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Antibiotic resistance in bacterial pathogens presents a substantial threat to the control of infectious diseases. Development of new classes of antibiotics has slowed in recent years due to pressures of cost and market profitability, and there is a strong need for new antimicrobial therapies. The therapeutic use of bacteriophages has long been considered, with numerous anecdotal reports of success. Interest in phage therapy has been renewed by recent clinical successes in case studies with personalized phage cocktails, and several clinical trials are in progress. We discuss recent progress in the therapeutic use of phages and contemplate the key factors influencing the opportunities and challenges. With strong safety profiles, the main challenges of phage therapeutics involve strain variation among clinical isolates of many pathogens, battling phage resistance, and the potential limitations of host immune responses. However, the opportunities are considerable, with the potential to enhance current antibiotic efficacy, protect newly developed antibiotics, and provide a last resort in response to complete antibiotic failure.

Rates of antimicrobial resistance are increasing globally while the pipeline of new antibiotics is drying up, putting patients with disease caused by drug-resistant bacteria at increased risk of complications and death. The growing costs for diagnosis and management of drug resistance threaten tuberculosis control where the disease is endemic and resources limited. Bacteriophages are viruses that attack bacteria. Phage preparations served as anti-infective agents long before antibiotics were discovered. Though small in size, phages are the most abundant and diverse biological entity on earth. Phages have co-evolved with their hosts and possess all the tools needed to infect and kill bacteria, independent of drug resistance. Modern biotechnology has improved our understanding of the biology of phages and their possible uses. Phage preparations are available to treat meat, fruit, vegetables, and dairy products against parasites or to prevent contamination with human pathogens, such as Listeria monocytogenes, Escherichia coli, or Staphylococcus aureus. Such phage-treated products are considered fit for human consumption. A number of recent case reports describe in great detail the successful treatment of highly drug-resistant infections with individualized phage preparations. Formal clinical trials with standardized products are slowly emerging. With its highly conserved genome and relative paucity of natural phage defence mechanisms Mycobacterium tuberculosis appears to be a suitable target for phage treatment. A phage cocktail with diverse and strictly lytic phages that kill all lineages of M. tuberculosis, and can be propagated on Mycobacterium smegmatis, has been assembled and is available for the evaluation of optimal dosage and suitable routes of administration for tuberculosis in humans. Phage treatment can be expected to be safe and active on extracellular organisms, but phage penetration to intracellular and granulomatous environments as well as synergistic effects with antibiotics are important questions to address during further evaluation.

An 81-year-old immunocompetent patient with bronchiectasis and refractory Mycobacterium abscessus lung disease was treated for 6 months with a three-phage cocktail active against the strain. In this case study of phage to lower infectious burden, intravenous administration was safe and reduced the M. abscessus sputum load tenfold within one month. However, after two months, M. abscessus counts increased as the patient mounted a robust IgM- and IgG-mediated neutralizing antibody response to the phages, which was associated with limited therapeutic efficacy.

As programs move closer toward the World Health Organization (WHO) goals of reduction in morbidity, elimination as a public health problem or elimination of transmission, countries will be faced with planning the next stages of surveillance and control in low prevalence settings. Mathematical models of neglected tropical diseases (NTDs) will need to go beyond predicting the effect of different treatment programs on these goals and on to predicting whether the gains can be sustained. One of the most important challenges will be identifying the policy goal and the right constraints on interventions and surveillance over the long term, as a single policy option will not achieve all aims—for example, minimizing morbidity and minimizing costs cannot both be achieved. As NTDs move toward 2030 and beyond, more nuanced intervention choices will be informed by quantitative analyses which are adapted to national context.

According to the Kenya National School-Based Deworming program launched in 2012 and implemented for the first 5 years (2012–2017), the prevalence of soil-transmitted helminths (STH) and schistosomiasis substantially reduced over the mentioned period among the surveyed schools. However, this reduction is heterogeneous. In this study, we aimed to determine the factors associated with the 5-year school-level infection prevalence and relative reduction (RR) in prevalence in Kenya following the implementation of the program. Multiple variables related to treatment, water, sanitation, and hygiene (WASH) and environmental factors were assembled and included in mixed-effects linear regression models to identify key determinants of the school location STH and schistosomiasis prevalence and RR. Reduced prevalence of Ascaris lumbricoides was associated with low (< 1%) baseline prevalence, seven rounds of treatment, high (50–75%) self-reported coverage of household handwashing facility equipped with water and soap, high (20–25°C) land surface temperature, and community population density of 5–10 people per 100 m2. Reduced hookworm prevalence was associated with low (< 1%) baseline prevalence and the presence of a school feeding program. Reduced Trichuris trichiura prevalence was associated with low (< 1%) baseline prevalence. Reduced Schistosoma mansoni prevalence was associated with low (< 1%) baseline prevalence, three treatment rounds, and high (> 75%) reported coverage of a household improved water source. Reduced Schistosoma haematobium was associated with high aridity index. Analysis indicated that a combination of factors, including the number of treatment rounds, multiple related program interventions, community- and school-level WASH, and several environmental factors had a major influence on the school-level infection transmission and reduction.

Background: National immunisation programmes globally are at risk of suspension due to the severe health system constraints and physical distancing measures in place to mitigate the ongoing COVID-19 pandemic. We aimed to compare the health benefits of sustaining routine childhood immunisation in Africa with the risk of acquiring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection through visiting routine vaccination service delivery points. Methods: We considered a high-impact scenario and a low-impact scenario to approximate the child deaths that could be caused by immunisation coverage reductions during COVID-19 outbreaks. In the high-impact scenario, we used previously reported country-specific child mortality impact estimates of childhood immunisation for diphtheria, tetanus, pertussis, hepatitis B, Haemophilus influenzae type b, Streptococcus pneumoniae, rotavirus, measles, meningitis A, rubella, and yellow fever to approximate the future deaths averted before 5 years of age by routine childhood vaccination during a 6-month COVID-19 risk period without catch-up campaigns. In the low-impact scenario, we approximated the health benefits of sustaining routine childhood immunisation on only the child deaths averted from measles outbreaks during the COVID-19 risk period. We assumed that contact-reducing interventions flattened the outbreak curve during the COVID-19 risk period, that 60% of the population will have been infected by the end of that period, that children can be infected by either vaccinators or during transport, and that upon child infection the whole household will be infected. Country-specific household age structure estimates and age-dependent infection-fatality rates were applied to calculate the number of deaths attributable to the vaccination clinic visits. We present benefit–risk ratios for routine childhood immunisation, with 95% uncertainty intervals (UIs) from a probabilistic sensitivity analysis. Findings: In the high-impact scenario, for every one excess COVID-19 death attributable to SARS-CoV-2 infections acquired during routine vaccination clinic visits, 84 (95% UI 14–267) deaths in children could be prevented by sustaining routine childhood immunisation in Africa. The benefit–risk ratio for the vaccinated children is 85 000 (4900–546 000), for their siblings (60 years) is 96 (14–307). In the low-impact scenario that approximates the health benefits to only the child deaths averted from measles outbreaks, the benefit–risk ratio to the households of vaccinated children is 3 (0–10); if the risk to only the vaccinated children is considered, the benefit–risk ratio is 3000 (182–21 000). Interpretation: The deaths prevented by sustaining routine childhood immunisation in Africa outweigh the excess risk of COVID-19 deaths associated with vaccination clinic visits, especially for the vaccinated children. Routine childhood immunisation should be sustained in Africa as much as possible, while considering other factors such as logistical constraints, staff shortages, and reallocation of resources during the COVID-19 pandemic. Funding: Gavi, the Vaccine Alliance; Bill & Melinda Gates Foundation.

