Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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11 pages, 1369 KiB  
Article
Phytophthora Species Involved in Alnus glutinosa Decline in Portugal
by Carlo Bregant, Eduardo Batista, Sandra Hilário, Benedetto T. Linaldeddu and Artur Alves
Pathogens 2023, 12(2), 276; https://doi.org/10.3390/pathogens12020276 - 8 Feb 2023
Cited by 11 | Viewed by 2967
Abstract
Recent field surveys conducted in five common alder ecosystems in Portugal have shown the occurrence of severe canopy dieback, bleeding canker and root rot symptoms indicative of Phytophthora infections. Isolations from symptomatic tissues, rhizosphere and water samples yielded a total of 13 Phytophthora [...] Read more.
Recent field surveys conducted in five common alder ecosystems in Portugal have shown the occurrence of severe canopy dieback, bleeding canker and root rot symptoms indicative of Phytophthora infections. Isolations from symptomatic tissues, rhizosphere and water samples yielded a total of 13 Phytophthora species belonging to 6 phylogenetic clades, including P. lacustris (13 isolates), P. multivora (10), P. amnicola (9), P. chlamydospora (6), P. polonica (6), P. bilorbang (4), P. plurivora (4), P. cinnamomi (3), P. asparagi (2), P. cactorum (2), P. pseudocryptogea (2), P. gonapodyides (1) and P. rosacearum (1). Results of the pathogenicity test confirmed the complex aetiology of common alder decline and the additional risk posed by Phytophthora multivora to the riparian habitats in Portugal. At the same time, the diversity of Phytophthora assemblages detected among the investigated sites suggests that different species could contribute to causing the same symptoms on this host. Two species, P. amnicola and P. rosacearum, are reported here for the first time in natural ecosystems in Europe. Full article
(This article belongs to the Section Fungal Pathogens)
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15 pages, 866 KiB  
Review
A Review on the Immunological Response against Trypanosoma cruzi
by Giusi Macaluso, Francesca Grippi, Santina Di Bella, Valeria Blanda, Francesca Gucciardi, Alessandra Torina, Annalisa Guercio and Vincenza Cannella
Pathogens 2023, 12(2), 282; https://doi.org/10.3390/pathogens12020282 - 8 Feb 2023
Cited by 16 | Viewed by 4457
Abstract
Chagas disease is a chronic systemic infection transmitted by Trypanosoma cruzi. Its life cycle consists of different stages in vector insects and host mammals. Trypanosoma cruzi strains cause different clinical manifestations of Chagas disease alongside geographic differences in morbidity and mortality. Natural killer [...] Read more.
Chagas disease is a chronic systemic infection transmitted by Trypanosoma cruzi. Its life cycle consists of different stages in vector insects and host mammals. Trypanosoma cruzi strains cause different clinical manifestations of Chagas disease alongside geographic differences in morbidity and mortality. Natural killer cells provide the cytokine interferon-gamma in the initial phases of T. cruzi infection. Phagocytes secrete cytokines that promote inflammation and activation of other cells involved in defence. Dendritic cells, monocytes and macrophages modulate the adaptive immune response, and B lymphocytes activate an effective humoral immune response to T. cruzi. This review focuses on the main immune mechanisms acting during T. cruzi infection, on the strategies activated by the pathogen against the host cells, on the processes involved in inflammasome and virulence factors and on the new strategies for preventing, controlling and treating this disease. Full article
(This article belongs to the Special Issue Current Research on Trypanosoma cruzi Infection)
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21 pages, 729 KiB  
Review
Borrelia miyamotoi: A Comprehensive Review
by Dawn W. Cleveland, Cassidy C. Anderson and Catherine A. Brissette
Pathogens 2023, 12(2), 267; https://doi.org/10.3390/pathogens12020267 - 7 Feb 2023
Cited by 18 | Viewed by 4661
Abstract
Borrelia miyamotoi is an emerging tick-borne pathogen in the Northern Hemisphere and is the causative agent of Borrelia miyamotoi disease (BMD). Borrelia miyamotoi is vectored by the same hard-bodied ticks as Lyme disease Borrelia, yet phylogenetically groups with relapsing fever Borrelia, and [...] Read more.
Borrelia miyamotoi is an emerging tick-borne pathogen in the Northern Hemisphere and is the causative agent of Borrelia miyamotoi disease (BMD). Borrelia miyamotoi is vectored by the same hard-bodied ticks as Lyme disease Borrelia, yet phylogenetically groups with relapsing fever Borrelia, and thus, has been uniquely labeled a hard tick-borne relapsing fever Borrelia. Burgeoning research has uncovered new aspects of B. miyamotoi in human patients, nature, and the lab. Of particular interest are novel findings on disease pathology, prevalence, diagnostic methods, ecological maintenance, transmission, and genetic characteristics. Herein, we review recent literature on B. miyamotoi, discuss how findings adapt to current Borrelia doctrines, and briefly consider what remains unknown about B. miyamotoi. Full article
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16 pages, 3502 KiB  
Review
A Review of Major Patents on Potential Malaria Vaccine Targets
by Reysla Maria da Silveira Mariano, Ana Alice Maia Gonçalves, Diana Souza de Oliveira, Helen Silva Ribeiro, Diogo Fonseca Soares Pereira, Ingrid Soares Santos, Daniel Ferreira Lair, Augusto Ventura da Silva, Alexsandro Sobreira Galdino, Miguel Angel Chávez-Fumagalli, Denise da Silveira-Lemos, Walderez Ornelas Dutra and Rodolfo Cordeiro Giunchetti
Pathogens 2023, 12(2), 247; https://doi.org/10.3390/pathogens12020247 - 3 Feb 2023
Cited by 6 | Viewed by 3586
Abstract
Malaria is a parasitic infection that is a great public health concern and is responsible for high mortality rates worldwide. Different strategies have been employed to improve disease control, demonstrating the ineffectiveness of controlling vectors, and parasite resistance to antimalarial drugs requires the [...] Read more.
Malaria is a parasitic infection that is a great public health concern and is responsible for high mortality rates worldwide. Different strategies have been employed to improve disease control, demonstrating the ineffectiveness of controlling vectors, and parasite resistance to antimalarial drugs requires the development of an effective preventive vaccine. There are countless challenges to the development of such a vaccine directly related to the parasite’s complex life cycle. After more than four decades of basic research and clinical trials, the World Health Organization (WHO) has recommended the pre-erythrocytic Plasmodium falciparum (RTS, S) malaria vaccine for widespread use among children living in malaria-endemic areas. However, there is a consensus that major improvements are needed to develop a vaccine with a greater epidemiological impact in endemic areas. This review discusses novel strategies for malaria vaccine design taking the target stages within the parasite cycle into account. The design of the multi-component vaccine shows considerable potential, especially as it involves transmission-blocking vaccines (TBVs) that eliminate the parasite’s replication towards sporozoite stage parasites during a blood meal of female anopheline mosquitoes. Significant improvements have been made but additional efforts to achieve an efficient vaccine are required to improve control measures. Different strategies have been employed, thus demonstrating the ineffectiveness in controlling vectors, and parasite resistance to antimalarial drugs requires the development of a preventive vaccine. Despite having a vaccine in an advanced stage of development, such as the RTS, S malaria vaccine, the search for an effective vaccine against malaria is far from over. This review discusses novel strategies for malaria vaccine design taking into account the target stages within the parasite’s life cycle. Full article
(This article belongs to the Special Issue Neglected and Emergent Diseases)
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25 pages, 7078 KiB  
Review
Epidemiology of Ebolaviruses from an Etiological Perspective
by Sahil Jain, Svetlana Khaiboullina, Ekaterina Martynova, Sergey Morzunov and Manoj Baranwal
Pathogens 2023, 12(2), 248; https://doi.org/10.3390/pathogens12020248 - 3 Feb 2023
Cited by 6 | Viewed by 5445
Abstract
Since the inception of the ebolavirus in 1976, 32 outbreaks have resulted in nearly 15,350 deaths in more than ten countries of the African continent. In the last decade, the largest (2013–2016) and second largest (2018–2020) ebolavirus outbreaks have occurred in West Africa [...] Read more.
Since the inception of the ebolavirus in 1976, 32 outbreaks have resulted in nearly 15,350 deaths in more than ten countries of the African continent. In the last decade, the largest (2013–2016) and second largest (2018–2020) ebolavirus outbreaks have occurred in West Africa (mainly Guinea, Liberia, and Sierra Leone) and the Democratic Republic of the Congo, respectively. The 2013–2016 outbreak indicated an alarming geographical spread of the virus and was the first to qualify as an epidemic. Hence, it is imperative to halt ebolavirus progression and develop effective countermeasures. Despite several research efforts, ebolaviruses’ natural hosts and secondary reservoirs still elude the scientific world. The primary source responsible for infecting the index case is also unknown for most outbreaks. In this review, we summarize the history of ebolavirus outbreaks with a focus on etiology, natural hosts, zoonotic reservoirs, and transmission mechanisms. We also discuss the reasons why the African continent is the most affected region and identify steps to contain this virus. Full article
(This article belongs to the Special Issue Surveillance of Zoonotic Pathogens Carried by Wildlife)
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27 pages, 3767 KiB  
Review
SARS-CoV-2-Specific T Cell Responses in Immunocompromised Individuals with Cancer, HIV or Solid Organ Transplants
by David B. Reeg, Maike Hofmann, Christoph Neumann-Haefelin, Robert Thimme and Hendrik Luxenburger
Pathogens 2023, 12(2), 244; https://doi.org/10.3390/pathogens12020244 - 3 Feb 2023
Cited by 11 | Viewed by 4005
Abstract
Adaptive immune responses play an important role in the clinical course of SARS-CoV-2 infection. While evaluations of the virus-specific defense often focus on the humoral response, cellular immunity is crucial for the successful control of infection, with the early development of cytotoxic T [...] Read more.
Adaptive immune responses play an important role in the clinical course of SARS-CoV-2 infection. While evaluations of the virus-specific defense often focus on the humoral response, cellular immunity is crucial for the successful control of infection, with the early development of cytotoxic T cells being linked to efficient viral clearance. Vaccination against SARS-CoV-2 induces both CD4+ and CD8+ T cell responses and permits protection from severe COVID-19, including infection with the currently circulating variants of concern. Nevertheless, in immunocompromised individuals, first data imply significantly impaired SARS-CoV-2-specific immune responses after both natural infection and vaccination. Hence, these high-risk groups require particular consideration, not only in routine clinical practice, but also in the development of future vaccination strategies. In order to assist physicians in the guidance of immunocompromised patients, concerning the management of infection or the benefit of (booster) vaccinations, this review aims to provide a concise overview of the current knowledge about SARS-CoV-2-specific cellular immune responses in the vulnerable cohorts of cancer patients, people living with HIV (PLWH), and solid organ transplant recipients (SOT). Recent findings regarding the virus-specific cellular immunity in these differently immunocompromised populations might influence clinical decision-making in the future. Full article
(This article belongs to the Special Issue 10th Anniversary of Pathogens: T Cells in Pathogenic Infections)
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16 pages, 685 KiB  
Review
Factors Affecting Arbovirus Midgut Escape in Mosquitoes
by Alexis Carpenter and Rollie J. Clem
Pathogens 2023, 12(2), 220; https://doi.org/10.3390/pathogens12020220 - 31 Jan 2023
Cited by 9 | Viewed by 6013
Abstract
Arboviral diseases spread by mosquitoes cause significant morbidity and mortality throughout much of the world. The treatment and prevention of these diseases through medication and vaccination is often limited, which makes controlling arboviruses at the level of the vector ideal. One way to [...] Read more.
