Pathogens

12 pages, 270 KB

Open AccessEditor’s ChoiceArticle

Assessment of the Impact of the Recombinant Porcine Reproductive and Respiratory Syndrome Virus Horsens Strain on the Reproductive Performance in Pregnant Sows

by Sandra Genís, Lise K. Kvisgaard, Lars E. Larsen, Lucas P. Taylor, Jay G. Calvert and Mònica Balasch

Pathogens 2020, 9(9), 772; https://doi.org/10.3390/pathogens9090772 - 21 Sep 2020

Cited by 5 | Viewed by 3058

Abstract

This study assessed the impact of a PRRSV (porcine reproductive and respiratory syndrome virus) recombinant strain (Horsens strain) on the reproductive performance of naïve pregnant sows in the last third of gestation. Fifteen sows were included: four negative reproductive controls (NTX), five infected [...] Read more.

This study assessed the impact of a PRRSV (porcine reproductive and respiratory syndrome virus) recombinant strain (Horsens strain) on the reproductive performance of naïve pregnant sows in the last third of gestation. Fifteen sows were included: four negative reproductive controls (NTX), five infected with a PRRSV-1 field strain (Olot/91, T01), and six infected with the recombinant PRRSV-1 strain (Horsens strain, T02). Piglets were monitored until weaning. Reproductive performance was the primary variable. In sows, viremia and nasal shedding (T01 and T02 groups), and, in piglets, viral load in blood and in lungs, as well as macroscopic lung lesions (T01 and T02 groups), were the secondary variables. The reproductive performance results were numerically different between the two challenged groups. Moreover, viral loads in blood were 1.83 × 10⁶ ± 9.05 × 10⁶ copies/mL at farrowing, 1.05 × 10⁷ ± 2.21 × 10⁷ copies/mL at weaning from piglets born from T01 animals and 1.64 × 10³ ± 7.62 × 10³ copies/mL at farrowing, 1.95 × 10³ ± 1.17 × 10⁴ copies/mL at weaning from piglets born from T02 sows. Overall, 68.8% of T01 piglets and 38.1% of T02 piglets presented mild lung lesions. In conclusion, the results suggest that Horsens strain is less virulent than the field strain Olot/91 under these experimental conditions. Full article

(This article belongs to the Section Animal Pathogens)

19 pages, 1577 KB

Open AccessEditor’s ChoiceReview

Long Noncoding RNAs in Plant Viroids and Viruses: A Review

by Nipin Shrestha and Józef J. Bujarski

Pathogens 2020, 9(9), 765; https://doi.org/10.3390/pathogens9090765 - 18 Sep 2020

Cited by 16 | Viewed by 8505

Abstract

Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle [...] Read more.

Infectious long-noncoding (lnc) RNAs related to plants can be of both viral and non-viral origin. Viroids are infectious plant lncRNAs that are not related to viruses and carry the circular, single-stranded, non-coding RNAs that replicate with host enzymatic activities via a rolling circle mechanism. Viroids interact with host processes in complex ways, emerging as one of the most productive tools for studying the functions of lncRNAs. Defective (D) RNAs, another category of lnc RNAs, are found in a variety of plant RNA viruses, most of which are noncoding. These are derived from and are replicated by the helper virus. D RNA-virus interactions evolve into mutually beneficial combinations, enhancing virus fitness via competitive advantages of moderated symptoms. Yet the satellite RNAs are single-stranded and include either large linear protein-coding ss RNAs, small linear ss RNAs, or small circular ss RNAs (virusoids). The satellite RNAs lack sequence homology to the helper virus, but unlike viroids need a helper virus to replicate and encapsidate. They can attenuate symptoms via RNA silencing and enhancement of host defense, but some can be lethal as RNA silencing suppressor antagonists. Moreover, selected viruses produce lncRNAs by incomplete degradation of genomic RNAs. They do not replicate but may impact viral infection, gene regulation, and cellular functions. Finally, the host plant lncRNAs can also contribute during plant-virus interactions, inducing plant defense and the regulation of gene expression, often in conjunction with micro and/or circRNAs. Full article

(This article belongs to the Special Issue The Structure-to-Function Relationship of Long Non-coding RNAs in Various Biological Systems)

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9 pages, 234 KB

Open AccessEditor’s ChoiceArticle

Statin Use Is Associated with Decreased Risk of Invasive Mechanical Ventilation in COVID-19 Patients: A Preliminary Study

by Sophia L. Song, Sarah B. Hays, Constance E. Panton, Evangelia K. Mylona, Markos Kalligeros, Fadi Shehadeh and Eleftherios Mylonakis

Pathogens 2020, 9(9), 759; https://doi.org/10.3390/pathogens9090759 - 17 Sep 2020

Cited by 45 | Viewed by 5144

Abstract

COVID-19 disproportionately affects patients with medical comorbidities such as cardiovascular disease (CVD). Patients with CVD are widely prescribed 3-hydroxy-3-methyl-glutayl-CoA (HMG-CoA) reductase inhibitors (statins), a class of lipid-lowering medications known for their pleiotropic anti-inflammatory and immunomodulatory effects. However, the relationship between statin use and [...] Read more.

COVID-19 disproportionately affects patients with medical comorbidities such as cardiovascular disease (CVD). Patients with CVD are widely prescribed 3-hydroxy-3-methyl-glutayl-CoA (HMG-CoA) reductase inhibitors (statins), a class of lipid-lowering medications known for their pleiotropic anti-inflammatory and immunomodulatory effects. However, the relationship between statin use and COVID-19 outcomes is not fully understood. In this preliminary study, we explored the association between statin use and severe COVID-19 outcomes in hospitalized patients, including intensive care unit (ICU) admission, the need for invasive mechanical ventilation (IMV), and in-hospital death. We performed a retrospective cohort study of 249 patients hospitalized with COVID-19 from 3 March 2020 to 10 April 2020 in Rhode Island, USA. Patient demographics, past medical history, current medications, and hospital course were recorded and analyzed. A multivariate logistic regression analysis was conducted to examine associations. After adjusting for age, sex, race, cardiovascular disease, chronic pulmonary disease, diabetes, and obesity, statin use was significantly associated with decreased risk for IMV (adjusted Odds Ratio (aOR) = 0.45, 95% Confidence Interval (CI): 0.20–0.99). Our results support the continued use of statins among COVID-19 patients and could have implications for future prospective studies on the management of COVID-19. Full article

(This article belongs to the Collection SARS-CoV Infections)

17 pages, 941 KB

Open AccessEditor’s ChoiceReview

Zoonotic Implications of Onchocerca Species on Human Health

by Maria Cambra-Pellejà, Javier Gandasegui, Rafael Balaña-Fouce, José Muñoz and María Martínez-Valladares

Pathogens 2020, 9(9), 761; https://doi.org/10.3390/pathogens9090761 - 17 Sep 2020

Cited by 21 | Viewed by 8513

Abstract

The genus Onchocerca includes several species associated with ungulates as hosts, although some have been identified in canids, felids, and humans. Onchocerca species have a wide geographical distribution, and the disease they produce, onchocerciasis, is generally seen in adult individuals because of its [...] Read more.

The genus Onchocerca includes several species associated with ungulates as hosts, although some have been identified in canids, felids, and humans. Onchocerca species have a wide geographical distribution, and the disease they produce, onchocerciasis, is generally seen in adult individuals because of its large prepatency period. In recent years, Onchocerca species infecting animals have been found as subcutaneous nodules or invading the ocular tissues of humans; the species involved are O. lupi, O. dewittei japonica, O. jakutensis, O. gutturosa, and O. cervicalis. These findings generally involve immature adult female worms, with no evidence of being fertile. However, a few cases with fertile O. lupi, O. dewittei japonica, and O. jakutensis worms have been identified recently in humans. These are relevant because they indicate that the parasite’s life cycle was completed in the new host—humans. In this work, we discuss the establishment of zoonotic Onchocerca infections in humans, and the possibility of these infections to produce symptoms similar to human onchocerciasis, such as dermatitis, ocular damage, and epilepsy. Zoonotic onchocerciasis is thought to be an emerging human parasitic disease, with the need to take measures such as One Health Strategies, in order to identify and control new cases in humans. Full article

(This article belongs to the Special Issue Onchocerciasis and River Epilepsy)

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16 pages, 1597 KB

Open AccessEditor’s ChoiceArticle

Role of TRP Channels in Shaping the Gut Microbiome

by Ravinder Nagpal, Santosh Kumar Mishra, Gagan Deep and Hariom Yadav

Pathogens 2020, 9(9), 753; https://doi.org/10.3390/pathogens9090753 - 16 Sep 2020

Cited by 17 | Viewed by 5243

Abstract

Transient receptor potential (TRP) channel family proteins are sensors for pain, which sense a variety of thermal and noxious chemicals. Sensory neurons innervating the gut abundantly express TRPA1 and TRPV1 channels and are in close proximity of gut microbes. Emerging evidence indicates a [...] Read more.

Transient receptor potential (TRP) channel family proteins are sensors for pain, which sense a variety of thermal and noxious chemicals. Sensory neurons innervating the gut abundantly express TRPA1 and TRPV1 channels and are in close proximity of gut microbes. Emerging evidence indicates a bi-directional gut–brain cross-talk in several entero-neuronal pathologies; however, the direct evidence of TRP channels interacting with gut microbial populations is lacking. Herein, we examine whether and how the knockout (KO) of TRPA1 and TRPV1 channels individually or combined TRPA1/V1 double-knockout (dKO) impacts the gut microbiome in mice. We detect distinct microbiome clusters among the three KO mouse models versus wild-type (WT) mice. All three TRP-KO models have reduced microbial diversity, harbor higher abundance of Bacteroidetes, and a reduced proportion of Firmicutes. Specifically distinct arrays in the KO models are determined mainly by S24-7, Bacteroidaceae, Clostridiales, Prevotellaceae, Helicobacteriaceae, Rikenellaceae, and Ruminococcaceae. A1KO mice have lower Prevotella, Desulfovibrio, Bacteroides, Helicobacter and higher Rikenellaceae and Tenericutes; V1KO mice demonstrate higher Ruminococcaceae, Lachnospiraceae, Ruminococcus, Desulfovibrio and Mucispirillum; and A1V1dKO mice exhibit higher Bacteroidetes, Bacteroides and S24-7 and lower Firmicutes, Ruminococcaceae, Oscillospira, Lactobacillus and Sutterella abundance. Furthermore, the abundance of taxa involved in biosynthesis of lipids and primary and secondary bile acids is higher while that of fatty acid biosynthesis-associated taxa is lower in all KO groups. To our knowledge, this is the first study demonstrating distinct gut microbiome signatures in TRPA1, V1 and dKO models and should facilitate prospective studies exploring novel diagnostic/ therapeutic modalities regarding the pathophysiology of TRP channel proteins. Full article

(This article belongs to the Section Animal Pathogens)

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14 pages, 1771 KB

Open AccessEditor’s ChoiceReview

Pathogenic Delivery: The Biological Roles of Cryptococcal Extracellular Vesicles

by Haroldo C. de Oliveira, Rafael F. Castelli, Flavia C. G. Reis, Juliana Rizzo and Marcio L. Rodrigues

Pathogens 2020, 9(9), 754; https://doi.org/10.3390/pathogens9090754 - 16 Sep 2020

Cited by 19 | Viewed by 6095

Abstract

Extracellular vesicles (EVs) are produced by all domains of life. In fungi, these structures were first described in Cryptococcus neoformans and, since then, they were characterized in several pathogenic and non-pathogenic fungal species. Cryptococcal EVs participate in the export of virulence factors that [...] Read more.