Significance Methods for analyzing individual-level geo-located disease data have existed for some time, but have rarely been used to analyze endemic human diseases. Here we apply such methods to nearly a decade’s worth of uniquely detailed epidemiological data on incidence of the deadly vector-borne disease visceral leishmaniasis (VL) and its secondary condition, post–kala-azar dermal leishmaniasis (PKDL), to quantify the spread of infection around cases in space and time by inferring who infected whom, and estimate the relative contribution of different infection states to transmission. Our findings highlight the key role long diagnosis delays and PKDL play in maintaining VL transmission. This detailed characterization of the spatiotemporal transmission of VL will help inform targeting of interventions around VL and PKDL cases., Understanding of spatiotemporal transmission of infectious diseases has improved significantly in recent years. Advances in Bayesian inference methods for individual-level geo-located epidemiological data have enabled reconstruction of transmission trees and quantification of disease spread in space and time, while accounting for uncertainty in missing data. However, these methods have rarely been applied to endemic diseases or ones in which asymptomatic infection plays a role, for which additional estimation methods are required. Here, we develop such methods to analyze longitudinal incidence data on visceral leishmaniasis (VL) and its sequela, post–kala-azar dermal leishmaniasis (PKDL), in a highly endemic community in Bangladesh. Incorporating recent data on VL and PKDL infectiousness, we show that while VL cases drive transmission when incidence is high, the contribution of PKDL increases significantly as VL incidence declines (reaching 55% in this setting). Transmission is highly focal: 85% of mean distances from inferred infectors to their secondary VL cases were

Objectives New HIV infections remain higher in women than men in sub-Saharan Africa. Preexposure prophylaxis (PrEP) is an effective HIV prevention measure, currently prioritized for those at highest risk, such as female sex workers (FSWs), for whom it is most cost-effective. However, the greatest number of HIV infections in sub-Saharan Africa occurs in women in the general population. As countries consider wider PrEP scale-up, there is a need to weigh the population-level impact, cost, and relative cost-effectiveness to inform priority setting. Methods We developed mathematical models of HIV risk to women and derived tools to highlight key considerations for PrEP programming. The models were fitted to South Africa, Zimbabwe, and Kenya, spanning a range of HIV burden in sub-Saharan Africa. The impact, cost, and cost-effectiveness of PrEP scale-up for adolescent girls and young women (AGYW), women 25 to 34 years old, and women 35 to 49 years old were assessed, accounting for differences in population sizes and the low program retention levels reported in demonstration projects. Results Preexposure prophylaxis could avert substantially more infections a year among women in general population than among FSW. The greatest number of infections could be averted annually among AGYW in South Africa (24-fold that for FSW). In Zimbabwe, the greatest number of infections could be averted among women 25 to 34 years old (8-fold that for FSW); and in Kenya, similarly between AGYW and women 25 to 34 years old (3-fold that for FSW). However, the unit costs of PrEP delivery for AGYW, women 25 to 34 years old, and women 35 to 49 years old would have to reduce considerably (by 70.8%-91.0% across scenarios) for scale-up to these populations to be as cost-effective as for FSW. Conclusions Preexposure prophylaxis has the potential to substantially reduce new HIV infections in HIV-endemic countries in sub-Saharan Africa. This will necessitate PrEP being made widely available beyond those at highest individual risk and continued integration into a range of national services and at community level to significantly bring down the costs and improve cost-effectiveness.

The widespread detection of per- and polyfluoroalkyl substances (PFAS) throughout the world and the ongoing proliferation of environmental regulations has prompted the need for a forensic approach ...

Background As the World Health Organization seeks to eliminate trachoma by 2020, countries are beginning to control the transmission of trachomatous inflammation–follicular (TF) and discontinue mass drug administration (MDA) with oral azithromycin. We evaluated the effect of MDA discontinuation on TF1–9 prevalence at the district level. Methods We extracted from the available data districts with an impact survey at the end of their program cycle that initiated discontinuation of MDA (TF1–9 prevalence Results Of the 220 districts included, TF1–9 prevalence increased to >5% from impact to surveillance survey in 9% of districts. Regression analysis indicated that impact survey TF1–9 prevalence was a significant predictor of surveillance survey TF1–9 prevalence. The proportion of simulations with >5% TF1–9 prevalence in the surveillance survey was 2%, assuming the survey was conducted 4 years after MDA. Conclusion An increase in TF1–9 prevalence may represent disease resurgence but could also be due to measurement error. Improved diagnostic tests are crucial to elimination of TF1–9 as a public health problem.

The World Health Organization (WHO) has set elimination as a public health problem (EPHP) as a goal for schistosomiasis. As the WHO treatment guidelines for schistosomiasis are currently under revision, we investigate whether school-based or community-wide treatment strategies are required for achieving the EPHP goal. In low- to moderate-transmission settings with good school enrolment, we find that school-based treatment is sufficient for achieving EPHP. However, community-wide treatment is projected to be necessary in certain high-transmission settings as well as settings with low school enrolment. Hence, the optimal treatment strategy depends on setting-specific factors such as the species present, prevalence prior to treatment, and the age profile of infection.

Summary Many infection prevention and control (IPC) interventions have been adopted by hospitals to limit nosocomial transmission of SARS-CoV-2. The aim of this systematic review is to identify evidence on the effectiveness of these interventions. We conducted a literature search of five databases (OVID MEDLINE, Embase, CENTRAL, COVID-19 Portfolio(pre-print), Web of Science). SWIFT ActiveScreener software was used to screen English titles and abstracts published between 1st January 2020 and 6th April 2021. Intervention studies, defined by Cochrane Effective Practice and Organisation of Care, that evaluated IPC interventions with an outcome of SARS-CoV-2 infection in either patients or healthcare workers were included. Personal protective equipment (PPE) was excluded as this intervention had been previously reviewed. Risks of bias were assessed using the Cochrane tool for randomised trials (RoB2) and non-randomized studies of interventions (ROBINS-I). From 23,156 screened articles, we identified seven articles that met the inclusion criteria, all of which evaluated interventions to prevent infections in healthcare workers and the majority of which were focused on effectiveness of prophylaxes. Due to heterogeneity in interventions, we did not conduct a meta-analysis. All agents used for prophylaxes have little to no evidence of effectiveness against SARS-CoV-2 infections. We did not find any studies evaluating the effectiveness of interventions including but not limited to screening, isolation and improved ventilation. There is limited evidence from interventional studies, excluding PPE, evaluating IPC measures for SARS-CoV-2. This review calls for urgent action to implement such studies to inform policies to protect our most vulnerable populations and healthcare workers.

Lateral flow device (LFD) rapid tests for SARS-CoV-2 antigens are used for asymptomatic testing (including for people who are presymptomatic or paucisymptomatic) in various settings, including in the UK. As of April 9, 2021, LFD tests were made available for twice per week rapid testing to the general population in England. News articles reported pressures within the UK Government to rescind asymptomatic testing due to concerns that, despite high specificity (estimated to be 99·9%),1 the proportion of people testing positive who had COVID-19 (ie, the positive predictive value) was falling in line with the reducing prevalence, leading to greater proportions of individuals having to unnecessarily isolate because of a false-positive test result.2 Asking people to isolate on the basis of what might be a false-positive result is associated with a perceived unfairness and, in some cases, moral indignation.\ud \ud The risk of people without COVID-19 self-isolating due to false-positive test results is a cost to the individual, their household, and their workplace that needs consideration and mitigation. However, this cost should be considered in the context of the costs of failing to identify true-positive results. In the UK, the epidemic control strategies implemented during the past year, including lockdowns, have all, to varying extents, required people who do not have COVID-19 to isolate or quarantine and to greatly restrict their social contacts, while shutting down entire economic sectors. These restrictions have had massive implications for the incomes, education, and wellbeing of many people, including children and young people.3 Any discussions concerning LFD testing policy should incorporate the trade-off between the negative effects of false positives and the onwards transmission prevented. This trade-off is particularly pertinent when considering the contribution of LFD testing to preventing the need for additional widespread restrictive measures.

Infection by multidrug-resistant Mycobacterium abscessus is increasingly prevalent in cystic fibrosis (CF) patients, leaving clinicians with few therapeutic options. A compassionate study showed the clinical improvement of a CF patient with a disseminated M. abscessus (GD01) infection, following injection of a phage cocktail, including phage Muddy. Broadening the use of phage therapy in patients as a potential antibacterial alternative necessitates the development of biological models to improve the reliability and successful prediction of phage therapy in the clinic. Herein, we demonstrate that Muddy very efficiently lyses GD01 in vitro, an effect substantially increased with standard drugs. Remarkably, this cooperative activity was retained in an M. abscessus model of infection in CFTR-depleted zebrafish, associated with a striking increase in larval survival and reduction in pathological signs. The activity of Muddy was lost in macrophage-ablated larvae, suggesting that successful phage therapy relies on functional innate immunity. CFTR-depleted zebrafish represent a practical model to rapidly assess phage treatment efficacy against M. abscessus isolates, allowing the identification of drug combinations accompanying phage therapy and treatment prediction in patients. This article has an associated First Person interview with the first author of the paper.

Many countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission is unknown. We used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the population attributable fraction (PAF) due to groups as the relative change in the basic reproduction number when groups are prevented. Groups of 50+ individuals accounted for 0.5% of reported contact events, and we estimate that the PAF due to groups of 50+ people is 5.4% (95% confidence interval 1.4%, 11.5%). The PAF due to groups of 20+ people is 18.9% (12.7%, 25.7%) and the PAF due to groups of 10+ is 25.2% (19.4%, 31.4%). Under normal circumstances with pre-COVID-19 contact patterns, large groups of individuals have a relatively small epidemiological impact; small- and medium-sized groups between 10 and 50 people have a larger impact on an epidemic. This article is part of the theme issue ‘Modelling that shaped the early COVID-19 pandemic response in the UK’.

This work presents results of macro, micro, and nanoscale surface characterization for a set of Roman denarii, ranging from 136 BCE to 240 CE, using large-scale X-ray fluorescence (XRF) mapping, particle-induced X-ray emission (PIXE) spectroscopy, focused-ion-beam-assisted scanning electron microscopy (FIB-SEM) with energy dispersive spectroscopy (EDS). The combination of XRF and PIXE, with varying beam energies, allowed for visualization and quantification of individual elements as a function of the surface distribution. These results helped to select suitable areas for FIB-SEM-EDS analysis. The edges of selected coins were polished to image the inner composition and surface morphology of the coins using a backscattering electron (BSE) imaging method and EDS mapping. Nanosized lamellas extracted from the coins were investigated by transmission electron microscopy (TEM) as well. The combination of these methods enabled the surface, the subsurface, and volume composition of these coins to be probed to better understand their production methods, their surface treatment methods, and their corrosion. The results also provide evidence that a particular surface treatment method, amalgam silvering, had been used to make authentic Roman coins as early as the third century CE.

A 15-year-old patient with cystic fibrosis with a disseminated Mycobacterium abscessus infection was treated with a three-phage cocktail following bilateral lung transplantation. Effective lytic phage derivatives that efficiently kill the infectious M. abscessus strain were developed by genome engineering and forward genetics. Intravenous phage treatment was well tolerated and associated with objective clinical improvement, including sternal wound closure, improved liver function, and substantial resolution of infected skin nodules. Clinical use of engineered bacteriophages for the treatment of disseminated mycobacterial infection.

Telehealth is a promising innovation in HIV care and services. It holds promise to leverage health information technology, (HIT), for expanding the benefits of treatment to underserved groups and Persons Living With HIV/AIDS, (PLWHA) dwelling in remote areas. The exploration of telehealth service structure, processes and effects is a useful starting point for clarifying expectations and setting benchmarks. Northeast Florida Ryan White network is in an early stage of telemedicine development and implementation. Learning from others is key to the design of effective telehealth services. Outlined here are essential tenets for framing consensus regarding the delivery, oversight, and evaluation of teleservices in Jacksonville, Florida. Multiple stakeholders are vested in the implementation of telehealth. Health services policy can inform the evolution of HIV teleservices in Northeast Florida and elsewhere.

Per- and polyfluoroalkyl substances (PFASs) are used in a wide range of consumer products for their water- and grease-resistant properties, but few studies have explored this exposure route. We used multiple regression to investigate associations between six self-reported behaviors hypothesized to influence PFAS exposure and serum concentrations of six PFAS chemicals in 178 middle-aged women enrolled in the Child Health and Development Studies, about half of whom are African American. Blood samples were collected in 2010-2013, and participants were interviewed about behavior in 2015-2016. Results showed that African American women had lower levels of perfluorooctanoic acid (PFOA) and perfluorohexanesulfonic acid (PFHxS) compared with non-Hispanic white women. In African Americans, but not others, frequent consumption of prepared food in coated cardboard containers was associated with higher levels of four PFASs. Flossing with Oral-B Glide, having stain-resistant carpet or furniture, and living in a city served by a PFAS-contaminated water supply were also associated with higher levels of some PFASs. Product testing using particle-induced γ-ray emission (PIGE) spectroscopy confirmed that Oral-B Glide and competitor flosses contained detectable fluorine. Despite the delay between blood collection and interview, these results strengthen the evidence for exposure to PFASs from food packaging and implicate exposure from polytetrafluoroethylene (PTFE)-based dental floss for the first time.

Due to the COVID-19 pandemic, many key neglected tropical disease (NTD) activities have been postponed. This hindrance comes at a time when the NTDs are progressing towards their ambitious goals for 2030. Mathematical modelling on several NTDs, namely gambiense sleeping sickness, lymphatic filariasis, onchocerciasis, schistosomiasis, soil-transmitted helminthiases (STH), trachoma, and visceral leishmaniasis, shows that the impact of this disruption will vary across the diseases. Programs face a risk of resurgence, which will be fastest in high-transmission areas. Furthermore, of the mass drug administration diseases, schistosomiasis, STH, and trachoma are likely to encounter faster resurgence. The case-finding diseases (gambiense sleeping sickness and visceral leishmaniasis) are likely to have fewer cases being detected but may face an increasing underlying rate of new infections. However, once programs are able to resume, there are ways to mitigate the impact and accelerate progress towards the 2030 goals., The COVID-19 pandemic has disrupted neglected tropical disease programs. Modelling shows the impact of this will vary across diseases. Once interventions are reintroduced, there are opportunities for mitigating the delay and accelerating progress towards the 2030 goals.

IntroductionThe natural history and transmission patterns of endemic human coronaviruses are of increased interest following the emergence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).MethodsIn rural Kenya 483 individuals from 47 households were followed for six months (2009-10) with nasopharyngeal swabs collected twice weekly regardless of symptoms. A total of 16,918 swabs were tested for human coronavirus (hCoV) OC43, NL63 and 229E and other respiratory viruses using polymerase chain reaction.ResultsFrom 346 (71.6%) household members 629 hCoV infection episodes were defined with 36.3% being symptomatic: varying by hCoV type and decreasing with age. Symptomatic episodes (aHR=0.6 (95% CI:0.5-0.8) or those with elevated peak viral load (medium aHR=0.4 (0.3-0.6); high aHR=0.31 (0.2-0.4)) had longer viral shedding compared to their respective counterparts. Homologous reinfections were observed in 99 (19.9%) of 497 first infections. School-age children (55%) were the most common index cases with those having medium (aOR=5.3 (2.3 – 12.0)) or high (8.1 (2.9 - 22.5)) peak viral load most often generating secondary cases.ConclusionHousehold coronavirus infection was common, frequently asymptomatic and mostly introduced by school-age children. Secondary transmission was influenced by viral load of index cases. Homologous-type reinfection was common. These data may be insightful for SARS-CoV-2.

