Pathogens

14 pages, 2925 KiB

Open AccessArticle

Comparison of Chicken Cecal Microbiota after Metaphylactic Treatment or Following Administration of Feed Additives in a Broiler Farm with Enterococcal Spondylitis History

by Julia Hankel, Björn Bodmann, Matthias Todte, Eric Galvez, Till Strowig, Dimitri Radko, Ali Antakli and Christian Visscher

Pathogens 2021, 10(8), 1068; https://doi.org/10.3390/pathogens10081068 - 23 Aug 2021

Cited by 5 | Viewed by 3046

Abstract

Minimizing the clinical signs of Enterococcus cecorum infections causing enterococcal spondylitis in broiler herds is successful when initiated as metaphylaxis in the first week of life. Mechanistically, either the Enterococcus species present at that time are reduced by antibiotic treatment or antibiotic treatment [...] Read more.

Minimizing the clinical signs of Enterococcus cecorum infections causing enterococcal spondylitis in broiler herds is successful when initiated as metaphylaxis in the first week of life. Mechanistically, either the Enterococcus species present at that time are reduced by antibiotic treatment or antibiotic treatment might induce changes in intestinal microbiota composition with an indirect and subsequent influence. The aim of the present study was to examine the cecal microbiota of chickens after administering lincospectin or different additives to evaluate whether these additives have lincospectin-like effects on microbiota. Therefore, 157,400 broiler chickens were reared in four chicken houses (~40,000 birds each) on a broiler farm with history of enterococcal spondylitis. Each flock was treated either with lincospectin or water soluble esterified butyrins, Bacillus (B.) licheniformis or palm oil was added via drinking water during the first days of life. Ten birds per house were dissected at days 11, 20 and 33 of life and cecal microbiota were analyzed (16S rRNA gene sequencing). Lincospectin treatment elicited significant changes in the cecal microbiota composition until slaughter age. Among the tested additives, effects of B. licheniformis on cecal microbiota composition were most similar to those seen after the treatment with lincospectin at day 11. Full article

(This article belongs to the Section Bacterial Pathogens)

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15 pages, 299 KiB

Open AccessArticle

Low Sensitivity of Real Time PCRs Targeting Retrotransposon Sequences for the Detection of Schistosoma japonicum Complex DNA in Human Serum

by Hagen Frickmann, Ulrike Loderstädt, Beatrice Nickel, Sven Poppert, Peter Odermatt, Somphou Sayasone, Marjan Van Esbroeck, Isabel Micalessi, Lieselotte Cnops, Poom Adisakwattana, Gérard Leboulle, Olfert Landt, Thorsten Thye and Egbert Tannich

Pathogens 2021, 10(8), 1067; https://doi.org/10.3390/pathogens10081067 - 22 Aug 2021

Cited by 5 | Viewed by 2363

Abstract

While hybridization probe-based real-time PCR assays targeting highly repetitive multi-copy genome sequences for the diagnosis of S. mansoni complex or S. haematobium complex from human serum are well established, reports on the evaluation of respective assays for the identification of S. japonicum complex [...] Read more.

While hybridization probe-based real-time PCR assays targeting highly repetitive multi-copy genome sequences for the diagnosis of S. mansoni complex or S. haematobium complex from human serum are well established, reports on the evaluation of respective assays for the identification of S. japonicum complex DNA in human serum are scarce. Here, we assessed the potential use of the retrotransposon sequences SjR2 and SjCHGCS19 from S. japonicum, S. mekongi and S. malayensis for the diagnosis of Asian Schistosoma infections. Based on available S. japonicum sequences and newly provided S. mekongi and S. malayensis sequences, hybridization probe-based real-time PCRs targeting SjR2 and SjCHGCS19 of the S. japonicum complex were designed both as consensus primer assays as well as multi-primer assays for the coverage of multiple variants of the target sequences. The assays were established using plasmids and S. mekongi DNA. While the consensus primer assays failed to detect S. mekongi DNA in human serum samples, the multi-primer assays showed positive or borderline positive results but only in 9.8% (6/61) of serum samples from patients with confirmed S. mekongi infections. Some cross-reactions with samples positive for S. mansoni or S. haematobium were observed but with the SjCHGCS19-PCR only. In spite of the low sensitivity, the presented experience may guide future evaluations of S. japonicum-complex-specific PCRs from human serum. Full article

(This article belongs to the Special Issue Molecular Diagnostics for Infectious Diseases)

15 pages, 2627 KiB

Open AccessArticle

Antibacterial Agents Adsorbed on Active Carbon: A New Approach for S. aureus and E. coli Pathogen Elimination

by Ewa Burchacka, Katarzyna Pstrowska, Elżbieta Beran, Hanna Fałtynowicz, Katarzyna Chojnacka and Marek Kułażyński

Pathogens 2021, 10(8), 1066; https://doi.org/10.3390/pathogens10081066 - 22 Aug 2021

Cited by 15 | Viewed by 3323

Abstract

Antibiotic overuse and mass production have led to a global problem with the treatment of antibacterial infections. Thus, any possibility to limit the number of antibacterial drugs used will contribute to a decrease in the development of pathogenic bacterial resistance. In this study, [...] Read more.

Antibiotic overuse and mass production have led to a global problem with the treatment of antibacterial infections. Thus, any possibility to limit the number of antibacterial drugs used will contribute to a decrease in the development of pathogenic bacterial resistance. In this study, the enhanced bacterial growth reduction of pharmaceutical activated carbon (PAC) material with adsorbed antimicrobial agents compared to the activity of pure antibacterial drugs was investigated. Sulfamethoxazole (SMZ) at a concentration of 1.1 mg/mL retained the growth of S. aureus and E. coli at 20.5% and 26.5%, respectively, whereas SMZ adsorbed on PAC increased the reduction of the tested bacteria in the range of 47–72%. The use of PAC with adsorbed gentamycin (G) over 24 h improved the effectiveness of E. coli growth reduction by 50% compared to the application of pure antibiotic (3.6 µg/mL). The increased reduction of S. aureus growth by 6% using G with PAC for a 24-h incubation time compared to the use of pure antibiotics at a concentration of 3.6 µg/mL was observed. The results provide proof-of-principle that the new approach of activated carbon with adsorbed antimicrobial agents could yield an attractive background with potential as a new starting material for S. aureus and E. coli pathogen elimination, e.g., in wound-healing treatment in the future. Full article

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17 pages, 1583 KiB

Open AccessReview

TNF Decoy Receptors Encoded by Poxviruses

by Francisco Javier Alvarez-de Miranda, Isabel Alonso-Sánchez, Antonio Alcamí and Bruno Hernaez

Pathogens 2021, 10(8), 1065; https://doi.org/10.3390/pathogens10081065 - 22 Aug 2021

Cited by 12 | Viewed by 4423

Abstract

Tumour necrosis factor (TNF) is an inflammatory cytokine produced in response to viral infections that promotes the recruitment and activation of leukocytes to sites of infection. This TNF-based host response is essential to limit virus spreading, thus poxviruses have evolutionarily adopted diverse molecular [...] Read more.