Extracellular vesicles (EVs) are produced by all domains of life. In fungi, these structures were first described in Cryptococcus neoformans and, since then, they were characterized in several pathogenic and non-pathogenic fungal species. Cryptococcal EVs participate in the export of virulence factors that directly impact the Cryptococcus–host interaction. Our knowledge of the biogenesis and pathogenic roles of Cryptococcus EVs is still limited, but recent methodological and scientific advances have improved our understanding of how cryptococcal EVs participate in both physiological and pathogenic events. In this review, we will discuss the importance of cryptococcal EVs, including early historical studies suggesting their existence in Cryptococcus, their putative mechanisms of biogenesis, methods of isolation, and possible roles in the interaction with host cells. Full article

(This article belongs to the Special Issue Pathogenesis of Cryptococcus neoformans)

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11 pages, 6043 KB

Open AccessEditor’s ChoiceArticle

Elevated Baseline Salivary Protease Activity May Predict the Steadiness of Gingival Inflammation During Periodontal Healing: A 12-Week Follow-Up Study on Adults

by Ulvi Kahraman Gürsoy, Dareen Fteita, Floris J. Bikker, Maria Anastasia Grande, Kamran Nazmi, Mervi Gürsoy, Eija Könönen and Daniel Belstrøm

Pathogens 2020, 9(9), 751; https://doi.org/10.3390/pathogens9090751 - 15 Sep 2020

Cited by 8 | Viewed by 3322

Abstract

Aim was to profile salivary total protease, Porphyromonas gingivalis gingipain, and neutrophil elastase activities in relation to the resolution of periodontal inflammation, salivary macrophage-derived chemokine (MDC), and macrophage inflammatory protein-1α concentrations. Nonsurgical periodontal treatment was performed in 24 periodontitis patients in a prospective [...] Read more.

Aim was to profile salivary total protease, Porphyromonas gingivalis gingipain, and neutrophil elastase activities in relation to the resolution of periodontal inflammation, salivary macrophage-derived chemokine (MDC), and macrophage inflammatory protein-1α concentrations. Nonsurgical periodontal treatment was performed in 24 periodontitis patients in a prospective interventional study design. Periodontal clinical parameters were recorded, and stimulated saliva samples were collected at baseline and 2, 6, and 12 weeks after treatment. Salivary total protease and gingipain activities were determined using fluorogenic substrates, elastase activity by chromogenic substrates, and cytokine concentrations by Luminex immunoassay. For statistical analyses, generalized linear mixed models for repeated measures were used. Salivary total protease activity elevated, while gingival inflammation and plaque accumulation decreased 2 and 6 weeks after periodontal therapy. Salivary MDC concentration was elevated 12 weeks after periodontal treatment. Patients with elevated protease activities at baseline in comparison to patients with low baseline total protease activities, had higher levels of gingival inflammation before and after periodontal treatment. In conclusion, elevations in salivary total protease activity seem to be part of periodontal healing at its early phases. Higher levels of salivary total protease activities before periodontal treatment may predict the severity and steadiness of unresolved gingival inflammation. Full article

(This article belongs to the Special Issue Oral Immunology and Periodontitis)

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9 pages, 513 KB

Open AccessEditor’s ChoiceReview

Current Perspectives on Uniparental Mitochondrial Inheritance in Cryptococcus neoformans

by Amber R. Matha and Xiaorong Lin

Pathogens 2020, 9(9), 743; https://doi.org/10.3390/pathogens9090743 - 10 Sep 2020

Cited by 9 | Viewed by 3669

Abstract

The mitochondrion is a vital organelle in most eukaryotic cells. It contains its own DNA which differs from nuclear DNA, since it is often inherited from only one parent during sexual reproduction. In anisogamous mammals, this is largely due to the fact that [...] Read more.

The mitochondrion is a vital organelle in most eukaryotic cells. It contains its own DNA which differs from nuclear DNA, since it is often inherited from only one parent during sexual reproduction. In anisogamous mammals, this is largely due to the fact that the oocyte has over 1000 times more copies of mitochondrial DNA than the sperm. However, in the isogamous fungus Cryptococcus neoformans, uniparental mitochondrial inheritance (UMI) still occurs during sexual reproduction. It is proposed that UMI might have evolved in the last common ancestor of eukaryotes. Thus, understanding the fundamental process of UMI in lower eukaryotes may give insights into how the process might have evolved in eukaryotic ancestors. In this review, we discuss the current knowledge regarding the cellular features as well as the molecular underpinnings of UMI in Cryptococcus during the mating process, and open questions that need to be answered to solve the mystery of UMI in this eukaryotic microbe. Full article

(This article belongs to the Special Issue Pathogenesis of Cryptococcus neoformans)

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15 pages, 5018 KB

Open AccessEditor’s ChoiceArticle

Comparative Analysis of Infection by Rickettsia rickettsii Sheila Smith and Taiaçu Strains in a Murine Model

by Eliane Esteves, Chanida Fongsaran, Ingeborg M. Langohr, Sean P. Riley, Marcelo B. Labruna, Sirlei Daffre, Andréa C. Fogaça and Kevin R. Macaluso

Pathogens 2020, 9(9), 744; https://doi.org/10.3390/pathogens9090744 - 10 Sep 2020

Cited by 8 | Viewed by 4574

Abstract

Rocky Mountain spotted fever (RMSF) is a life-threatening tick-borne disease caused by Rickettsia rickettsii, which is widely distributed throughout the Americas. Over 4000 cases of RMSF are recorded annually in the United States, while only around 100 cases are reported in Brazil. [...] Read more.

Rocky Mountain spotted fever (RMSF) is a life-threatening tick-borne disease caused by Rickettsia rickettsii, which is widely distributed throughout the Americas. Over 4000 cases of RMSF are recorded annually in the United States, while only around 100 cases are reported in Brazil. Conversely, while case fatality rates in the United States oscillate around 5%, in Brazil they can surpass 70%, suggesting that differences in tick vectoring capacity, population sensitivity, and/or variability in virulence of the rickettsial strains may exist. In this study, we compared the susceptibility of C3H/HeN mice to two highly virulent strains of R. rickettsii, one from the United States (Sheila Smith) and the other from Brazil (Taiaçu). Animals inoculated with the Taiaçu strain succumbed to infection earlier and exhibited severe histological lesions in both liver and spleen sooner than mice infected with the Sheila Smith strain. These differences in survival and signs of the disease are not related to a greater proliferation of the Taiaçu strain, as there were no significant differences in the rickettsial load in mice tissues inoculated with either strain. The present study is the first step to experimentally assess differences in fatality rates of RMSF in two different regions of the American continent. Full article

(This article belongs to the Special Issue Virulence Mechanisms of Rickettsiae)

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30 pages, 2265 KB

Open AccessEditor’s ChoiceReview

Control Measures for SARS-CoV-2: A Review on Light-Based Inactivation of Single-Stranded RNA Viruses

by Joshua Hadi, Magdalena Dunowska, Shuyan Wu and Gale Brightwell

Pathogens 2020, 9(9), 737; https://doi.org/10.3390/pathogens9090737 - 8 Sep 2020

Cited by 80 | Viewed by 13934

Abstract

SARS-CoV-2 is a single-stranded RNA virus classified in the family Coronaviridae. In this review, we summarize the literature on light-based (UV, blue, and red lights) sanitization methods for the inactivation of ssRNA viruses in different matrixes (air, liquid, and solid). The rate [...] Read more.

SARS-CoV-2 is a single-stranded RNA virus classified in the family Coronaviridae. In this review, we summarize the literature on light-based (UV, blue, and red lights) sanitization methods for the inactivation of ssRNA viruses in different matrixes (air, liquid, and solid). The rate of inactivation of ssRNA viruses in liquid was higher than in air, whereas inactivation on solid surfaces varied with the type of surface. The efficacy of light-based inactivation was reduced by the presence of absorptive materials. Several technologies can be used to deliver light, including mercury lamp (conventional UV), excimer lamp (UV), pulsed-light, and light-emitting diode (LED). Pulsed-light technologies could inactivate viruses more quickly than conventional UV-C lamps. Large-scale use of germicidal LED is dependent on future improvements in their energy efficiency. Blue light possesses virucidal potential in the presence of exogenous photosensitizers, although femtosecond laser (ultrashort pulses) can be used to circumvent the need for photosensitizers. Red light can be combined with methylene blue for application in medical settings, especially for sanitization of blood products. Future modelling studies are required to establish clearer parameters for assessing susceptibility of viruses to light-based inactivation. There is considerable scope for improvement in the current germicidal light-based technologies and practices. Full article

(This article belongs to the Section Human Pathogens)

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23 pages, 6213 KB

Open AccessEditor’s ChoiceReview

Mayaro Virus Pathogenesis and Transmission Mechanisms

by Cheikh Tidiane Diagne, Michèle Bengue, Valérie Choumet, Rodolphe Hamel, Julien Pompon and Dorothée Missé

Pathogens 2020, 9(9), 738; https://doi.org/10.3390/pathogens9090738 - 8 Sep 2020

Cited by 70 | Viewed by 10424

Abstract

Mayaro virus (MAYV), isolated for the first time in Trinidad and Tobago, has captured the attention of public health authorities worldwide following recent outbreaks in the Americas. It has a propensity to be exported outside its original geographical range, because of the vast [...] Read more.

Mayaro virus (MAYV), isolated for the first time in Trinidad and Tobago, has captured the attention of public health authorities worldwide following recent outbreaks in the Americas. It has a propensity to be exported outside its original geographical range, because of the vast distribution of its vectors. Moreover, most of the world population is immunologically naïve with respect to infection with MAYV which makes this virus a true threat. The recent invasion of several countries by Aedesalbopictus underscores the risk of potential urban transmission of MAYV in both tropical and temperate regions. In humans, the clinical manifestations of MAYV disease range from mild fever, rash, and joint pain to arthralgia. In the absence of a licensed vaccine and clinically proven therapeutics against Mayaro fever, prevention focuses mainly on household mosquito control. However, as demonstrated for other arboviruses, mosquito control is rather inefficient for outbreak management and alternative approaches to contain the spread of MAYV are therefore necessary. Despite its strong epidemic potential, little is currently known about MAYV. This review addresses various aspects of MAYV, including its epidemiology, vector biology, mode of transmission, and clinical complications, as well as the latest developments in MAYV diagnosis. Full article

(This article belongs to the Special Issue Untargeted Alternative Routes of Arbovirus Transmission)

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18 pages, 2649 KB

Open AccessEditor’s ChoiceArticle

Trends of the Dengue Serotype-4 Circulation with Epidemiological, Phylogenetic, and Entomological Insights in Lao PDR between 2015 and 2019

by Elodie Calvez, Virginie Pommelet, Somphavanh Somlor, Julien Pompon, Souksakhone Viengphouthong, Phaithong Bounmany, Thep Aksone Chindavong, Thonglakhone Xaybounsou, Phoyphaylinh Prasayasith, Sitsana Keosenhom, Paul T. Brey, Olivier Telle, Marc Choisy, Sébastien Marcombe and Marc Grandadam

Pathogens 2020, 9(9), 728; https://doi.org/10.3390/pathogens9090728 - 3 Sep 2020

Cited by 22 | Viewed by 6475

Abstract

Dengue outbreaks have regularly been recorded in Lao People’s Democratic Republic (PDR) since the first detection of the disease in 1979. In 2012, an integrated arbovirus surveillance network was set up in Lao PDR and an entomological surveillance has been implemented since 2016 [...] Read more.

Dengue outbreaks have regularly been recorded in Lao People’s Democratic Republic (PDR) since the first detection of the disease in 1979. In 2012, an integrated arbovirus surveillance network was set up in Lao PDR and an entomological surveillance has been implemented since 2016 in Vientiane Capital. Here, we report a study combining epidemiological, phylogenetic, and entomological analyzes during the largest DENV-4 epidemic ever recorded in Lao PDR (2015–2019). Strikingly, from 2015 to 2019, we reported the DENV-4 emergence and spread at the country level after two large epidemics predominated by DENV-3 and DENV-1, respectively, in 2012–2013 and 2015. Our data revealed a significant difference in the median age of the patient infected by DENV-4 compared to the other serotypes. Phylogenetic analysis demonstrated the circulation of DENV-4 Genotype I at the country level since at least 2013. The entomological surveillance showed a predominance of Aedesaegypti compared to Aedesalbopictus and high abundance of these vectors in dry and rainy seasons between 2016 and 2019, in Vientiane Capital. Overall, these results emphasized the importance of an integrated approach to evaluate factors, which could impact the circulation and the epidemiological profile of dengue viruses, especially in endemic countries like Lao PDR. Full article

(This article belongs to the Special Issue Untargeted Alternative Routes of Arbovirus Transmission)

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29 pages, 4775 KB

Open AccessEditor’s ChoiceArticle

Differences in the Endophytic Microbiome of Olive Cultivars Infected by Xylella fastidiosa across Seasons

by Annalisa Giampetruzzi, Paula Baptista, Massimiliano Morelli, Cristina Cameirão, Teresa Lino Neto, Daniela Costa, Giusy D’Attoma, Raied Abou Kubaa, Giuseppe Altamura, Maria Saponari, José Alberto Pereira and Pasquale Saldarelli

Pathogens 2020, 9(9), 723; https://doi.org/10.3390/pathogens9090723 - 2 Sep 2020

Cited by 51 | Viewed by 7898

Abstract

The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on [...] Read more.

