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Molecular Epidemiology and Diagnosis of Parasitic Zoonosis

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Parasitology".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 28129

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Prof. Dr. Simonetta Mattiucci

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Section of Parasitology, Department of Public Health and Infectious Diseases, "Sapienza - University of Rome" and "Umberto I" University Hospital, Rome, Italy
Interests: parasitology; population genetics; genetic diversity; gene expression analysis; Transcriptomics; molecular markers; genetics; molecular systematics; sequencing; phylogenetics; molecular population genetics; diagnostics

Prof. Dr. Antonio Varcasia

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Guest Editor

Parasitology and Parasitic Diseases of the Department of Veterinary Medicine, University of Sassari, via Vienna 2, 07100 Sassari, Italy
Interests: genotyping; molecular biology; immunology; sequencing; DNA extraction; PCR; infectious disease epidemiology; infection; genetics; DNA

Dr. Simona Gabrielli

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Guest Editor

Department of Public Health and Infectious Diseases, Sapienza University of Rome, P.le Aldo Moro, 5, 00185 Rome, Italy
Interests: tropical diseases; parasitic diseases; infectious disease epidemiology; PCR; molecular biology; antibodies; ELISA; genetics; DNA; infection
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The current pandemic of SARS-CoV-2 has once again pointed out the possible occurrence of the phenomenon known as "spillover" as a cause of zoonotic infections. The majority of the human parasitic diseases due to protozoa and helminths are of zoonotic origin. Several factors in the last decades have modified and sometimes increased the diffusion of parasitic zoonosis, such as habitat disturbance and ecosystems deterioration with increased contacts with wildlife species; climate change possibly affecting the distribution range of parasites and vectors; eating habits; military action and wars; increasing popularity for exotic pets; and others.

Despite the extensive research that has so far been performed on parasitic zoonoses, most of them still remain not fully investigated and underestimated. However, in recent years, the application of genetic molecular methodologies—attempts in the genomics, transcriptomics, and proteomics of these parasites—have provided new insights and knowledge on their molecular epidemiology, host–parasite interaction, and diagnosis. This Special Issue aims to collect updated studies on zoonotic parasites, highlighting aspects of the molecular epidemiology and diagnosis of parasitic diseases achieved by using innovative approaches.

In detail, the main topics of the Issue will be:

Advances in the genomics of parasites, etiological agents of zoonosis;
Host–parasite interface studies;
Transcriptomic profiles of parasites, etiological agents of zoonosis;
Interactions between parasites and the host’s microbiome;
Emerging and re-emerging zoonotic parasites;
Immune response to zoonotic parasites;
Epidemiological updates on the most important parasitic zoonoses;
Possible effects of climate change and anthropogenic impacts on the epidemiology of parasitic zoonosis

Prof. Dr. Simonetta Mattiucci
Dr. Antonio Varcasia
Dr. Simona Gabrielli
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Research

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16 pages, 2651 KiB

Open AccessArticle

A Novel Relapsing Fever Group Borrelia Isolated from Ornithodoros Ticks of the Brazilian Caatinga

by Glauber M. B. de Oliveira, Sebastián Muñoz-Leal, Adriana Santodomingo, Barbara C. Weck, Álvaro A. Faccini-Martínez, Maurício C. Horta and Marcelo B. Labruna

Microorganisms 2023, 11(2), 370; https://doi.org/10.3390/microorganisms11020370 - 01 Feb 2023

Cited by 4 | Viewed by 1615

Abstract

Tick-borne relapsing fever group (RFG) borreliosis remains neglected as a human disease and little is known on its maintenance in ticks and vertebrates, especially in South America. Therefore, this study investigated borrelial infection in Ornithodoros ticks collected in rodent-inhabited rock formations in the Brazilian semiarid region, within the Caatinga biome. Collected ticks (Ornithodoros rietcorreai and Ornithodoros cf. tabajara) were allowed to feed under laboratory conditions on guinea pigs, which had blood samples examined daily by dark-field microscopy. No spirochetes were visualized in the blood of any of four O. rietcorreai-infested guinea pigs. Contrastingly, spirochetes were visualized between 9 and 39 days after tick feeding in the blood of three guinea pigs, each infested with O. cf. tabajara ticks from a different locality. Guinea pig infection was confirmed by passages into experimental animals and by generating DNA sequences of Borrelia spp. from the blood of spirochetemic guinea pigs. Three O. cf. tabajara populations were infected by the same borrelial organism, which was characterized as a novel RFG agent (named as ‘Candidatus Borrelia caatinga’) based on 10 Borrelia loci (rrs, flaB, glpQ, gyrB, clpX, pepX, pyrG, recG, rplB and uvrA). We demonstrated that O. cf. tabajara is a competent vector of the novel Borrelia sp. isolates, although none of the infected rodents developed clinical illness. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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12 pages, 301 KiB

