A desalination guide for South African municipal engineers

Municipalities need to develop Water Services Development Plans (WSDPs) as a first requirement in their budgetary process, and need to be made aware of the options that are available to provide more than basic services. While 25./personEd has been set as the minimum basic water supply and while many consumers receive far in excess of this amount, there are areas of the country where water of acceptable quality is not available for household use. However, in many areas adequate quantities of saline water may be, or are, readily available. This is especially the case for coastal cities and towns.The cost of treating water is only part of the total cost of making drinking water available to the consumer. This together with the fact that membrane technology is becoming more affordable and that energy can be recovered, makes the desalination of water viable for domestic purposes.A desk study, funded by the Department Water Affairs and Forestry and managed by the Water Research Commission, was undertaken to identify treatment options for desalinating seawater from both the Indian and Atlantic oceans or brackish water from boreholes. The specific objectives of the project were to compile a Guide on the technologies that can be implemented in South Africa to treat saline water to drinking water standards, to identify the pretreatment that is necessary, and to present guidelines on operational, maintenance, management and environmental aspects relevant to the selection and use of these technologies. An important aspect was also to quantify the capital and operating costs for planning purposes of the different components needed to successfully bring the water to the accepted standards for potable and domestic use.Of particular importance for the South African application was to identify the level of skills required for daily operation of the desalination plants, the level of skills required to provide technical back-up and advice, and to identify and advise on the competencies, training needs and capacity building required at operator and management levels. Lastly, the relevant local environmental legislations governing desalination were also identified

Consensus statement on the use of high sensitivity cardiac troponins

The increased sensitivity of high sensitivity cardiac troponin assays comes at a cost of decreased specificity, and “false positive” diagnosis of acute coronary syndromes has made clinicians wary of their use, fearing unnecessary hospitalisations, angiography and revascularisation. The Ethics and Guidelines Standing Committee of SA Heart Association convened a meeting of cardiologists, chemical pathologists, emergency medicine specialists and industry representatives to discuss the role of high sensitivity troponin (hsTn) testing. An international expert provided guidance, and this Consensus Statement is the product of that meeting. It is recommended that hsTn assays be widely adopted as the preferred biomarker for diagnosis of myocardial infarction. Pathology laboratories will standardise the units of measurement and the reporting of results. Rules for interpretation of results and algorithms for their application are provided. Separate algorithms apply to troponin T and troponin I, and the several troponin I assays on the market each have different numerical values. Use of high sensitivity troponin assays will result in earlier diagnosis of myocardial infarction, more reliable ruling out of myocardial infarction, and shortening of chest pain triage (to 4 hours), compared to former assays

Putative novel cps loci in a large global collection of pneumococci

The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18  000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6  % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis

International genomic definition of pneumococcal lineages, to contextualise disease, antibiotic resistance and vaccine impact

Background: Pneumococcal conjugate vaccines have reduced the incidence of invasive pneumococcal disease, caused by vaccine serotypes, but non-vaccine-serotypes remain a concern. We used whole genome sequencing to study pneumococcal serotype, antibiotic resistance and invasiveness, in the context of genetic background. / Methods: Our dataset of 13,454 genomes, combined with four published genomic datasets, represented Africa (40%), Asia (25%), Europe (19%), North America (12%), and South America (5%). These 20,027 pneumococcal genomes were clustered into lineages using PopPUNK, and named Global Pneumococcal Sequence Clusters (GPSCs). From our dataset, we additionally derived serotype and sequence type, and predicted antibiotic sensitivity. We then measured invasiveness using odds ratios that relating prevalence in invasive pneumococcal disease to carriage. / Findings: The combined collections (n = 20,027) were clustered into 621 GPSCs. Thirty-five GPSCs observed in our dataset were represented by >100 isolates, and subsequently classed as dominant-GPSCs. In 22/35 (63%) of dominant-GPSCs both non-vaccine serotypes and vaccine serotypes were observed in the years up until, and including, the first year of pneumococcal conjugate vaccine introduction. Penicillin and multidrug resistance were higher (p < .05) in a subset dominant-GPSCs (14/35, 9/35 respectively), and resistance to an increasing number of antibiotic classes was associated with increased recombination (R2 = 0.27 p < .0001). In 28/35 dominant-GPSCs, the country of isolation was a significant predictor (p < .05) of its antibiogram (mean misclassification error 0.28, SD ± 0.13). We detected increased invasiveness of six genetic backgrounds, when compared to other genetic backgrounds expressing the same serotype. Up to 1.6-fold changes in invasiveness odds ratio were observed. / Interpretation: We define GPSCs that can be assigned to any pneumococcal genomic dataset, to aid international comparisons. Existing non-vaccine-serotypes in most GPSCs preclude the removal of these lineages by pneumococcal conjugate vaccines; leaving potential for serotype replacement. A subset of GPSCs have increased resistance, and/or serotype-independent invasiveness