The dynamics of Xylella fastidiosa infections in the context of the endophytic microbiome was studied in field-grown plants of the susceptible and resistant olive cultivars Kalamata and FS17. Whole metagenome shotgun sequencing (WMSS) coupled with 16S/ITS rRNA gene sequencing was carried out on the same trees at two different stages of the infections: In Spring 2017 when plants were almost symptomless and in Autumn 2018 when the trees of the susceptible cultivar clearly showed desiccations. The progression of the infections detected in both cultivars clearly unraveled that Xylella tends to occupy the whole ecological niche and suppresses the diversity of the endophytic microbiome. However, this trend was mitigated in the resistant cultivar FS17, harboring lower population sizes and therefore lower Xylella average abundance ratio over total bacteria, and a higher α-diversity. Host cultivar had a negligible effect on the community composition and no clear associations of a single taxon or microbial consortia with the resistance cultivar were found with both sequencing approaches, suggesting that the mechanisms of resistance likely reside on factors that are independent of the microbiome structure. Overall, Proteobacteria, Actinobacteria, Firmicutes, and Bacteriodetes dominated the bacterial microbiome while Ascomycota and Basidiomycota those of Fungi. Full article

(This article belongs to the Special Issue Endophytes in Plant Health and Disease)

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13 pages, 3545 KB

Open AccessEditor’s ChoiceArticle

In Vitro Characterization of Multidrug-Resistant Influenza A(H1N1)pdm09 Viruses Carrying a Dual Neuraminidase Mutation Isolated from Immunocompromised Patients

by Emi Takashita, Seiichiro Fujisaki, Masaru Yokoyama, Masayuki Shirakura, Hiroko Morita, Kazuya Nakamura, Noriko Kishida, Tomoko Kuwahara, Hironori Sato, Ikuko Doi, Yuji Sato, Shinichi Takao, Yukie Shimazu, Takeshi Shimomura, Takuo Ito, Shinji Watanabe, Takato Odagiri and on behalf of The Influenza Virus Surveillance Group of Japan

Pathogens 2020, 9(9), 725; https://doi.org/10.3390/pathogens9090725 - 2 Sep 2020

Cited by 11 | Viewed by 4327

Abstract

Influenza A(H1N1)pdm09 viruses carrying a dual neuraminidase (NA) substitution were isolated from immunocompromised patients after administration of one or more NA inhibitors. These mutant viruses possessed an H275Y/I223R, H275Y/I223K, or H275Y/G147R substitution in their NA and showed enhanced cross-resistance to oseltamivir and peramivir [...] Read more.

Influenza A(H1N1)pdm09 viruses carrying a dual neuraminidase (NA) substitution were isolated from immunocompromised patients after administration of one or more NA inhibitors. These mutant viruses possessed an H275Y/I223R, H275Y/I223K, or H275Y/G147R substitution in their NA and showed enhanced cross-resistance to oseltamivir and peramivir and reduced susceptibility to zanamivir compared to single H275Y mutant viruses. Baloxavir could be a treatment option against the multidrug-resistant viruses because these dual H275Y mutant viruses showed susceptibility to this drug. The G147R substitution appears to stabilize the NA structure, with the fitness of the H275Y/G147R mutant virus being similar or somewhat better than that of the wild-type virus. Since the multidrug-resistant viruses may be able to transmit between humans, surveillance of these viruses must continue to improve clinical management and to protect public health. Full article

(This article belongs to the Special Issue Advance in Influenza A Virus)

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13 pages, 709 KB

Open AccessEditor’s ChoiceArticle

Comparison of Japanese Encephalitis Force of Infection in Pigs, Poultry and Dogs in Cambodian Villages

by Héléna Ladreyt, Heidi Auerswald, Sothyra Tum, Sreymom Ken, Leangyi Heng, Saraden In, Sokchea Lay, Chakriyouth Top, Sowath Ly, Veasna Duong, Philippe Dussart, Benoit Durand and Véronique Chevalier

Pathogens 2020, 9(9), 719; https://doi.org/10.3390/pathogens9090719 - 1 Sep 2020

Cited by 24 | Viewed by 5192

Abstract

Japanese encephalitis virus (JEV) is the main cause of human viral encephalitis in Asia, with a mortality rate reaching 30%, mostly affecting children. The traditionally described cycle involving wild birds as reservoirs, pigs as amplifying hosts and Culex mosquitoes as vectors is questioned, [...] Read more.

Japanese encephalitis virus (JEV) is the main cause of human viral encephalitis in Asia, with a mortality rate reaching 30%, mostly affecting children. The traditionally described cycle involving wild birds as reservoirs, pigs as amplifying hosts and Culex mosquitoes as vectors is questioned, with increasing evidence of a more complex multi-host system involved in areas where densities of pigs are low, such as in Cambodia. In 2018, we examined pigs, chickens, ducks and dogs from Kandal province, Cambodia, for antibody response against JEV by hemagglutination inhibition and virus neutralization assays. Forces of infection (FOI) for flaviviruses and JEV were estimated per species and per unit of body surface area (BSA). JEV seroprevalence reached 31% (95% CI: 23–41%) in pigs, 1% (95% CI: 0.1–3%) in chickens, 12% (95% CI: 7–19%) in ducks and 35% (95% CI: 28–42%) in dogs. Pigs were most likely to be infected (FOI: 0.09 per month), but the FOI was higher in ducks than in pigs for a given BSA (ratio of 0.13). Dogs had a lower FOI than ducks but a higher FOI than chickens (0.01 per month). For a given BSA, dogs were less likely to be infected than pigs (ratio of 1.9). In Cambodia, the virus may be circulating between multiple hosts. Dogs live in close contact with humans, and estimating their exposure to JEV infection could be a relevant indicator of the risk for humans to get infected, which is poorly known due to underdiagnosis. Understanding the JEV cycle and developing tools to quantify the exposure of humans is essential to adapt and support control measures for this vaccine-preventable disease. Full article

(This article belongs to the Special Issue Japanese Encephalitis and Rift Valley Fever)

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19 pages, 3375 KB

Open AccessEditor’s ChoiceReview

Epidemiology of Usutu Virus: The European Scenario

by Tatjana Vilibic-Cavlek, Tamas Petrovic, Vladimir Savic, Ljubo Barbic, Irena Tabain, Vladimir Stevanovic, Ana Klobucar, Anna Mrzljak, Maja Ilic, Maja Bogdanic, Iva Benvin, Marija Santini, Krunoslav Capak, Federica Monaco, Eddy Listes and Giovanni Savini

Pathogens 2020, 9(9), 699; https://doi.org/10.3390/pathogens9090699 - 26 Aug 2020

Cited by 107 | Viewed by 10164

Abstract

Usutu virus (USUV) is an emerging arbovirus isolated in 1959 (Usutu River, Swaziland). Previously restricted to sub-Saharan Africa, the virus was introduced in Europe in 1996. While the USUV has received little attention in Africa, the virus emergence has prompted numerous studies with [...] Read more.

Usutu virus (USUV) is an emerging arbovirus isolated in 1959 (Usutu River, Swaziland). Previously restricted to sub-Saharan Africa, the virus was introduced in Europe in 1996. While the USUV has received little attention in Africa, the virus emergence has prompted numerous studies with robust epidemiological surveillance programs in Europe. The natural transmission cycle of USUV involves mosquitoes (vectors) and birds (amplifying hosts) with humans and other mammals considered incidental (“dead-end”) hosts. In Africa, the virus was isolated in mosquitoes, rodents and birds and serologically detected in horses and dogs. In Europe, USUV was detected in bats, whereas antibodies were found in different animal species (horses, dogs, squirrels, wild boar, deer and lizards). While bird mortalities were not reported in Africa, in Europe USUV was shown to be highly pathogenic for several bird species, especially blackbirds (Turdus merula) and great gray owls (Strix nebulosa). Furthermore, neurotropism of USUV for humans was reported for the first time in both immunocompromised and immunocompetent patients. Epizootics and genetic diversity of USUV in different bird species as well as detection of the virus in mosquitoes suggest repeated USUV introductions into Europe with endemization in some countries. The zoonotic potential of USUV has been reported in a growing number of human cases. Clinical cases of neuroinvasive disease and USUV fever, as well as seroconversion in blood donors were reported in Europe since 2009. While most USUV strains detected in humans, birds and mosquitoes belong to European USUV lineages, several reports indicate the presence of African lineages as well. Since spreading trends of USUV are likely to continue, continuous multidisciplinary interventions (“One Health” concept) should be conducted for monitoring and prevention of this emerging arboviral infection. Full article

(This article belongs to the Special Issue Usutu Virus Infection)

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18 pages, 9060 KB

Open AccessEditor’s ChoiceArticle

Atypical Non-H₂S-Producing Monophasic Salmonella Typhimurium ST3478 Strains from Chicken Meat at Processing Stage Are Adapted to Diverse Stresses

by Joana Mourão, Andreia Rebelo, Sofia Ribeiro, Luísa Peixe, Carla Novais and Patrícia Antunes

Pathogens 2020, 9(9), 701; https://doi.org/10.3390/pathogens9090701 - 26 Aug 2020

Cited by 21 | Viewed by 7046

Abstract

Poultry products are still an important cause of Salmonella infections worldwide, with an increasingly reported expansion of less-frequent serotypes or atypical strains that are frequently multidrug-resistant. Nevertheless, the ability of Salmonella to survive antimicrobials promoted in the context of antibiotic reducing/replacing and farming [...] Read more.

Poultry products are still an important cause of Salmonella infections worldwide, with an increasingly reported expansion of less-frequent serotypes or atypical strains that are frequently multidrug-resistant. Nevertheless, the ability of Salmonella to survive antimicrobials promoted in the context of antibiotic reducing/replacing and farming rethinking (e.g., organic acids and copper in feed/biocides) has been scarcely explored. We investigated Salmonella occurrence (conventional and molecular assays) among chicken meat at the processing stage (n = 53 batches/29 farms) and characterized their tolerance to diverse stress factors (antibiotics, copper, acid pH, and peracetic acid). Whole-genome sequencing was used to assess adaptive features and to perform comparative analysis. We found a low Salmonella occurrence (4%) and identified S. Enteritidis/ST11 plus atypical non-H₂S-producing S. 1,4,[5],12:i:-/ST3478. The ST3478 presented the ability to grow under diverse stresses (antibiotics, copper, and acid-pH). Comparative genomics among ST3478 isolates showed similar antibiotic/metal resistance gene repertoires and identical nonsense phsA thiosulfate reductase mutations (related to H₂S-negative phenotype), besides their close phylogenetic relationship by cgMLST and SNPs. This study alerts for the ongoing national and international spread of an emerging monophasic Salmonella Typhimurium clonal lineage with an enlarged ability to survive to antimicrobials/biocides commonly used in poultry production, being unnoticed by conventional Salmonella detection approaches due to an atypical non-H₂S-producing phenotype. Full article

(This article belongs to the Special Issue Advances on Control of Foodborne Pathogens: From Conventional to Cutting-Edge Approaches)

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9 pages, 2189 KB

Open AccessEditor’s ChoiceArticle

Detection of Feline Coronavirus in Feline Effusions by Immunofluorescence Staining and Reverse Transcription Polymerase Chain Reaction

by Yi-Chen Luo, I-Li Liu, Yu-Tan Chen and Hui-Wen Chen

Pathogens 2020, 9(9), 698; https://doi.org/10.3390/pathogens9090698 - 25 Aug 2020

Cited by 8 | Viewed by 5276

Abstract

Feline coronavirus (FCoV), the pathogen for feline infectious peritonitis, is a lethal infectious agent that can cause effusions in the pleural and abdominal cavities in domestic cats. To study the epidemiology of FCoV in Taiwan, 81 FIP-suspected sick cats with effusive specimens were [...] Read more.

