Cost-effective method of DNA extraction from taeniid eggs

Plasma Circulating Cell-Free DNA Facilitated the Detection of an Alveolar Echinococcosis Patient Initially Misdiagnosed as Cystic Echinococcosis: A Case Report

Echinococcosis, especially alveolar echinococcosis (AE), is becoming an emerging/re-emerging disease with a growing number of cases reported globally. The diagnosis of echinococcosis is based mainly on imaging, which may be challenging when the image presentation is atypical. We reported one patient with suspected cystic echinococcosis (CE) by imaging. The cell-free DNA (cfDNA) obtained from sequencing the patient's plasma before the operation showed that this patient probably had AE with 45 reads mapped to the Echinococcus multilocularis reference genome (Read-Pairs Per Million = 0.24). The patients underwent surgery, and the pathological result showed that the patient had AE. The conventional polymerase chain reaction (PCR) of her lesion sample extraction also indicated that the infection was caused by Echinococcus multilocularis. The follow-up ultrasound after three months indicated no recurrence. We demonstrated that the differentiation of CE and AE by imaging may not be that easy, with further elaboration on the differentiation between AE and CE in different aspects. We demonstrated that it is possible to use patients' plasma cfDNA mapped to Echinococcus references before the operation to obtain the objective clue of the lesion to facilitate diagnosis.

Cultivation-free sample preparation and DNA purification for direct real-time qPCR of intracellular or spore-like Coxiella burnetii in beef, goat, and lamb meat

Coxiella burnetii is a zoonotic pathogen that has been associated with foodborne outbreaks in products with ruminant origins. However, a method to detect C. burnetii in meat has been merely studied, and commercial kits cannot efficiently fulfill this purpose. In this study, an in-house preparation method for direct real-time qPCR of C. burnetii in beef, goat, and lamb meat was designed. In the sample preparation step (step 1), trypsin digestion and cell disruption techniques were introduced to target C. burnetii in an obligate intracellular or spore-like form. Afterward, 16 DNA purification protocols involving the following steps (steps 2-3) were assessed: the precipitation of meat proteins (step 2; using 2.5, 5.0 M NaCl or 1:1, 2:1 ethanol as the precipitant) and binding of DNA to silicon dioxide particles with chaotropic salts (step 3; using 2.5, 5.0 M NaCl or 2.5, 5.0 M guanidine thiocyanate as the salt). The protocols with superior performance in high-spiked loins (estimated 4-5 log cells/g) were verified in low-spiked (1-2 log cells/g) or Bacillus thuringiensis spore-inoculated (1-2 log CFU/g) loins, ribs, and hind legs. During the protein precipitation, 5.0 M NaCl induced significantly lower protein level as demonstrated by A280, when compared to 2.5 M NaCl or ethanol (P < 0.05). For the DNA binding step, Ct values were lowered in high-spiked goat or lamb loins (3.5-6.0▾; P < 0.05) when the concentration of NaCl was doubled or guanidine thiocyanate was introduced instead of NaCl as a chaotropic salt. Based on these results, two protocols using 5.0 M NaCl as the protein precipitant and 5.0 M NaCl (N2 + N2) or guanidine thiocyanate (N2 + G2) as the chaotropic salt were selected, which demonstrated successful detection in low-spiked (Ct values of N2 + N2, 32.9-35.6; N2 + G2, 32.3-36.4) or spore-inoculated meat (N2 + N2, 30.9-37.5; N2 + G2, 29.7-32.7). Verification in low-spiked meat showed that meat type/part significantly impacted the Ct values of N2 + G2 but not those of N2 + N2. To our knowledge, this is the first study that developed a highly accessible method for detecting C. burnetii in meat which could reveal the possibility of meat-borne Q fever in humans.

Overview of renicolid digeneans (Digenea, Renicolidae) from marine gulls of northern Holarctic with remarks on their species statuses, phylogeny and phylogeography

