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Filariasis, a neglected tropical disease caused by roundworms, is a significant public health concern in many tropical countries. Microscopic examination of blood samples can detect and differentiate parasite species, but it is time consuming and requires expert microscopists, a resource that is not always available. In this context, artificial intelligence (AI) can assist in the diagnosis of this disease by automatically detecting and differentiating microfilariae. In line with the target product profile for lymphatic filariasis as defined by the World Health Organization, we developed an edge AI system running on a smartphone whose camera is aligned with the ocular of an optical microscope that detects and differentiates filarias species in real time without the internet connection. Our object detection algorithm that uses the Single-Shot Detection (SSD) MobileNet V2 detection model was developed with 115 cases, 85 cases with 1903 fields of view and 3342 labels for model training, and 30 cases with 484 fields of view and 873 labels for model validation before clinical validation, is able to detect microfilarias at 10x magnification and distinguishes four species of them at 40x magnification: Loa loa, Mansonella perstans, Wuchereria bancrofti, and Brugia malayi. We validated our augmented microscopy system in the clinical environment by replicating the diagnostic workflow encompassed examinations at 10x and 40x with the assistance of the AI models analyzing 18 samples with the AI running on a middle range smartphone. It achieved an overall precision of 94.14%, recall of 91.90% and F1 score of 93.01% for the screening algorithm and 95.46%, 97.81% and 96.62% for the species differentiation algorithm respectively. This innovative solution has the potential to support filariasis diagnosis and monitoring, particularly in resource-limited settings where access to expert technicians and laboratory equipment is scarce. Author summary: Filariasis is a common tropical infectious disease. Depending on the parasite, it causes lymphoedema, elephantiasis, itching, blindness, etc. It is estimated that more than 1 billion people require preventive chemotherapy to stop the spread of this infection. The diagnosis of this disease is made through microscopical examination of a blood smear by a human expert, which is not always available. In this study we propose an edge Artificial Intelligence (AI) system that detects and quantifies four species of microfilariae (Loa loa, Mansonella perstans, Wuchereria bancrofti and Brugia malayi) using the camera of a smartphone attached to an optical microscope with a 3D printed adapter. The system works in real time and does not need internet connectivity as the AI models are run locally in a medium range smartphone. We have replicated the diagnostic workflow that is typically performed by an expert microscopist augmented by the support of the AI system. [ABSTRACT FROM AUTHOR]

Soil-transmitted helminths (STH) are the most prevalent pathogens among the group of neglected tropical diseases (NTDs). The Kato-Katz technique is the diagnosis method recommended by the World Health Organization (WHO) although it often presents a decreased sensitivity in low transmission settings and it is labour intensive. Visual reading of Kato-Katz preparations requires the samples to be analyzed in a short period of time since its preparation. Digitizing the samples could provide a solution which allows to store the samples in a digital database and perform remote analysis. Artificial intelligence (AI) methods based on digitized samples can support diagnosis by performing an objective and automatic quantification of disease infection. In this work, we propose an end-to-end pipeline for microscopy image digitization and automatic analysis of digitized images of STH. Our solution includes (a) a digitization system based on a mobile app that digitizes microscope samples using a 3D printed microscope adapter, (b) a telemedicine platform for remote analysis and labelling, and (c) novel deep learning algorithms for automatic assessment and quantification of parasitological infections by STH. The deep learning algorithm has been trained and tested on 51 slides of stool samples containing 949 Trichuris spp. eggs from 6 different subjects. The algorithm evaluation was performed using a cross-validation strategy, obtaining a mean precision of 98.44% and a mean recall of 80.94%. The results also proved the potential of generalization capability of the method at identifying different types of helminth eggs. Additionally, the AI-assisted quantification of STH based on digitized samples has been compared to the one performed using conventional microscopy, showing a good agreement between measurements. In conclusion, this work has presented a comprehensive pipeline using smartphone-assisted microscopy. It is integrated with a telemedicine platform for automatic image analysis and quantification of STH infection using AI models. Author summary: Soil-transmitted helminths (STH), including hookworm, Ascaris lumbricoides and Trichuris trichiura, are common intestinal infections in low-income countries. Global estimates indicate that more than 1.5 billion people are infected with at least one STH species. They cause anaemia, gastro-intestinal problems, tiredness amongst other