Feline coronavirus (FCoV), the pathogen for feline infectious peritonitis, is a lethal infectious agent that can cause effusions in the pleural and abdominal cavities in domestic cats. To study the epidemiology of FCoV in Taiwan, 81 FIP-suspected sick cats with effusive specimens were recruited to test for FCoV infection using immunofluorescence staining and reverse transcription-polymerase chain reaction as detection methods, and viral RNAs were recovered from the specimens to conduct genotyping and phylogenetic analysis based on the spike (S) protein gene. The results revealed that a total of 47 (47/81, 58%) of the sick cats were positive for FCoV in the effusion samples, of which 39 were successfully sequenced and comprised of 21 type I strains, 9 type II strains, and 9 co-infections. The signalment analysis of these sick cats revealed that only the sex of cats showed a significant association (odds ratio = 2.74, 95% confidence interval = 1.06–7.07, p = 0.03) with the infection of FCoV, while age and breed showed no association. FCoV-positive cats demonstrated a significantly lower albumin to globulin ratio than negative individuals (p = 0.0004). The partial S gene-based phylogenetic analysis revealed that the type I strains demonstrated genetic diversity forming several clades, while the type II strains were more conserved. This study demonstrates the latest epidemiological status of FCoV infection in the northern part of Taiwan among sick cats and presents comparisons of Taiwan and other countries. Full article

(This article belongs to the Special Issue Feline Infectious Peritonitis)

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13 pages, 3881 KB

Open AccessEditor’s ChoiceArticle

Giardia duodenalis Induces Apoptosis in Intestinal Epithelial Cells via Reactive Oxygen Species-Mediated Mitochondrial Pathway In Vitro

by Lin Liu, Rui Fang, Ziyan Wei, Jingxue Wu, Xiaoyun Li and Wei Li

Pathogens 2020, 9(9), 693; https://doi.org/10.3390/pathogens9090693 - 23 Aug 2020

Cited by 26 | Viewed by 4880

Abstract

The intestinal protozoan parasite, Giardia duodenalis, infects a large number of people in the world annually. Giardia infection has been considered a negative effect on intestinal epithelial cell growth, while the underlying mechanisms remain to be explored. Here we evaluated reactive oxygen [...] Read more.

The intestinal protozoan parasite, Giardia duodenalis, infects a large number of people in the world annually. Giardia infection has been considered a negative effect on intestinal epithelial cell growth, while the underlying mechanisms remain to be explored. Here we evaluated reactive oxygen species (ROS) production and apoptotic events in Giardia trophozoites-stimulated Caco-2 cells via fluorescence microscopy, transmission electron microscopy, flow cytometry, western blot, and cell counting kit-8 analyses. The results showed that Giardia trophozoite treatment could induce lactate dehydrogenase release and Caco-2 cell apoptosis. The ROS levels were increased post treatment. The observed typical characteristics of mitochondria damage include significant swelling and degeneration of matrix and cristae. After trophozoite treatment, the level of Bax protein expression was increased, while Bcl-2 protein decreased. Trophozoite stimulation also led to reduction of mitochondrial membrane potential and release of cytochrome c from the mitochondria to the cytoplasm, and this process was accompanied by activation of caspase-9 and caspase-3 and poly (ADP-ribose) polymerase 1 cleavage. Pretreatment with N-acetyl-L-cysteine, a ROS inhibitor, reversed G. duodenalis-induced Caco-2 cell apoptosis. Taken together, we indicated that G. duodenalis could induce Caco-2 cell apoptosis through a ROS- and mitochondria-mediated caspase-dependent pathway. This study furthers our understanding of the cellular mechanism of the interaction between Giardia trophozoites and host cells. Full article

(This article belongs to the Section Human Pathogens)

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17 pages, 2256 KB

Open AccessEditor’s ChoiceArticle

Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission

by Jakob Thannesberger, Nicolas Rascovan, Anna Eisenmann, Ingeborg Klymiuk, Carina Zittra, Hans-Peter Fuehrer, Thea Scantlebury-Manning, Marquita Gittens-St.Hilaire, Shane Austin, Robert Clive Landis and Christoph Steininger

Pathogens 2020, 9(9), 686; https://doi.org/10.3390/pathogens9090686 - 21 Aug 2020

Cited by 13 | Viewed by 5226

Abstract

Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and [...] Read more.

Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and Culex pipiens complex), from different geographic locations and environments (central Europe and the Caribbean) for highly sensitive next-generation sequencing-based virome characterization. We found a rich virus community associated with a great diversity of host species. Among those, we detected a large diversity of novel virus sequences that we could predominately assign to circular Rep-encoding single-stranded (CRESS) DNA viruses, including the full-length genome of a yet undescribed Gemykrogvirus species. Moreover, we report for the first time the detection of a potentially zoonotic CRESS-DNA virus (Cyclovirus VN) in mosquito vectors. This study expands the knowledge on virus diversity in medically important mosquito vectors, especially for CRESS-DNA viruses that have previously been shown to easily recombine and jump the species barrier. Full article

(This article belongs to the Special Issue Translational Research for Zoonotic Parasites: New Findings toward Improved Diagnostics, Therapy and Prevention)

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9 pages, 629 KB

Open AccessEditor’s ChoiceReview

Buffalopox Virus: An Emerging Virus in Livestock and Humans

by Kamal H. Eltom, Abdallah M. Samy, Ahmed Abd El Wahed and Claus-Peter Czerny

Pathogens 2020, 9(9), 676; https://doi.org/10.3390/pathogens9090676 - 20 Aug 2020

Cited by 26 | Viewed by 6800

Abstract

Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease [...] Read more.

Buffalopox virus (BPXV) is the cause of buffalopox, which was recognized by the FAO/WHO Joint Expert Committee on Zoonosis as an important zoonotic disease. Buffalopox was first described in India, later in other countries, and has become an emerging contagious viral zoonotic disease infecting milkers with high morbidity among affected domestic buffalo and cattle. BPXV is a member of the genus Orthopoxvirus and a close variant of the vaccinia virus (VACV). Recent genome data show that BPXV shares a most recent common ancestor of VACV Lister strain, which had been used for inoculating buffalo calves to produce a Smallpox vaccine. Over time, VACV evolved into BPXV by establishing itself in buffaloes to be increasingly pathogenic to this host and to make infections in cattle and humans. Together with the current pandemic of SARS-COV2/COVID 19, BPXV infections illustrate how vulnerable the human population is to the emergence and re-emergence of viral pathogens from unsuspected sources. In view that majority of the world population are not vaccinated against smallpox and are most vulnerable in the event of its re-emergence, reviewing and understanding the biology of vaccinia-like viruses are necessary for developing a new generation of safer smallpox vaccines in the smallpox-free world. Full article

(This article belongs to the Section Animal Pathogens)

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15 pages, 1034 KB

Open AccessEditor’s ChoiceArticle

Molecular Epidemiology Reveals Low Genetic Diversity among Cryptococcus neoformans Isolates from People Living with HIV in Lima, Peru, during the Pre-HAART Era

by Nathalie van de Wiele, Edgar Neyra, Carolina Firacative, Felix Gilgado, Carolina Serena, Beatriz Bustamante and Wieland Meyer

Pathogens 2020, 9(8), 665; https://doi.org/10.3390/pathogens9080665 - 18 Aug 2020

Cited by 7 | Viewed by 3933

Abstract

Cryptococcosis, a mycosis presenting mostly as meningoencephalitis, affecting predominantly human immunodeficiency virus (HIV)-infected people, is mainly caused by Cryptococcus neoformans. The genetic variation of 48 C. neoformans isolates, recovered from 20 HIV-positive people in Lima, Peru, during the pre-highly active antiretroviral therapy [...] Read more.

Cryptococcosis, a mycosis presenting mostly as meningoencephalitis, affecting predominantly human immunodeficiency virus (HIV)-infected people, is mainly caused by Cryptococcus neoformans. The genetic variation of 48 C. neoformans isolates, recovered from 20 HIV-positive people in Lima, Peru, during the pre-highly active antiretroviral therapy (HAART) era, was studied retrospectively. The mating type of the isolates was determined by PCR, and the serotype by agglutination and CAP59-restriction fragment length polymorphism (RFLP). Genetic diversity was assessed by URA5-RFLP, PCR-fingerprinting, amplified fragment length polymorphism (AFLP), and multilocus sequence typing (MLST). All isolates were mating type alpha, with 39 molecular type VNI, seven VNII, corresponding to C. neoformans var. grubii serotype A, and two VNIII AD hybrids. Overall, the cryptococcal population from HIV-positive people in Lima shows a low degree of genetic diversity. In most patients with persistent cryptococcal infection, the same genotype was recovered during the follow-up. In four patients with relapse and one with therapy failure, different genotypes were found in isolates from the re-infection and from the isolate recovered at the end of the treatment. In one patient, two genotypes were found in the first cryptococcosis episode. This study contributes data from Peru to the ongoing worldwide population genetic analysis of Cryptococcus. Full article

(This article belongs to the Section Human Pathogens)

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14 pages, 933 KB

Open AccessEditor’s ChoiceArticle

Cystatin C and α-1-Microglobulin Predict Severe Acute Kidney Injury in Patients with Hemorrhagic Fever with Renal Syndrome

by Magnus Hansson, Rasmus Gustafsson, Chloé Jacquet, Nedia Chebaane, Simon Satchell, Therese Thunberg, Clas Ahlm and Anne-Marie Fors Connolly

Pathogens 2020, 9(8), 666; https://doi.org/10.3390/pathogens9080666 - 18 Aug 2020

Cited by 24 | Viewed by 4973

Abstract

Puumala orthohantavirus causes hemorrhagic fever with renal syndrome (HFRS) characterized by acute kidney injury (AKI), an abrupt decrease in renal function. Creatinine is routinely used to detect and quantify AKI; however, early AKI may not be reflected in increased creatinine levels. Therefore, kidney [...] Read more.

Puumala orthohantavirus causes hemorrhagic fever with renal syndrome (HFRS) characterized by acute kidney injury (AKI), an abrupt decrease in renal function. Creatinine is routinely used to detect and quantify AKI; however, early AKI may not be reflected in increased creatinine levels. Therefore, kidney injury markers that can predict AKI are needed. The potential of the kidney injury markers urea, cystatin C, α1-microglobulin (A1M) and neutrophil gelatinase-associated lipocalin (NGAL) to detect early AKI during HFRS was studied by quantifying the levels of these markers in consecutively obtained plasma (P) and urine samples (U) for 44 HFRS patients. P-cystatin C and U-A1M levels were significantly increased during early HFRS compared to follow-up. In a receiver operating characteristic (ROC) curve analysis, P-cystatin C, U-A1M and P-urea predicted severe AKI with area under the curve 0.72, 0.73 and 0.71, respectively, whereas the traditional kidney injury biomarkers creatinine and U-albumin did not predict AKI. Nearly half of the HFRS patients (41%) fulfilled the criteria for shrunken pore syndrome, which was associated with the level of inflammation as measured by P-CRP. P-cystatin C and U-A1M are more sensitive and earlier markers compared to creatinine in predicting kidney injury during HFRS. Full article

(This article belongs to the Special Issue Hemorrhagic Fever Viruses)

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21 pages, 409 KB

Open AccessEditor’s ChoiceReview

Water as a Source of Antimicrobial Resistance and Healthcare-Associated Infections

by Claire Hayward, Kirstin E. Ross, Melissa H. Brown and Harriet Whiley

Pathogens 2020, 9(8), 667; https://doi.org/10.3390/pathogens9080667 - 18 Aug 2020

Cited by 50 | Viewed by 7979

Abstract

Healthcare-associated infections (HAIs) are one of the most common patient complications, affecting 7% of patients in developed countries each year. The rise of antimicrobial resistant (AMR) bacteria has been identified as one of the biggest global health challenges, resulting in an estimated 23,000 [...] Read more.

Healthcare-associated infections (HAIs) are one of the most common patient complications, affecting 7% of patients in developed countries each year. The rise of antimicrobial resistant (AMR) bacteria has been identified as one of the biggest global health challenges, resulting in an estimated 23,000 deaths in the US annually. Environmental reservoirs for AMR bacteria such as bed rails, light switches and doorknobs have been identified in the past and addressed with infection prevention guidelines. However, water and water-related devices are often overlooked as potential sources of HAI outbreaks. This systematic review examines the role of water and water-related devices in the transmission of AMR bacteria responsible for HAIs, discussing common waterborne devices, pathogens, and surveillance strategies. AMR strains of previously described waterborne pathogens including Pseudomonas aeruginosa, Mycobacterium spp., and Legionella spp. were commonly isolated. However, methicillin-resistant Staphylococcus aureus and carbapenem-resistant Enterobacteriaceae that are not typically associated with water were also isolated. Biofilms were identified as a hot spot for the dissemination of genes responsible for survival functions. A limitation identified was a lack of consistency between environmental screening scope, isolation methodology, and antimicrobial resistance characterization. Broad universal environmental surveillance guidelines must be developed and adopted to monitor AMR pathogens, allowing prediction of future threats before waterborne infection outbreaks occur. Full article

(This article belongs to the Section Waterborne/Foodborne/Airborne Pathogens)

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16 pages, 2594 KB

Open AccessEditor’s ChoiceArticle

Continuous Reassortment of Clade 2.3.4.4 H5N6 Highly Pathogenetic Avian Influenza Viruses Demonstrating High Risk to Public Health

by Huanan Li, Qian Li, Bo Li, Yang Guo, Jinchao Xing, Qiang Xu, Lele Liu, Jiahao Zhang, Wenbao Qi, Weixin Jia and Ming Liao

Pathogens 2020, 9(8), 670; https://doi.org/10.3390/pathogens9080670 - 18 Aug 2020

Cited by 24 | Viewed by 4456

Abstract

Since it firstly emerged in China in 2013, clade 2.3.4.4 H5N6 highly pathogenic avian influenza viruses (HPAIVs) has rapidly replaced predominant H5N1 to become the dominant H5 subtype in China, especially in ducks. Not only endemic in China, it also crossed the geographical [...] Read more.

