Impact of the addition of azithromycin to antimalarials used for seasonal malaria chemoprevention on antimicrobial resistance of Streptococcus pneumoniae.

OBJECTIVE: A trial was conducted in Burkina Faso and Mali to investigate whether addition of azithromycin to the antimalarials used for seasonal malaria chemoprevention reduces mortality and hospital admissions of children. We tested the sensitivity of nasal isolates of Streptococcus pneumoniae obtained during this trial to azithromycin and other antibiotics. METHODS: Azithromycin or placebo was administered monthly, in combination with the antimalarials used for seasonal malaria chemoprevention, for four months, over the annual malaria transmission seasons of 2014, 2015, and 2016. Nasopharyngeal swabs were collected from 2773 Burkinabe and 2709 Malian children on seven occasions: in July and December each year prior to and after drug administration, and at a final survey in early 2018. Pneumococci were isolated from nasopharyngeal swabs and tested for sensitivity to azithromycin and other antibiotics. RESULTS: A total of 5482 samples were collected. In Burkina Faso, the percentage of pneumococcal isolates resistant to azithromycin among children who had received it increased from 4.9% (95% CI: 2.4%, 9.9%) before the intervention to 25.6% (95% CI: 17.6%, 35.7%) afterward. In Mali, the increase was from 7.6% (95% CI: 3.8%, 14.4%) to 68.5% (95% CI: 55.1%, 79.4%). The percentage of resistant isolates remained elevated (17.7% (95% CI: 11.1%, 27.1%) in Burkina Faso and 19.1% (95% CI: 13.5%, 26.3%) in Mali) among children who had received azithromycin 1 year after stopping the intervention. An increase in resistance to azithromycin was also observed in children who had received a placebo but it was less marked. CONCLUSION: Addition of azithromycin to the antimalarial combination used for seasonal malaria chemoprevention was associated with an increase in resistance of pneumococci to azithromycin and erythromycin, which persisted 1 year after the last administration of azithromycin

Standardization of Laboratory Methods for the PERCH Study.

The Pneumonia Etiology Research for Child Health study was conducted across 7 diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1-59 months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal and external quality assurance testing. Targeted confirmatory testing and testing by specialized assays were done at a central reference laboratory

Colonization Density of the Upper Respiratory Tract as a Predictor of Pneumonia-Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii.

BACKGROUND.: There is limited information on the association between colonization density of upper respiratory tract colonizers and pathogen-specific pneumonia. We assessed this association for Haemophilus influenzae, Moraxella catarrhalis, Staphylococcus aureus, and Pneumocystis jirovecii. METHODS.: In 7 low- and middle-income countries, nasopharyngeal/oropharyngeal swabs from children with severe pneumonia and age-frequency matched community controls were tested using quantitative polymerase chain reaction (PCR). Differences in median colonization density were evaluated using the Wilcoxon rank-sum test. Density cutoffs were determined using receiver operating characteristic curves. Cases with a pathogen identified from lung aspirate culture or PCR, pleural fluid culture or PCR, blood culture, and immunofluorescence for P. jirovecii defined microbiologically confirmed cases for the given pathogens. RESULTS.: Higher densities of H. influenzae were observed in both microbiologically confirmed cases and chest radiograph (CXR)-positive cases compared to controls. Staphylococcus aureus and P. jirovecii had higher densities in CXR-positive cases vs controls. A 5.9 log10 copies/mL density cutoff for H. influenzae yielded 86% sensitivity and 77% specificity for detecting microbiologically confirmed cases; however, densities overlapped between cases and controls and positive predictive values were poor (<3%). Informative density cutoffs were not found for S. aureus and M. catarrhalis, and a lack of confirmed case data limited the cutoff identification for P. jirovecii. CONCLUSIONS.: There is evidence for an association between H. influenzae colonization density and H. influenzae-confirmed pneumonia in children; the association may be particularly informative in epidemiologic studies. Colonization densities of M. catarrhalis, S. aureus, and P. jirovecii are unlikely to be of diagnostic value in clinical settings

Standardization of laboratory methods for the PERCH study

The Pneumonia Etiology Research for Child Health study was conducted across diverse research sites and relied on standardized clinical and laboratory methods for the accurate and meaningful interpretation of pneumonia etiology data. Blood, respiratory specimens, and urine were collected from children aged 1-5months hospitalized with severe or very severe pneumonia and community controls of the same age without severe pneumonia and were tested with an extensive array of laboratory diagnostic tests. A standardized testing algorithm and standard operating procedures were applied across all study sites. Site laboratories received uniform training, equipment, and reagents for core testing methods. Standardization was further assured by routine teleconferences, in-person meetings, site monitoring visits, and internal

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Les ligneux à usages multiples dans les jachères et les champs du Plateau Central du Burkina Faso