Background: Soil-transmitted helminths (STH) are among the most common parasitic infections globally, disproportionately affecting children. Treatment of STH in Kenya is often targeted at preschool (PSAC) and school aged (SAC) children delivered through annual mass drug administration (MDA) in primary schools. Understanding group-specific prevalence and dynamics between treatment and coverage is critical for continued treatment success. This study aims to provide detailed information on group-specific infection prevalence and relative reductions (RR), and their relationships with treatment coverage over time. Additionally, it aims to quantify the correlation between the observed school level infection prevalence and treatment coverage.Methods: Secondary analysis of existing data collected between 2012 and 2018 by the monitoring and evaluation (M&E) program of the National School-Based Deworming (NSBD) program was used. The M&E program conducted surveys utilizing cross-sectional study design, at four survey time points, in a nationally-representative sample of schoolchildren across counties in Kenya. In each participating school, the program randomly sampled 108 children per school, of both groups. Infection prevalence was estimated using binomial regression, RR in prevalence using multivariable mixed effects model, statistical correlations using structural equation modeling, and change-point-analysis using the binary segmentation algorithm.Results: Overall, STH prevalence for PSAC was 33.7, 20.2, 19.0, and 17.9% during Year 1 (Y1), Year 3 (Y3), Year 5 (Y5), and Year 6 (Y6) surveys, respectively with an overall RR of 46.9% (p = 0.001) from Y1 to Y6. Similarly, overall STH prevalence for SAC was 33.6, 18.4, 14.7, and 12.5% during Y1, Y3, Y5, and Y6 surveys, respectively with an overall RR of 62.6% (p < 0.001). An overall (all time points) significant but very weak negative correlation was found between treatment coverage and undifferentiated STH prevalence (r = −0.144, p = 0.002) among PSAC but not in SAC. Further, we observed inter-county heterogeneity variation in infection prevalence, RR, as well as correlations.Conclusion: The analysis showed that after six rounds of MDA, prevalence of STH has significantly declined among both groups of children, however not to a point where it is not a public health problem (below 1%). The analysis, additionally established an overall significant but weak negative correlation between treatment coverage and prevalence, indicating that the current treatment coverage might not be sufficient to drive the overall STH prevalence to below 1%. These findings will allow STH control programs in Kenya to make decisions that will accelerate the attainment of STH elimination as a public health problem.

Summary: Background: In most countries, contacts of confirmed COVID-19 cases are asked to quarantine for 14 days after exposure to limit asymptomatic onward transmission. While theoretically effective, this policy places a substantial social and economic burden on both the individual and wider society, which might result in low adherence and reduced policy effectiveness. We aimed to assess the merit of testing contacts to avert onward transmission and to replace or reduce the length of quarantine for uninfected contacts. Methods: We used an agent-based model to simulate the viral load dynamics of exposed contacts, and their potential for onward transmission in different quarantine and testing strategies. We compared the performance of quarantines of differing durations, testing with either PCR or lateral flow antigen (LFA) tests at the end of quarantine, and daily LFA testing without quarantine, against the current 14-day quarantine strategy. We also investigated the effect of contact tracing delays and adherence to both quarantine and self-isolation on the effectiveness of each strategy. Findings: Assuming moderate levels of adherence to quarantine and self-isolation, self-isolation on symptom onset alone can prevent 37% (95% uncertainty interval [UI] 12–56) of onward transmission potential from secondary cases. 14 days of post-exposure quarantine reduces transmission by 59% (95% UI 28–79). Quarantine with release after a negative PCR test 7 days after exposure might avert a similar proportion (54%, 95% UI 31–81; risk ratio [RR] 0·94, 95% UI 0·62–1·24) to that of the 14-day quarantine period, as would quarantine with a negative LFA test 7 days after exposure (50%, 95% UI 28–77; RR 0·88, 0·66–1·11) or daily testing without quarantine for 5 days after tracing (50%, 95% UI 23–81; RR 0·88, 0·60–1·43) if all tests are returned negative. A stronger effect might be possible if individuals isolate more strictly after a positive test and if contacts can be notified faster. Interpretation: Testing might allow for a substantial reduction in the length of, or replacement of, quarantine with a small excess in transmission risk. Decreasing test and trace delays and increasing adherence will further increase the effectiveness of these strategies. Further research is required to empirically evaluate the potential costs (increased transmission risk, false reassurance) and benefits (reduction in the burden of quarantine, increased adherence) of such strategies before adoption as policy. Funding: National Institute for Health Research, UK Research and Innovation, Wellcome Trust, EU Horizon 2021, and the Bill & Melinda Gates Foundation.

Background Effective case identification strategies are fundamental to capturing the remaining visceral leishmaniasis (VL) cases in India. To inform government strategies to reach and sustain elimination benchmarks, this study presents costs of active- and passive- case detection (ACD and PCD) strategies used in India’s most VL-endemic state, Bihar, with a focus on programme outcomes stratified by district-level incidence. Methods Expenditure analysis was complemented by onsite micro-costing to compare the cost of PCD in hospitals alongside index case-based ACD and a combination of blanket (house-to-house) and camp ACD from January to December 2018. From the provider’s perspective, a cost analysis evaluated the overall programme cost of each activity, the cost per case detected, and the cost of scaling up ACD. Results During 2018, index case-based ACD, blanket and camp ACD, and PCD reported 1,497, 131, and 1,983 VL-positive cases at a unit cost of $522.81, $4,186.81, and $246.79, respectively. In high endemic districts, more VL cases were identified through PCD while in meso- and low-endemic districts more cases were identified through ACD. The cost of scaling up ACD to identify 3,000 additional cases ranged from $1.6–4 million, depending on the extent to which blanket and camp ACD was relied upon. Conclusion Cost per VL test conducted (rather than VL-positive case identified) may be a better metric estimating unit costs to scale up ACD in Bihar. As more VL cases were identified in meso-and low-endemic districts through ACD than PCD, health authorities in India should consider bolstering ACD in these areas. Blanket and camp ACD identified fewer cases at a higher unit cost than index case-based ACD. However, the value of detecting additional VL cases early outweighs long-term costs for reaching and sustaining VL elimination benchmarks in India., Author summary Visceral leishmaniasis (VL) is targeted for elimination in India by 2020, where early identification and prompt treatment are essential measures for reaching and sustaining incidence benchmarks. Both active- and passive- case detection (ACD and PCD) strategies have been employed in recent years, and evaluating the cost and outputs of each is now important for sustaining funding and political momentum. This study presents overall and unit costs for PCD, index case-based ACD (where neighbours in the vicinity of a recent VL case are screened), and a combination of blanket and camp ACD (involving house-to-house case searching and weekly diagnostic camps) in Bihar, India during 2018. Results of this study indicate that a larger proportion of VL cases were found through PCD in high incidence districts, which may be related to increased interaction with ACD officers. ACD can be bolstered in meso- and low-incidence districts where educational exposure to VL is low and risk of resurgence is high. Although blanket and camp ACD unit costs were at least four times higher than index case-based ACD, the number of VL cases identified through this approach may warrant the investment to achieve VL elimination. Cost and outcomes of VL case finding approaches need to be continuously evaluated until elimination benchmarks are reached and integrated into sustained surveillance programmes.