Arboviral diseases spread by mosquitoes cause significant morbidity and mortality throughout much of the world. The treatment and prevention of these diseases through medication and vaccination is often limited, which makes controlling arboviruses at the level of the vector ideal. One way to prevent the spread of an arbovirus would be to stop its vector from developing a disseminated infection, which is required for the virus to make its way to the saliva of the mosquito to be potentially transmitted to a new host. The midgut of the mosquito provides one such opportunity to stop an arbovirus in its tracks. It has been known for many years that in certain arbovirus–vector combinations, or under certain circumstances, an arbovirus can infect and replicate in the midgut but is unable to escape from the tissue to cause disseminated infection. This situation is known as a midgut escape barrier. If we better understand why this barrier occurs, it might aid in the development of more informed control strategies. In this review, we discuss how the midgut escape barrier contributes to virus–vector specificity and possible mechanisms that may allow this barrier to be overcome in successful virus–vector combinations. We also discuss several of the known factors that either increase or decrease the likelihood of midgut escape. Full article
(This article belongs to the Special Issue Advances in Mosquito-Borne Pathogens and Diseases)
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20 pages, 543 KiB  
Article
Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012–2020
by Marie Anne Chattaway, Anaïs Painset, Gauri Godbole, Saheer Gharbia and Claire Jenkins
Pathogens 2023, 12(2), 223; https://doi.org/10.3390/pathogens12020223 - 31 Jan 2023
Cited by 7 | Viewed by 4169
Abstract
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. [...] Read more.
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012–2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella. Full article
(This article belongs to the Special Issue Genomic Epidemiology of Foodborne Pathogens 2.0)
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19 pages, 1628 KiB  
Article
Seroprevalence of Tick-Borne Encephalitis (TBE) Virus Antibodies in Wild Rodents from Two Natural TBE Foci in Bavaria, Germany
by Philipp Johannes Brandenburg, Anna Obiegala, Hannah Maureen Schmuck, Gerhard Dobler, Lidia Chitimia-Dobler and Martin Pfeffer
Pathogens 2023, 12(2), 185; https://doi.org/10.3390/pathogens12020185 - 25 Jan 2023
Cited by 7 | Viewed by 2185
Abstract
Tick-borne encephalitis (TBE) is Eurasia’s most important tick-borne viral disease. Rodents play an important role as natural hosts. Longitudinal studies on the dynamics of the seroprevalence rates in wild rodents in natural foci over the year are rare, and the dynamics of the [...] Read more.
Tick-borne encephalitis (TBE) is Eurasia’s most important tick-borne viral disease. Rodents play an important role as natural hosts. Longitudinal studies on the dynamics of the seroprevalence rates in wild rodents in natural foci over the year are rare, and the dynamics of the transmission cycle still need to be understood. To better understand the infection dynamics, rodents were captured in a capture-mark-release-recapture-study in two natural foci in Bavaria, Germany, monthly from March 2019 to October 2022. Overall, 651 blood and thoracic lavage samples from 478 different wild rodents (Clethrionomys glareolus and Apodemus flavicollis) were analyzed for antibodies against tick-borne encephalitis virus (TBEV) by indirect immunofluorescence assay (IIFA) and confirmed using a serum neutralization test (SNT). Furthermore, a generalized linear mixed model (GLMM) analysis was performed to investigate ecological and individual factors for the probability of infection in rodents. Clethrionomys glareolus (19.4%) had a higher seroprevalence than A. flavicollis (10.5%). Within Cl. glareolus, more males (40.4%) than females (15.6%) were affected, and more adults (25.4%) than juveniles (9.8%). The probability of infection of rodents rather depends on factors such as species, sex, and age than on the study site of a natural focus, year, and season. The high incidence rates of rodents, particularly male adult bank voles, highlight their critical role in the transmission cycle of TBEV in a natural focus and demonstrate that serologically positive rodents can be reliably detected in a natural focus regardless of season or year. In addition, these data contribute to a better understanding of the TBEV cycle and thus could improve preventive strategies for human infections. Full article
(This article belongs to the Special Issue Tick-Borne Encephalitis Virus)
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32 pages, 1237 KiB  
Review
Pathogenesis of Anemia in Canine Babesiosis: Possible Contribution of Pro-Inflammatory Cytokines and Chemokines—A Review
by Wojciech Zygner, Olga Gójska-Zygner and Luke J. Norbury
Pathogens 2023, 12(2), 166; https://doi.org/10.3390/pathogens12020166 - 20 Jan 2023
Cited by 10 | Viewed by 7264
Abstract
Canine babesiosis is a tick-borne protozoan disease caused by intraerythrocytic parasites of the genus Babesia. The infection may lead to anemia in infected dogs. However, anemia is not directly caused by the pathogen. The parasite’s developmental stages only have a marginal role [...] Read more.
Canine babesiosis is a tick-borne protozoan disease caused by intraerythrocytic parasites of the genus Babesia. The infection may lead to anemia in infected dogs. However, anemia is not directly caused by the pathogen. The parasite’s developmental stages only have a marginal role in contributing to a decreased red blood cell (RBC) count. The main cause of anemia in affected dogs is the immune response to the infection. This response includes antibody production, erythrophagocytosis, oxidative damage of RBCs, complement activation, and antibody-dependent cellular cytotoxicity. Moreover, both infected and uninfected erythrocytes are retained in the spleen and sequestered in micro-vessels. All these actions are driven by pro-inflammatory cytokines and chemokines, especially IFN-γ, TNF-α, IL-6, and IL-8. Additionally, imbalance between the actions of pro- and anti-inflammatory cytokines plays a role in patho-mechanisms leading to anemia in canine babesiosis. This article is a review of the studies on the pathogenesis of anemia in canine babesiosis and related diseases, such as bovine or murine babesiosis and human or murine malaria, and the role of pro-inflammatory cytokines and chemokines in the mechanisms leading to anemia in infected dogs. Full article
(This article belongs to the Special Issue Immune Response of the Host and Vaccine Development)
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11 pages, 3758 KiB  
Article
Zoonotic Mutation of Highly Pathogenic Avian Influenza H5N1 Virus Identified in the Brain of Multiple Wild Carnivore Species
by Sandra Vreman, Marja Kik, Evelien Germeraad, Rene Heutink, Frank Harders, Marcel Spierenburg, Marc Engelsma, Jolianne Rijks, Judith van den Brand and Nancy Beerens
Pathogens 2023, 12(2), 168; https://doi.org/10.3390/pathogens12020168 - 20 Jan 2023
Cited by 32 | Viewed by 29666
Abstract
Wild carnivore species infected with highly pathogenic avian influenza (HPAI) virus subtype H5N1 during the 2021–2022 outbreak in the Netherlands included red fox (Vulpes vulpes), polecat (Mustela putorius), otter (Lutra lutra), and badger (Meles meles). [...] Read more.
Wild carnivore species infected with highly pathogenic avian influenza (HPAI) virus subtype H5N1 during the 2021–2022 outbreak in the Netherlands included red fox (Vulpes vulpes), polecat (Mustela putorius), otter (Lutra lutra), and badger (Meles meles). Most of the animals were submitted for testing because they showed neurological signs. In this study, the HPAI H5N1 virus was detected by PCR and/or immunohistochemistry in 11 animals and was primarily present in brain tissue, often associated with a (meningo) encephalitis in the cerebrum. In contrast, the virus was rarely detected in the respiratory tract and intestinal tract and associated lesions were minimal. Full genome sequencing followed by phylogenetic analysis demonstrated that these carnivore viruses were related to viruses detected in wild birds in the Netherlands. The carnivore viruses themselves were not closely related, and the infected carnivores did not cluster geographically, suggesting that they were infected separately. The mutation PB2-E627K was identified in most carnivore virus genomes, providing evidence for mammalian adaptation. This study showed that brain samples should be included in wild life surveillance programs for the reliable detection of the HPAI H5N1 virus in mammals. Surveillance of the wild carnivore population and notification to the Veterinary Authority are important from a one-heath perspective, and instrumental to pandemic preparedness. Full article
(This article belongs to the Collection Emerging and Re-emerging Pathogens)
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25 pages, 1993 KiB  
Review
Endogenous Retroviruses as Modulators of Innate Immunity
by Eric Russ and Sergey Iordanskiy
Pathogens 2023, 12(2), 162; https://doi.org/10.3390/pathogens12020162 - 19 Jan 2023
Cited by 23 | Viewed by 6357
Abstract
Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations [...] Read more.
Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations that rendered them non-infectious; thereby, the genome could co-opt them into constructive roles with important biological functions. In the past two decades, with the help of advances in sequencing technology, ERVs are increasingly considered to be important components of the innate immune response. While typically silenced, expression of HERVs can be induced in response to traumatic, toxic, or infection-related stress, leading to a buildup of viral transcripts and under certain circumstances, proteins, including functionally active reverse transcriptase and viral envelopes. The biological activity of HERVs in the context of the innate immune response can be based on the functional effect of four major viral components: (1) HERV LTRs, (2) HERV-derived RNAs, (3) HERV-derived RNA:DNA duplexes and cDNA, and (4) HERV-derived proteins and ribonucleoprotein complexes. In this review, we will discuss the implications of HERVs in all four contexts in relation to innate immunity and their association with various pathological disease states. Full article
(This article belongs to the Special Issue Host Immune Responses to RNA Viruses)
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17 pages, 904 KiB  
Review
Prevention and Treatment Strategies for Respiratory Syncytial Virus (RSV)
by Dvir Gatt, Isaac Martin, Rawan AlFouzan and Theo J. Moraes
Pathogens 2023, 12(2), 154; https://doi.org/10.3390/pathogens12020154 - 17 Jan 2023
Cited by 31 | Viewed by 15600
Abstract
Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease, especially in young children. Despite its global impact on healthcare, related to its high prevalence and its association with significant morbidity, the current therapy is still mostly supportive. Moreover, [...] Read more.
Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract disease, especially in young children. Despite its global impact on healthcare, related to its high prevalence and its association with significant morbidity, the current therapy is still mostly supportive. Moreover, while more than 50 years have passed since the first trial of an RSV vaccine (which unfortunately caused enhanced RSV disease), no vaccine has been approved for RSV prevention. In the last two decades, our understanding of the pathogenesis and immunopathology of RSV have continued to evolve, leading to significant advancements in RSV prevention strategies. These include both the development of new potential vaccines and the successful implementation of passive immunization, which, together, will provide coverage from infancy to old age. In this review, we provide an update of the current treatment options for acute disease (RSV-specific and -non-specific) and different therapeutic approaches focusing on RSV prevention. Full article
(This article belongs to the Special Issue The Changing Landscape of Respiratory Syncytial Virus Infections)
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20 pages, 2889 KiB  
Article
Fusarium Yellows of Ginger (Zingiber officinale Roscoe) Caused by Fusarium oxysporum f. sp. zingiberi Is Associated with Cultivar-Specific Expression of Defense-Responsive Genes
by Duraisamy Prasath, Andrea Matthews, Wayne T. O’Neill, Elizabeth A. B. Aitken and Andrew Chen
Pathogens 2023, 12(1), 141; https://doi.org/10.3390/pathogens12010141 - 14 Jan 2023
Cited by 9 | Viewed by 3930
Abstract
Ginger (Zingiber officinale Roscoe) is an important horticultural crop, valued for its culinary and medicinal properties. Fusarium yellows of ginger, caused by Fusarium oxysporum f. sp. zingiberi (Foz), is a devastating disease that has significantly reduced the quality and crop [...] Read more.