Since it firstly emerged in China in 2013, clade 2.3.4.4 H5N6 highly pathogenic avian influenza viruses (HPAIVs) has rapidly replaced predominant H5N1 to become the dominant H5 subtype in China, especially in ducks. Not only endemic in China, it also crossed the geographical barrier and emerged in South Korea, Japan, and Europe. Here, we analyzed the genetic properties of the clade 2.3.4.4 H5N6 HPAIVs with full genome sequences available online together with our own isolates. Phylogenetic analysis showed that clade 2.3.4.4 H5N6 HPAIVs continuously reassorted with local H5, H6, and H7N9/H9N2. Species analysis reveals that aquatic poultry and migratory birds became the dominant hosts of H5N6. Adaption to aquatic poultry might help clade 2.3.4.4 H5N6 better adapt to migratory birds, thus enabling it to become endemic in China. Besides, migratory birds might help clade 2.3.4.4 H5N6 transmit all over the world. Clade 2.3.4.4 H5N6 HPAIVs also showed a preference for α2,6-SA receptors when compared to other avian origin influenza viruses. Experiments in vitro and in vivo revealed that clade 2.3.4.4 H5N6 HPAIVs exhibited high replication efficiency in both avian and mammal cells, and it also showed high pathogenicity in both mice and chickens, demonstrating high risk to public health. Considering all the factors together, adaption to aquatic poultry and migratory birds helps clade 2.3.4.4 H5N6 overcome the geographical isolation, and it has potential to be the next influenza pandemic in the world, making it worthy of our attention. Full article

(This article belongs to the Special Issue Current Research on Infectious Diseases of Domestic Animals in a One Health Perspective)

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22 pages, 1268 KB

Open AccessEditor’s ChoiceArticle

Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

by Wairimu M. Maringa, Peter N. Mwangi, Julia Simwaka, Evans M. Mpabalwani, Jason M. Mwenda, Ina Peenze, Mathew D. Esona, M. Jeffrey Mphahlele, Mapaseka L. Seheri and Martin M. Nyaga

Pathogens 2020, 9(8), 663; https://doi.org/10.3390/pathogens9080663 - 17 Aug 2020

Cited by 18 | Viewed by 5332

Abstract

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 [...] Read more.

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans. Full article

(This article belongs to the Special Issue Rotaviruses and Rotavirus Vaccines)

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17 pages, 653 KB

Open AccessEditor’s ChoiceReview

Recent Advances in the Diagnosis of Classical Swine Fever and Future Perspectives

by Lihua Wang, Rachel Madera, Yuzhen Li, David Scott McVey, Barbara S. Drolet and Jishu Shi

Pathogens 2020, 9(8), 658; https://doi.org/10.3390/pathogens9080658 - 15 Aug 2020

Cited by 28 | Viewed by 7657

Abstract

Classical swine fever (CSF) is a highly contagious viral disease of pigs, including wild boar. It is regarded as one of the major problems in the pig industry as it is still endemic in many regions of the world and has the potential [...] Read more.

Classical swine fever (CSF) is a highly contagious viral disease of pigs, including wild boar. It is regarded as one of the major problems in the pig industry as it is still endemic in many regions of the world and has the potential to cause devastating epidemics, particularly in countries free of the disease. Rapid and reliable diagnosis is of utmost importance in the control of CSF. Since clinical presentations of CSF are highly variable and may be confused with other viral diseases in pigs, laboratory diagnosis is indispensable for an unambiguous diagnosis. On an international level, well-established diagnostic tests of CSF such as virus isolation, fluorescent antibody test (FAT), antigen capture antibody enzyme-linked immunosorbent assay (ELISA), reverse-transcription polymerase chain reaction (RT-PCR), virus neutralization test (VNT), and antibody ELISA have been described in detail in the OIE Terrestrial Manual. However, improved CSF diagnostic methods or alternatives based on modern technologies have been developed in recent years. This review thus presents recent advances in the diagnosis of CSF and future perspectives. Full article

(This article belongs to the Special Issue Classical Swine Fever)

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20 pages, 1719 KB

Open AccessEditor’s ChoiceArticle

BLIGHTSIM: A New Potato Late Blight Model Simulating the Response of Phytophthora infestans to Diurnal Temperature and Humidity Fluctuations in Relation to Climate Change

by Hossein A. Narouei-Khandan, Shankar K. Shakya, Karen A. Garrett, Erica M. Goss, Nicholas S. Dufault, Jorge L. Andrade-Piedra, Senthold Asseng, Daniel Wallach and Ariena H.C van Bruggen

Pathogens 2020, 9(8), 659; https://doi.org/10.3390/pathogens9080659 - 15 Aug 2020

Cited by 25 | Viewed by 7530

Abstract

Temperature response curves under diurnal oscillating temperatures differ from those under constant conditions for all stages of the Phytophthora infestans infection cycle on potatoes. We developed a mechanistic model (BLIGHTSIM) with an hourly time step to simulate late blight under fluctuating environmental conditions [...] Read more.

Temperature response curves under diurnal oscillating temperatures differ from those under constant conditions for all stages of the Phytophthora infestans infection cycle on potatoes. We developed a mechanistic model (BLIGHTSIM) with an hourly time step to simulate late blight under fluctuating environmental conditions and predict late blight epidemics in potato fields. BLIGHTSIM is a modified susceptible (S), latent (L), infectious (I) and removed (R) compartmental model with hourly temperature and relative humidity as driving variables. The model was calibrated with growth chamber data covering one infection cycle and validated with field data from Ecuador. The model provided a good fit to all data sets evaluated. There was a significant interaction between average temperature and amplitude in their effects on the area under the disease progress curve (AUDPC) as predicted from growth chamber data on a single infection cycle. BLIGHTSIM can be incorporated in a potato growth model to study effects of diurnal temperature range on late blight impact under climate change scenarios. Full article

(This article belongs to the Section Plant Pathogens)

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21 pages, 3464 KB

Open AccessEditor’s ChoiceArticle

Analyses of the Root-Knot Nematode (Meloidogyne graminicola) Transcriptome during Host Infection Highlight Specific Gene Expression Profiling in Resistant Rice Plants

by Anne-Sophie Petitot, Alexis Dereeper, Corinne Da Silva, Julie Guy and Diana Fernandez

Pathogens 2020, 9(8), 644; https://doi.org/10.3390/pathogens9080644 - 8 Aug 2020

Cited by 21 | Viewed by 5528

Abstract

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection [...] Read more.

The plant-parasitic nematode Meloidogyne graminicola causes considerable damages to rice (Oryza sativa) culture. Resistance to M. graminicola in the related species Oryza glaberrima reduces root penetration by juveniles and stops further nematode development. M. graminicola genes expressed during O. sativa infection were previously characterized but no information is available about the molecular dialogue established with a resistant plant. We compared the M. graminicola transcriptomes of stage-two juveniles (J2s) before and during infection of susceptible or resistant rice. Among 36,121 M. graminicola genes surveyed, 367 were differentially expressed during infection of resistant or susceptible plants. Genes encoding cell wall-degrading enzymes, peptidases and neuropeptides were expressed for a longer time in resistant plants compared to susceptible plants. Conversely, genes related to nematode development were not activated in the resistant host. The majority of M. graminicola effector genes had similar expression patterns, whatever the host genotype. However, two venom allergen-like protein (VAP)-encoding genes were specifically induced in resistant plants and Mg-VAP1 silencing in J2s reduced their ability to colonize roots. This study highlighted that M. graminicola adapts its gene expression to the host susceptibility. Further investigation is required to assess the role of Mg-VAPs in the rice–nematode interaction. Full article

(This article belongs to the Section Plant Pathogens)

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15 pages, 1062 KB

Open AccessEditor’s ChoiceArticle

Field Experience of Antibody Testing against Mycoplasma bovis in Adult Cows in Commercial Danish Dairy Cattle Herds

by Mette Bisgaard Petersen, Lars Pedersen, Lone Møller Pedersen and Liza Rosenbaum Nielsen

Pathogens 2020, 9(8), 637; https://doi.org/10.3390/pathogens9080637 - 6 Aug 2020

Cited by 14 | Viewed by 4525

Abstract

Mycoplasma bovis in cattle is difficult to diagnose. Recently, the ID screen^® mycoplasma bovis indirect ELISA (ID screen) was commercially released by IDVet. The objectives of this study were to: (1) gain and share experience of using the ID screen in adult [...] Read more.

Mycoplasma bovis in cattle is difficult to diagnose. Recently, the ID screen^® mycoplasma bovis indirect ELISA (ID screen) was commercially released by IDVet. The objectives of this study were to: (1) gain and share experience of using the ID screen in adult dairy cows under field conditions; (2) determine the correlation between antibody levels in milk and serum and (3) compare the ID screen results with those of the Bio K 302 (BioX 302) ELISA from BioX Diagnostics. Paired serum and milk samples were collected from 270 cows from 12 Danish dairy herds with three categories of M. bovis disease history. The ID screen tested nearly all cows positive in all, but the three non-infected herds, while the BioX 302 tested very few cows positive. The ID screen is therefore a much more sensitive test than the BioX 302. However, cows in five exposed herds without signs of ongoing infection and two herds with no history of M. bovis infection also tested ID screen positive. Therefore, the performance and interpretation of the test must be investigated under field conditions in best practice test evaluation setups. A concordance correlation coefficient of 0.66 (95% CI: 0.59–0.72) between the ID screen serum and milk results indicates that milk samples can replace serum samples for the ID screen diagnosis of M. bovis in adult cows. Full article

(This article belongs to the Special Issue Mycoplasma bovis Infections: Occurrence, Pathogenesis, Diagnosis and Control, Including Prevention and Therapy)

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19 pages, 634 KB

Open AccessEditor’s ChoiceReview

Factoring in the Complexity of the Cystic Fibrosis Lung to Understand Aspergillus fumigatus and Pseudomonas aeruginosa Interactions

by Emily Beswick, Jorge Amich and Sara Gago

Pathogens 2020, 9(8), 639; https://doi.org/10.3390/pathogens9080639 - 6 Aug 2020

Cited by 17 | Viewed by 6950

Abstract

Pseudomonas aeruginosa has long been established as the most prevalent respiratory pathogen in Cystic Fibrosis (CF) patients, with opportunistic infection causing profound morbidity and mortality. Recently, Aspergillus fumigatus has also been recognised as a key contributor to CF lung deterioration, being consistently associated [...] Read more.

Pseudomonas aeruginosa has long been established as the most prevalent respiratory pathogen in Cystic Fibrosis (CF) patients, with opportunistic infection causing profound morbidity and mortality. Recently, Aspergillus fumigatus has also been recognised as a key contributor to CF lung deterioration, being consistently associated with decreased lung function and worsened prognosis in these patients. As clinical evidence for the common occurrence of combined infection with these two pathogens increases, research into the mechanism and consequences of their interaction is becoming more relevant. Clinical evidence suggests a synergistic effect of combined infection, which translates into a poorer prognosis for the patients. In vitro results from the laboratory have identified a variety of possible synergistic and antagonistic interactions between A. fumigatus and P. aeruginosa. Here, we present a comprehensive overview of the complex environment of the CF lung and discuss how it needs to be considered to determine the exact molecular interactions that A. fumigatus and P. aeruginosa undergo during combined infection and their effects on the host. Full article

(This article belongs to the Special Issue Aspergillosis)

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21 pages, 1187 KB

Open AccessEditor’s ChoiceReview

Mycoplasma bovis Infections—Occurrence, Diagnosis and Control

by Katarzyna Dudek, Robin A. J. Nicholas, Ewelina Szacawa and Dariusz Bednarek

Pathogens 2020, 9(8), 640; https://doi.org/10.3390/pathogens9080640 - 6 Aug 2020

Cited by 82 | Viewed by 13002

Abstract

Mycoplasma bovis is a cause of bronchopneumonia, mastitis and arthritis but may also affect other main organs in cattle such us the eye, ear or brain. Despite its non-zoonotic character, M. bovis infections are responsible for substantial economic health and welfare problems worldwide. [...] Read more.