Utilization of the ART approach in a group of public oral health operators in South Africa: a 5-year longitudinal study

Contains fulltext : 80990.pdf (publisher's version ) (Open Access)BACKGROUND: A significant increase in the proportion of restorations to the number of tooth extractions was reported after the introduction of ART in an academic mobile dental service in South Africa. The changes were ascribed to its less threatening procedure. Based on these findings, ART was subsequently introduced into the public oral health service of Ekurhuleni district in the South African province of Gauteng. This article reports on the 5-year restorative treatment pattern of operators in the Ekurhuleni district, who adopted the ART approach into their daily dental practice. METHODS: Of the 21 trained operators, 11 had placed more than 10% of restorations using ART at year 1 and were evaluated after 5 years. Data, including number of restored and extracted teeth and type of restoration, were drawn from clinical records 4 months before, and up to 5 years after training. The restoration/extraction ratio (REX score) and the proportion of ART restorations to the total number of restorations were calculated. The paired sample t-test and linear regression analysis were applied. RESULTS: The mean percentage of ART restorations after 1 year was 24.0% (SE 7.2) and significantly increased annually to 42.7% (SE 9.2) after 5 years in permanent dentitions. In primary dentitions the mean percentage of ART restorations after 1 year was 80.6% (SE 4.9) and 72.6% (SE 8.8) after 5 years. The mean REX score before ART training was 0.08 (SE 0.03) and 0.07 (SE 0.04) for permanent and primary teeth, respectively and 0.11 (SE 0.03) and 0.17 (SE 0.05) after 5 years. CONCLUSION: Five years after training, ART had been used consistently in this selected group of operators as the predominant restorative treatment used for primary teeth and showed a significant annual increase in permanent teeth. However, this change had not resulted in an increase in the REX score in both dentitions

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates

Knowledge of pneumococcal lineages, their geographic distribution and antibiotic resistance patterns, can give insights into global pneumococcal disease. We provide interactive bioinformatic outputs to explore such topics, aiming to increase dissemination of genomic insights to the wider community, without the need for specialist training. We prepared 12 country-specific phylogenetic snapshots, and international phylogenetic snapshots of 73 common Global Pneumococcal Sequence Clusters (GPSCs) previously defined using PopPUNK, and present them in Microreact. Gene presence and absence defined using Roary, and recombination profiles derived from Gubbins are presented in Phandango for each GPSC. Temporal phylogenetic signal was assessed for each GPSC using BactDating. We provide examples of how such resources can be used. In our example use of a country-specific phylogenetic snapshot we determined that serotype 14 was observed in nine unrelated genetic backgrounds in South Africa. The international phylogenetic snapshot of GPSC9, in which most serotype 14 isolates from South Africa were observed, highlights that there were three independent sub-clusters represented by South African serotype 14 isolates. We estimated from the GPSC9-dated tree that the sub-clusters were each established in South Africa during the 1980s. We show how recombination plots allowed the identification of a 20kb recombination spanning the capsular polysaccharide locus within GPSC97. This was consistent with a switch from serotype 6A to 19A estimated to have occured in the 1990s from the GPSC97-dated tree. Plots of gene presence/absence of resistance genes (tet, erm, cat) across the GPSC23 phylogeny were consistent with acquisition of a composite transposon. We estimated from the GPSC23-dated tree that the acquisition occurred between 1953 and 1975. Finally, we demonstrate the assignment of GPSC31 to 17 externally generated pneumococcal serotype 1 assemblies from Utah via Pathogenwatch. Most of the Utah isolates clustered within GPSC31 in a USA-specific clade with the most recent common ancestor estimated between 1958 and 1981. The resources we have provided can be used to explore to data, test hypothesis and generate new hypotheses. The accessible assignment of GPSCs allows others to contextualize their own collections beyond the data presented here