Background Pre-exposure prophylaxis (PrEP) is highly effective in preventing HIV and has the potential to significantly impact the HIV epidemic. Given limited resources for HIV prevention, identifying PrEP provision strategies that maximize impact is critical. Methods We used a stochastic individual-based network model to evaluate the direct (infections prevented among PrEP users) and indirect (infections prevented among non-PrEP users as a result of PrEP) benefits of PrEP, the person-years of PrEP required to prevent one HIV infection, and the community-level impact of providing PrEP to populations defined by gender and age in western Kenya and South Africa. We examined sensitivity of results to scale-up of antiretroviral therapy (ART) and voluntary medical male circumcision (VMMC) by comparing two scenarios: maintaining current coverage (“status quo”) and rapid scale-up to meet programmatic targets (“fast-track”). Results The community-level impact of PrEP was greatest among women aged 15–24 due to high incidence, while PrEP use among men aged 15–24 yielded the highest proportion of indirect infections prevented in the community. These indirect infections prevented continue to increase over time (western Kenya: 0.4–5.5 (status quo); 0.4–4.9 (fast-track); South Africa: 0.5–1.8 (status quo); 0.5–3.0 (fast-track)) relative to direct infections prevented among PrEP users. The number of person-years of PrEP needed to prevent one HIV infection was lower (59 western Kenya and 69 in South Africa in the status quo scenario; 201 western Kenya and 87 in South Africa in the fast-track scenario) when PrEP was provided only to women compared with only to men over time horizons of up to 5 years, as the indirect benefits of providing PrEP to men accrue in later years. Conclusions Providing PrEP to women aged 15–24 prevents the greatest number of HIV infections per person-year of PrEP, but PrEP provision for young men also provides indirect benefits to women and to the community overall. This finding supports existing policies that prioritize PrEP use for young women, while also illuminating the community-level benefits of PrEP availability for men when resources permit.

Background: \ud The risk of severe COVID-19 if an individual becomes infected is known to be higher in older individuals and those with underlying health conditions. Understanding the number of individuals at increased risk of severe COVID-19 and how this varies between countries should inform the design of possible strategies to shield or vaccinate those at highest risk.\ud \ud Methods: \ud We estimated the number of individuals at increased risk of severe disease (defined as those with at least one condition listed as “at increased risk of severe COVID-19” in current guidelines) by age (5-year age groups), sex, and country for 188 countries using prevalence data from the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2017 and UN population estimates for 2020. The list of underlying conditions relevant to COVID-19 was determined by mapping the conditions listed in GBD 2017 to those listed in guidelines published by WHO and public health agencies in the UK and the USA. We analysed data from two large multimorbidity studies to determine appropriate adjustment factors for clustering and multimorbidity. To help interpretation of the degree of risk among those at increased risk, we also estimated the number of individuals at high risk (defined as those that would require hospital admission if infected) using age-specific infection–hospitalisation ratios for COVID-19 estimated for mainland China and making adjustments to reflect country-specific differences in the prevalence of underlying conditions and frailty. We assumed males were twice at likely as females to be at high risk. We also calculated the number of individuals without an underlying condition that could be considered at increased risk because of their age, using minimum ages from 50 to 70 years. We generated uncertainty intervals (UIs) for our estimates by running low and high scenarios using the lower and upper 95% confidence limits for country population size, disease prevalences, multimorbidity fractions, and infection–hospitalisation ratios, and plausible low and high estimates for the degree of clustering, informed by multimorbidity studies.\ud \ud Findings: \ud We estimated that 1·7 billion (UI 1·0–2·4) people, comprising 22% (UI 15–28) of the global population, have at least one underlying condition that puts them at increased risk of severe COVID-19 if infected (ranging from 66% of those aged 70 years or older). We estimated that 349 million (186–787) people (4% [3–9] of the global population) are at high risk of severe COVID-19 and would require hospital admission if infected (ranging from

Summary Background Non-pharmaceutical interventions have been implemented to reduce transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been crucial to support evidence-based policy making during the early stages of the epidemic. This study assesses the potential impact of different control measures for mitigating the burden of COVID-19 in the UK. Methods We used a stochastic age-structured transmission model to explore a range of intervention scenarios, tracking 66·4 million people aggregated to 186 county-level administrative units in England, Wales, Scotland, and Northern Ireland. The four base interventions modelled were school closures, physical distancing, shielding of people aged 70 years or older, and self-isolation of symptomatic cases. We also modelled the combination of these interventions, as well as a programme of intensive interventions with phased lockdown-type restrictions that substantially limited contacts outside of the home for repeated periods. We simulated different triggers for the introduction of interventions, and estimated the impact of varying adherence to interventions across counties. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (ie, admission to the intensive care units [ICU]) treatment, and deaths, and compared the effect of each intervention on the basic reproduction number, R0. Findings We projected a median unmitigated burden of 23 million (95% prediction interval 13–30) clinical cases and 350 000 deaths (170 000–480 000) due to COVID-19 in the UK by December, 2021. We found that the four base interventions were each likely to decrease R0, but not sufficiently to prevent ICU demand from exceeding health service capacity. The combined intervention was more effective at reducing R0, but only lockdown periods were sufficient to bring R0 near or below 1; the most stringent lockdown scenario resulted in a projected 120 000 cases (46 000–700 000) and 50 000 deaths (9300–160 000). Intensive interventions with lockdown periods would need to be in place for a large proportion of the coming year to prevent health-care demand exceeding availability. Interpretation The characteristics of SARS-CoV-2 mean that extreme measures are probably required to bring the epidemic under control and to prevent very large numbers of deaths and an excess of demand on hospital beds, especially those in ICUs. Funding Medical Research Council.

SummaryBackgroundMany countries have banned groups and gatherings as part of their response to the pandemic caused by the coronavirus, SARS-CoV-2. Although there are outbreak reports involving mass gatherings, the contribution to overall transmission is unknown.MethodsWe used data from a survey of social contact behaviour that specifically asked about contact with groups to estimate the Population Attributable Fraction (PAF) due to groups as the relative change in the Basic Reproduction Number when groups are prevented.FindingsGroups of 50+ individuals accounted for 0.5% of reported contact events, and we estimate that the PAF due to groups of 50+ people is 5.4% (95%CI 1.4%, 11.5%). The PAF due to groups of 20+ people is 18.9% (12.7%, 25.7%) and the PAF due to groups of 10+ is 25.2% (19.4%, 31.4%)InterpretationLarge groups of individuals have a relatively small epidemiological impact; small and medium sized groups between 10 and 50 people have a larger impact on an epidemic.

Background Mathematical models can be powerful policymaking tools. Simple, static models are user-friendly for policymakers. More complex, dynamic models account for time-dependent changes but are complicated to understand and produce. Under which conditions are static models adequate? We compare static and dynamic model predictions of whether behavioural disinhibition could undermine the impact of HIV pre-exposure prophylaxis (PrEP) provision to female sex workers in South Africa. Methods A static model of HIV risk was developed and adapted into a dynamic model. Both models were used to estimate the possible reduction in condom use, following PrEP introduction, without increasing HIV risk. The results were compared over a 20-year time horizon, in two contexts: at epidemic equilibrium and during an increasing epidemic. Results Over time horizons of up to 5 years, the models are consistent. Over longer timeframes, the static model overstates the tolerated reduction in condom use where initial condom use is reasonably high ($\ge$50%) and/or PrEP effectiveness is low ($\le$45%), especially during an increasing epidemic. Conclusions Static models can provide useful deductions to guide policymaking around the introduction of a new HIV intervention over short–medium time horizons of up to 5 years. Over longer timeframes, static models may not sufficiently emphasise situations of programmatic importance, especially where underlying epidemics are still increasing.