symptoms. Diagnosis of STH infection is mainly performed by analyzing stool samples under the microscope using the so-called Kato-Katz technique. However, the analysis of Kato-Katz samples, which is usually performed by microscopy experts, is a subjective procedure based on visual inspection of the samples and requires to be done in a short period of time since the sample preparation. In this work we proposed a novel system to digitize the microscopy samples using an affordable 3D-printed adapter and smartphones. Digitized images were uploaded to a telemedicine platform enabling remote diagnosis. Additionally, the digitized images were automatically analyzed by an Artificial Intelligence (AI) algorithm which was fully-integrated in the telemedicine platform, performing an automatic and objective count of different types of STH parasites (A. lumbricoides and T. trichiura). [ABSTRACT FROM AUTHOR]

Background: Human infections by the gastrointestinal helminth Strongyloides stercoralis and the enteric protozoans Giardia duodenalis, Cryptosporidium spp. and Blastocystis spp. are not formally included in the list of 20 neglected tropical diseases prioritised by the World Health Organization. Although largely underdiagnosed and considered of lower public health relevance, these infections have been increasingly demonstrated to cause significant morbidity and even mortality globally, particularly among children living in resource-poor settings. Methods: In this cross-sectional survey the prevalence, frequency and molecular diversity of S. stercoralis, G. duodenalis, Cryptosporidium spp. and Blastocystis spp. were investigated in a school children population in the province of Benguela (Angola). A total of 351 stool samples were collected during January to June 2015. The presence of S. stercoralis and G. duodenalis was confirmed by qPCR methods. Giardia duodenalis assemblages and sub-assemblages were determined by multilocus sequence-based genotyping of the glutamate dehydrogenase and β-giardin genes of the parasite. Detection and identification of Cryptosporidium and Blastocystis species and subtypes was carried out by amplification and sequencing of a partial fragment of the small-subunit ribosomal RNA gene of both protozoan. Analyses of risk factors potentially associated with the transmission of these pathogens were also conducted. Results: Prevalences of S. stercoralis, G. duodenalis, Cryptosporidium spp., and Blastocystis spp. were estimated at 21.4% (95% CI: 17.1-25.7%), 37.9% (95% CI: 32.8-43.0%), 2.9% (95% CI: 1.1-4.5%) and 25.6% (95% CI: 21.18-30. 2%), respectively. Overall, 64.1% (225/351) of the children were infected by at least one of the pathogens investigated. Sequence analyses of the 28 G. duodenalis isolates that were successfully genotyped allowed the identification of sub-assemblages AI (14.3%), AII (14.3%), BIII (7.1%) and BIV (25.0%). Discordant typing results AII/AIII and BIII/BIV were identified in 7.1% and 14.3% of the isolates, respectively. A total of five additional isolates (17.9%) were identified as assemblage B. Three Cryptosporidium species including C. hominis (70%), C. parvum (20%) and C. canis (10%) were found circulating in the children population under study. A total of 75 Blastocystis isolates were assigned to the subtypes ST1 (30.7%), ST2 (30.7%), ST3 (36.0%), ST5 (1.3%) and ST7 (1.3%), respectively. Children younger than seven years of age had significantly higher risk of infections by protozoan enteropathogens (PRR: 1.35, P< 0.01), whereas being underweight seemed to have a protective effect against these infections (PRR: 0.74, P = 0.005). Conclusions: The burden of disease attributable to human strongyloidiasis, giardiosis, cryptosporidiosis and blastocystosis in Angola is considerably higher than initially estimated in previous surveys. Surveillance and control of these infections should be jointly tackled with formally considered neglected tropical diseases in order to maximize effort and available resources. Our data also demonstrate the added value of using molecular diagnostic methods in high transmission areas. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the performance of Rapid-Heat LAMPellet assay in field conditions for diagnosis of urogenital schistosomiasis in an endemic area in Cubal, Angola, and to assess the reproducibility in a reference laboratory.Methods: A total of 172 urine samples from school-age children were tested for microhaematuria, microscopic detection of Schistosoma haematobium eggs and LAMP for DNA detection. Urine samples were stored in a basic equipped laboratory. Field-LAMP tests were performed with and without prior DNA extraction from urine samples, and the results were read by turbidity and by colour change. When field procedures were finished, samples were sent to a reference laboratory to be reanalysed by LAMP.Results: A total of 83 of 172 (48.3%) were positive for microhaematuria, 87/172 (50.6%) were microscopy-positive for S. haematobium eggs detection, and 127/172 (73.8%) showed LAMP-positive results for detecting S. haematobium using purified DNA and 109/172 (63.4%) without prior DNA extraction. MacNemar's test showed a statistical significant relation between LAMP results and microscopy-detected S. haematobium infections and microhaematuria (P < 0.001 in both cases), respectively. When samples of purified DNA were reanalysed in a reference laboratory in Spain using the same LAMP methodology, the overall reproducibility achieved 72.1%.Conclusions: The ease of use, simplicity and feasibility demonstrated by LAMP assay in field conditions together with the acceptable level of reproducibility achieved in a reference laboratory support the use of LAMP assay as an effective test for molecular diagnosis of urogenital schistosomiasis in endemic remote areas. [ABSTRACT FROM AUTHOR]

