Human pathogenic microsporidia detection in agricultural samples: method development and assessment

First identification and coinfection detection of Enterocytozoon bieneusi, Encephalitozoon spp., Cryptosporidium spp. and Giardia duodenalis in diarrheic pigs in Southwest China

BACKGROUND

Enterocytozoon bieneusi, Encephalitozoon spp., Cryptosporidium spp., and Giardia duodenalis (G. intestinalis) are enteric pathogens that cause diarrhea in pigs. This study aimed to determine the prevalence of these enteric parasites and their coinfection with E. bieneusi in diarrheic pigs in Southwest China (Chongqing and Sichuan) using nested polymerase chain reaction (nPCR) based methods.

RESULTS

A total of 514 fecal samples were collected from diarrheic pigs from 14 pig farms in Chongqing (five farms) and Sichuan (nine farms) Provinces. The prevalence of Encephalitozoon spp., Cryptosporidium spp. and G. duodenalis was 16.14% (83/514), 0% (0/514), and 8.95% (46/514), respectively. Nested PCR revealed 305 mono-infections of E. bieneusi, six of E. cuniculi, two of E. hellem, and nine of G. duodenalis and 106 concurrent infections of E. bieneusi with the other enteric pathogens. No infections of E. intestinalis and Cryptosporidium species were detected. The highest coinfection was detected between E. bieneusi and E. cuniculi (10.5%, 54/514), followed by E. bieneusi and G. duodenalis (5.8%, 30/514) and E. bieneusi and E. hellem (2.9%, 15/514). E. bieneusi was the most frequently detected enteric pathogen, followed by E. cuniculi, G. duodenalis and E. hellem. There was a significant age-related difference in the prevalence of E. cuniculi in fattening pigs (χ2 = 15.266, df = 3, P = 0.002) and G. duodenalis in suckling pigs (χ2 = 11.92, df = 3, P = 0.008) compared with the other age groups. Sequence analysis of the ITS region of Encephalitozoon species showed two genotypes (II and III) for E. cuniculi and one (TURK1B) for E. hellem. Only G. duodenalis assemblage A was identified in all nested PCR-positive samples. E. bieneusi was found more often than other enteric pathogens.

CONCLUSIONS

This study showed that E. bieneusi, Encephalitozoon spp. [E. cuniculi and E. hellem] and G. duodenalis were common enteric parasites in diarrheic pigs in Chongqing and Sichuan Provinces. In case of both mono-infection and coinfection, E. bieneusi was the most common enteric pathogen in diarrheic pigs. Thus, it may be a significant cause of diarrhea in pigs. Precautions should be taken to prevent the spread of these enteric parasites.

Exploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems

Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem structure and function. Unfortunately, their ecological role is not well understood. Present also as highly resistant spores in the environment, their characterisation requires special attention. Different techniques based on direct isolation and/or molecular approaches can be considered to elucidate their role in the ecosystems, but integrating environmental and genomic data (for example, genome architecture, core genome, transcriptional and translational signals) is crucial to better understand the diversity and adaptive capacities of Microsporidia. Here, we review the current status of Microsporidia in trophic networks; the various genomics tools that could be used to ensure identification and evaluate diversity and abundance of these organisms; and how these tools could be used to explore the microsporidian life cycle in different environments. Our understanding of the evolution of these widespread parasites is currently impaired by limited sampling, and we have no doubt witnessed but a small subset of their diversity.

Molecular detection of microsporidiosis in various samples of Iranian immunocompromised patients

Microsporidia infections occur in virtually all invertebrate and vertebrate hosts, including humans. The aim of this study is detection of microsporidiosis in various samples of Iranian immunosuppressed patients during 2011-2012 by molecular methods. The samples included stool samples from the healthy participants and samples from biological fluids of the patients according to consult of their physician and the site of infection. The sample size was determined as 258 for each group. Clinical and demographical data related to each participant was collected. DNA extraction and nested polymerase chain reaction were carried out on all the samples. In the control group, the rates of Encephalitozoon and Enterocytozoon infections were 5.3 and 4 % respectively higher in males and in the age range of 30-45, and all positive cases had gastrointestinal symptoms. In the patient group, most infection cases occurred in male patients and in the age range of 60 and above. Patients with microsporidiosis mostly had the symptoms of chronic diarrhea, vomiting, weight loss, dyspepsia, and malabsorption. In BAL samples from patients 2 % Encephalitozoon and 0.7 % Enterocytozoon, in the sampling bone marrow transplantation from patients 5.7 % Encephalitozoon, 1.43 % Enterocytozoon and from patients who underwent kidney transplantation 5.26 % Enterocytozoon were detected. The most cases of human microsporidiosis are associated with human immunodeficiency virus infection or other states of immunosuppression, particularly in organ transplant recipients; the result of this study confirms this claim.