Tumour necrosis factor (TNF) is an inflammatory cytokine produced in response to viral infections that promotes the recruitment and activation of leukocytes to sites of infection. This TNF-based host response is essential to limit virus spreading, thus poxviruses have evolutionarily adopted diverse molecular mechanisms to counteract TNF antiviral action. These include the expression of poxvirus-encoded soluble receptors or proteins able to bind and neutralize TNF and other members of the TNF ligand superfamily, acting as decoy receptors. This article reviews in detail the various TNF decoy receptors identified to date in the genomes from different poxvirus species, with a special focus on their impact on poxvirus pathogenesis and their potential use as therapeutic molecules. Full article

(This article belongs to the Special Issue Poxviruses: Novel Concepts and Emerging Trends)

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4 pages, 593 KiB

Open AccessCase Report

Intracellular S. aureus in Osteoblasts in a Clinical Sample from a Patient with Chronic Osteomyelitis—A Case Report

by Nike Walter, Daniel Mendelsohn, Christoph Brochhausen, Markus Rupp and Volker Alt

Pathogens 2021, 10(8), 1064; https://doi.org/10.3390/pathogens10081064 - 22 Aug 2021

Cited by 12 | Viewed by 2682

Abstract

The pathophysiological role of intracellular bacteria in osteomyelitis is still a matter of debate. Here, we demonstrate for the first time the presence of Staphylococcus aureus internalized into osteoblasts in human tissue samples of a case with a chronic osteomyelitis using ultrastructural transmission [...] Read more.

The pathophysiological role of intracellular bacteria in osteomyelitis is still a matter of debate. Here, we demonstrate for the first time the presence of Staphylococcus aureus internalized into osteoblasts in human tissue samples of a case with a chronic osteomyelitis using ultrastructural transmission electron microscope analysis. Full article

(This article belongs to the Special Issue Advances in Human Pathogens Infections)

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27 pages, 5294 KiB

Open AccessArticle

Gut Microbiota in Military International Travelers with Doxycycline Malaria Prophylaxis: Towards the Risk of a Simpson Paradox in the Human Microbiome Field

by Emilie Javelle, Aurélie Mayet, Matthieu Million, Anthony Levasseur, Rodrigue S. Allodji, Catherine Marimoutou, Chrystel Lavagna, Jérôme Desplans, Pierre Edouard Fournier, Didier Raoult and Gaëtan Texier

Pathogens 2021, 10(8), 1063; https://doi.org/10.3390/pathogens10081063 - 21 Aug 2021

Cited by 2 | Viewed by 3637

Abstract

Dysbiosis, developed upon antibiotic administration, results in loss of diversity and shifts in the abundance of gut microbes. Doxycycline is a tetracycline antibiotic widely used for malaria prophylaxis in travelers. We prospectively studied changes in the fecal microbiota of 15 French soldiers after [...] Read more.

Dysbiosis, developed upon antibiotic administration, results in loss of diversity and shifts in the abundance of gut microbes. Doxycycline is a tetracycline antibiotic widely used for malaria prophylaxis in travelers. We prospectively studied changes in the fecal microbiota of 15 French soldiers after a 4-month mission to Mali with doxycycline malaria prophylaxis, compared to changes in the microbiota of 28 soldiers deployed to Iraq and Lebanon without doxycycline. Stool samples were collected with clinical data before and after missions, and 16S rRNA sequenced on MiSeq targeting the V3-V4 region. Doxycycline exposure resulted in increased alpha-biodiversity and no significant beta-dissimilarities. It led to expansion in Bacteroides, with a reduction in Bifidobacterium and Lactobacillus, as in the group deployed without doxycycline. Doxycycline did not alter the community structure and was specifically associated with a reduction in Escherichia and expression of Rothia. Differences in the microbiota existed at baseline between military units but not within the studied groups. This group-effect highlighted the risk of a Simpson paradox in microbiome studies. Full article

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23 pages, 10218 KiB

Open AccessReview

Murine Models of Central Nervous System Disease following Congenital Human Cytomegalovirus Infections

by Jerome Moulden, Cathy Yea Won Sung, Ilija Brizic, Stipan Jonjic and William Britt

Pathogens 2021, 10(8), 1062; https://doi.org/10.3390/pathogens10081062 - 21 Aug 2021

Cited by 15 | Viewed by 3097

Abstract

Human cytomegalovirus infection of the developing fetus is a leading cause of neurodevelopmental disorders in infants and children, leading to long-term neurological sequela in a significant number of infected children. Current understanding of the neuropathogenesis of this intrauterine infection is limited because of [...] Read more.

Human cytomegalovirus infection of the developing fetus is a leading cause of neurodevelopmental disorders in infants and children, leading to long-term neurological sequela in a significant number of infected children. Current understanding of the neuropathogenesis of this intrauterine infection is limited because of the complexity of this infection, which includes maternal immunological responses that are overlaid on virus replication in the CNS during neurodevelopment. Furthermore, available data from human cases are observational, and tissues from autopsy studies have been derived from only the most severe infections. Animal models of this human infection are also limited by the strict species specificity of cytomegaloviruses. However, informative models including non-human primates and small animal models have been developed. These include several different murine models of congenital HCMV infection for the study of CMV neuropathogenesis. Although individual murine models do not completely recapitulate all aspects of the human infection, each model has provided significant information that has extended current understanding of the neuropathogenesis of this human infection. This review will compare and contrast different murine models in the context of available information from human studies of CNS disease following congenital HCMV infections. Full article

(This article belongs to the Special Issue Murine Models of Cytomegalovirus Infection)

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12 pages, 1024 KiB

Open AccessArticle

General Characteristics of Children with Single- and Co-Infections and Febrile Seizures with a Main Focus on Respiratory Pathogens: Preliminary Results

by Henriette Rudolph, Katharina Gress, Christel Weiss, Horst Schroten, Ortwin Adams and Tobias Tenenbaum

Pathogens 2021, 10(8), 1061; https://doi.org/10.3390/pathogens10081061 - 20 Aug 2021

Cited by 9 | Viewed by 3092

Abstract

Febrile seizures (FS) affect up to 5% of children. The pathogen etiology in regard of viral loads has never been investigated. In a prospective cohort study we investigated the correlation between virus type and quantity in nasopharyngeal aspirates (NPAs) and the clinical characteristics [...] Read more.

Febrile seizures (FS) affect up to 5% of children. The pathogen etiology in regard of viral loads has never been investigated. In a prospective cohort study we investigated the correlation between virus type and quantity in nasopharyngeal aspirates (NPAs) and the clinical characteristics in pediatric patients with a FS. From January 2014 to April 2016, 184 children with a FS were prospectively enrolled. The mean age of all included children was 26.7 ± 18.3 months with a male to female ratio of 1.4:1. Males with an acute disease and a short duration or absence of prior symptoms had a higher risk for complex FS. The majority of patients with FS presented with a generalized convulsion (180; 98%) and was admitted to hospital (178; 97%). Overall, 79 (43%) single and in 59 (32%) co-infections were detected. Human herpes virus 6 (HHV6), influenza, adenovirus (AV) and rhinovirus (RV) were the dominant pathogens, all detected with clinically significant high viral loads. HHV6 positive cases were significantly younger and less likely to have a positive family/personal history for FS. Influenza positives showed a higher rate of complex seizures, lower leukocyte and higher monocyte counts. AV positive cases were more likely to have a positive family history for FS and showed higher C-reactive protein values. In conclusion, a high viral load may contribute to the development of a FS in respiratory tract infections. Full article

(This article belongs to the Special Issue Respiratory Tract Infections in Children)

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8 pages, 694 KiB

Open AccessCommunication

Propagation of CJD Prions in Primary Murine Glia Cells Expressing Human PrP^c

by Joo-Hee Wälzlein, Karla A. Schwenke and Michael Beekes

Pathogens 2021, 10(8), 1060; https://doi.org/10.3390/pathogens10081060 - 20 Aug 2021

Cited by 6 | Viewed by 2449

Abstract

There are various existing cell models for the propagation of animal prions. However, in vitro propagation of human prions has been a long-standing challenge. This study presents the establishment of a long-term primary murine glia culture expressing the human prion protein homozygous for [...] Read more.