Background: Soil transmitted helminths are highly prevalent worldwide. Globally, approximately 1.5 billion people are infected with Ascaris lumbricoides, Trichuris trichiura or hookworm. Endemic countries carry out periodic mass treatment of at-risk populations with albendazole or mebendazole as a control measure. Most prevalence studies have focused on school aged children and therefore control programs are implemented at school level, not at community level. In this study, the prevalence of intestinal helminths, including Strongyloides stercoralis, was examined using a comprehensive laboratory approach in a community in north-western Ethiopia. Methods: A cross-sectional survey was conducted on 792 individuals ≥5 years old in randomly selected houses in a rural district. Stools were examined using three techniques: a formol-ether concentration, the Baermann technique and a real time polymerase chain reaction test (these last two specific for S. stercoralis). Statistical analyses were performed between two large age groups, children (≤14 years old) and adults (≥15 years old). Results: The prevalence of helminths was 91.3%; (95% CI: 89.3–93.3%). Hookworm was the most prevalent, 78.7% (95% CI 75.6–81.4%), followed by S. stercoralis 55.7% (95% CI 52.2–59.1%). Co-infection with both was detected in 45.4% (95% CI 42.0–49.0%) of the participants. The mean age of hookworm-infected individuals was significantly higher than non-infected ones (p = 0.003). Also, S. stercoralis infection was significantly associated with age, being more prevalent in adults (p = 0.002). Conclusions: This is the highest prevalence of S. stercoralis detected in Ethiopia so far. Our results highlight the need of searching specifically for infection by this parasite since it usually goes unnoticed if helminth studies rely only on conventional diagnostic techniques, i.e. Kato-Katz. Moreover, the focus of these programs on children undermines the actual prevalence of hookworm. The adult population acts as a reservoir for both hookworm and S. stercoralis and this fact may negatively impact the current control programs in Ethiopia which only target treatment of school aged children. This reservoir, together with a lack of adequate water, sanitation and hygiene, increases the probability of re-infection in children. Finally, the high prevalence of S. stercoralis found calls for a comprehensive diagnostic approach in endemic areas in addition to a revision of control measures that is, adding ivermectin to current albendazole/mebendazole, since it is the drug of choice for S. stercoralis. Author summary: Soil-transmitted-helminthiases and schistosomiasis have major programs for control within the neglected tropical diseases agenda. Deworming programs, that is, periodic mass drug administration, with albendazole or mebendazole and praziquantel, for at-risk populations, are the main strategy for control and success in interrupting the transmission of these diseases. But despite huge efforts made, programs are still unsuccessful in controlling STH in endemic areas in Africa. In Ethiopia most parts of the country are suitable for helminth transmission. Mapping for identification of risk areas for hookworm, A. lumbricoides, T. trichiura and Schistosoma spp., has been conducted by the government, in order to prioritize the health agenda. The focus of the interventions are school- aged children. Another species of soil-transmitted helminth, Strongyloides stercoralis, of high morbidity, which requires special laboratory methods for diagnosis and a different treatment drug, is highly underestimated and not included in control programs. With the aim of knowing the prevalence of S. stercoralis and other intestinal helminths at the community level, a population in the rural area of north-western Ethiopia was studied using parasitological and molecular techniques. A high prevalence of helminths at the community level and specifically a high prevalence of S. stercoralis were detected. These results suggest there is a need to revise control programs in order to be able to cut transmission and to ensure universal health coverage that "leaves no one behind". [ABSTRACT FROM AUTHOR]

