Identification of the Unwinding Region in the Clostridioides difficile Chromosomal Origin of Replication

Faithful DNA replication is crucial for viability of cells across all kingdoms. Targeting DNA replication is a viable strategy for inhibition of bacterial pathogens. Clostridioides difficile is an important enteropathogen that causes potentially fatal intestinal inflammation. Knowledge about DNA replication in this organism is limited and no data is available on the very first steps of DNA replication. Here, we use a combination of in silico predictions and in vitro experiments to demonstrate that C. difficile employs a bipartite origin of replication that shows DnaA-dependent melting at oriC2, located in the dnaA-dnaN intergenic region. Analysis of putative origins of replication in different clostridia suggests that the main features of the origin architecture are conserved. This study is the first to characterize aspects of the origin region of C. difficile and contributes to our understanding of the initiation of DNA replication in clostridia

Infant and child mortality in relation to malaria transmission in KEMRI/CDC HDSS, Western Kenya: validation of verbal autopsy

Malaria transmission reduction is a goal of many malaria control programmes. Little is known of how much mortality can be reduced by specific reductions in transmission. Verbal autopsy (VA) is widely used for estimating malaria specific mortality rates, but does not reliably distinguish malaria from other febrile illnesses. Overall malaria attributable mortality includes both direct and indirect deaths. It is unclear what proportion of the deaths averted by reducing malaria transmission are classified as malaria in VA.; Both all-cause, and cause-specific mortality reported by VA for children under 5 years of age, were assembled from the KEMRI/CDC health and demographic surveillance system in Siaya county, rural Western Kenya for the years 2002-2004. These were linked to household-specific estimates of the Plasmodium falciparum entomological inoculation rate (EIR) based on high resolution spatio-temporal geostatistical modelling of entomological data. All-cause and malaria specific mortality (by VA), were analysed in relation to EIR, insecticide-treated net use (ITN), socioeconomic status (SES) and parameters describing space-time correlation. Time at risk for each child was analysed using Bayesian geostatistical Cox proportional hazard models, with time-dependent covariates. The outputs were used to estimate the diagnostic performance of VA in measuring mortality that can be attributed to malaria exposure.; The overall under-five mortality rate was 80 per 1000 person-years during the study period. Eighty-one percent of the total deaths were assigned causes of death by VA, with malaria assigned as the main cause of death except in the neonatal period. Although no trend was observed in malaria-specific mortality assessed by VA, ITN use was associated with reduced all-cause mortality in infants (hazard ratio 0.15, 95% CI 0.02, 0.63) and the EIR was strongly associated with both all-cause and malaria-specific mortality. 48.2% of the deaths could be attributed to malaria by analysing the exposure-response relationship, though only 20.5% of VAs assigned malaria as the cause and the sensitivity of VAs was estimated to be only 26%. Although VAs assigned some deaths to malaria even in areas where there was estimated to be no exposure, the specificity of the VAs was estimated to be 85%.; Interventions that reduce P. falciparum transmission intensity will not only significantly reduce malaria-diagnosed mortality, but also mortality assigned to other causes in under-5 year old children in endemic areas. In this setting, the VA tool based on clinician review substantially underestimates the number of deaths that could be averted by reducing malaria exposure in childhood, but has a reasonably high specificity. This suggests that malaria transmission-reducing interventions such as ITNs can potentially reduce overall child mortality by as much as twice the total direct malaria burden estimated from VAs

Impact of COVID-19 lockdowns on adolescent pregnancy and school dropout among secondary schoolgirls in Kenya

Introduction Secondary school closures aimed at limiting the number of infections and deaths due to COVID-19 may have amplified the negative sexual and reproductive health (SRH) and schooling outcomes of vulnerable adolescent girls. This study aimed to measure pandemic-related effects on adolescent pregnancy and school dropout among school-going girls in Kenya. Methods We report longitudinal findings of 910 girls in their last 2 years of secondary school. The study took place in 12 secondary day schools in rural western Kenya between 2018 and 2021. Using a causal-comparative design, we compared SRH and schooling outcomes among 403 girls who graduated after completion of their final school examinations in November 2019 pre-pandemic with 507 girls who experienced disrupted schooling due to COVID-19 and sat examinations in March 2021. Unadjusted and adjusted generalised linear mixed models were used to investigate the effect of COVID-19-related school closures and restrictions on all outcomes of interest and on incident pregnancy. Results At study initiation, the mean age of participants was 17.2 (IQR: 16.4–17.9) for girls in the pre-COVID-19 cohort and 17.5 (IQR: 16.5–18.4) for girls in the COVID-19 cohort. Girls experiencing COVID-19 containment measures had twice the risk of falling pregnant prior to completing secondary school after adjustment for age, household wealth and orphanhood status (adjusted risk ratio (aRR)=2.11; 95% CI:1.13 to 3.95, p=0.019); three times the risk of school dropout (aRR=3.03; 95% CI: 1.55 to 5.95, p=0.001) and 3.4 times the risk of school transfer prior to examinations (aRR=3.39; 95% CI: 1.70 to 6.77, p=0.001) relative to pre-COVID-19 learners. Girls in the COVID-19 cohort were more likely to be sexually active (aRR=1.28; 95% CI: 1.09 to 1.51, p=0.002) and less likely to report their first sex as desired (aRR=0.49; 95% CI: 0.37 to 0.65, p<0.001). These girls reported increased hours of non-school-related work (3.32 hours per day vs 2.63 hours per day in the pre-COVID-19 cohort, aRR=1.92; 95% CI: 1.92 to 2.99, p=0.004). In the COVID-19 cohort, 80.5% reported worsening household economic status and COVID-19-related stress was common. Conclusion The COVID-19 pandemic deleteriously affected the SRH of girls and amplified school transfer and dropout. Appropriate programmes and interventions that help buffer the effects of population-level emergencies on school-going adolescents are warranted

