Post-deployment effectiveness of malaria control interventions on Plasmodium infections in Madagascar: a comprehensive phase IV assessment

Additional file 1. Definition of variables

Detection of co-infection and recombination cases with Omicron and local Delta variants of SARS-CoV-2 in Vietnam

The first nationwide outbreak of COVID-19 in Vietnam started in late April 2021 and was caused almost exclusively by a single Delta lineage, AY.57. In early 2022, multiple Omicron variants co-circulated with Delta variants and quickly became dominant. The co-circulation of Delta and Omicron happened leading to possibility of co-infection and recombination events which can be revealed by viral genomic data. From January to October 2022, a total of 1028 viral RNA samples out of 4852 positive samples (Ct < 30) were sequenced by the long pooled amplicons method on Illumina platforms. All sequencing data was analysed by the workflow for SARS-CoV-2 on CLC genomics workbench and Illumina Dragen Covid application. Among those sequenced samples, we detected a case of Delta AY.57/Omicron BA.1 co-infection and two cases of infection with Delta AY.57/Omicron BA.2 recombinants which were nearly identical and had different epidemiological characteristics. Since the AY.57 lineage circulated almost exclusively in Vietnam, these results strongly suggest domestic events of co-infection and recombination. These findings highlight the strengths of genomic surveillance in monitoring the circulating variants in the community enabling rapid identification of viral changes that may affect viral properties and evolutionary events

Apramycin susceptibility of multidrug-resistant Gram-negative blood culture isolates in five countries in South-East Asia

Bloodstream infections (BSIs) are a leading cause of sepsis, a life-threatening condition that contributes significantly to the mortality of bacterial infections. Aminoglycoside antibiotics such as gentamicin or amikacin are essential medicines in the treatment of BSIs, but their clinical efficacy is increasingly compromised by antimicrobial resistance. The aminoglycoside apramycin has demonstrated preclinical efficacy against aminoglycoside- and multidrug-resistant (MDR) Gram-negative bacilli (GNB) and is currently in clinical development for the treatment of critical systemic infections. Here, we collected a panel of 470 MDR GNB isolates from health care facilities in Cambodia, Laos, Singapore, Thailand, and Vietnam for a multi-centre assessment of their antimicrobial susceptibility to apramycin in comparison to other aminoglycosides and colistin by broth microdilution assays. Apramycin and amikacin MICs ≤ 16 µg/mL were found for 462 (98.3%) and 408 (86.8%) GNB isolates, respectively. Susceptibility to gentamicin and tobramycin (MIC ≤ 4 µg/mL) was significantly lower at 122 (26.0%) and 101 (21.5%) susceptible isolates, respectively. Of note, all carbapenem- and third-generation cephalosporin (3GC) resistant Enterobacterales, all Acinetobacter baumannii, and all Pseudomonas aeruginosa isolates tested in this study appeared to be susceptible to apramycin. Of the 65 colistin-resistant isolates tested, only four (6.2%) had an apramycin MIC > 16 µg/mL. Apramycin demonstrated best-in-class activity against a panel of GNB isolates with resistances to other aminoglycosides, carbapenems, 3GC, and colistin, warranting continued consideration of apramycin as a drug candidate for the treatment of multidrug-resistant BSIs. Keywords: Bloodstream infection; Gram negative; aminoglycoside; antimicrobial resistance; apramycin; blood culture isolates

Investigating Pneumonia Etiology Among Refugees and the Lebanese population (PEARL): A study protocol