A portable near infrared spectroscopy system for bedside monitoring of newborn brain

BACKGROUND: Newborns with critical health conditions are monitored in neonatal intensive care units (NICU). In NICU, one of the most important problems that they face is the risk of brain injury. There is a need for continuous monitoring of newborn's brain function to prevent any potential brain injury. This type of monitoring should not interfere with intensive care of the newborn. Therefore, it should be non-invasive and portable. METHODS: In this paper, a low-cost, battery operated, dual wavelength, continuous wave near infrared spectroscopy system for continuous bedside hemodynamic monitoring of neonatal brain is presented. The system has been designed to optimize SNR by optimizing the wavelength-multiplexing parameters with special emphasis on safety issues concerning burn injuries. SNR improvement by utilizing the entire dynamic range has been satisfied with modifications in analog circuitry. RESULTS AND CONCLUSION: As a result, a shot-limited SNR of 67 dB has been achieved for 10 Hz temporal resolution. The system can operate more than 30 hours without recharging when an off-the-shelf 1850 mAh-7.2 V battery is used. Laboratory tests with optical phantoms and preliminary data recorded in NICU demonstrate the potential of the system as a reliable clinical tool to be employed in the bedside regional monitoring of newborn brain metabolism under intensive care

A mosaic tetracycline resistance gene tet(S/M) detected in an MDR pneumococcal CC230 lineage that underwent capsular switching in South Africa

Objectives: We reported tet(S/M) in Streptococcus pneumoniae and investigated its temporal spread in relation to nationwide clinical interventions. Methods: We whole-genome sequenced 12 254 pneumococcal isolates from 29 countries on an Illumina HiSeq sequencer. Serotype, multilocus ST and antibiotic resistance were inferred from genomes. An SNP tree was built using Gubbins. Temporal spread was reconstructed using a birth–death model. Results: We identified tet(S/M) in 131 pneumococcal isolates and none carried other known tet genes. Tetracycline susceptibility testing results were available for 121 tet(S/M)-positive isolates and all were resistant. A majority (74%) of tet(S/M)-positive isolates were from South Africa and caused invasive diseases among young children (59% HIV positive, where HIV status was available). All but two tet(S/M)-positive isolates belonged to clonal complex (CC) 230. A global phylogeny of CC230 (n=389) revealed that tet(S/M)-positive isolates formed a sublineage predicted to exhibit resistance to penicillin, co-trimoxazole, erythromycin and tetracycline. The birth–death model detected an unrecognized outbreak of this sublineage in South Africa between 2000 and 2004 with expected secondary infections (effective reproductive number, R) of ∼2.5. R declined to ∼1.0 in 2005 and <1.0 in 2012. The declining epidemic could be related to improved access to ART in 2004 and introduction of pneumococcal conjugate vaccine (PCV) in 2009. Capsular switching from vaccine serotype 14 to non-vaccine serotype 23A was observed within the sublineage. Conclusions: The prevalence of tet(S/M) in pneumococci was low and its dissemination was due to an unrecognized outbreak of CC230 in South Africa. Capsular switching in this MDR sublineage highlighted its potential to continue to cause disease in the post-PCV13 era

Quality of Computationally Inferred Gene Ontology Annotations

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation