Publications by authors named "Cheikh Sokhna"

191 Publications

COVID-19-related attitudes, risk perceptions, preventive behaviours and economic impact in sub-Saharan African countries: implementing a longitudinal phone-based survey protocol in rural Senegalese households.

BMJ Open 2021 07 16;11(7):e050090. Epub 2021 Jul 16.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.

Introduction: Rural areas are considered safe havens against the increased spread of COVID-19 and associated restrictive measures, especially in contexts where public authorities are not in a position to systematically and substantially ease COVID-19-induced economic shocks. In the current sub-Saharan Africa context, still marked by uncertainty surrounding the spread of COVID-19, we present the protocol of an ongoing longitudinal study aimed at investigating COVID-19-related attitudes, risks perceptions, preventive behaviours and economic impact in rural areas in Senegal.

Methods And Analysis: A prospective randomised longitudinal study of 600 households located in three semiurban villages and nine randomly selected rural villages in the Niakhar area (located 135 km East of Dakar). Three ad hoc phone surveys are administered to 600 heads of households, their housewives in charge of managing the household and a relative living temporarily in the household, respectively. In addition to sharing identical sets of questions on several topics (risks perceptions, attitudes to curfew, attitudes to vaccines, beliefs about COVID-19 infection), the three separate survey questionnaires also include other topics (economic impact, local preventive strategies) whose related questions differ between questionnaires. As analysing evolutions is the study's primary focus, data on all the topics covered will be collected in three waves unless the spread of COVID-19 by mid-2021 justifies extending data collection. The present article presents the study protocol and details about the implementation of the first wave of data collection which started in July 2020. The decision to wait before presenting the protocol was based on the unprecedented context the COVID-19 pandemic.

Ethics And Dissemination: The survey's protocol was approved by the Senegalese National Ethical Committee for Research in Health (131/MSAS/CNERS/Sec) and received authorisation from both the Senegalese Ministry of Health (619/MSAS/DPRS/DR) and the French Commission on Information Technology and Liberties (CNIL 2220771).
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http://dx.doi.org/10.1136/bmjopen-2021-050090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8288240PMC
July 2021

Bacterial Infections in Humans and Nonhuman Primates from Africa: Expanding the Knowledge.

Yale J Biol Med 2021 Jun 30;94(2):227-248. Epub 2021 Jun 30.

IHU Méditerranée Infection, Marseille, France.

The close phylogenetic relationship between humans and other primates creates exceptionally high potential for pathogen exchange. The surveillance of pathogens in primates plays an important role in anticipating possible outbreaks. In this study, we conducted a molecular investigation of pathogenic bacteria in feces from African nonhuman primates (NHPs). We also investigated the pathogens shared by the human population and gorillas living in the same territory in the Republic of Congo. In total, 93% of NHPs (n=176) and 95% (n=38) of humans were found to carry at least one bacterium. Non- spp. (including , , and several potential new species) were recovered from stools of 70% of great apes, 88% of monkeys, and 79% of humans. Non- spp. were also common in almost all NHP species as well as in humans. In addition, spp., members of the primate gut microbiota, were mainly prevalent in human and gorilla. Pathogenic spp. were highly present in humans (82%) and gorillas (66%) stool samples in Congo, but were absent in the other NHPs, therefore suggesting a possible gorillas-humans exchange. Particular attention will be necessary for enteropathogenic bacteria detected in humans such as , spp. (including ), , and , some of which were also present in gorillas in the same territory ( and ). This study enhances our knowledge of pathogenic bacteria that threaten African NHPs and humans by using a non-invasive sampling technique. Contact between humans and NHPs results in an exchange of pathogens. Ongoing surveillance, prevention, and treatment strategies alone will limit the spread of these infectious agents.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8223552PMC
June 2021

A Listeria monocytogenes clone in human breast milk associated with severe acute malnutrition in West Africa: A multicentric case-controlled study.

PLoS Negl Trop Dis 2021 Jun 29;15(6):e0009555. Epub 2021 Jun 29.

IHU-Méditerranée Infection, Marseille, France.

Background: Severe acute malnutrition (SAM) is a major public health problem affecting children under the age of five in many low- and middle-income countries, and its resolution would contribute towards achieving the several sustainable development goals. The etiology of SAM is pluri-factorial, including delayed maturation of the gut microbiota, suboptimal feeding practices and dysfunctional breastfeeding. The recent serendipitous detection of Listeria monocytogenes in the breast milk of Malian women, in contrast to French women, suggests a possible association with SAM.

Methodology/ Principal Findings: To investigate the possible association of L. monocytogenes carriage in breast milk and SAM, a case-control study was performed in Senegal, with subjects recruited from two areas. Using 16S amplicon sequencing, a culture independent method, 100% (152/152) of the mothers were positive for L. monocytogenes in their breast milk while qPCR analysis gave lower recovery rates. Interestingly, after enrichment in Fraser broth and seeding on PALCALM agar, all 10 isolated strains were isolated from the milk of 10 mothers who had SAM children which also had a significantly increased relative abundance of L. monocytogenes (0.34 (SD 0.35) vs 0.05 (SD 0.07) in controls, p<0.0001). The high genomic similarity between these strains and Malian breast milk strains from a previous study supports the hypothesis of endemic clone carriage in West Africa. Moreover, the in vitro growth inhibition of L. monocytogenes using breast milk samples was obtained from only 50% of the milk of mothers who had SAM children, in contrast to control samples which systematically inhibited the growth of L. monocytogenes with a higher inhibition diameter (15.7 mm (SD 2.3) in controls versus 3.5 mm (SD 4.6) in SAM, p = 0.0001). Lactobacillus and Streptococcus isolated from the breast milk of controls inhibit L. monocytogenes in a species-dependent manner.