Mycoplasma bovis is a cause of bronchopneumonia, mastitis and arthritis but may also affect other main organs in cattle such us the eye, ear or brain. Despite its non-zoonotic character, M. bovis infections are responsible for substantial economic health and welfare problems worldwide. M. bovis has spread worldwide, including to countries for a long time considered free of the pathogen. Control of M. bovis infections is hampered by a lack of effective vaccines and treatments due to increasing trends in antimicrobial resistance. This review summarizes the latest data on the epizootic situation of M. bovis infections and new sources/routes of transmission of the infection, and discusses the progress in diagnostics. The review includes various recommendations and suggestions which could be applied to infection control programs. Full article

(This article belongs to the Special Issue Mycoplasma bovis Infections: Occurrence, Pathogenesis, Diagnosis and Control, Including Prevention and Therapy)

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24 pages, 432 KB

Open AccessEditor’s ChoiceReview

Preclinical Models of Nontuberculous Mycobacteria Infection for Early Drug Discovery and Vaccine Research

by Elisa Rampacci, Valentina Stefanetti, Fabrizio Passamonti and Marcela Henao-Tamayo

Pathogens 2020, 9(8), 641; https://doi.org/10.3390/pathogens9080641 - 6 Aug 2020

Cited by 18 | Viewed by 5874

Abstract

Nontuberculous mycobacteria (NTM) represent an increasingly prevalent etiology of soft tissue infections in animals and humans. NTM are widely distributed in the environment and while, for the most part, they behave as saprophytic organisms, in certain situations, they can be pathogenic, so much [...] Read more.

Nontuberculous mycobacteria (NTM) represent an increasingly prevalent etiology of soft tissue infections in animals and humans. NTM are widely distributed in the environment and while, for the most part, they behave as saprophytic organisms, in certain situations, they can be pathogenic, so much so that the incidence of NTM infections has surpassed that of Mycobacterium tuberculosis in developed countries. As a result, a growing body of the literature has focused attention on the critical role that drug susceptibility tests and infection models play in the design of appropriate therapeutic strategies against NTM diseases. This paper is an overview of the in vitro and in vivo models of NTM infection employed in the preclinical phase for early drug discovery and vaccine development. It summarizes alternative methods, not fully explored, for the characterization of anti-mycobacterial compounds. Full article

(This article belongs to the Section Vaccines and Therapeutic Developments)

23 pages, 10380 KB

Open AccessEditor’s ChoiceReview

Comparative Pathology of Pseudorabies in Different Naturally and Experimentally Infected Species—A Review

by Julia Sehl and Jens Peter Teifke

Pathogens 2020, 9(8), 633; https://doi.org/10.3390/pathogens9080633 - 4 Aug 2020

Cited by 75 | Viewed by 14327

Abstract

The pseudorabies virus (PRV) is an alphaherpesvirus and the causative agent of Aujeszky’s disease (AD). PRV infects a wide range of animal species including swine as the natural host as well as ruminants, carnivores, rodents and lagomorphs. In these species, except for the [...] Read more.

The pseudorabies virus (PRV) is an alphaherpesvirus and the causative agent of Aujeszky’s disease (AD). PRV infects a wide range of animal species including swine as the natural host as well as ruminants, carnivores, rodents and lagomorphs. In these species, except for the pig, PRV infection causes acute, severe disease, characterized by insatiable itching, and is always lethal. Horses, chickens and non-human primates have been shown to be largely resistant to PRV infection, while disease in humans is still controversial. PRV is a pantropic virus, which preferably invades neural tissue, but also infects epithelia of various organs, whereupon multisystemic lesions may result. Although AD is mainly associated with severe pruritus, also known as “mad itch”, there are notable differences regarding infection route, clinical signs, viral distribution and lesion patterns in different animal species. In this comprehensive review, we will present clinico-pathologic findings from different species, which have been either shown to be susceptible to PRV infection or have been tested experimentally. Full article

(This article belongs to the Special Issue Pseudorabies Virus Infections)

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14 pages, 1723 KB

Open AccessEditor’s ChoiceArticle

Combining Computed Tomography and Histology Leads to an Evolutionary Concept of Hepatic Alveolar Echinococcosis

by Johannes Grimm, Annika Beck, Juliane Nell, Julian Schmidberger, Andreas Hillenbrand, Ambros J. Beer, Balázs Dezsényi, Rong Shi, Meinrad Beer, Peter Kern, Doris Henne-Bruns, Wolfgang Kratzer, Peter Moller, Thomas FE Barth, Beate Gruener and Tilmann Graeter

Pathogens 2020, 9(8), 634; https://doi.org/10.3390/pathogens9080634 - 4 Aug 2020

Cited by 15 | Viewed by 4182

Abstract

Alveolar echinococcosis (AE) is caused by the intermediate stage of Echinococcus multilocularis. We aimed to correlate computed tomography (CT) data with histology to identify distinct characteristics for different lesion types. We classified 45 samples into five types with the Echinococcus multilocularis Ulm [...] Read more.

Alveolar echinococcosis (AE) is caused by the intermediate stage of Echinococcus multilocularis. We aimed to correlate computed tomography (CT) data with histology to identify distinct characteristics for different lesion types. We classified 45 samples into five types with the Echinococcus multilocularis Ulm Classification for Computed Tomography (EMUC-CT). The various CT lesions exhibited significantly different histological parameters, which led us to propose a progression model. The initial lesion fit the CT type IV classification, which comprises a single necrotic area with the central located laminated layer, a larger distance between laminated layer and border zone, a small fibrotic peripheral zone, and few small particles of Echinococcus multilocularis (spems). Lesions could progress through CT types I, II, and III, characterized by shorter distances between laminated layer and border zone, more spems inside and surrounding the lesion, and a pronounced fibrotic rim (mostly in type III). Alternatively, lesions could converge to a highly calcified, regressive state (type V). Our results suggest that the CT types mark sequential stages of the infection, which progress over time. These distinct histological patterns advance the understanding of interactions between AE and human host; moreover, they might become prognostically and therapeutically relevant. Full article

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12 pages, 2000 KB

Open AccessEditor’s ChoiceArticle

The Clinical Infection with Pigeon Circovirus (PiCV) Leads to Lymphocyte B Apoptosis But Has No Effect on Lymphocyte T Subpopulation

by Tomasz Stenzel, Daria Dziewulska, Bartłomiej Tykałowski and Andrzej Koncicki

Pathogens 2020, 9(8), 632; https://doi.org/10.3390/pathogens9080632 - 3 Aug 2020

Cited by 21 | Viewed by 3957

Abstract

The pathology of pigeon circovirus (PiCV) is still unknown, but it is regarded as an immunosuppressant. This study aimed to find a correlation between PiCV natural infection and immunosuppression. The study was conducted with 56 pigeons divided into the following groups: PiCV-positive but [...] Read more.

The pathology of pigeon circovirus (PiCV) is still unknown, but it is regarded as an immunosuppressant. This study aimed to find a correlation between PiCV natural infection and immunosuppression. The study was conducted with 56 pigeons divided into the following groups: PiCV-positive but showing (group S) or not (group I) non-specific clinical symptoms and asymptomatic pigeons negative for PiCV (group H). The percentage and apoptosis of T CD3⁺ and B IgM⁺ splenocytes; the expression of CD4, CD8, and IFN-γ genes in splenic mononuclear cells; the number of PiCV viral loads in the bursa of Fabricius; and the level of anti-PiCV antibodies were analyzed. The results showed that the percentage of B IgM⁺ cells was almost two-fold lower in group S than in group H, and that ca. 20% of the lymphocytes were apoptotic. No increased apoptosis was detected in TCD3⁺ subpopulation. The PiCV viral loads were approximately one thousand and ten thousand times higher in group S than in groups I and H, respectively. Our results indicate a possible correlation between the number of PiCV viral loads and severity of PiCV infection and confirm that PiCV infection leads to the suppression of humoral immunity by inducing B lymphocyte apoptosis. Full article

(This article belongs to the Section Animal Pathogens)

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15 pages, 610 KB

Open AccessEditor’s ChoiceArticle

A Sensitive, One-Way Sequential Sieving Method to Isolate Helminths’ Eggs and Protozoal Oocysts from Lettuce for Genetic Identification

by Annina R. Guggisberg, Cristian A. Alvarez Rojas, Philipp A. Kronenberg, Nadia Miranda and Peter Deplazes

Pathogens 2020, 9(8), 624; https://doi.org/10.3390/pathogens9080624 - 31 Jul 2020

Cited by 23 | Viewed by 4894

Abstract

Different helminths and protozoa are transmitted to humans by oral uptake of environmentally resistant parasite stages after hand-to-mouth contact or by contaminated food and water. The aim of this study was to develop and validate a method for the simultaneous detection of parasite [...] Read more.

Different helminths and protozoa are transmitted to humans by oral uptake of environmentally resistant parasite stages after hand-to-mouth contact or by contaminated food and water. The aim of this study was to develop and validate a method for the simultaneous detection of parasite stages from fresh produce (lettuce) by a one-way isolation test kit followed by genetic identification (PCR, sequencing). Three sentinel zoonotic agents (eggs of Toxocara canis, Echinococcus multilocularis and oocysts of Toxoplasma gondii) were used to investigate the practicability and sensitivity of the method. The detection limits (100% positive results) in the recovery experiments were four Toxocara eggs, two E. multilocularis eggs and 18 T. gondii oocysts (in 4/5 replicates). In a field study, helminth DNA was detected in 14 of 157 lettuce samples including Hydatigera taeniaeformis (Syn. Taenia taeniaeformis) (four samples), T. polyacantha (three), T. martis (one), E. multilocularis (two) and Toxocara cati (four). Toxoplasma gondii was detected in six of 100 samples. In vivo testing in mice resulted in metacestode growth in all animals injected with 40–60 E. multilocularis eggs, while infection rates were 20–40% with 2–20 eggs. The developed diagnostic strategy is highly sensitive for the isolation and genetic characterisation of a broad range of parasite stages from lettuce, whereas the sensitivity of the viability tests needs further improvement. Full article

(This article belongs to the Special Issue Tackling Foodborne Parasitic Infections)

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22 pages, 1392 KB

Open AccessEditor’s ChoiceReview

Modulation of Host Lipid Pathways by Pathogenic Intracellular Bacteria

by Paige E. Allen and Juan J. Martinez

Pathogens 2020, 9(8), 614; https://doi.org/10.3390/pathogens9080614 - 28 Jul 2020

Cited by 20 | Viewed by 5295

Abstract

Lipids are a broad group of molecules required for cell maintenance and homeostasis. Various intracellular pathogens have developed mechanisms of modulating and sequestering host lipid processes for a large array of functions for both bacterial and host cell survival. Among the host cell [...] Read more.