There are various existing cell models for the propagation of animal prions. However, in vitro propagation of human prions has been a long-standing challenge. This study presents the establishment of a long-term primary murine glia culture expressing the human prion protein homozygous for methionine at codon 129, which allows in vitro propagation of Creutzfeldt–Jakob disease (CJD) prions (variant CJD (vCJD) and sporadic CJD (sCJD) type MM2). Prion propagation could be detected by Western blotting of pathological proteinase K-resistant prion protein (PrP^Sc) from 120 days post exposure. The accumulation of PrP^Sc could be intensified by adding a cationic lipid mixture to the infectious brain homogenate at the time of infection. Stable propagation of human prions in a long-term murine glia cell culture represents a new tool for future drug development and for mechanistic studies in the field of human prion biology. In addition, our cell model can reduce the need for bioassays with human prions and thereby contributes to further implementation of the 3R principles aiming at replacement, reduction and refinement of animal experiments. Full article

(This article belongs to the Special Issue Human Prion Disease)

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14 pages, 644 KiB

Open AccessArticle

Antibiotic Resistance and Virulence Profiles of Escherichia coli Strains Isolated from Wild Birds in Poland

by Anna Nowaczek, Marta Dec, Dagmara Stępień-Pyśniak, Renata Urban-Chmiel, Agnieszka Marek and Paweł Różański

Pathogens 2021, 10(8), 1059; https://doi.org/10.3390/pathogens10081059 - 20 Aug 2021

Cited by 14 | Viewed by 3420

Abstract

Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds [...] Read more.

Wild animals are increasingly reported as carriers of antibiotic-resistant and pathogenic bacteria including Enterobacteriaceae. However, the role of free-living birds as reservoirs for potentially dangerous microbes is not yet thoroughly understood. In our work, we examined Escherichia coli strains from wild birds in Poland in relation to their antimicrobial agents susceptibility, virulence and phylogenetic affiliation. Identification of E. coli was performed using MALDI-TOF mass spectrometry. The antibiotic susceptibility of the isolates was determined by the broth microdilution method, and resistance and virulence genes were detected by PCR. E. coli bacteria were isolated from 32 of 34 samples. The strains were most often classified into phylogenetic groups B1 (50%) and A (25%). Resistance to tetracycline (50%), ciprofloxacin (46.8%), gentamicin (34.3%) and ampicillin (28.1%) was most frequently reported, and as many as 31.2% of E. coli isolates exhibited a multidrug resistance phenotype. Among resistance genes, sul2 (31.2% of isolates) and bla_TEM (28.1%) were identified most frequently, while irp-2 (31.2%) and ompT (28.1%) were the most common virulence-associated genes. Five strains were included in the APEC group. The study indicates that wild birds can be carriers of potentially dangerous E. coli strains and vectors for the spread of resistant bacteria and resistance determinants in the environment. Full article

(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)

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14 pages, 820 KiB

Open AccessReview

Medical Imaging in the Diagnosis of Schistosomiasis: A Review

by Andrea Cimini, Maria Ricci, Paola Elda Gigliotti, Luca Pugliese, Agostino Chiaravalloti, Roberta Danieli and Orazio Schillaci

Pathogens 2021, 10(8), 1058; https://doi.org/10.3390/pathogens10081058 - 20 Aug 2021

Cited by 9 | Viewed by 4403

Abstract

Schistosomiasis is one of the most important parasitic diseases and it is endemic in tropical and subtropical areas. Clinical and laboratory data are fundamental for the diagnosis of schistosomiasis, but diagnostic imaging techniques such as x-rays, ultrasound (US), computed tomography (CT), magnetic resonance [...] Read more.

Schistosomiasis is one of the most important parasitic diseases and it is endemic in tropical and subtropical areas. Clinical and laboratory data are fundamental for the diagnosis of schistosomiasis, but diagnostic imaging techniques such as x-rays, ultrasound (US), computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography/computed tomography (PET/CT) may be helpful in the evaluation of disease severity and complications. In this context, the aim of this review is to explore the actual role of diagnostic imaging in the diagnosis of schistosomiasis, underlining advantages and drawbacks providing information about the utilization of diagnostic imaging techniques in this context. Furthermore, we aim to provide a useful guide regarding imaging features of schistosomiasis for radiology and nuclear medicine physicians of non-endemic countries: in fact, in the last years non-endemic countries have experienced important flows of migrants from endemic areas, therefore it is not uncommon to face cases of this disease in daily practice. Full article

(This article belongs to the Special Issue Schistosomiasis: Host-Pathogen Biology)

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31 pages, 9358 KiB

Open AccessSystematic Review

A Systematic Review of Epstein–Barr Virus Latent Membrane Protein 1 (LMP1) Gene Variants in Nasopharyngeal Carcinoma

by Ana Banko, Danijela Miljanovic, Ivana Lazarevic and Andja Cirkovic

Pathogens 2021, 10(8), 1057; https://doi.org/10.3390/pathogens10081057 - 20 Aug 2021

Cited by 10 | Viewed by 3507

Abstract

Nasopharyngeal carcinoma (NPC) is an aggressive tumor with a complex etiology. Although Epstein–Barr virus (EBV) infection is known environmental factor for NPC development, the degree to which EBV naturally infects nasopharyngeal epithelium and the moment when and why the virus actively begins to [...] Read more.

Nasopharyngeal carcinoma (NPC) is an aggressive tumor with a complex etiology. Although Epstein–Barr virus (EBV) infection is known environmental factor for NPC development, the degree to which EBV naturally infects nasopharyngeal epithelium and the moment when and why the virus actively begins to affect cell transformation remains questionable. The aim of this study was to explore the association between LMP1 gene variability and potential contribution to NPC development. A systematic review was performed through searches of PubMed, Web of Science (WoS) and SCOPUS electronic databases. Additionally, meta-analysis of the difference in the frequency of seven LMP1 gene variants in NPC and control individuals was accomplished. The results from this study give a proof of concept for the association between 30 bp deletion (OR = 3.53, 95% CI = 1.48–8.43) and Xhol loss (OR = 14.17, 95% CI = 4.99–40.20) and NPC susceptibility when comparing biopsies from NPC and healthy individuals. Otherwise, 30 bp deletion from NPC biopsies could not distinguish NPC from EBV-associated non-NPC tumors (OR = 1.74, 95% CI = 0.81–3.75). However, B95-8, China1 and North Carolina variants were uncommon for NPC individuals. Much more efforts remains to be done to verify the biological significance of the differences observed, define so-called “high-risk” EBV variants and make it available for clinical application. Full article

(This article belongs to the Special Issue Epstein-Barr Virus (EBV) and Nasopharyngeal Carcinoma (NPC): Pathogenesis, Viral-Host Interaction and Therapeutic Strategies)

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10 pages, 1572 KiB

Open AccessArticle

Acute Inflammatory Mediators in Young Adult Patients with COVID-19 in Mexico

by Anahí Maldonado-Cabrera, Aracely Angulo-Molina, Ubydul Haque, Carlos Velazquez, Andrea S. Álvarez-Villaseñor, Karla J. Santacruz-Gómez and Ana L. Gallego-Hernández

Pathogens 2021, 10(8), 1056; https://doi.org/10.3390/pathogens10081056 - 20 Aug 2021

Cited by 6 | Viewed by 3863

Abstract

Young adults (18–40 years old) are an active population with high risk of infection and transmission of COVID-19. They are considered a low-risk population due to its low 1.0% case fatality rate (CFR). Despite their high clinical usefulness to prevent fatal cases, inflammatory [...] Read more.