Open AccessArticle

Comparative Evaluation of Real-Time Screening PCR Assays for Giardia duodenalis and of Assays Discriminating the Assemblages A and B

by Felix Weinreich, Andreas Hahn, Kirsten Alexandra Eberhardt, Simone Kann, Torsten Feldt, Fred Stephen Sarfo, Veronica Di Cristanziano, Hagen Frickmann and Ulrike Loderstädt

Microorganisms 2022, 10(7), 1310; https://doi.org/10.3390/microorganisms10071310 - 28 Jun 2022

Cited by 1 | Viewed by 1727

Abstract

Due to superior sensitivity compared to traditional microscopy, real-time PCR has been well established for the diagnosis of Giardia duodenalis in human stool samples. In this study, screening real-time PCRs for different target genes of G. duodenalis, i.e., the 18S rRNA gene, the gdh (glutamate dehydrogenase) gene and the bg (beta-giardin) gene, were comparatively assessed next to various real-time PCR assays for the discrimination of the assemblages A and B of G. duodenalis targeting the bg gene with and without locked nucleic acid–containing probes as well as the tpi (triose phosphate isomerase) gene. The screening PCRs were assessed by including 872 non-preselected samples with a high pre-test probability for G. duodenalis in the statistical analysis, while 53 G. duodenalis-positive samples as indicated by at least two screening PCRs were finally included in the assessment of the assemblage-specific PCRs. For the screening PCRs, sensitivity estimated with latent class analysis (LCA) ranged from 17.5% to 100%, specificity from 92.3% to 100% with an accuracy-adjusted prevalence of 7.2% for G. duodenalis within the non-preselected sample collection. In detail, sensitivity and specificity were 100% and 100% for the 18S rRNA gene-specific assay, 17.5% and 92.3% for the gdh gene-specific assay, and 31.7% and 100% for the bg gene-specific assay, respectively. Agreement kappa was slight with only 15.5%. For the assemblage-specific PCRs, estimated sensitivity ranged from 82.1% to 100%, specificity from 84.0% to 100% with nearly perfect agreement kappa of 90.1% for assemblage A and yet substantial agreement of 74.8% for assemblage B. In detail for assemblage A, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without locked nucleic acids (LNA) as well as 100% and 97.8% for both the bg gene-specific assay with LNA and the tri gene-specific assay, respectively. For assemblage B, sensitivity and specificity were 100% and 100% for the bg gene-specific assay without LNA, 96.4% and 84.0% for the bg gene-specific assay with LNA, and 82.1% and 100% for the tri gene-specific assay, respectively. Within the assessed sample collection, the observed proportion comprised 15.1% G. duodenalis assemblage A, 52.8% G. duodenalis assemblage B and 32.1% non-resolved assemblages. Only little differences were observed regarding the cycle threshold (Ct) values when comparing the assays. In conclusion, best diagnostic accuracy was shown for an 18S rRNA gene-specific screening assay for G. duodenalis and for a differentiation assay discriminating the G. duodenalis assemblages A and B by targeting the bg gene with probes not containing locked nucleic acids. By adding additional highly specific competitor assays for confirmation testing, diagnostic specificity can be further increased on the cost of sensitivity if optimized specificity is desired. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

10 pages, 2879 KiB

Open AccessArticle

Molecular Subtyping of Blastocystis sp. Isolated from Farmed Animals in Southern Italy

by Simona Gabrielli, Marialetizia Palomba, Federica Furzi, Emanuele Brianti, Gabriella Gaglio, Ettore Napoli, Laura Rinaldi, Renato Aco Alburqueque and Simonetta Mattiucci

Microorganisms 2021, 9(8), 1656; https://doi.org/10.3390/microorganisms9081656 - 03 Aug 2021