Background: The MMed in Family Medicine is a professional Master’s qualification spanning 4 years of training. The outcomes were predetermined by national consensus. While these outcomes are measured in the form of a national exit examination, there has been no exploration of the experiences of registrars (residents) in this relatively new programme. To evaluate the experiences of registrars in one of the nine training programmes in South Africa and to identify areas for improvement. Methods: This study used purposive sampling to recruit registrar ( n = 9) and supervisor ( n = 8) participants into respective groups. Data were collected via semi-structured interviews and analysed thematically, and consensus was built using the nominal group technique. Results: Supervisors identified the strengths and weaknesses of the programme which will impact on further strategic planning. Data from registrar interviews yielded two themes: affirmation, referring to the positive social engagement and facilitation of professional identity formation; and frustrations, referring to structural aspects of the programme which hindered academic progress. Conclusion: Qualitative programme evaluation is a useful tool in understanding the learning environment. The student perspective helped to identify the unintended consequences of the programme. It was also shown that the nominal group consensus building technique worked well in a resource-constrained environment.

Background Our goal was to identify clinically relevant immunotherapies that synergize with microencapsulation to protect adult porcine islet (API) xenografts in diabetic NOD mice. We have shown previously that dual costimulatory blockade (CTLA4-Ig plus anti-CD154 mAb) combined with encapsulation protects APIs long-term in NOD mice. Since no anti-CD154 mAbs currently are approved for use in humans, we tested the efficacy of other targeted immunosuppression regimens that might be used for diabetic patients receiving encapsulated islets. Methods Microencapsulated APIs were transplanted i.p. in diabetic NOD mice given either no immunosuppression or combinations immunosuppressive reagents. Graft function was monitored by blood glucose levels, i.p. glucose tolerance tests, and histology. Mechanisms of rejection were investigated by phenotyping host peritoneal cells and measuring graft site cytokine and chemokine levels. Results New immunosuppressive therapies were compared to CTLA4-Ig plus anti-CD154 mAb, used here as a control. The most effective was triple treatment with CTLA4-Ig, anti-CD154 mAb, and intracapsular CXCL12, and the next most effective was a non-depleting anti-CD4 mAb (YTS177.9) plus intracapsular CXCL12. Three additional regimens (CTLA4-Ig plus YTS177.9, YTS177.9 alone, and anti-OX40-Ligand mAb alone) significantly prolonged encapsulated API function. Dual treatment with CTLA4-Ig plus anti-CD40 mAb was as effective as CTLA4-Ig plus anti-CD154 mAb. Five other monotherapies and three combination therapies did not augment encapsulated API survival. Most peritoneal cytokines and chemokines were either absent or minimal. At necropsy, the capsules were intact, not fibrosed, and clean when function was maintained, but were coated with host cells if rejection had occurred. Conclusions Multiple different immunotherapies which specifically inhibit CD4+ T cells, modulate T-cell trafficking, or interfere with antigen presentation can substitute for anti-CD154 mAb to prolong encapsulated islet xenograft function in diabetic NOD mice.

BackgroundHepatocellular carcinoma (HCC) continues to be a leading challenge in modern oncology. Early detection via blood-based screening tests has the potential to cause a stage-shift at diagnosis and improve clinical outcomes. Tumor associated autoantibodies (TA-AAbs) have previously shown the ability to distinguish HCC from patients with high-risk liver disease. This research aimed to further show the utility of TA-AAbs as biomarkers of HCC and assess their use in combination with Alpha-fetoprotein (AFP) for detection of HCC across multiple tumor stages.MethodsLevels of circulating G class antibodies to 44 recombinant tumor associated antigens and circulating AFP were measured in the serum of patients with HCC, non-cancerous chronic liver disease (NCCLD) and healthy controls via enzyme-linked immunosorbent assay (ELISA). TA-AAb cut-offs were set at the highest Youden's J statistic at a specificity ≥95.00%. Panels of TA-AAbs were formed using net reclassification improvement. AFP was assessed at a cut-off of 200 ng/ml.ResultsSensitivities ranged from 1.01% to 12.24% at specificities of 95.96% to 100.00% for single TA-AAbs. An ELISA test measuring a panel of 10 of these TA-AAbs achieved a combined sensitivity of 36.73% at a specificity of 89.89% when distinguishing HCC from NCCLD controls. At a cut-off of 200 ng/ml, AFP achieved a sensitivity of 31.63% at a specificity of 100.00% in the same cohort. Combination of the TA-AAb panel with AFP significantly increased the sensitivity for stage one (40.00%) and two (55.00%) HCC over the TA-AAb panel or AFP alone.ConclusionsA panel of TA-AAbs in combination with AFP could be clinically relevant as a replacement for measuring levels of AFP alone in surveillance and diagnosis strategies. The increased early stage sensitivity could lead to a stage shift with positive prognostic outcomes.

Background Control of visceral leishmaniasis (VL) on the Indian subcontinent relies on prompt detection and treatment of symptomatic cases. Detection efforts influence the observed VL incidence and how well it reflects the underlying true incidence. As control targets are defined in terms of observed cases, there is an urgent need to understand how changes in detection delay and population coverage of improved detection affect VL control. Methods Using a mathematical model for transmission and control of VL, we predict the impact of reduced detection delays and/or increased population coverage of the detection programs on observed and true VL incidence and mortality. Results Improved case detection, either by higher coverage or reduced detection delay, causes an initial rise in observed VL incidence before a reduction. Relaxation of improved detection may lead to an apparent temporary (1 year) reduction in VL incidence, but comes with a high risk of resurging infection levels. Duration of symptoms in detected cases shows an unequivocal association with detection effort. Conclusions VL incidence on its own is not a reliable indicator of the performance of case detection programs. Duration of symptoms in detected cases can be used as an additional marker of the performance of case detection programs.

Globally, more people die annually from tuberculosis than from any other single infectious agent. Unfortunately, there is no commercially-available vaccine that is sufficiently effective at preventing acquisition of pulmonary tuberculosis in adults. In this study, pre-exposure prophylactic pulmonary delivery of active aerosolized anti-tuberculosis bacteriophage D29 was evaluated as an option for protection against Mycobacterium tuberculosis infection. An average bacteriophage concentration of approximately 1 PFU/alveolus was achieved in the lungs of mice using a nose-only inhalation device optimized with a dose simulation technique and adapted for use with a vibrating mesh nebulizer. Within 30 minutes of bacteriophage delivery, the mice received either a low dose (∼50-100 CFU), or an ultra-low dose (∼5-10 CFU), of M. tuberculosis H37Rv aerosol to the lungs. A prophylactic effect was observed with bacteriophage aerosol pre-treatment significantly decreasing M. tuberculosis burden in mouse lungs 24 hours and 3 weeks post-challenge (p < 0.05). These novel results indicate that a sufficient dose of nebulized mycobacteriophage aerosol to the lungs may be a valuable intervention to provide extra protection to health care professionals and other individuals at risk of exposure to M. tuberculosis.

Background Juvenile dermatomyositis (JDM) is an auto-immune muscle disease which presents with skin manifestations and muscle weakness. At least 10% of the patients with JDM present with acquired lipodystrophy. Laminopathies are caused by mutations in the lamin genes and cover a wide spectrum of diseases including muscular dystrophies and lipodystrophy. The p.T10I LMNA variant is associated with a phenotype of generalized lipodystrophy that has also been called atypical progeroid syndrome. Case presentation A previously healthy female presented with bilateral proximal lower extremity muscle weakness at age 4. She was diagnosed with JDM based on her clinical presentation, laboratory tests and magnetic resonance imaging (MRI). She had subcutaneous fat loss which started in her extremities and progressed to her whole body. At age 7, she had diabetes, hypertriglyceridemia, low leptin levels and low body fat on dual energy X-ray absorptiometry (DEXA) scan, and was diagnosed with acquired generalized lipodystrophy (AGL). Whole exome sequencing (WES) revealed a heterozygous c.29C > T; p.T10I missense pathogenic variant in LMNA, which encodes lamins A and C. Muscle biopsy confirmed JDM rather than muscular dystrophy, showing perifascicular atrophy and perivascular mononuclear cell infiltration. Immunofluroscence of skin fibroblasts confirmed nuclear atypia and fragmentation. Conclusions This is a unique case with p.T10I LMNA variant displaying concurrent JDM and AGL. This co-occurrence raises the intriguing possibility that LMNA, and possibly p.T10I, may have a pathogenic role in not only the occurrence of generalized lipodystrophy, but also juvenile dermatomyositis. Careful phenotypic characterization of additional patients with laminopathies as well as individuals with JDM is warranted. Electronic supplementary material The online version of this article (10.1186/s40842-018-0058-3) contains supplementary material, which is available to authorized users.

