Frontiers in tropical diseases最新文献

{"title":"Metabarcoding mosquitoes: MinION sequencing of bulk samples gives accurate species profiles for vector surveillance (Culicidae)","authors":"Rebecca Ker Loh, Tyrone Ren Hao Tan, Huiqing Yeo, Tze Xuan Yeoh, T. T. M. Lee, S. N. Kutty, Nalini Puniamoorthy","doi":"10.3389/fitd.2024.1223435","DOIUrl":"https://doi.org/10.3389/fitd.2024.1223435","url":null,"abstract":"Mosquitoes (Family: Culicidae) are dominant vectors of pathogens, and their surveillance has been incorporated into major disease control programs worldwide. However, routine, species-level identification of mosquitoes is often a bottleneck for management, and Next Generation Sequencing (NGS) platforms and DNA metabarcoding can revolutionize this process. MinION nanopore technologies promise on-site sequencing and rapid sample processing rates ideal for time-sensitive biosurveillance. Here, we benchmark the results of DNA metabarcoding on the MinION against the Illumina MiSeq platform, which is known for its higher sequencing accuracy. We used metazoan COI mini-barcode primers to carry out DNA metabarcoding of mosquito bulk samples caught during a real vector survey, then compared the mosquito species profiles recovered on each sequencing platform. We also tested the influence of using different trap lures, storage methods, and pooling different specimen body parts on the number of species recovered. We report that mosquito species-level identifications were highly congruent between MinION and Illumina (93% overlap). We also find that CO2 gas cylinders outperformed biogenic CO2 sources significantly, by two-fold. Notably, we demonstrated the feasibility of detecting zoonotic reservoirs and pathogen signals from mosquito bulk samples. We present the first use of DNA metabarcoding on the MinION for vector surveillance and discuss future applications.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"340 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139841490","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Antimicrobial resistance profile of Enterococcus species and molecular characterization of Vancomycin resistant Enterococcus faecium from the fecal samples of newly diagnosed adult HIV patients in Dar es Salaam, Tanzania","authors":"U. Kibwana, J. Manyahi, S. Moyo, Bjørn Blomberg, Adam P. Roberts, N. Langeland, S. Mshana","doi":"10.3389/fitd.2024.1307379","DOIUrl":"https://doi.org/10.3389/fitd.2024.1307379","url":null,"abstract":"Enterococci are becoming clinically more important especially among immunocompromised patients. Of concern are vancomycin resistant enterococci (VRE) which have both intrinsic and acquired forms of resistance. This work aimed to determine the antimicrobial resistance patterns of Enterococcus spp. and characterize VRE isolate obtained from HIV-infected patient using whole genome sequencing (WGS).Antimicrobial susceptibility testing was done on 57 enterococci isolates by both the disk diffusion method and Epsilometer test (E-Test). WGS was performed on VRE isolate determined by E-test.Out of the 57 enterococci isolates; 58% (33/57) were E. faecalis, 39% (22/57) E. faecium and 4% (2/57) were E. gallinarum. The highest antimicrobial resistance was observed in E. faecalis isolates. The most prevalent antimicrobial resistance was observed towards quinupristin-dalfopristin (56%, 32/57), followed by ciprofloxacin (28%), tigecycline (18%), daptomycin (16%), chloramphenicol (14%), ampicillin and teicoplanin (2%). Multidrug resistance (MDR) was detected in 11% (6/57) of the isolates. Vancomycin resistance and high-level gentamycin resistance (HLGR) were observed in one E. faecium and one E. faecalis isolates respectively. The VRE was typed as ST80, carried vanA and other resistance genes for aminoglycosides, tetracyclines, quinolones and ampicillin. Furthermore, the isolate had chromosomal mutations responsible for quinolone (gyrA (p.S83I) and parC (p.S80I) and ampicillin (pbp5) resistance.The detection of VRE, HLGR and MDR in the study settings underscores the sustained surveillance of VRE in high-risk groups and institution of infection control measures for prompt identification and isolation of carriers to prevent the spread of VRE in the community and hospital settings.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"134 31","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139780765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabarcoding mosquitoes: MinION sequencing of bulk samples gives accurate species profiles for vector surveillance (Culicidae)","authors":"Rebecca Ker Loh, Tyrone Ren Hao Tan, Huiqing Yeo, Tze Xuan Yeoh, T. T. M. Lee, S. N. Kutty, Nalini Puniamoorthy","doi":"10.3389/fitd.2024.1223435","DOIUrl":"https://doi.org/10.3389/fitd.2024.1223435","url":null,"abstract":"Mosquitoes (Family: Culicidae) are dominant vectors of pathogens, and their surveillance has been incorporated into major disease control programs worldwide. However, routine, species-level identification of mosquitoes is often a bottleneck for management, and Next Generation Sequencing (NGS) platforms