Cited by 16 | Viewed by 2604

Abstract

Blastocystis is a common intestinal protist distributed worldwide, infecting humans and a wide range of domestic and wild animals. It exhibits an extensive genetic diversity and, so far, 25 distinct small subunit ribosomal RNA (SSU rRNA) lineages termed subtypes (STs)) have been characterized; among them, 12 have thus far been reported in humans. The aims of the present study were to detect and genetically characterize Blastocystis sp. in synantropic animals to improve our current knowledge on the distribution and zoonotic transmission of Blastocystis STs in Italy. Samples were collected from N = 193 farmed animals and submitted to DNA extraction and PCR amplification of the SSU rRNA. Blastocystis was detected in 60 samples (31.08%) and successfully subtyped. Phylogenetic analysis evidenced that the isolates from fallow deer, goats, and pigs (N = 9) clustered within the ST5; those from pheasants (N = 2) in the ST6; those from chickens (N = 8) in the ST7; those from sheep (N = 6) in the ST10; and those from water buffaloes (N = 9) in the ST14 clade. The comparison between the present isolates from animals and those previously detected in humans in Italy suggested the animal-to-human spillover for ST6 and ST7. The present study represents the widest Blastocystis survey performed thus far in farmed animals in Italy. Further epidemiological studies using molecular approaches are required to determine the occurrence and distribution of Blastocystis STs in other potential animal reservoirs in Italy and to define the pathways of zoonotic transmission. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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21 pages, 2469 KiB

Open AccessEditor’s ChoiceArticle

Mind the Gap: New Full-Length Sequences of Blastocystis Subtypes Generated via Oxford Nanopore Minion Sequencing Allow for Comparisons between Full-Length and Partial Sequences of the Small Subunit of the Ribosomal RNA Gene

by Jenny G. Maloney and Monica Santin

Microorganisms 2021, 9(5), 997; https://doi.org/10.3390/microorganisms9050997 - 05 May 2021

Cited by 56 | Viewed by 4547

Abstract

Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subunit ribosomal (SSU rRNA) RNA gene. Though full-length reference sequences of the SSU rRNA gene are a current requirement to name a novel Blastocystis subtype, full-length reference sequences are not currently available for all subtypes. In the present study, Oxford Nanopore MinION long-read sequencing was employed to generate full-length SSU rRNA sequences for seven new Blastocystis subtypes for which no full-length references currently exist: ST21, ST23, ST24, ST25, ST26, ST27, and ST28. Phylogenetic analyses and pairwise distance matrixes were used to compare full-length and partial sequences of the two regions that are most commonly used for subtyping. Analyses included Blastocystis nucleotide sequences obtained in this study (ST21 and ST23–ST28) and existing subtypes for which full-length reference sequences were available (ST1–ST17 and ST29). The relationships and sequence variance between new and existing subtypes observed in analyses of different portions of the SSU rRNA gene are discussed. The full-length SSU rRNA reference sequences generated in this study provide essential new data to study and understand the relationships between the genetic complexity of Blastocystis and its host specificity, pathogenicity, and epidemiology. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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11 pages, 696 KiB

Open AccessArticle

Molecular Characterization of Giardia duodenalis in Children and Adults Sampled in Algeria

by Salem Belkessa, Daniel Thomas-Lopez, Karim Houali, Farida Ghalmi and Christen Rune Stensvold

Microorganisms 2021, 9(1), 54; https://doi.org/10.3390/microorganisms9010054 - 28 Dec 2020

Cited by 9 | Viewed by 2877

Abstract

The molecular epidemiology of giardiasis in Africa remains unclear. A study was carried out across four hospitals in Algeria. A total of 119 fecal samples from 55 children, 37 adults, and 27 individuals of undetermined age, all scored positive for intestinal parasites by microscopy, and were screened by real-time PCR for Giardia. Molecular characterization of Giardia was performed by assemblage-specific PCR and PCR targeting the triose phosphate isomerase gene (tpi). Of the 119 samples, 80 (67%) were Giardia-positive by real-time PCR. For 48 moderately-highly real-time PCR-positive samples, tpi genotyping assigned 22 samples to Assemblage A and 26 to Assemblage B. Contrary to Assemblage A, Assemblage B exhibited substantial genetic diversity and allelic heterozygosity. Assemblage-specific PCR proved to be specific for discriminating Assemblage A or B but not as sensitive as tpi genotyping. We confirmed that real-time PCR is more sensitive than microscopy for detecting Giardia in stool samples and that robust amplification and sequencing of the tpi gene is feasible when moderate-to-strongly real-time PCR-positive samples are used. This study is one of the few performed in Africa providing genotyping data on Giardia infections in humans. Both assemblages A and B were commonly seen and not associated with specific sociodemographic data. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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Review

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25 pages, 1182 KiB

Open AccessReview

Detection of Cryptosporidium spp. and Giardia spp. in Environmental Water Samples: A Journey into the Past and New Perspectives

by Marie-Stéphanie Fradette, Alexander I. Culley and Steve J. Charette

Microorganisms 2022, 10(6), 1175; https://doi.org/10.3390/microorganisms10061175 - 07 Jun 2022

