and cross-sector cooperation are crucial for reducing financial losses and protecting human and animal health. 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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19 pages, 6831 KiB

Open AccessEditor’s ChoiceArticle

Conformational and Stability Analysis of SARS-CoV-2 Spike Protein Variants by Molecular Simulation

by Gustavo E. Olivos-Ramirez, Luis F. Cofas-Vargas, Tobias Madl and Adolfo B. Poma

Pathogens 2025, 14(3), 274; https://doi.org/10.3390/pathogens14030274 - 12 Mar 2025

Cited by 1 | Viewed by 2197

Abstract

We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of [...] Read more.

We performed a comprehensive structural analysis of the conformational space of several spike (S) protein variants using molecular dynamics (MD) simulations. Specifically, we examined four well-known variants (Delta, BA.1, XBB.1.5, and JN.1) alongside the wild-type (WT) form of SARS-CoV-2. The conformational states of each variant were characterized by analyzing their distributions within a selected space of collective variables (CVs), such as inter-domain distances between the receptor-binding domain (RBD) and the N-terminal domain (NTD). Our primary focus was to identify conformational states relevant to potential structural transitions and to determine the set of native contacts (NCs) that stabilize these conformations. The results reveal that genetically more distant variants, such as XBB.1.5, BA.1, and JN.1, tend to adopt more compact conformational states compared to the WT. Additionally, these variants exhibit novel NC profiles, characterized by an increased number of specific contacts distributed among ionic, polar, and nonpolar residues. We further analyzed the impact of specific mutations, including T478K, N500Y, and Y504H. These mutations not only enhance interactions with the human host receptor but also alter inter-chain stability by introducing additional NCs compared to the WT. Consequently, these mutations may influence the accessibility of certain protein regions to neutralizing antibodies. Overall, these findings contribute to a deeper understanding of the structural and functional variations among S protein variants. Full article

(This article belongs to the Section Viral Pathogens)

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13 pages, 1850 KiB

Open AccessEditor’s ChoiceArticle

Acid Tolerance of Coxiella burnetii Is Strain-Specific and Might Depend on Stomach Content

by Katharina Sobotta, Jan Schulze-Luehrmann, Martha Ölke, Katharina Boden and Anja Lührmann

Pathogens 2025, 14(3), 272; https://doi.org/10.3390/pathogens14030272 - 12 Mar 2025

Viewed by 1472

Abstract

Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella (C.) burnetii. Human infections occur mainly via inhalation, but infections via the oral route have been observed. Gastric acidic conditions (pH 2–4) are the first defense mechanism [...] Read more.

Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella (C.) burnetii. Human infections occur mainly via inhalation, but infections via the oral route have been observed. Gastric acidic conditions (pH 2–4) are the first defense mechanism to limit food-associated infections. In this study, we tested the ability of C. burnetii to survive extremely acidic conditions (pH 2–3) to assess the risk of oral infection in humans. We treated different C. burnetii strains with different pH values and calculated the recovery rate by counting colony-forming units. The analysis of an additional eight C. burnetii strains showed that some strains are acid-resistant, while others are not. Importantly, the presence of pepsin, an endopeptidase and the main digestive enzyme in the gastrointestinal tract, increases the survival rate of C. burnetii. Similarly, the presence of milk might also increase the survival rate. These results suggest that oral infections by C. burnetii are possible and depend on the bacterial strain and the stomach microenvironment. Consequently, the digestive infection route of C. burnetii could play a role in the transmission of the pathogen. Full article

(This article belongs to the Special Issue Coxiella burnetii: The Host Immune Response, Host-Pathogen Interaction and Pathogenesis)

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13 pages, 6620 KiB

Open AccessEditor’s ChoiceReview

Encystment and Excystment Processes in Acanthamoeba castellanii: An Emphasis on Cellulose Involvement

by Mathew Choaji, Ascel Samba-Louaka, Zineb Fechtali-Moute, Willy Aucher and Sébastien Pomel

Pathogens 2025, 14(3), 268; https://doi.org/10.3390/pathogens14030268 - 10 Mar 2025

Viewed by 1719

Abstract

The free-living amoeba Acanthamoeba castellanii is a unicellular eukaryote distributed in a wide range of soil or aquatic environments, either natural or human-made, such as rivers, lakes, drinking water, or swimming pools. Besides its capacity to transport potential pathogens, such as bacteria or [...] Read more.

The free-living amoeba Acanthamoeba castellanii is a unicellular eukaryote distributed in a wide range of soil or aquatic environments, either natural or human-made, such as rivers, lakes, drinking water, or swimming pools. Besides its capacity to transport potential pathogens, such as bacteria or viruses, Acanthamoeba spp. can have intrinsic pathogenic properties by causing severe infections at the ocular and cerebral level, named granulomatous amoebic encephalitis and amoebic keratitis, respectively. During its life cycle, A. castellanii alternates between a vegetative and mobile form, named the trophozoite, and a resistant, latent, and non-mobile form, named the cyst. The cyst wall of Acanthamoeba is double-layered, with an inner endocyst and an outer ectocyst, and is mainly composed of cellulose and proteins. The resistance of cysts to many environmental stresses and disinfection treatments has been assigned to the presence of cellulose. The current review aims to present the importance of this glycopolymer in Acanthamoeba cysts and to further report the pathways involved in encystment and excystment. Full article

(This article belongs to the Special Issue Acanthamoeba Infections)

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21 pages, 2438 KiB

Open AccessEditor’s ChoiceArticle

Development of Low-Cost In-House Assays for Quantitative Detection of HBsAg, HBeAg, and HBV DNA to Enhance Hepatitis B Virus Diagnostics and Antiviral Screening in Resource-Limited Settings

by Simmone D’souza, Layla Al-Yasiri, Annie Chen, Dan T. Boghici, Guido van Marle, Jennifer A. Corcoran, Trushar R. Patel and Carla S. Coffin

Pathogens 2025, 14(3), 258; https://doi.org/10.3390/pathogens14030258 - 5 Mar 2025

Viewed by 1573

Abstract

Globally, an estimated 254 million people are living with chronic hepatitis B virus (HBV) infection, yet only 10.5% have been diagnosed, underscoring the urgent need to expand testing to meet the World Health Organization’s HBV elimination targets by 2030. Many HBV diagnostic tests [...] Read more.

Globally, an estimated 254 million people are living with chronic hepatitis B virus (HBV) infection, yet only 10.5% have been diagnosed, underscoring the urgent need to expand testing to meet the World Health Organization’s HBV elimination targets by 2030. Many HBV diagnostic tests remain expensive and inaccessible in resource-limited settings. In this study, we demonstrate how individually sourced, commercially available reagents can be used to develop cost-effective in-house assays for total DNA isolation, HBV viral load quantification by (q)PCR, and qHBsAg and qHBeAg measurement using sandwich ELISA. These assays were validated using known HBV-positive and HBV-negative plasma samples (genotypes A–F) and HepAD38 cells treated with tenofovir disoproxil fumarate (TDF). DNA isolation using a commercial column-based kit was compared to a high-throughput, column-free method, allowing for HBV quantification from 50 µL of plasma with lower limits of detection (LLOD) of 1.8 × 10³ and 1.8 × 10⁴ HBV DNA copies IU/mL, respectively. Both commercial and in-house DNA isolation methods yielded comparable half-maximal effective concentration (EC₅₀) values in TDF-treated HepAD38 cells. Additionally, in-house sandwich ELISA assays were developed for quantitative HBsAg and HBeAg detection, with LLOD values of 0.78 IU/mL and 0.38 PEI U/mL (Paul Ehrlich Institute), respectively. The in-house reagents for DNA isolation, molecular testing, and serological detection of HBV were estimated to be at least 10 times more cost-effective than commercially available kits, highlighting their potential for broader application in resource-limited regions. Full article

(This article belongs to the Special Issue Remaining Challenges of HBV Infection: Pathogenesis, Immune Response, Diagnosis and Therapeutic Strategies)

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15 pages, 2282 KiB

Open AccessEditor’s ChoiceArticle

Development and Characterization of Fluorescent Protein-Tagged Vibrio harveyi Strains as a Versatile Tool for Studying Infection Dynamics and Strain Interactions

by Charalampos Chalmoukis, Stavros Droubogiannis, Vassiliki A. Michalopoulou, Adriana Triga, Panagiotis F. Sarris and Pantelis Katharios

Pathogens 2025, 14(3), 247; https://doi.org/10.3390/pathogens14030247 - 3 Mar 2025

Cited by 2 | Viewed by 1559

Abstract

Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using [...] Read more.

Fluorescent protein-tagged bacterial strains are widely used tools for studying host-pathogen interactions and microbial dynamics. In this study, we developed and characterized Vibrio harveyi strains genetically modified to express green fluorescent protein (GFP) and red fluorescent protein (RFP). These strains were constructed using triparental mating and evaluated for phenotypic, genomic, and virulence attributes. Genomic analyses revealed strain-specific variations, including mutations in key regulatory and metabolic genes, such as luxO and transketolase. While plasmid acquisition imposed metabolic costs, resulting in altered growth and antibiotic sensitivities in certain transconjugants, others demonstrated robust phenotypic stability. Virulence assays using gilthead seabream larvae revealed that most tagged strains retained moderate pathogenicity, with visualization of co-infections highlighting the potential for studying strain-specific interactions. Furthermore, fluorescent microscopy confirmed the successful colonization and localization of tagged bacteria within host tissues. These findings underscore the utility of GFP- and RFP-tagged Vibrio harveyi as versatile tools for infection dynamics, offering a foundation for future research on strain interactions and pathogen-host relationships. Full article

(This article belongs to the Special Issue Fish Pathogens: An Ongoing Challenge for Aquaculture)

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21 pages, 702 KiB

Open AccessEditor’s ChoiceReview

Latency Reversing Agents and the Road to an HIV Cure

by Louis Tioka, Rafael Ceña Diez, Anders Sönnerborg and Maarten A. A. van de Klundert

Pathogens 2025, 14(3), 232; https://doi.org/10.3390/pathogens14030232 - 27 Feb 2025

Viewed by 3391

Abstract

HIV-1 infection cannot be cured due to the presence of HIV-1 latently infected cells. These cells do not produce the virus, but they can resume virus production at any time in the absence of antiretroviral therapy. Therefore, people living with HIV (PLWH) need [...] Read more.

HIV-1 infection cannot be cured due to the presence of HIV-1 latently infected cells. These cells do not produce the virus, but they can resume virus production at any time in the absence of antiretroviral therapy. Therefore, people living with HIV (PLWH) need to take lifelong therapy. Strategies have been coined to eradicate the viral reservoir by reactivating HIV-1 latently infected cells and subsequently killing them. Various latency reversing agents (LRAs) that can reactivate HIV-1 in vitro and ex vivo have been identified. The most potent LRAs also strongly activate T cells and therefore cannot be applied in vivo. Many LRAs that reactivate HIV in the absence of general T cell activation have been identified and have been tested in clinical trials. Although some LRAs could reduce the reservoir size in clinical trials, so far, they have failed to eradicate the reservoir. More recently, immune modulators have been applied in PLWH, and the first results seem to indicate that these may reduce the reservoir and possibly improve immunological control after therapy interruption. Potentially, combinations of LRAs and immune modulators could reduce the reservoir size, and in the future, immunological control may enable PLWH to live without developing HIV-related disease in the absence of therapy. Full article

(This article belongs to the Section Viral Pathogens)

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20 pages, 3172 KiB

Open AccessEditor’s ChoiceArticle

Integrated One Health Surveillance of West Nile Virus and Usutu Virus in the Veneto Region, Northeastern Italy, from 2022 to 2023

by Federica Gobbo, Giulia Chiarello, Sofia Sgubin, Federica Toniolo, Francesco Gradoni, Lidia Iustina Danca, Sara Carlin, Katia Capello, Giacomo De Conti, Alessio Bortolami, Maria Varotto, Laura Favero, Michele Brichese, Francesca Russo, Franco Mutinelli, Stefania Vogiatzis, Monia Pacenti, Luisa Barzon and Fabrizio Montarsi

Pathogens 2025, 14(3), 227; https://doi.org/10.3390/pathogens14030227 - 25 Feb 2025

Viewed by 1990

Abstract

West Nile virus (WNV) and Usutu virus (USUV) are neurotropic mosquito-borne orthoflaviviruses maintained in an enzootic cycle, in which birds are amplifying/reservoir hosts, while humans and equids are dead-end hosts. As northern Italy, especially the Veneto Region, is considered an endemic area for [...] Read more.