Conclusions/significance: Our study reveals a previously unsuspected carriage of L. monocytogenes in the breast milk of West African women, which is associated with SAM. The inhibitory effect of human selected lactic acid bacterial species against L. monocytogenes might provide new therapeutic and inexpensive options to prevent and treat this neglected public health issue.
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http://dx.doi.org/10.1371/journal.pntd.0009555DOI Listing
June 2021

Multidrug-resistant clones from wild chimpanzees and termites in Senegal.

Antimicrob Agents Chemother 2021 Jun 21:AAC0255720. Epub 2021 Jun 21.

Aix Marseille Univ, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, 19-21 Boulevard Jean Moulin, 13385 Marseille CEDEX 05, France.

Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant a common pathogen of chimpanzees and humans. We screened antibiotic-resistant from 48 chimpanzee stools and 38 termite mounds (N=415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (N=13). Whole genome sequencing was performed on complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The and the genes were carried by international pOXA-48 and pKPC-2 plasmids respectively. The ESBL plasmid carried , and genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.
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http://dx.doi.org/10.1128/AAC.02557-20DOI Listing
June 2021

Respiratory infections among pilgrims at the Grand Magal of Touba: A comparative cohort controlled survey.

Travel Med Infect Dis 2021 Jun 4;43:102104. Epub 2021 Jun 4.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

Background: The Grand Magal of Touba (GMT) is a large event gathering around 4-5 million participants every year. A pilot study conducted in 2017 among GMT pilgrims showed that 41.8% of participants reported respiratory symptoms, mostly due to rhinovirus (13.0%), coronaviruses (16.0%) and adenovirus (4.6%).

Methods: A PCR-based prospective cohort study was conducted among GMT pilgrims and controls (who did not participate to the event) in two rural villages in South Senegal, in 2019.

Results: 93 pilgrims and 84 controls were included in the study. There were no significant differences between pilgrims and controls regarding demographic characteristics and chronic conditions. 60.2% of pilgrims reported respiratory symptoms during their stay in Touba, or soon after their return. By contrast, only 8.3% of controls reported respiratory symptoms after the GMT. The acquisition of rhinovirus, coronaviruses, Streptococcus pneumoniae and Moraxella catarrhalis was 22.6%, 6.5%, 17.2% and 6.8% respectively in pilgrims and was significantly higher than in controls (3.6%, 0%, 4.8% and 1.2% respectively). Respiratory symptoms post-GMT were five times more frequent in S. pneumoniae carriers (aOR = 5.18, 95%CI = [1.98-13.57]).

Conclusion: This study demonstrates that individuals who participated in the GMT were at higher risk of suffering from respiratory symptoms and that this was linked to the acquisition of S. pneumoniae.
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http://dx.doi.org/10.1016/j.tmaid.2021.102104DOI Listing
June 2021

The Costs of Introducing the Hepatitis B Birth Dose Vaccine into the National Immunization Programme in Senegal (NéoVac Study).

Vaccines (Basel) 2021 May 18;9(5). Epub 2021 May 18.

Aix Marseille Univ, INSERM, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, ISSPAM, 13385 Marseille, France.

Some African countries are still reluctant to introduce the hepatitis B vaccine birth dose (HepB-BD) into their expanded program of immunization (EPI), partly because of logistical, economic, and cost information constraints. To assist decision-makers in these countries, we assessed the economic and financial costs of HepB-BD introduction in Senegal in 2016. We performed a micro-costing study in a representative sample of Senegal's EPI sites at all levels in 2018. Information on EPI and HepB-BD activity-related inputs and costs was collected using standardized questionnaires and semi-structured interviews. Using inverse probability weighting, we computed weighted average costs associated with HepB-BD introduction for each EPI level, country-level aggregated costs and estimated costs per newborn. Economic and financial costs from a government perspective were estimated in US dollars for 2015, 2016 and 2017. Total economic costs were USD 143,364 in 2015, USD 759,406 in 2016 and USD 867,311 in 2017, while financial costs were USD 127,745, USD 82,519 and USD 29,853, respectively. When annualizing pre-introduction and initial training costs, the economic (financial) cost per vaccinated newborn was USD 2.10 (USD 0.30) in 2016 and USD 1.90 (USD 0.20) in 2017. Our estimates provide valuable information to implement HepB-BD in Sub-Saharan African countries that have not yet integrated this vaccine.
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http://dx.doi.org/10.3390/vaccines9050521DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8158493PMC
May 2021

Hepatitis B Vaccination in Senegalese Children: Coverage, Timeliness, and Sociodemographic Determinants of Non-Adherence to Immunisation Schedules (ANRS 12356 AmBASS Survey).

Vaccines (Basel) 2021 May 15;9(5). Epub 2021 May 15.

Inserm, IRD, SESSTIM, Sciences Economiques & Sociales de la Santé & Traitement de l'Information Médicale, ISSPAM, Aix Marseille University, 13385 Marseille, France.

