True versus apparent malaria infection prevalence: the contribution of a Bayesian approach

Aims

To present a new approach for estimating the “true prevalence” of malaria and apply it to datasets from Peru, Vietnam, and Cambodia.

Methods

Bayesian models were developed for estimating both the malaria prevalence using different diagnostic tests (microscopy, PCR & ELISA), without the need of a gold standard, and the tests'' characteristics. Several sources of information, i.e. data, expert opinions and other sources of knowledge can be integrated into the model. This approach resulting in an optimal and harmonized estimate of malaria infection prevalence, with no conflict between the different sources of information, was tested on data from Peru, Vietnam and Cambodia.

Results

Malaria sero-prevalence was relatively low in all sites, with ELISA showing the highest estimates. The sensitivity of microscopy and ELISA were statistically lower in Vietnam than in the other sites. Similarly, the specificities of microscopy, ELISA and PCR were significantly lower in Vietnam than in the other sites. In Vietnam and Peru, microscopy was closer to the “true” estimate than the other 2 tests while as expected ELISA, with its lower specificity, usually overestimated the prevalence.

Conclusions

Bayesian methods are useful for analyzing prevalence results when no gold standard diagnostic test is available. Though some results are expected, e.g. PCR more sensitive than microscopy, a standardized and context-independent quantification of the diagnostic tests'' characteristics (sensitivity and specificity) and the underlying malaria prevalence may be useful for comparing different sites. Indeed, the use of a single diagnostic technique could strongly bias the prevalence estimation. This limitation can be circumvented by using a Bayesian framework taking into account the imperfect characteristics of the currently available diagnostic tests. As discussed in the paper, this approach may further support global malaria burden estimation initiatives.     

Prevalence of Toxoplasma gondii infection in feral cats in Seoul, Korea

The present study assessed the prevalence of Toxoplasma gondii infection in feral cat populations in Seoul using enzyme-linked immunosorbent assay (ELISA) and nested polymerase chain reaction (PCR). A total of 456 feral cats from 17 wards in Seoul was surveyed. The overall prevalence of T. gondii infection was 15.8% (69/456) by ELISA and 17.5% (80/456) by PCR; by gender, 17% (44/259) by ELISA and 16.2% (42/259) by PCR in males and 14.3% (28/196) by ELISA and 19.4% (38/196) by PCR in females. On a baseline of the Han River, prevalence was 15.1% (29/192) by ELISA and 15.6% (30/192) by PCR in the upper region and 16.4% (43/264) by ELISA and 18.9% (50/264) by PCR in the lower area. This suggested that toxoplasmosis is widespread throughout Seoul's feral cat population and it is critical that the city institute policies for the control of the feral cat population to reduce the risk of toxoplasmosis transmission to animals, including humans.     

A comparative analysis of microscopy and PCR-based detection methods for blood parasites

We compared information obtained by both microscopy and nested mitochondrial cytochrome b PCR in determining prevalence of haemosporidian infections in naturally infected birds. Blood samples from 472 birds of 11 species belonging to 7 families and 4 orders were collected in Europe, Africa and North America. Skilled investigators investigated them using the PCR-based screening and microscopic examination of stained blood films. The overall prevalence of haemosporidian infections, which was determined combining results of both these methods, was 60%. Both methods slightly underestimated the overall prevalence of infection, which was 54.2% after the PCR diagnostics and 53.6% after microscopic examination. Importantly, both these tools showed the same trends of prevalence of Haemoproteus spp. (21% by PCR and 22% by microscopy), Plasmodium spp. (17% and 22%) and Leucocytozoon spp. (30% and 25%) in the same sample, testifying that microscopy is a reliable tool in determining patterns of distribution of blood haemosporidian parasites in naturally infected birds. We encourage using optical microscopy in studies of blood parasites in parallel to the now widely employed molecular methods. Microscopy is relatively inexpensive and provides valuable information about directions how molecular methods can be further improved and most effectively applied, especially in the field studies of parasites. Importantly, blood films, which are used for microscopic examination, should be of good quality; they should be examined properly by skilled investigators. In spite of relatively long duration of microscopy of each sample, such examination provides opportunities for simultaneous determination and verification of taxonomically different parasites. Presently, different PCR protocols must be used for the detection of parasites belonging to different genera; this is expensive and time-consuming.     