Renicolid digeneans parasitize aquatic birds. Their intramolluscan stages develop in marine and brackish-water gastropods, while metacercariae develop in molluscs and fishes. The systematics of renicolids is poorly developed, their life cycles are mostly unknown, and the statuses of many species require revision. Here, we establish based on integrated morphological and molecular data that adult renicolids from gulls Larus argentatus and Larus schistisagus and sporocysts and cercariae of Cercaria parvicaudata from marine snails Littorina spp. are life-cycle stages of the same species. We name it Renicola parvicaudatus and synonymized with it Renicola roscovitus. An analysis of the cox1 gene of R. parvicaudatus from Europe, North America and North Asia demonstrates a low genetic divergence, suggesting that this species has formed quite recently (perhaps during last glacial maximum) and that interregional gene flow is high. In Littorina saxatilis and L. obtusata from the Barents Sea, molecular analysis has revealed intramolluscan stages of Cercaria littorinae saxatilis VIII, a cryptic species relative to R. parvicaudatus. In the molecular trees, Renicola keimahuri from L. schistisagus belongs to another clade than R. parvicaudatus. We show that the species of this clade have cercariae of Rhodometopa group and outline morphological and behavioural transformations leading from xiphidiocercariae to these larvae. Molecular analysis has revealed 3 main phylogenetic branches of renicolids, differing in structure of adults, type of cercariae and host range. Our results elucidate the patterns of host colonization and geographical expansion of renicolids and pave the way to the solution of some long-standing problems of their classification.

Copro-Molecular Identification of Tapeworms in Introduced Invasive Carnivores in Poland

The raccoon (Procyon lotor) and the raccoon dog (Nyctereutes procyonoides) were introduced to Europe and, in the past decades, their populations have increased and adapted to synanthropic environments across Europe. In view of their possible further spread in Europe, the invasive species should be examined as potential reservoirs for helminths, including tapeworms. This study aims to investigate the prevalence and diversity of tapeworms in introduced wild carnivores in Poland by identifying cestode species based on copro-DNA analysis. A total of 214 individual fecal samples from non-native invasive carnivores, i.e., raccoons and raccoon dogs, and additionally 47 samples from native carnivores, i.e., European badgers (Meles meles), were analyzed for the presence of cestodes. PCR analysis of fecal samples targeting a fragment of mitochondrial (mt) 12S rRNA gene revealed the presence of cestode DNA in 19 of 103 (18.4%) raccoons, in 13 of 111 (11.7%) raccoon dogs and in 23 of 47 (48.9%) badgers. Sequence analysis demonstrated the presence of Mesocestoides litteratus in raccoons and raccoon dogs, while Mesocestoides lineatus was identified only in two samples derived from raccoon dogs. Moreover, in this study, Atriotaenia incisa was for the first time molecularly characterized by using fragments of mt 12S rRNA gene, and the DNA of this cestode species was detected in the fecal samples of all the examined host species.

A Survey of Intestinal Helminths of Dogs in Slovakia with an Emphasis on Zoonotic Species

Simple Summary

Dogs are the most popular pet animals worldwide; however, frequent and close contact with people increases the risk of transmission of different zoonotic parasites. As the occurrence of intestinal parasites in the dog population is affected by several factors, understanding the epidemiology of zoonotic parasitic infections is important to minimize the risks for humans. This study presents results about the prevalence of gastrointestinal helminths in seven different groups of dogs (pet, shelter, guard, working, and hunting dogs, as well as dogs from segregated Roma settlements) in Slovakia. Out of 495 faecal samples collected between 2016 and 2021, eggs of intestinal helminths were detected in 134 (27.1%) samples. Altogether, six different species/genera/families, namely, Toxocara canis (14.7%), Toxascaris leonina (1.6%), Trichuris vulpis (6.3%), Capillaria spp. (1.4%), Ancylostoma/Uncinaria spp. (8.3%), and taeniid eggs (4.0%), were recorded. Infection with Echinococcus multilocularis was confirmed in 2.2% of dogs and 0.4% of the animals were infested with Taenia hydatigena. The results showed that the occurrence of intestinal helminths is quite frequent in the majority of analyzed dog groups, with a close correlation between the occurrence of intestinal helminths and availability of veterinary care and anthelmintic therapy.

Abstract

Dogs are the most popular pets worldwide; however, close contact with people increases the risk of transmission of different zoonotic parasites. This study aims to determine the prevalence of gastrointestinal helminths in dogs in Slovakia. A total of 495 faecal samples collected from pet, shelter, guard, working (police), and hunting dogs, as well as dogs from segregated Roma settlements between 2016 and 2021, were examined using flotation and molecular methods. Eggs of intestinal helminths were detected in 134 (27.1%) samples. Microscopically, six different species/genera/families, namely, Toxocara canis (14.7%), Toxascaris leonina (1.6%), Trichuris vulpis (6.3%), Capillaria spp. (1.4%), Ancylostoma/Uncinaria spp. (8.3%), and taeniid eggs (4.0%), were recorded. Molecular analyses revealed infection with Echinococcus multilocularis in 2.2% of dogs and 0.4% of the animals were infected with Taenia hydatigena. The results showed a correlation between the occurrence of intestinal helminths and the availability of veterinary care, as dogs from Roma settlements and shelter dogs were the most often infected (66.7% and 39.2%, respectively). On the other hand, working animals were in the best health condition, with only 2.5% being positive. The relatively frequent occurrence of zoonotic species points to the constant need for preventive measures and regular deworming of dogs.

