Pooled testing conserves SARS-CoV-2 laboratory resources and improves test turn-around time: experience on the Kenyan Coast.
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ABSTRACT:
SUBMITTER: Agoti CN
PROVIDER: S-EPMC7590893 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundPrompt and accurate identification of carbapenemase production is essential for appropriate treatment and infection control. NG-Test Carba 5 (termed herein "Carba 5"; NG Biotech, Guipry, France) is a multiplex immunochromatographic assay for the rapid phenotypic identification of five major carbapenemases (KPC, NDM, VIM, IMP, and OXA-48-like) from bacterial isolates. This study aimed to evaluate the diagnostic performance of Carba 5 and its impact on the turn-around-time in a clinical microbiology laboratory.ResultsCarba 5 was retrospectively evaluated using 78 carbapenemase producers and 23 non-carbapenemase producers confirmed by PCR and sequencing. The performance and time required for carbapenemase identification were prospectively evaluated using 47 carbapenem resistant Enterobacteriaceae isolates, and the results were compared to those obtained using Xpert Carba-R (Cepheid, Sunnyvale, CA, USA). For the bacterial isolates included in retrospective and prospective evaluation, the Carba 5 assay correctly identified 147 isolates except one isolate with a sensitivity of 99.13% (95% CI 95.25-99.98%) and specificity of 100% (95% CI 89.42-100%). The Carba 5 assay missed one VIM-1 among 13 VIM producers. The assay showed a sensitivity of 92.31% (95% CI 63.97-99.81%) for detecting VIM and 100% for detecting KPC, NDM, OXA-48-like, and IMP. Compared to the Xpert Carba-R assay, Carba 5 exhibited 100% agreement and was more time-efficient (median time 24 min vs. 1 h 11 min).ConclusionsThe Carba 5 assay has potential as an alternative to molecular methods for detecting major carbapenemases from bacterial isolates in a clinical microbiology laboratory. Compared to the Xpert Carba-R, Carba 5 turns out to be more affordable and time-efficient while showing a comparable performance, and may accelerate therapeutic and infection control decisions.
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Project description:BackgroundIn South Africa’s National Health Laboratory Service, ad hoc mean turn-around time (TAT) reporting is an important indicator of performance. However, historic static TAT reporting did not assess very long or very short times. An interactive TAT dashboard was developed using the following TAT measures; (1) median, (2) 75th percentile and (3) percentage of within cut-off TAT to allow for improved differentiation of TAT performance.ObjectivesThe objective of our study was to demonstrate increased efficiency achieved by using an interactive TAT dashboard.MethodsA retrospective descriptive study design was used. Creatinine TAT outcomes were reported over 122 weeks from a high-volume laboratory in Gauteng, South Africa. The percentage of within cut-off and 75th percentile TAT were analysed and reported using Microsoft Excel. A focus group session was used to populate a cause and effect diagram.ResultsThe percentage of within cut-off TAT increased from 10% in week 4 to 90% and higher from week 81. The 75th percentile decreased from 10 hours in week 4 to under 5 h from week 71. Component TAT analysis revealed that the 75th percentile testing was 5 h or longer for weeks 4, 5 and 48. The 75th percentile review TAT ranged from 1 h to 15 h. From week 41, the review TAT was under 1 h.ConclusionOur study demonstrated that the use of an interactive TAT dashboard coupled with good management can dramatically improve TAT and efficiency in a high-volume laboratory.
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Project description:We surveyed tree hyrax populations living in forests, limestone rocky formations, and caves in coastal Kenya to identify the species and estimate the threat-level populations are in. Tree hyrax vocalizations were recorded in three different habitats with passive acoustic monitoring (PAM) for a total of 84 h in January and February 2022. We also observed tree hyrax behavior with thermal imaging camera and photographed individuals. Tree hyraxes in coastal Kenya are vocally active throughout the night, with most calls emitted between 23.00 and 04.00. We identified four different calls: snort, hac, hac ping-pong, and wheeze. Their calling range is between 220 and 15,000 Hz. Calls of tree hyraxes from the coast of Kenya were compared with calls stored by the Oxford Brookes University's Nocturnal Primate Research Group and identified as eastern tree hyrax, previously recorded from Tanzania. Here, we present what are, to our knowledge, the first photographs of live D. validus from Kenya. These tree hyraxes live in social groups. Due to strong pressure from humans, conservation measures are necessary to prevent the extinction of these isolated D. validus populations in Kenya.