Spatially explicit predictions of blood parasites in a widely distributed African rainforest bird

Critical to the mitigation of parasitic vector-borne diseases is the development of accurate spatial predictions that integrate environmental conditions conducive to pathogen proliferation. Species of Plasmodium and Trypanosoma readily infect humans, and are also common in birds. Here, we develop predictive spatial models for the prevalence of these blood parasites in the olive sunbird (Cyanomitra olivacea). Since this species exhibits high natural parasite prevalence and occupies diverse habitats in tropical Africa, it represents a distinctive ecological model system for studying vector-borne pathogens. We used PCR and microscopy to screen for haematozoa from 28 sites in Central and West Africa. Species distribution models were constructed to associate ground-based and remotely sensed environmental variables with parasite presence. We then used machine-learning algorithm models to identify relationships between parasite prevalence and environmental predictors. Finally, predictive maps were generated by projecting model outputs to geographically unsampled areas. Results indicate that for Plasmodium spp., the maximum temperature of the warmest month was most important in predicting prevalence. For Trypanosoma spp., seasonal canopy moisture variability was the most important predictor. The models presented here visualize gradients of disease prevalence, identify pathogen hotspots and will be instrumental in studying the effects of ecological change on these and other pathogens.     

Investigation of the prevalence of amoebiasis in Izmir province and determination of Entamoeba spp. using PCR and enzyme immunoassay

Amoebiasis is a common and life-threatening disease. The discrimination of the pathogenic Entamoeba histolytica from the non-pathogenic Entamoeba dispar could be done by advanced methods such as enzyme immunoassay (EIA) and PCR. The aim of this study was to investigate the prevalence of amoebiasis in Izmir province, and differentiate the Entamoeba species by PCR and EIA. Stool samples of 2,047 individuals were examined by direct microscopy, formalin ethyl acetate concentration, trichrome staining and culture, and those found to be positive for E. histolytica/dispar by any of these methods were further analyzed by PCR and EIA for species identification. Fifty-nine of 2,047 (2.9%) stool samples were found to be positive for E. histolytica/dispar with microscopy and/or culture. Among these positive samples, E. histolytica was detected in 14 (23.7%) and 5 (8.5%) samples with PCR and antigen-specific ELISA (EIA), respectively. E. dispar was diagnosed in 31 (52.5%) and 52 (88.1%) of 59 samples with species-specific PCR and EIA, respectively. Risk factors related to infection with Entamoeba spp. and other intestinal parasites included living in shanty houses (p < 0.01), a history of recent immigration to Izmir (p < 0.01), having no social security (p < 0.05) and living with a crowded family (p < 0.01). The results demonstrated the significance of amoebiasis as a public health problem among people with low socio-economic status in Izmir province.     

PCR and Mosquito dissection as tools to monitor filarial infection levels following mass treatment

BACKGROUND: Entomological methods may provide important tools for monitoring the progress of lymphatic filariasis elimination programs. In this study, we compared dissection of the vector, Culex quinquefasciatus, with the polymerase chain reaction (PCR) to assess filarial infection levels in mosquitoes in the context of a lymphatic filariasis elimination program in Leogane, Haiti. METHODS: Mosquitoes were collected using gravid traps located in 4 sentinel communities with Wuchereria bancrofti microfilaria prevalence that ranged from 0.8% to 15.9%. Captured mosquitoes were divided between dissection, to enumerate W. bancrofti larvae (L1, L2, L3) and desiccation for later analysis by PCR. PCR was conducted on DNA extracts from pooled mosquitoes (1-15 pooled females) utilizing a competitive PCR system with primers specific for the Ssp I repeat. PCR products were analyzed with a hybridization ELISA using probes specific for a control sequence and the Ssp I repeat. RESULTS: The prevalence of mosquito infection with W. bancrofti ranged from 0%-3.66% by dissection (L1-L3) and point estimates of infection prevalence, as assayed by PCR, ranged from 0.25% - 9.16%. Following mass treatment, W. bancrofti infection prevalence dropped significantly as determined by PCR and dissection in 2 of the 4 sentinel sites (Leogane and Barrier Jeudi, P = 0.04 and P = 0.005, respectively). Although transmission declined in the other two sites, larval recoveries were low and these changes were not statistically significant. DISCUSSION: Our results suggest that a single round of mass treatment can have an impact on transmission of lymphatic filariasis. The use of entomologic methods as a tool to monitor filariasis programs and the statistical limitations of mosquito trapping are discussed.     