Young adults (18–40 years old) are an active population with high risk of infection and transmission of COVID-19. They are considered a low-risk population due to its low 1.0% case fatality rate (CFR). Despite their high clinical usefulness to prevent fatal cases, inflammatory and coagulation biomarkers studies are limited. For this reason, we performed a retrospective cohort study with COVID-19 patients in Hermosillo, Mexico, to assess inflammation, coagulopathy profile, and severity outcomes in young adults. We analyzed blood samples to determine the neutrophil/lymphocyte ratio (NLR), neutrophil/monocyte ratio (NMR), lymphocyte/monocyte ratio (LMR), platelet/lymphocyte ratio (PLR), and C-reactive protein (C-RP). We included epidemiological features and comorbidities, and compared them to the severity status. Only 359 COVID-19-confirmed young adults were included in the ambulatory (44.8%), hospitalized (42.9%), and death (12%) severity groups. Laboratory results showed an increase in NMR, LMR, and C-RP associated with the aggravated patients. Additionally, obesity, arterial hypertension, and type-2 diabetes mellitus (T2DM) were associated with the COVID-19 severity outcome. We found that 9.1% and 30.3% of young adults presented the novel COVID-19-associated coagulopathy (CAC) and the risk of CAC, respectively. These parameters can be considered independent biomarkers reflecting an enhanced inflammatory process related to the COVID-19 prognosis. Full article

(This article belongs to the Collection SARS-CoV-2 Infection and COVID-19 Disease)

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10 pages, 963 KiB

Open AccessReview

Equine Coital Exanthema: New Insights on the Knowledge and Leading Perspectives for Treatment and Prevention

by María Aldana Vissani, Armando Mario Damiani and María Edith Barrandeguy

Pathogens 2021, 10(8), 1055; https://doi.org/10.3390/pathogens10081055 - 20 Aug 2021

Cited by 5 | Viewed by 4829

Abstract

Equine coital exanthema (ECE) is a highly contagious, venereally-transmitted mucocutaneous disease, characterized by the formation of papules, vesicles, pustules and ulcers on the external genital organs of mares and stallions, and caused by equid alphaherpesvirus 3 (EHV-3). The infection is endemic worldwide and [...] Read more.

Equine coital exanthema (ECE) is a highly contagious, venereally-transmitted mucocutaneous disease, characterized by the formation of papules, vesicles, pustules and ulcers on the external genital organs of mares and stallions, and caused by equid alphaherpesvirus 3 (EHV-3). The infection is endemic worldwide and the virus is transmitted mainly through direct contact during sexual intercourse and by contaminated instruments during reproductive maneuvers in breeding facilities. The disease does not result in systemic illness, infertility or abortion, yet it does have a negative impact on the equine industry as it forces the temporary withdrawal of affected animals with the consequent disruption of mating activities in breeding facilities. The purpose of this review is to provide up-to-date relevant information on the knowledge of EHV-3 infection and to analyze new approaches on diagnostics, treatment and prevention in the interest of minimizing the negative consequences of ECE in light of the current situation of the equine industry. Full article

(This article belongs to the Special Issue Equine Herpesviruses)

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9 pages, 438 KiB

Open AccessCommunication

The Risk of False-Positive Serological Results for Paratuberculosis in Mycobacterium bovis-Infected Cattle

by Anna Didkowska, Monika Krajewska-Wędzina, Daniel Klich, Kinga Prolejko, Blanka Orłowska and Krzysztof Anusz

Pathogens 2021, 10(8), 1054; https://doi.org/10.3390/pathogens10081054 - 19 Aug 2021

Cited by 6 | Viewed by 3481

Abstract

Both bovine tuberculosis (BTB) and paratuberculosis (paraTB) continue to cause significant economic losses in cattle breeding; in addition, their etiological agents have zoonotic potential. Although the diagnostics of both diseases are still being improved, problems still remain, such as the potential for cross-reactivity [...] Read more.

Both bovine tuberculosis (BTB) and paratuberculosis (paraTB) continue to cause significant economic losses in cattle breeding; in addition, their etiological agents have zoonotic potential. Although the diagnostics of both diseases are still being improved, problems still remain, such as the potential for cross-reactivity to the antigens used in tests. The aim of the present study was to confirm whether animals known to harbor Mycobacterium bovis antibodies are at increased risk of yielding positive results in paraTB serotesting and, additionally, to verify the accuracy of three commonly used methods for confirming M. bovis infection: ELISA, the tuberculin skin test (TST), and the presence of gross lesions. Material was collected from 98 dairy cattle suspected of BTB due to TST-positive results. During postmortem examination, gross lesions were assessed visually. Blood, lymph nodes, and TB-suspected organs were collected. Serum was obtained from the collected blood and tested serologically for TB and paraTB. The tissues underwent standard microbiological testing for M. tuberculosis complex. Among the 98 TST-positive individuals, tuberculous gross lesions were detected in 57 (58.1%), MTBC were isolated in 83 (84.7%), and the ELISA test was positive for 21 (21.4%). None of the lesions characteristic for paraTB were detected. The chance of obtaining a positive TB result by ELISA was seven times higher using the ELISA-paraTB method; hence, there is a significant risk of obtaining false-positive serological results for paraTB in M. bovis-infected cattle. However, the hypothesis that infection of M. bovis or prior TST performance may have boosted the host immune response and therefore increased the sensitivity of the paraTB-ELISA cannot be excluded. Full article

(This article belongs to the Special Issue Immunopathogenesis and Diagnostics to Control Tuberculosis in Cattle and Wildlife)

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9 pages, 294 KiB

Open AccessArticle

Comparison of Two Real-Time PCR Assays Targeting Ribosomal Sequences for the Identification of Cystoisospora belli in Human Stool Samples

by Martin Blohm, Andreas Hahn, Ralf Matthias Hagen, Kirsten Alexandra Eberhardt, Holger Rohde, Gérard Leboulle, Torsten Feldt, Fred Stephen Sarfo, Veronica Di Cristanziano, Hagen Frickmann and Ulrike Loderstädt

Pathogens 2021, 10(8), 1053; https://doi.org/10.3390/pathogens10081053 - 19 Aug 2021

Cited by 5 | Viewed by 3068

Abstract

Cystoisospora (C.) belli is a coccidian parasite associated with acute or chronic gastroenteritis in immunocompromised patients. Dissatisfactory sensitivity of microscopy as the diagnostic standard approach has been described. Here, we comparatively evaluated two real-time PCRs targeting ribosomal RNA gene sequences of C. belli [...] Read more.

