Establishing a metagenomic workflow for eukaryotic analysis in drinking water system

The analysis of metagenomic short-reads derived from drinking water systems has traditionally focused on the study of prokaryotes (i.e., bacteria and archaea) neglecting the presence of eukaryotes, even though such (micro)-organisms can have an impact on water quality. This limitation stems from the fact that traditional prokaryotic-centric bioinformatic tools are not suited for eukaryotic genomes due to their higher complexity and typically lower abundance in comparison with prokaryotes. Noticeably, while established bioinformatic pipelines exist for the analysis of prokaryotic-derived genomes, only recently researchers have started to develop tools suitable for the identification and subsequent analysis of eukaryotic populations in mixed communities; for this reason, there is currently no validated and widely accepted bioinformatic workflow for analyses of eukaryotes in metagenomes. In this study we propose a workflow tailored for the identification and analysis of eukaryotic genomes derived from metagenomic drinking water system surveys by comparing the performances of several tools for the identification of eukaryotic contigs, contigs binning, and gene prediction on both synthetically generated metagenomes and a representative drinking water system case study, consisting of samples collected for over 6 months. Our findings indicate that the performance of eukaryotic-centric tools differs between the analysis of real-world and synthetic data. However, an ensemble approach involving the combination of reference-dependent and reference-independent tools was found to be beneficial for the eukaryotic identification and analysis and was included in the workflow. For example, several k-mer-based (i.e., EukRep, Tiara, Whokaryote) and a reference-based (i.e., CAT) contigs classifiers were selected for the identification of eukaryotic contigs, leveraging the benefits of both approaches. Overall, the workflow proposed in this study will enable a more systematic metagenomic characterization of eukaryotic populations in the drinking water microbiome and thus help to better understand their ecological role in drinking water systems

Microbial quality of drinking water from groundtanks and tankers at source and point-of-use in eThekwini Municipality, South Africa, and its relationship to health outcomes

Drinking water quality was investigated at source and corresponding point-of-use in 2 peri-urban areas receiving drinking water either by communal water tanker or by delivery directly from the distribution system to household-based groundtanks with taps. Water quality variables measured were heterotrophic bacteria, total coliforms, E. coli, conductivity, turbidity, pH, and total and residual chlorine. Water quality data were analysed together with an existing epidemiological database to investigate links between microbial quality of drinking water, household demographics, health outcomes, socio-economic status, hygiene and sanitation practices. Groundtank households had better quality drinking water than households using storage containers filled from communal tankers. Uncovered storage containers had the poorest microbial water quality among all storage containers. All stored water did not meet drinking water standards, although mains water did. Households with children under 5 years and using open-topped containers had the poorest water quality overall. Households with groundtanks had the best water quality at point-of-use, but did not have the lowest occurrence of health effects. Although groundtanks were supplied together with urine diversion (UD) toilets and hygiene education, groundtank households showed overall poorer hygiene practices than tanker-supplied households, and some groundtank households with UD toilets preferred to continue using open defecation. Households that practised open defecation had higher levels of E. coli in their drinking water and higher rates of adverse health outcomes. Poorer socio-economic standing and lower educational standard were associated with poorer water quality, poorer hygiene practices and higher rates of diarrhoea and vomiting.Keywords: drinking water; point of use; water quality; water quantity; hygiene; sanitatio

Sequence-based prediction for vaccine strain selection and identification of antigenic variability in foot-and-mouth disease virus

Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics, but the prediction of viral cross-protection remains an important unsolved problem. For foot-and-mouth disease virus (FMDV) research in particular, improved methods for predicting this cross-protection are critical for predicting the severity of outbreaks within endemic settings where multiple serotypes and subtypes commonly co-circulate, as well as for deciding whether appropriate vaccine(s) exist and how much they could mitigate the effects of any outbreak. To identify antigenic relationships and their predictors, we used linear mixed effects models to account for variation in pairwise cross-neutralization titres using only viral sequences and structural data. We identified those substitutions in surface-exposed structural proteins that are correlates of loss of cross-reactivity. These allowed prediction of both the best vaccine match for any single virus and the breadth of coverage of new vaccine candidates from their capsid sequences as effectively as or better than serology. Sub-sequences chosen by the model-building process all contained sites that are known epitopes on other serotypes. Furthermore, for the SAT1 serotype, for which epitopes have never previously been identified, we provide strong evidence - by controlling for phylogenetic structure - for the presence of three epitopes across a panel of viruses and quantify the relative significance of some individual residues in determining cross-neutralization. Identifying and quantifying the importance of sites that predict viral strain cross-reactivity not just for single viruses but across entire serotypes can help in the design of vaccines with better targeting and broader coverage. These techniques can be generalized to any infectious agents where cross-reactivity assays have been carried out. As the parameterization uses pre-existing datasets, this approach quickly and cheaply increases both our understanding of antigenic relationships and our power to control disease

Post-modern ‘languagers’: the effects of texting by university students on three South African languages

The present post-modern society has witnessed a growth spurt in technology, and with the development of Information and Communication Technologies (ICTs), mobile text messaging (texting) is now seen as the norm among the youth. For these late-modern languagers (Lytra and Jørgensen 2008: 5), it has become a common if not almost natural process to send and receive an SMS (Short Message Service) in different languages. Although some studies have examined the transformation and modification of the English language by mobile communication, hardly any, apart from Deumert and Masinyana (2008), have looked at how local South African languages are being reshaped and modified through this medium. Drawing on texting data from university undergraduate students, this paper examines the ways in which three South African languages – Afrikaans, isiXhosa and Setswana – are used, transformed and modified through this medium of communication. It is argued here that the intense creativity displayed by these young cell phone users as they play with the multilingual resources at their disposal may lead to some form of language revitalisation for these languages