Prevalence of human African trypanosomiasis in the Democratic Republic of the Congo

Human African Trypanosomiasis (HAT) is a major public health problem in the Democratic Republic of the Congo (DRC). Active and passive surveillance for HAT is conducted but may underestimate the true prevalence of the disease. We used ELISA to screen 7,769 leftover dried blood spots from a nationally representative population-based survey, the 2007 Demographic and Health Survey. 26 samples were positive by ELISA. Three of these were also positive by trypanolysis and/or PCR. From these data, we estimate that there were 18,592 people with HAT (95% confidence interval, 4,883-32,302) in the DRC in 2007, slightly more than twice as many as were reported.     

Sensitive assays for simian foamy viruses reveal a high prevalence of infection in commensal, free-ranging Asian monkeys

Foamy viruses (FV) are retroviruses that naturally infect many hosts, including most nonhuman primates (NHPs). Zoonotic infection by primate FV has been documented in people in Asia who reported contact with free-ranging macaques. FV transmission in Asia is a concern, given abundant human-NHP contact, particularly at monkey temples and in urban settings. We have developed three assays capable of detecting the presence of FV in Asian NHP species that are commensal with humans: enzyme-linked immunosorbent assay (ELISA), Western blot assays using recombinant viral Gag protein, and an indicator cell line that can detect macaque FV. The recombinant ELISA correlates very well with the presence of FV sequences detected by PCR. We have used these assays to demonstrate both that FV is highly prevalent among free-ranging NHPs and that seroconversion occurs at a young age in these animals. These assays should also prove useful for large-scale analysis of the prevalence of FV infections in human populations in Asia that are commensal with free-ranging NHPs.     

Detection of Campylobacter jejuni and Campylobacter coli in environmental waters by PCR enzyme-linked immunosorbent assay

A PCR enzyme-linked immunosorbent assay (ELISA) assay was applied to the detection of Campylobacter jejuni and Campylobacter coli in environmental water samples after enrichment culture. Bacterial cells were concentrated from 69 environmental water samples by using filtration, and the filtrates were cultured in Campylobacter blood-free broth. After enrichment culture, DNA was extracted from the samples by using a rapid-boiling method, and the DNA extracts were used as a template in a PCR ELISA assay. A total of 51 samples were positive by either PCR ELISA or culture; of these, 43 were found to be positive by PCR ELISA and 43 were found to be positive by culture. Overall, including positive and negative results, 59 samples were concordant in both methods. Several samples were positive in the PCR ELISA assay but were culture negative; therefore, this assay may be able to detect sublethally damaged or viable nonculturable forms of campylobacters. The method is rapid and sensitive, and it significantly reduces the time needed for the detection of these important pathogens by 2 to 3 days.     

Cystic echinococcosis in Greece. Past and present

Cystic echinococcosis is a zoonotic disease with a wide geographical distribution, Greece included, and is considered to be a serious problem for the public health and the livestock economy. Although the disease was widespread in Greece since ancient times, cystic echinococcosis was identified as a serious problem around 1970, and since then national surveillance programmes are running, based on meat inspection and stray dogs management. Ever since, there are official records of the parasite's prevalence in humans and livestock which show a continuous decline. More precisely, human hydatidosis, according to the official records, declines from an annual incidence of 14.8 per 100,000 inhabitants during 1967-1971 to 0.3 in 2008. Late surveys reveal that in Greece the prevalence of echinococcosis was 23-39.2% for sheep, 7.6-14.7% for goats, 0% in cattle and 0.6% in pigs, while further molecular analyses in Southern Greece showed the existence of the genotypes G1 and G3 in sheep and G7 in goats in that area. All data presented demonstrate that the parasite is still present in Greece. Surveillance is nowadays being performed under EU regulations but it is highly important to improve and adopt corrective and preventive measures to avoid animal and human infection.     