and DNA metabarcoding can revolutionize this process. MinION nanopore technologies promise on-site sequencing and rapid sample processing rates ideal for time-sensitive biosurveillance. Here, we benchmark the results of DNA metabarcoding on the MinION against the Illumina MiSeq platform, which is known for its higher sequencing accuracy. We used metazoan COI mini-barcode primers to carry out DNA metabarcoding of mosquito bulk samples caught during a real vector survey, then compared the mosquito species profiles recovered on each sequencing platform. We also tested the influence of using different trap lures, storage methods, and pooling different specimen body parts on the number of species recovered. We report that mosquito species-level identifications were highly congruent between MinION and Illumina (93% overlap). We also find that CO2 gas cylinders outperformed biogenic CO2 sources significantly, by two-fold. Notably, we demonstrated the feasibility of detecting zoonotic reservoirs and pathogen signals from mosquito bulk samples. We present the first use of DNA metabarcoding on the MinION for vector surveillance and discuss future applications.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"40 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139781653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing climate change impacts on public health in Haiti: a comprehensive study of disease distribution, modeling, and adaptation strategies","authors":"Ibrahima Diouf, Ibrahima Sy, Moussa Diakhaté","doi":"10.3389/fitd.2023.1287499","DOIUrl":"https://doi.org/10.3389/fitd.2023.1287499","url":null,"abstract":"This study examines the relationship between climate change and public health in Haiti, a country already facing socioeconomic challenges. The well-being of Haiti’s vulnerable population is expected to be further affected by climate change, leading to an increase in vector-borne, water-borne, and heat-related diseases. As one of the most vulnerable countries to climate change effects, Haiti is currently experiencing an increase in vector-borne diseases such as malaria, dengue, and chikungunya, as well as water-borne diseases and emerging zoonotic outbreaks. This study aims to improve planning, decision-making, and responses to public health challenges by utilizing health data, climatic information, and impact models. The methodology involves the creation of a comprehensive climate and health database to uncover detailed spatial-temporal relationships on a national scale. By evaluating disease indicators from historical periods (1950-2014) and future projections (2015-2100) using the Shared Socio-Economic Pathways (SSPs) from the multi-model ensemble mean of the CMIP6 models, target diseases, including malaria, meningitis, dengue, and heat-sensitive chronic diseases are assessed. Our results highlight a decrease in rainfall and a strong increase in temperatures, especially within western Haiti under the extreme SSP585 scenario. The ability of the impact models to simulate the seasonality and spatial distribution of malaria incidence, dengue and heatwaves was performed. The analysis of risks related to climate-sensitive diseases’ climatic parameters shows that Haiti’s west and central regions are mostly exposed to vector-borne and water-borne diseases. Models predict a decrease in malaria cases due to climate change with hot temperatures and a decline in rainfall, while dengue transmission patterns may undergo changes. These findings will inform the implementation of context-specific early-warning systems and adaptation strategies for climate-sensitive diseases while acknowledging the challenges of integrating climate-altered data into health policies.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":" 34","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139790418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing climate change impacts on public health in Haiti: a comprehensive study of disease distribution, modeling, and adaptation strategies","authors":"Ibrahima Diouf, Ibrahima Sy, Moussa Diakhaté","doi":"10.3389/fitd.2023.1287499","DOIUrl":"https://doi.org/10.3389/fitd.2023.1287499","url":null,"abstract":"This study examines the relationship between climate change and public health in Haiti, a country already facing socioeconomic challenges. The well-being of Haiti’s vulnerable population is expected to be further affected by climate change, leading to an increase in vector-borne, water-borne, and heat-related diseases. As one of the most vulnerable countries to climate change effects, Haiti is currently experiencing an increase in vector-borne diseases such as malaria, dengue, and chikungunya, as well as water-borne diseases and emerging zoonotic outbreaks. This study aims to improve planning, decision-making, and responses to public health challenges by utilizing health data, climatic information, and impact models. The methodology involves the creation of a comprehensive climate and health database to uncover detailed spatial-temporal relationships on a national scale. By evaluating disease indicators