Ginger (Zingiber officinale Roscoe) is an important horticultural crop, valued for its culinary and medicinal properties. Fusarium yellows of ginger, caused by Fusarium oxysporum f. sp. zingiberi (Foz), is a devastating disease that has significantly reduced the quality and crop yield of ginger worldwide. The compatible interaction between ginger and Foz leading to susceptibility is dissected here. The pathogenicity of two Foz isolates on ginger was confirmed by their ability to colonise ginger and in turn induce both internal and external plant symptoms typical of Fusarium yellows. To shed light on Foz susceptibility at the molecular level, a set of defense-responsive genes was analysed for expression in the roots of ginger cultivars challenged with Foz. These include nucleotide-binding site (NBS) type of resistant (R) genes with a functional role in pathogen recognition, transcription factors associated with systemic acquired resistance, and enzymes involved in terpenoid biosynthesis and cell wall modifications. Among three R genes, the transcripts of ZoNBS1 and ZoNBS3 were rapidly induced by Foz at the onset of infection, and the expression magnitude was cultivar-dependent. These expression characteristics extend to the other genes. This study is the first step in understanding the mechanisms of compatible host–pathogen interactions in ginger. Full article
(This article belongs to the Special Issue Current Research on Fusarium)
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15 pages, 1257 KiB  
Review
Self-Amplifying RNA Vaccine Candidates: Alternative Platforms for mRNA Vaccine Development
by Christin Schmidt and Barbara S. Schnierle
Pathogens 2023, 12(1), 138; https://doi.org/10.3390/pathogens12010138 - 13 Jan 2023
Cited by 25 | Viewed by 19360
Abstract
The present use of mRNA vaccines against COVID-19 has shown for the first time the potential of mRNA vaccines for infectious diseases. Here we will summarize the current knowledge about improved mRNA vaccines, i.e., the self-amplifying mRNA (saRNA) vaccines. This approach may enhance [...] Read more.
The present use of mRNA vaccines against COVID-19 has shown for the first time the potential of mRNA vaccines for infectious diseases. Here we will summarize the current knowledge about improved mRNA vaccines, i.e., the self-amplifying mRNA (saRNA) vaccines. This approach may enhance antigen expression by amplification of the antigen-encoding RNA. RNA design, RNA delivery, and the innate immune responses induced by RNA will be reviewed. Full article
(This article belongs to the Special Issue Infectious Diseases and Vaccine Technology Research)
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24 pages, 392 KiB  
Review
Molecular Targets for Foodborne Pathogenic Bacteria Detection
by Spiros Paramithiotis
Pathogens 2023, 12(1), 104; https://doi.org/10.3390/pathogens12010104 - 8 Jan 2023
Cited by 5 | Viewed by 3689
Abstract
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the [...] Read more.
The detection of foodborne pathogenic bacteria currently relies on their ability to grow on chemically defined liquid and solid media, which is the essence of the classical microbiological approach. Such procedures are time-consuming and the quality of the result is affected by the selectivity of the media employed. Several alternative strategies based on the detection of molecular markers have been proposed. These markers may be cell constituents, may reside on the cell envelope or may be specific metabolites. Each marker provides specific advantages and, at the same time, suffers from specific limitations. The food matrix and chemical composition, as well as the accompanying microbiota, may also severely compromise detection. The aim of the present review article is to present and critically discuss all available information regarding the molecular targets that have been employed as markers for the detection of foodborne pathogens. Their strengths and limitations, as well as the proposed alleviation strategies, are presented, with particular emphasis on their applicability in real food systems and the challenges that are yet to be effectively addressed. Full article
(This article belongs to the Special Issue 10th Anniversary of Pathogens—Feature Papers)
28 pages, 7699 KiB  
Article
Genomics of Tenacibaculum Species in British Columbia, Canada
by Joseph P. Nowlan, Ashton N. Sies, Scott R. Britney, Andrew D. S. Cameron, Ahmed Siah, John S. Lumsden and Spencer Russell
Pathogens 2023, 12(1), 101; https://doi.org/10.3390/pathogens12010101 - 6 Jan 2023
Cited by 4 | Viewed by 3716
Abstract
Tenacibaculum is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing Tenacibaculum genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of Tenacibaculum [...] Read more.
Tenacibaculum is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing Tenacibaculum genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of Tenacibaculum spp., yet no Canadian Tenacibaculum genomes are publicly available. Ribosomal DNA sequencing of 16S and four species-specific 16S quantitative-PCR assays were used to select isolates cultured from Atlantic salmon with mouthrot in British Columbia (BC), Canada. Ten isolates representing four known and two unknown species of Tenacibaculum were selected for shotgun whole genome sequencing using the Oxford Nanopore’s MinION platform. The genome assemblies achieved closed circular chromosomes for seven isolates and long contigs for the remaining three isolates. Average nucleotide identity analysis identified T. ovolyticum, T. maritimum, T. dicentrarchi, two genomovars of T. finnmarkense, and two proposed novel species T. pacificus sp. nov. type strain 18-2881-AT and T. retecalamus sp. nov. type strain 18-3228-7BT. Annotation in most of the isolates predicted putative virulence and antimicrobial resistance genes, most-notably toxins (i.e., hemolysins), type-IX secretion systems, and oxytetracycline resistance. Comparative analysis with the T. maritimum type-strain predicted additional toxins and numerous C-terminal secretion proteins, including an M12B family metalloprotease in the T. maritimum isolates from BC. The genomic prediction of virulence-associated genes provides important targets for studies of mouthrot disease, and the annotation of the antimicrobial resistance genes provides targets for surveillance and diagnosis in veterinary medicine. Full article
(This article belongs to the Special Issue Emerging Infections in Aquatic Animals)
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17 pages, 1878 KiB  
Article
Systematic Review and Modelling of Age-Dependent Prevalence of Toxoplasma gondii in Livestock, Wildlife and Felids in Europe
by Filip Dámek, Arno Swart, Helga Waap, Pikka Jokelainen, Delphine Le Roux, Gunita Deksne, Huifang Deng, Gereon Schares, Anna Lundén, Gema Álvarez-García, Martha Betson, Rebecca K. Davidson, Adriana Györke, Daniela Antolová, Zuzana Hurníková, Henk J. Wisselink, Jacek Sroka, Joke W. B. van der Giessen, Radu Blaga and Marieke Opsteegh
Pathogens 2023, 12(1), 97; https://doi.org/10.3390/pathogens12010097 - 6 Jan 2023
Cited by 16 | Viewed by 5992
Abstract
Toxoplasma gondii is a zoonotic parasite of importance to both human and animal health. The parasite has various transmission routes, and the meat of infected animals appears to be a major source of human infections in Europe. We aimed to estimate T. gondii [...] Read more.
Toxoplasma gondii is a zoonotic parasite of importance to both human and animal health. The parasite has various transmission routes, and the meat of infected animals appears to be a major source of human infections in Europe. We aimed to estimate T. gondii prevalence in a selection of animal host species. A systematic literature review resulting in 226 eligible publications was carried out, and serological data were analyzed using an age-dependent Bayesian hierarchical model to obtain estimates for the regional T. gondii seroprevalence in livestock, wildlife, and felids. Prevalence estimates varied between species, regions, indoor/outdoor rearing, and types of detection methods applied. The lowest estimated seroprevalence was observed for indoor-kept lagomorphs at 4.8% (95% CI: 1.8–7.5%) and the highest for outdoor-kept sheep at 63.3% (95% CI: 53.0–79.3%). Overall, T. gondii seroprevalence estimates were highest within Eastern Europe, whilst being lowest in Northern Europe. Prevalence data based on direct detection methods were scarce and were not modelled but rather directly summarized by species. The outcomes of the meta-analysis can be used to extrapolate data to areas with a lack of data and provide valuable inputs for future source attribution approaches aiming to estimate the relative contribution of different sources of T. gondii human infection. Full article
(This article belongs to the Special Issue Epidemiology and Management of Foodborne Parasitic Diseases)
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18 pages, 963 KiB  
Article
Risk Factors for Exposure of Wild Birds to West Nile Virus in A Gradient of Wildlife-Livestock Interaction
by Laia Casades-Martí, Rocío Holgado-Martín, Pilar Aguilera-Sepúlveda, Francisco Llorente, Elisa Pérez-Ramírez, Miguel Ángel Jiménez-Clavero and Francisco Ruiz-Fons
Pathogens 2023, 12(1), 83; https://doi.org/10.3390/pathogens12010083 - 3 Jan 2023
Cited by 7 | Viewed by 3447
Abstract
West Nile virus (WNV) transmission rate is shaped by the interaction between virus reservoirs and vectors, which may be maximized in farm environments. Based on this hypothesis, we screened for WNV in wild birds in three scenarios with decreasing gradient of interaction with [...] Read more.
West Nile virus (WNV) transmission rate is shaped by the interaction between virus reservoirs and vectors, which may be maximized in farm environments. Based on this hypothesis, we screened for WNV in wild birds in three scenarios with decreasing gradient of interaction with horses: (i) the farm (A1); (ii) the neighborhood (A2); and (iii) a wild area (A3). We captured wild birds and analyzed their sera for WNV antibodies by blocking ELISA and micro-virus neutralization test. Flavivirus infections were tested with generic and specific PCR protocols. We parameterized linear mixed models with predictors (bird abundance and diversity, vector abundance, vector host abundance, and weather quantities) to identify Flavivirus spp. and WNV exposure risk factors. We detected a low rate of Flavivirus infections by PCR (0.8%) and 6.9% of the birds were seropositive by ELISA. Exposure to Flavivirus spp. was higher in A1 (9%) than in A2 and A3 (5.6% and 5.8%, respectively). Bird diversity was the most relevant predictor of exposure risk and passerines dominated the on-farm bird community. Our results suggest that measures deterring the use of the farm by passerines should be implemented because the environmental favorability of continental Mediterranean environments for WNV is increasing and more outbreaks are expected. Full article
(This article belongs to the Special Issue Surveillance of Zoonotic Pathogens Carried by Wildlife)
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15 pages, 2022 KiB  
Article
Occurrence of Escherichia coli Pathotypes in Diarrheic Calves in a Low-Income Setting
by Wagaw Sendeku Chekole, Haileeyesus Adamu, Susanna Sternberg-Lewrein, Ulf Magnusson and Tesfaye Sisay Tessema
Pathogens 2023, 12(1), 42; https://doi.org/10.3390/pathogens12010042 - 27 Dec 2022
Cited by 4 | Viewed by 2951
Abstract
Different E. coli pathotypes are common zoonotic agents. Some of these pathotypes cause recurrent and widespread calf diarrhea and contribute to significant economic losses in the livestock sector worldwide in addition to putting humans at risk. Here, we investigated the occurrence of E. [...] Read more.
Different E. coli pathotypes are common zoonotic agents. Some of these pathotypes cause recurrent and widespread calf diarrhea and contribute to significant economic losses in the livestock sector worldwide in addition to putting humans at risk. Here, we investigated the occurrence of E. coli pathotypes in diarrheic calves in Ethiopia kept under various calf management practices. One hundred fecal samples were collected from diarrheic calves in 98 different farms. E. coli was isolated in the samples from 99 of the diarrheic calves, and virulence genes were detected in 80% of the samples. The occurrence of E. coli pathotypes in the samples was 32% ETEC, 23% STEC, 18% STEC/ETEC, 3% EPEC, 2% EAEC, and 1% EHEC. No diarrheic calves were positive for the EIEC and DAEC pathotypes. The occurrence of pathotypes was positively associated with female calves (EPEC, p = 0.006), aged less than 2 weeks (STEC, p = 0.059), and calves fed colostrum via the hand method (STEC, p = 0.008 and EAEC, p = 0.003). This study revealed that several E. coli pathotypes occurred among calves affected with diarrhea. Moreover, the presence of a mixed STEC/ETEC pathotypes infection was present in the studied low-income setting. These findings indicate a considerable risk for the zoonotic transmission from calves to humans and the options to provide the better management for younger calves in order to reduce the economic loss. Full article
(This article belongs to the Section Bacterial Pathogens)
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18 pages, 8135 KiB  
Article
Genomic Analysis Unveils the Pervasiveness and Diversity of Prophages Infecting Erwinia Species
by Tulio Morgan, Rafael Reis de Rezende, Thamylles Thuany Mayrink Lima, Flávia de Oliveira Souza and Poliane Alfenas-Zerbini
Pathogens 2023, 12(1), 44; https://doi.org/10.3390/pathogens12010044 - 27 Dec 2022
Cited by 1 | Viewed by 3647
Abstract
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus [...] Read more.
