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A cornucopia of research resources for the fourth rodent malaria parasite species [Letter]

Carlton, Jane M
The study of human malaria caused by species of Plasmodium has undoubtedly been enriched by the use of model systems, such as the rodent malaria parasites originally isolated from African thicket rats. A significant gap in the arsenal of resources of the species that make up the rodent malaria parasites has been the lack of any such tools for the fourth of the species, Plasmodium vinckei. This has recently been rectified by Abhinay Ramaprasad and colleagues, whose pivotal paper published in BMC Biology describes a cornucopia of new P. vinckei 'omics datasets, mosquito transmission experiments, transfection protocols, and virulence phenotypes, to propel this species firmly into the twenty-first century.
PMID: 33888109
ISSN: 1741-7007
CID: 4847932

Spatial and temporal village-level prevalence of Plasmodium infection and associated risk factors in two districts of Meghalaya, India

Kessler, Anne; Shylla, Badondor; Singh, Upasana Shyamsunder; Lyngdoh, Rilynti; Mawkhlieng, Bandapkupar; van Eijk, Anna Maria; Sullivan, Steven A; Das, Aparup; Walton, Catherine; Wilson, Mark L; Carlton, Jane M; Albert, Sandra
BACKGROUND:Despite declining incidence over the past decade, malaria remains an important health burden in India. This study aimed to assess the village-level temporal patterns of Plasmodium infection in two districts of the north-eastern state of Meghalaya and evaluate risk factors that might explain these patterns. METHODS:Primary Health Centre passive malaria case data from 2014 to 2018 were analysed to characterize village-specific annual incidence and temporal trends. Active malaria case detection was undertaken in 2018 and 2019 to detect Plasmodium infections using PCR. A questionnaire collected socio-demographic, environmental, and behavioural data, and households were spatially mapped via GPS. Adult mosquitoes were sampled at a subset of subjects' houses, and Anopheles were identified by PCR and sequencing. Risk factors for Plasmodium infection were evaluated using bivariate and multivariate logistic regression analysis, and spatial cluster analysis was undertaken. RESULTS:The annual malaria incidence from PHC-based passive surveillance datasets in 2014-2018 was heterogenous but declining across villages in both districts. Active surveillance in 2018 enrolled 1468 individuals from 468 households (West Jaintia Hills) and 1274 individuals from 359 households (West Khasi Hills). Plasmodium falciparum prevalence per 100 people varied from 0 to 4.1% in the nine villages of West Jaintia Hills, and from 0 to 10.6% in the 12 villages of West Khasi Hills. Significant clustering of P. falciparum infections [observed = 11, expected = 2.15, Relative Risk (RR) = 12.65; p < 0.001] was observed in West Khasi Hills. A total of 13 Anopheles species were found at 53 houses in five villages, with Anopheles jeyporiensis being the most abundant. Risk of infection increased with presence of mosquitoes and electricity in the households [Odds Ratio (OR) = 1.19 and 1.11], respectively. Households with reported animals had reduced infection risk (OR = 0.91). CONCLUSION/CONCLUSIONS:Malaria incidence during 2014-2018 declined in all study villages covered by the passive surveillance data, a period that includes the first widespread insecticide-treated net campaign. The survey data from 2018 revealed a significant association between Plasmodium infection and certain household characteristics. Since species of Plasmodium-competent mosquito vectors continue to be abundant, malaria resurgence remains a threat, and control efforts should continue.
PMCID:7859895
PMID: 33541366
ISSN: 1475-2875
CID: 4793182

Small RNAs Are Implicated in Regulation of Gene and Transposable Element Expression in the Protist Trichomonas vaginalis