from historical periods (1950-2014) and future projections (2015-2100) using the Shared Socio-Economic Pathways (SSPs) from the multi-model ensemble mean of the CMIP6 models, target diseases, including malaria, meningitis, dengue, and heat-sensitive chronic diseases are assessed. Our results highlight a decrease in rainfall and a strong increase in temperatures, especially within western Haiti under the extreme SSP585 scenario. The ability of the impact models to simulate the seasonality and spatial distribution of malaria incidence, dengue and heatwaves was performed. The analysis of risks related to climate-sensitive diseases’ climatic parameters shows that Haiti’s west and central regions are mostly exposed to vector-borne and water-borne diseases. Models predict a decrease in malaria cases due to climate change with hot temperatures and a decline in rainfall, while dengue transmission patterns may undergo changes. These findings will inform the implementation of context-specific early-warning systems and adaptation strategies for climate-sensitive diseases while acknowledging the challenges of integrating climate-altered data into health policies.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"8 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139850379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Operationalising transdisciplinary remote methods in epidemic and pandemic preparedness and response in Sub-Saharan Africa","authors":"Catherine Grant","doi":"10.3389/fitd.2024.1356329","DOIUrl":"https://doi.org/10.3389/fitd.2024.1356329","url":null,"abstract":"","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"163 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139793795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Operationalising transdisciplinary remote methods in epidemic and pandemic preparedness and response in Sub-Saharan Africa","authors":"Catherine Grant","doi":"10.3389/fitd.2024.1356329","DOIUrl":"https://doi.org/10.3389/fitd.2024.1356329","url":null,"abstract":"","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"3 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139853651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trichuris trichiura infection is associated with changes in gut microbiome composition and function among women of reproductive age from Pemba, Tanzania","authors":"Aristide Toussaint Nguélé, Matteo Mozzicafreddo, Hongliang Chen, Angela Piersanti, Salum Seif Salum, Said M. Ali, Junjie Zhang, Cristina Miceli","doi":"10.3389/fitd.2024.1276210","DOIUrl":"https://doi.org/10.3389/fitd.2024.1276210","url":null,"abstract":"Large intestine-dwelling helminths affect microbiome composition. In sub-Saharan Africa, where helminth infections are endemic, the use of chemotherapeutic drugs is the primary strategy for controlling soil-transmitted helminthiases (STHs). However, the emergence of anthelmintic resistance necessitates the urgent exploration of alternative and complementary treatments to achieve the World Health Organization’s goal of eliminating STHs. One promising avenue involves the manipulation of gut microbiota in at-risk populations. This study aimed to enhance the understanding of the interplay between Trichuris trichiura and the gut microbiome. In this study, we used the Mini-FLOTAC technique for parasitological analyses and a shotgun metagenomic sequencing approach to investigate the effect of T. trichiura on the gut microbiome by comparing infected and non-infected women of reproductive age (WRA) from Pemba. Structural and functional analyses of the gut microbiome revealed that T. trichiura infection shaped the host gut microbiome in WRA. Some taxa vary according to infection status. Prevotella genus was more abundant in healthy participants, whereas species such as Weissella cibaria, Leuconostoc citreum (new emergent probiotics), and Leuconostoc lactis (starter) decreased in infected individuals, suggesting the use of potential probiotic treatments to mitigate dysbiosis induced by STHs. Furthermore, the overall number of common fungi, irrespective of species, was significantly higher in the mycobiome of Trichuris infected participants. Functional analysis revealed significant differences in metabolic pathways (p < 0.05), with cholesterol metabolism and pathogenic infections being more abundant in the infected samples than in the non-infected samples. In conclusion, this study sheds light on the intricate interactions between helminth infections and the gut microbiome in the WRA, particularly in STH-endemic regions. The identified associations between specific gut microbial changes and T. trichiura infection may pave the way for innovative complementary treatments to effectively combat STHs.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"24 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139804199","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Trichuris trichiura infection is associated with changes in gut microbiome composition and function among women of reproductive age from Pemba, Tanzania","authors":"Aristide Toussaint Nguélé, Matteo Mozzicafreddo, Hongliang Chen, Angela Piersanti, Salum Seif Salum, Said M. Ali, Junjie Zhang, Cristina Miceli","doi":"10.3389/fitd.2024.1276210","DOIUrl":"https://doi.org/10.3389/fitd.2024.1276210","url":null,"abstract":"Large intestine-dwelling helminths affect microbiome composition. In sub-Saharan Africa, where helminth infections are endemic, the use of chemotherapeutic drugs is the primary strategy for controlling soil-transmitted helminthiases (STHs). However, the emergence of anthelmintic resistance necessitates the urgent exploration of alternative and complementary treatments to achieve the World Health Organization’s goal of eliminating STHs. One promising avenue involves the manipulation of gut microbiota in at-risk populations. This study aimed to enhance the understanding of the interplay between Trichuris trichiura and the gut microbiome. In this study, we used the Mini-FLOTAC technique for parasitological analyses and a shotgun metagenomic sequencing approach to investigate the effect of T. trichiura on the gut microbiome by comparing infected and non-infected women of reproductive age (WRA) from Pemba. Structural and functional analyses of the gut microbiome revealed that T. trichiura infection shaped the host gut microbiome in WRA. Some taxa vary according to infection status. Prevotella genus was more abundant in healthy participants, whereas species such as Weissella cibaria, Leuconostoc citreum (new emergent probiotics), and Leuconostoc lactis (starter) decreased in infected individuals, suggesting the use of potential probiotic treatments to mitigate dysbiosis induced by STHs. Furthermore, the overall number of common fungi, irrespective of species, was significantly higher in the mycobiome of Trichuris infected participants. Functional analysis revealed significant differences in metabolic pathways (p < 0.05), with cholesterol metabolism and pathogenic infections being more abundant in the infected samples than in the non-infected samples. In conclusion, this study sheds light on the intricate interactions between helminth infections and the gut microbiome in the WRA, particularly in STH-endemic regions. The identified associations between specific gut microbial changes and T. trichiura infection may pave the way for innovative complementary treatments to effectively combat STHs.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"14 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139864302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing different lymphatic filariasis patient estimate approaches and results in Ethiopia","authors":"B. Mengistu, F. Kebede, Biruck Kebede Negash, Addisalem Miheret, Biruk Kebede Beyene, Solomon Abetew, Berihu Gebremariam Tedla, Asfaw Kejella Oucha, Shigute Alene, Sharone Backers, Clara Burgert, Emily Toubali, Molly Brady, Scott McPherson","doi":"10.3389/fitd.2023.1286274","DOIUrl":"https://doi.org/10.3389/fitd.2023.1286274","url":null,"abstract":"The World Health Organization (WHO) recommends that countries ensure morbidity management and disability prevention (MMDP) services are available to all lymphedema and hydrocele patients in lymphatic filariasis (LF)-endemic areas. The first step in ensuring the availability of MMDP services is to understand the number and distribution of people with lymphedema and hydrocele. We examined the burden of lymphoedema and hydrocoele using different patient estimation approaches employed in endemic districts of the Beneshangul-Gumuz and Tigray regions of Ethiopia.In Approach I, trained health extension workers (HEWs) conducted the patient estimates during a door-to-door pre-mass drug administration (MDA) census. Validation of a sample of the data collected was integrated with a post-MDA coverage survey. In Approach II, trained HEWs conducted a stand-alone patient estimation, and clinical officers validated all suspected patients. In 15 districts, 753,557 individuals were surveyed. A total of 1,645 lymphedema (1:1.6 male-to-female ratio) and 517 hydrocele cases were identified. The prevalence of lymphedema and hydrocele was 40 per 10,000 in the adult population and 25 per 10,000 in the adult male population, with wide variation across districts. Validation in Approach I showed that 94% of the lymphedema cases and 77% of hydrocele cases were correctly identified by the HEWs, while 60% and 53% were correctly identified in Approach II.Patient estimation is important for planning, prioritization, targeting interventions, and monitoring progress in LF-endemic areas. Trained HEWs can correctly identify most cases using a standardized patient estimate job aid and questionnaire, even when cascade training is used. For the purposes of LF elimination, these results are sufficient and at a low cost per district. Ethiopia’s LF program could integrate patient estimations into MDA activities in the remaining LF-endemic districts with minimal cost and effort.","PeriodicalId":73112,"journal":{"name":"Frontiers in tropical diseases","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139802952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}