Cited by 13 | Viewed by 4959

Abstract

Among the major issues linked with producing safe water for consumption is the presence of the parasitic protozoa Cryptosporidium spp. and Giardia spp. Since they are both responsible for gastrointestinal illnesses that can be waterborne, their monitoring is crucial, especially in water sources feeding treatment plants. Although their discovery was made in the early 1900s and even before, it was only in 1999 that the U.S. Environmental Protection Agency (EPA) published a standardized protocol for the detection of these parasites, modified and named today the U.S. EPA 1623.1 Method. It involves the flow-through filtration of a large volume of the water of interest, the elution of the biological material retained on the filter, the purification of the (oo)cysts, and the detection by immunofluorescence of the target parasites. Since the 1990s, several molecular-biology-based techniques were also developed to detect Cryptosporidium and Giardia cells from environmental or clinical samples. The application of U.S. EPA 1623.1 as well as numerous biomolecular methods are reviewed in this article, and their advantages and disadvantages are discussed guiding the readers, such as graduate students, researchers, drinking water managers, epidemiologists, and public health specialists, through the ever-expanding number of techniques available in the literature for the detection of Cryptosporidium spp. and Giardia spp. in water. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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17 pages, 1664 KiB

Open AccessReview

Vaccination against Tick-Borne Encephalitis (TBE) in Italy: Still a Long Way to Go

by Donatella Panatto, Alexander Domnich, Daniela Amicizia, Paolo Reggio and Raffaella Iantomasi

Microorganisms 2022, 10(2), 464; https://doi.org/10.3390/microorganisms10020464 - 18 Feb 2022

Cited by 11 | Viewed by 4894

Abstract

Tick-borne encephalitis (TBE) is endemic in several European countries, and its incidence has recently increased. Various factors may explain this phenomenon: social factors (changes in human behavior, duration and type of leisure activities and increased tourism in European high-risk areas), ecological factors (e.g., effects of climate change on the tick population and reservoir animals), and technological factors (improved diagnostics, increased medical awareness). Furthermore, the real burden of TBE is not completely known, as the performance of surveillance systems is suboptimal and cases of disease are under-reported in several areas. Given the potentially severe clinical course of the disease, the absence of any antiviral therapy, and the impossibility of interrupting the transmission of the virus in nature, vaccination is the mainstay of prevention and control. TBE vaccines are effective (protective effect of approximately 95% after completion of the basic vaccination—three doses) and well tolerated. However, their uptake in endemic areas is suboptimal. In the main endemic countries where vaccination is included in the national/regional immunization program (with reimbursed vaccination programs), this decision was driven by a cost-effectiveness assessment (CEA), which is a helpful tool in the decision-making process. All CEA studies conducted have demonstrated the cost-effectiveness of TBE vaccination. Unfortunately, CEA is still lacking in many endemic countries, including Italy. In the future, it will be necessary to fill this gap in order to introduce an effective vaccination strategy in endemic areas. Finally, raising awareness of TBE, its consequences and the benefit of vaccination is critical in order to increase vaccination coverage and reduce the burden of the disease. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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19 pages, 1164 KiB

Open AccessSystematic Review

Parasites of Free-Ranging and Captive American Primates: A Systematic Review

by Silvia Rondón, Serena Cavallero, Erika Renzi, Andrés Link, Camila González and Stefano D’Amelio

Microorganisms 2021, 9(12), 2546; https://doi.org/10.3390/microorganisms9122546 - 09 Dec 2021

Cited by 6 | Viewed by 3163

Abstract

The diversity, spread, and evolution of parasites in non-human primates (NHPs) is a relevant issue for human public health as well as for NHPs conservation. Although previous reviews have recorded information on parasites in NHPs (Platyrrhines) in the Americas, the increasing number of recent studies has made these inventories far from complete. Here, we summarize information about parasites recently reported in Platyrrhines, attempting to build on earlier reviews and identify information gaps. A systematic literature search was conducted in PubMed, ISI Web of Science, and Latin American and Caribbean Health Sciences Literature (LILACS), and following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines. Ninety-three studies were included after the screening process. Records for 20 genera of NHPs, including 90 species were found. Most of the studies were conducted on captive individuals (54.1%), and morphological approaches were the most used for parasite identification. The most commonly collected biological samples were blood and stool, and Protozoa was the most frequent parasite group found. There is still scarce (if any) information on the parasites associated to several Platyrrhine species, especially for free-ranging populations. The use of molecular identification methods can provide important contributions to the field of NHPs parasitology in the near future. Finally, the identification of parasites in NHPs populations will continue to provide relevant information in the context of pervasive habitat loss and fragmentation that should influence both human public health and wildlife conservation strategies. Full article

(This article belongs to the Special Issue Molecular Epidemiology and Diagnosis of Parasitic Zoonosis)

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