West Nile virus (WNV) and Usutu virus (USUV) are neurotropic mosquito-borne orthoflaviviruses maintained in an enzootic cycle, in which birds are amplifying/reservoir hosts, while humans and equids are dead-end hosts. As northern Italy, especially the Veneto Region, is considered an endemic area for WNV and USUV circulation, a surveillance plan based on a One Health approach has been implemented since 2008. This work reports the results of entomological, veterinary and human surveillances for WNV and USUV in the Veneto Region in 2022 and 2023, through virological and/or serological examinations. In 2022, 531 human WNV infections were recorded, and 93,213 mosquitoes and 2193 birds were virologically tested, showing infection rates (IRs) of 4.85% and 8.30%, respectively. The surveillance effort in 2023 provided these results: 56 human WNV infections were confirmed, and 133,648 mosquitoes and 1812 birds were virologically tested, showing IRs of 1.78% and 4.69%, respectively. This work highlights the exceptional circulation of WNV in the Veneto Region, due to the new re-introduction of WNV lineage 1 and co-circulation with WNV lineage 2. This paper confirms the efficacy of integrated surveillance for early warning of viral circulation and gives new insights about avian hosts involved in the enzootic cycle of orthoflavivirus in the endemic region of Italy. Full article

(This article belongs to the Section Viral Pathogens)

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42 pages, 5461 KiB

Open AccessEditor’s ChoiceReview

Anisakidae and Anisakidosis: A Public Health Perspective

by Diana Nonković, Vanja Tešić, Vida Šimat, Svjetlana Karabuva, Alan Medić and Jerko Hrabar

Pathogens 2025, 14(3), 217; https://doi.org/10.3390/pathogens14030217 - 22 Feb 2025

Cited by 2 | Viewed by 2518

Abstract

Fish and seafood are increasingly recognised as safe and nutritiously valuable foods of animal origin, being a source of about 17% of animal protein globally. Novel culinary trends encourage the consumption of raw or thermally lightly processed fishery products. At the same time, [...] Read more.

Fish and seafood are increasingly recognised as safe and nutritiously valuable foods of animal origin, being a source of about 17% of animal protein globally. Novel culinary trends encourage the consumption of raw or thermally lightly processed fishery products. At the same time, consumers prefer wild, fresh and whole fish over farmed or processed fish. However, the consumption of raw or undercooked fish and other marine organisms poses a risk of contracting parasitic infections, potentially representing a public health risk. Among the most common seafoodborne parasites are members of the Anisakidae family, especially the genus Anisakis, which can cause potentially detrimental effects to human health. These parasites are the causative agent of a zoonosis termed anisakidosis that is prevalent in countries with high per capita fish consumption. Although the number of annual clinical cases varies among countries and regions and is generally not high, sensitisation to this parasite in the general population seems to be considerably higher. Therefore, anisakidosis is still significantly underreported and misdiagnosed globally, making it a disease of rising public health concerns. To prevent infection and mitigate potential negative effects on human health, proper preventive measures such as gutting the fish, freezing or thermal processing are needed. Moreover, a holistic approach implementing One Health principles together with educational campaigns towards the general public and primary care physicians can extend the knowledge on the occurrence of these parasites in their natural hosts and the diagnosis and incidence of anisakidosis, with a final goal to minimize risks for human health and reducing costs for health systems. Full article

(This article belongs to the Section Parasitic Pathogens)

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18 pages, 10968 KiB

Open AccessEditor’s ChoiceArticle

The Historical Baseline of Hard Tick Records in Spain (1985–2024)

by Agustín Estrada-Peña, Miguel A. Habela Martínez-Estéllez, Carlos Pradera and Joaquim Castellà

Pathogens 2025, 14(2), 173; https://doi.org/10.3390/pathogens14020173 - 9 Feb 2025

Cited by 1 | Viewed by 2482

Abstract

Ticks are important vectors of pathogens, producing diseases in animals and humans. The planning of information campaigns or prevention programs is heavily based on the knowledge of highly detailed data on tick distribution. This study reports unpublished data on the distribution of more [...] Read more.

Ticks are important vectors of pathogens, producing diseases in animals and humans. The planning of information campaigns or prevention programs is heavily based on the knowledge of highly detailed data on tick distribution. This study reports unpublished data on the distribution of more than 30,000 tick specimens, collected by active surveys in the years 1985–2024 in Spain, from 2285 surveys in 1636 unique sites, providing coordinates with variable accuracy. The report covers new records of Dermacentor marginatus, Dermacentor reticulatus, Haemaphysalis punctata, Haemaphysalis sulcata, Hyalomma marginatum, Hyalomma lusitanicum, Ixodes ricinus, Rhipicephalus bursa, Rhipicephalus hibericus, and Rhipicephalus sanguineus (either s.s. or s.l.). Other species were sporadically collected. Many specimens have been re-examined for accurate identification according to current taxonomic views, mainly in the genus Rhipicephalus. We summarized this newly available information using the Köppen–Geiger climate classification. This compilation of unpublished tick records pinpoints the importance of the systematic monitoring of ticks. It is intended as the baseline over which the ongoing national tick collection program is built in order to track the long-term changes of tick distribution in Spain, because of the land use changes, the spread of invasive vertebrates, or the climate trends. Full article

(This article belongs to the Section Ticks)

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13 pages, 1026 KiB

Open AccessEditor’s ChoiceArticle

Molecular and Clinical Characterization of Invasive Streptococcus pyogenes Isolates: Insights from Two Northern-Italy Centers

by Carmelo Bonomo, Eva Mannino, Dafne Bongiorno, Caterina Vocale, Armando Amicucci, Dalida Bivona, Davide Guariglia, Emanuele Nicitra, Grete Francesca Privitera, Giuseppe Sangiorgio, Stefania Stefani and Simone Ambretti

Pathogens 2025, 14(2), 152; https://doi.org/10.3390/pathogens14020152 - 5 Feb 2025

Cited by 1 | Viewed by 1789

Abstract

Streptococcus pyogenes (Group A Streptococcus, GAS) is a Gram-positive pathogen responsible for both superficial and invasive infections (iGAS), with increasing global incidence in recent years. This study aims to characterize the molecular and clinical features of iGAS cases in Bologna and Imola (Italy) [...] Read more.

Streptococcus pyogenes (Group A Streptococcus, GAS) is a Gram-positive pathogen responsible for both superficial and invasive infections (iGAS), with increasing global incidence in recent years. This study aims to characterize the molecular and clinical features of iGAS cases in Bologna and Imola (Italy) between 2022 and 2024. Thirty-five invasive isolates were analyzed through whole-genome sequencing (WGS) to investigate the distribution of emm types, antimicrobial resistance (AMR) genes, and virulence factors. Clinical and epidemiological data were retrospectively collected and analyzed. The majority of cases (80%) were recorded in 2023, predominantly among patients aged over 65 (60%). Bloodstream infections were present in 97.1% of cases, and comorbidities such as diabetes and immunosuppression were common. Empirical antibiotic therapy often involved penicillin/β-lactam inhibitors, while oxazolidinones were the most frequently used in targeted regimens. The in-hospital mortality rate was 20%. Genomic analysis identified emm1, emm12, and emm89 as the most prevalent types, associated with specific virulence profiles and resistance determinants. This study highlights the critical role of emm typing and genomic characterization in understanding the pathogenicity of GAS. These findings contribute to the identification of risk factors for severe outcomes and underscore the need for targeted prevention and treatment strategies in vulnerable populations. Full article

(This article belongs to the Section Bacterial Pathogens)

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15 pages, 2841 KiB

Open AccessEditor’s ChoiceArticle

Biocontrol Potential of Trichoderma spp. Against Phytophthora ramorum

by Elisa Becker, Nirusan Rajakulendran and Simon Francis Shamoun

Pathogens 2025, 14(2), 136; https://doi.org/10.3390/pathogens14020136 - 2 Feb 2025

Cited by 1 | Viewed by 1910

Abstract

Phytophthora ramorum, the cause of Sudden Oak Death and related diseases, threatens over 130 tree and shrub species. We evaluated the biocontrol potential of isolates from nine Trichoderma species against P. ramorum using growth-rate studies, dual-culture assays, and culture-filtrate assays. Results showed [...] Read more.

Phytophthora ramorum, the cause of Sudden Oak Death and related diseases, threatens over 130 tree and shrub species. We evaluated the biocontrol potential of isolates from nine Trichoderma species against P. ramorum using growth-rate studies, dual-culture assays, and culture-filtrate assays. Results showed significant variation in Trichoderma growth rates and biocontrol potential. Some isolates exhibited rapid growth, effective overgrowth, and lethal effects against P. ramorum and produced potent antagonistic metabolites. Faster growth rates only partially correlated with biocontrol efficacy, indicating that factors beyond growth, such as metabolite production, play significant roles. Notably, isolates of T. koningii, T. viride, and the commercial product SoilGard™ (T. virens) showed promising efficacy. We calculated a combined biocontrol variable to rank isolates based on vigour and efficacy to aid in identifying promising candidates. Our findings support the use of Trichoderma spp. as biocontrol agents against P. ramorum and underscore the need for a multifaceted approach to selecting and optimizing isolates. Our evaluation demonstrated the importance of using different assays to assess specific mechanisms of action of biocontrol candidates. Future research should further explore these interactions to enhance the sustainable management of P. ramorum. Full article

(This article belongs to the Special Issue The Paths of Plant Pathogens—Interactions with Host and Nonhosts and Insight of Mechanisms of Pathogenesis)

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14 pages, 698 KiB

Open AccessEditor’s ChoiceArticle

Long-Term Surveillance of Food Products of Diverse Origins: A Five-Year Survey of Hepatitis A and Norovirus in Greece, 2019–2024

by Rafail Fokas, Zoi Anastopoulou, Kalypso-Angeliki Koukouvini, Maria-Eleni Dimitrakopoulou, Zoi Kotsiri, Eleftheria Chorti-Tripsa, Chrysoula Kotsalou, Dimosthenis Tzimotoudis and Apostolos Vantarakis

Pathogens 2025, 14(2), 135; https://doi.org/10.3390/pathogens14020135 - 2 Feb 2025

Viewed by 1320

Abstract

This study examines at the prevalence and spread of Hepatitis A Virus (HAV) and norovirus GI/GII in local and imported food products in Greece over a five-year period (2019–2024). A total of two hundred sixty-six food samples were evaluated using obligatory inspections and [...] Read more.

This study examines at the prevalence and spread of Hepatitis A Virus (HAV) and norovirus GI/GII in local and imported food products in Greece over a five-year period (2019–2024). A total of two hundred sixty-six food samples were evaluated using obligatory inspections and virus detection procedures, including 202 for Hepatitis A and 64 for Norovirus. High-risk categories analyzed were vegetables [138 (HAV), 17 (NoV)], fruits [16 (HAV), 7 (NoV)], soft fruits/berries [37 (HAV), 31 (NoV)], processed meals [4 (HAV), 4 (NoV)], and animal-based products [1 (HAV), 5 (NoV)]. Viral RNA was isolated using QIAamp Viral RNA Mini Kit and detected using established RT-qPCR procedures that met ISO requirements for high sensitivity and reproducibility. The results demonstrated HAV contamination mostly in vegetables (4.35% positive rate), with sporadic findings in other categories. Norovirus GI/GII was detected primarily in soft fruits/berries, with a category-specific positive rate of 6.45%. A temporal study revealed that HAV peaks in 2020, while Norovirus contaminations were detected in 2021 and 2024. The findings highlight the important need to incorporate viral testing into routine food safety procedures, especially for high-risk product categories. This study establishes a basic framework for public health initiatives that address gaps in foodborne virus surveillance in Greece. The study’s ramifications extend to global efforts to monitor and reduce foodborne virus contamination, pushing for higher regulatory requirements and targeted preventative actions. Full article

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23 pages, 3056 KiB

Open AccessEditor’s ChoiceArticle

Putrescine Depletion in Leishmania donovani Parasites Causes Immediate Proliferation Arrest Followed by an Apoptosis-like Cell Death

by Julia Johnston, Jonathan Taylor, Surbhi Nahata, Angelica Gatica-Gomez, Yvette L. Anderson, Sophia Kiger, Thong Pham, Kayhan Karimi, Jasmin-Faith Lacar, Nicola S. Carter and Sigrid C. Roberts

Pathogens 2025, 14(2), 137; https://doi.org/10.3390/pathogens14020137 - 2 Feb 2025

Cited by 1 | Viewed by 1788

Abstract

The polyamine pathway in Leishmania parasites has emerged as a promising target for therapeutic intervention, yet the functions of polyamines in parasites remain largely unexplored. Ornithine decarboxylase (ODC) and spermidine synthase (SPDSYN) catalyze the sequential conversion of ornithine to putrescine and spermidine. We [...] Read more.