Warring, Sally D; Blow, Frances; Avecilla, Grace; Orosco, Jordan C; Sullivan, Steven A; Carlton, Jane M
Trichomonas vaginalis is the causative agent of trichomoniasis, the most prevalent nonviral sexually transmitted infection worldwide. Repetitive elements, including transposable elements (TEs) and virally derived repeats, comprise more than half of the ∼160-Mb T. vaginalis genome. An intriguing question is how the parasite controls its potentially lethal complement of mobile elements, which can disrupt transcription of protein-coding genes and genome functions. In this study, we generated high-throughput RNA sequencing (RNA-Seq) and small RNA-Seq data sets in triplicate for the T. vaginalis G3 reference strain and characterized the mRNA and small RNA populations and their mapping patterns along all six chromosomes. Mapping the RNA-Seq transcripts to the genome revealed that the majority of genes predicted within repetitive elements are not expressed. Interestingly, we identified a novel species of small RNA that maps bidirectionally along the chromosomes and is correlated with reduced protein-coding gene expression and reduced RNA-Seq coverage in repetitive elements. This novel small RNA family may play a regulatory role in gene and repetitive element expression. Our results identify a possible small RNA pathway mechanism by which the parasite regulates expression of genes and TEs and raise intriguing questions as to the role repeats may play in shaping T. vaginalis genome evolution and the diversity of small RNA pathways in general.IMPORTANCE Trichomoniasis, caused by the protozoan Trichomonas vaginalis, is the most common nonviral sexually transmitted infection in humans. The millions of cases each year have sequelae that may include complications during pregnancy and increased risk of HIV infection. Given its evident success in this niche, it is paradoxical that T. vaginalis harbors in its genome thousands of transposable elements that have the potential to be extremely detrimental to normal genomic function. In many organisms, transposon expression is regulated by the activity of endogenously expressed short (∼21 to 35 nucleotides [nt]) small RNA molecules that effect gene silencing by targeting mRNAs for degradation or by recruiting epigenetic silencing machinery to locations in the genome. Our research has identified small RNA molecules correlated with reduced expression of T. vaginalis genes and transposons. This suggests that a small RNA pathway is a major contributor to gene expression patterns in the parasite and opens up new avenues for investigation into small RNA biogenesis, function, and diversity.
PMID: 33408230
ISSN: 2379-5042
CID: 4739092

The effectiveness of malaria camps as part of the Durgama Anchalare Malaria Nirakaran (DAMaN) program in Odisha, India: study protocol for a cluster-assigned quasi-experimental study

Ompad, Danielle C; Kessler, Anne; Van Eijk, Anna Maria; Padhan, Timir K; Haque, Mohammed A; Sullivan, Steven A; Tozan, Yesim; Rocklöv, Joacim; Mohanty, Sanjib; Pradhan, Madan M; Sahu, Praveen K; Carlton, Jane M
The Indian state of Odisha has a longstanding battle with forest malaria. Many remote and rural villages have poor access to health care, a problem that is exacerbated during the rainy season when malaria transmission is at its peak. Approximately 62% of the rural population consists of tribal groups who are among the communities most negatively impacted by malaria. To address the persistently high rates of malaria in these remote regions, the Odisha State Malaria Control Program introduced 'malaria camps' in 2017 where teams of health workers visit villages to educate the population, enhance vector control methods, and perform village-wide screening and treatment. Malaria rates declined statewide, particularly in forested areas, following the introduction of the malaria camps, but the impact of the intervention is yet to be externally evaluated. This study protocol describes a cluster-assigned quasi-experimental stepped-wedge study with a pretest-posttest control group design that evaluates if malaria camps reduce the prevalence of malaria, compared to control villages which receive the usual malaria control interventions (e.g. IRS, ITNs), as detected by PCR.
PMID: 33866961
ISSN: 1654-9880
CID: 4846562

EukRef-excavates: seven curated SSU ribosomal RNA gene databases

Kolisko, Martin; Flegontova, Olga; Karnkowska, Anna; Lax, Gordon; Maritz, Julia M; Pánek, Tomáš; Táborský, Petr; Carlton, Jane M; Čepička, Ivan; Horák, Aleš; Lukeš, Julius; Simpson, Alastair G B; Tai, Vera
The small subunit ribosomal RNA (SSU rRNA) gene is a widely used molecular marker to study the diversity of life. Sequencing of SSU rRNA gene amplicons has become a standard approach for the investigation of the ecology and diversity of microbes. However, a well-curated database is necessary for correct classification of these data. While available for many groups of Bacteria and Archaea, such reference databases are absent for most eukaryotes. The primary goal of the EukRef project (eukref.org) is to close this gap and generate well-curated reference databases for major groups of eukaryotes, especially protists. Here we present a set of EukRef-curated databases for the excavate protists-a large assemblage that includes numerous taxa with divergent SSU rRNA gene sequences, which are prone to misclassification. We identified 6121 sequences, 625 of which were obtained from cultures, 3053 from cell isolations or enrichments and 2419 from environmental samples. We have corrected the classification for the majority of these curated sequences. The resulting publicly available databases will provide phylogenetically based standards for the improved identification of excavates in ecological and microbiome studies, as well as resources to classify new discoveries in excavate diversity.
PMID: 33216898
ISSN: 1758-0463
CID: 4673182