Designing strategies to introduce new HIV prevention technologies requires balancing equitable access with sustainable distribution, particularly in resource constrained settings with high HIV prevalence. This paper explores how knowledge of preference heterogeneity can guide the equitable targeting of HIV prevention products using differentiated advertising and product placement to balance increased access with sustainability. A discrete choice experiment elicited 1016 women's preferences for distribution of HIV prevention products in South Africa. Qualitative research guided the experimental design which considered distribution outlet, collection method, advertising message, and price. A range of choice models, including random parameters logit, latent class and latent class random parameters logit models, were compared for fit. A latent class model showed the best fit and distinguished two classes of women: Class 1 were significantly more likely to be cohabiting and unemployed, who preferred products advertised for HIV prevention distributed through clinics and were highly price sensitive. Class 2 significantly preferred distribution through pharmacies and advertising around women's empowerment, while price was not a key factor. This analysis suggests that equity in access to new products could be advanced through exploiting preference heterogeneity between groups. The identified groups can be then used to design social marketing differentiated distribution strategies. Distributing free products promoted for HIV prevention could discourage ‘leakage’ of highly subsidised products to women with some capacity to pay, while priced products marketed for women's empowerment through pharmacies could encourage cost recovery with minimal reductions in coverage among employed women.

Mycobacterium tuberculosis and other non-tuberculous mycobacteria are responsible for a variety of different infections affecting millions of patients worldwide. Their diagnosis is often problematic and delayed until late in the course of disease, requiring a high index of suspicion and the combined efforts of clinical and laboratory colleagues. Molecular methods, such as PCR platforms, are available, but expensive, and with limited sensitivity in the case of paucibacillary disease. Treatment of mycobacterial infections is also challenging, typically requiring months of multiple and combined antibiotics, with associated side effects and toxicities. The presence of innate and acquired drug resistance further complicates the picture, with dramatic cases without effective treatment options. Bacteriophages (viruses that infect bacteria) have been used for decades in Eastern Europe for the treatment of common bacterial infections, but there is limited clinical experience of their use in mycobacterial infections. More recently, bacteriophages’ clinical utility has been re-visited and their use has been successfully demonstrated both as diagnostic and treatment options. This review will focus specifically on how mycobacteriophages have been used recently in the diagnosis and treatment of different mycobacterial infections, as potential emerging technologies, and as an alternative treatment option.

BackgroundFollowing success demonstrated with the HIV Self-Testing AfRica Initiative, HIV self-testing (HIVST) is being added to national HIV testing strategies in Southern Africa. An analysis of the costs of scaling up HIVST is needed to inform national plans, but there is a dearth of evidence on methods for forecasting costs at scale from pilot projects. Econometric cost functions (ECFs) apply statistical inference to predict costs; however, we often do not have the luxury of collecting large amounts of location-specific data. We fit an ECF to identify key drivers of costs, then use a simpler model to guide cost projections at scale.MethodsWe estimated the full economic costs of community-based HIVST distribution in 92 locales across Malawi, Zambia, Zimbabwe, South Africa and Lesotho between June 2016 and June 2019. We fitted a cost function with determinants related to scale, locales organisational and environmental characteristics, target populations, and per capita Growth Domestic Product (GDP). We used models differing in data intensity to predict costs at scale. We compared predicted estimates with scale-up costs in Lesotho observed over a 2-year period.ResultsThe scale of distribution, type of community-based intervention, percentage of kits distributed to men, distance from implementer’s warehouse and per capita GDP predicted average costs per HIVST kit distributed. Our model simplification approach showed that a parsimonious model could predict costs without losing accuracy. Overall, ECF showed a good predictive capacity, that is, forecast costs were close to observed costs. However, at larger scale, variations of programme efficiency over time (number of kits distributed per agent monthly) could potentially influence cost predictions.DiscussionOur empirical cost function can inform community-based HIVST scale-up in Southern African countries. Our findings suggest that a parsimonious ECF can be used to forecast costs at scale in the context of financial planning and budgeting.

Background\ud \ud Brazil has the second highest annual number of new leprosy cases. The aim of this study is to formally compare predictions of future new case detection rate (NCDR) trends and the annual probability of NCDR falling below 10/100,000 of four different modelling approaches in four states of Brazil: Rio Grande do Norte, Amazonas, Ceará, Tocantins.\ud \ud Methods\ud \ud A linear mixed model, a back-calculation approach, a deterministic compartmental model and an individual-based model were used. All models were fitted to leprosy data obtained from the Brazilian national database (SINAN). First, models were fitted to the data up to 2011, and predictions were made for NCDR for 2012–2014. Second, data up to 2014 were considered and forecasts of NCDR were generated for each year from 2015 to 2040. The resulting distributions of NCDR and the probability of NCDR being below 10/100,000 of the population for each year were then compared between approaches.\ud \ud Results\ud \ud Each model performed well in model fitting and the short-term forecasting of future NCDR. Long-term forecasting of NCDR and the probability of NCDR falling below 10/100,000 differed between models. All agree that the trend of NCDR will continue to decrease in all states until 2040. Reaching a NCDR of less than 10/100,000 by 2020 was only likely in Rio Grande do Norte. Prediction until 2040 showed that the target was also achieved in Amazonas, while in Ceará and Tocantins the NCDR most likely remain (far) above 10/100,000.\ud \ud Conclusions\ud \ud All models agree that, while incidence is likely to decline, achieving a NCDR below 10/100,000 by 2020 is unlikely in some states. Long-term prediction showed a downward trend with more variation between models, but highlights the need for further control measures to reduce the incidence of new infections if leprosy is to be eliminated.

Background: Low-dose computed tomography (CT) screening reduces lung cancer mortality but costs are prohibitive for most healthcare budgets due to high false positive rates. An adjunctive test able to distinguish malignant from benign pulmonary nodules would be hugely beneficial. EarlyCDT-Lung measures serum autoantibodies to tumor-associated antigens and has found clinical acceptance to aid early detection of lung cancer for high risk patients. However performance was optimized for screening. The construction of a receiver-operating characteristic (ROC) curve would enable optimization of performance for alternative settings, including nodule malignancy. Methods: A Monte-Carlo search method was used to construct a ROC curve using a case-control cohort, enabling high and low specificity versions of EarlyCDT-Lung to be determined. These were used for a theoretical evaluation of a nodule cohort, and positive predictive value (PPV) was calculated under the assumption of independence of risk source. Patients or their nodules are typically classified into three risk groups: low (0% - 10%), intermediate (10% - 65%) and high (>65%) risk of malignancy. The predicted shift in risk group by application of the high and low specificity versions, along with the current commercial EarlyCDT-Lung, was then estimated. Results: The ROC curve, with an area under the curve of 0.743, was constructed. The high specificity (98%), low specificity (49%) and current commercial (91% specificity) versions of EarlyCDT-Lung re-classified 27%, 23% and 26% of intermediate nodules, respectively, to either a higher (10%, 8% and 10%) or lower (17%, 15% and 16%) risk group. Conclusion: A ROC curve was constructed to allow performance prediction of EarlyCDT-Lung at different specificities in the indeterminate nodule setting. This enabled risk re-classification of intermediate risk nodules, and could therefore facilitate alternative more appropriate intervention. We have shown how a multivariate biomarker test can add to the interpretation of pulmonary nodules and therefore aid patient management.