Serological profile of foot-and-mouth disease in wildlife populations of West and Central Africa with special reference to Syncerus caffer subspecies

The role which West and Central African wildlife populations might play in the transmission dynamics of FMD is not known nor have studies been performed in order to assess the distribution and prevalence of FMD in wild animal species inhabiting those specific regions of Africa. This study reports the FMD serological profile extracted from samples (n = 696) collected from wildlife of West and Central Africa between 1999 and 2003. An overall prevalence of FMDV NSP reactive sera of 31.0% (216/696) was estimated, where a significant difference in seropositivity (p = 0.000) was reported for buffalo (64.8%) as opposed to other wild animal species tested (17.8%). Different levels of exposure to the FMDV resulted for each of the buffalo subspecies sampled (p = 0.031): 68.4%, 50.0% and 0% for Nile Buffalo, West African Buffalo and African Forest Buffalo, respectively. The characterisation of the FMDV serotypes tested for buffalo found presence of antibodies against all the six FMDV serotypes tested, although high estimates for type O and SAT 3 were reported for Central Africa. Different patterns of reaction to the six FMDV serotypes tested were recorded, from sera only positive for a single serotype to multiple reactivities. The results confirmed that FMDV circulates in wild ruminants populating both West and Central Africa rangelands and in particular in buffalo, also suggesting that multiple FMDV serotypes might be involved with type O, SAT 2 and SAT 1 being dominant. Differences in serotype and spill-over risk between wildlife and livestock likely reflect regional geography, historical circulation and differing trade and livestock systems

Evaluating the potential for the environmentally sustainable control of foot and mouth disease in Sub-Saharan Africa

Strategies to control transboundary diseases have in the past generated unintended negative consequences for both the environment and local human populations. Integrating perspectives from across disciplines, including livestock, veterinary and conservation sectors, is necessary for identifying disease control strategies that optimise environmental goods and services at the wildlife-livestock interface. Prompted by the recent development of a global strategy for the control and elimination of foot-and-mouth disease (FMD), this paper seeks insight into the consequences of, and rational options for potential FMD control measures in relation to environmental, conservation and human poverty considerations in Africa. We suggest a more environmentally nuanced process of FMD control that safe-guards the integrity of wild populations and the ecosystem dynamics on which human livelihoods depend while simultaneously improving socio-economic conditions of rural people. In particular, we outline five major issues that need to be considered: 1) improved understanding of the different FMD viral strains and how they circulate between domestic and wildlife populations; 2) an appreciation for the economic value of wildlife for many African countries whose presence might preclude the country from ever achieving an FMD-free status; 3) exploring ways in which livestock production can be improved without compromising wildlife such as implementing commodity-based trading schemes; 4) introducing a participatory approach involving local farmers and the national veterinary services in the control of FMD; and 5) finally the possibility that transfrontier conservation might offer new hope of integrating decision-making at the wildlife-livestock interface

Foot-and-Mouth Disease Virus Persists in the Light Zone of Germinal Centres

Foot-and-mouth disease virus (FMDV) is one of the most contagious viruses of animals and is recognised as the most important constraint to international trade in animals and animal products. Two fundamental problems remain to be understood before more effective control measures can be put in place. These problems are the FMDV “carrier state” and the short duration of immunity after vaccination which contrasts with prolonged immunity after natural infection. Here we show by laser capture microdissection in combination with quantitative real-time reverse transcription polymerase chain reaction, immunohistochemical analysis and corroborate by in situ hybridization that FMDV locates rapidly to, and is maintained in, the light zone of germinal centres following primary infection of naïve cattle. We propose that maintenance of non-replicating FMDV in these sites represents a source of persisting infectious virus and also contributes to the generation of long-lasting antibody responses against neutralising epitopes of the virus

Advocacy at the Eighth World Congress of Pediatric Cardiology and Cardiac Surgery

The Eighth World Congress of Pediatric Cardiology and Cardiac Surgery (WCPCCS) will be held in Washington DC, USA, from Saturday, 26 August, 2023 to Friday, 1 September, 2023, inclusive. The Eighth World Congress of Pediatric Cardiology and Cardiac Surgery will be the largest and most comprehensive scientific meeting dedicated to paediatric and congenital cardiac care ever held. At the time of the writing of this manuscript, The Eighth World Congress of Pediatric Cardiology and Cardiac Surgery has 5,037 registered attendees (and rising) from 117 countries, a truly diverse and international faculty of over 925 individuals from 89 countries, over 2,000 individual abstracts and poster presenters from 101 countries, and a Best Abstract Competition featuring 153 oral abstracts from 34 countries. For information about the Eighth World Congress of Pediatric Cardiology and Cardiac Surgery, please visit the following website: [www.WCPCCS2023.org]. The purpose of this manuscript is to review the activities related to global health and advocacy that will occur at the Eighth World Congress of Pediatric Cardiology and Cardiac Surgery. Acknowledging the need for urgent change, we wanted to take the opportunity to bring a common voice to the global community and issue the Washington DC WCPCCS Call to Action on Addressing the Global Burden of Pediatric and Congenital Heart Diseases. A copy of this Washington DC WCPCCS Call to Action is provided in the Appendix of this manuscript. This Washington DC WCPCCS Call to Action is an initiative aimed at increasing awareness of the global burden, promoting the development of sustainable care systems, and improving access to high quality and equitable healthcare for children with heart disease as well as adults with congenital heart disease worldwide