Virus infections in wild plant populations are both frequent and often unapparent

? Premise of the study: Pathogens are thought to regulate host populations. In agricultural crops, virus infection reduces yield. However, in wild plants little is known about the spatial and temporal patterns of virus prevalence. Thus, pathogen effects on plant population dynamics are unclear. Prevalence data provide necessary background for (1) evaluating the effects of virus infection on plant population size and dynamics and (2) improving risk assessment of virus-resistant transgenic crops. ? Methods: We used ELISA and RT-PCR to survey wild Cucurbita pepo populations over 4 years for five viruses, aphid-transmitted viruses of the genus Potyvirus as a group and PCR to survey for virus-resistance transgenes. In addition, we surveyed the literature for reports of virus prevalence in wild populations. ? Key results: In 21 C. pepo populations, virus prevalence (0-74%) varied greatly among populations, years, and virus species. In samples analyzed by both ELISA and RT-PCR, RT-PCR detected 6-44% more viruses than did ELISA. Eighty percent of these infections did not cause any visually apparent symptoms. In our samples, the virus-resistance transgene was not present. In 30 published studies, 92 of 146 tested species were infected with virus, and infection rates ranged from 0.01-100%. Most published studies used ELISA, suggesting virus prevalence is higher than reported. ? Conclusions: In wild C. pepo, the demographic effects of virus are likely highly variable in space and time. Further, our literature survey suggests that such variation is probably common across plant species. Our results indicate that risk assessments for virus-resistant transgenic crops should not rely on visual symptoms or ELISA and should include data from multiple populations over multiple years.     

Serological and molecular studies on Dirofilaria immitis in dogs from Turkey

We estimated the prevalence of Dirofilaria immitis infection in domestic dogs in five Turkish provinces - Sakarya, Kocaeli, Ankara, Elazig and Mersin - using a commercial ELISA kit for detecting circulating antigen and a PCR test for detecting circulating microfilarial DNA. A total of 211 whole-blood and serum samples were collected from dogs of various breeds, ages and life status (owned or stray). Sample population characteristics were recorded and examined for differences in prevalence. Additionally, we collected 15 blood samples from cats (14 owned and 1 stray) from Ankara province and used PCR to detect D. immitis infection. Twenty-seven (12.8%) of 211 dog samples were positive for D. immitis antigen by ELISA. No differences in prevalence were observed by sex (female: 14.4%; male: 10.7%; P>0.05). The prevalence of D. immitis infection varied with age: 11.8% in younger dogs (0.5-2 years) and 17.5% in older dogs (3-5 years). Prevalence between stray dogs (15.2%) and owned dogs (9.3%) did not differ (P>0.05). Prevalence rates were highest in Kocaeli province (18.3%), followed by Ankara (14.8%), Sakarya (12.3%) and Mersin (10.5%) provinces. Prevalence in Elazig province was 0%. No dogs or cats had microfilarial DNA detectable by PCR.     

A comparison of the prevalence of Spirocerca lupi in three groups of dogs with different life and hunting styles

The prevalence of Spirocerca lupi in 260 privately owned dogs with different life and hunting styles in Greece was based on the examination of randomly taken faecal samples using Teleman's sedimentation technique. The dogs did not demonstrate any clinical signs of spirocerciasis. Although the prevalence was 10%, it was found to be significantly higher in trace hunting dogs (21%), than in scent hunting dogs (5%) and household pets (0%). There was no relationship between prevalence and age/sex of dogs. The impact of life and hunting styles on the prevalence of S. lupi in the dog and that of the faecal examination technique, are discussed.     

Comparative evaluation of the efficacy of Borrelia indication in ixodes ticks (Ixodidae) using dark field microscopy and polymerase chain reaction (PCR)

Indication of Borrelia (B. burgdorferi sensu lato) in 205 adult unfed I. persulcatus ticks from a natural focus was carried out simultaneously by methods of PCR and dark-field microscopy of vital preparations. PCR method revealed Borrelia prevalence in considerable number of ticks, in which Borrelia were not found by microscopy of 250 microscopic fields in a preparation from each individual tick. At the same time, PCR method didn't give positive results for approximately 8% of ticks, which contained rather high concentration of Borrelia (more than 10 per 100 microscopic fields). In general, PCR method doesn't have advantages in comparison with a microscopy of vital preparations for study the Borrelia prevalence in ticks.     