Prophages are abundant elements integrated into bacterial genomes and contribute to inter-strain genetic variability and, in some cases, modulate the environmental behavior of bacteria, such as pathogen virulence. Here, we described prophage occurrence and diversity in publicly available Erwinia genome assemblies, a genus containing plant pathogens. Prophage-like sequences were identified and taxonomically classified. Sequence diversity was analyzed through intergenomic similarities. Furthermore, we searched for anti-phage defense systems in Erwinia spp., such as DISARM, BREX, and CRISPR-Cas systems, and identified the putative targets of CRISPR spacers. We identified 939 prophage-like sequences in 221 Erwinia spp. genome assemblies. Only 243 prophage-like sequences were classified, all belonging to the Caudoviricetes class. The set of putative Erwinia prophages was mostly unique since only three sequences showed more than 70% intergenomic similarities to known Erwinia phages. Overall, the number and type of CRISPR-Cas systems were conserved within Erwinia species, with many spacers directed to the putative prophages identified. This study increased the knowledge of the diversity and distribution of Erwinia prophages, contributing to the characterization of genetic and ecological factors influencing Erwinia spp. environmental fitness. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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18 pages, 986 KiB  
Review
The Use of Natural Methods to Control Foodborne Biofilms
by Michelle Marie Esposito and Sara Turku
Pathogens 2023, 12(1), 45; https://doi.org/10.3390/pathogens12010045 - 27 Dec 2022
Cited by 7 | Viewed by 3305
Abstract
Biofilms are large aggregates of various species of bacteria or other microorganisms tightly attached to surfaces through an intricate extracellular matrix. These complex microbial communities present quite the challenge in the food processing industry, as conditions such as raw meats and diverse food [...] Read more.
Biofilms are large aggregates of various species of bacteria or other microorganisms tightly attached to surfaces through an intricate extracellular matrix. These complex microbial communities present quite the challenge in the food processing industry, as conditions such as raw meats and diverse food product content in contact with workers, drains, machinery, and ventilation systems, make for prime circumstances for contamination. Adding to the challenge is the highly resistant nature of these biofilm growths and the need to keep in mind that any antimicrobials utilized in these situations risk health implications with human consumption of the products that are being processed in these locations. For that reason, the ideal means of sanitizing areas of foodborne biofilms would be natural means. Herein, we review a series of innovative natural methods of targeting foodborne biofilms, including bacteriocins, bacteriophages, fungi, phytochemicals, plant extracts, essential oils, gaseous and aqueous control, photocatalysis, enzymatic treatments, and ultrasound mechanisms. Full article
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19 pages, 1587 KiB  
Review
Many Ways to Communicate—Crosstalk between the HBV-Infected Cell and Its Environment
by Annika Jasmin Walter, Maarten A. van de Klundert and Stephanie Jung
Pathogens 2023, 12(1), 29; https://doi.org/10.3390/pathogens12010029 - 24 Dec 2022
Cited by 3 | Viewed by 3313
Abstract
Chronic infection with the hepatitis B virus (HBV) affects an estimated 257 million people worldwide and can lead to liver diseases such as cirrhosis and liver cancer. Viral replication is generally considered not to be cytopathic, and although some HBV proteins may have [...] Read more.
Chronic infection with the hepatitis B virus (HBV) affects an estimated 257 million people worldwide and can lead to liver diseases such as cirrhosis and liver cancer. Viral replication is generally considered not to be cytopathic, and although some HBV proteins may have direct carcinogenic effects, the majority of HBV infection-related disease is related to chronic inflammation resulting from disrupted antiviral responses and aberrant innate immune reactions. Like all cells, healthy and HBV-infected cells communicate with each other, as well as with other cell types, such as innate and adaptive immune cells. They do so by both interacting directly and by secreting factors into their environment. Such factors may be small molecules, such as metabolites, single viral proteins or host proteins, but can also be more complex, such as virions, protein complexes, and extracellular vesicles. The latter are small, membrane-enclosed vesicles that are exchanged between cells, and have recently gained a lot of attention for their potential to mediate complex communication and their potential for therapeutic repurposing. Here, we review how HBV infection affects the communication between HBV-infected cells and cells in their environment. We discuss the impact of these interactions on viral persistence in chronic infection, as well as their relation to HBV infection-related pathology. Full article
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13 pages, 1496 KiB  
Review
The Never-Ending Presence of Phytophthora Species in Italian Nurseries
by Chiara Antonelli, Margherita Biscontri, Dania Tabet and Anna Maria Vettraino
Pathogens 2023, 12(1), 15; https://doi.org/10.3390/pathogens12010015 - 22 Dec 2022
Cited by 12 | Viewed by 3563
Abstract
Plant trade coupled with climate change has led to the increased spread of well-known and new Phytophthora species, a group of fungus-like organisms placed in the Kingdom Chromista. Their presence in plant nurseries is of particular concern because they are responsible for many [...] Read more.
Plant trade coupled with climate change has led to the increased spread of well-known and new Phytophthora species, a group of fungus-like organisms placed in the Kingdom Chromista. Their presence in plant nurseries is of particular concern because they are responsible for many plant diseases, with high environmental, economic and social impacts. This paper offers a brief overview of the current status of Phytophthora species in European plant nurseries. Focus was placed on Italian sites. Despite the increasing awareness of the risk of Phytophthora spread and the management strategies applied for controlling it, the complexity of the Phytophthora community in the horticulture industry is increasing over time. Since the survey carried out by Jung et al. (2016), new Phytophthora taxa and Phytophthora-host associations were identified. Phytophthorahydropathica, P. crassamura, P. pseudocryptogea and P. meadii were reported for the first time in European plant nurseries, while P. pistaciae, P. mediterranea and P. heterospora were isolated from Italian ornamental nurseries. Knowledge of Phytophthora diversity in plant nurseries and the potential damage caused by them will help to contribute to the development of early detection methods and sustainable management strategies to control Phytophthora spread in the future. Full article
(This article belongs to the Section Fungal Pathogens)
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13 pages, 3277 KiB  
Review
The History of the Intestinal Microbiota and the Gut-Brain Axis
by Zuzanna Lewandowska-Pietruszka, Magdalena Figlerowicz and Katarzyna Mazur-Melewska
Pathogens 2022, 11(12), 1540; https://doi.org/10.3390/pathogens11121540 - 15 Dec 2022
Cited by 8 | Viewed by 5314
Abstract
The gut-brain axis and the intestinal microbiota have been an area of an intensive research in the last few years. However, it is not a completely novel area of interest for physicians and scientists. From the earliest centuries, both professionals and patients turned [...] Read more.
The gut-brain axis and the intestinal microbiota have been an area of an intensive research in the last few years. However, it is not a completely novel area of interest for physicians and scientists. From the earliest centuries, both professionals and patients turned their attention to the gastrointestinal system in order to find the root of physical and mental disturbances. The approach to the gut-brain axis and the therapeutic methods have changed alongside the development of different medical approaches to health and illness. They often reflected the social changes. The authors of this article aim to provide a brief history of the gut-brain axis and the intestinal microbiota in order to demonstrate how important the study of these systems is for both scientists and medical professionals, as well as for the general public. We analysed the publications accessible through PubMed regarding the microbiota and gut-brain axis history. If available, we accessed the original historical sources. We conclude that although the history of this science might be long, there are still many areas that need to be researched, analysed, and understood in future projects. The interest in the subject is not diminishing, but rather it has increased throughout the years. Full article
(This article belongs to the Special Issue The Role of the Gut Microbiome in Health and Disease)
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18 pages, 2263 KiB  
Article
Artificial Insemination as an Alternative Transmission Route for African Swine Fever Virus
by Virginia Friedrichs, Darwin Reicks, Tobias Hasenfuß, Elisabeth Gerstenkorn, Jeffrey J. Zimmerman, Eric A. Nelson, Tessa Carrau, Paul Deutschmann, Julia Sehl-Ewert, Hanna Roszyk, Martin Beer, Jane Christopher-Hennings and Sandra Blome
Pathogens 2022, 11(12), 1539; https://doi.org/10.3390/pathogens11121539 - 14 Dec 2022
Cited by 6 | Viewed by 7399
Abstract
The rapid spread of the African swine fever virus (ASFV), causing severe disease with often high fatality rates in Eurasian suids, prevails as a threat for pig populations and dependent industries worldwide. Although advancing scientific progress continually enhances our understanding of ASFV pathogenesis, [...] Read more.
The rapid spread of the African swine fever virus (ASFV), causing severe disease with often high fatality rates in Eurasian suids, prevails as a threat for pig populations and dependent industries worldwide. Although advancing scientific progress continually enhances our understanding of ASFV pathogenesis, alternative transmission routes for ASFV have yet to be assessed. Here, we demonstrate that ASFV can efficiently be transferred from infected boars to naïve recipient gilts through artificial insemination (AI). In modern pig production, semen from boar studs often supplies many sow herds. Thus, the infection of a boar stud presents the risk of rapidly and widely distributing ASFV within or between countries. Daily blood and semen collection from four boars after intramuscular inoculation with ASFV strain ‘Estonia 2014’ resulted in the detection of ASFV genomes in the semen as early as 2 dpi, in blood at 1 dpi while semen quality remained largely unaffected. Ultimately, after insemination with extended semen, 7 of 14 gilts were ASFV positive by 7 days post insemination, and all gilts were ASFV positive by 35 days post insemination. Twelve out of 13 pregnant gilts aborted or resorbed at the onset of fever. A proportion of fetuses originating from the remaining gilt showed both abnormalities and replication of ASFV in fetal tissues. Thus, we present evidence for the efficient transmission of ASFV to gilts via AI and also to implanted embryos. These results underline the critical role that boar semen could play in ASFV transmission. Full article
(This article belongs to the Special Issue An Update on African Swine Fever)
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13 pages, 3082 KiB  
Article
Monitoring Wind-Borne Particle Matter Entering Poultry Farms via the Air-Inlet: Highly Pathogenic Avian Influenza Virus and Other Pathogens Risk
by Armin R. W. Elbers, José L. Gonzales, Miriam G. J. Koene, Evelien A. Germeraad, Renate W. Hakze-van der Honing, Marleen van der Most, Henk Rodenboog and Francisca C. Velkers
Pathogens 2022, 11(12), 1534; https://doi.org/10.3390/pathogens11121534 - 14 Dec 2022
Cited by 7 | Viewed by 4098
Abstract
Wind-supported transport of particle matter (PM) contaminated with excreta from highly pathogenic avian influenza virus (HPAIv)-infected wild birds may be a HPAIv-introduction pathway, which may explain infections in indoor-housed poultry. The primary objective of our study was therefore to measure the nature and [...] Read more.
Wind-supported transport of particle matter (PM) contaminated with excreta from highly pathogenic avian influenza virus (HPAIv)-infected wild birds may be a HPAIv-introduction pathway, which may explain infections in indoor-housed poultry. The primary objective of our study was therefore to measure the nature and quantity of PM entering poultry houses via air-inlets. The air-inlets of two recently HPAIv-infected poultry farms (a broiler farm and a layer farm) were equipped with mosquito-net collection bags. PM was harvested every 5 days for 25 days. Video-camera monitoring registered wild bird visits. PM was tested for avian influenza viruses (AIV), Campylobacter and Salmonella with PCR. Insects, predominantly mosquitoes, were tested for AIV, West Nile, Usutu and Schmallenberg virus. A considerable number of mosquitoes and small PM amounts entered the air-inlets, mostly cobweb and plant material, but no wild bird feathers. Substantial variation in PM entering between air-inlets existed. In stormy periods, significantly larger PM amounts may enter wind-directed air-inlets. PM samples were AIV and Salmonella negative and insect samples were negative for all viruses and bacteria, but several broiler and layer farm PM samples tested Campylobacter positive. Regular wild (water) bird visits were observed near to the poultry houses. Air-borne PM and insects—potentially contaminated with HPAIv or other pathogens—can enter poultry air-inlets. Implementation of measures limiting this potential introduction route are recommended. Full article
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22 pages, 345 KiB  
Review
Therapeutic Approaches for Chronic Obstructive Pulmonary Disease (COPD) Exacerbations
by Yehudis Rosenwasser, Irene Berger and Zvi G. Loewy
Pathogens 2022, 11(12), 1513; https://doi.org/10.3390/pathogens11121513 - 10 Dec 2022
Cited by 8 | Viewed by 3486
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a progressive pulmonary disorder underpinned by poorly reversible airflow resulting from chronic bronchitis or emphysema. The prevalence and mortality of COPD continue to increase. Pharmacotherapy for patients with COPD has included antibiotics, bronchodilators, and anti-inflammatory corticosteroids (but [...] Read more.
Chronic Obstructive Pulmonary Disease (COPD) is a progressive pulmonary disorder underpinned by poorly reversible airflow resulting from chronic bronchitis or emphysema. The prevalence and mortality of COPD continue to increase. Pharmacotherapy for patients with COPD has included antibiotics, bronchodilators, and anti-inflammatory corticosteroids (but with little success). Oral diseases have long been established as clinical risk factors for developing respiratory diseases. The establishment of a very similar microbiome in the mouth and the lung confirms the oral-lung connection. The aspiration of pathogenic microbes from the oral cavity has been implicated in several respiratory diseases, including pneumonia and chronic obstructive pulmonary disease (COPD). This review focuses on current and future pharmacotherapeutic approaches for COPD exacerbation including antimicrobials, mucoregulators, the use of bronchodilators and anti-inflammatory drugs, modifying epigenetic marks, and modulating dysbiosis of the microbiome. Full article
(This article belongs to the Section Bacterial Pathogens)
12 pages, 600 KiB  
Article
Characteristics of Staphylococcus aureus Isolated from Patients in Busia County Referral Hospital, Kenya
by Benear Apollo Obanda, Elizabeth A. J. Cook, Eric M. Fèvre, Lilly Bebora, William Ogara, Shu-Hua Wang, Wondwossen Gebreyes, Ronald Ngetich, Dolphine Wandede, Johnstone Muyodi, Beth Blane, Francesc Coll, Ewan M. Harrison, Sharon J. Peacock and George C. Gitao
Pathogens 2022, 11(12), 1504; https://doi.org/10.3390/pathogens11121504 - 9 Dec 2022
Cited by 5 | Viewed by 2580
Abstract
Staphylococcus aureus is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of S. [...] Read more.
Staphylococcus aureus is an important pathogen associated with hospital, community, and livestock-acquired infections, with the ability to develop resistance to antibiotics. Nasal carriage by hospital inpatients is a risk for opportunistic infections. Antibiotic susceptibility patterns, virulence genes and genetic population structure of S. aureus nasal isolates, from inpatients at Busia County Referral Hospital (BCRH) were analyzed. A total of 263 inpatients were randomly sampled, from May to July 2015. The majority of inpatients (85.9%) were treated empirically with antimicrobials, including ceftriaxone (65.8%) and metronidazole (49.8%). Thirty S. aureus isolates were cultured from 29 inpatients with a prevalence of 11% (10.3% methicillin-susceptible S. aureus (MSSA), 0.8% methicillin resistant S. aureus (MRSA)). Phenotypic and genotypic resistance was highest to penicillin-G (96.8%), trimethoprim (73.3%), and tetracycline (13.3%) with 20% of isolates classified as multidrug resistant. Virulence genes, Panton-Valentine leukocidin (pvl), toxic shock syndrome toxin-1 (tsst-1), and sasX gene were detected in 16.7%, 23.3% and 3.3% of isolates. Phylogenetic analysis showed 4 predominant clonal complexes CC152, CC8, CC80, and CC508. This study has identified that inpatients of BCRH were carriers of S. aureus harbouring virulence genes and resistance to a range of antibiotics. This may indicate a public health risk to other patients and the community. Full article
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12 pages, 652 KiB  
Article
Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies
by Ansgar Schulz, Balal Sadeghi, Franziska Stoek, Jacqueline King, Kerstin Fischer, Anne Pohlmann, Martin Eiden and Martin H. Groschup
Pathogens 2022, 11(12), 1502; https://doi.org/10.3390/pathogens11121502 - 8 Dec 2022
Cited by 3 | Viewed by 2659
Abstract
On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the [...] Read more.
On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean–Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses. Full article
(This article belongs to the Special Issue Molecular Diagnostics of Emerging Pathogens)
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25 pages, 810 KiB  
Review
Listeria monocytogenes—How This Pathogen Uses Its Virulence Mechanisms to Infect the Hosts
by Jacek Osek and Kinga Wieczorek
Pathogens 2022, 11(12), 1491; https://doi.org/10.3390/pathogens11121491 - 7 Dec 2022
Cited by 26 | Viewed by 6947
Abstract
Listeriosis is a serious food-borne illness, especially in susceptible populations, including children, pregnant women, and elderlies. The disease can occur in two forms: non-invasive febrile gastroenteritis and severe invasive listeriosis with septicemia, meningoencephalitis, perinatal infections, and abortion. Expression of each symptom depends on [...] Read more.
Listeriosis is a serious food-borne illness, especially in susceptible populations, including children, pregnant women, and elderlies. The disease can occur in two forms: non-invasive febrile gastroenteritis and severe invasive listeriosis with septicemia, meningoencephalitis, perinatal infections, and abortion. Expression of each symptom depends on various bacterial virulence factors, immunological status of the infected person, and the number of ingested bacteria. Internalins, mainly InlA and InlB, invasins (invasin A, LAP), and other surface adhesion proteins (InlP1, InlP4) are responsible for epithelial cell binding, whereas internalin C (InlC) and actin assembly-inducing protein (ActA) are involved in cell-to-cell bacterial spread. L. monocytogenes is able to disseminate through the blood and invade diverse host organs. In persons with impaired immunity, the elderly, and pregnant women, the pathogen can also cross the blood–brain and placental barriers, which results in the invasion of the central nervous system and fetus infection, respectively. The aim of this comprehensive review is to summarize the current knowledge on the epidemiology of listeriosis and L. monocytogenes virulence mechanisms that are involved in host infection, with a special focus on their molecular and cellular aspects. We believe that all this information is crucial for a better understanding of the pathogenesis of L. monocytogenes infection. Full article
(This article belongs to the Section Bacterial Pathogens)
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21 pages, 2131 KiB  
Review
Giant Viruses as a Source of Novel Enzymes for Biotechnological Application
by Ellen Gonçalves de Oliveira, João Victor Rodrigues Pessoa Carvalho, Bruna Barbosa Botelho, Clécio Alonso da Costa Filho, Lethícia Ribeiro Henriques, Bruna Luiza de Azevedo and Rodrigo Araújo Lima Rodrigues
Pathogens 2022, 11(12), 1453; https://doi.org/10.3390/pathogens11121453 - 1 Dec 2022
Cited by 5 | Viewed by 2868
Abstract
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry [...] Read more.
The global demand for industrial enzymes has been increasing in recent years, and the search for new sources of these biological products is intense, especially in microorganisms. Most known viruses have limited genetic machinery and, thus, have been overlooked by the enzyme industry for years. However, a peculiar group of viruses breaks this paradigm. Giant viruses of the phylum Nucleocytoviricota infect protists (i.e., algae and amoebae) and have complex genomes, reaching up to 2.7 Mb in length and encoding hundreds of genes. Different giant viruses have robust metabolic machinery, especially those in the Phycodnaviridae and Mimiviridae families. In this review, we present some peculiarities of giant viruses that infect protists and discuss why they should be seen as an outstanding source of new enzymes. We revisited the genomes of representatives of different groups of giant viruses and put together information about their enzymatic machinery, highlighting several genes to be explored in biotechnology involved in carbohydrate metabolism, DNA replication, and RNA processing, among others. Finally, we present additional evidence based on structural biology using chitinase as a model to reinforce the role of giant viruses as a source of novel enzymes for biotechnological application. Full article
(This article belongs to the Special Issue Viruses of Microbes: From Basics to Biotechnological Application)
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30 pages, 1333 KiB  
Review
Enhancing the Effect of Nucleic Acid Vaccines in the Treatment of HPV-Related Cancers: An Overview of Delivery Systems
by Ingrid Andrêssa de Moura, Anna Jéssica Duarte Silva, Larissa Silva de Macêdo, Maria da Conceição Viana Invenção, Mylenna Máyra Gois de Sousa and Antonio Carlos de Freitas
Pathogens 2022, 11(12), 1444; https://doi.org/10.3390/pathogens11121444 - 30 Nov 2022
Cited by 9 | Viewed by 3412
Abstract
Prophylactic vaccines against human papillomavirus (HPV) have proven efficacy in those who have not been infected by the virus. However, they do not benefit patients with established tumors. Therefore, the development of therapeutic options for HPV-related malignancies is critical. Third-generation vaccines based on [...] Read more.
Prophylactic vaccines against human papillomavirus (HPV) have proven efficacy in those who have not been infected by the virus. However, they do not benefit patients with established tumors. Therefore, the development of therapeutic options for HPV-related malignancies is critical. Third-generation vaccines based on nucleic acids are fast and simple approaches to eliciting adaptive immune responses. However, techniques to boost immunogenicity, reduce degradation, and facilitate their capture by immune cells are frequently required. One option to overcome this constraint is to employ delivery systems that allow selective antigen absorption and help modulate the immune response. This review aimed to discuss the influence of these different systems on the response generated by nucleic acid vaccines. The results indicate that delivery systems based on lipids, polymers, and microorganisms such as yeasts can be used to ensure the stability and transport of nucleic acid vaccines to their respective protein synthesis compartments. Thus, in view of the limitations of nucleic acid-based vaccines, it is important to consider the type of delivery system to be used—due to its impact on the immune response and desired final effect. Full article
(This article belongs to the Special Issue Latest Advances in Human Papillomavirus (HPV) Research)
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15 pages, 3495 KiB  
Article
SARS-CoV-2 Antibody Effectiveness Is Influenced by Non-Epitope Mutation/Binding-Induced Denaturation of the Epitope 3D Architecture
by Moffat M. Malisheni, Matthew Bates, Albert A. Rizvanov and Paul A. MacAry
Pathogens 2022, 11(12), 1437; https://doi.org/10.3390/pathogens11121437 - 29 Nov 2022
Cited by 3 | Viewed by 1906
Abstract
The public health threat from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to intensify with emerging variants of concern (VOC) aiming to render COVID-19 vaccines/infection-induced antibodies redundant. The SARS-CoV-2 spike protein is responsible for receptor binding and infection of host cells making [...] Read more.