Detailed knowledge about hepatitis B virus (HBV) vaccination coverage and timeliness for sub-Saharan Africa is scarce. We used data from a community-based cross-sectional survey conducted in 2018-2019 in the area of Niakhar, Senegal, to estimate coverage, timeliness, and factors associated with non-adherence to the World Health Organisation-recommended vaccination schedules in children born in 2016 (year of the birth dose (BD) introduction in Senegal) and 2017-2018. Vaccination status was assessed from vaccination cards, surveillance data, and healthcare post vaccination records. Among 241 children with available data, for 2016 and 2017-2018, respectively, 31.0% and 66.8% received the BD within 24 h of birth (BD schedule), and 24.3% and 53.7% received the BD plus at least two pentavalent vaccine doses within the recommended timeframes (three-dose schedule). In logistic regression models, home birth, dry season birth, and birth in 2016 were all associated with non-adherence to the recommended BD and three-dose schedules. Living over three kilometres from the nearest healthcare post, being the firstborn, and living in an agriculturally poorer household were only associated with non-adherence to the three-dose schedule. The substantial proportion of children not vaccinated according to recommended schedules highlights the importance of considering vaccination timeliness when evaluating vaccination programme effectiveness. Outreach vaccination activities and incentives to bring children born at home to healthcare facilities within 24 h of birth, must be strengthened to improve timely HBV vaccination.
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http://dx.doi.org/10.3390/vaccines9050510DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8155976PMC
May 2021

Tick-borne relapsing fever Borreliosis, a major public health problem overlooked in Senegal.

PLoS Negl Trop Dis 2021 04 22;15(4):e0009184. Epub 2021 Apr 22.

Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France.

Background: Tick-borne relapsing fever (TBRF) is the most common vector-borne bacterial disease in humans in West Africa. It is frequently clinically confused with malaria. Our study aims to determine, on a micro-geographic scale, the conditions for the maintenance and spread of TBRF in the Niakhar district of Senegal.

Methodology/principal Findings: We conducted clinical, entomological and animal reservoir investigations. Field surveys were carried out in order to investigate the presence of Ornithodoros sonrai vector ticks and to detect Borrelia spp. by qPCR using the 16S rRNA and glpQ genes, respectively. Micromammal trapping series were carried out inside homes and Borrelia infection was detected using brain tissue qPCR. Capillary blood samples from febrile patients were also tested for Borrelia using qPCR. More than 97% (40/41) of the villages surveyed were infested with O. sonrai ticks. The prevalence of Borrelia spp. infections in ticks was 13% (116/910), and over 73% (85/116) were positively confirmed as being Borrelia crocidurae. Borreliosis cases accounted for 12% (94/800) of episodes of fever and all age groups were infected, with children and young people between the ages of 8-14 and 22-28 being the most infected by the disease (16% and 18.4%). TBRF cases occurred in all seasons, with a peak in August. In two species of small rodents that were found to be infected (Arvicanthis niloticus, Mus musculus), the proportion of Borrelia infection was 17.5% (10/57), and the highest prevalence of infection (40.9%, 9/22) was observed in A. niloticus.

Conclusion/significance: Our study indicates that TBRF is an endemic disease in the Niakhar district, where children and young people are the most infected. Arvicanthis niloticus and O. sonrai ticks are massively present and appear to be the main epidemiological reservoirs causing its extensive spread to humans.
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http://dx.doi.org/10.1371/journal.pntd.0009184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8096072PMC
April 2021

Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant.

J Clin Virol 2021 06 31;139:104814. Epub 2021 Mar 31.

IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005, Marseille, France; Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005, Marseille, France. Electronic address:

Introduction: The SARS-CoV-2 pandemic has been associated with the occurrence since summer 2020 of several viral variants that overlapped or succeeded each other in time. Those of current concern harbor mutations within the spike receptor binding domain (RBD) that may be associated with viral escape to immune responses. In our geographical area a viral variant we named Marseille-4 harbors a S477 N substitution in this RBD.

Materials And Methods: We aimed to implement an in-house one-step real-time reverse transcription-PCR (qPCR) assay with a hydrolysis probe that specifically detects the SARS-CoV-2 Marseille-4 variant.

Results: All 6 cDNA samples from Marseille-4 variant strains identified in our institute by genome next-generation sequencing (NGS) tested positive using our Marseille-4 specific qPCR, whereas all 32 cDNA samples from other variants tested negative. In addition, 39/42 (93 %) respiratory samples identified by NGS as containing a Marseille-4 variant strain and 0/26 samples identified as containing non-Marseille-4 variant strains were positive. Finally, 2018/3960 (51%) patients SARS-CoV-2-diagnosed in our institute, 10/277 (3.6 %) respiratory samples collected in Algeria, and none of 207 respiratory samples collected in Senegal, Morocco, or Lebanon tested positive using our Marseille-4 specific qPCR.

Discussion: Our in-house qPCR system was found reliable to detect specifically the Marseille-4 variant and allowed estimating it is involved in about half of our SARS-CoV-2 diagnoses since December 2020. Such approach allows the real-time surveillance of SARS-CoV-2 variants, which is warranted to monitor and assess their epidemiological and clinical characterics based on comprehensive sets of data.
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http://dx.doi.org/10.1016/j.jcv.2021.104814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8011323PMC
June 2021

Fine-scale spatio-temporal mapping of asymptomatic and clinical P. falciparum infections: epidemiological evidence for targeted malaria elimination interventions.