Development and validation of a flexible DNA extraction (PAN) method for liquid biopsy of multiple sample types

BACKGROUND

Liquid biopsy is gaining increasing popularity in cancer screening and diagnosis. However, there is no relatively mature DNA isolation method or commercial kit available that is compatible with different LB sample types. This study developed a PAN-sample DNA isolation method (PAN method) for liquid biopsy samples.

METHODS

The PAN method has two key steps, including biosample-specific pretreatments for various LB sample types and high concentration guanidine thiocyanate buffer for lysis and denaturation procedure. Subsequently, the performance of PAN method was validated by a series of molecular analyses.

RESULTS

The PAN method was used to isolate DNA from multiple sample types related to LB, including plasma, serum, saliva, nasopharyngeal swab, and stool. All purified DNA products showed good quality and high quantity. Comparison of KRAS mutation analysis using DNA purified using PAN method versus QIAamp methods showed similar efficiency. Epstein-Barr virus DNA was detected via Q-PCR using DNA purified from serum, plasma, nasopharyngeal swab, and saliva samples collected from nasopharyngeal carcinoma patients. Similarly, methylation sequencing of swab and saliva samples revealed good coverage of target region and high methylation of HLA-DPB1 gene. Finally, 16S rDNA gene sequencing of saliva, swab, and stool samples successfully defines the relative abundance of microbial communities.

CONCLUSIONS

This study developed and validated a PAN-sample DNA isolation method that can be used for different LB samples, which can be applied to molecular epidemiological research and other areas.

A rapid competitive method for bacteriophage genomic DNA extraction

The bacteriophage (phage) DNA extraction methods for genomics analysis is a critical and time-consuming process. Hence, a rapid and cost-effective method for DNA extraction of phages is favorable for phage biologists. In the present study, a cost-effective, simple and rapid procedure for phage genome extraction in less than 10 min is introduced. Highly concentrated phage lysates were prepared using acetone precipitation followed by extraction using various methods such as commercial kits, TES lysis buffer, potassium iodide, and sodium iodide. The quality of the extracted DNA was analyzed by agarose gel electrophoresis and UV absorbance of DNA at 260 and 280 nm. Finally, the extracted DNA was subjected to restriction digestion and next-generation sequencing to approve the efficiency of the method. Based on the time, cost, and quality of obtained DNA, the acetone precipitation of phages and extraction by potassium iodide or sodium iodide method was determined to be the best method for phage DNA extraction tested in this study. Moreover, the extracted genomic DNA using this method is suitable for phage genomic analysis such as restriction enzyme studies, preparation of DNA library, and also next-generation sequencing.

Echinococcus multilocularis in Red Foxes in Turkey: Increasing risk in urban

This study was conducted to determine the occurrence of E. multilocularis in foxes and environmental fecal contamination by E. multilocularis in Erzurum, the most highly endemic region for AE in Turkey. The study materials consisted of 50 red fox carcasses collected from 20 counties of Erzurum, Turkey, between October 2015 and February 2016. After the application of the sedimentation and counting technique (SCT), E. multilocularis was identified through the identification of typical morphological structures. Fox fecal samples (n = 600) were also collected from these counties for the isolation of taeniid eggs using the sequential sieving and flotation method (SSFM). Then, the collected adult worms and taeniid eggs were subjected to molecular and sequence analyses. Mature E. multilocularis parasites were found in 42% (21/50) of the fox intestines, with a mean number of 7,806 (150-31,644). The severity of infection was higher in carcasses obtained from the central district (48.6%, 17/35) than in those obtained from the peripheral district (26.7%, 4/15). The prevalence of environmental fecal contamination with E. multilocularis was 10.5% (63/600) in fecal samples collected from all counties of Erzurum. This infection rate was higher in the central district (32.1%, 36/112) than in the peripheral district (5.5%, 27/488; P < 0.0001). In conclusion, contrary to expectation, the prevalence of E. multilocularis positivity was high in urban areas. This could have been due to alterations in the dietary habitats of definitive and intermediate hosts. Therefore, new control strategies are essential to eliminate human AE cases in the future as urbanization advances.