Malaria in Sundargarh district, Odisha, India: Epidemiological and behavioral aspects from surveys

van Eijk, Anna Maria; Choubey, Sandhya; Barla, Punam; Haque, Mohammed A; Nandini, P; Acharya, Subrata; Sullivan, Steven A; Mohanty, Sanjib; Satpathi, Sanghamitra; Carlton, Jane M
To characterize malaria and assist in prevention efforts, we conducted a series of epidemiological studies in Sundargarh district, India, as part of an NIH-funded International Center of Excellence for Malaria Research. In a published survey around Rourkela in 2013-2014 (N = 1307), malaria prevalence was found to be 8.3%. Using these data, villages were divided into low (<2%), medium (2-10%) and high (>10%) malaria prevalence, and risk factors assessed by type of village. In the six low malaria villages, four persons were positive by PCR; in the four medium malaria villages, prevalence was 7% (35 infections, 7 P. vivax); and in the three high malaria villages, prevalence was 21% (62 infections, 10 P. vivax and 5 mixed with P. vivax and P. falciparum). A total of 30.6% infections were submicroscopic and 40.6% were asymptomatic. Our analyses showed that the rainy season and male gender were risk factors for malaria; in high malaria villages, young age was an additional risk factor, and indoor and outdoor spraying was protective compared to no spraying. We undertook a subsequent behavioral survey in four of the medium and high malaria villages in 2017 to investigate the behavioral aspects of malaria risk. Among 500 participants in 237 households, adult men (15+ years) were more likely to be outside in the evening (34.5% vs. 7.9% among adult women 15+ years and 0.7% among children, p < 0.001), or to sleep outside (7.5% vs. 0.5% and 0%, respectively, p < 0.001). Although women were more likely to get up before 6 a.m. (86.6%, vs. 70.5% among men, 50.7% among children, p < 0.001), men were more likely to be outside in the early morning (77.6% among men, 11.2% among women, and 11.1% among children, p < 0.001). More children used insecticide treated nets the previous night (73.4%) than men (45.6%) or women (39.6%), and repellents were used by 29.5% of 234 households (insecticide creams were not used at all). Malaria control and elimination in India will need local approaches, and the promotion of repellent cream use by at-risk groups could be further explored in addition to mass-screen or treat programs in high-risk villages.
PMCID:7494530
PMID: 32735794
ISSN: 1873-6254
CID: 4669932

Defining symptoms of malaria in India in an era of asymptomatic infections

van Eijk, Anna Maria; Mannan, Asad S; Sullivan, Steven A; Carlton, Jane M
BACKGROUND:Malaria is a major public health problem in India. Data from surveys totaling 3031 participants at three sites revealed a high proportion of asymptomatic infections, complicating diagnosis. The aim of this study was to identify differences in complaints and symptoms between sites, and factors associated with asymptomatic Plasmodium infections. METHODS:Published data from community-based cross-sectional studies conducted between 2012 and 2015 in Nadiad (Gujarat), Chennai (Tamil Nadu), and Rourkela (Odisha) as part of the Center for the Study of Complex Malaria in India were analysed. Complaints and symptoms were systematically recorded, and Plasmodium infections confirmed using microscopy, rapid diagnostic tests (RDTs), and polymerase chain reaction (PCR). Multivariate analyses were conducted to determine the association between general symptoms and age, season, or gender, and factors associated with asymptomatic Plasmodium infections were assessed. RESULTS:Complaints of any illness were lowest in Chennai (17.7%), 30.6% in Rourkela and 42.7% in Nadiad. Complaints were more often reported for children; gender differences were noted in Rourkela only. In Nadiad, 7.0% of 796 participants were positive for malaria by PCR (32% Plasmodium falciparum); 78.6% had a history of fever or documented fever, 14.3% had other symptoms, and 7.1% were "truly asymptomatic". For Chennai this was 29.2%, 4.2% and 66.7% respectively, with a malaria prevalence of 2.6% by PCR of 928 participants (29% P. falciparum). In Rourkela, with 7.7% of 1307 participants positive for malaria by PCR (82% P. falciparum), the percentages were 35.6%, 24.8% and 39.6%, respectively. In Rourkela, asymptomatic infections were associated with young age and male gender (microscopy or RDT), and with rainy season (PCR). In the same site, participants with Plasmodium vivax were more likely to be asymptomatic (11/18 or 61.1%) than persons with P. falciparum mono-infections (27/78 or 34.6%); gametocytes for P. falciparum were evenly distributed between symptomatic and asymptomatic infections (2/53 vs. 2/49, respectively). The addition of the symptoms "headache", "aches" and "chills" to fever improved the case-definition of symptomatic malaria. CONCLUSION/CONCLUSIONS:There were considerable differences in complaints at the three sites in India. Malaria and asymptomatic infections differ by region, indicating that malaria elimination will require localized approaches.
PMCID:7339403
PMID: 32631326
ISSN: 1475-2875
CID: 4669922

Clinical and epidemiological characterization of severe Plasmodium vivax malaria in Gujarat, India