Prevalence and diversity of Encephalitozoon spp. and Enterocytozoon bieneusi in wild boars (Sus scrofa) in Central Europe

From 2011 to 2012, the occurrence of Enterocytozoon bieneusi and Encephalitozoon spp. was surveyed at 29 randomly selected localities (both forest areas and enclosures) across four Central European countries: Austria, the Czech Republic, Poland, and the Slovak Republic. Isolates were genotyped by PCR amplification and characterization of the internal transcribed spacer (ITS) region using Enterocytozoon and Encephalitozoon-specific protocols. PCR revealed 16 mono-infections of Encephalitozoon cuniculi, 33 mono-infections of Enterocytozoon bieneusi and 5 concurrent infections of both Encephalitozoon cuniculi and Enterocytozoon bieneusi out of 460 faecal samples. Two genotypes (I and II) were revealed by sequence analysis of the ITS region of Encephalitozoon cuniculi. Eleven genotypes, five previously found in other hosts including domestic pigs (D, EbpA, EbpC, G and Henan-I) and six novel (WildBoar1-6), were identified in Enterocytozoon bieneusi. No other microsporidia infection was found in the examined faecal samples. Prevalence of microsporidia at the locality level ranged from 0 to 58.8 %; the prevalence was less than 25 % at more than 86 % of localities. Enterocytozoon bieneusi was detected as a predominant species infecting Eurasian wild boars (Sus scrofa). The present report is the most comprehensive survey of microsporidia infections in wild boars within the Czech Republic and selected Central European countries.

Comparative analysis of detection limits and specificity of molecular diagnostic markers for three pathogens (Microsporidia, Nosema spp.) in the key pollinators Apis mellifera and Bombus terrestris

Global pollinator decline has recently been discussed in the context of honey and bumble bee infections from various pathogens including viruses, bacteria, microsporidia and mites. The microsporidian pathogens Nosema apis, Nosema ceranae and Nosema bombi may in fact be major candidates contributing to this decline. Different molecular and non-molecular detection methods have been developed; however, a comparison, especially of the highly sensitive PCR based methods, is currently lacking. Here, we present the first comparative quantitative real-time PCR study of nine Nosema spp. primers within the framework of primer specificity and sensitivity. With the help of dilution series of defined numbers of spores, we reveal six primer pairs amplifying N. apis, six for N. bombi and four for N. ceranae. All appropriate primer pairs detected an amount of at least 10(4) spores, the majority of which were even as sensitive to detect such low amounts as 10(3) to ten spores. Species specificity of primers was observed for N. apis and N. bombi, but not for N. ceranae. Additionally, we did not find any significant correlation for the amplified fragments with PCR efficiency or the limit of detection. We discuss our findings on the background of false positive and negative results using quantitative real-time PCR. On the basis of these results, future research might be based on appropriate primer selection depending on the experimental needs. Primers may be selected on the basis of specificity or sensitivity. Pathogen species and load may be determined with higher precision enhancing all kinds of diagnostic studies.

Identification and genotyping of Enterocytozoon bieneusi in China

In this study, the prevalence of Enterocytozoon bieneusi in China was investigated. Twelve genotypes of E. bieneusi were identified, of which 10 were novel genotypes. Further, 41.6% of the genotypes were found in both humans and animals. This is the first report of E. bieneusi in China.

First detection and genotyping of Encephalitozoon cuniculi in a new host species, gyrfalcon (Falco rusticolus)

Recently, the pathogenic species of microsporidia of the genus Encephalitozoon have been detected increasingly, also in representatives of the Aves class. Our study presents laboratory proof of Encephalitozoon cuniculi (E. cuniculi) genotype II in a new host, gyrfalcon (Falco rusticolus), with suspect microsporidiosis. E. cuniculi is an obligate intracellular microsporidian parasite that infects a wide range of mammalian hosts, including humans. Characterization of the internal transcribed spacer of the rRNA gene has identified three genotypes of E. cuniculi based on the number of 5'-GTTT-3' repeats present: a genotype I from rabbits and mice, containing three repeats; a genotype II from mice and dogs, containing two repeats; and a genotype III from dogs and fox, containing four repeats. Samples of faeces from 30 gyrfalcons were examined for the presence of microsporidia spores, using microscopical, molecular methods and sequencing. Microscopic analysis showed presence of brightly fluorescing oval shapes of size 1.5 × 3 μm, characteristic of the strain Microsporidia in five samples. The PCR method, using species non-specific (530F/580R) and species-specific (ECUNR/ECUNF) primers, proved the presence of E. cuniculi spores in two samples. After sequencing were confirmed, E. cuniculi genotype II which implies new host species for this parasite.