Cystoisospora (C.) belli is a coccidian parasite associated with acute or chronic gastroenteritis in immunocompromised patients. Dissatisfactory sensitivity of microscopy as the diagnostic standard approach has been described. Here, we comparatively evaluated two real-time PCRs targeting ribosomal RNA gene sequences of C. belli in stool in a test comparison without a reference standard applying latent class analysis. Therefore, 1000 stool samples from Ghanaian HIV (human immunodeficiency virus) patients (n = 905) as well as military returnees from the tropics (n = 95) were assessed by both assays in parallel. After the exclusion of 33 samples showing PCR inhibition, 29 and 33 positive results were recorded with the 5.8S rRNA gene/ITS-2 sequence PCR and the ITS-2 sequence PCR, respectively, resulting in an accuracy-adjusted prevalence of 3.2%. Nearly perfect agreement between both assays was indicated by Fleiss’ kappa of 0.933 with sensitivity and specificity of 92.8% and 100% as well as 100% and 99.8% for the 5.8S rRNA gene/ITS-2 sequence PCR and the ITS-2 sequence PCR, respectively. Both assays proved to be suitable for the diagnosis of C. belli in human stool samples with slightly better sensitivity of the ITS-2 sequence assay, while the 5.8S rRNA gene/ITS-2 sequence PCR may be considered for confirmatory testing. Full article

(This article belongs to the Special Issue Molecular Diagnostics for Infectious Diseases)

11 pages, 590 KiB

Open AccessArticle

Relationship between Latent Toxoplasmosis and Depression in Clients of a Center for Assisted Reproduction

by Jana Hlaváčová, Jaroslav Flegr, Kateřina Fiurašková and Šárka Kaňková

Pathogens 2021, 10(8), 1052; https://doi.org/10.3390/pathogens10081052 - 19 Aug 2021

Cited by 9 | Viewed by 3727

Abstract

Latent infection of the globally spread parasite Toxoplasma gondii in humans has been associated with changes in personality and behavior. Numerous studies have investigated the effect of toxoplasmosis on depression, but their results are inconsistent. Our study focused on the effect of latent [...] Read more.

Latent infection of the globally spread parasite Toxoplasma gondii in humans has been associated with changes in personality and behavior. Numerous studies have investigated the effect of toxoplasmosis on depression, but their results are inconsistent. Our study focused on the effect of latent toxoplasmosis on depression in men and women in association with their fertility. In 2016–2018, we recruited clients (677 men and 664 women) of the Center for Assisted Reproduction and asked them to complete a standardized Beck Depression Inventory-II. In women without fertility problems, we found higher depression scores in Toxoplasma-positive than in Toxoplasma-negative (p = 0.010, Cohen’s d = 0.48). Toxoplasma-positive infertile men, on the other hand, had lower depression scores than Toxoplasma-negative infertile men (p ≤ 0.001, Cohen’s d = 0.48). Our results are consistent with the previously described effects of latent toxoplasmosis, which seem to go in opposite directions regarding the effect on personality and behavior of men and women. Our results could be explained by gender-contrasting reactions to chronic stress associated with lifelong infection. This suggests that due to gender differences in the impact of latent toxoplasmosis, future studies ought to perform separate analyses for women and men. Full article

(This article belongs to the Special Issue Effects of Toxoplasma gondii Infection on Human Behaviour)

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18 pages, 661 KiB

Open AccessReview

Potential for Developing Plant-Derived Candidate Vaccines and Biologics against Emerging Coronavirus Infections

by Balamurugan Shanmugaraj, Konlavat Siriwattananon, Ashwini Malla and Waranyoo Phoolcharoen

Pathogens 2021, 10(8), 1051; https://doi.org/10.3390/pathogens10081051 - 19 Aug 2021

Cited by 17 | Viewed by 6343

Abstract

The emerging human coronavirus infections in the 21st century remain a major public health crisis causing worldwide impact and challenging the global health care system. The virus is circulating in several zoonotic hosts and continuously evolving, causing occasional outbreaks due to spill-over events [...] Read more.

The emerging human coronavirus infections in the 21st century remain a major public health crisis causing worldwide impact and challenging the global health care system. The virus is circulating in several zoonotic hosts and continuously evolving, causing occasional outbreaks due to spill-over events occurring between animals and humans. Hence, the development of effective vaccines or therapeutic interventions is the current global priority in order to reduce disease severity, frequent outbreaks, and to prevent future infections. Vaccine development for newly emerging pathogens takes a long time, which hinders rapid immunization programs. The concept of plant-based pharmaceuticals can be readily applied to meet the recombinant protein demand by means of transient expression. Plants are evolved as an expression platform, and they bring a combination of unique interests in terms of rapid scalability, flexibility, and economy for industrial-scale production of effective vaccines, diagnostic reagents, and other biopharmaceuticals. Plants offer safe biologics to fulfill emergency demands, especially during pandemic situations or outbreaks caused by emerging strains. This review highlights the features of a plant expression platform for producing recombinant biopharmaceuticals to combat coronavirus infections with emphasis on COVID-19 vaccine and biologics development. Full article

(This article belongs to the Collection Emerging and Re-emerging Pathogens)

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22 pages, 2226 KiB

Open AccessEditor’s ChoiceArticle

The History of Anti-Trypanosome Vaccine Development Shows That Highly Immunogenic and Exposed Pathogen-Derived Antigens Are Not Necessarily Good Target Candidates: Enolase and ISG75 as Examples

by Stefan Magez, Zeng Li, Hang Thi Thu Nguyen, Joar Esteban Pinto Torres, Pieter Van Wielendaele, Magdalena Radwanska, Jakub Began, Sebastian Zoll and Yann G.-J. Sterckx

Pathogens 2021, 10(8), 1050; https://doi.org/10.3390/pathogens10081050 - 19 Aug 2021

Cited by 11 | Viewed by 4480

Abstract

Salivarian trypanosomes comprise a group of extracellular anthroponotic and zoonotic parasites. The only sustainable method for global control of these infection is through vaccination of livestock animals. Despite multiple reports describing promising laboratory results, no single field-applicable solution has been successful so far. [...] Read more.

Salivarian trypanosomes comprise a group of extracellular anthroponotic and zoonotic parasites. The only sustainable method for global control of these infection is through vaccination of livestock animals. Despite multiple reports describing promising laboratory results, no single field-applicable solution has been successful so far. Conventionally, vaccine research focusses mostly on exposed immunogenic antigens, or the structural molecular knowledge of surface exposed invariant immunogens. Unfortunately, extracellular parasites (or parasites with extracellular life stages) have devised efficient defense systems against host antibody attacks, so they can deal with the mammalian humoral immune response. In the case of trypanosomes, it appears that these mechanisms have been perfected, leading to vaccine failure in natural hosts. Here, we provide two examples of potential vaccine candidates that, despite being immunogenic and accessible to the immune system, failed to induce a functionally protective memory response. First, trypanosomal enolase was tested as a vaccine candidate, as it was recently characterized as a highly conserved enzyme that is readily recognized during infection by the host antibody response. Secondly, we re-addressed a vaccine approach towards the Invariant Surface Glycoprotein ISG75, and showed that despite being highly immunogenic, trypanosomes can avoid anti-ISG75 mediated parasitemia control. Full article

(This article belongs to the Special Issue Immunity and Vaccine Development Efforts against Trypanosomatid Parasites)

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13 pages, 1641 KiB

Open AccessArticle

Pragmatic Strategy for Fecal Specimen Storage and the Corresponding Test Methods for Clostridioides difficile Diagnosis

by Seong Won Nho, Minjae Kim, Seong-Jae Kim, Steven L. Foley, Rajesh Nayak, Ohgew Kweon and Carl E. Cerniglia

Pathogens 2021, 10(8), 1049; https://doi.org/10.3390/pathogens10081049 - 18 Aug 2021

Cited by 2 | Viewed by 3056

Abstract

The quality of fecal specimens is one of the factors responsible for successful Clostridioides difficile infection (CDI) diagnosis. The quality depends largely on the storage conditions, including the temperature and time period. In this study, we organized the outputs of previous studies, filled [...] Read more.