Clin Infect Dis 2021 Mar 2. Epub 2021 Mar 2.

Institut Pasteur Dakar, Pôle Immunophysiopathologie & Maladies Infectieuses, Dakar, Sénégal.

Background: A detailed understanding of the contribution of the asymptomatic Plasmodium reservoir to the occurrence of clinical malaria at individual and community levels is needed to guide effective elimination interventions. This study investigated the relationship between asymptomatic P. falciparum carriage and subsequent clinical malaria episodes in Dielmo and Ndiop villages in Senegal.

Methods: The study used a total of 2,792 venous and capillary blood samples obtained from asymptomatic individuals and clinical malaria datasets collected from 2013 to 2016. Mapping, spatial clustering of infections and risk analysis were performed using georeferenced households.

Results: High incidences of clinical malaria episodes were observed to occur predominantly in households of asymptomatic P. falciparum carriers. A statistically significant association was found between asymptomatic carriage in a household and subsequent episode of clinical malaria occurring in that household for each individual year (p-values were 0.0017, 6x10 -5, 0.005, and 0.008 for 2013, 2014, 2015, and 2016 respectively) and the combined years (p=8.5x10 -8), which was not found at the individual level. In both villages, no significant patterns of spatial clustering of P. falciparum clinical cases was found, but there was a higher risk of clinical episodes <25m from asymptomatic individuals in Ndiop attributable to clustering within households.

Conclusion: The findings provide strong epidemiological evidence linking the asymptomatic P. falciparum reservoir to clinical malaria episodes at household scale in Dielmo and Ndiop villagers. This argues for a likely success of a mass testing and treatment intervention to move towards the elimination of malaria in Dielmo and Ndiop villages.
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http://dx.doi.org/10.1093/cid/ciab161DOI Listing
March 2021

The Grand Magal of Touba was spared by the COVID-19 pandemic.

Int J Infect Dis 2021 Apr 9;105:470-471. Epub 2021 Jan 9.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.

In the context of the coronavirus disease-2019 (COVID-19) pandemic, all mass gathering (MG) events have been cancelled. The Grand Magal took place on October 6, 2020, in Touba, Senegal, which was the only MG event organized in 2020. This Muslim pilgrimage gathers about four million Muslim Mourides from Senegal and beyond. No significant increase in COVID-19 cases was therefore observed at the national level in the weeks following the Grand Magal. This successful strategy is an invitation to better promote community commitments by public authorities in their various strategies.
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http://dx.doi.org/10.1016/j.ijid.2021.01.006DOI Listing
April 2021

Errors in reported ages and dates in surveys of adult mortality: A record linkage study in Niakhar (Senegal).

Popul Stud (Camb) 2021 Jul 4;75(2):269-287. Epub 2021 Jan 4.

Johns Hopkins University.

Sibling survival histories are a major source of adult mortality estimates in countries with incomplete death registration. We evaluate age and date reporting errors in sibling histories collected during a validation study in the Niakhar Health and Demographic Surveillance System (Senegal). Participants were randomly assigned to either the Demographic and Health Survey questionnaire or a questionnaire incorporating an event history calendar, recall cues, and increased probing strategies. We linked 60-62 per cent of survey reports of siblings to the reference database using manual and probabilistic approaches. Both questionnaires showed high sensitivity (>96 per cent) and specificity (>97 per cent) in recording siblings' vital status. Respondents underestimated the age of living siblings, and age at and time since death of deceased siblings. These reporting errors introduced downward biases in mortality estimates. The revised questionnaire improved reporting of age of living siblings but not of age at or timing of deaths.
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http://dx.doi.org/10.1080/00324728.2020.1854332DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178157PMC
July 2021

Lack of SARS-CoV-2 among Grand Magal de Touba pilgrims consulting for respiratory symptoms in October 2020.

Travel Med Infect Dis 2021 Jan-Feb;39:101916. Epub 2020 Nov 13.

IHU-Méditerranée Infection, Marseille, France; Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.tmaid.2020.101916DOI Listing
February 2021

The Impact of Renewing Long-Lasting Insecticide-Treated Nets in the Event of Malaria Resurgence: Lessons from 10 Years of Net Use in Dielmo, Senegal.

Am J Trop Med Hyg 2021 01;104(1):255-262

1VITROME, UMR 257 IRD, Campus UCAD-IRD, Dakar, Senegal.

The occurrence of malaria resurgences could threaten progress toward elimination of the disease. This study investigated the impact of repeated renewal of long-lasting insecticide-treated net (LLIN) universal coverage on malaria resurgence over a period of 10 years of net implementation in Dielmo (Senegal). A longitudinal study was carried out in Dielmo between August 2007 and July 2018. In July 2008, LLINs were offered to all villagers through universal campaign distribution which was renewed in July 2011, August 2014, and May 2016. Malaria cases were treated with artemisinin-based combination therapy. Two resurgences of malaria occurred during the 10 years in which LLINs have been in use. Since the third renewal of the nets, malaria decreased significantly compared with the first year the nets were implemented (adjusted incidence rate ratio) (95% CI) = 0.35 (0.15-0.85), during the ninth year after net implementation). During the tenth year of net implementation, no cases of malaria were observed among the study population. The use of nets increased significantly after the third time the nets were renewed when compared with the year after the first and the second times the nets were renewed ( < 0.001). The third renewal of nets, which took place after 2 years instead of 3 years together with a higher use of LLINs especially among the young, probably prevented the occurrence of a third malaria upsurge in this village.
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http://dx.doi.org/10.4269/ajtmh.20-0127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7790102PMC
January 2021

A latent class analysis of attitudes concerning the acceptability of intimate partner violence in rural Senegal.

Popul Health Metr 2020 10 15;18(1):27. Epub 2020 Oct 15.

Harvard University, Cambridge, USA.

Background: Research concerning the causes and consequences of intimate partner violence (IPV), particularly in less developed areas of the world, has become prominent in the last two decades. Although a number of potential causal factors have been investigated the current consensus is that attitudes toward IPV on the individual level, likely representing perceptions of normative behavior, and the normative acceptability of IPV on the aggregate level likely play key roles. Measurement of both is generally approached through either binary indicators of acceptability of any type of IPV or additive composite indexes of multiple indicators. Both strategies imply untested assumptions which potentially have important implications for both research into the causes and consequences of IPV as well as interventions aimed to reduce its prevalence.

Methods: Using survey data from rural Senegal collected in 2014, this analysis estimates latent class measurement models of attitudes concerning the acceptability of IPV. We investigate the dimensional structure of IPV ideation and test the parallel indicator assumption implicit in common measurement strategies, as well as structural and measurement invariance between men and women.

Results: We find that a two-class model of the acceptability of IPV in which the conditional probability of class membership is allowed to vary between the sexes is preferred for both men and women. Though the assumption of structural invariance between men and women is supported, measurement invariance and the assumption of parallel indicators (or equivalence of indicators used) are not.

Conclusions: Measurement strategies conventionally used to operationalize the acceptability of IPV, key to modeling perceptions of norms around IPV, are a poor fit to the data used here. Research concerning the measurement characteristics of IPV acceptability is a precondition for adequate investigation of its causes and consequences, as well as for intervention efforts aimed at reducing or eliminating IPV.
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http://dx.doi.org/10.1186/s12963-020-00233-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566139PMC
October 2020

Establishing Medical Coverage and Epidemiological Surveillance during the Grand Magal of Touba in Senegal: A Public Health Need.

J Epidemiol Glob Health 2020 12 26;10(4):247-249. Epub 2020 Jun 26.

Aix Marseille University, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France.

The Grand Magal is a religious pilgrimage that takes place in Senegal. An estimated 4-5 million individuals yearly gather in the holy city of Touba. Pilgrims comes from the whole Senegal and surrounding countries and from countries outside of Africa where Mouride Senegalese emigrated. It is the largest Mass Gathering (MG) event of the Mouride community and the largest Muslim religious MG in West Africa. The context of the Grand Magal MG is unique given its location in a tropical developing country and its international component which may favour the globalization of local endemic diseases and warrants investment in modern methods for public health surveillance and planning of the event.
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http://dx.doi.org/10.2991/jegh.k.200620.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758853PMC
December 2020

The 2020 Grand Magal of Touba, Senegal in the time of the COVID-19 pandemic.

Travel Med Infect Dis 2020 Nov - Dec;38:101880. Epub 2020 Sep 17.

IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD de L'IRD, Dakar, Senegal.

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http://dx.doi.org/10.1016/j.tmaid.2020.101880DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7494441PMC
January 2021

Towards harmonization of microscopy methods for malaria clinical research studies.

Malar J 2020 Sep 4;19(1):324. Epub 2020 Sep 4.

UMR 257 IRD VITROME, Campus IRD-UCAD, Dakar, Senegal.

Microscopy performed on stained films of peripheral blood for detection, identification and quantification of malaria parasites is an essential reference standard for clinical trials of drugs, vaccines and diagnostic tests for malaria. The value of data from such research is greatly enhanced if this reference standard is consistent across time and geography. Adherence to common standards and practices is a prerequisite to achieve this. The rationale for proposed research standards and procedures for the preparation, staining and microscopic examination of blood films for malaria parasites is presented here with the aim of improving the consistency and reliability of malaria microscopy performed in such studies. These standards constitute the core of a quality management system for clinical research studies employing microscopy as a reference standard. They can be used as the basis for the design of training and proficiency testing programmes as well as for procedures and quality assurance of malaria microscopy in clinical research.
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http://dx.doi.org/10.1186/s12936-020-03352-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7471592PMC
September 2020

Epidemiology of human common coronavirus acquisition in pilgrims.

Travel Med Infect Dis 2020 Sep - Oct;37:101845. Epub 2020 Aug 14.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France. Electronic address:

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http://dx.doi.org/10.1016/j.tmaid.2020.101845DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7427599PMC
October 2020

Parasitic Infections in African Humans and Non-Human Primates.

Pathogens 2020 Jul 11;9(7). Epub 2020 Jul 11.

Aix Marseille Univ, IRD, AP-HM, MEPHI, 13385 Marseille, France.

Different protozoa and metazoa have been detected in great apes, monkeys and humans with possible interspecies exchanges. Some are either nonpathogenic or their detrimental effects on the host are not yet known. Others lead to serious diseases that can even be fatal. Their survey remains of great importance for public health and animal conservation. Fecal samples from gorillas () and humans living in same area in the Republic of Congo, chimpanzees () from Senegal and one other from the Republic of Congo, Guinea baboons ( from Senegal, hamadryas baboons () from Djibouti and Barbary macaques ) from Algeria, were collected. DNA was extracted and screened using specific qPCR assays for the presence of a large number of helminths and protozoa. Positive samples were then amplified in standard PCRs and sequenced when possible. Overall, infection rate was 36.5% in all non-human primates (NHPs) and 31.6% in humans. Great apes were more often infected (63.6%) than monkeys (7.3%). At least twelve parasite species, including ten nematodes and two protozoa were discovered in NHPs and five species, including four nematodes and a protozoan in humans. The prevalences of , were similar between gorillas and human community co-habiting the same forest ecosystem in the Republic of Congo. In addition, human specific (5.1%) and other spp. (5.1%) detected in these gorillas suggest a possible cross-species exchange. Low prevalence (2%) of were observed in chimpanzees, as well as a high prevalence of (57.1%), which should be considered carefully as this parasite can affect other NHPs, animals and humans. The Barbary macaques were less infected (7.2%) and was the main parasite detected (5.8%). Finally, we report the presence of sp. and an environmental Nematoda DNAs in chimpanzee feces, sp. and sp. in gorillas, as well as DNA of uncharacterized Nematoda in apes and humans, but with a relatively lower prevalence in humans. Prevalence of extraintestinal parasites remains underestimated since feces are not the suitable sampling methods. Using non-invasive sampling (feces) we provide important information on helminths and protozoa that can infect African NHPs and human communities living around them. Public health and animal conservation authorities need to be aware of these infections, as parasites detected in African NHPs could affect both human and other animals' health.
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http://dx.doi.org/10.3390/pathogens9070561DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400533PMC
July 2020

Zoonotic in Wild Chimpanzees () from Senegal.

Pathogens 2020 Jun 27;9(7). Epub 2020 Jun 27.

IRD, AP-HM, Microbes, Evolution, Phylogeny and Infection (MEPHI), IHU Méditerranée Infection, Aix Marseille Univ, 19-21, Bd Jean Moulin, 13005 Marseille, France.

(syn. ) has been reported in human and various non-human primates including great apes. The identification of this nematode is seldom performed and relies on egg characterization at the coproscopy, in the absence of any molecular tool. Following the recovery of two adult females of from the feces of wild Senegalese chimpanzees, morphometric characteristics were reported and new data on the width of the esophagus (0.268-0.287 mm) and on the cuticle structure (0.70-0.122 mm) were provided. The molecular characterization of a set of mitochondrial (1, 16S rRNA, 12S rRNA) and nuclear (18S rRNA and ITS2) partial genes was performed. Our phylogenetic analysis indicates for the first time that is monophyletic with species. A novel molecular tool was developed for the routine diagnosis of and the surveillance of Nematoda infestations. An -specific qPCR targeting the 12S gene was assessed. The assay was able to detect up to 1.13 × 10 eggs/g of fecal matter irrespective of its consistency, with an efficiency of 101.8% and a perfect adjustment (R = 0.99). The infection rate by in the chimpanzee fecal samples was 52.08%. Only 6.19% of the environmental samples were positive for nematode DNA and any for . Our findings indicate the need for further studies to clarify the epidemiology, circulation, life cycle, and possible pathological effects of this infestation using the molecular tool herein developed.
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http://dx.doi.org/10.3390/pathogens9070517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7400140PMC
June 2020

Anopheles arabiensis and Anopheles funestus biting patterns in Dielmo, an area of low level exposure to malaria vectors.

Malar J 2020 Jun 26;19(1):230. Epub 2020 Jun 26.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.

Background: In Dielmo, Senegal, the widespread use of long-lasting insecticidal nets has decreased both the incidence of malaria and the density of the Anopheles population. However, persistent low-level malaria transmission may hamper efforts to eliminate the disease. Therefore, continuous monitoring of the vector population is needed in order to improve knowledge of Anopheles biting behaviour and to readjust control interventions.

Methods: In 2015, Anopheles were collected every month for a whole year and each specimen was identified using morphological and molecular techniques. The biting pattern of each species was analysed according to night (7 pm-7am) and morning (7am-11am) periods, the place of biting and the season. The ELISA CSP technique was used to assess the Plasmodium falciparum sporozoite rate to evaluate the entomological inoculation rate (EIR).

Results: Anopheles arabiensis and Anopheles funestus sensu stricto were found to be the main vectors biting humans. Overall, the biting rate was low, at 3.84bites per night (bpn) and 1.27 bites per morning (bpm), respectively (IRR = 3.04, CI [1.84-5.00], p < 0.001). The EIR was 2.51 and 5.03 infectious bites per year during the night and morning, respectively. During the night, the An. arabiensis and An. funestus biting rate was 1.81 bpn and 1.71 bpn, respectively (IRR = 0.95, CI [0.46-1.92], p = 0.88). During the morning, their density decreased to 0.51 bpm and 0.73 bpm for An. arabiensis and An. funestus, respectively (IRR = 1.47, CI [0.58-3.71], p = 0.41). During the night and the morning, no specific trend of indoor or outdoor biting was observed in the dry and rainy season for both vectors.

Conclusion: This study highlighted low level Anopheles nocturnal and diurnal biting and the associated risk of malaria transmission. It showed also the influence of the season on the indoor and outdoor biting pattern, indicating that the human population could be exposed all year round to a low level of Anopheles bites. Control programmes should increase awareness of the use of bed nets throughout the year and promote the development and implementation of complimentary tools to target Anopheles biting shortly after dawn when people are still indoors and outside the bed nets.
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http://dx.doi.org/10.1186/s12936-020-03302-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320554PMC
June 2020

Adenovirus Infections in African Humans and Wild Non-Human Primates: Great Diversity and Cross-Species Transmission.

Viruses 2020 06 18;12(6). Epub 2020 Jun 18.

IHU Méditerranée Infection, 13385 Marseille CEDEX 05, France.

Non-human primates (NHPs) are known hosts for adenoviruses (AdVs), so there is the possibility of the zoonotic or cross-species transmission of AdVs. As with humans, AdV infections in animals can cause diseases that range from asymptomatic to fatal. The aim of this study was to investigate the occurrence and diversity of AdVs in: (i) fecal samples of apes and monkeys from different African countries (Republic of Congo, Senegal, Djibouti and Algeria), (ii) stool of humans living near gorillas in the Republic of Congo, in order to explore the potential zoonotic risks. Samples were screened by real-time and standard PCRs, followed by the sequencing of the partial DNA polymerase gene in order to identify the AdV species. The prevalence was 3.3 folds higher in NHPs than in humans. More than 1/3 (35.8%) of the NHPs and 1/10 (10.5%) of the humans excreted AdVs in their feces. The positive rate was high in great apes (46%), with a maximum of 54.2% in chimpanzees () and 35.9% in gorillas (), followed by monkeys (25.6%), with 27.5% in Barbary macaques () and 23.1% in baboons (seven and six ). No green monkeys () were found to be positive for AdVs. The AdVs detected in NHPs were members of (HAdV-E), HAdV-C or HAdV-B, and those in the humans belonged to HAdV-C or HAdV-D. HAdV-C members were detected in both gorillas and humans, with evidence of zoonotic transmission since phylogenetic analysis revealed that gorilla AdVs belonging to HAdV-C were genetically identical to strains detected in humans who had been living around gorillas, and, inversely, a HAdV-C member HAdV type was detected in gorillas. This confirms the gorilla-to-human transmission of adenovirus. which has been reported previously. In addition, HAdV-E members, the most often detected here, are widely distributed among NHP species regardless of their origin, i.e., HAdV-E members seem to lack host specificity. Virus isolation was successful from a human sample and the strain of the Mbo024 genome, of 35 kb, that was identified as belonging to HAdV-D, exhibited close identity to HAdV-D members for all genes. This study provides information on the AdVs that infect African NHPs and the human populations living nearby, with an evident zoonotic transmission. It is likely that AdVs crossed the species barrier between different NHP species (especially HAdV-E members), between NHPs and humans (especially HAdV-C), but also between humans, NHPs and other animal species.
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http://dx.doi.org/10.3390/v12060657DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7354429PMC
June 2020

Spatio-temporal variation of malaria hotspots in Central Senegal, 2008-2012.

BMC Infect Dis 2020 Jun 17;20(1):424. Epub 2020 Jun 17.

Aix Marseille Univ, APHM, INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Biostatistic & ICT, Marseille, France.

Background: In malaria endemic areas, identifying spatio-temporal hotspots is becoming an important element of innovative control strategies targeting transmission bottlenecks. The aim of this work was to describe the spatio-temporal variation of malaria hotspots in central Senegal and to identify the meteorological, environmental, and preventive factors that influence this variation.

Methods: This study analysed the weekly incidence of malaria cases recorded from 2008 to 2012 in 575 villages of central Senegal (total population approximately 500,000) as part of a trial of seasonal malaria chemoprevention (SMC). Data on weekly rainfall and annual vegetation types were obtained for each village through remote sensing. The time series of weekly malaria incidence for the entire study area was divided into periods of high and low transmission using change-point analysis. Malaria hotspots were detected during each transmission period with the SaTScan method. The effects of rainfall, vegetation type, and SMC intervention on the spatio-temporal variation of malaria hotspots were assessed using a General Additive Mixed Model.

Results: The malaria incidence for the entire area varied between 0 and 115.34 cases/100,000 person weeks during the study period. During high transmission periods, the cumulative malaria incidence rate varied between 7.53 and 38.1 cases/100,000 person-weeks, and the number of hotspot villages varied between 62 and 147. During low transmission periods, the cumulative malaria incidence rate varied between 0.83 and 2.73 cases/100,000 person-weeks, and the number of hotspot villages varied between 10 and 43. Villages with SMC were less likely to be hotspots (OR = 0.48, IC95%: 0.33-0.68). The association between rainfall and hotspot status was non-linear and depended on both vegetation type and amount of rainfall. The association between village location in the study area and hotspot status was also shown.

Conclusion: In our study, malaria hotspots varied over space and time according to a combination of meteorological, environmental, and preventive factors. By taking into consideration the environmental and meteorological characteristics common to all hotspots, monitoring of these factors could lead targeted public health interventions at the local level. Moreover, spatial hotspots and foci of malaria persisting during LTPs need to be further addressed.

Trial Registration: The data used in this work were obtained from a clinical trial registered on July 10, 2008 at www.clinicaltrials.gov under NCT00712374.
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http://dx.doi.org/10.1186/s12879-020-05145-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7301493PMC
June 2020

Application of Functional Data Analysis to Identify Patterns of Malaria Incidence, to Guide Targeted Control Strategies.