Molecular diagnostic tests for microsporidia

The Microsporidia are a ubiquitous group of eukaryotic obligate intracellular parasites which were recognized over 100 years ago with the description of Nosema bombycis, a parasite of silkworms. It is now appreciated that these organisms are related to the Fungi. Microsporidia infect all major animal groups most often as gastrointestinal pathogens; however they have been reported from every tissue and organ, and their spores are common in environmental sources such as ditch water. Several different genera of these organisms infect humans, but the majority of infections are due to either Enterocytozoon bieneusi or Encephalitozoon species. These pathogens can be difficult to diagnose, but significant progress has been made in the last decade in the development of molecular diagnostic reagents for these organisms. This report reviews the molecular diagnostic tests that have been described for the identification of the microsporidia that infect humans.

Propagation of human enteropathogens in constructed horizontal wetlands used for tertiary wastewater treatment

Constructed subsurface flow (SSF) and free-surface flow (FSF) wetlands are being increasingly implemented worldwide into wastewater treatments in response to the growing need for microbiologically safe reclaimed waters, which is driven by an exponential increase in the human population and limited water resources. Wastewater samples from four SSF and FSF wetlands in northwestern Ireland were tested qualitatively and quantitatively for Cryptosporidium spp., Giardia duodenalis, and human-pathogenic microsporidia, with assessment of their viability. Overall, seven species of human enteropathogens were detected in wetland influents, vegetated areas, and effluents: Cryptosporidium parvum, C. hominis, C. meleagridis, C. muris, G. duodenalis, Encephalitozoon hellem, and Enterocytozoon bieneusi. SSF wetland had the highest pathogen removal rate (i.e., Cryptosporidium, 97.4%; G. duodenalis, 95.4%); however, most of these values for FSF were in the negative area (mean, -84.0%), meaning that more pathogens were discharged by FSF wetlands than were delivered to wetlands with incoming wastewater. We demonstrate here that (i) the composition of human enteropathogens in wastewater entering and leaving SSF and FSF wetlands is highly complex and dynamic, (ii) the removal and inactivation of human-pathogenic microorganisms were significantly higher at the SSF wetland, (iii) FSF wetlands may not always provide sufficient remediation for human enteropathogens, (iv) wildlife can contribute a substantial load of human zoonotic pathogens to wetlands, (v) most of the pathogens discharged by wetlands were viable, (vi) large volumes of wetland effluents can contribute to contamination of surface waters used for recreation and drinking water abstraction and therefore represent a serious public health threat, and (vii) even with the best pathogen removal rates achieved by SSF wetland, the reduction of pathogens was not enough for a safety reuse of the reclaimed water. To our knowledge, this is the first report of C. meleagridis from Ireland.

Identification of Encephalitozoon cuniculi genotype III and two novel genotypes of Enterocytozoon bieneusi in swine

Samples of intestinal content from thirty fattened pigs of six farms slaughtered at an abattoir in North-Western Germany, and faecal samples of four pigs kept as laboratory animals at the Federal Institute for Risk Assessment (BfR, Berlin, Germany) were investigated for the occurrence of microsporidia by light microscopy, PCR and sequencing. A modified Webers trichrome staining and the immunohistochemistry (the Avidin-Biotin-Peroxidase-Complex technique with a polyclonal anti-Encephalitozoon cuniculi-serum and monoclonal antibodies against Encephalitozoon intestinalis and Enterocytozoon bieneusi) was used as a screening method for the light microscopical detection of these pathogenic eukaryotes. By this light microscopically methods microsporidia suspected organisms were found in all samples (100%). By the use of PCR, microsporidia were identified in fourteen samples (41.2%). The prevalence of microsporidia infections among the farms diversifies from 0 to 80% as considered by PCR. E. bieneusi was the most prevalent species and was identified in twelve fattened pigs (40%) from five of the six tested farms (83.3%) and in two of the four laboratory animals (50%). Three of the E. bieneusi species belonged to the genotype O, one to the genotype E, and one to the genotype F. Two isolates were identified as novel genotypes and two samples showed a mixed infection of different genotypes. In three faecal samples of the pigs from two farms E. cuniculi genotype III was identified. One sample contained both microsporidia species. To our knowledge, this is the first time that the genotype III of E. cuniculi was identified in swine.

Detection of Encephalitozoon cuniculi in a new host--cockateel (Nymphicus hollandicus) using molecular methods

A total of 123 avian faecal specimens randomly collected in Bohemian commercial aviaries, Zoo parks and countryside were screened for the presence of human pathogenic microsporidia by both calcofluor M2R staining and polymerase chain reaction. Of these, no positive sample was detected using microscopical examination, and one isolate was detected by polymerase chain reaction and identified as Encephalitozoon cuniculi. Cockateel (Nymphicus hollandicus) represents a new avian host of this microsporidian.