In Burkina Faso, the central plateau region is part of the North Sudan agro- sylvo-pastoral system. Most of the vegetation in this system is found in fallows of various ages. Consequently, fallows play an important role in local production (hunting, collecting, tilling). Semi-structured questionnaires of land users were used to collect data in order to evaluate the perception and usage of woody plants found in fallows and fields. The study shows the existence of 38 multi-purpose woody plants.Six species were common to all of the provinces studied : Adansonia digitata, Lannea microcarpa., Tamarindus indica, Bombax costatum, Parkia biglobosa (néré), and Butyrospermum paradoxum (Shea tree), the most abundant woody plants were always Butyrospermum paradoxum and Parkia biglobosa.. Fodder species are found in all provinces although they are used differently. All fodder plants but only 25% of the fruit species are used directly, while the remaining 75% are sold before or after transformation.Le Plateau central appartient au système agro-sylvo-pastoral nord soudanien du Burkina Faso. Les jachères qu'on y trouve ont des âges divers et jouent un rôle important dans la production (cueillette, chasse, cultures). Les enquêtes par questionnaires semi-structures ont appréhendé la perception et l'utilisation des ligneux dans les champs et les jachères. Elles portent sur 38 ligneux à usages multiples dont 6 se rencontrent dans toutes les provinces. Il s'agit de Adansonia digit ata (Baobab), Lannea microcarpa (Raisinier), Tamarindus indica (Tamarinier), Bombax costatum (Kapokier), Parkia biglobosa (Néré) et Butyrospermum paradoxum (Karité), ces deux dernières espèces étant les plus employées. Beaucoup d'espèces ont un intérêt alimentaire pour le bétail et se rencontrent dans toutes les provinces mais leur intensité d'utilisation diffère d'un lieu à l'autre. Si toutes les productions ligneuses fourragères sont directement utilisées, seulement 25% des espèces fruitières le sont, les 75% autres étant vendues directement ou après transformation.Belem Mamounata, Bognounou Ouétian, Ouedraogo Sibiri Jean, Maiga Abdoul Aziz. Les ligneux à usages multiples dans les jachères et les champs du Plateau Central du Burkina Faso. In: Journal d'agriculture traditionnelle et de botanique appliquée, 38ᵉ année, bulletin n°1,1996. "Biodiversité, friches et jachères" sous la direction de Bernard Roussel, Claude Sastre et Paul Arnould. pp. 251-272

First report of V1016I, F1534C and V410L kdr mutations associated with pyrethroid resistance in Aedes aegypti populations from Niamey, Niger

Background: Ae. aegypti is the vector of important μ arboviruses, including dengue, Zika, chikungunya and yellow fever. Despite not being specifically targeted by insecticide-based control programs in West Africa, resistance to insecticides in Ae. aegypti has been reported in countries within this region. In this study, we investigated the status and mechanisms of Ae. aegypti resistance in Niamey, the capital of Niger. This research aims to provide baseline data necessary for arbovirus outbreak prevention and preparedness in the country. Methods: Ovitraps were used to collect Ae. aegypti eggs, which were subsequently hatched in the insectary for bioassay tests. The hatched larvae were then reared to 3–5-day-old adults for WHO tube and CDC bottle bioassays, including synergist tests. The kdr mutations F1534C, V1016I, and V410L were genotyped using allele-specific PCR and TaqMan qPCR methods. Results: Ae. aegypti from Niamey exhibited moderate resistance to pyrethroids but susceptibility to organophosphates and carbamates. The kdr mutations, F1534C, V1016I and V410L were detected with the resistant tri-locus haplotype 1534C+1016L+410L associated with both permethrin and deltamethrin resistance. Whereas the homozygote tri-locus resistant genotype 1534CC+1016LL+410LL was linked only to permethrin resistance. The involvement of oxidase and esterase enzymes in resistance mechanisms was suggested by partial restoration of mosquitoes’ susceptibility to pyrethroids in synergist bioassays. Conclusion: This study is the first report of Ae. aegypti resistance to pyrethroid insecticides in Niamey. The resistance is underpinned by target site mutations and potentially involves metabolic enzymes. The observed resistance to pyrethroids coupled with susceptibility to other insecticides, provides data to support evidence-based decision-making for Ae. aegypti control in Niger

Insecticide resistance in Anopheles gambiae sensu lato (Diptera: Culicidae) across different agroecosystems in Niamey, Niger

International audienceMalaria vector control in Niger is currently based on the distribution of insecticide treated nets. However, vectors resistance to insecticides represents a major threat to the current national strategy against malaria. This study aims to characterize the impact of agroecosystems on insecticide resistance in Anopheles gambiae s.l. at Niamey. Larvae collected were reared until emergence. Adults aged 2-5 days were used to assess susceptibility to insecticides (pyrethroids, DDT and bendiocarb) after pre-exposure to piperonyl butoxide (PBO) synergist according to WHO protocols. PCRs were performed to identify the sibling species of An. gambiae complex and characterization resistance mutations (Kdr and ace-1). Overall, An. gambiae s.l. was resistance to pyrethroids and DDT (mortality rates from 1% to 55%) and susceptible to bendiocarb at most sites. Pre-exposure to the PBO synergist resulted in partial restoration of pyrethroid susceptibility. Two species of An. gambiae complex were found: An. arabiensis and An. coluzzii. The presence of An. coluzzii was strongly correlated with agricultural practices (99% in rice cultivation sites). Kdr mutations were found at all sites with kdr-w ranging from 45% to 70% in mosquitoes collected in unirrigated and rice field, respectively, and kdr-e found at 37% to 47% at each type of site, respectively. The ace-1 mutation was detected at low frequency (1%) and only from two rice cultivation sites. The high levels of pyrethroid and DDT resistance detected in Niamey had a strong link with rice cultivation, shown that agriculture is a driver of resistance that can compromise control malaria efforts