The quality of fecal specimens is one of the factors responsible for successful Clostridioides difficile infection (CDI) diagnosis. The quality depends largely on the storage conditions, including the temperature and time period. In this study, we organized the outputs of previous studies, filled experimental gaps in the knowledge of storage conditions, and introduced a pragmatic strategy for fecal storage for CDI diagnosis. A 5-step pathway was adopted to develop the fecal specimen storage strategy as follows: step 1, bibliomic analysis; step 2, experimental gap-filling; step 3, comparative evaluation; step 4, strategy development; step 5, internal review. Step 1 identified eight articles providing experimental information on the effects of fecal specimen storage conditions on the effectiveness of C. difficile detection methods. Step 2 provided additional quantitative data on C. difficile vegetative and spore cell viability and DNA stability. All previous and current results were compared (step 3). In step 4, fir general and nine special strategies were developed, followed by an internal review of the overall approaches (step 5). It is recommended to separate fecal samples into aliquots before testing and storing them. It is particularly recommended that fecal specimen samples be stored for CDI diagnosis at 4 °C for up to 60 days for all test methods. Full article

(This article belongs to the Special Issue Molecular Diagnostics for Infectious Diseases)

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21 pages, 2104 KiB

Open AccessReview

Artificial Intelligence in Surveillance, Diagnosis, Drug Discovery and Vaccine Development against COVID-19

by Gunjan Arora, Jayadev Joshi, Rahul Shubhra Mandal, Nitisha Shrivastava, Richa Virmani and Tavpritesh Sethi

Pathogens 2021, 10(8), 1048; https://doi.org/10.3390/pathogens10081048 - 18 Aug 2021

Cited by 48 | Viewed by 15754

Abstract

As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment [...] Read more.

As of August 6th, 2021, the World Health Organization has notified 200.8 million laboratory-confirmed infections and 4.26 million deaths from COVID-19, making it the worst pandemic since the 1918 flu. The main challenges in mitigating COVID-19 are effective vaccination, treatment, and agile containment strategies. In this review, we focus on the potential of Artificial Intelligence (AI) in COVID-19 surveillance, diagnosis, outcome prediction, drug discovery and vaccine development. With the help of big data, AI tries to mimic the cognitive capabilities of a human brain, such as problem-solving and learning abilities. Machine Learning (ML), a subset of AI, holds special promise for solving problems based on experiences gained from the curated data. Advances in AI methods have created an unprecedented opportunity for building agile surveillance systems using the deluge of real-time data generated within a short span of time. During the COVID-19 pandemic, many reports have discussed the utility of AI approaches in prioritization, delivery, surveillance, and supply chain of drugs, vaccines, and non-pharmaceutical interventions. This review will discuss the clinical utility of AI-based models and will also discuss limitations and challenges faced by AI systems, such as model generalizability, explainability, and trust as pillars for real-life deployment in healthcare. Full article

(This article belongs to the Special Issue Detection and Characterization of Drug-Resistant Organisms)

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12 pages, 616 KiB

Open AccessArticle

A Three-Year Biocrime Sanitary Surveillance on Illegally Imported Companion Animals

by Monia Cocchi, Patrizia Danesi, Gabrita De Zan, Marta Leati, Laura Gagliazzo, Margherita Ruggeri, Manlio Palei, Alessandro Bremini, Marie-Christin Rossmann, Melanie Lippert-Petscharnig, Michael-Dieter Mansfeld, Silvia Deotto, Sofia Leardini, Federica Gobbo, Paolo Zucca and Paola De Benedictis

Pathogens 2021, 10(8), 1047; https://doi.org/10.3390/pathogens10081047 - 18 Aug 2021

Cited by 5 | Viewed by 3630

Abstract

The illegal trade of companion animals in the European Union poses several legal, ethical and health issues to the entire community. In the framework of the Biocrime Interreg project between Italy and Austria, we surveyed puppies and kittens confiscated at the borders to [...] Read more.

The illegal trade of companion animals in the European Union poses several legal, ethical and health issues to the entire community. In the framework of the Biocrime Interreg project between Italy and Austria, we surveyed puppies and kittens confiscated at the borders to identify the most frequent pathogens associated with (i) the risk of spread within the shelter, (ii) the development of fatal disease and (iii) the zoonotic potential. From January 2018 to December 2020, we examined a total of 613 puppies and 62 kittens coming from 44 requisitions. Feces, skin specimens and blood sera from confiscated animals were tested to verify the presence of major infections and to assess the rabies post-vaccination immunity. Out of the total of individuals under investigation, necropsies and laboratory investigations were also performed on 79 puppies and three kittens that had died during the observation period. Results indicated a high prevalence of Canine Parvovirus (CPV) and Giardia spp. infections, CPV as the most likely cause of fatal gastroenteritis in puppies and Salmonella and Microsporum canis as major zoonotic pathogens. Conversely, both extended spectrum beta lactamases Escherichia coli and methicillin resistant Staphylococcus pseudintermedius strains as rare findings. Results highlighted that illegal animal trade could expose the human population to potential zoonotic risk and naïve animal population to potentially disrupting epidemic waves, both of these issues being largely underestimated when buying companion animals. Full article

(This article belongs to the Special Issue Epidemiology, Surveillance and Control of Infectious Diseases)

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15 pages, 5561 KiB

Open AccessCase Report

First Report of a Case of Ocular Infection Caused by Purpureocillium lilacinum in Poland

by Robert Kuthan, Anna K. Kurowska, Justyna Izdebska, Jacek P. Szaflik, Anna Lutyńska and Ewa Swoboda-Kopeć

Pathogens 2021, 10(8), 1046; https://doi.org/10.3390/pathogens10081046 - 18 Aug 2021

Cited by 1 | Viewed by 2918

Abstract

This report describes the first case of an ocular infection induced by Purpureocillium lilacinum in Poland. The patient was a 51-year-old immunocompetent contact lens user who suffered from subacute keratitis and progressive granulomatous uveitis. He underwent penetrating keratoplasty for corneal perforation, followed by [...] Read more.