Background: Community-acquired pneumonia (CAP), a leading cause of mortality, mainly affects children in developing countries. The harsh circumstances experienced by refugees include various factors associated with respiratory pathogen transmission, and clinical progression of CAP. Consequently, the etiology of CAP in humanitarian crisis situations may differ to that of settled populations, which would impact appropriate case management. Therefore, the Pneumonia Etiology Among Refugees and the Lebanese population (PEARL) study was initiated with the objective of identifying the causal pathogenic microorganisms in the respiratory tract of children and adults from both the refugee and host country population presenting with signs of CAP during a humanitarian crisis. Methods: PEARL, a prospective, multicentric, case-control study, will be conducted at four primary healthcare facilities in Tripoli and the Bekaa valley over 15 months (including two high-transmission seasons/winters). Sociodemographic and medical data, and biological samples will be collected from at least 600 CAP cases and 600 controls. Nasopharyngeal swabs, sputum, urine and blood samples will be analyzed at five clinical pathology laboratories in Lebanon to identify the bacterial and viral etiological agents of CAP. Transcriptomic profiling of host le

Spatiotemporal evolution of SARS-CoV-2 Alpha and Delta variants during large nationwide outbreak of COVID-19, Vietnam, 2021

We analyzed 1,303 SARS-CoV-2 whole-genome sequences from Vietnam, and found the Alpha and Delta variants were responsible for a large nationwide outbreak of COVID-19 in 2021. The Delta variant was confined to the AY.57 lineage and caused >1.7 million infections and >32,000 deaths. Viral transmission was strongly affected by nonpharmaceutical interventions

The seeds of divergence: the economy of French North America, 1688 to 1760

Generally, Canada has been ignored in the literature on the colonial origins of divergence with most of the attention going to the United States. Late nineteenth century estimates of income per capita show that Canada was relatively poorer than the United States and that within Canada, the French and Catholic population of Quebec was considerably poorer. Was this gap long standing? Some evidence has been advanced for earlier periods, but it is quite limited and not well-suited for comparison with other societies. This thesis aims to contribute both to Canadian economic history and to comparative work on inequality across nations during the early modern period. With the use of novel prices and wages from Quebec—which was then the largest settlement in Canada and under French rule—a price index, a series of real wages and a measurement of Gross Domestic Product (GDP) are constructed. They are used to shed light both on the course of economic development until the French were defeated by the British in 1760 and on standards of living in that colony relative to the mother country, France, as well as the American colonies. The work is divided into three components. The first component relates to the construction of a price index. The absence of such an index has been a thorn in the side of Canadian historians as it has limited the ability of historians to obtain real values of wages, output and living standards. This index shows that prices did not follow any trend and remained at a stable level. However, there were episodes of wide swings—mostly due to wars and the monetary experiment of playing card money. The creation of this index lays the foundation of the next component. The second component constructs a standardized real wage series in the form of welfare ratios (a consumption basket divided by nominal wage rate multiplied by length of work year) to compare Canada with France, England and Colonial America. Two measures are derived. The first relies on a “bare bones” definition of consumption with a large share of land-intensive goods. This measure indicates that Canada was poorer than England and Colonial America and not appreciably richer than France. However, this measure overestimates the relative position of Canada to the Old World because of the strong presence of land-intensive goods. A second measure is created using a “respectable” definition of consumption in which the basket includes a larger share of manufactured goods and capital-intensive goods. This second basket better reflects differences in living standards since the abundance of land in Canada (and Colonial America) made it easy to achieve bare subsistence, but the scarcity of capital and skilled labor made the consumption of luxuries and manufactured goods (clothing, lighting, imported goods) highly expensive. With this measure, the advantage of New France over France evaporates and turns slightly negative. In comparison with Britain and Colonial America, the gap widens appreciably. This element is the most important for future research. By showing a reversal because of a shift to a different type of basket, it shows that Old World and New World comparisons are very sensitive to how we measure the cost of living. Furthermore, there are no sustained improvements in living standards over the period regardless of the measure used. Gaps in living standards observed later in the nineteenth century existed as far back as the seventeenth century. In a wider American perspective that includes the Spanish colonies, Canada fares better. The third component computes a new series for Gross Domestic Product (GDP). This is to avoid problems associated with using real wages in the form of welfare ratios which assume a constant labor supply. This assumption is hard to defend in the case of Colonial Canada as there were many signs of increasing industriousness during the eighteenth and nineteenth centuries. The GDP series suggest no long-run trend in living standards (from 1688 to circa 1765). The long peace era of 1713 to 1740 was marked by modest economic growth which offset a steady decline that had started in 1688, but by 1760 (as a result of constant warfare) living standards had sunk below their 1688 levels. These developments are accompanied by observations that suggest that other indicators of living standard declined. The flat-lining of incomes is accompanied by substantial increases in the amount of time worked, rising mortality and rising infant mortality. In addition, comparisons of incomes with the American colonies confirm the results obtained with wages— Canada was considerably poorer. At the end, a long conclusion is provides an exploratory discussion of why Canada would have diverged early on. In structural terms, it is argued that the French colony was plagued by the problem of a small population which prohibited the existence of scale effects. In combination with the fact that it was dispersed throughout the territory, the small population of New France limited the scope for specialization and economies of scale. However, this problem was in part created, and in part aggravated, by institutional factors like seigneurial tenure. The colonial origins of French America’s divergence from the rest of North America are thus partly institutional