The polyamine pathway in Leishmania parasites has emerged as a promising target for therapeutic intervention, yet the functions of polyamines in parasites remain largely unexplored. Ornithine decarboxylase (ODC) and spermidine synthase (SPDSYN) catalyze the sequential conversion of ornithine to putrescine and spermidine. We previously found that Leishmania donovani Δodc and Δspdsyn mutants exhibit markedly reduced growth in vitro and diminished infectivity in mice, with the effect being most pronounced in putrescine-depleted Δodc mutants. Here, we report that, in polyamine-free media, ∆odc mutants arrested proliferation and replication, while ∆spdsyn mutants showed a slow growth and replication phenotype. Starved ∆odc parasites also exhibited a marked reduction in metabolism, which was not observed in the starved ∆spdsyn cells. In contrast, both mutants displayed mitochondrial membrane hyperpolarization. Hallmarks of apoptosis, specifically DNA fragmentation and membrane modifications, were observed in Δodc mutants incubated in polyamine-free media. These results show that putrescine depletion had an immediate detrimental effect on cell growth, replication, and mitochondrial metabolism and caused an apoptosis-like death phenotype. Our findings establish ODC as the most promising therapeutic target within the polyamine biosynthetic pathway for treating leishmaniasis. Full article

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12 pages, 258 KiB

Open AccessEditor’s ChoiceReview

Novel Strategies for Preventing Fungal Infections—Outline

by Damilola J. Agbadamashi and Claire L. Price

Pathogens 2025, 14(2), 126; https://doi.org/10.3390/pathogens14020126 - 1 Feb 2025

Cited by 3 | Viewed by 1817

Abstract

Fungal infections are a significant global health challenge, causing approximately 3.8 million deaths annually, with immunocompromised populations particularly at risk. Traditional antifungal therapies, including azoles, echinocandins, and polyenes, face limitations due to rising antifungal resistance, toxicity, and inadequate treatment options. This review explores [...] Read more.

Fungal infections are a significant global health challenge, causing approximately 3.8 million deaths annually, with immunocompromised populations particularly at risk. Traditional antifungal therapies, including azoles, echinocandins, and polyenes, face limitations due to rising antifungal resistance, toxicity, and inadequate treatment options. This review explores innovative strategies for preventing and managing fungal infections, such as vaccines, antifungal peptides, nanotechnology, probiotics, and immunotherapy. Vaccines offer promising avenues for long-term protection, despite difficulties in their development due to fungal complexity and immune evasion mechanisms. Antifungal peptides provide a novel class of agents with broad-spectrum activity and reduced resistance risk, whilst nanotechnology enables targeted, effective drug delivery systems. Probiotics show potential in preventing fungal infections, particularly vulvovaginal candidiasis, by maintaining microbial balance. Immunotherapy leverages immune system modulation to enhance antifungal defenses, and omics technologies deliver comprehensive insights into fungal biology, paving the way for novel therapeutic and vaccine targets. While these approaches hold immense promise, challenges such as cost, accessibility, and translational barriers remain. A coordinated effort among researchers, clinicians, and policymakers is critical to advancing these strategies and addressing the global burden of fungal infections effectively. Full article

(This article belongs to the Section Fungal Pathogens)

13 pages, 271 KiB

Open AccessEditor’s ChoiceReview

An Update on Vaccines Against Trypanosoma cruzi and Chagas Disease

by Nisha J. Garg

Pathogens 2025, 14(2), 124; https://doi.org/10.3390/pathogens14020124 - 30 Jan 2025

Cited by 2 | Viewed by 1792

Abstract

Chagas disease (CD) is a global health concern, with no existing therapies to prophylactically treat adults traveling to endemic countries or those who may already be infected with Trypanosoma cruzi. The economic burden of Chagas cardiomyopathy and heart failure, due to healthcare [...] Read more.

Chagas disease (CD) is a global health concern, with no existing therapies to prophylactically treat adults traveling to endemic countries or those who may already be infected with Trypanosoma cruzi. The economic burden of Chagas cardiomyopathy and heart failure, due to healthcare costs and lost productivity from premature deaths, provides a strong rationale for investment in the development of immune therapies against CD. Vaccine efficacy is proposed to depend heavily on the induction of a robust Th1 response for the clearance of intracellular pathogens like T. cruzi. In this review, updated information on the efforts for vaccine development against CD is provided. Full article

(This article belongs to the Special Issue Chagas Disease: Celebrating the 115th Anniversary of the Discovery of Trypanosoma cruzi)

18 pages, 14380 KiB

Open AccessEditor’s ChoiceArticle

Optimization of Enterovirus-like Particle Production and Purification Using Design of Experiments

by Louis Kuijpers, Wouter J. P. van den Braak, Abbas Freydoonian, Nynke H. Dekker and Leo A. van der Pol

Pathogens 2025, 14(2), 118; https://doi.org/10.3390/pathogens14020118 - 27 Jan 2025

Cited by 1 | Viewed by 1681

Abstract

Hand, foot, and mouth disease (HFMD) represents an emerging health concern whose main causative agents are Coxsackievirus A6 (CVA6) and enterovirus A71 (EV71). The lack of a CVA6 vaccine and the rise of new HFMD-causing strains due to the containment of established HFMD-causing [...] Read more.

Hand, foot, and mouth disease (HFMD) represents an emerging health concern whose main causative agents are Coxsackievirus A6 (CVA6) and enterovirus A71 (EV71). The lack of a CVA6 vaccine and the rise of new HFMD-causing strains due to the containment of established HFMD-causing viruses necessitates the search for alternative vaccine technologies, including virus-like particle (VLP) vaccine candidates. While studies have demonstrated that production of enterovirus-like particles in various organisms can be achieved by expression of the viral P1 structural proteins and the 3CD protease, optimization based on the interplay between the three most commonly altered infection parameters (multiplicity of infection (MOI), viable cell density at the time of infection (VCD), and the infection period) is often not investigated. To address this challenge, we have performed Design of Experiments (DoE) to optimize the production of CVA6 and EV71 VLPs. Our results indicate that CVA6 VLP production peaks at high MOI, high VCD, and long infection periods. Our subsequent downstream purification processes yielded 38 mg and 158 mg of purified CVA6 and EV71 VLPs from 1 L crude harvest, respectively. This translates into thousands of potential vaccine doses and highlights the economic potential of enterovirus-like particles for vaccine purposes. Full article

(This article belongs to the Special Issue Hand–Foot–Mouth Disease)

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11 pages, 839 KiB

Open AccessEditor’s ChoiceArticle

Prevalence of T. rubrum and T. interdigitale Exhibiting High MICs to Terbinafine in Clinical Samples Analyzed in the Portuguese Mycology Reference Laboratory

by Helena Schirmer, Camila Henriques, Helena Simões, Cristina Veríssimo and Raquel Sabino

Pathogens 2025, 14(2), 115; https://doi.org/10.3390/pathogens14020115 - 25 Jan 2025

Cited by 5 | Viewed by 1210

Abstract

Cutaneous fungal infections represent a significant burden worldwide with a high impact on public health. Accurate identification of dermatophyte species causing these infections is vital for an appropriate treatment. Terbinafine is the primary agent against Trichophyton species due to its clinical efficacy; however, [...] Read more.

Cutaneous fungal infections represent a significant burden worldwide with a high impact on public health. Accurate identification of dermatophyte species causing these infections is vital for an appropriate treatment. Terbinafine is the primary agent against Trichophyton species due to its clinical efficacy; however, cases of elevated minimum inhibitory concentration (MIC) have been reported, raising clinical and epidemiological concerns. Herein, we aimed to detect Trichophyton rubrum and Trichophyton interdigitale isolates collected from clinical samples with terbinafine-high MICs (TRB-hMIC). A total of 168 isolates, recovered from 2017 to 2023, were identified as T. rubrum complex (140/83.4%) or T. interdigitale (28/16.7%) and further screened regarding their terbinafine susceptibility. Four isolates with capacity to grow in terbinafine media were detected by screening, and these and a further sixteen random isolates were submitted to the broth microdilution method. This methodology confirmed the four (2.4%) isolates as TRB-hMIC. One T. rubrum and three T. interdigitale showed a minimum inhibitory concentration (MIC) higher than 1 mg/L. Partial sequencing of the SQLE gene identified point mutations in T. rubrum (Phe397Iso) and in one T. interdigitale (Phe397Leu) isolate. Notably, in the other two T. interdigitale isolates with TRB-hMIC, no point mutations in the SQLE gene were identified. In conclusion, TRB-hMIC isolates (T. rubrum and T. interdigitale) were identified in clinical samples analyzed in Portugal, as antifungal susceptibility testing is a crucial routine for identifying treatment failures and also for epidemiological purposes aiming to monitor the dynamics of terbinafine resistance. Full article

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

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25 pages, 393 KiB

Open AccessEditor’s ChoiceReview

The Body of Chagas Disease Vectors

by Jean-Pierre Dujardin

Pathogens 2025, 14(1), 98; https://doi.org/10.3390/pathogens14010098 - 20 Jan 2025

Cited by 3 | Viewed by 1258

Abstract

Morphometry is an effort to describe or measure the morphology of the body, or parts of it. It also provides quantitative data on the interactions of living organisms with their environment, external or internal. As a discipline, morphometrics has undergone significant developments in [...] Read more.

Morphometry is an effort to describe or measure the morphology of the body, or parts of it. It also provides quantitative data on the interactions of living organisms with their environment, external or internal. As a discipline, morphometrics has undergone significant developments in the last decade, making its implementation more visual and less laborious. Chagas disease vectors, often referred to by the common name of “kissing bugs”, belong to the subfamily Triatominae. Due to their apparent morphological plasticity, they have been the subject of numerous morphometric studies. Most of these have been applied taking into account the particularities of this group of vectors, such as domesticity (synanthropy), food preferences, dispersal ability, insecticide resistance, as well as some taxonomic issues. This brief review over nearly three decades is organized here according to the body organs considered by the authors. Full article

(This article belongs to the Special Issue Chagas Disease: Celebrating the 115th Anniversary of the Discovery of Trypanosoma cruzi)

12 pages, 949 KiB

Open AccessEditor’s ChoiceArticle

Seroprevalence of Borrelia, Anaplasma, Bartonella, Toxoplasma, Mycoplasma, Yersinia, and Chlamydia in Human Population from Eastern Poland

by Angelina Wójcik-Fatla, Anna Sawczyn-Domańska, Anna Kloc, Joanna Krzowska-Firych and Jacek Sroka

Pathogens 2025, 14(1), 96; https://doi.org/10.3390/pathogens14010096 - 18 Jan 2025

Viewed by 2024

Abstract

The epidemiological situation related to infectious diseases is influenced by many factors. To monitor actual trends in selected zoonoses, a total of 473 serum samples from farmers, forestry workers, and veterinarians were collected for serological examination. Anti-Borrelia burgdorferi sensu lato (s.l.) antibodies [...] Read more.

The epidemiological situation related to infectious diseases is influenced by many factors. To monitor actual trends in selected zoonoses, a total of 473 serum samples from farmers, forestry workers, and veterinarians were collected for serological examination. Anti-Borrelia burgdorferi sensu lato (s.l.) antibodies were tested with ELISA and Western blot (WB) tests; the detection of anti-Toxoplasma gondii antibodies was performed using an enzyme linked fluorescence assay (ELFA). Antibodies to bartonellosis, anaplasmosis, and chlamydiosis were determined by indirect immunofluorescent test (IFA), whereas antibodies to yersiniosis and mycoplasmosis were confirmed in the ELISA test. Positive or borderline results of antibodies against B. burgdorferi s.l. in the ELISA test were detected in 33.8% of the study population. The borderline or positive ELISA test results for at least one antibody class were confirmed by WB in 58.7% of cases. The IgG antibodies against Anaplasma phagocytophilum, Toxoplasma gondii, and Mycoplasma pneumoniae were detected in 9.6%, 51.7%, and 63.6% of samples, respectively. Antibodies against Yersinia spp., Bartonella henselae, and Chlamydia pneumoniae were found to vary between 43 and 47%. Full article

(This article belongs to the Special Issue Exploring the Biodiversity of Parasites in Humans, Wild and Domestic Animals)

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12 pages, 2329 KiB

Open AccessEditor’s ChoiceArticle

Epidemiological Analysis of Fungal Infection Disease in Pediatric Population: Focus on Hospitalization from 2007 to 2022 in Veneto Region in Italy

by Lorenzo Chiusaroli, Claudia Cozzolino, Silvia Cocchio, Mario Saia, Carlo Giaquinto, Daniele Donà and Vincenzo Baldo

Pathogens 2025, 14(1), 93; https://doi.org/10.3390/pathogens14010093 - 18 Jan 2025

Viewed by 979

Abstract

Fungal infections (FIs) are widespread globally, affecting both immunocompromised and immunocompetent children, with varying clinical implications based on age and comorbidities. In immunocompromised children, particularly those with hematologic oncological conditions, FI leads to substantially longer hospital stays and increased in-hospital mortality, with reported [...] Read more.