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Project description:Plastic pollution represents a pervasive and increasing threat to marine ecosystems worldwide and there is a need to better understand the extent to which microplastics (<5?mm) are ingested by high trophic-level taxa, such as marine mammals. Here, we perform a comprehensive assessment by examining whole digestive tracts of 50 individuals from 10 species whilst operating strict contamination controls. Microplastics were ubiquitous with particles detected in every animal examined. The relatively low number per animal (mean?=?5.5) suggests these particles are transitory. Stomachs, however, were found to contain a greater number than intestines, indicating a potential site of temporary retention. The majority of particles were fibres (84%) while the remaining 16% was fragments. Particles were mainly blue and black (42.5% and 26.4%) in colour and Nylon was the most prevalent (60%) polymer type. A possible relationship was found between the cause of death category and microplastic abundance, indicating that animals that died due to infectious diseases had a slightly higher number of particles than those that died of trauma and other drivers of mortality. It is not possible, however, to draw any firm conclusions on the potential biological significance of this observation and further research is required to better understand the potential chronic effects of microplastic exposure on animal health, particularly as marine mammals are widely considered important sentinels for the implications of pollution for the marine environment.
| S-EPMC6355900 | biostudies-other
Project description:BackgroundProgress toward reducing the malaria burden in Africa has been measured, or modeled, using datasets with relatively short time-windows. These restricted temporal analyses may miss the wider context of longer-term cycles of malaria risk and hence may lead to incorrect inferences regarding the impact of intervention.Methods1147 age-corrected Plasmodium falciparum parasite prevalence (PfPR2-10) surveys among rural communities along the Kenyan coast were assembled from 1974 to 2014. A Bayesian conditional autoregressive generalized linear mixed model was used to interpolate to 279 small areas for each of the 41 years since 1974. Best-fit polynomial splined curves of changing PfPR2-10 were compared to a sequence of plausible explanatory variables related to rainfall, drug resistance and insecticide-treated bed net (ITN) use.ResultsP. falciparum parasite prevalence initially rose from 1974 to 1987, dipped in 1991-92 but remained high until 1998. From 1998 onwards prevalence began to decline until 2011, then began to rise through to 2014. This major decline occurred before ITNs were widely distributed and variation in rainfall coincided with some, but not all, short-term transmission cycles. Emerging resistance to chloroquine and introduction of sulfadoxine/pyrimethamine provided plausible explanations for the rise and fall of malaria transmission along the Kenyan coast.ConclusionsProgress towards elimination might not be as predictable as we would like, where natural and extrinsic cycles of transmission confound evaluations of the effect of interventions. Deciding where a country lies on an elimination pathway requires careful empiric observation of the long-term epidemiology of malaria transmission.
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Project description:BackgroundSevere childhood illnesses present a major public health challenge for Africa, which is aggravated by a suboptimal response to the child's health problems with reference to the health-seeking behaviour of the parents or guardians. We examined the health-seeking behaviour of parents at the Kenyan coast because understanding impediments to optimal health-seeking behaviour could greatly contribute to reducing the impact of severe illness on children's growth and development.Methods and resultsHealth-seeking behaviour, and the factors influencing this behaviour, were examined in two traditional communities. We held in-depth interviews with 53 mothers, fathers and caregivers from two rural clinics at the Kenyan Coast. Biomedical medicine (from health facilities and purchased over the counter) was found to be the most popular first point of treatment. However, traditional healing still plays a salient role in the health care within these two communities. Traditional healers were consulted for various reasons: a) attribution of causation of ill-health to supernatural sources, b) chronic illness (inability of modern medicine to cure the problem) and c) as prevention against possible ill-health. In developing an explanatory model of decision-making, we observed that this was a complex process involving consultation at various levels, with elders, but also between both parents, depending on the perceived nature and chronicity of the illness. However, it was reported that fathers were the ultimate decision makers in relation to decisions concerning where the child would be taken for treatment.ConclusionsHealth systems need to see traditional healing as a complementary system in order to ensure adequate access to health care. Importantly, fathers also need to be addressed in intervention and education programs.
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Project description:The ability to automatically segment an image into distinct regions is a critical aspect in many visual processing applications. Because inaccuracies often exist in automatic segmentation, manual segmentation is necessary in some application domains to correct mistakes, such as required in the reconstruction of neuronal processes from microscopic images. The goal of the automated segmentation tool is traditionally to produce the highest-quality segmentation, where quality is measured by the similarity to actual ground truth, so as to minimize the volume of manual correction necessary. Manual correction is generally orders-of-magnitude more time consuming than automated segmentation, often making handling large images intractable. Therefore, we propose a more relevant goal: minimizing the turn-around time of automated/manual segmentation while attaining a level of similarity with ground truth. It is not always necessary to inspect every aspect of an image to generate a useful segmentation. As such, we propose a strategy to guide manual segmentation to the most uncertain parts of segmentation. Our contributions include 1) a probabilistic measure that evaluates segmentation without ground truth and 2) a methodology that leverages these probabilistic measures to significantly reduce manual correction while maintaining segmentation quality.