This report describes the first case of an ocular infection induced by Purpureocillium lilacinum in Poland. The patient was a 51-year-old immunocompetent contact lens user who suffered from subacute keratitis and progressive granulomatous uveitis. He underwent penetrating keratoplasty for corneal perforation, followed by cataract surgery due to rapid uveitic cataract. A few weeks later, intraocular lens removal and pars plana vitrectomy were necessary due to endophthalmitis. The patient was treated with topical, systemic, and intravitreal voriconazole with improvement; however, the visual outcome was poor. The pathogen was identified by MALDI-TOF MS. Full article

(This article belongs to the Special Issue Filamentous Fungal Pathogens)

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5 pages, 1174 KiB

Open AccessCase Report

Renal Thrombotic Microangiopathy in Concurrent COVID-19 Vaccination and Infection

by Marco De Fabritiis, Maria Laura Angelini, Benedetta Fabbrizio, Giovanna Cenacchi, Claudio Americo, Stefania Cristino, Maria Francesca Lifrieri, Maria Cappuccilli, Alessandra Spazzoli, Loretta Zambianchi and Giovanni Mosconi

Pathogens 2021, 10(8), 1045; https://doi.org/10.3390/pathogens10081045 - 17 Aug 2021

Cited by 22 | Viewed by 3305

Abstract

We report on the development of nephrotic proteinuria and microhematuria, with histological features of renal thrombotic microangiopathy (TMA), following the first dose of BNT162b2 COVID-19 vaccine (Pfizer-BioNTech) and COVID-19 diagnosis. A 35-year-old previously healthy man was admitted at our hospital due to the [...] Read more.

We report on the development of nephrotic proteinuria and microhematuria, with histological features of renal thrombotic microangiopathy (TMA), following the first dose of BNT162b2 COVID-19 vaccine (Pfizer-BioNTech) and COVID-19 diagnosis. A 35-year-old previously healthy man was admitted at our hospital due to the onset of foamy urine. Previously, 40 days earlier, he had received the first injection of the vaccine, and 33 days earlier, the RT-PCR for SARS-CoV-2 tested positive. Laboratory tests showed nephrotic proteinuria (7.9 gr/day), microhematuria, serum creatinine 0.91 mg/dL. Kidney biopsy revealed ultrastructural evidence of severe endothelial cell injury suggestive of a starting phase of TMA. After high-dose steroid treatment administration, complete remission of proteinuria was achieved in a few weeks. The association of COVID-19 with renal TMA has been previously described only in patients with acute renal injury. Besides, the correlation with COVID-19 vaccine has not been reported so far. The close temporal proximity (7 days) between the two events opens the question whether the histological findings should be ascribed to COVID-19 itself or to vaccine injection. Full article

(This article belongs to the Special Issue Advances in Human Pathogens Infections)

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23 pages, 3866 KiB

Open AccessSystematic Review

Pathogens Spillover from Honey Bees to Other Arthropods

by Antonio Nanetti, Laura Bortolotti and Giovanni Cilia

Pathogens 2021, 10(8), 1044; https://doi.org/10.3390/pathogens10081044 - 17 Aug 2021

Cited by 64 | Viewed by 9158

Abstract

Honey bees, and pollinators in general, play a major role in the health of ecosystems. There is a consensus about the steady decrease in pollinator populations, which raises global ecological concern. Several drivers are implicated in this threat. Among them, honey bee pathogens [...] Read more.

Honey bees, and pollinators in general, play a major role in the health of ecosystems. There is a consensus about the steady decrease in pollinator populations, which raises global ecological concern. Several drivers are implicated in this threat. Among them, honey bee pathogens are transmitted to other arthropods populations, including wild and managed pollinators. The western honey bee, Apis mellifera, is quasi-globally spread. This successful species acted as and, in some cases, became a maintenance host for pathogens. This systematic review collects and summarizes spillover cases having in common Apis mellifera as the mainteinance host and some of its pathogens. The reports are grouped by final host species and condition, year, and geographic area of detection and the co-occurrence in the same host. A total of eighty-one articles in the time frame 1960–2021 were included. The reported spillover cases cover a wide range of hymenopteran host species, generally living in close contact with or sharing the same environmental resources as the honey bees. They also involve non-hymenopteran arthropods, like spiders and roaches, which are either likely or unlikely to live in close proximity to honey bees. Specific studies should consider host-dependent pathogen modifications and effects on involved host species. Both the plasticity of bee pathogens and the ecological consequences of spillover suggest a holistic approach to bee health and the implementation of a One Health approach. Full article

(This article belongs to the Special Issue Infection in Honey Bees: Host–Pathogen Interaction and Spillover)

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26 pages, 4503 KiB

Open AccessFeature PaperArticle

Survey of Ticks and Tick-Borne Rickettsial and Protozoan Pathogens in Eswatini

by Kimberly J. Ledger, Lorenza Beati and Samantha M. Wisely

Pathogens 2021, 10(8), 1043; https://doi.org/10.3390/pathogens10081043 - 17 Aug 2021

Cited by 12 | Viewed by 4421

Abstract

Ticks are widespread parasites of vertebrates and major vectors of pathogens to humans, domestic animals, and wildlife. In southern Africa, numerous tick species transmit diseases of economic and health importance. This study aimed to describe the occurrence of ticks and tick-borne pathogens in [...] Read more.

Ticks are widespread parasites of vertebrates and major vectors of pathogens to humans, domestic animals, and wildlife. In southern Africa, numerous tick species transmit diseases of economic and health importance. This study aimed to describe the occurrence of ticks and tick-borne pathogens in multiple land-use types and the possible role of ticks in the transmission of pathogen species. Using molecular techniques, we screened 1716 ticks for infection by rickettsial bacteria and protozoans. To characterize pathogen identity, we sequenced multiple loci from positive samples and analyzed sequences within a phylogenetic framework. Across the seven tick species collected as nymphs or adults, we detected Rickettsia, Anaplasma, Ehrlichia, Babesia, Hepatozoon, and Theileira species. We found that some tick species and tick-borne pathogens differed according to land use. For example, we found a higher density of Haemaphysalis elliptica and higher prevalence of Rickettsia in H. elliptica collected from savanna grasses used for livestock grazing near human settlements than savanna grasses in conservation areas. These findings highlight the importance of comprehensive surveillance to achieve a full understanding of the diversity and ecology of the tick-borne pathogens that can infect humans, domestic animals, and wildlife. Full article

(This article belongs to the Special Issue Ticks and Tick-Borne Diseases―Pathogens, Parasites and People)

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14 pages, 1892 KiB

Open AccessArticle

Monitoring the Circulation of SARS-CoV-2 Variants by Genomic Analysis of Wastewater in Marseille, South-East France

by Nathalie Wurtz, Océane Revol, Priscilla Jardot, Audrey Giraud-Gatineau, Linda Houhamdi, Christophe Soumagnac, Alexandre Annessi, Alexandre Lacoste, Philippe Colson, Sarah Aherfi and Bernard La Scola

Pathogens 2021, 10(8), 1042; https://doi.org/10.3390/pathogens10081042 - 17 Aug 2021

Cited by 20 | Viewed by 4141

Abstract

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to [...] Read more.