Lipids are a broad group of molecules required for cell maintenance and homeostasis. Various intracellular pathogens have developed mechanisms of modulating and sequestering host lipid processes for a large array of functions for both bacterial and host cell survival. Among the host cell lipid functions that intracellular bacteria exploit for infection are the modulation of host plasma membrane microdomains (lipid rafts) required for efficient bacterial entry; the recruitment of specific lipids for membrane integrity of intracellular vacuoles; and the utilization of host lipid droplets for the regulation of immune responses and for energy production through fatty acid β-oxidation and oxidative phosphorylation. The majority of published studies on the utilization of these host lipid pathways during infection have focused on intracellular bacterial pathogens that reside within a vacuole during infection and, thus, have vastly different requirements for host lipid metabolites when compared to those intracellular pathogens that are released into the host cytosol upon infection. Here we summarize the mechanisms by which intracellular bacteria sequester host lipid species and compare the modulation of host lipid pathways and metabolites during host cell infection by intracellular pathogens residing in either a vacuole or within the cytosol of infected mammalian cells. This review will also highlight common and unique host pathways necessary for intracellular bacterial growth that could potentially be targeted for therapeutic intervention. Full article

(This article belongs to the Special Issue Virulence Mechanisms of Rickettsiae)

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24 pages, 2145 KB

Open AccessEditor’s ChoiceReview

Ticks and Tick-Borne Diseases in Cuba, Half a Century of Scientific Research

by Dasiel Obregón Alvarez, Belkis Corona-González, Alina Rodríguez-Mallón, Islay Rodríguez Gonzalez, Pastor Alfonso, Angel A. Noda Ramos, Adrian A. Díaz-Sánchez, Maylin González Navarrete, Rafmary Rodríguez Fernández, Luis Méndez Mellor, Helen N. Catanese, Manuel Peláez, Yousmel Alemán Gainza, Roxana Marrero-Perera, Lisset Roblejo-Arias, Evelyn Lobo-Rivero, Claudia B. Silva, Adivaldo H. Fonseca, Eugenio Roque López and Alejandro Cabezas-Cruz

Pathogens 2020, 9(8), 616; https://doi.org/10.3390/pathogens9080616 - 28 Jul 2020

Cited by 19 | Viewed by 7956

Abstract

Ticks and the vast array of pathogens they transmit, including bacteria, viruses, protozoa, and helminths, constitute a growing burden for human and animal health worldwide. In Cuba, the major tropical island in the Caribbean, ticks are an important cause of vector-borne diseases affecting [...] Read more.

Ticks and the vast array of pathogens they transmit, including bacteria, viruses, protozoa, and helminths, constitute a growing burden for human and animal health worldwide. In Cuba, the major tropical island in the Caribbean, ticks are an important cause of vector-borne diseases affecting livestock production, pet animal health and, to a lesser extent, human health. The higher number of tick species in the country belong to the Argasidae family and, probably less known, is the presence of an autochthonous tick species in the island, Ixodes capromydis. Herein, we provide a comprehensive review of the ticks and tick-borne pathogens (TBPs) affecting animal and human health in Cuba. The review covers research results including ecophysiology of ticks, the epidemiology of TBPs, and the diagnostic tools used currently in the country for the surveillance of TBPs. We also introduce the programs implemented in the country for tick control and the biotechnology research applied to the development of anti-tick vaccines. Full article

(This article belongs to the Collection Advances in Tick Research)

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20 pages, 580 KB

Open AccessEditor’s ChoiceReview

Zebrafish as a Model for Fish Diseases in Aquaculture

by Louise von Gersdorff Jørgensen

Pathogens 2020, 9(8), 609; https://doi.org/10.3390/pathogens9080609 - 27 Jul 2020

Cited by 62 | Viewed by 7037

Abstract

The use of zebrafish as a model for human conditions is widely recognized. Within the last couple of decades, the zebrafish has furthermore increasingly been utilized as a model for diseases in aquacultured fish species. The unique tools available in zebrafish present advantages [...] Read more.

The use of zebrafish as a model for human conditions is widely recognized. Within the last couple of decades, the zebrafish has furthermore increasingly been utilized as a model for diseases in aquacultured fish species. The unique tools available in zebrafish present advantages compared to other animal models and unprecedented in vivo imaging and the use of transgenic zebrafish lines have contributed with novel knowledge to this field. In this review, investigations conducted in zebrafish on economically important diseases in aquacultured fish species are included. Studies are summarized on bacterial, viral and parasitic diseases and described in relation to prophylactic approaches, immunology and infection biology. Considerable attention has been assigned to innate and adaptive immunological responses. Finally, advantages and drawbacks of using the zebrafish as a model for aquacultured fish species are discussed. Full article

(This article belongs to the Special Issue Fish Parasites and Immunology)

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11 pages, 11945 KB

Open AccessEditor’s ChoiceArticle

Mycobacterium pseudoshottsii in Mediterranean Fish Farms: New Trouble for European Aquaculture?

by Davide Mugetti, Katia Varello, Andrea Gustinelli, Paolo Pastorino, Vasco Menconi, Daniela Florio, Maria Letizia Fioravanti, Elena Bozzetta, Simona Zoppi, Alessandro Dondo and Marino Prearo

Pathogens 2020, 9(8), 610; https://doi.org/10.3390/pathogens9080610 - 27 Jul 2020

Cited by 20 | Viewed by 4871

Abstract

Mycobacterium pseudoshottsii, a slow-growing mycobacterium closely related to M. marinum, has been isolated only in wild fish in the United States and in Japanese fish farms to date. Here, we report cases of mortality in three farmed fish species (Dicentrarchus [...] Read more.

Mycobacterium pseudoshottsii, a slow-growing mycobacterium closely related to M. marinum, has been isolated only in wild fish in the United States and in Japanese fish farms to date. Here, we report cases of mortality in three farmed fish species (Dicentrarchus labrax, Sparus aurata, and Sciaenops ocellatus) caused by M. pseudoshottsii in Italy. Samples underwent necropsy, histology, and culture with pathogen identification based on PCR and sequencing of housekeeping genes (16S rRNA, hsp65, rpoB). Multifocal to coalescing granulomatous and necrotizing inflammation with acid-fast bacilli were observed in the parenchymatous organs, from which M. pseudoshottsii was isolated and identified. Phylogenetic analysis confirmed the results of gene sequencing and allowed subdivision of the isolates into three distinct groups. M. pseudoshottsii poses a potential threat for Mediterranean aquaculture. Its origin in the area under study needs to be clarified, as well as the threat to the farmed fish species. Full article

(This article belongs to the Special Issue Emerging Infectious Diseases in Aquaculture)

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14 pages, 1518 KB

Open AccessEditor’s ChoiceArticle

Dolphins Stranded along the Tuscan Coastline (Central Italy) of the “Pelagos Sanctuary”: A Parasitological Investigation

by Giuliana Terracciano, Gianluca Fichi, Antonia Comentale, Enrica Ricci, Cecilia Mancusi and Stefania Perrucci

Pathogens 2020, 9(8), 612; https://doi.org/10.3390/pathogens9080612 - 27 Jul 2020

Cited by 17 | Viewed by 4198

Abstract

Parasite monitoring is considered a necessary step for cetacean management and conservation. Between February 2013 and July 2015, 26 dolphins (15 Stenella coeruleoalba, 10 Tursiops truncatus, and one Grampus griseus) stranded along the Tuscan coastline of the protected marine area [...] Read more.

Parasite monitoring is considered a necessary step for cetacean management and conservation. Between February 2013 and July 2015, 26 dolphins (15 Stenella coeruleoalba, 10 Tursiops truncatus, and one Grampus griseus) stranded along the Tuscan coastline of the protected marine area “Pelagos Sanctuary”, were examined. Organs, tissues, and faecal and blood samples taken from all animals were analysed by parasitological, immunological, and molecular techniques. Twenty-one out of 26 dolphins (80.77%) tested positive for at least one parasite species, and 13/15 (86.7%) S. coeruleoalba, 7/10 (70%) T. truncatus, and the single G. griseus were found positive. Identified parasites included the nematodes Skrjabinalius guevarai (7.69%, 2/26), Halocercus lagenorhynchi (3.85%, 1/26), Halocercus delphini (7.69%, 2/26), Stenurus ovatus (7.69%, 2/26), Crassicauda spp. (7.69%, 2/26); the trematodes Pholeter gastrophilus (26.92%, 7/26), Campula palliata (3.85%, 1/26); the cestodes Phyllobothrium delphini (42.31%, 11/26), Monorygma grimaldii (23.08%, 6/26), Tetrabothrium forsteri (7.69%, 2/26), Strobilocephalus triangularis (7.69%, 2/26), and the acanthocephalan Bolbosoma vasculosum (7.69%, 2/26). Moreover, 6/26 (23%) animals scored positive to Toxoplasma gondii at serology, but PCR confirmed the infection (T. gondii Type II genotype) in a single animal. In examined dolphins, obtained results showed a high prevalence of endoparasites, which included species considered as a cause of severe debilitation or death. Full article

(This article belongs to the Special Issue Animal Parasitic Diseases)

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19 pages, 7966 KB

Open AccessEditor’s ChoiceArticle

Specific Detection of Yersinia pestis Based on Receptor Binding Proteins of Phages

by Friederike Born, Peter Braun, Holger C. Scholz and Gregor Grass

Pathogens 2020, 9(8), 611; https://doi.org/10.3390/pathogens9080611 - 27 Jul 2020

Cited by 27 | Viewed by 5961

Abstract

The highly pathogenic bacterium Yersinia pestis is the causative agent of plague, a notorious infectious zoonotic disease. When transmitted from person to person as pneumonic plague via droplets, Y. pestis is highly contagious and in most cases is fatal if left untreated. Thus, [...] Read more.

The highly pathogenic bacterium Yersinia pestis is the causative agent of plague, a notorious infectious zoonotic disease. When transmitted from person to person as pneumonic plague via droplets, Y. pestis is highly contagious and in most cases is fatal if left untreated. Thus, when plague is suspected, rapid diagnosis is crucial, as a serious course of the infection is only averted by early antibiotic therapy. The bacterium is easy to cultivate, accessible and has a high potential for nefarious use such as bioterrorism. Highly specific, rapid and easy-to-use confirmatory diagnostic methods are required to reliably identify the pathogen independently from PCR-based methods or F1 antigen-based immunological detection. Yersinia pestis specific phages such as L-413C and ΦA1122 are already used for detection of Y. pestis in bacterial plaque or biosensor assays. Here, we made use of the host specificities conferred by phage receptor binding (or tail fiber/spike) proteins (RBP) for developing a specific, fast and simple fluorescence-microscopy-based detection method for Y. pestis. Genes of putative RBP of phages L-413C (gpH) and ΦA1122 (gp17) were fused with those of fluorescent proteins and recombinant receptor-reporter fusion proteins were produced heterologously in Escherichia coli. When first tested on attenuated Y. pestis strain EV76, RBP-reporters bound to the bacterial cell surface. This assay could be completed within a few minutes using live or formaldehyde-inactivated cells. Specificity tests using cultures of closely related Yersinia species and several inactivated fully virulent Y. pestis strains exhibited high specificities of the RBP-reporters against Y. pestis. The L-413C RBP proved to be especially specific, as it only detected Y. pestis at all temperatures tested, whereas the RBP of ΦA1122 also bound to Y. pseudotuberculosis strains at 37 °C (but not at 28, 20 or 6 °C). Finally, the Y. pestis-specific capsule, produced when grown at 37 °C, significantly reduced binding of phage ΦA1122 RBP, whereas the capsule only slightly diminished binding of L-413C RBP. Full article

(This article belongs to the Special Issue Advances in Yersinia Infection: Epidemiology, Omics Diagnosis and Control/Prevention)

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14 pages, 1967 KB

Open AccessEditor’s ChoiceArticle

Cyclic Hypoxia Exposure Accelerates the Progression of Amoebic Gill Disease

by Tina Oldham, Tim Dempster, Philip Crosbie, Mark Adams and Barbara Nowak

Pathogens 2020, 9(8), 597; https://doi.org/10.3390/pathogens9080597 - 22 Jul 2020

Cited by 16 | Viewed by 3304

Abstract

Amoebic gill disease (AGD), caused by the amoeba Neoparamoeba perurans, has led to considerable economic losses in every major Atlantic salmon producing country, and is increasing in frequency. The most serious infections occur during summer and autumn, when temperatures are high and [...] Read more.