Background: Several studies have independently evaluated the occurrence of hepatitis E virus (HEV) and enteroparasites in swine, but no surveys have been conducted to jointly assess the prevalence and genetic diversity of enteroparasites in pigs and wild boars, their sympatric transmission between hosts, and their potential interaction with HEV. Methods: We prospectively collected serum and faecal samples from black Iberian domestic pigs and wild boars from southern Spain between 2015‒2016. We evaluated for HEV in serum and faeces, and for the presence of enteroparasites (Giardia duodenalis, Cryptosporidium spp., Blastocystis sp., Neobalantidium coli and Strongyloides spp.) in the same faecal samples. The prevalence of each intestinal parasite species was calculated. Results: A total of 328 animals (56.7% black Iberian pigs and 43.3% wild boars) were included in the study. The overall global prevalence of HEV in serum was 16.8%. The overall global prevalence of each enteroparasite species was 19.5% for G. duodenalis, 8.2% for Cryptosporidium spp., 41.8% for Blastocystis sp., 31.4% for N. coli, and 8.8% for Strongyloides spp. HEV-infected animals showed a significantly lower prevalence of G. duodenalis (3.2 vs 20%; P = 0.002) and Blastocystis sp. (38.7 vs 80%; P < 0.001) than those uninfected by HEV. Animals carrying G. duodenalis and Blastocystis sp. infections showed a significantly lower rate of HEV infection than those not harbouring these enteroparasites (P < 0.001). Conclusions: Our study found a high prevalence of enteroparasites in black Iberian pigs and wild boars in southern Spain, suggesting a sympatric co-transmission of some of the species investigated. It is suggested that extracellular G. duodenalis and Blastocystis sp. might have a protective effect on HEV acquisition in swine. [ABSTRACT FROM AUTHOR]

The diversity and frequency of enteric parasites in dog populations in the Castellón province (Eastern Spain) were assessed using a prospective cross-sectional epidemiological survey. A total of 263 canine fecal samples were collected between July 2014 and July 2016. Detection of intestinal parasites was conducted by routine coprological methods. In addition, identification of Giardia duodenalis and Cryptosporidium spp. was carried out by direct immunofluorescence microscopy, whereas the presence of Strongyloides spp. was assessed by real-time PCR in a selected number of specimens. Based on conventional and/or immunofluorescence microscopy examination, 65.8% (95% confidence interval: 59.7–71.5) of the investigated dogs were found infected by at least one gastrointestinal parasite. G. duodenalis (35.4%) and members of the family Ancylostomatidae (27.0%) were the most prevalent protozoan and helminth parasites found, respectively. Other pathogens potentially infective to humans included Toxocara canis (8.0%), Cryptosporidium spp. (6.8%), and Strongyloides spp. (1.1%). Frequency of occurrence of helminthic, but not protozoan, enteroparasites was geographical origin dependent (p = 0.02), with dogs living in coastal areas presenting higher infection rates than those living in inland regions. Similarly, rural dogs were significantly more infected than urban dogs (p < 0.001). Our results revealed that zoonotic agents were common in dogs from the Castellón province. Animals from rural areas and sheltered dogs were particularly at risk of these infections. [ABSTRACT FROM AUTHOR]

Gut parasites exert an important influence on the gut microbiome, with many studies focusing on the human gut microbiome. It has, however, undergone severe richness depletion. Hygienic lifestyle, antimicrobial treatments and altered gut homeostasis (e.g., chronic inflammation) reduce gut microbiome richness and also parasite prevalence; which may confound results. Studying species closely related to humans could help overcome this problem by providing insights into the ancestral relationship between humans, their gut microbiome and their gut parasites. Chimpanzees are a particularly promising model as they have similar gut microbiomes to humans and many parasites infect both species. We study the interaction between gut microbiome and enteric parasites in chimpanzees. Investigating what novel insights a closely related species can reveal when compared to studies on humans. Using eighty-seven faecal samples from wild western chimpanzees (Pan troglodytes verus) in Senegal, we combine 16S rRNA gene amplicon sequencing for gut microbiome characterization with PCR detection of parasite taxa (Blastocystis sp., Strongyloides spp., Giardia duodenalis , Cryptosporidium spp., Plasmodium spp., Filariae and Trypanosomatidae). We test for differences in gut microbiota ecosystem traits and taxonomical composition between Blastocystis and Strongyloides bearing and non-bearing samples. For Blastocystis , twelve differentially abundant taxa (e.g., Methanobrevibacter), including Prevotella and Ruminococcus - Methanobrevibacter enterotype markers, replicate findings in humans. However, several richness indices are lower in Blastocystis carriers, contradicting human studies. This indicates Blastocystis , unlike Strongyloides , is associated to a "poor health" gut microbiome, as does the fact that Faecalibacterium , a bacterium with gut protective traits, is absent in Blastocystis -positive samples. Strongyloides was associated to Alloprevotella and five other taxonomic groups. Each parasite had its unique impact on the gut microbiota indicating parasite-specific niches. Our results suggest that studying the gut microbiomes of wild chimpanzees could help disentangle biological from artefactual associations between gut microbiomes and parasites. • Microbial variation was explained by group affiliation, diet and parasite carriage • Blastocystis is associated to increases in Methanobrevibacter and Prevotella _1; and Ruminococcus and Prevotella enterotypes • At the taxonomic level, Blastocystis ' associations reflect those found in humans • Blastocystis is associated to decreased prokaryote richness and poor health markers • Strongyloides is associated to Alloprevotella and Mollicutes_RF9 increases [ABSTRACT FROM AUTHOR]