Fungal infections (FIs) are widespread globally, affecting both immunocompromised and immunocompetent children, with varying clinical implications based on age and comorbidities. In immunocompromised children, particularly those with hematologic oncological conditions, FI leads to substantially longer hospital stays and increased in-hospital mortality, with reported rates ranging from 15% to 20%. Our study aims to analyze the epidemiological trends of fungal infections in the pediatric population within a specific region of Italy. We extracted ICD-9 codes related to fungal infections from hospital discharge records (HDRs) in the pediatric population of Veneto, located in the north-east of Italy, between 2007 and 2022. We included all children admitted to the hospital with a primary or secondary diagnosis during admission for other reasons. Data were stratified based on age, year, ward of admission, and type of diagnosis. Patients older than eighteen and HDRs related to a second admission within thirty days from the previous admission were excluded. A total of 1433 diagnoses were analyzed during the period, with 241 (16.8%) as main diagnoses and 1192 (83.2%) as secondary diagnoses. The overall hospitalization rate was 1084 cases/100,000 (1.69 cases/100,000 as primary diagnosis and 8.95 cases/100,000 as secondary). The hospitalization rate stratified for age was 11,055 cases/100,000 among infants younger than 1 year, 8.48 cases/100,000 among those aged 1-4 years, and 4.4 cases/100,000 among children older than 5. The more frequent infection was Candida spp. (62.8%), followed by Aspergillus spp. (14.6%) and skin mycosis (9.5%). Overall, the pediatric in-hospital case fatality rate due to FI was 2.09%. Our study elucidated the overall experience of fungal infections in the pediatric population of the Veneto region in Italy. Specifically, we underscored a relatively stable hospitalization rate for fungal diseases and a noteworthy mortality rate. Full article

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

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14 pages, 3787 KiB

Open AccessEditor’s ChoiceArticle

A Four-Year Study of Antibiotic Resistance, Prevalence and Biofilm-Forming Ability of Uropathogens Isolated from Community- and Hospital-Acquired Urinary Tract Infections in Southern Italy

by Marilena Trinchera, Angelina Midiri, Giuseppe Mancuso, Maria Antonietta Lagrotteria, Carmelo Antonio De Ani and Carmelo Biondo

Pathogens 2025, 14(1), 59; https://doi.org/10.3390/pathogens14010059 - 11 Jan 2025

Cited by 1 | Viewed by 2350

Abstract

The aim of this study was to investigate the differences between nosocomial and community microorganisms isolated from patients with UTI by determining their bacterial profile, antibiotic resistance and ability to produce biofilms. A retrospective study, based on bacterial isolates from consecutive urine samples [...] Read more.

The aim of this study was to investigate the differences between nosocomial and community microorganisms isolated from patients with UTI by determining their bacterial profile, antibiotic resistance and ability to produce biofilms. A retrospective study, based on bacterial isolates from consecutive urine samples collected between January 2019 and December 2023, was conducted at a university hospital. The main pathogens isolated from both community and hospital samples were the same, but their frequency of isolation differed. Compared with community-associated cases, hospital-associated infections have more isolates of Acinetobacter baumanii complex. In contrast, Proteus mirabilis isolates were more prevalent in community than in hospital infections. In both hospital and community isolates, gram-positive bacteria showed a lower overall antimicrobial resistance (22%) compared to gram-negative bacteria (30%). The data demonstrated that individual strains exhibited disparate degrees of capacity for biofilm formation. Additionally, the data indicate an inverse correlation between biofilm production and antibiotic resistance. Isolates from community patients exhibited lower capacities for biofilm production in comparison to the capacities demonstrated by microorganisms isolated from nosocomial patients (29% and 35%, respectively). Area-specific surveillance studies can provide valuable information on UTI pathogens and antimicrobial resistance patterns, which can be useful in guiding empirical treatment. Full article

(This article belongs to the Special Issue Virulence and Resistance Mechanisms in Multidrug-Resistant Gram-Negative Bacteria)

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27 pages, 914 KiB

Open AccessEditor’s ChoiceReview

Cytomegalovirus Genetic Diversity and Evolution: Insights into Genotypes and Their Role in Viral Pathogenesis

by Cristina Venturini and Judith Breuer

Pathogens 2025, 14(1), 50; https://doi.org/10.3390/pathogens14010050 - 9 Jan 2025

Cited by 4 | Viewed by 2396

Abstract

Cytomegalovirus (CMV) is a ubiquitous virus that infects most of the human population and causes significant morbidity and mortality, particularly among immunocompromised individuals. Understanding CMV’s genetic diversity and evolutionary dynamics is crucial for elucidating its pathogenesis and developing effective therapeutic interventions. This review [...] Read more.

Cytomegalovirus (CMV) is a ubiquitous virus that infects most of the human population and causes significant morbidity and mortality, particularly among immunocompromised individuals. Understanding CMV’s genetic diversity and evolutionary dynamics is crucial for elucidating its pathogenesis and developing effective therapeutic interventions. This review provides a comprehensive examination of CMV’s genetic diversity and evolution, focussing on the role of different genotypes in viral pathogenesis. Full article

(This article belongs to the Special Issue Understanding Human Cytomegalovirus Pathogenesis: Evidence from the Clinic and Laboratory Models)

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17 pages, 3157 KiB

Open AccessEditor’s ChoiceArticle

Relationships Between Candida auris and the Rest of the Candida World—Analysis of Dual-Species Biofilms and Infections

by Monika Janeczko and Tomasz Skrzypek

Pathogens 2025, 14(1), 40; https://doi.org/10.3390/pathogens14010040 - 8 Jan 2025

Viewed by 1491

Abstract

In this study, we investigated the interactions between Candida auris and C. albicans, C. tropicalis, C. glabrata, and C. krusei in mixed infections. Initially, these interactions were studied qualitatively and quantitatively in dual-species biofilms formed in vitro. The MTT assays, [...] Read more.

In this study, we investigated the interactions between Candida auris and C. albicans, C. tropicalis, C. glabrata, and C. krusei in mixed infections. Initially, these interactions were studied qualitatively and quantitatively in dual-species biofilms formed in vitro. The MTT assays, determination of the total CFU/mL, and SEM analysis showed that C. auris interacted differentially with the other Candida spp. during the dual-species biofilm formation. Depending on the stage of the biofilm development, C. auris was found to be a particularly dominant species during its interaction with the C. krusei biofilms but significantly submissive in the C. auris-C. albicans biofilms. These studies were then extended to in vivo host models of experimental candidiasis. G. mellonella larvae were inoculated with monotypic and heterotypic suspensions of Candida. The survival rates and quantification of fungal cells in the hemolymph showed that the highest mortality was exhibited by larvae in the C. auris-C. albicans co-infection (100% mortality after 36 h). The CFU/mL values of C. auris from the larval hemolymph were lower in the interactive groups compared to the mono-species group. As a newly emerging species, C. auris persists in environments in the presence of other Candida species and is involved in both competitive and noncompetitive interactions with other Candida species during biofilm formation and development of experimental candidiasis. Full article

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10 pages, 488 KiB

Open AccessEditor’s ChoiceReview

Influence of Aging and Immune Alterations on Susceptibility to Pneumococcal Pneumonia in the Elderly

by Nathan Kang, Veedamali S. Subramanian and Anshu Agrawal

Pathogens 2025, 14(1), 41; https://doi.org/10.3390/pathogens14010041 - 8 Jan 2025

Viewed by 2337

Abstract

Pneumonia is a common respiratory infection affecting individuals of all ages, with a significantly higher incidence among the elderly. As the aging population grows, pneumonia is expected to become an increasingly critical health concern. In non-institutionalized elderly individuals, the annual incidence ranges from [...] Read more.

Pneumonia is a common respiratory infection affecting individuals of all ages, with a significantly higher incidence among the elderly. As the aging population grows, pneumonia is expected to become an increasingly critical health concern. In non-institutionalized elderly individuals, the annual incidence ranges from 25 to 44 per 1000, approximately four times higher than in those under 65. Streptococcus pneumoniae, a Gram-positive diplococcus, is the leading cause of pneumonia-related deaths in older adults. Management of S. pneumoniae infections in the elderly is challenging due to impaired antibody responses to polysaccharides and surface proteins, compounded by rising antibiotic resistance. The underlying mechanisms for increased susceptibility remain unclear, but age-related changes in the immune system, particularly in dendritic cells and T cells, are implicated. This review explores how aging-related immune alterations contribute to the heightened vulnerability of the elderly to S. pneumoniae infections. Full article

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17 pages, 4303 KiB

Open AccessEditor’s ChoiceArticle

Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing

by Smriti Shringi, Devendra H. Shah, Kimberly Carney and Ashutosh Verma

Pathogens 2025, 14(1), 33; https://doi.org/10.3390/pathogens14010033 - 5 Jan 2025

Cited by 1 | Viewed by 1726

Abstract

According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also [...] Read more.

According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses. Full article

(This article belongs to the Special Issue One Health: New Approaches, Research and Innovation to Zoonoses)

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11 pages, 1525 KiB

Open AccessEditor’s ChoiceArticle

A Novel Strain of Orientia tsutsugamushi Detected from Chiggers (Acari: Trombiculidae) on Wild Rodents

by Hak Seon Lee, Seong Yoon Kim and Hee Il Lee

Pathogens 2025, 14(1), 29; https://doi.org/10.3390/pathogens14010029 - 3 Jan 2025

Cited by 1 | Viewed by 1345

Abstract

Scrub typhus is caused by intracellular bacteria belonging to the genus Orientia. Until 2010, the endemic region was thought to be restricted to the Asia–Pacific region. Orientia species have recently been discovered in South America, Africa, Europe, and North America. In accordance [...] Read more.

Scrub typhus is caused by intracellular bacteria belonging to the genus Orientia. Until 2010, the endemic region was thought to be restricted to the Asia–Pacific region. Orientia species have recently been discovered in South America, Africa, Europe, and North America. In accordance with these circumstances, we tried to find new or novel bacterial strains in the Republic of Korea (ROK). We found that a new strain of O. tsutsugamushi formed a unique clade based on a 56-kDa type-specific antigen gene and showed 63.2–77.8% similarity to other strains of the same species. Additionally, we identified another sequence with 99.8% similarity to the O3 strain, which has not been recorded in the ROK and whose pathogenicity remains unknown. These findings confirm the diversity of O. tsutsugamushi strains in the ROK, and highlight the need for continued surveillance and further studies to characterize the pathogenicity of this novel bacterial strain. Full article

(This article belongs to the Special Issue Host-Vector-Pathogen Relationships: One-Health Approach to Vector-Borne Diseases)

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19 pages, 359 KiB

Open AccessEditor’s ChoiceReview

Flaviviruses—Induced Neurological Sequelae

by Samantha Gabrielle Cody, Awadalkareem Adam, Andrei Siniavin, Sam S. Kang and Tian Wang

Pathogens 2025, 14(1), 22; https://doi.org/10.3390/pathogens14010022 - 31 Dec 2024

Cited by 3 | Viewed by 1630

Abstract

Flaviviruses, a group of single-stranded RNA viruses spread by mosquitoes or ticks, include several significant neurotropic viruses, such as West Nile virus (WNV), Japanese encephalitis virus (JEV), tick-borne encephalitis virus (TBEV), and Zika virus (ZIKV). These viruses can cause a range of neurological [...] Read more.