Amoebic gill disease (AGD), caused by the amoeba Neoparamoeba perurans, has led to considerable economic losses in every major Atlantic salmon producing country, and is increasing in frequency. The most serious infections occur during summer and autumn, when temperatures are high and poor dissolved oxygen (DO) conditions are most common. Here, we tested if exposure to cyclic hypoxia at DO saturations of 40–60% altered the course of infection with N. perurans compared to normoxic controls maintained at ≥90% DO saturation. Although hypoxia exposure did not increase initial susceptibility to N. perurans, it accelerated progression of the disease. By 7 days post-inoculation, amoeba counts estimated from qPCR analysis were 1.7 times higher in the hypoxic treatment than in normoxic controls, and cumulative mortalities were twice as high (16 ± 4% and 8 ± 2%), respectively. At 10 days post-inoculation, however, there were no differences between amoeba counts in the hypoxic and normoxic treatments, nor in the percentage of filaments with AGD lesions (control = 74 ± 2.8%, hypoxic = 69 ± 3.3%), or number of lamellae per lesion (control = 30 ± 0.9%, hypoxic = 27.9 ± 0.9%) as determined by histological examination. Cumulative mortalities at the termination of the experiment were similarly high in both treatments (hypoxic = 60 ± 2%, normoxic = 53 ± 11%). These results reveal that exposure to cyclic hypoxia in a diel pattern, equivalent to what salmon are exposed to in marine aquaculture cages, accelerated the progression of AGD in post-smolts. Full article

(This article belongs to the Special Issue Pathogen Characterization, Host Immune Response and Development of Strategies to Reduce Losses to Disease in Aquaculture)

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13 pages, 789 KB

Open AccessEditor’s ChoiceArticle

Correlation of Feline Coronavirus Shedding in Feces with Coronavirus Antibody Titer

by Sandra Felten, Ute Klein-Richers, Regina Hofmann-Lehmann, Michèle Bergmann, Stefan Unterer, Christian M. Leutenegger and Katrin Hartmann

Pathogens 2020, 9(8), 598; https://doi.org/10.3390/pathogens9080598 - 22 Jul 2020

Cited by 36 | Viewed by 6755

Abstract

Background: Feline coronavirus (FCoV) infection is ubiquitous in multi-cat households. Responsible for the continuous presence are cats that are chronically shedding a high load of FCoV. The aim of the study was to determine a possible correlation between FCoV antibody titer and frequency [...] Read more.

Background: Feline coronavirus (FCoV) infection is ubiquitous in multi-cat households. Responsible for the continuous presence are cats that are chronically shedding a high load of FCoV. The aim of the study was to determine a possible correlation between FCoV antibody titer and frequency and load of fecal FCoV shedding in cats from catteries. Methods: Four fecal samples from each of 82 cats originating from 19 German catteries were examined for FCoV viral loads by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). Additionally, antibody titers were determined by an immunofluorescence assay. Results: Cats with antibodies were more likely to be FCoV shedders than non-shedders, and there was a weak positive correlation between antibody titer and mean fecal virus load (Spearman r = 0.2984; p = 0.0072). Antibody titers were significantly higher if cats shed FCoV more frequently throughout the study period (p = 0.0063). When analyzing only FCoV shedders, cats that were RT-qPCR-positive in all four samples had significantly higher antibody titers (p = 0.0014) and significantly higher mean fecal virus loads (p = 0.0475) than cats that were RT-qPCR-positive in only one, two, or three samples. Conclusions: The cats’ antibody titers correlate with the likelihood and frequency of FCoV shedding and fecal virus load. Chronic shedders have higher antibody titers and shed more virus. This knowledge is important for the management of FCoV infections in multi-cat environments, but the results indicate that antibody measurement cannot replace fecal RT-qPCR. Full article

(This article belongs to the Special Issue Feline Infectious Peritonitis)

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15 pages, 2267 KB

Open AccessEditor’s ChoiceArticle

Monitoring Mycoplasma bovis Diversity and Antimicrobial Susceptibility in Calf Feedlots Undergoing a Respiratory Disease Outbreak

by Claire A.M. Becker, Chloé Ambroset, Anthéa Huleux, Angélique Vialatte, Adélie Colin, Agnès Tricot, Marie-Anne Arcangioli and Florence Tardy

Pathogens 2020, 9(7), 593; https://doi.org/10.3390/pathogens9070593 - 21 Jul 2020

Cited by 25 | Viewed by 4506

Abstract

Bovine respiratory diseases (BRD) are widespread in veal calf feedlots. Several pathogens are implicated, both viruses and bacteria, one of which, Mycoplasma bovis, is under-researched. This worldwide-distributed bacterium has been shown to be highly resistant in vitro to the main antimicrobials used [...] Read more.

Bovine respiratory diseases (BRD) are widespread in veal calf feedlots. Several pathogens are implicated, both viruses and bacteria, one of which, Mycoplasma bovis, is under-researched. This worldwide-distributed bacterium has been shown to be highly resistant in vitro to the main antimicrobials used to treat BRD. Our objective was to monitor the relative prevalence of M. bovis during BRD episodes, its diversity, and its resistance phenotype in relation to antimicrobial use. For this purpose, a two-year longitudinal follow-up of 25 feedlots was organized and 537 nasal swabs were collected on 358 veal calves at their arrival in the lot, at the BRD peak and 4 weeks after collective antimicrobial treatments. The presence of M. bovis was assessed by real-time PCR and culture. The clones isolated were then subtyped (polC subtyping and PFGE analysis), and their susceptibility to five antimicrobials was determined. The course of the disease and the antimicrobials used had no influence on the genetic diversity of the M. bovis strains: The subtype distribution was the same throughout the BRD episode and similar to that already described in France, with a major narrowly-variable subtype circulating, st2. The same conclusion holds for antimicrobial resistance (AMR) phenotypes: All the clones were already multiresistant to the main antimicrobials used (except for fluoroquinolones) prior to any treatments. By contrast, changes of AMR phenotypes could be suspected for Pasteurellaceae in two cases in relation to the treatments registered. Full article

(This article belongs to the Special Issue Mycoplasma bovis Infections: Occurrence, Pathogenesis, Diagnosis and Control, Including Prevention and Therapy)

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23 pages, 16329 KB

Open AccessEditor’s ChoiceArticle

The Epstein-Barr Virus-Encoded EBNA1 Protein Activates the Bone Morphogenic Protein (BMP) Signalling Pathway to Promote Carcinoma Cell Migration

by Hannah E. Bridgewater, Kathryn L. Date, John D. O’Neil, Chunfang Hu, John R. Arrand, Christopher W. Dawson and Lawrence S. Young

Pathogens 2020, 9(7), 594; https://doi.org/10.3390/pathogens9070594 - 21 Jul 2020

Cited by 10 | Viewed by 4189

Abstract

The Epstein-Barr virus (EBV)-encoded nuclear antigen 1 (EBNA1) protein is expressed in all virus-associated malignancies, where it performs an essential role in the maintenance, replication and transcription of the EBV genome. In recent years, it has become apparent that EBNA1 can also influence [...] Read more.

The Epstein-Barr virus (EBV)-encoded nuclear antigen 1 (EBNA1) protein is expressed in all virus-associated malignancies, where it performs an essential role in the maintenance, replication and transcription of the EBV genome. In recent years, it has become apparent that EBNA1 can also influence cellular gene transcription. Here, we demonstrate that EBNA1 is able to stimulate the expression of the Transforming growth factor-beta (TGFβ) superfamily member, bone morphogenic protein 2 (BMP2), with consequential activation of the BMP signalling pathway in carcinoma cell lines. We show that BMP pathway activation is associated with an increase in the migratory capacity of carcinoma cells, an effect that can be ablated by the BMP antagonist, Noggin. Gene expression profiling of authentic EBV-positive nasopharyngeal carcinoma (NPC) tumours revealed the consistent presence of BMP ligands, established BMP pathway effectors and putative target genes, constituting a prominent BMP “signature” in this virus-associated cancer. Our findings show that EBNA1 is the major viral-encoded protein responsible for activating the BMP signalling pathway in carcinoma cells and supports a role for this pathway in promoting cell migration and possibly, metastatic spread. Full article

(This article belongs to the Section Human Pathogens)

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9 pages, 433 KB

Open AccessEditor’s ChoiceReview

Understanding HCMV Latency Using Unbiased Proteomic Analyses

by Emma Poole and John Sinclair

Pathogens 2020, 9(7), 590; https://doi.org/10.3390/pathogens9070590 - 20 Jul 2020

Cited by 14 | Viewed by 4315

Abstract

Human cytomegalovirus (HCMV) establishes either a latent (non-productive) or lytic (productive) infection depending upon cell type, cytokine milieu and the differentiation status of the infected cell. Undifferentiated cells, such as precursor cells of the myeloid lineage, support a latent infection whereas terminally differentiated [...] Read more.

Human cytomegalovirus (HCMV) establishes either a latent (non-productive) or lytic (productive) infection depending upon cell type, cytokine milieu and the differentiation status of the infected cell. Undifferentiated cells, such as precursor cells of the myeloid lineage, support a latent infection whereas terminally differentiated cells, such as monocytes or dendritic cells are an environment conducive to reactivation and support a lytic infection. The mechanisms which regulate HCMV in either a latent or lytic infection have been the focus of intense investigation with a view to developing novel treatments for HCMV-associated disease which can have a heavy clinical burden after reactivation or primary infection in, especially, the immune compromised. To this end, a number of studies have been carried out in an unbiased manner to address global changes occurring within the latently infected cell to address the molecular changes associated with HCMV latency. In this review, we will concentrate on the proteomic analyses which have been carried out in undifferentiated myeloid cells which either stably express specific viral latency associated genes in isolation or on cells which have been latently infected with virus. Full article

(This article belongs to the Special Issue Cytomegalovirus (CMV) Infection and Latency)

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51 pages, 2593 KB

Open AccessEditor’s ChoiceReview

West Nile Virus: An Update on Pathobiology, Epidemiology, Diagnostics, Control and “One Health” Implications

by Gervais Habarugira, Willy W. Suen, Jody Hobson-Peters, Roy A. Hall and Helle Bielefeldt-Ohmann

Pathogens 2020, 9(7), 589; https://doi.org/10.3390/pathogens9070589 - 19 Jul 2020

Cited by 139 | Viewed by 22448

Abstract

West Nile virus (WNV) is an important zoonotic flavivirus responsible for mild fever to severe, lethal neuroinvasive disease in humans, horses, birds, and other wildlife species. Since its discovery, WNV has caused multiple human and animal disease outbreaks in all continents, except Antarctica. [...] Read more.

West Nile virus (WNV) is an important zoonotic flavivirus responsible for mild fever to severe, lethal neuroinvasive disease in humans, horses, birds, and other wildlife species. Since its discovery, WNV has caused multiple human and animal disease outbreaks in all continents, except Antarctica. Infections are associated with economic losses, mainly due to the cost of treatment of infected patients, control programmes, and loss of animals and animal products. The pathogenesis of WNV has been extensively investigated in natural hosts as well as in several animal models, including rodents, lagomorphs, birds, and reptiles. However, most of the proposed pathogenesis hypotheses remain contentious, and much remains to be elucidated. At the same time, the unavailability of specific antiviral treatment or effective and safe vaccines contribute to the perpetuation of the disease and regular occurrence of outbreaks in both endemic and non-endemic areas. Moreover, globalisation and climate change are also important drivers of the emergence and re-emergence of the virus and disease. Here, we give an update of the pathobiology, epidemiology, diagnostics, control, and “One Health” implications of WNV infection and disease. Full article

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14 pages, 4534 KB

Open AccessEditor’s ChoiceArticle

Genetic Diversity Among SARS-CoV2 Strains in South America may Impact Performance of Molecular Detection

by Juan David Ramírez, Marina Muñoz, Carolina Hernández, Carolina Flórez, Sergio Gomez, Angelica Rico, Lisseth Pardo, Esther C. Barros and Alberto E. Paniz-Mondolfi

Pathogens 2020, 9(7), 580; https://doi.org/10.3390/pathogens9070580 - 17 Jul 2020

Cited by 30 | Viewed by 7282

Abstract

Since its emergence in Wuhan (China) on December 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020, the virus has expanded throughout the region, infecting over 900,000 individuals with approximately [...] Read more.

Since its emergence in Wuhan (China) on December 2019, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has rapidly spread worldwide. After its arrival in South America in February 2020, the virus has expanded throughout the region, infecting over 900,000 individuals with approximately 41,000 reported deaths to date. In response to the rapidly growing number of cases, a number of different primer-probe sets have been developed. However, despite being highly specific, most of these primer-probe sets are known to exhibit variable sensitivity. Currently, there are more than 300 SARS-CoV2 whole genome sequences deposited in databases from Brazil, Chile, Ecuador, Colombia, Uruguay, Peru, and Argentina. To test how regional viral diversity may impact oligo binding sites and affect test performance, we reviewed all available primer-probe sets targeting the E, N, and RdRp genes against available South American SARS-CoV-2 genomes checking for nucleotide variations in annealing sites. Results from this in silico analysis showed no nucleotide variations on the E-gene target region, in contrast to the N and RdRp genes which showed massive nucleotide variations within oligo binding sites. In lines with previous data, our results suggest that the E-gene stands as the most conserved and reliable target when considering single-gene target testing for molecular diagnosis of SARS-CoV-2 in South America. Full article

(This article belongs to the Collection SARS-CoV Infections)

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