The public health threat from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to intensify with emerging variants of concern (VOC) aiming to render COVID-19 vaccines/infection-induced antibodies redundant. The SARS-CoV-2 spike protein is responsible for receptor binding and infection of host cells making it a legitimate antibody target. Antibodies mostly target epitopes in the receptor binding domain (RBD). Mutations occurring within epitopes influence antibody specificity and function by altering their 3D architecture. However, the mechanisms by which non-epitope mutations in the RBD influence antibody specificity and function remain a mystery. We used Protein Data Bank (PDB) deposited 3D structures for the original, Beta, Delta, BA.1, and BA.2 RBD proteins in complex with either neutralizing antibodies or Angiotensin-Converting Enzyme 2 (ACE2) to elucidate the structural and mechanistic basis for neutralizing antibody evasion driven by non-epitope amino acid substitutions in the RBD. Since the mechanism behind the extensively reported functional discrepancies between the same antibody when used individually and when used in an antibody cocktail is lacking, we explored the structural basis for this inconsistency. Finally, since SARS-CoV-2 antibodies are viral mutagens, we deciphered determinants for antibody-pressured amino acid substitutions. On the one hand, we show that non-epitope mutations in the RBD domain of SARS-CoV-2 VOC influence the formation of hydrogen bonds in the paratope-epitope interface by repositioning RBD amino-acid sidechains (AASCs). This increases the distance between complementary donor/acceptor atoms on paratope and epitope AASCs leading to weaker or the complete prevention of the formation of hydrogen bonds in the paratope-epitope interface. On the other hand, we show that SARS-CoV-2 VOC employ the same strategy to simultaneously search for complementary donor/acceptor atoms on ACE2 AASCs to form new interactions, potentially favoring increased viral transmission. Additionally, we illustrate that converting the spike protein to an RBD, a deletion mutation, also repositions epitope AASCs and that AASC interactions in the paratope-epitope interface vary when an antibody is used individually versus when utilized as a cocktail with other antibodies. Finally, we show that the process of substituting immunogenic RBD amino acids begins with the repositioning of their AASCs induced by immune/antibody pressure. We show that donor/acceptor atoms from any amino acid can determine cross-reactivity instead, provided they possess and present spatially pairing donor/acceptor atoms. By studying structural alignments for PDB deposited antibody-RBD 3D structures and relating them to published binding and neutralization profiles of the same antibodies, we demonstrate that minor structural alterations such as epitope AASC repositioning have a major impact on antibody effectiveness and, hence, should receive adequate attention given that protein structure dictates protein function. Full article
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22 pages, 1348 KiB  
Review
The Tapeworm Hymenolepis diminuta as an Important Model Organism in the Experimental Parasitology of the 21st Century
by Anna Sulima-Celińska, Alicja Kalinowska and Daniel Młocicki
Pathogens 2022, 11(12), 1439; https://doi.org/10.3390/pathogens11121439 - 29 Nov 2022
Cited by 8 | Viewed by 5667
Abstract
The tapeworm Hymenolepis diminuta is a common parasite of the small intestine in rodents but it can also infect humans. Due to its characteristics and ease of maintenance in the laboratory, H. diminuta is also an important model species in studies of cestodiasis, [...] Read more.
The tapeworm Hymenolepis diminuta is a common parasite of the small intestine in rodents but it can also infect humans. Due to its characteristics and ease of maintenance in the laboratory, H. diminuta is also an important model species in studies of cestodiasis, including the search for new drugs, treatments, diagnostics and biochemical processes, as well as its host–parasite interrelationships. A great deal of attention has been devoted to the immune response caused by H. diminuta in the host, and several studies indicate that infection with H. diminuta can reduce the severity of concomitant disease. Here, we present a critical review of the experimental research conducted with the use of H. diminuta as a model organism for over more than two decades (in the 21st century). The present review evaluates the tapeworm H. diminuta as a model organism for studying the molecular biology, biochemistry and immunology aspects of parasitology, as well as certain clinical applications. It also systematizes the latest research on this species. Its findings may contribute to a better understanding of the biology of tapeworms and their adaptation to parasitism, including complex correlations between H. diminuta and invertebrate and vertebrate hosts. It places particular emphasis on its value for the further development of modern experimental parasitology. Full article
(This article belongs to the Special Issue Biology of Parasitism)
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19 pages, 1792 KiB  
Review
Filoviruses: Innate Immunity, Inflammatory Cell Death, and Cytokines
by Jianlin Lu, Jessica M. Gullett and Thirumala-Devi Kanneganti
Pathogens 2022, 11(12), 1400; https://doi.org/10.3390/pathogens11121400 - 23 Nov 2022
Cited by 7 | Viewed by 7896
Abstract
Filoviruses are a group of single-stranded negative sense RNA viruses. The most well-known filoviruses that affect humans are ebolaviruses and marburgviruses. During infection, they can cause life-threatening symptoms such as inflammation, tissue damage, and hemorrhagic fever, with case fatality rates as high as [...] Read more.
Filoviruses are a group of single-stranded negative sense RNA viruses. The most well-known filoviruses that affect humans are ebolaviruses and marburgviruses. During infection, they can cause life-threatening symptoms such as inflammation, tissue damage, and hemorrhagic fever, with case fatality rates as high as 90%. The innate immune system is the first line of defense against pathogenic insults such as filoviruses. Pattern recognition receptors (PRRs), including toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors, AIM2-like receptors, and NOD-like receptors, detect pathogens and activate downstream signaling to induce the production of proinflammatory cytokines and interferons, alert the surrounding cells to the threat, and clear infected and damaged cells through innate immune cell death. However, filoviruses can modulate the host inflammatory response and innate immune cell death, causing an aberrant immune reaction. Here, we discuss how the innate immune system senses invading filoviruses and how these deadly pathogens interfere with the immune response. Furthermore, we highlight the experimental difficulties of studying filoviruses as well as the current state of filovirus-targeting therapeutics. Full article
(This article belongs to the Special Issue New Research on Filovirus Infections)
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22 pages, 8563 KiB  
Article
Antagonistic Activity of Potentially Probiotic Lactic Acid Bacteria against Honeybee (Apis mellifera L.) Pathogens
by Aleksandra Leska, Adriana Nowak, Justyna Szulc, Ilona Motyl and Karolina Henryka Czarnecka-Chrebelska
Pathogens 2022, 11(11), 1367; https://doi.org/10.3390/pathogens11111367 - 16 Nov 2022
Cited by 10 | Viewed by 5712
Abstract
Lactic acid bacteria (LAB) are an essential part of the microbiota of the digestive tract of honeybees (Apis mellifera L.). Antagonistic activity of 103 LAB strains (isolates from different environments) against 21 honeybee pathogens/opportunistic pathogens (with agar slab method) was screened. The [...] Read more.
Lactic acid bacteria (LAB) are an essential part of the microbiota of the digestive tract of honeybees (Apis mellifera L.). Antagonistic activity of 103 LAB strains (isolates from different environments) against 21 honeybee pathogens/opportunistic pathogens (with agar slab method) was screened. The growth of Paenibacillus genus was inhibited to the most extent. The highest antagonistic activity was demonstrated by Lacticaseibacillus casei 12AN, while the lowest by Apilactobacillus kunkeei DSM 12361, a species naturally inhabiting the honeybee gut. LAB isolated from the honeybee environment demonstrated stronger antagonism against pathogens than collection strains. The antagonistic activity of cell-free supernatants (CFSs) from 24 LAB strains against 7 honeybee pathogens was additionally assessed at physiological pH with the microtitration method. The same was determined for selected CFSs at neutralized pH. CFSs with physiological pH showed significantly stronger antibacterial activity than CFSs with neutralized pH. The results confirmed that the mechanism of antimicrobial activity of LAB is acidification of the environment. The obtained results may, in the future, contribute to a better understanding of the antagonistic properties of LAB and the construction of a probiotic preparation to increase the viability of honeybee colonies. Full article
(This article belongs to the Special Issue Diseases of Insect Pollinators)
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17 pages, 3634 KiB  
Article
Isolation of a New Infectious Pancreatic Necrosis Virus (IPNV) Variant from Genetically Resistant Farmed Atlantic Salmon (Salmo salar) during 2021–2022
by Marcos Godoy, Molly J. T. Kibenge, Marco Montes de Oca, Juan Pablo Pontigo, Yoandy Coca, Diego Caro, Karina Kusch, Rudy Suarez, Ian Burbulis and Frederick S. B. Kibenge
Pathogens 2022, 11(11), 1368; https://doi.org/10.3390/pathogens11111368 - 16 Nov 2022
Cited by 4 | Viewed by 3937
Abstract
Infectious pancreatic necrosis (IPN), caused by IPNV, affects several species of farmed fish, particularly Atlantic salmon, and is responsible for significant economic losses in salmon aquaculture globally. Despite the introduction of genetically resistant farmed Atlantic salmon and vaccination strategies in the Chilean salmon [...] Read more.
Infectious pancreatic necrosis (IPN), caused by IPNV, affects several species of farmed fish, particularly Atlantic salmon, and is responsible for significant economic losses in salmon aquaculture globally. Despite the introduction of genetically resistant farmed Atlantic salmon and vaccination strategies in the Chilean salmon industry since 2019, the number of IPN outbreaks has been increasing in farmed Atlantic salmon in the freshwater phase. This study examined gross and histopathological lesions of IPNV-affected fish, as well as the IPNV nucleotide sequence encoding the VP2 protein in clinical cases. The mortality reached 0.4% per day, and the cumulative mortality was from 0.4 to 3.5%. IPNV was isolated in the CHSE-214 cell line and was confirmed by RT-PCR, and VP2 sequence analysis. The analyzed viruses belong to IPNV genotype 5 and have 11 mutations in their VP2 protein. This is the first report of IPN outbreaks in farmed Atlantic salmon genetically resistant to IPNV in Chile. Similar outbreaks were previously reported in Scotland and Norway during 2018 and 2019, respectively. This study highlights the importance of maintaining a comprehensive surveillance program in conjunction with the use of farmed Atlantic salmon genetically resistant to IPNV. Full article
(This article belongs to the Special Issue Virulence Mechanisms, Detection and Control of Aquatic Animal Viruses)
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25 pages, 1015 KiB  
Article
Bacterial Pathogens in the Food Industry: Antibiotic Resistance and Virulence Factors of Salmonella enterica Strains Isolated from Food Chain Links
by Michał Wójcicki, Agnieszka Chmielarczyk, Olga Świder, Paulina Średnicka, Magdalena Strus, Tomasz Kasperski, Dziyana Shymialevich, Hanna Cieślak, Paulina Emanowicz, Monika Kowalczyk, Barbara Sokołowska and Edyta Juszczuk-Kubiak
Pathogens 2022, 11(11), 1323; https://doi.org/10.3390/pathogens11111323 - 10 Nov 2022
Cited by 8 | Viewed by 3195
Abstract
Salmonella is one of the most important foodborne pathogens. Fifty-three strains of Salmonella deposited in the Culture Collection of Industrial Microorganisms—Microbiological Resources Center (IAFB) were identified using molecular and proteomic analyses. Moreover, the genetic similarity of the tested strains was determined using the [...] Read more.