Outbreak of COVID-19 on an industrial ship

Background: People on ships are at high risk for outbreaks of infectious diseases including coronavirus disease 2019 (COVID-19). A rapid and well-coordinated response is important to curb transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We studied an outbreak on an industrial ship to improve outbreak control for ships and coordination between participating harbour partners.Materials and methods: Public Health Service (PHS) Rotterdam-Rijnmond performed an epidemiological investigation during the outbreak of COVID-19 among 77 seafarers on a ship in their port. The captain was interviewed about ship details and his experiences during the outbreak. The seafarers were asked to fill in questionnaires about symptoms suspicious of COVID-19 and date of symptom onset. Information about stakeholders involved in outbreak control was registered.Results: The captain first contacted PHS about probable cases on March 31st 2020 via a physician ashore. One crewmember was hospitalised on April 8th and another died unexpectedly aboard on April 10th. Questionnaires distributed mid-April to the 75 remaining seafarers showed that 38 of 60 responders (63%) had had suspicious symptoms between February 15th and April 13th. None of them were tested but a total of 8 other crewmembers tested positive for COVID-19 after leaving the ship, including the hospitalised crewmember and the one who died aboard. On May 5th, the last case left isolation and the quarantine ended. Many different stakeholders were involved in the outbreak response and responsibilities were not always fully clear beforehand, causing coordination issues.Conclusions: Testing crew with COVID-19 symptoms underpins control measures and clarifies communication between stakeholders. Building a network beforehand to develop outbreak guidelines tailored to ships and local circumstances is essential to control future outbreaks on ships

Outbreak of COVID-19 on an industrial ship.

Background: People on ships are at high risk for outbreaks of infectious diseases including Coronavirus disease 2019 (COVID-19). A rapid and well-coordinated response is important to curb transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We studied an outbreak on an industrial ship to improve outbreak control for ships and coordination between participating harbour partners. Materials and methods: Public Health Service (PHS) Rotterdam-Rijnmond performed an epidemiological investigation during the outbreak of COVID-19 among 77 seafarers on a ship in their port. The captain was interviewed about ship details and his experiences during the outbreak. The seafarers were asked to fill in questionnaires about symptoms suspicious of COVID-19 and date of symptom onset. Information about stakeholders involved in outbreak control was registered. Results: The captain first contacted PHS about probable cases on March 31st 2020 via a physician ashore. One crewmember was hospitalised on April 8th and another died unexpectedly aboard on April 10th. Questionnaires distributed mid-April to the 75 remaining seafarers showed that 38 of 60 responders (63%) had had suspicious symptoms between February 15th and April 13th. None of them were tested but a total of 8 other crewmembers tested positive for COVID-19 after leaving the ship, including the hospitalised crewmember and the one who died aboard. On May 5th, the last case left isolation and the quarantine ended. Many different stakeholders were involved in the outbreak response and responsibilities were not always fully clear beforehand, causing coordination issues. Conclusions: Testing crew with COVID-19 symptoms underpins control measures and clarifies communication between stakeholders. Building a-network beforehand to develop outbreak guidelines tailored to ships and local circumstances is essential to control future outbreaks on ships

A comparison between bioelectrical impedance analysis and air-displacement plethysmography in assessing fat-free mass in patients with motor neurone diseases: a cross-sectional study

To determine the validity of bioelectrical impedance analysis (BIA) in quantifying fat-free mass (FFM) compared to air-displacement plethysmography (ADP) in patients with a motor neurone disease (MND). FFM of 140 patients diagnosed with MND was determined by ADP using the BodPod (i.e. the gold standard), and by BIA using the whole-body Bodystat. FFM values were translated to predicted resting energy expenditure (REE); the actual REE was measured using indirect calorimetry, resulting in a metabolic index. Validity of the BIA compared to the ADP was assessed using Bland-Altman analysis and Pearson’s r. To assess the clinical relevance of differences, we evaluated changes in metabolic index and in individualized protein demand. Despite the high correlation between ADP and BIA (r = 0.93), averaged across patients, the assessed mean fat-free mass was 51.7 kg (± 0.9) using ADP and 54.2 kg (± 1.0) using BIA. Hence, BIA overestimated fat-free mass by 2.5 kg (95% CI 1.8–3.2, p p = 0.048). A clinically relevant overestimation of ≥ 15 g in protein demand was observed for 4 (2.9%) patients using BIA. BIA systematically overestimates FFM in patients with MND. Although the differences are limited with ADP, underscoring the utility of BIA for research, overestimation of fat-free mass may have consequences for clinical decision-making, especially when interest lies in determining the metabolic index.</p

Norovirus outbreak in a natural playground: A One Health

Norovirus constitutes the most frequently identified infectious cause of disease outbreaks associated with untreated recreational water. When investigating outbreaks related to surface water, a One Health approach is insightful. Historically, there has been a focus on potential contamination of recreational water by bird droppings and a recent publication demonstrating human noroviruses in bird faeces suggested this should be investigated in future water-related norovirus outbreaks. Here, we describe a One Health approach investigating a norovirus outbreak in a natural playground. On social media, a large amount of waterfowl were reported to defecate near these playground premises leading to speculations about their potential involvement. Surface water, as well as human and bird faecal specimens, was tested for human noroviruses. Norovirus was found to be the most likely cause of the outbreak but there was no evidence for transmission via waterfowl. Cases had become known on social media prior to notification to the public health service underscoring the potential of online media as an early warning system. In view of known risk factors, advice was given for future outbreak investigations and natural playground design