Int J Environ Res Public Health 2020 06 11;17(11). Epub 2020 Jun 11.

Aix Marseille Université, Assistance Publique-Hôpitaux de Marseille(APHM), INSERM, IRD, SESSTIM, Hop Timone, BioSTIC, Biostatistic and ICT, 13005 Marseille, France.

We introduce an approach based on functional data analysis to identify patterns of malaria incidence to guide effective targeting of malaria control in a seasonal transmission area. Using functional data method, a smooth function (functional data or curve) was fitted from the time series of observed malaria incidence for each of 575 villages in west-central Senegal from 2008 to 2012. These 575 smooth functions were classified using hierarchical clustering (Ward's method), and several different dissimilarity measures. Validity indices were used to determine the number of distinct temporal patterns of malaria incidence. Epidemiological indicators characterizing the resulting malaria incidence patterns were determined from the velocity and acceleration of their incidences over time. We identified three distinct patterns of malaria incidence: high-, intermediate-, and low-incidence patterns in respectively 2% (12/575), 17% (97/575), and 81% (466/575) of villages. Epidemiological indicators characterizing the fluctuations in malaria incidence showed that seasonal outbreaks started later, and ended earlier, in the low-incidence pattern. Functional data analysis can be used to identify patterns of malaria incidence, by considering their temporal dynamics. Epidemiological indicators derived from their velocities and accelerations, may guide to target control measures according to patterns.
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http://dx.doi.org/10.3390/ijerph17114168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7312547PMC
June 2020

Risk perceptions of infectious diseases at the Grand Magal of Touba. A pilot study in two senegalese villages.

Travel Med Infect Dis 2020 Nov - Dec;38:101767. Epub 2020 Jun 3.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD de l'IRD, Dakar, Senegal.

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http://dx.doi.org/10.1016/j.tmaid.2020.101767DOI Listing
July 2021

The impact of daily soap use in rural areas of Senegal on respiratory infectious diseases, fevers and skin microbiota.

Int J Infect Dis 2020 Jul 1;96:408-415. Epub 2020 May 1.

Aix-Marseille Univ., IRD, AP-HM, MEPHI, Marseille, France; IHU Mediterranée Infection, Marseille, France.

Objectives: Children aged <5 years are the group most affected by infectious diseases, more specifically in underdeveloped countries. A study was performed to assess the effects of daily soap use on the incidence of diarrhoea, fever, respiratory infection, and the prevalence of pathogenic bacteria on the skin.

Methods: Soap was distributed to the population of the village of Ndiop (test) for use in their daily hygiene but not to the population of the village of Dielmo (control). Fieldworkers daily recorded the clinical events in the two villages and encouraged the use of soap in Ndiop.

Results: A total of 638 people participated in the study. The incidence rates of cough, runny nose and fever significantly decreased in 2016 compared with 2015, unlike that of diarrhoea. In 2016, significant reductions in the incidence rates of cough, runny nose and fever were observed in children aged <15 years in Ndiop. The prevalence of Streptococcus pneumoniae, Staphylococcus aureus and Streptococcus pyogenes in the palms of the hands significantly dropped in Ndiop.

Conclusion: Using soap reduces the incidence of respiratory infections, fevers and the prevalence of pathogenic bacteria on the skin. However, for diarrhoea, additional strategies are needed to improve outcomes.
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http://dx.doi.org/10.1016/j.ijid.2020.04.076DOI Listing
July 2020

Role of plants in the transmission of Asaia sp., which potentially inhibit the Plasmodium sporogenic cycle in Anopheles mosquitoes.

Sci Rep 2020 04 28;10(1):7144. Epub 2020 Apr 28.

MEФI, IRD, Aix Marseille Univ, AP-HM, Marseille, France.

Biological control against malaria and its transmission is currently a considerable challenge. Plant-associated bacteria of the genus Asaia are frequently found in nectarivorous arthropods, they thought to have a natural indirect action on the development of plasmodium in mosquitoes. However, virtually nothing is known about its natural cycle. Here, we show the role of nectar-producing plants in the hosting and dissemination of Asaia. We isolated Asaia strains from wild mosquitoes and flowers in Senegal and demonstrated the transmission of the bacteria from infected mosquitoes to sterile flowers and then to 26.6% of noninfected mosquitoes through nectar feeding. Thus, nectar-producing plants may naturally acquire Asaia and then colonize Anopheles mosquitoes through food-borne contamination. Finally, Asaia may play an indirect role in the reduction in the vectorial capacity of Anopheles mosquitoes in a natural environment (due to Plasmodium-antagonistic capacities of Asaia) and be used in the development of tools for Asaia-based paratransgenetic malaria control.
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http://dx.doi.org/10.1038/s41598-020-64163-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189373PMC
April 2020

Senegal faces the coronavirus disease -19 challenge.

Authors:
Cheikh Sokhna

Travel Med Infect Dis 2020 Sep - Oct;37:101687. Epub 2020 Apr 22.

Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, IHU-Méditerranée Infection, Marseille, France; VITROME, Campus International IRD-UCAD, Dakar, Senegal. Electronic address:

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http://dx.doi.org/10.1016/j.tmaid.2020.101687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7195138PMC
October 2020
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