Salmonella is one of the most important foodborne pathogens. Fifty-three strains of Salmonella deposited in the Culture Collection of Industrial Microorganisms—Microbiological Resources Center (IAFB) were identified using molecular and proteomic analyses. Moreover, the genetic similarity of the tested strains was determined using the PFGE method. Main virulence genes were identified, and phenotypical antibiotic susceptibility profiles and prevalence of resistance genes were analyzed. Subsequently, the occurrence of the main mechanisms of β-lactam resistance was determined. Virulence genes, invA, fimA, and stn were identified in all tested strains. Phenotypic tests, including 28 antibiotics, showed that 50.9% of the strains were MDR. The tet genes associated with tetracyclines resistance were the most frequently identified genes. Concerning the genes associated with ESBL-producing Salmonella, no resistance to the TEM and CTX-M type was identified, and only two strains (KKP 1597 and KKP 1610) showed resistance to SHV. No strains exhibited AmpC-type resistance but for six Salmonella strains, the efflux-related resistance of PSE-1 was presented. The high number of resistant strains in combination with multiple ARGs in Salmonella indicates the possible overuse of antibiotics. Our results showed that it is necessary to monitor antimicrobial resistance profiles in all food chain links constantly and to implement a policy of proper antibiotic stewardship to contain or at least significantly limit the further acquisition of antibiotic resistance among Salmonella strains. Full article
(This article belongs to the Section Bacterial Pathogens)
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26 pages, 1041 KiB  
Review
Transmission Cycle of Tick-Borne Infections and Co-Infections, Animal Models and Diseases
by Sandra C. Rocha, Clara Vásquez Velásquez, Ahmed Aquib, Aya Al-Nazal and Nikhat Parveen
Pathogens 2022, 11(11), 1309; https://doi.org/10.3390/pathogens11111309 - 8 Nov 2022
Cited by 16 | Viewed by 5594
Abstract
Tick-borne pathogens such as species of Borrelia, Babesia, Anaplasma, Rickettsia, and Ehrlichia are widespread in the United States and Europe among wildlife, in passerines as well as in domestic and farm animals. Transmission of these pathogens occurs by infected [...] Read more.
Tick-borne pathogens such as species of Borrelia, Babesia, Anaplasma, Rickettsia, and Ehrlichia are widespread in the United States and Europe among wildlife, in passerines as well as in domestic and farm animals. Transmission of these pathogens occurs by infected ticks during their blood meal, carnivorism, and through animal bites in wildlife, whereas humans can become infected either by an infected tick bite, through blood transfusion and in some cases, congenitally. The reservoir hosts play an important role in maintaining pathogens in nature and facilitate transmission of individual pathogens or of multiple pathogens simultaneously to humans through ticks. Tick-borne co-infections were first reported in the 1980s in white-footed mice, the most prominent reservoir host for causative organisms in the United States, and they are becoming a major concern for public health now. Various animal infection models have been used extensively to better understand pathogenesis of tick-borne pathogens and to reveal the interaction among pathogens co-existing in the same host. In this review, we focus on the prevalence of these pathogens in different reservoir hosts, animal models used to investigate their pathogenesis and host responses they trigger to understand diseases in humans. We also documented the prevalence of these pathogens as correlating with the infected ticks’ surveillance studies. The association of tick-borne co-infections with other topics such as pathogens virulence factors, host immune responses as they relate to diseases severity, identification of vaccine candidates, and disease economic impact are also briefly addressed here. Full article
(This article belongs to the Special Issue Understanding Host-Tick-Pathogen Interactions through Animal Models)
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19 pages, 1942 KiB  
Article
Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields
by Pilar Marcos, Paul Whyte, Catherine Burgess, Daniel Ekhlas and Declan Bolton
Pathogens 2022, 11(11), 1310; https://doi.org/10.3390/pathogens11111310 - 8 Nov 2022
Cited by 11 | Viewed by 4691
Abstract
Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach [...] Read more.
Despite an increased incidence of Clostridioides difficile infections, data on the reservoirs and dissemination routes of this bacterium are limited. This study examined the prevalence and characteristics of C. difficile isolates in spinach fields. C. difficile was detected in 2/60 (3.3%) of spinach and 6/60 (10%) of soil samples using culture-based techniques. Whole genome sequencing (WGS) analysis identified the spinach isolates as belonging to the hypervirulent clade 5, sequence type (ST) 11, ribotypes (RT) 078 and 126 and carried the genes encoding toxins A, B and CDT. The soil isolates belonged to clade 1 with different toxigenic ST/RT (ST19/RT614, ST12/RT003, ST46/RT087, ST16/RT050, ST49/RT014/0) strains and one non-toxigenic ST79/RT511 strain. Antimicrobial resistance to erythromycin (one spinach isolate), rifampicin (two soil isolates), clindamycin (one soil isolate), both moxifloxacin and rifampicin (one soil isolate), and multi-drug resistance to erythromycin, vancomycin and rifampicin (two soil isolates) were observed using the E test, although a broader range of resistance genes were detected using WGS. Although the sample size was limited, our results demonstrate the presence of C. difficile in horticulture and provide further evidence that there are multiple sources and dissemination routes for these bacteria. Full article
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25 pages, 1211 KiB  
Review
Potential Hybridization of Fasciola hepatica and F. gigantica in Africa—A Scoping Review
by Sophy Nukeri, Mokgadi Pulane Malatji, Mita Eva Sengupta, Birgitte Jyding Vennervald, Anna-Sofie Stensgaard, Mamohale Chaisi and Samson Mukaratirwa
Pathogens 2022, 11(11), 1303; https://doi.org/10.3390/pathogens11111303 - 6 Nov 2022
Cited by 5 | Viewed by 4776
Abstract
The occurrence of Fasciola gigantica and F. hepatica in Africa is well documented; however, unlike in Asia, there is a paucity of information on the existence of hybrids or parthenogenetic species on the continent. Nonetheless, these hybrid species may have beneficial characteristics, such as [...] Read more.
The occurrence of Fasciola gigantica and F. hepatica in Africa is well documented; however, unlike in Asia, there is a paucity of information on the existence of hybrids or parthenogenetic species on the continent. Nonetheless, these hybrid species may have beneficial characteristics, such as increased host range and pathogenicity. This study provides evidence of the potential existence of Fasciola hybrids in Africa. A literature search of articles published between 1980 and 2022 was conducted in PubMed, Google Scholar, and Science Direct using a combination of search terms and Boolean operators. Fasciola species were documented in 26 African countries with F. hepatica being restricted to 12 countries, whilst F. gigantica occurred in 24 countries, identified based on morphological features of adult Fasciola specimens or eggs and molecular techniques. The co-occurrence of both species was reported in 11 countries. However, the occurrence of potential Fasciola hybrids was only confirmed in Egypt and Chad but is suspected in South Africa and Zimbabwe. These were identified based on liver fluke morphometrics, assessment of the sperms in the seminal vesicle, and molecular techniques. The occurrence of intermediate host snails Galba truncatula and Radix natalensis was reported in Ethiopia, Egypt, South Africa, Tanzania, and Uganda, where F. hepatica and F. gigantica co-occurrences were reported. The invasive Pseudosuccinea columella snails naturally infected with F. gigantica were documented in South Africa and Egypt. In Zimbabwe, P. columella was infected with a presumed parthenogenetic Fasciola. This suggests that the invasive species might also be contributing to the overlapping distributions of the two Fasciola species since it can transmit both species. Notwithstanding the limited studies in Africa, the potential existence of Fasciola hybrids in Africa is real and might mimic scenarios in Asia, where parthenogenetic Fasciola exist in most Asian countries. In South Africa, aspermic F. hepatica and Fasciola sp. have been reported already, and Fasciola hybrids have been reported? in Chad and Egypt. Thus, the authors recommend future surveys using molecular markers recommended to identify Fasciola spp. and their snail intermediate hosts to demarcate areas of overlapping distribution where Fasciola hybrids and/or parthenogenetic Fasciola may occur. Further studies should also be conducted to determine the presence and role of P. columella in the transmission of Fasciola spp. in these geographical overlaps to help prevent parasite spillbacks. Full article
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17 pages, 1781 KiB  
Review
Host-Directed Therapies for Tuberculosis
by Eui-Kwon Jeong, Hyo-Ji Lee and Yu-Jin Jung
Pathogens 2022, 11(11), 1291; https://doi.org/10.3390/pathogens11111291 - 3 Nov 2022
Cited by 12 | Viewed by 7667
Abstract
Tuberculosis (TB) is one of the leading causes of death worldwide, consistently threatening public health. Conventional tuberculosis treatment requires a long-term treatment regimen and is associated with side effects. The efficacy of antitubercular drugs has decreased with the emergence of drug-resistant TB; therefore, [...] Read more.
Tuberculosis (TB) is one of the leading causes of death worldwide, consistently threatening public health. Conventional tuberculosis treatment requires a long-term treatment regimen and is associated with side effects. The efficacy of antitubercular drugs has decreased with the emergence of drug-resistant TB; therefore, the development of new TB treatment strategies is urgently needed. In this context, we present host-directed therapy (HDT) as an alternative to current tuberculosis therapy. Unlike antitubercular drugs that directly target Mycobacterium tuberculosis (Mtb), the causative agent of TB, HDT is an approach for treating TB that appropriately modulates host immune responses. HDT primarily aims to enhance the antimicrobial activity of the host in order to control Mtb infection and attenuate excessive inflammation in order to minimize tissue damage. Recently, research based on the repositioning of drugs for use in HDT has been in progress. Based on the overall immune responses against Mtb infection and the immune-evasion mechanisms of Mtb, this review examines the repositioned drugs available for HDT and their mechanisms of action. Full article
(This article belongs to the Special Issue Drugs Repurposing for Multi-Drug Resistant Bacterial Infections)
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13 pages, 807 KiB  
Article
Incidence and Treatments of Bovine Mastitis and Other Diseases on 37 Dairy Farms in Wisconsin
by Juliano L. Gonçalves, Juliana L. de Campos, Andrew J. Steinberger, Nasia Safdar, Ashley Kates, Ajay Sethi, John Shutske, Garret Suen, Tony Goldberg, Roger I. Cue and Pamela L. Ruegg
Pathogens 2022, 11(11), 1282; https://doi.org/10.3390/pathogens11111282 - 1 Nov 2022
Cited by 13 | Viewed by 3392
Abstract
The aim of this research was to describe the incidence and treatments of mastitis and other common bovine diseases using one year of retrospective observational data (n = 50,329 cow-lactations) obtained from herd management software of 37 large dairy farms in Wisconsin. Incidence [...] Read more.
The aim of this research was to describe the incidence and treatments of mastitis and other common bovine diseases using one year of retrospective observational data (n = 50,329 cow-lactations) obtained from herd management software of 37 large dairy farms in Wisconsin. Incidence rate (IR) was defined as the number of first cases of each disease divided by the number of lactations per farm. Clinical mastitis (CM) remains the most diagnosed disease of dairy cows. Across all herds, the mean IR (cases per 100 cow-lactations) was 24.4 for clinical mastitis, 14.5 for foot disorders (FD), 11.2 for metritis (ME), 8.6 for ketosis (KE), 7.4 for retained fetal membranes (RFM), 4.5 for diarrhea (DI), 3.1 for displaced abomasum (DA), 2.9 for pneumonia (PN) and 1.9 for milk fever (MF). More than 30% of cows that had first cases of CM, DA, RFM, DI, and FD did not receive antibiotics. Of those treated, more than 50% of cows diagnosed with PN, ME and CM received ceftiofur as a treatment. The IR of mastitis and most other diseases was greater in older cows (parity ≥ 3) during the first 100 days of lactation and these cows were more likely to receive antibiotic treatments (as compared to younger cows diagnosed in later lactation). Cows of first and second parities in early lactation were more likely to remain in the herd after diagnosis of disease, as compared to older cows and cows in later stages of lactation. Most older cows diagnosed with CM in later lactation were culled before completion of the lactation. These results provide baseline data for disease incidence in dairy cows on modern U.S. dairy farms and reinforce the role of mastitis as an important cause of dairy cow morbidity. Full article
(This article belongs to the Collection Mastitis in Dairy Ruminants)
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12 pages, 276 KiB  
Article
“Monkeypox: What Do You Know about That?” Italian Adults’ Awareness of a New Epidemic
by Francesca Gallè, Lavinia Bianco, Giovanna Da Molin, Rita Mancini, Salvatore Sciacchitano, Stefano Ferracuti, Giorgio Liguori, Giovanni Battista Orsi and Christian Napoli
Pathogens 2022, 11(11), 1285; https://doi.org/10.3390/pathogens11111285 - 1 Nov 2022
Cited by 25 | Viewed by 2876
Abstract
In the course of 2022, an epidemic of monkeypox (MPX) arose worldwide. In order to assess the level of knowledge of the Italian adults regarding the new emerging disease, its prevention and their level of worrying and the acceptance of a possible vaccination, [...] Read more.