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Project description:The emergence of artemisinin-resistant P. falciparum malaria in South-East Asia highlights the need for continued global surveillance of the efficacy of artemisinin-based combination therapies.On the Kenyan coast we studied the treatment responses in 474 children 6-59 months old with uncomplicated P. falciparum malaria in a randomized controlled trial of dihydroartemisinin-piperaquine vs. artemether-lumefantrine from 2005 to 2008. (ISRCTN88705995).The proportion of patients with residual parasitemia on day 1 rose from 55% in 2005-2006 to 87% in 2007-2008 (odds ratio, 5.4, 95%CI, 2.7-11.1; P<0.001) and from 81% to 95% (OR, 4.1, 95%CI, 1.7-9.9; P?=?0.002) in the DHA-PPQ and AM-LM groups, respectively. In parallel, Kaplan-Meier estimated risks of apparent recrudescent infection by day 84 increased from 7% to 14% (P?=?0.1) and from 6% to 15% (P?=?0.05) with DHA-PPQ and AM-LM, respectively. Coinciding with decreasing transmission in the study area, clinical tolerance to parasitemia (defined as absence of fever) declined between 2005-2006 and 2007-2008 (OR body temperature >37.5°C, 2.8, 1.9-4.1; P<0.001). Neither in vitro sensitivity of parasites to DHA nor levels of antibodies against parasite extract accounted for parasite clearance rates or changes thereof.The significant, albeit small, decline through time of parasitological response rates to treatment with ACTs may be due to the emergence of parasites with reduced drug sensitivity, to the coincident reduction in population-level clinical immunity, or both. Maintaining the efficacy of artemisinin-based therapy in Africa would benefit from a better understanding of the mechanisms underlying reduced parasite clearance rates.Controlled-Trials.com ISRCTN88705995.
| S-EPMC3213089 | biostudies-literature
Project description:BackgroundThe over-distributed pattern of malaria transmission has led to attempts to define malaria "hotspots" that could be targeted for purposes of malaria control in Africa. However, few studies have investigated the use of routine health facility data in the more stable, endemic areas of Africa as a low-cost strategy to identify hotspots. Here the objective was to explore the spatial and temporal dynamics of fever positive rapid diagnostic test (RDT) malaria cases routinely collected along the Kenyan Coast.MethodsData on fever positive RDT cases between March 2018 and February 2019 were obtained from patients presenting to six out-patients health-facilities in a rural area of Kilifi County on the Kenyan Coast. To quantify spatial clustering, homestead level geocoded addresses were used as well as aggregated homesteads level data at enumeration zone. Data were sub-divided into quarterly intervals. Kulldorff's spatial scan statistics using Bernoulli probability model was used to detect hotspots of fever positive RDTs across all ages, where cases were febrile individuals with a positive test and controls were individuals with a negative test.ResultsAcross 12 months of surveillance, there were nine significant clusters that were identified using the spatial scan statistics among RDT positive fevers. These clusters included 52% of all fever positive RDT cases detected in 29% of the geocoded homesteads in the study area. When the resolution of the data was aggregated at enumeration zone (village) level the hotspots identified were located in the same areas. Only two of the nine hotspots were temporally stable accounting for 2.7% of the homesteads and included 10.8% of all fever positive RDT cases detected.ConclusionTaking together the temporal instability of spatial hotspots and the relatively modest fraction of the malaria cases that they account for; it would seem inadvisable to re-design the sub-county control strategies around targeting hotspots.
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Project description:Since Barbara McClintock's groundbreaking discovery of mobile DNA sequences some 70 years ago, transposable elements have come to be recognized as important mutagenic agents impacting genome composition, genome evolution, and human health. Transposable elements are a major constituent of prokaryotic and eukaryotic genomes, and the transposition mechanisms enabling transposon proliferation over evolutionary time remain engaging topics for study, suggesting complex interactions with the host, both antagonistic and mutualistic. The impact of transposition is profound, as over 100 human heritable diseases have been attributed to transposon insertions. Transposition can be highly mutagenic, perturbing genome integrity and gene expression in a wide range of organisms. This mutagenic potential has been exploited in the laboratory, where transposons have long been utilized for phenotypic screening and the generation of defined mutant libraries. More recently, barcoding applications and methods for RNA-directed transposition are being used towards new phenotypic screens and studies relevant for gene therapy. Thus, transposable elements are significant in affecting biology both in vivo and in the laboratory, and this review will survey advances in understanding the biological role of transposons and relevant laboratory applications of these powerful molecular tools.
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