Detection of Campylobacter jejuni and Campylobacter coli in Environmental Waters by PCR Enzyme-Linked Immunosorbent Assay

A PCR enzyme-linked immunosorbent assay (ELISA) assay was applied to the detection of Campylobacter jejuni and Campylobacter coli in environmental water samples after enrichment culture. Bacterial cells were concentrated from 69 environmental water samples by using filtration, and the filtrates were cultured in Campylobacter blood-free broth. After enrichment culture, DNA was extracted from the samples by using a rapid-boiling method, and the DNA extracts were used as a template in a PCR ELISA assay. A total of 51 samples were positive by either PCR ELISA or culture; of these, 43 were found to be positive by PCR ELISA and 43 were found to be positive by culture. Overall, including positive and negative results, 59 samples were concordant in both methods. Several samples were positive in the PCR ELISA assay but were culture negative; therefore, this assay may be able to detect sublethally damaged or viable nonculturable forms of campylobacters. The method is rapid and sensitive, and it significantly reduces the time needed for the detection of these important pathogens by 2 to 3 days.     

Low Parasitemia in Submicroscopic Infections Significantly Impacts Malaria Diagnostic Sensitivity in the Highlands of Western Kenya

Asymptomatic malaria infections represent a major challenge in malaria control and elimination in Africa. They are reservoirs of malaria parasite that can contribute to disease transmission. Therefore, identification and control of asymptomatic infections are important to make malaria elimination feasible. In this study, we investigated the extent and distribution of asymptomatic malaria in Western Kenya and examined how varying parasitemia affects performance of diagnostic methods including microscopy, conventional PCR, and quantitative PCR. In addition, we compared parasite prevalence rates and parasitemia levels with respect to topography and age in order to explore factors that influence malaria infection. Over 11,000 asymptomatic blood samples from children and adolescents up to 18 years old representing broad areas of Western Kenya were included. Quantitative PCR revealed the highest parasite positive rate among all methods and malaria prevalence in western Kenya varied widely from less than 1% to over 50%. A significantly lower parasitemia was detected in highland than in lowland samples and this contrast was also observed primarily among submicroscopic samples. Although we found no correlation between parasitemia level and age, individuals of younger age group (aged <14) showed significantly higher parasite prevalence. In the lowlands, individuals of aged 5–14 showed significantly higher prevalence than those under age 5. Our findings highlight the need for a more sensitive and time-efficient assay for asymptomatic malaria detection particularly in areas of low-transmission. Combining QPCR with microscopy can enhance the capacity of detecting submicroscopic asymptomatic malaria infections.     

Genetically Diverse Clostridium difficile Strains Harboring Abundant Prophages in an Estuarine Environment

Clostridium difficile is the leading cause of antibiotic-associated diarrheal disease in health care settings across the world. Despite its pathogenic capacity, it can be carried asymptomatically and has been found in terrestrial and marine ecosystems outside hospital environments. Little is known about these environmental strains, and few studies have been conducted on estuarine systems. Although prophage abundance and diversity are known to occur within clinical strains, prophage carriage within environmental strains of C. difficile has not previously been explored. In this study, we isolated C. difficile from sites sampled in two consecutive years in an English estuarine system. Isolates were characterized by PCR ribotype, antibiotic resistance, and motility. The prevalence and diversity of prophages were detected by transmission electron microscopy (TEM) and a phage-specific PCR assay. We show that a dynamic and diverse population of C. difficile exists within these sediments and that it includes isolates of ribotypes which are associated with severe clinical infections and those which are more frequently isolated from outside the hospital environment. Prophage carriage was found to be high (75%), demonstrating that phages play a role in the biology of these strains.     

Tomato spotted wilt virus (TSWV) in Greece: its incidence following the expansion of Frankliniella occidentalis, and characterisation of isolates collected from various hosts

Leaf samples were collected from plants with tospovirus‐like symptoms from various hosts in different regions of Greece where Thrips tabaci, Frankliniella occidentalis or both vectors occur. The viruses infecting these plants were identified with polyclonal antibodies raised against the N proteins of Tomato spotted wilt virus (TSWV) and Impatiens necrotic spot virus (INSV) by ELISA. All samples tested positive for TSWV, but not for INSV. ELISA of thirty three isolates, using monoclonal antibodies against the N protein of TSWV, revealed the existence of five epitopes on the N protein. RT‐PCR tests on a few randomly‐selected isolates, using a pair of universal primers, a pair of primers specific for the L gene and a pair of primers specific for the N gene, as well as sequence analysis of a part of the S gene of one isolate, confirmed the authenticity of the virus isolated as TSWV. Host range studies showed differences in susceptibility, especially among species belonging to the Leguminosae and Cucurbitaceae. The species Beloporone guttata and Coleus sp. are reported for the first time as hosts of the virus, whereas Solanum melongena, Celosia cristata, Dianthus chinensis, Stephanotis floribunda and Catharanthus roseus were identified as new hosts of TSWV in Greece.     

Prevalence of chlamydiae in semen and genital tracts of bulls, rams and bucks

Chlamydiae infect male genital organs of ruminants. However, little is known about their prevalence. Hence, we investigated fresh and cryopreserved semen (bulls: n=304; rams: n=78; bucks: n=44) by polymerase chain reaction (PCR), as well as genital organs (bulls: n=13; rams: n=10; bucks: n=6) by immunohistochemistry (IHC) and PCR. Sera from bulls (n=104) and small ruminants (n=61) were tested by LPS and rMOMP (recombinant major outer membrane protein) ELISA and competitive ELISA (cELISA), respectively. Three PCR assays were compared in this study for detection of chlamydial DNA in semen: 16S rRNA, IGS-S (intergenic spacer 16S/23S-short), and IGS-L (intergenic spacer 16S/23S-long) PCRs. PCR sensitivity and inhibitory effects were determined by spiking semen with Chlamydophila (Cp.) abortus DNA. In bull semen, detection limits of the 16S, IGS-S and IGS-L PCRs were 10, 10, 100 templates, respectively. However, PCR sensitivity was reduced in ram and buck semen suggesting the presence of potential PCR inhibitors. Of 304 bull semen samples, the 16S PCR revealed DNA of chlamydiae in 20 samples (6.6%), including Cp. abortus (n=2), Cp. psittaci (n=1), Chlamydia suis (n=2), and Chlamydia-like organisms (n=15). In rams, one semen sample was positive for Chlamydia-like organism. All investigated male genital organs were negative for Chlamydia. Serology revealed 47.1% (49/104) positive bulls by LPS ELISA. Of these, 30 samples were positive by rMOMP ELISA, predominantly for Cp. pecorum. In small ruminants, cELISA displayed 34.8% (16/46) and 60% (9/15) positivity for Cp. abortus in rams and bucks, respectively. There was no correlation between serology and PCR of semen. The presence of chlamydiae in semen suggests the possibility of venereal transmission, although risk may be low in Switzerland.     

Pseudorabies virus in European wild boar from central Italy

Tissue and blood samples were collected from 152 wild boars (Sus scrofa) from the Maremma area (Grosseto district, Central Italy) between November 2002 and January 2003. The presence of pseudorabies virus (PRV) antibodies, antigen, and DNA were confirmed by an enzyme-linked immunosorbent assay (ELISA), immunohistochemistry, and polymerase chain reaction (PCR), respectively. Of 152 animals, 62 (41%) were positive for viral antigen in tonsillar tissue. Of the 80 serum samples that were suitable for testing, 41 (51%) were positive for PRV antibodies. Positive immunohistochemistry results were confirmed by PCR. A significantly higher prevalence of PRV antigen and seroprevalence was detected in older animals. No differences were detected between males and females or for animals coming from different areas sampled. Results confirm that PRV is endemic in this wild boar population with a high prevalence of infection. The results of immunohistochemistry investigations demonstrated that a large number of wild boars harbor PRV in tonsillar tissues and should be considered as an important reservoir of PRV.