Flaviviruses, a group of single-stranded RNA viruses spread by mosquitoes or ticks, include several significant neurotropic viruses, such as West Nile virus (WNV), Japanese encephalitis virus (JEV), tick-borne encephalitis virus (TBEV), and Zika virus (ZIKV). These viruses can cause a range of neurological diseases during acute infection, from mild, flu-like symptoms to severe and fatal encephalitis. A total of 20–50% of patients who recovered from acute flavivirus infections experienced long-term cognitive issues. Here, we discuss these major neurotropic flaviviruses-induced clinical diseases in humans and the recent findings in animal models and provide insights into the underlying disease mechanisms. Full article

(This article belongs to the Special Issue Neuropathogenesis of Arboviruses)

16 pages, 9146 KiB

Open AccessEditor’s ChoiceArticle

Tracing the Origin, Spread, and Molecular Evolution of Dengue Type 1 Cases That Occurred in Northern Italy in 2023

by Greta Romano, Guglielmo Ferrari, Antonino Maria Guglielmo Pitrolo, Francesca Rovida, Antonio Piralla and Fausto Baldanti

Pathogens 2024, 13(12), 1124; https://doi.org/10.3390/pathogens13121124 - 19 Dec 2024

Cited by 1 | Viewed by 1326

Abstract

The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world’s [...] Read more.

The dengue virus (DENV) is a mosquito-borne flavivirus endemic to many tropical and subtropical regions. Over the past few decades, the global incidence of dengue has risen dramatically, with the virus now present in over 100 countries, putting nearly half of the world’s population at risk. This increase is attributed to several factors, including urbanization, climate change, and global travel, which facilitate the spread of both the virus and its mosquito vectors. While dengue is primarily associated with tropical regions, outbreaks in temperate areas are becoming increasingly common due to the spread of Aedes albopictus, a competent vector for DENV that can adapt to cooler climates. This study investigates the molecular dynamics and geographic evolution of DENV type 1 (DENV-1) strains isolated from 13 patients during an autochthonous outbreak in Lombardy, Northern Italy, between August and September 2023. Additionally, Aedes albopictus mosquitoes were collected from a neighboring area to assess their potential role in the outbreak. A metagenomic approach was used to recover DENV-1 consensus sequences from clinical samples. Genotype classification and phylogenetic analyses were performed using Bayesian methods and a comprehensive dataset of DENV-1 sequences from other countries. The Italian autochthonous strains clustered with South American strains collected between 2020 and 2023, specifically those belonging to genotype V, subtype D. Bayesian analysis estimated a mean evolutionary substitution rate of 8.234 × 10⁻⁴ substitutions per site per year (95% HPD interval: 7.1448 × 10⁻⁴–9.3343 × 10⁻⁴), with the time to the most recent common ancestor (tMRCA) dating back to 1972 (95% HPD interval: 1968–1976). These findings suggest the likely introduction of the virus into the region from endemic areas in South America, followed by local transmission. This study offers valuable insights into the dynamics of the DENV-1 outbreak in Lombardy, underscoring the importance of genomic surveillance in monitoring viral spread and evolution. The findings emphasize the critical need for enhanced molecular and entomological surveillance to detect and respond to emerging autochthonous DENV cases in temperate regions where competent vectors, such as Aedes albopictus, are present. Public health strategies should prioritize integrated vector management, real-time genomic monitoring, and awareness campaigns to mitigate the risk of future outbreaks. These measures are essential to address the growing threat posed by the geographic expansion of the dengue virus. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Molecular Epidemiology, Diagnostics and Management of Viral Pathogens)

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32 pages, 1091 KiB

Open AccessEditor’s ChoiceReview

Antimicrobial Resistance in the Context of Animal Production and Meat Products in Poland—A Critical Review and Future Perspective

by Patryk Wiśniewski, Miłosz Trymers, Wioleta Chajęcka-Wierzchowska, Katarzyna Tkacz, Anna Zadernowska and Monika Modzelewska-Kapituła

Pathogens 2024, 13(12), 1123; https://doi.org/10.3390/pathogens13121123 - 19 Dec 2024

Cited by 4 | Viewed by 4212

Abstract

The prevalence of antimicrobial-resistant bacteria in meat and meat products is a significant public health challenge, largely driven by the excessive and inappropriate use of antimicrobials in animal husbandry. In Poland, a key meat producer in Europe, antibiotic-resistant pathogens such as Campylobacter spp., [...] Read more.

The prevalence of antimicrobial-resistant bacteria in meat and meat products is a significant public health challenge, largely driven by the excessive and inappropriate use of antimicrobials in animal husbandry. In Poland, a key meat producer in Europe, antibiotic-resistant pathogens such as Campylobacter spp., Staphylococcus spp., Enterococcus spp., Listeria monocytogenes, and Enterobacterales have been detected in meat, posing serious risks to consumers. This review examines the use of antimicrobial agents in meat production and the resulting antimicrobial resistance (AMR) in microorganisms isolated from meat products in Poland. The mechanisms of AMR, genetic factors, and prevalence in Poland are presented. It highlights key factors contributing to AMR, such as antibiotic misuse in livestock farming, and discusses the legal regulations governing veterinary drug residues in food. This review emphasizes the importance of monitoring and enforcement to safeguard public health and calls for further research on AMR in the meat industry. Antimicrobial resistance in meat and meat products in Poland is a huge challenge, requiring stricter antibiotic controls in animal husbandry and improved surveillance systems. Additionally, the impact of husbandry practices on the environment and food requires further research. Future efforts should focus on nationwide monitoring, alternative strategies to reduce antibiotic use, and stronger enforcement to combat antimicrobial resistance and protect public health. Full article

(This article belongs to the Special Issue Microbial Resistance, a Worldwide Concern a Global Sight)

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12 pages, 6118 KiB

Open AccessEditor’s ChoiceArticle

Pathology and VP2-Based Characterization of Infectious Bursal Disease Virus Associated with an Outbreak in Layer Chickens in Ghana

by Ben Enyetornye, Henry A. Abugri, Ama K. Kusi-Appiah, Grazieli Maboni, Theophilus Odoom, Nicole L. Gottdenker and Binu T. Velayudhan

Pathogens 2024, 13(12), 1115; https://doi.org/10.3390/pathogens13121115 - 17 Dec 2024

Viewed by 1933

Abstract

Infectious bursal disease (IBD) continues to threaten poultry production globally, with highly virulent strains circulating in many parts of Africa. In this study, molecular characterization was performed on a circulating infectious bursal disease virus (IBDV) strain from an outbreak in a layer flock [...] Read more.

Infectious bursal disease (IBD) continues to threaten poultry production globally, with highly virulent strains circulating in many parts of Africa. In this study, molecular characterization was performed on a circulating infectious bursal disease virus (IBDV) strain from an outbreak in a layer flock in Ghana. Layer chicks presented for necropsy had markedly enlarged and hemorrhagic bursae of Fabricius, with necrotic foci and catarrhal exudate on the serosal surface. Histopathology of the bursa of Fabricius revealed scattered to effacing hemorrhages on the plicae, extensive necrosis with expansion of the stroma between the follicles, and depletion of lymphocytes within the interfollicular epithelium. Reverse transcription polymerase chain reaction (RT-PCR) and subsequent sequencing of the VP2 gene showed the presence of IBDV in formalin-fixed paraffin-embedded tissues. A phylogenetic analysis compared 62 other IBDV sequences from different parts of the world and placed the Ghanaian IBDV in genogroup 3 (vvIBDV), closely related to IBDV from Nigeria. In comparison to reference vvIBDV, there were amino acid substitutions at positions 252, 254, and 300. To the best of our knowledge, this is the first report in which an IBDV from a disease outbreak in Ghana has been sequenced and compared with other IBDVs in a phylogenetic analysis. Full article

(This article belongs to the Special Issue Genomic Epidemiology of High-Consequence Viruses)

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16 pages, 3878 KiB

Open AccessEditor’s ChoiceArticle

Development of Multiplex Assays for the Identification of Zoonotic Babesia Species

by Ana Cláudia Calchi, Charlotte O. Moore, Lillianne Bartone, Emily Kingston, Marcos Rogério André, Edward B. Breitschwerdt and Ricardo G. Maggi

Pathogens 2024, 13(12), 1094; https://doi.org/10.3390/pathogens13121094 - 11 Dec 2024

Cited by 4 | Viewed by 1514

Abstract

More than one-hundred Babesia species that affect animals and humans have been described, eight of which have been associated with emerging and underdiagnosed zoonoses. Most diagnostic studies in humans have used serology or molecular assays based on the 18S rRNA gene. Because the [...] Read more.

More than one-hundred Babesia species that affect animals and humans have been described, eight of which have been associated with emerging and underdiagnosed zoonoses. Most diagnostic studies in humans have used serology or molecular assays based on the 18S rRNA gene. Because the 18S rRNA gene is highly conserved, obtaining an accurate diagnosis at the species level is difficult, particularly when the amplified DNA fragment is small. Also, due to its low copy number, sequencing of the product is often unsuccessful. In contrast, because the Babesia internal transcribed regions (ITS), between 18S rRNA and 5.8S rRNA, and between 5.8S rRNA and 28S rRNA, contain highly variable non-coding regions, the sequences in these regions provide a good option for developing molecular assays that facilitate differentiation at the species level. In this study, the complete ITS1 and ITS2 intergenic regions of different Piroplasmida species were sequenced to add to the existing GenBank database. Subsequently, ITS1 and ITS2 sequences were used to develop species-specific PCR assays and specific single-plex and multiplex conventional (c)PCR, quantitative real-time (q)PCR, and digital (d)PCR assays for four zoonotic Babesia species (Babesia divergens, Babesia odocoilei, Babesia duncani, and Babesia microti). The efficacy of the assay protocols was confirmed by testing DNA samples extracted from human blood or enrichment blood cultures. Primers were first designed based on the 18S rRNA-5.8S rRNA and 5.8S rRNA-28S rRNA regions to obtain the ITS1 and ITS2 sequences derived from different Piroplasmida species (B. odocoilei, Babesia vulpes, Babesia canis, Babesia vogeli, Babesia gibsoni, Babesia lengau, Babesia divergens-like, B. duncani, B. microti, Babesia capreoli, Babesia negevi, Babesia conradae, Theileria bicornis, and Cytauxzoon felis). Subsequently, using these sequences, single-plex or multiplex protocols were optimized targeting the ITS1 region of B. divergens, B. microti, and B. odocoilei. Each protocol proved to be sensitive and specific for the four targeted Babesia sp., detecting 10⁻² (for B. microti and B. odocoilei) and 10⁻¹ (for B. divergens and B. duncani) DNA copies per microliter. There was no cross-amplification among the Babesia species tested. Using 226 DNA extractions from blood or enrichment blood cultures obtained from 82 humans, B. divergens (seven individuals), B. odocoilei (seven individuals), and B. microti (two individuals) were detected and identified as a single infection, whereas co-infection with more than one Babesia sp. was documented by DNA sequencing in six (7.3%) additional individuals (representing a 26.8% overall prevalence). These newly developed protocols proved to be effective in detecting DNA of four Babesia species and facilitated documentation of co-infection with more than one Babesia sp. in the same individual. Full article

(This article belongs to the Section Parasitic Pathogens)

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10 pages, 673 KiB

Open AccessEditor’s ChoiceArticle

Characterization of Tick-Borne Encephalitis Virus Isolates from Ixodes persulcatus Ticks Collected During 2020 in Selenge, Mongolia

by Bazartseren Boldbaatar, Nora G. Cleary, Julia E. Paoli, Dong-Wook Lee, Doniddemberel Altantogtokh, Graham A. Matulis, Noel Cote, Jodi Fiorenzano, Irina V. Etobayeva, Jung-Hoon Kwon, Carla Mavian, Andrew G. Letizia and Michael E. von Fricken

Pathogens 2024, 13(12), 1086; https://doi.org/10.3390/pathogens13121086 - 10 Dec 2024

Cited by 2 | Viewed by 2011

Abstract

Tick-borne encephalitis virus (TBEV) causes neurological disease in humans, with varied clinical severity influenced by the viral subtype. TBEV is endemic to Mongolia, where both Siberian and Far-Eastern subtypes are present. Ixodes persulcatus is considered the main vector of TBEV in Mongolia; although, the [...] Read more.