Elucidation of Himasthla leptosoma (Creplin, 1829) Dietz, 1909 (Digenea, Himasthlidae) life cycle with insights into species composition of the north Atlantic Himasthla associated with periwinkles Littorina spp

Trematodes of the genus Himasthla are usual parasites of coastal birds in nearshore ecosystems of northern European seas and the Atlantic coast of North America. Their first intermediate hosts are marine and brackish-water gastropods, while second intermediate hosts are various invertebrates. We analysed sequences of partial 28S rRNA and nad1 genes and the morphology of intramolluscan stages, particularly cercariae of Himasthla spp. parasitizing intertidal molluscs Littorina spp. in the White Sea, the Barents Sea and coasts of North Norway and Iceland. We showed that only three Himasthla spp. are associated with periwinkles in these regions. Intramolluscan stages of H. elongata were found in Littorina littorea, of H. littorinae, in both L. saxatilis and L. obtusata, and of Cercaria littorinae obtusatae, predominantly, in L. obtusata. Other Himasthla spp. previously reported from Littorina spp. in North Atlantic are either synonymous with one of these species or described erroneously. Based on a comparison of newly generated 28S rDNA sequences with GenBank data, rediae and cercariae of C. littorinae obtusatae were identified as belonging to H. leptosoma. Some previously unknown morphological features of young and mature rediae and cercariae of the three Himasthla spp. are described. We provide a key to the rediae and highlight characters important for identification of cercariae. Genetic diversity within the studied species was only partially determined by their specificity to the molluscan host. The nad1 network constructed for H. leptosoma lacked geographical structure, which is explained by a high gene flow owing to highly vagile definitive hosts, shorebirds.

The fox tapeworm, Echinococcus multilocularis, in grey wolves and dogs in Slovakia: epidemiology and genetic analysis

Echinococcus multilocularis, the causative agent of human alveolar echinococcosis, is an important emerging parasite in the northern hemisphere. In epidemiological studies, the highest attention is being paid to foxes as the main reservoir hosts responsible for geographic expansion from multiple focal populations and the invasion of urban habitats, but little information is available on the parasite distribution in other carnivores. Hence, the study was designed to obtain updated information about the occurrence and genetic diversity of E. multilocularis in grey wolves and dogs in Slovakia. Faecal samples of wolves were collected from three locations under a certain level of environmental protection in the central and eastern parts of the country, and the presence of the parasite DNA was detected in 35.7% of 112 samples, with the highest rate (51.2%) recorded in the Poloniny National Park in north-eastern Slovakia. Among 110 faecal dog samples, E. multilocularis was detected in three faeces from segregated Roma settlements in the eastern part of the country, which accounted for an overall positivity of 2.7%. Sequence analysis of two mitochondrial genes, 12S rRNA and NADH dehydrogenase subunit 1, revealed four haplotypes in 13 isolates from wolves and dogs originating from four sites in eastern and central Slovakia, with all samples bearing a European-type pattern of E. multilocularis. The more than one-third positivity rate of E. multilocularis in wolf faecal samples dispersed over a large part of the country has corroborated the extensive circulation of the parasite in wildlife and confirmed the need to improve intervention control strategies.

Molecular Characterization of Echinococcus multilocularis and Echinococcus granulosus from Cysts and Formalin-Fixed Paraffin-Embedded Tissue Samples of Human Isolates in Northeastern Turkey

Erzurum province of Turkey is known to be highly endemic for alveolar echinococcosis (AE) and cystic echinococcosis (CE). In this study, we confirmed Echinococcus multilocularis cases, searched genetic variations of the isolates, and-for the first time-determined the genotypes of Echinococcus granulosus s.l. infecting humans in the province. A total of 5 alveolar and 106 hydatid cysts as well as 23 formalin-fixed paraffin-embedded (FFPE) samples that were diagnosed as AE were collected from hospitals between 2015 and 2017. Partial sequences of two mitochondrial genes were amplified to detect E. multilocularis and E. granulosus sensu lato with conventional polymerase chain reactions (PCRs) and genotypes confirmed by sequencing. PCR amplification of a partial 12S rRNA gene on an alveolar cyst and FFPE tissue samples yielded the expected bp in 5 cysts and 19 of 23 FFPE samples; all Erzurum E. multilocularis isolates were confirmed by sequencing. Phylogenetic analysis of the isolates indicated that some of them were identical to European isolates, whereas some of them were identical to Asian isolates. Off all hydatid cyst samples, 101 (95.2%) yielded the expected bp (94 with 12S rRNA-PCR and 7 with COI-PCR). Sequence analysis showed that 98 (97%) of them corresponded to the G1 genotype, whereas 3 (3%) corresponded to the G3 genotype. Results of the study emphasize that E. multilocularis isolates of Erzurum, based on short sequencing, are similar to both European and Asian isolates, and the G1 genotype of E. granulosus is the main causative agent of human CE in Erzurum.