Gastrointestinal anisakiasis is an uncommon zoonotic parasitic infection caused by consumption of raw or undercooked seafood infected with nematodes of genus Anisakis. Given the non-specific clinical presentation of acute abdomen, nausea, and vomiting these patients are often subject to radiologic imaging. We present ultrasound and computed tomography imaging features in a case of gastric anisakiasis demonstrating characteristic features of diffuse gastric submucosal edema, perigastric stranding and trace ascites that helped to further elaborate the clinical history of uncooked fish consumption prompting timely endoscopic diagnosis and management.

Persons living with HIV also experience other comorbidities, some of which are related to prolonged use of antiretroviral therapy. The increased burden of chronic conditions along with HIV infection can reduce quality of life. Two exploratory studies, conducted in Duval County, Jacksonville Florida, USA, pursued justification for development of a cumulative chronic disease severity index of common non-communicable diseases, which co-occurred with HIV. Study one used a sample of 121 client charts. Study two screened 96 HIV positive clients for nutritional risk using a patient care, disease-specific screening tool. Both studies relied on convenience sampling, were non-comparable, yet each provided evidence of poor metabolic health indicator. This shared finding portends risks for future health complications such as heart disease and stroke, among others. Given the excess burden of chronic diseases that exist in Duval County, strengthening the HIV health care system data coordination and collection infrastructure can facilitate the provision of patient centered care.

Background Human papillomavirus (HPV) is the most widespread sexually transmitted infection worldwide. It causes several health consequences, in particular accounting for the majority of cervical cancer cases in women. In the United Kingdom, a vaccination campaign targeting 12-year-old girls started in 2008; this campaign has been successful, with high uptake and reduced HPV prevalence observed in vaccinated cohorts. Recently, attention has focused on vaccinating both sexes, due to HPV-related diseases in males (particularly for high-risk men who have sex with men) and an equity argument over equalising levels of protection. Methods We constructed an epidemiological model for HPV transmission in the UK, accounting for nine of the most common HPV strains. We complemented this with an economic model to determine the likely health outcomes (healthcare costs and quality-adjusted life years) for individuals from the epidemiological model. We then tested vaccination with the three HPV vaccines currently available, vaccinating either girls alone or both sexes. For each strategy we calculated the threshold price per vaccine dose, i.e. the maximum amount paid for the added health benefits of vaccination to be worth the cost of each vaccine dose. We calculated results at 3.5% discounting, and also 1.5%, to consider the long-term health effects of HPV infection. Results At 3.5% discounting, continuing to vaccinate girls remains highly cost-effective compared to halting vaccination, with threshold dose prices of £56-£108. Vaccination of girls and boys is less cost-effective (£25-£53). Compared to vaccinating girls only, adding boys to the programme is not cost-effective, with negative threshold prices (-£6 to -£3) due to the costs of administration. All threshold prices increase when using 1.5% discounting, and adding boys becomes cost-effective (£36-£47). These results are contingent on the UK’s high vaccine uptake; for lower uptake rates, adding boys (at the same uptake rate) becomes more cost effective. Conclusions Vaccinating girls is extremely cost-effective compared with no vaccination, vaccinating both sexes is less so. Adding boys to an already successful girls-only programme has a low cost-effectiveness, as males have high protection through herd immunity. If future health effects are weighted more heavily, threshold prices increase and vaccination becomes cost-effective. Electronic supplementary material The online version of this article (10.1186/s12879-019-4108-y) contains supplementary material, which is available to authorized users.

Graphical abstract, Introduction Respiratory syncytial virus (RSV) causes a significant respiratory disease burden in the under 5 population. The transmission pathway to young children is not fully quantified in low-income settings, and this information is required to design interventions. Methods We used an individual level transmission model to infer transmission parameters using data collected from 493 individuals distributed across 47 households over a period of 6 months spanning the 2009/2010 RSV season. A total of 208 episodes of RSV were observed from 179 individuals. We model competing transmission risk from within household exposure and community exposure while making a distinction between RSV groups A and B. Results We find that 32–53% of all RSV transmissions are between members of the same household; the rate of pair-wise transmission is 58% (95% CrI: 30–74%) lower in larger households (≥8 occupants) than smaller households; symptomatic individuals are 2–7 times more infectious than asymptomatic individuals i.e. 2.48 (95% CrI: 1.22–5.57) among symptomatic individuals with low viral load and 6.7(95% CrI: 2.56–16) among symptomatic individuals with high viral load; previous infection reduces susceptibility to re-infection within the same epidemic by 47% (95% CrI: 17%–68%) for homologous RSV group and 39% (95%CrI: -8%-69%) for heterologous group; RSV B is more frequently introduced into the household, and RSV A is more rapidly transmitted once in the household. Discussion Our analysis presents the first transmission modelling of cohort data for RSV and we find that it is important to consider the household social structuring and household size when modelling transmission. The increased infectiousness of symptomatic individuals implies that a vaccine against RSV related disease would also have an impact on infection transmission. Together, the weak cross immunity between RSV groups and the possibility of different transmission niches could form part of the explanation for the group co-existence.

We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3–4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5–13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to, Through an intensive, active surveillance of human rhinovirus (HRV) in households, we observed continuous invasion and high diversity of HRV. Individual repeat infections were frequent, decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection.

Background There is no safe level of lead in children's bodies. The US Centers for Disease Control and Prevention (CDC) estimate that more than half a million children under the age of 6 years are affected by low-level lead exposure in the USA. Low levels of lead can cause irreversible neurological and physiological damage in children. Currently, lead is investigated in the home and environment after a child has been identified as having elevated concentrations of lead in their blood; the source of lead exposure is then sought and removed. However, we seek to reverse this paradigm and allow families to engage in prevention by testing their home and environment before their child is exposed to lead. The aim of this study was to design and pilot a screening device to allow families to test their homes for lead. Methods We recruited participants for this blinded case-control study in Saint Joseph County, Indiana, USA, through community partnerships, a community lead testing event, and flyers. Participants were divided into three groups based on the age of their home: homes built before 1950; homes built between 1951 and 1978; and homes built after 1978. The post-1978 group acted as a control because lead paint was banned in 1978. Participants collected eight samples from their homes, including from soil, dust, and paint. The field team measured the concentration of lead levels in each of the eight samples at the site of collection using an X-ray fluorescence analyser. Samples were then tested at the laboratory where all identifying information was removed and workers were unaware of the age of the home the samples came from. Results from the field were then correlated with results from the laboratory using Bland-Altman plots, linear regression, and ROC curves. Informed consent was obtained and this study was approved by the University of Notre Dame Institutional Review Board. Findings We included results from 45 homes in the analysis: 17 from pre-1950 homes, 11 from 1951–78 homes; and 17 from post-1978 houses. Of the 17 pre-1950 homes, 94% had at least one finding of a lead concentration that exceeded the action level laid out by the US Environmental Protection Agency. Of the 11 1951–78 homes, 36% (4) had at least one elevated lead result, and none of the 1978 homes had an elevated lead result. Bland-Altman plot analysis showed good agreement between onsite and laboratory measurement with biases very close to zero. Correlation coefficients between field and laboratory measurements were 0·97, 0·89, and 0·92 for the soil, dust, and paint samples, respectively. The ROC curves show high sensitivity (87%), specificity (98%), and accuracy (96%). At the time of the study, the cost of the kit was approximately US$7.00, excluding laboratory fees. Interpretation This study lays the foundation for the creation of a lead sample collection kit model that can be implemented in homes, day-care centres, and schools. Although this model will not provide the participant with an in-depth lead risk assessment, it has the potential to be a tool to allow proactive screening of homes for environmental lead hazards. Our team will now work to scale up implementation with our community partners. Our goal is to distribute and test 500 kits in 2019. Funding A local private donor.