Tick-borne encephalitis virus (TBEV) causes neurological disease in humans, with varied clinical severity influenced by the viral subtype. TBEV is endemic to Mongolia, where both Siberian and Far-Eastern subtypes are present. Ixodes persulcatus is considered the main vector of TBEV in Mongolia; although, the virus has also been detected in Dermacentor species. To further characterize the disease ecology of TBEV within the endemic Selenge province of Mongolia, 1300 Ixodes persulcatus ticks were collected in May 2020 from regions outside Ulaanbaatar. Pooled tick samples (n = 20–50) were homogenized and the supernatant was inoculated into Vero cells. Two RT-PCR assays were conducted on the cell supernatant following an observed cytopathic effect: one for TBEV detection and the second for viral subtyping. Lysed cell cultures were processed for next-generation sequencing (NGS) using Illumina technology. TBEV was detected in 10.7% of tick pools (3/28), and isolates were identified as the Siberian subtype. Phylogenetic analysis showed PQ479142 clustering within the Siberian subtype and sharing high similarity with published isolates collected in Selenge in 2012 from Ixodes persulcatus. Subtype analysis of circulating TBEV isolates and sequencing analytics to track viral evolution in ticks are vital to continued understanding of the risk to local populations. Full article

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14 pages, 2872 KiB

Open AccessEditor’s ChoiceArticle

Vaccination Schedule and Age Influence Impaired Responsiveness to Hepatitis B Vaccination: A Randomized Trial in Central Asia

by Janyn Heisig, Zuridin Sh. Nurmatov, Peggy Riese, Stephanie Trittel, Gulsunai J. Sattarova, Saikal N. Temirbekova, Gulnara Zh. Zhumagulova, Zhanylai N. Nuridinova, Aisuluu A. Derkenbaeva, Bubuzhan K. Arykbaeva, Bakyt I. Dzhangaziev, Jana Prokein, Norman Klopp, Thomas Illig, Carlos A. Guzmán, Omor T. Kasymov, Manas K. Akmatov and Frank Pessler

Pathogens 2024, 13(12), 1082; https://doi.org/10.3390/pathogens13121082 - 9 Dec 2024

Viewed by 1627

Abstract

Vaccination against hepatitis B virus (HBV) is the most cost-efficient measure to prevent infection. Still, vaccination coverage among adults in Central Asia, including Kyrgyzstan, remains suboptimal, and data about immune responses to HBV vaccination are lacking. HBV vaccination is given as three injections, [...] Read more.

Vaccination against hepatitis B virus (HBV) is the most cost-efficient measure to prevent infection. Still, vaccination coverage among adults in Central Asia, including Kyrgyzstan, remains suboptimal, and data about immune responses to HBV vaccination are lacking. HBV vaccination is given as three injections, whereby the second and third doses are given 1 and 6 months after the first (0-1-6 scheme). However, compliance with the third dose is low in Kyrgyzstan, presumably due to the long time interval between the second and third doses, suggesting that a shortened vaccination schedule could result in better adherence and increased seroconversion. Thus, we conducted a randomized trial of individuals aged 17–66 years comparing the 0-1-6 scheme against a shorter 0-1-3 scheme. Primary outcome measures were post-vaccination titers and the percentage of participants with protective post-vaccination titers (≥10 mIU/mL). Compliance with the completeness of blood draws and administered third vaccine dose was better with the 0-1-3 scheme than with the 0-1-6 scheme. In both study arms combined, younger age (<40 years) was associated with better vaccine protection. The 0-1-6 scheme resulted in higher post-vaccination titers (52 versus 15 mIU/mL, p = 0.002) and a higher seroprotection rate (85% versus 64%, p = 0.01) than the 0-1-3 scheme, whereby post-vaccination titers correlated negatively with age in the 0-1-3 scheme. Thus, the 0-1-6 scheme should continue to be the preferred HBV vaccination schedule, but interventions to improve compliance with the third vaccine dose are needed. Full article

(This article belongs to the Special Issue Biomarkers for Human and Veterinary Infectious Diseases)

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18 pages, 2264 KiB

Open AccessEditor’s ChoiceReview

Advancements in Detection Methods for Salmonella in Food: A Comprehensive Review

by Aayushi Patel, Andrew Wolfram and Taseen S. Desin

Pathogens 2024, 13(12), 1075; https://doi.org/10.3390/pathogens13121075 - 7 Dec 2024

Cited by 3 | Viewed by 5806

Abstract

Non-typhoidal Salmonella species are one of the leading causes of gastrointestinal disease in North America, leading to a significant burden on the healthcare system resulting in a huge economic impact. Consequently, early detection of Salmonella species in the food supply, in accordance with [...] Read more.

Non-typhoidal Salmonella species are one of the leading causes of gastrointestinal disease in North America, leading to a significant burden on the healthcare system resulting in a huge economic impact. Consequently, early detection of Salmonella species in the food supply, in accordance with food safety regulations, is crucial for protecting public health, preventing outbreaks, and avoiding serious economic losses. A variety of techniques have been employed to detect the presence of this pathogen in the food supply, including culture-based, immunological, and molecular methods. The present review summarizes these methods and highlights recent updates on promising emerging technologies, including aptasensors, Surface Plasmon Resonance (SPR), and Surface Enhanced Raman Spectroscopy (SERS). Full article

(This article belongs to the Special Issue Development and Evaluation of Detection Method for Pathogenic Bacteria from Food)

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13 pages, 958 KiB

Open AccessEditor’s ChoiceArticle

Antimicrobial Susceptibility Trends in E. coli Causing Pediatric Urinary Tract Infections in the United States

by Simren Mahajan, Neena Kanwar, Gina M. Morgan, Rodrigo E. Mendes, Brian R. Lee, Dithi Banerjee and Rangaraj Selvarangan

Pathogens 2024, 13(12), 1068; https://doi.org/10.3390/pathogens13121068 - 6 Dec 2024

Cited by 1 | Viewed by 1720

Abstract

Urinary tract infections (UTIs) are among the most common pediatric infections. This study evaluated the antimicrobial susceptibility patterns of 3511 uropathogenic E. coli (UPEC) isolated from pediatric patients in the United States from 2014 to 2023. The database from the SENTRY antimicrobial surveillance [...] Read more.

Urinary tract infections (UTIs) are among the most common pediatric infections. This study evaluated the antimicrobial susceptibility patterns of 3511 uropathogenic E. coli (UPEC) isolated from pediatric patients in the United States from 2014 to 2023. The database from the SENTRY antimicrobial surveillance program from 89 medical centers was utilized as a data source. The antimicrobial susceptibility was tested using the microbroth dilution technique against 24 antimicrobial agents. MICs were determined using the CLSI/EUCAST/FDA breakpoint criteria. All the antimicrobials reported susceptibility rates above 80% except for tetracycline (76.2%), trimethoprim–sulfamethoxazole (69.7%), and ampicillin–sulbactam (55.7%). During the study period, the susceptibility rates remained stable for most antimicrobial agents. However, significant differences were observed among age, gender, and U.S. census regions, with the Middle Atlantic showing the lowest and the Mountain region the highest susceptibility rates, for most antimicrobials. The incidence of ESBL UPEC increased from 7.1% to 10.8% between 2014 and 2023, while the prevalence of the MDR phenotype remained relatively stable. The prevalence of both ESBL and MDR phenotypes was highest among infants and young children (0–24 months), with the highest resistance rates from the Pacific region. Knowledge of the landscape of antibiotic resistance in pediatric UPEC will help healthcare providers to better tailor empiric treatment regimens for most UTI infections. Full article

(This article belongs to the Special Issue New Insight in Pathogenic Escherichia coli: Infections, Pathogenesis and Therapies)

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16 pages, 3024 KiB

Open AccessEditor’s ChoiceArticle

Genomic Insights into Fusarium verticillioides Diversity: The Genome of Two Clinical Isolates and Their Demethylase Inhibitor Fungicides Susceptibility

by Luca Degradi, Valeria Tava, Maria Carmela Esposto, Anna Prigitano, Daniela Bulgari, Andrea Kunova, Marco Saracchi, Paolo Cortesi and Matias Pasquali

Pathogens 2024, 13(12), 1062; https://doi.org/10.3390/pathogens13121062 - 3 Dec 2024

Viewed by 1369

Abstract

Fusarium verticillioides is an important plant pathogen in maize and other cereals that is seldom detected as the cause of human fusariosis. Here, we provide the analysis of the available diversity of F. verticillioides sequenced worldwide and report the first two genome assemblies [...] Read more.

Fusarium verticillioides is an important plant pathogen in maize and other cereals that is seldom detected as the cause of human fusariosis. Here, we provide the analysis of the available diversity of F. verticillioides sequenced worldwide and report the first two genome assemblies and annotations (including mitochondrial DNA) of Fusarium verticillioides from clinical settings. Fusarium verticillioides 05-0160 (IUM05-0160) and Fusarium verticillioides 09-1037 (IUM09-1037) strains were obtained from the bone marrow and blood of two immunocompromised patients, respectively. The phylogenomic analysis confirmed the species identity of our two strains. Comparative genomic analyses among the reannotated F. verticillioides genomes (n = 46) did not lead to the identification of unique genes specific to the clinical samples. Two subgroups in the F. verticillioides clade were also identified and confirmed by a mitochondrial diversity study. Clinical strains (n = 4) were positioned in the multigene phylogenetic tree without any correlation between the host and the tree branches, grouping with plant-derived strains. To investigate the existence of a potential fitness advantage of our two clinical strains, we compared demethylase inhibitor fungicides susceptibility against the reference Fusarium verticillioides 7600, showing, on average, lower susceptibility to agricultural and medical-used antifungals. A significant reduction in susceptibility was observed for itraconazole and tetraconazole, which might be explained by structural changes in CYP51A and CYP51C sequences. By providing the first two annotated genomes of F. verticillioides from clinical settings comprehensive of their mitogenomes, this study can serve as a base for exploring the fitness and adaptation capacities of Fusarium verticillioides infecting different kingdoms. Full article

(This article belongs to the Section Fungal Pathogens)

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21 pages, 6589 KiB

Open AccessEditor’s ChoiceReview

Papillomaviruses and Papillomaviral Disease in Dogs and Cats: A Comprehensive Review

by John S. Munday and Cameron G. Knight

Pathogens 2024, 13(12), 1057; https://doi.org/10.3390/pathogens13121057 - 1 Dec 2024

Cited by 5 | Viewed by 5381

Abstract

Papillomaviruses (PVs) frequently infect humans as well as non-human species. While most PV infections are asymptomatic, PVs can also cause hyperplastic papillomas (warts) as well as pre-neoplastic and neoplastic lesions. In this review, the life cycle of PVs is discussed, along with the [...] Read more.

Papillomaviruses (PVs) frequently infect humans as well as non-human species. While most PV infections are asymptomatic, PVs can also cause hyperplastic papillomas (warts) as well as pre-neoplastic and neoplastic lesions. In this review, the life cycle of PVs is discussed, along with the mechanisms by which PVs cause hyperplastic and neoplastic diseases. The humoral and cell-mediated immune responses to PVs are reviewed, giving context to the later discussion on the use of vaccines to reduce canine and feline PV-associated disease. Both dogs and cats are infected by numerous different PV types classified into multiple different PV genera. The taxonomic classification of PVs is reviewed, along with the significance of this classification. The PV-associated diseases of dogs and cats are then described. These descriptions include the clinical presentation of the disease, the causative PV types, the histological features that allow diagnosis, and, where appropriate, possible treatment options. The review is comprehensive and contains the latest information about PVs and the diseases they cause in dogs and cats. Full article

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

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15 pages, 2923 KiB

Open AccessEditor’s ChoiceArticle

Coxsackievirus A6 U.K. Genetic and Clinical Epidemiology Pre- and Post-SARS-CoV-2 Emergence

by Alice M. Joyce, Jack D. Hill, Theocharis Tsoleridis, Stuart Astbury, Louise Berry, Hannah C. Howson-Wells, Nancy Allen, Ben Canning, Carl B. Jones, Gemma Clark, William L. Irving, Alexander W. Tarr and C. Patrick McClure

Pathogens 2024, 13(11), 1020; https://doi.org/10.3390/pathogens13111020 - 20 Nov 2024

Cited by 1 | Viewed by 1964

Abstract

Coxsackievirus A6 (CVA6) has become increasingly clinically relevant as a cause of Hand, Foot and Mouth Disease (HFMD) globally since 2008. However, most laboratories do not routinely determine the enteroviral type of positive samples. The non-pharmaceutical measures introduced to curb transmission during the [...] Read more.