Clinical, pathological and parasitological examinations of a German spaniel with alveolar echinococcosis, Germany, 2018

Alveolar echinococcosis (AE) is a parasitic zoonosis occurring in most European countries and also emerging in parts of Asia and North America. AE is caused by the larval stage of Echinococcus multilocularis in intermediate and also in accidental hosts. The principal definitive host is the red fox, but domestic dogs and cats are also potential definitive hosts. Several species of rodents serve as intermediate hosts of this parasite. However, there are also some species acting as accidental intermediate hosts, among them dogs. Since the late 1980s cases of canine AE have been diagnosed. Here, we present a case of canine AE in a two-year old female intact German spaniel from Thuringia, Central Germany. The dog was used as a hunting dog and presented to a small animal clinic for subacute lethargy and inappetence. Abdominal ultrasound and contrast computed tomography (CT) scan were performed and revealed intrahepatic lesions. Multinodular changes of the liver and the greater omentum were demonstrated by exploratory laparotomy. After euthanasia, a necropsy was performed and histological sections of representative tissue samples were prepared. PCR followed by sequencing was conducted with DNA extracted from tissue samples of the liver, hepatic lymph nodes and greater omentum. The sequence herein obtained showed very high similarity with other partial nad2 sequences of E. multilocularis from the GenBank database by BLASTn analysis and was analysed using the maximum likelihood method. The presented case combines the clinical presentation and pathological, parasitological and phylogenetic analyses.

Contamination of wastewater with Echinococcus multilocularis - possible implications for drinking water resources in the QTP China

Echinococcus multilocularis is a parasite that causes a dangerous zoonosis, alveolar echinococcosis (AE). Its presence in water sources, however, has scarcely been studied heretofore. Accordingly, 222 samples of different origin including wastewater from wastewater treatment plants (WWTPs) (n = 137), slaughterhouse (n = 49) as well as water from rivers (n = 26) and a cattle farm (n = 10) were collected from Xining City and a rural area in Qinghai-Tibet Plateau (QTP), an endemic area. Material obtained after processing of 10 L volume samples was subsequently analysed using three molecular detection methods: nested PCR, real-time PCR and LAMP. E. multilocularis DNA was found in 13 (5.85%) water samples; including 8 (5.8%), 3 (6%), 2 (20%) and 0 positive samples found in WWTPs, a slaughterhouse, a cattle farm and rivers, respectively. All three (LAMP, PCR, RT-PCR) molecular tools displayed high agreement and effectiveness in their ability of detecting the parasite's DNA in environmental material. This is the first investigation describing E. multilocularis detection in wastewater samples, using three sensitive molecular diagnostic tools. Results indicate the role of wastewater in dissemination of E. multilocularis and the risk of contamination of water sources.

First detection of Echinococcus multilocularis in environmental water sources in endemic areas using capsule filtration and molecular detection methods

Water is one of the possible transmission routes for water- and foodborne parasites to humans. Echinococcus multilocularis is a parasite, which causes alveolar echinococcosis (AE). Nevertheless, no environmental studies have been performed as yet to confirm the occurrence of E. multilocularis in water supplies. Accordingly, 105 water samples of 50 L volume were collected from surface waters (lakes, rivers, canals) and wells in the Warmia-Masuria Province (Echinococcus endemic area) and Pomerania Province (Echinococcus non-endemic area), Poland. The water was filtered and subsequently analysed with nested PCR and real-time PCR. E. multilocularis DNA was found in two (1.9%) samples, which originated from two lakes localised in the Warmia-Masuria Province. Sequencing of the positive samples confirmed that the PCR products were fragments of the E. multilocularis mitochondrial 12S rRNA gene. This is the first investigation describing E. multilocularis detection in environmental water samples, using molecular diagnostic tools. The results indicate that water could be considered as a potential source of E. multilocularis infections in humans and animals, in endemic areas.