Anvikar, Anupkumar R; van Eijk, Anna Maria; Shah, Asha; Upadhyay, Kamlesh J; Sullivan, Steven A; Patel, Ankita J; Joshi, Jaykumar M; Tyagi, Suchi; Singh, Ranvir; Carlton, Jane M; Gupta, Himanshu; Wassmer, Samuel C
The mounting evidence supporting the capacity of Plasmodium vivax to cause severe disease has prompted the need for a better characterization of the resulting clinical complications. India is making progress with reducing malaria, but epidemics of severe vivax malaria in Gujarat, one of the main contributors to the vivax malaria burden in the country, have been reported recently and may be the result of a decrease in transmission and immune development. Over a period of one year, we enrolled severe malaria patients admitted at the Civil Hospital in Ahmedabad, the largest city in Gujarat, to investigate the morbidity of severe vivax malaria compared to severe falciparum malaria. Patients were submitted to standard thorough clinical and laboratory investigations and only PCR-confirmed infections were selected for the present study. Severevivax malaria (30 patients) was more frequent than severe falciparum malaria (8 patients) in our setting, and it predominantly affected adults (median age 32 years, interquartile range 22.5 years). This suggests a potential age shift in anti-malarial immunity, likely to result from the recent decrease in transmission across India. The clinical presentation of severe vivax patients was in line with previous reports, with jaundice as the most common complication. Our findings further support the need for epidemiological studies combining clinical characterization of severe vivax malaria and serological evaluation of exposure markers to monitor the impact of elimination programmes.
PMID: 32490754
ISSN: 2150-5608
CID: 4482022

Antibody responses within two leading Plasmodium vivax vaccine candidate antigens in three geographically diverse malaria-endemic regions of India

Kale, Sonal; Yadav, Chander P; Rao, Pavitra N; Shalini, Sneh; Eapen, Alex; Srivasatava, Harish C; Sharma, Surya K; Pande, Veena; Carlton, Jane M; Singh, Om P; Mallick, Prashant K
BACKGROUND:antigens in individuals living in three geographically diverse malaria endemic regions of India. METHODS:antigens. The difference in seroprevalence and factors associated with antibody responses at each site was statistically analysed. RESULTS:. CONCLUSION/CONCLUSIONS:appears to be highly immunogenic in Indian population and has great potential as a malaria vaccine candidate. The differences in immune response against vaccine candidate antigens in different endemic settings should be taken into account for development of asexual stage based P. vivax malaria vaccine, which in turn can enhance malaria control efforts.
PMCID:6916228
PMID: 31842894
ISSN: 1475-2875
CID: 4669912

The burden of submicroscopic and asymptomatic malaria in India revealed from epidemiology studies at three varied transmission sites in India

van Eijk, Anna Maria; Sutton, Patrick L; Ramanathapuram, Lalitha; Sullivan, Steven A; Kanagaraj, Deena; Priya, G Sri Lakshmi; Ravishankaran, Sangamithra; Asokan, Aswin; Sangeetha, V; Rao, Pavitra N; Wassmer, Samuel C; Tandel, Nikunj; Patel, Ankita; Desai, Nisha; Choubey, Sandhya; Ali, Syed Zeeshan; Barla, Punam; Oraon, Rajashri Rani; Mohanty, Stuti; Mishra, Shobhna; Kale, Sonal; Bandyopadhyay, Nabamita; Mallick, Prashant K; Huck, Jonathan; Valecha, Neena; Singh, Om P; Pradhan, K; Singh, Ranvir; Sharma, S K; Srivastava, Harish C; Carlton, Jane M; Eapen, Alex
Malaria in India, while decreasing, remains a serious public health problem, and the contribution of submicroscopic and asymptomatic infections to its persistence is poorly understood. We conducted community surveys and clinic studies at three sites in India differing in their eco-epidemiologies: Chennai (Tamil Nadu), Nadiad (Gujarat), and Rourkela (Odisha), during 2012-2015. A total of 6,645 subject blood samples were collected for Plasmodium diagnosis by microscopy and PCR, and an extensive clinical questionnaire completed. Malaria prevalence ranged from 3-8% by PCR in community surveys (24 infections in Chennai, 56 in Nadiad, 101 in Rourkela), with Plasmodium vivax dominating in Chennai (70.8%) and Nadiad (67.9%), and Plasmodium falciparum in Rourkela (77.3%). A proportional high burden of asymptomatic and submicroscopic infections was detected in community surveys in Chennai (71% and 71%, respectively, 17 infections for both) and Rourkela (64% and 31%, 65 and 31 infections, respectively). In clinic studies, a proportional high burden of infections was identified as submicroscopic in Rourkela (45%, 42 infections) and Chennai (19%, 42 infections). In the community surveys, anemia and fever were significantly more common among microscopic than submicroscopic infections. Exploratory spatial analysis identified a number of potential malaria hotspots at all three sites. There is a considerable burden of submicroscopic and asymptomatic malaria in malarious regions in India, which may act as a reservoir with implications for malaria elimination strategies.
PMCID:6863831
PMID: 31745160
ISSN: 2045-2322
CID: 4256782