Coxsackievirus A6 (CVA6) has become increasingly clinically relevant as a cause of Hand, Foot and Mouth Disease (HFMD) globally since 2008. However, most laboratories do not routinely determine the enteroviral type of positive samples. The non-pharmaceutical measures introduced to curb transmission during the COVID-19 pandemic may also have perturbed CVA6 epidemiology. We thus aimed to determine the prevalence, clinical presentation and genetic relationship of CVA6 across three complete epidemic seasons: one pre-SARS-CoV-2 emergence and two post-SARS-CoV-2 emergence in our regional healthcare setting. Surplus diagnostic nucleic acid from diagnosed enteroviral positives diagnosed between September and December of 2018 and between May 2021 and April of 2023 was subject to VP1 gene sequencing to determine the CVA6 cases and interrogate their phylogenetic relationship. The confirmed CVA6 cases were also retrospectively clinically audited. CVA6 infections were identified in 33 and 69 individuals pre- and post-pandemic, respectively, with cases peaking in November of 2018 and 2022, but in October of 2021. HFMD was the primary diagnosis in 85.5% of the post-pandemic cases, but only 69.7% of the pre-pandemic cases, where respiratory and neurological symptoms (45.5% and 12.1%, respectively) were significantly elevated. A complete VP1 sequence was retrieved for 94% of the CVA6 cases, revealing that studied infections were genetically diverse and suggestive of multiple local and international transmission chains. CVA6 presented a significant clinical burden in our regional U.K. hospital setting both pre- and post-pandemic and was subject to dynamic clinical and genetic epidemiology. Full article

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

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12 pages, 922 KiB

Open AccessEditor’s ChoiceArticle

Highly Pathogenic H5N1 Influenza A Virus (IAV) in Blue-Winged Teal in the Mississippi Flyway Is Following the Historic Seasonal Pattern of Low-Pathogenicity IAV in Ducks

by David E. Stallknecht, Deborah L. Carter, Lyndon Sullivan-Brügger, Paul Link, Emily Ferraro, Ciara McCarty, Bruce Davis, Lynda Knutsen, James Graham and Rebecca L. Poulson

Pathogens 2024, 13(11), 1017; https://doi.org/10.3390/pathogens13111017 - 19 Nov 2024

Cited by 1 | Viewed by 2406

Abstract

Highly pathogenic H5N1 (HP H5N1) influenza A virus (IAV) has been detected annually in North American ducks since its introduction during 2021, but it is unknown if this virus will follow the same seasonal and geographic patterns that have been observed with low-pathogenicity [...] Read more.

Highly pathogenic H5N1 (HP H5N1) influenza A virus (IAV) has been detected annually in North American ducks since its introduction during 2021, but it is unknown if this virus will follow the same seasonal and geographic patterns that have been observed with low-pathogenicity (LP) IAV in this reservoir. We monitored blue-winged teal in the Mississippi flyway prior to the detection of HP H5N1 and during two post-introduction migration cycles from spring 2022 to spring 2024, testing birds for infection and antibodies to IAV nucleoprotein (NP), hemagglutinin subtype H5, and neuraminidase subtype N1. Antigens representing clade 2.3.4.4b HP H5 and LP North American H5 were used for hemagglutination inhibition (HI) and virus neutralization (VN) tests for H5 antibodies. Virologic results were consistent with historic seasonal and geographic patterns reported for LP IAV with peak infections occurring in pre-migration staging areas in Minnesota during fall 2022. However, the high prevalence of the H5 subtype was exceptional compared to historic prevalence estimates at this same site and for the Mississippi flyway. HP H5N1 was detected on wintering areas in Louisiana and Texas during the fall of that same year and this was followed by an increase in estimated antibody prevalence to NP, H5, and N1 with no HP H5N1 detections during the wintering or spring migration periods of 2022/2023. HP H5N1 was not detected in Minnesota during fall 2023 but was detected from a single bird in Louisiana. However, a similar increase in antibody prevalence was observed during the winter and spring period of 2023 and 2024. Over the two migration cycles, there was a temporal shift in observed prevalence and relative titers against the H5 antigens with a higher proportion of ducks testing positive to the 2.3.4.4b H5 antigen and higher relative titer to that antigen compared to the representative LP North American H5 antigen. The seasonal and geographic patterns observed appear to be driven by population immunity during the migration cycle. Results support an initial high infection rate of HP H5N1 in blue-winged teal in the Mississippi flyway followed by a high prevalence of antibodies to NP, H5, and N1. Although prevalence was much reduced in the second migration cycle following introduction, it is not known if this pattern will persist in the longer term or affect historic patterns of subtype diversity in this reservoir. Full article

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

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22 pages, 7188 KiB

Open AccessEditor’s ChoiceReview

In Silico Genomic Analysis of Avian Influenza Viruses Isolated From Marine Seal Colonies

by Klaudia Chrzastek and Darrell R. Kapczynski

Pathogens 2024, 13(11), 1009; https://doi.org/10.3390/pathogens13111009 - 16 Nov 2024

Viewed by 2232

Abstract

Genetically diverse avian influenza viruses (AIVs) are maintained in wild aquatic birds with increasingly frequent spillover into mammals, yet these represent a small proportion of the overall detections. The isolation of AIVs in marine mammals, including seals, has been reported sporadically over the [...] Read more.

Genetically diverse avian influenza viruses (AIVs) are maintained in wild aquatic birds with increasingly frequent spillover into mammals, yet these represent a small proportion of the overall detections. The isolation of AIVs in marine mammals, including seals, has been reported sporadically over the last 45 years. Prior to 2016, all reports of AIVs detected in seals were of low-pathogenicity AIVs. In spite of this, the majority of reported AIV outbreaks caused fatal respiratory diseases, with harbor seals particularly susceptible to infection. The H5 clade 2.3.4.4b highly pathogenic AIV (HPAIV) was detected in seals for the first time in 2016. Recently, many cases of mass seal die-offs have occurred because of 2.3.4.4b HPAIV and are attributed to spillover from wild bird species. The potential for seal-to-seal transmission has been considered after the mass mortality of southern elephant seals off the coast of Argentina. Close contact between seals and wild birds, the rapid evolution of H5N1 AIVs, and the possibility of efficient mammal-to-mammal transmission are increasing concerns due to the potential for the establishment of a marine mammal reservoir and public health risks associated with the pandemic potential of the virus. This manuscript details the detection of AIVs in the seal population, comparing interesting features of various subtypes with an emphasis on avian-to-mammal-to-mammal transmission. Phylogenetic characterizations of the representative seal isolates were performed to demonstrate the relationships within the different virus isolates. Furthermore, we demonstrate that the reassortment events between different LPAIVs occurred before and after the viruses reached the seal population. The reassortment of viral segments plays an important role in the evolution of influenza viruses. Taken together, these data report on the 45 year history between seals and AIVs. Full article

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

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18 pages, 6479 KiB

Open AccessEditor’s ChoiceArticle

Antimicrobial Resistance Profile of Zoonotic Clinically Relevant WHO Priority Pathogens

by Elaine Meade, Mark Anthony Slattery and Mary Garvey

Pathogens 2024, 13(11), 1006; https://doi.org/10.3390/pathogens13111006 - 15 Nov 2024

Cited by 1 | Viewed by 1675

Abstract

The World Health Organization announced critically important bacterial and fungal pathogens displaying alarming levels of antimicrobial resistance, which currently represent difficult-to-treat cases of morbidity. Within this grouping, the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, [...] Read more.

The World Health Organization announced critically important bacterial and fungal pathogens displaying alarming levels of antimicrobial resistance, which currently represent difficult-to-treat cases of morbidity. Within this grouping, the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are causative of significant morbidity and mortality. Studies described herein demonstrate the presence of critically important fungal and ESKAPE bacterial species in companion animals which are zoonotic in nature. The relationship between the environment, animals, and human infectious disease has long been recognized as part of One Health. This research investigates the resistance patterns of isolated zoonotic pathogens using recognized in vitro methodologies, namely disk diffusion, minimum inhibitory concentration testing, and genetic screening. Antibiotic susceptibility testing and gene analysis demonstrated an association between multi-drug resistance and extended beta spectrum lactamase production in critical-priority bacteria. Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa exhibit great levels of multi-drug resistance. Fungal isolates demonstrated high levels of resistance, with Amphotericin B proving the most effective antifungal agent investigated. The level of antimicrobial resistance present in clinically relevant bacterial and fungal pathogens isolated from animal cases of morbidity in this study is alarming. In conclusion, this study shows that animals can act as a reservoir facilitating the transmission of antibiotic-resistant pathogens and genes zoonotically. Full article

(This article belongs to the Section Bacterial Pathogens)

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22 pages, 1584 KiB

Open AccessEditor’s ChoiceArticle

Development and Validation of an Indirect and Blocking ELISA for the Serological Diagnosis of African Swine Fever

by Chukwunonso Onyilagha, Kaye Quizon, Dmytro Zhmendak, Ian El Kanoa, Thang Truong, Thanuja Ambagala, Alfonso Clavijo, Van Phan Le, Shawn Babiuk and Aruna Ambagala

Pathogens 2024, 13(11), 981; https://doi.org/10.3390/pathogens13110981 - 8 Nov 2024

Cited by 2 | Viewed by 2033

Abstract

African swine fever (ASF) is an economically devastating viral disease of pigs caused by the ASF virus (ASFV). The rapid global spread of ASF has increased the demand for ASF diagnostics to be readily available and accessible. No commercial ASF enzyme-linked immunosorbent assay [...] Read more.

African swine fever (ASF) is an economically devastating viral disease of pigs caused by the ASF virus (ASFV). The rapid global spread of ASF has increased the demand for ASF diagnostics to be readily available and accessible. No commercial ASF enzyme-linked immunosorbent assay (ELISA) kits are manufactured and licensed in North America. Here, we report the development of two serological diagnostic assays, a blocking ELISA (bELISA) based on ASFV glycoprotein p54 and an indirect ELISA (iELISA) based on ASFV glycoproteins p54 and p72. The assays showed high sensitivity and specificity and detected anti-ASFV antibodies in serum samples from experimentally infected animals as early as 8 days post-infection. The two assays were produced commercially (AsurDx^™ bELISA and iELISA) and subjected to extensive validation. Based on data from a set of characterized reference sera, the prototype commercial assays, while maintaining 100.00% specificity, showed 97.67% (AsurDx^™ bELISA) and 83.72% (AsurDx^™ iELISA) sensitivity. Both prototype assays detected anti-ASFV antibodies in serum samples collected from pigs experimentally infected with multiple ASFV strains and field samples collected from sick, recovering, and vaccinated animals. The two commercially available assays can be used in routine ASF diagnostics, serological surveys, and for evaluating serological responses to ASF vaccine candidates. Full article

(This article belongs to the Section Viral Pathogens)

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20 pages, 1804 KiB

Open AccessEditor’s ChoiceReview

Multidrug Resistant Pseudomonas aeruginosa in Clinical Settings: A Review of Resistance Mechanisms and Treatment Strategies

by Beth Schwartz, Katherine Klamer, Justin Zimmerman, Pramodini B. Kale-Pradhan and Ashish Bhargava

Pathogens 2024, 13(11), 975; https://doi.org/10.3390/pathogens13110975 - 7 Nov 2024

Cited by 11 | Viewed by 5814

Abstract

Pseudomonas aeruginosa is causing increasing concern among clinicians due to its high mortality and resistance rates. This bacterium is responsible for various infections, especially in hospital settings, affecting some of the most vulnerable patients. Pseudomonas aeruginosa has developed resistance through multiple mechanisms, making [...] Read more.

Pseudomonas aeruginosa is causing increasing concern among clinicians due to its high mortality and resistance rates. This bacterium is responsible for various infections, especially in hospital settings, affecting some of the most vulnerable patients. Pseudomonas aeruginosa has developed resistance through multiple mechanisms, making treatment challenging. Diagnostic techniques are evolving, with rapid testing systems providing results within 4–6 h. New antimicrobial agents are continuously being developed, offering potential solutions to these complex clinical decisions. This article provides a review of the epidemiology, at-risk populations, resistance mechanisms, and diagnostic and treatment options for Pseudomonas aeruginosa. Full article

(This article belongs to the Section Bacterial Pathogens)

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25 pages, 467 KiB

Open AccessEditor’s ChoiceReview

Diseases Caused by and Behaviors Associated with Toxoplasma gondii Infection

by Ginger K. H. Akins, João M. Furtado and Justine R. Smith

Pathogens 2024, 13(11), 968; https://doi.org/10.3390/pathogens13110968 - 6 Nov 2024

Cited by 3 | Viewed by 3702

Abstract

Toxoplasma gondii is an Apicomplexan parasite that is estimated to infect at least one-third of the global human population. T. gondii infection may be transmitted horizontally or vertically. The main risk factors for transmission to humans are related to diet, especially the consumption [...] Read more.