Echinococcus multilocularis in a Eurasian lynx (Lynx lynx) in Turkey

Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), one of the most threatening zoonoses in Eurasia. Human AE is widespread in the Erzurum region of Turkey, but the situation of the disease in intermediate and definitive hosts is unknown. A Eurasian lynx (Lynx lynx) was killed in a traffic accident in the north of Erzurum, and was taken to our laboratory. Sedimentation and counting technique (SCT), DNA isolation and polymerase chain reaction (PCR) analysis were performed. The SCT results showed that the lynx was infected with E. multilocularis with a medium (745 worms) worm burden. The DNA of adult worms obtained from the lynx was analyzed with a species-specific PCR, and the worms were confirmed to be E. multilocularis by 12S rRNA gene sequence analysis. This is the first report of E. multilocularis from Eurasian lynx in Turkey.

First detection of Echinococcus multilocularis in rodent intermediate hosts in Turkey

Echinococcus multilocularis is the causative agent of alveolar echinococcosis (AE), a potentially fatal zoonotic disease. Large parts of Turkey are considered as endemic for E. multilocularis. The aim of this study was to determine the occurrence of metacestode of E. multilocularis in wild rodents in Erzurum, an endemic region for human AE in Turkey. During the sampling period, a total of 498 rodents were trapped in twenty counties of Erzurum Province. Suspected lesions were observed on the livers of 48 rodents, and then partial fragment of mitochondrial 12S rRNA gene was PCR-amplified. Five liver samples exhibited E. multilocularis infection. The prevalence of E. multilocularis for Microtus spp. was 1·3%. All of the infected rodents had fertile metacestodes. Infected rodents were morphologically and molecularly analysed and were confirmed to be Microtus irani by the mitochondrial cytochrome b gene sequence analysis. This is the first report of the presence of E. multilocularis in rodent intermediate hosts in Turkey. Our findings of infected M. irani with protoscoleces show that this rodent can act as suitable intermediate host for E. multilocularis’ life cycle in Turkey. However, there was a complete lack of data on the infection of carnivores from the country. An extensive survey is recommended to determine the prevalence of E. multilocularis in definitive hosts in this endemic region.

Detection of Echinococcus multilocularis DNA in fruit, vegetable, and mushroom samples collected in the non-endemic territory of the Pomerania province and comparison of the results with data from rural areas of the neighbouring highly endemic Warmia-Masuria province, Poland

Echinococcus multilocularis is a tapeworm that may cause alveolar echinococcosis (AE), one of the most dangerous parasitic zoonoses. As in the case of some foodborne diseases, unwashed fruits and vegetables contaminated with eggs of E. multilocularis may serve as an important transmission route for this parasite. The aim of this study was to investigate the presence of E. multilocularis DNA in fruit, vegetables, and mushrooms in rural areas of the Pomerania province, Poland (non-endemic territory). In total, 104 environmental fruit, vegetable, and mushroom samples collected in forests, plantations, and kitchen gardens were analysed using nested PCR based on the mitochondrial 12S rRNA gene. E. multilocularis DNA was detected in 6.7 % of the samples tested, which indicated that the environment of the Pomerania province is contaminated with this parasite, creating a potential risk for humans. Therefore, fresh fruit, vegetables, and mushrooms should be washed before consumption. Additionally, the results showed that the level of contamination is significantly lower than in the highly endemic Warmia-Masuria province. The differences in the occurrence of E. multilocularis in the environment of these neighbouring provinces appears to be connected with the general epidemiological situation of these two regions, but further study is required for an exact explanation.

Comparison of different commercial DNA extraction kits and PCR protocols for the detection of Echinococcus multilocularis eggs in faecal samples from foxes

Effective and sensitive methods for the molecular detection of Echinococcus multilocularis in faecal samples of final hosts are crucial for the prevention and control of human alveolar echinococcosis and for studies on the epidemiology of the parasite. Little is known about the suitability of commercial test kits for isolating DNA of E. multilocularis from fox faeces and the performance of standard Polymerase Chain Reaction (PCR) protocols in relation to the quality of DNA extracted by these kits. We compared four different kits: ZR Faecal DNA MiniPrep™ (Zymo Research), FastDNA^® SPIN Kit for Soil (MP Biomedicals), QIAamp^® Fast DNA Stool Mini Kit (QIAGEN) and NucleoSpin^® Soil Kit (Macherey-Nagel) for the extraction of DNA from E. multilocularis eggs present in faeces of foxes. Negative faecal samples were spiked with 600, 300, 150, 75, 37, 18, 9, 5 or 2 E. multilocularis eggs, and each egg concentration was tested 10 times with each of the DNA extraction kits. Each extracted DNA sample was amplified using three PCR protocols: i. conventional PCR (cPCR, Platinum^®Taq, Invitrogen), ii. qPCR with the iQ™ Supermix (Bio-Rad) and iii. qPCR with the QuantiTect^® Multiplex-Master Mix (QIAGEN). The highest analytical sensitivities for molecular detection of E. multilocularis eggs in spiked fox faeces were observed when combining either the QIAamp^® Fast DNA Stool Mini Kit or the ZR Faecal DNA MiniPrep™ kit with the qPCR using the QuantiTect^® Multiplex-Master Mix (Sensitivities 97% and 94%, respectively). Combinations including the remaining test kits (NucleoSpin^® Soil Kit and FastDNA^® SPIN Kit for Soil) showed a markedly lower analytical sensitivity for PCR examinations. The results of the present study indicate that it is of utmost importance to select suitable DNA extraction kits in combination with robust PCR methods or reagents to achieve acceptable analytical sensitivity in the molecular detection of E. multilocularis eggs in fox faecal samples.