The monitoring of SARS-CoV-2 RNA in sewage has been proposed as a simple and unbiased means of assessing epidemic evolution and the efficiency of the COVID-19 control measures. The past year has been marked by the emergence of variants that have led to a succession of epidemic waves. It thus appears that monitoring the presence of SARS-CoV-2 in wastewater alone is insufficient, and it may be important in the future to also monitor the evolution of these variants. We used a real-time RT-PCR screening test for variants in the wastewater of our city to assess the effectiveness of direct SARS-CoV-2 sequencing from the same wastewater. We compared the genome sequencing results obtained over the large RS network and the smaller B7 network with the different distributions of the variants observed by RT-PCR screening. The prevalence of the “UK variant” in the RS and B7 networks was estimated to be 70% and 8% using RT-PCR screening compared to 95% and 64% using genome sequencing, respectively. The latter values were close to the epidemiology observed in patients of the corresponding area, which were 91% and 58%, respectively. Genome sequencing in sewage identified SARS-CoV-2 of lineage B.1.525 in B7 at 27% (37% in patients), whereas it was completely missed by RT-PCR. We thus determined that direct sequencing makes it possible to observe, in wastewater, a distribution of the variants comparable to that revealed by genomic monitoring in patients and that this method is more accurate than RT-PCR. It also shows that, rather than a single large sample, it would be preferable to analyse several targeted samples if we want to more appropriately assess the geographical distribution of the different variants. In conclusion, this work supports the wider surveillance of SARS-CoV-2 variants in wastewater by genome sequencing and targeting small areas on the condition of having a sequencing capacity and, when this is not the case, to developing more precise screening tests based on the multiplexed detection of the mutations of interest. Full article

(This article belongs to the Special Issue SARS-CoV-2 in the Water Environment)

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13 pages, 6450 KiB

Open AccessArticle

Specific Secondary Bile Acids Control Chicken Necrotic Enteritis

by Mohit Bansal, Tahrir Alenezi, Ying Fu, Ayidh Almansour, Hong Wang, Anamika Gupta, Rohana Liyanage, Danielle B. Graham, Billy M. Hargis and Xiaolun Sun

Pathogens 2021, 10(8), 1041; https://doi.org/10.3390/pathogens10081041 - 17 Aug 2021

Cited by 18 | Viewed by 4001

Abstract

Necrotic enteritis (NE), mainly induced by the pathogens of Clostridium perfringens and coccidia, causes huge economic losses with limited intervention options in the poultry industry. This study investigated the role of specific bile acids on NE development. Day-old broiler chicks were assigned to [...] Read more.

Necrotic enteritis (NE), mainly induced by the pathogens of Clostridium perfringens and coccidia, causes huge economic losses with limited intervention options in the poultry industry. This study investigated the role of specific bile acids on NE development. Day-old broiler chicks were assigned to six groups: noninfected, NE, and NE with four bile diets of 0.32% chicken bile, 0.15% commercial ox bile, 0.15% lithocholic acid (LCA), or 0.15% deoxycholic acid (DCA). The birds were infected with Eimeria maxima at day 18 and C. perfringens at day 23 and 24. The infected birds developed clinical NE signs. The NE birds suffered severe ileitis with villus blunting, crypt hyperplasia, epithelial line disintegration, and massive immune cell infiltration, while DCA and LCA prevented the ileitis histopathology. NE induced severe body weight gain (BWG) loss, while only DCA prevented NE-induced BWG loss. Notably, DCA reduced the NE-induced inflammatory response and the colonization and invasion of C. perfringens compared to NE birds. Consistently, NE reduced the total bile acids in the ileal digesta, while dietary DCA and commercial bile restored it. Together, this study showed that DCA and LCA reduced NE histopathology, suggesting that secondary bile acids, but not total bile acid levels, play an essential role in controlling the enteritis. Full article

(This article belongs to the Special Issue Microbe-Mediated Intestinal Diseases in Humans and Animals)

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8 pages, 590 KiB

Open AccessArticle

Optimization of DNA Extraction from Field-Collected Mammalian Whole Blood on Filter Paper for Trypanosoma cruzi (Chagas Disease) Detection

by Bonnie E. Gulas-Wroblewski, Rebecca B. Kairis, Rodion Gorchakov, Anna Wheless and Kristy O. Murray

Pathogens 2021, 10(8), 1040; https://doi.org/10.3390/pathogens10081040 - 17 Aug 2021

Cited by 7 | Viewed by 3506

Abstract

Blood filter paper strips are cost-effective materials used to store body fluid specimens under challenging field conditions, extending the reach of zoonotic pathogen surveillance and research. We describe an optimized procedure for the extraction of parasite DNA from whole blood (WB) stored on [...] Read more.

Blood filter paper strips are cost-effective materials used to store body fluid specimens under challenging field conditions, extending the reach of zoonotic pathogen surveillance and research. We describe an optimized procedure for the extraction of parasite DNA from whole blood (WB) stored on Type I Advantec Nobuto strips from both experimentally spiked and field-collected specimens from canine and skunks, respectively. When comparing two commercial kits for extraction, Qiagen’s DNeasy Blood & Tissue Kit performed best for the detection of parasite DNA by PCR from Trypanosoma cruzi-spiked canine WB samples on Nobuto strips. To further optimize recovery of β-actin from field-collected skunk WB archived on Nobuto strips, we modified the extraction procedures for the Qiagen kit with a 90 °C incubation step and extended incubation post-addition of proteinase K, a method subsequently employed to identify a T. cruzi infection in one of the skunks. Using this optimized extraction method can efficaciously increase the accuracy and precision of future molecular epidemiologic investigations targeting neglected tropical diseases in field-collected WB specimens on filter strips. 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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14 pages, 2988 KiB

Open AccessArticle

Recombinant SARS-CoV-2 Nucleocapsid Protein: Expression, Purification, and Its Biochemical Characterization and Utility in Serological Assay Development to Assess Immunological Responses to SARS-CoV-2 Infection

by Da Di, Mythili Dileepan, Shamim Ahmed, Yuying Liang and Hinh Ly

Pathogens 2021, 10(8), 1039; https://doi.org/10.3390/pathogens10081039 - 16 Aug 2021

Cited by 13 | Viewed by 4292

Abstract

The SARS-CoV-2 nucleocapsid protein (N) binds a single-stranded viral RNA genome to form a helical ribonucleoprotein complex that is packaged into virion particles. N is relatively conserved among coronaviruses and consists of the N-terminal domain (NTD) and C-terminal domain (CTD), which are flanked [...] Read more.

The SARS-CoV-2 nucleocapsid protein (N) binds a single-stranded viral RNA genome to form a helical ribonucleoprotein complex that is packaged into virion particles. N is relatively conserved among coronaviruses and consists of the N-terminal domain (NTD) and C-terminal domain (CTD), which are flanked by three disorganized regions. N is highly immunogenic and has been widely used to develop a serological assay as a diagnostic tool for COVID-19 infection, although there is a concern that the natural propensity of N to associate with RNA might compromise the assay’s specificity. We expressed and purified from bacterial cells two recombinant forms of SARS-CoV-2 N, one from the soluble fraction of bacterial cell lysates that is strongly associated with bacterial RNAs and the other that is completely devoid of RNAs. We showed that both forms of N can be used to develop enzyme-linked immunosorbent assays (ELISAs) for the specific detection of human and mouse anti-N monoclonal antibodies (mAb) as well as feline SARS-CoV-2 seropositive serum samples, but that the RNA-free form of N exhibits a slightly higher level of sensitivity than the RNA-bound form to react to anti-N mouse mAb. Using the electrophoretic mobility shift assay (EMSA), we also showed that N preferentially binds ssRNA in a sequence-independent manner and that both NTD and CTD of N contribute to RNA-binding activity. Collectively, our study describes methods to express, purify, and biochemically characterize the SARS-CoV-2 N protein and to use it for the development of serological assays to detect SARS-CoV-2 infection. Full article

(This article belongs to the Collection Immunological Responses and Immune Defense Mechanism)

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