Evaluation of the effectiveness of malaria control interventions in Madagascar

Afin de guider les politiques de santé publique, il semble intéressant de vérifier l’efficacité des actions de lutte contre le paludisme (ALP). Pour ce faire, l’on tend à évaluer l’impact d’une ALP sur l’incidence de la maladie par exemple, mais cette approche permet difficilement d’isoler l’effet d’une ALP par rapport aux autres interventions déployées simultanément, et par rapport aux interférences environnementales et sociales. La modélisation mathématique est également d’un recours limité puisqu’elle établit des inférences à partir de l’efficacité théorique de l’intervention (efficacy en anglais) mesurée au cours d’essais contrôlés. La mesure directe de l’efficacité de l’intervention sur le terrain (effectiveness en anglais), c’est-à-dire sous l’influence de facteurs biologiques, environnementaux et humains, est cependant possible. En particulier, des enquêtes épidémiologiques appropriées permettent de mesurer l’association entre l’exposition aux ALP et le poids du paludisme.Dans le cadre de cette thèse, plusieurs études de ce type ont été menées pour évaluer l’effectiveness des ALP à Madagascar. Ce pays a l’avantage de présenter un contraste important en terme de transmission du paludisme, certaines parties étant en phase de pré-élimination et d’autres présentant une transmission du paludisme intense et continue. (...)Ce travail de thèse propose une méthodologie d’évaluation de l’effectiveness des ALP transposable dans d’autres contextes, et démontre l’utilité de cette approche. Dans un contexte mondial où les financements internationaux stagnent, ces résultats apportent des informations et outils utiles pour poursuivre la lutte contre le paludisme.In order to guide policy making in public health, it seems useful to confirm the effectiveness of malaria control interventions (MCI). To achieve this, one may evaluate the impact of a given MCI on the incidence of the disease, for example, but this approach won’t easily disentangle the effects of the intervention from those of other MCIs deployed simultaneously, and from influences of environmental and social factors. Mathematical modelling won’t be helpful in this purpose since it infers the impact from the efficacy measured in controlled trials. The direct estimation of the effectiveness of the intervention under fields conditions, i.e. under the influence of biological, environmental and human factors, is nevertheless possible. In particular, appropriate epidemiological surveys can estimate the association between exposure to MCIs and malaria.The present thesis describes the results of several studies conducted to evaluate the effectiveness of MCIs in Madagascar. This country has the advantage to include constrasted malaria transmission patterns, with areas earmarked for pre-elimination and others with intense and perennial malaria transmission. (...)Overall this thesis proposes a methodology for the evaluation of the effectiveness of MCIs that can be transferred to other settings, and demonstrates the usefulness of this approach. In a global context of stagnating international funding, these results provide valuable information and tools to carry on the fight against malaria