First Molecular Characterization of Echinococcus multilocularis in Turkey

This study aimed to find out the occurrence of Echinococcus multilocularis in foxes in Erzurum province, the highest endemic region for human alveolar echinococcosis in Turkey. The sedimentation and counting technique was used to reveal adult Echinococcus spp. in the intestines of foxes. One out of the 10 foxes was infected with E. multilocularis. The adult worms were analyzed morphologically and molecularly and were confirmed to be E. multilocularis by species-specific PCR. Pairwise comparisons between the 12S rRNA sequences of the E. multilocularis isolate from Erzurum and other E. multilocularis isolates showed 100% similarity of the Erzurum isolate with European isolates. With this study, the presence of E. multilocularis in a fox in Erzurum was confirmed by PCR, and molecular identification of E. multilocularis is reported for the first time in Turkey.

The first detection of Echinococcus multilocularis DNA in environmental fruit, vegetable, and mushroom samples using nested PCR

The aim of this study was to estimate the presence of Echinococcus multilocularis DNA in fruits, vegetables, and mushrooms in rural areas of Varmia-Masuria Province, Poland, which is the region with the highest number of human alveolar echinococcosis (AE) cases in this country. Recovery tests showed that E. multilocularis DNA is detectable in samples contaminated with at least 100 eggs of this tapeworm. In total, 103 environmental fruit, vegetable, and mushroom samples collected in forests, plantations, and kitchen gardens were analyzed using nested PCR assay based on the mitochondrial 12S ribosomal RNA (rRNA) gene. The parasite DNA was detected in 23.3 % of the samples. Sequencing confirmed that the obtained PCR products represented E. multilocularis. This study is the first environmental survey of the presence of E. multilocularis DNA in fruits, vegetables, and mushrooms intended for consumption. The results clearly demonstrate that it may be a direct source of human infections and shows the need to educate the public about the threat, especially people living in at-risk areas.

Echinococcus multilocularis detection in the intestines and feces of free-ranging domestic cats (Felis s. catus) and European wildcats (Felis s. silvestris) from northeastern France

Experimental studies have demonstrated that cats can be infected by Echinococcus multilocularis, although few data are available concerning their natural infection. This study was designed to compare experimental findings with information on the prevalence of natural E. multilocularis infections of cats in a rural high endemic area. Of 19 intestines of domestic cats (Felis s. catus) and five of European wildcats (Felis s. silvestris) analyzed by segmental sedimentation and counting technique (SSCT), infection by E. multilocularis was observed for one individual of each species, resulting in a prevalence estimated at 5%, (CI95%: 1-26) in domestic cats and at 20% (CI95%: 1-72) in wildcats. High worm burdens (680 and 7040) were noted, but comprised only immature worms. The same EmsB microsatellite profile obtained from the worms' DNA was observed in the two cats as in foxes from the same area and from other European countries. The presence of E. multilocularis DNA was diagnosed in 3.1% (10/321) of the domestic cat feces collected on the field in two villages. However, no E. multilocularis eggs were found after flotation with zinc chloride of the positive feces. The detection of DNA from E. multilocularis was thought to be due to the presence of cells from worms untied from the intestine and corresponding to prepatent infection or due to the digested metacestode. These results from E. multilocularis presence in wild and domestic cat populations agree with those previously obtained by experimental infections. These findings support that these cats play an insignificant role in E. multilocularis transmission, even in a "highly endemic" region. Nevertheless, since the presence of thick-shelled E. multilocularis eggs from cats has already been reported, the associated zoonotic risk cannot be totally ruled out, even if it is very low.