In the course of 2022, an epidemic of monkeypox (MPX) arose worldwide. In order to assess the level of knowledge of the Italian adults regarding the new emerging disease, its prevention and their level of worrying and the acceptance of a possible vaccination, a web questionnaire was spread nationwide. A total of 1352 individuals (mean age 54.5 ± 13.4, 52.4% males) completed the questionnaire. Only 26. 7% of the sample were aware of the burden of the epidemic at the moment of the investigation; 47.1% were not able to identify the transmission route, nor the main symptoms (48.9%); and 54.2% were hesitant toward a possible MPXV vaccination, mainly because of a lack of confident in vaccines (38.5%). A low level of worrying about the disease was registered (mean score 2.3 ± 1.2 on a 5-point scale). In the regression analysis performed considering MPX knowledge as outcome, a lower level of knowledge was associated with higher age (OR 1.378, CI95% 0.998–1.904), working or studying in a nonhealthcare setting (OR 0.046, CI95% 0.033–0.066), being single (OR 0.624, CI95% 0.455–0.856) and having mass media as the main source of information (OR 0.332, CI95% 0.158–0.696). These findings indicate as of the time of this investigation, the communication about the MPXV epidemic was not effective in determining a good level of knowledge about the disease and its transmission among Italian adults. This highlights the need to improve risk communication strategies. Full article
(This article belongs to the Special Issue Epidemiology and Outcomes Research in Infectious Diseases)
15 pages, 1082 KiB  
Article
Unlicensed Molnupiravir is an Effective Rescue Treatment Following Failure of Unlicensed GS-441524-like Therapy for Cats with Suspected Feline Infectious Peritonitis
by Meagan Roy, Nicole Jacque, Wendy Novicoff, Emma Li, Rosa Negash and Samantha J. M. Evans
Pathogens 2022, 11(10), 1209; https://doi.org/10.3390/pathogens11101209 - 20 Oct 2022
Cited by 15 | Viewed by 26568
Abstract
Feline infectious peritonitis (FIP) is a complex and historically fatal disease, though recent advances in antiviral therapy have uncovered potential treatments. A newer therapeutic option, unlicensed molnupiravir, is being used as a first-line therapy for suspect FIP and as a rescue therapy to [...] Read more.
Feline infectious peritonitis (FIP) is a complex and historically fatal disease, though recent advances in antiviral therapy have uncovered potential treatments. A newer therapeutic option, unlicensed molnupiravir, is being used as a first-line therapy for suspect FIP and as a rescue therapy to treat cats who have persistent or relapsed clinical signs of FIP after GS-441524 and/or GC376 therapy. Using owner-reported data, treatment protocols for 30 cats were documented. The 26 cats treated with unlicensed molnupiravir as a rescue therapy were treated with an average starting dosage of 12.8 mg/kg and an average ending dosage of 14.7 mg/kg twice daily for a median of 12 weeks (IQR = 10–15). In total, 24 of 26 cats were still living disease-free at the time of writing. One cat was euthanized after completing treatment due to a prolonged seizure, and the other cat underwent retreatment for relapsed clinical signs. Few adverse effects were reported, with the most notable—folded ears (1), broken whiskers (1), and severe leukopenia (1)—seen at dosages above 23 mg/kg twice daily. This study provides a proof of principle for the use of molnupiravir in cats and supports the need for future studies to further evaluate molnupiravir as a potentially safe and effective therapy for FIP. Full article
(This article belongs to the Special Issue Advances on Feline Coronavirus Infection)
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21 pages, 2959 KiB  
Review
Multidistrict Host–Pathogen Interaction during COVID-19 and the Development Post-Infection Chronic Inflammation
by Marialaura Fanelli, Vita Petrone, Margherita Buonifacio, Elisabetta Delibato, Emanuela Balestrieri, Sandro Grelli, Antonella Minutolo and Claudia Matteucci
Pathogens 2022, 11(10), 1198; https://doi.org/10.3390/pathogens11101198 - 18 Oct 2022
Cited by 4 | Viewed by 3841
Abstract
Due to the presence of the ACE2 receptor in different tissues (nasopharynx, lung, nervous tissue, intestine, liver), the COVID-19 disease involves several organs in our bodies. SARS-CoV-2 is able to infect different cell types, spreading to different districts. In the host, an uncontrolled [...] Read more.
Due to the presence of the ACE2 receptor in different tissues (nasopharynx, lung, nervous tissue, intestine, liver), the COVID-19 disease involves several organs in our bodies. SARS-CoV-2 is able to infect different cell types, spreading to different districts. In the host, an uncontrolled and altered immunological response is triggered, leading to cytokine storm, lymphopenia, and cellular exhaustion. Hence, respiratory distress syndrome (ARDS) and systemic multi-organ dysfunction syndrome (MODS) are established. This scenario is also reflected in the composition of the microbiota, the balance of which is regulated by the interaction with the immune system. A change in microbial diversity has been demonstrated in COVID-19 patients compared with healthy donors, with an increase in potentially pathogenic microbial genera. In addition to other symptoms, particularly neurological, the occurrence of dysbiosis persists after the SARS-CoV-2 infection, characterizing the post-acute COVID syndrome. This review will describe and contextualize the role of the immune system in unbalance and dysbiosis during SARS-CoV-2 infection, from the acute phase to the post-COVID-19 phase. Considering the tight relationship between the immune system and the gut–brain axis, the analysis of new, multidistrict parameters should be aimed at understanding and addressing chronic multisystem dysfunction related to COVID-19. Full article
(This article belongs to the Special Issue Role of Pathogens in Chronic Inflammatory Diseases and Cancer)
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18 pages, 4612 KiB  
Article
Microbial Genetics and Clonal Dissemination of Salmonella enterica Serotype Javiana Isolated from Human Populations in Arkansas, USA
by Yasser M. Sanad, Nesreen H. Aljahdali, Bijay K. Khajanchi, Rajesh Nayak, Ashraf Khan and Steven L. Foley
Pathogens 2022, 11(10), 1192; https://doi.org/10.3390/pathogens11101192 - 16 Oct 2022
Viewed by 2500
Abstract
Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period [...] Read more.
Salmonella is estimated to cause over a million infections and ~400 deaths annually in the U.S. Salmonella enterica serotype Javiana strains (n = 409) that predominantly originated from the State of Arkansas over a six-year period (2003 to 2008) were studied. This period coincided with a rapid rise in the incidence of S. Javiana infections in the U.S. Children under the age of 10 displayed the highest prevalence of S. Javiana infections, regardless of sex or year of detection. Antimicrobial susceptibility to 15 different antimicrobials was assessed and 92% (n = 375) were resistant to at least one of the antimicrobials. Approximately 89% of the isolates were resistant to sulfisoxazole alone and 3% (n = 11) were resistant to different antimicrobials, including gentamicin, ciprofloxacin or ceftiofur. The pulsed-field gel electrophoresis (PFGE) analyses assessed the genotypic diversity and distribution of S. Javiana strains using XbaI restriction. Nine major clusters were identified and isolates from each group were digested with the restriction enzyme AvrII. Isolates with identical profiles of XbaI and AvrII were found to be disseminated in human populations. These distinct “types” of S. Javiana were persistent in human populations for multiple years. A subset of isolates (n = 19) with unique resistance phenotypes underwent plasmid and incompatibility (Inc) type analyses and the isolates resistant to more than one antimicrobial harbored multiple plasmids (<3 to 165 kb). Furthermore, these strains possessed 14 virulence genes, including pagC, cdtB, and iroN. The whole genome sequences (WGS) of 18 isolates that mostly originated from Arkansas from 2003 to 2011 were compared with isolates collected from different areas in the U.S. in 1999, indicating the perseverance of S. Javiana in disseminating antimicrobial resistance and virulence genes. Full article
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22 pages, 1546 KiB  
Review
The Fight against Plant-Parasitic Nematodes: Current Status of Bacterial and Fungal Biocontrol Agents
by David Pires, Cláudia S. L. Vicente, Esther Menéndez, Jorge M. S. Faria, Leidy Rusinque, Maria J. Camacho and Maria L. Inácio
Pathogens 2022, 11(10), 1178; https://doi.org/10.3390/pathogens11101178 - 13 Oct 2022
Cited by 46 | Viewed by 13389
Abstract
Plant-parasitic nematodes (PPNs) are among the most notorious and underrated threats to food security and plant health worldwide, compromising crop yields and causing billions of dollars of losses annually. Chemical control strategies rely heavily on synthetic chemical nematicides to reduce PPN population densities, [...] Read more.
Plant-parasitic nematodes (PPNs) are among the most notorious and underrated threats to food security and plant health worldwide, compromising crop yields and causing billions of dollars of losses annually. Chemical control strategies rely heavily on synthetic chemical nematicides to reduce PPN population densities, but their use is being progressively restricted due to environmental and human health concerns, so alternative control methods are urgently needed. Here, we review the potential of bacterial and fungal agents to suppress the most important PPNs, namely Aphelenchoides besseyi, Bursaphelenchus xylophilus, Ditylenchus dipsaci, Globodera spp., Heterodera spp., Meloidogyne spp., Nacobbus aberrans, Pratylenchus spp., Radopholus similis, Rotylenchulus reniformis, and Xiphinema index. Full article
(This article belongs to the Special Issue Biological Plant Protection)
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9 pages, 1413 KiB  
Article
Toxoplasmosis in Captive Ring-Tailed Lemurs (Lemur catta)
by Guido Rocchigiani, Niccolò Fonti, Simona Nardoni, Paolo Cavicchio, Francesca Mancianti and Alessandro Poli
Pathogens 2022, 11(10), 1142; https://doi.org/10.3390/pathogens11101142 - 3 Oct 2022
Cited by 2 | Viewed by 3747
Abstract
Toxoplasma gondii is one of the most common protozoan parasites and is widely present in all warm-blooded animals. Although clinical disease is uncommon, some species, including ring-tailed lemurs (Lemur catta), have been found to develop acute and lethal toxoplasmosis. The aim [...] Read more.
Toxoplasma gondii is one of the most common protozoan parasites and is widely present in all warm-blooded animals. Although clinical disease is uncommon, some species, including ring-tailed lemurs (Lemur catta), have been found to develop acute and lethal toxoplasmosis. The aim of this study was to describe the pathologic, immunohistochemical, serological, and molecular findings of an outbreak of fatal toxoplasmosis in three captive ring-tailed lemurs in Central Italy in 2009. The animals died acutely within few days. The necropsy was immediately performed; necrotic lesions in the spleen, liver, and kidney, as well as interstitial pneumonia, were found histologically. All animals had high titers of anti–T. gondii-specific antibodies (1:1280 IgM and 1:640 IgG) according to a modified agglutination test (MAT) and immunohistochemistry showed scattered tachyzoites in the target organs. Diagnosis was confirmed by PCR and clonal type II was identified. In addition, the seven co-habiting lemurs were seronegative. This paper reports the first outbreak of acute disseminated toxoplasmosis in captive ring-tailed lemurs in Italy. These findings confirm the high susceptibility of this endangered species to toxoplasma infection, which may be considered a further threat to captive population viability. Full article
(This article belongs to the Special Issue Toxoplasma)
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