Toxoplasma gondii is an Apicomplexan parasite that is estimated to infect at least one-third of the global human population. T. gondii infection may be transmitted horizontally or vertically. The main risk factors for transmission to humans are related to diet, especially the consumption of undercooked meat, along with soil contact. In immunocompetent persons, the acute infection may go undetected as it typically produces minor, non-specific symptoms that are self-limited. After infection is established, recurrent retinochoroiditis is the most common clinical disease. In contrast, severe systemic or cerebral toxoplasmosis may be life-threatening for immunocompromised individuals. Furthermore, congenital toxoplasmosis acquired in utero may have devastating consequences if not recognized and promptly treated. A growing body of research has identified associations between latent T. gondii infection, and personality traits and risk-taking behaviors. Other studies have documented associations between latent infection and psychiatric conditions that include schizophrenia and bipolar affective disorder. With no current treatment regimens being curative of T. gondii infection, effective prevention measures at both the public health and individual levels are vitally important. Full article

(This article belongs to the Special Issue Women’s Special Issue Series: Pathogens)

14 pages, 1269 KiB

Open AccessEditor’s ChoiceArticle

Clinical Snapshot of Group A Streptococcal Isolates from an Australian Tertiary Hospital

by Phoebe K. Shaw, Andrew J. Hayes, Maree Langton, Angela Berkhout, Keith Grimwood, Mark R. Davies, Mark J. Walker and Stephan Brouwer

Pathogens 2024, 13(11), 956; https://doi.org/10.3390/pathogens13110956 - 1 Nov 2024

Viewed by 1544

Abstract

Streptococcus pyogenes (Group A Streptococcus, GAS) is a human-restricted pathogen that causes a wide range of diseases from pharyngitis and scarlet fever to more severe, invasive infections such as necrotising fasciitis and streptococcal toxic shock syndrome. There has been a global increase [...] Read more.

Streptococcus pyogenes (Group A Streptococcus, GAS) is a human-restricted pathogen that causes a wide range of diseases from pharyngitis and scarlet fever to more severe, invasive infections such as necrotising fasciitis and streptococcal toxic shock syndrome. There has been a global increase in both scarlet fever and invasive infections during the COVID-19 post-pandemic period. The aim of this study was the molecular characterisation of 17 invasive and non-invasive clinical non-emm1 GAS isolates from an Australian tertiary hospital collected between 2021 and 2022. Whole genome sequencing revealed a total of nine different GAS emm types with the most prevalent being emm22, emm12 and emm3 (each 3/17, 18%). Most isolates (14/17, 82%) carried at least one superantigen gene associated with contemporary scarlet fever outbreaks, and the carriage of these toxin genes was non-emm type specific. Several mutations within key regulatory genes were identified across the different GAS isolates, which may be linked to an increased expression of several virulence factors. This study from a single Australian centre provides a snapshot of non-emm1 GAS clinical isolates that are multiclonal and linked with distinct epidemiological markers commonly observed in high-income settings. These findings highlight the need for continual surveillance to monitor genetic markers that may drive future outbreaks. Full article

(This article belongs to the Special Issue Microbial Pathogenesis and Emerging Infections)

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18 pages, 9126 KiB

Open AccessEditor’s ChoiceArticle

Investigation of the Antimicrobial Resistance of Important Pathogens Isolated from Poultry from 2015 to 2023 in the United States

by Asher T. Wang, Liya Tang, Andrew Gao, Ethan Zhang, Grace Huang, Justin Shen, Qian Jia and Zuyi Huang

Pathogens 2024, 13(11), 919; https://doi.org/10.3390/pathogens13110919 - 22 Oct 2024

Cited by 2 | Viewed by 2374

Abstract

Foodborne pathogens cause around 47.8 million illnesses in the U.S. annually, with antimicrobial misuse in food production, particularly in poultry processing, contributing significantly to this public health challenge. Misuse of antimicrobials can contribute to antimicrobial resistance (AMR) and make the treatment of pathogens [...] Read more.

Foodborne pathogens cause around 47.8 million illnesses in the U.S. annually, with antimicrobial misuse in food production, particularly in poultry processing, contributing significantly to this public health challenge. Misuse of antimicrobials can contribute to antimicrobial resistance (AMR) and make the treatment of pathogens increasingly difficult. This emphasizes the need to investigate antimicrobial resistance in U.S. poultry. This study analyzes data from the NCBI Pathogen Isolates Browser (2015–2023) to explore the relationships between antimicrobial-resistant pathogens, AMR genes, and antimicrobials detected with resistance in pathogens isolated from chicken and turkey. Using principal component analysis and hierarchical clustering, we mapped and profiled regional and temporal patterns of antimicrobial resistance. Salmonella enterica was the most prevalent antimicrobial-resistant pathogen across both chicken and turkey, with notable outbreaks, particularly in the Northeast. Antimicrobial-resistant Campylobacter jejuni was more prevalent in chicken, particularly in California and Georgia, while Escherichia coli and Shigella were more prominent in turkey, with concentrated antimicrobial resistance in Texas for pathogen samples isolated from chicken. Resistance to tetracycline and streptomycin was widespread, with distinct regional clusters: antimicrobial resistance was concentrated in states like Minnesota for pathogens isolated from chicken, while AMR found in pathogens isolated from turkey was more evenly distributed across the Midwest. Key AMR genes, such as tet(A), mdsA, and mdsB, also followed similar patterns, peaking in 2019 and significantly declining by 2022. The observed decline in AMR cases may be linked to improved biosecurity measures and disruptions in detection due to the COVID-19 pandemic. This comprehensive study of antimicrobial resistance in U.S. poultry provides valuable insights into resistance trends, which provide useful information to inform targeted interventions and policies to mitigate AMR threats in the poultry production industry. For consumers, these findings emphasize the importance of proper food handling and cooking practices to reduce the risk of exposure to resistant pathogens. Regulatory authorities should focus on enforcing stricter antimicrobial usage policies and enhancing surveillance systems to sustain the reduction in AMR cases. Full article

(This article belongs to the Special Issue Foodborne Pathogens: The Antimicrobial Resistance from Farm to Fork)

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15 pages, 3279 KiB

Open AccessEditor’s ChoiceArticle

Genomic Analysis of Aeromonas salmonicida ssp. salmonicida Isolates Collected During Multiple Clinical Outbreaks Supports Association with a Single Epidemiological Unit

by Konrad Wojnarowski, Paulina Cholewińska, Peter Steinbauer, Tobias Lautwein, Wanvisa Hussein, Lisa-Marie Streb and Dušan Palić

Pathogens 2024, 13(10), 908; https://doi.org/10.3390/pathogens13100908 - 17 Oct 2024

Cited by 2 | Viewed by 1954

Abstract

Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease [...] Read more.

Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased scrutiny and availability of veterinary medical products to control this disease in production facilities. In such a regulatory environment, the utility of autogenous vaccines to assist with disease prevention and control as a veterinary-guided prophylactic measure is of high interest to the producers and veterinary services alike. However, evolving concepts of epidemiological units and epidemiological links need to be considered during approval and acceptance procedures for the application of autogenous vaccines in multiple aquaculture facilities. Here, we present the results of solid-state nanopore sequencing (Oxford Nanopore Technologies, ONT) performed on 54 isolates of Aeromonas salmonicida ssp. salmonicida sampled during clinical outbreaks of furunculosis in different aquaculture facilities from Bavaria, Germany, from 2017 to 2020. All of the performed analyses (phylogeny, single nucleotide polymorphism and 3D protein modeling for major immunogenic proteins) support a high probability that all studied isolates belong to the same epidemiological unit. Simultaneously, we describe a cost/effective method of whole genome analysis with the usage of ONT as a viable strategy to study outbreaks of other pathogens in the field of aquatic veterinary medicine for the purpose of developing the best autogenous vaccine candidates applicable to multiple aquaculture establishments. Full article

(This article belongs to the Special Issue Molecular Epidemiology of Pathogenic Agents)

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16 pages, 301 KiB

Open AccessEditor’s ChoiceReview

Phage-Based Therapy in Combination with Antibiotics: A Promising Alternative against Multidrug-Resistant Gram-Negative Pathogens

by Cleo Anastassopoulou, Stefanos Ferous, Aikaterini Petsimeri, Georgia Gioula and Athanasios Tsakris

Pathogens 2024, 13(10), 896; https://doi.org/10.3390/pathogens13100896 - 14 Oct 2024

Cited by 8 | Viewed by 6053

Abstract

The continued rise in antimicrobial resistance poses a serious threat to public health worldwide. The use of phages that can have bactericidal activity without disrupting the normal flora represents a promising alternative treatment method. This practice has been successfully applied for decades, mainly [...] Read more.

The continued rise in antimicrobial resistance poses a serious threat to public health worldwide. The use of phages that can have bactericidal activity without disrupting the normal flora represents a promising alternative treatment method. This practice has been successfully applied for decades, mainly in Eastern Europe, and has recently been used as an emergency therapy for compassionate care in the United States. Here, we provide a comprehensive review of the pre-clinical and clinical applications of phage therapy concerning three major Gram-negative pathogens: Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. The advantages and the challenges of expanding the usage of phages as an alternative or adjunctive treatment for antimicrobial-resistant bacterial infections are discussed. We emphasize the virologic complexities of using the highly adaptable phage populations as molecular tools, along with antibiotic chemical compounds, to effectively combat rapidly coevolving pathogenic bacteria in the host microenvironment. Pre-clinical studies, isolated clinical reports and a few randomized clinical trials have shown that bacteriophages can be effective in treating multidrug-resistant bacterial infections. The ability of some phages to revert the resistance against antibiotics, and possibly also against the human complement and other phages, appears to be a great advantage of phage therapy despite the inevitable emergence of phage-resistant strains. Bacteriophages (or specific phage-derived products) can enhance antimicrobial efficacy by reducing bacterial virulence via the alteration of basic bacterial structures, primarily of the cellular wall and membrane. Although several issues remain open regarding their effective clinical application, it appears that phage-based therapeutics in combination with antibiotics can provide an effective solution to the spread of antimicrobial resistance. Full article

(This article belongs to the Special Issue Pathogenesis Mechanisms and Antimicrobial Strategies against Multidrug-Resistant Pathogens)

19 pages, 5414 KiB

Open AccessEditor’s ChoiceReview

Ocular Toxoplasmosis: Advances in Toxoplasma gondii Biology, Clinical Manifestations, Diagnostics, and Therapy

by Miki Miyagaki, Yuan Zong, Mingming Yang, Jing Zhang, Yaru Zou, Kyoko Ohno-Matsui and Koju Kamoi

Pathogens 2024, 13(10), 898; https://doi.org/10.3390/pathogens13100898 - 14 Oct 2024

Cited by 10 | Viewed by 6497

Abstract

Toxoplasma gondii, an obligate intracellular parasite, is a globally prevalent pathogen capable of infecting a wide range of warm-blooded animals, including humans. Ocular toxoplasmosis (OT), a severe manifestation of T. gondii infection, can lead to potentially blinding complications. This comprehensive review delves [...] Read more.

Toxoplasma gondii, an obligate intracellular parasite, is a globally prevalent pathogen capable of infecting a wide range of warm-blooded animals, including humans. Ocular toxoplasmosis (OT), a severe manifestation of T. gondii infection, can lead to potentially blinding complications. This comprehensive review delves into the current understanding of T. gondii biology, exploring its complex life cycle, diverse transmission routes, and strain diversity. This article provides an in-depth analysis of the clinical manifestations of OT, which can result from both congenital and acquired infections, presenting a spectrum of signs and symptoms. The review examines various diagnostic strategies employed for OT, including clinical examination, multimodal imaging techniques such as fundus fluorescein angiography (FFA), indocyanine green angiography (ICGA), optical coherence tomography (OCT), and optical coherence tomography angiography (OCTA), as well as laboratory tests including serology and molecular methods. Despite extensive research, the specific mechanisms underlying ocular involvement in T. gondii infection remain elusive, and current diagnostic options have limitations. Moreover, the treatment of active and recurrent OT remains a challenge. While existing therapies, such as antimicrobial agents and immunosuppressants, can control active infections, they do not offer a definitive cure or completely prevent recurrence. The clinical endpoints for the management of active and recurrent OT are also not yet well-established, and the available treatment methods carry the potential for adverse effects. This article highlights the need for future research to elucidate the pathogenesis of OT, investigate genetic factors influencing susceptibility to infection, and develop more sensitive and specific diagnostic tools. Enhancing global surveillance, implementing robust prevention strategies, and fostering multidisciplinary collaborations will be crucial in reducing the burden of OT and improving patient outcomes. This comprehensive review aims to provide a valuable resource for clinicians, researchers, and policymakers, contributing to a better understanding of T. gondii infection and its impact on ocular health. Full article

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