Development of three PCR assays for the differentiation between Echinococcus shiquicus, E. granulosus (G1 genotype), and E. multilocularis DNA in the co-endemic region of Qinghai-Tibet plateau, China

To investigate echinococcosis in co-endemic regions, three polymerase chain reaction (PCR) assays based on the amplification of a fragment within the NADH dehydrogenase subunit 1 (ND1) mitochondrial gene were optimized for the detection of Echinococcus shiquicus, Echinococcus granulosus G1, and Echinococcus multilocularis DNA derived from parasite tissue or canid fecal samples. Specificity using parasite tissue-derived DNA was found to be 100% except for E. shiquicus primers that faintly detected E. equinus DNA. Sensitivity of the three assays for DNA detection was between 2 and 10 pg. Ethanol precipitation of negative PCR fecal samples was used to eliminate false negatives and served to increase sensitivity as exemplified by an increase in detection from 0% to 89% of E. shiquicus coproDNA using necropsy-positive fox samples.

Validation of a PicoGreen-based DNA quantification integrated in an RNA extraction method for two-dimensional and three-dimensional cell cultures

DNA measurement and RNA extraction are two frequently used methods for cell characterization. In the conventional protocols, they require similar, but separate samples and in most cases, different pretreatments. The few combined protocols that exist still include time-consuming steps. Hence, to establish an efficient combined RNA extraction and DNA measurement protocol for two-dimensional (2D) and three-dimensional (3D) cell cultures, a PicoGreen-based DNA measurement was integrated in an existing RNA extraction protocol. It was validated by analysis of the influence of different lysis buffers, RLT, RA1, or Trizol, used for RNA extraction on the measured DNA concentration. The DNA cell yield was evaluated both in cell suspensions (2D) and on 3D cell-seeded scaffolds. Results showed that the different RNA lysis buffers caused a concentration-dependent perturbation of the PicoGreen signal. The measured DNA concentrations in 2D and 3D using RLT and RA1 buffer were comparable, also to the positive control. We, therefore, concluded that RNA extraction protocols using RA1 or RLT buffer allow the integration of a DNA quantification step without the buffer influencing the results. Hence, the combined DNA measurement and RNA extraction offer an alternative for DNA measurement techniques that is time and sample saving, for both 2D cell cultures and specific 3D constructs.

Simultaneous DNA and RNA isolation from brain punches for epigenetics

BACKGROUND

Epigenetic modifications such as DNA methylation play an important role for gene expression and are regulated by developmental and environmental signals. DNA methylation typically occurs in a highly tissue- and cell-specific manner. This raises a severe challenge when studying discrete, small regions of the brain where cellular heterogeneity is high and tissue quantity limited. Because gene expression and methylation are often tightly linked it appears of interest to compare both parameters in the same sample.

FINDINGS

We present a refined method for the simultaneous extraction of DNA for bisulfite sequencing and RNA for expression analysis from small mouse brain tissue punches. This method can also be easily adapted for other small tissues or cell populations.

CONCLUSIONS

The method described herein results in DNA and RNA of a quantity and quality permitting highly reliable bisulfite analysis and quantitative RT-PCR measurements, respectively.

Occurrence and molecular characterization ofCryptosporidiumspp. genotypes in European hedgehogs (Erinaceus europaeusL.) in Germany

Juvenile hedgehogs having insufficient body weight are often brought for overwintering to hedgehog rehabilitation centres. Faecal samples of juvenile hedgehogs and overwintering hedgehogs (n=188) collected prior to releasing them back into the wilderness were examined for the presence ofCryptosporidiumcoproantigen and oocysts. Altogether 56 (29·8%) submitted samples were positive for coproantigen. Forty-five (39·5%,n=114) of the positive samples originated from newly rescued hedgehogs, while 11 (14·8%,n=74) positive samples were from animals that spent several months at the station. Fifteen samples subjected to PCR-RFLP analysis on the partial 18S rRNA locus suggested the presence ofC. parvum. Multilocus sequence typing on partial 60 kDa glycoprotein gene, 18S rRNA, actin gene, 70 kDa heat shock protein gene sequences revealed 3 different subtype families: IIa, IIc and a new, proposed as VIIa subtype family.Cryptosporidiumsp. genotype belonging to VIIa subtype family is closely related toC. parvumbut is genetically distinct being probably a hedgehog-specificCryptosporidiumsp. genotype with unknown zoonotical potential. Hedgehogs excretingCryptosporidiumoocysts represent a potential source for human infections, but also an anthroponotic nature of the IIc subtype family should be reviewed.