Cheikh Fall

Institut Pasteur de Dakar · Pole de virologie

In Senegal, the burden of dengue is increasing and expanding. As case management and traditional diagnostic techniques can be difficult to implement, rapid diagnostic tests (RDTs) deployed at point of care are ideal for investigating active outbreaks. The aim of this study was to evaluate the diagnostic performance of the Dengue NS1 and Dengue IgM/...

Antimicrobial resistance (AMR) is a global public health threat. Quality data on AMR are needed to tackle the rise of multidrug-resistant clones. These data are rare in low-income countries, especially in sub-Saharan Africa. In this study, we investigated the rise of extended-spectrum β-lactamase–producing (ESBL) Enterobacteriaceae in Bangui, Centr...

Zika virus (ZIKV) shows an enigmatic epidemiological profile in Africa. Despite its frequent detection in mosquitoes, few human cases have been reported. This could be due to the low infectious potential or low virulence of African ZIKV lineages. This study sought to assess the susceptibility of A. aegypti and C. quinquefasciatus to ZIKV strains fr...

On 10th September 2018, the Syndromic Sentinel Surveillance network that monitors febrile illnesses in all 14 regions of Senegal detected a peak of fever in the Fatick region. On 13 September 2018, 10 samples were sent to the WHO Collaborating Centre for Arboviruses and Viral Haemorrhagic Fevers at the Institut Pasteur de Dakar (IPD). Laboratory in...

Foodborne diseases are an important public health concern worldwide. Following a first global estimate of the burden of these diseases by the World Health Organization in 2015, many high-income countries implemented the generation of national data as a part of strategies to limit the transmission of pathogens through the food chain. In contrast, lo...

Yellow Fever (YF) is a mosquito-borne viral disease that is endemic in several African and South American countries. YF Virus (YFV) causes subclinical infections with mild and non-specific symptoms, to severe, potentially lethal illness. Despite the existence of efficient vaccines, epidemics continue to occur, mostly in Africa. One major drawback o...

This study aimed to determine drug-susceptibility profiles and characterize ESBL genes in 66 clinical strains of ESBL-producing K. pneumoniae in an university teaching hospital of Dakar.

Dengue virus (DENV) was detected in Senegal in 1979 for the first time. Since 2017, unprecedented frequent outbreaks of DENV were noticed yearly. In this context, epidemiological and molecular evolution data are paramount to decipher the virus diffusion route. In the current study, we focused on a dengue outbreak which occurred in Senegal in 2018 i...

Antimicrobial resistance (AMR) has become a global public health threat. Experts agree that unless proper actions are taken, the number of deaths due to AMR will increase. Many strategies are being pursued to tackle AMR, one of the most important being the development of efficient vaccines. Similar to other bacterial pathogens, AMR in Helicobacter...

Dengue virus (DENV) was detected in Senegal in 1979 for the first time. Since 2017, unprecedented frequent occurrence of DENV outbreaks was noticed yearly. In this context, epidemiological and molecular evolution data are paramount to decipher virus diffusion route. In the current study, a dengue outbreak occurred in Senegal in 2018 in the context...

Background The control of snails intermediate hosts remains an effective strategy to limit schistosomiasis transmission despite the widespread mass de-worming campaign based on praziquantel. Therefore, the study of snail biology could help to improve snails control strategies. This study evaluated the development of Biomphalaria pfeifferi, Bulinus...

Extra-intestinal pathogenic Escherichia coli (ExPEC), a predominant Gram-negative bacterial pathogen, express a wide range of virulence factors and is responsible of several diseases including urinary tract infections (UTI), nosocomial pneumonia, bacteremia, and neonatal meningitis. ExPEC isolates are often multidrug resistant (MDR) and clones prod...

Salmonella enterica is the most common foodborne pathogen worldwide. It causes two types of diseases, a self-limiting gastroenteritis and an invasive, more threatening, infection. Salmonella gastroenteritis is caused by several serotypes and is common worldwide. In contrast, invasive salmonellosis is rare in high-income countries (HIC) while freque...

Background Dengue fever is a mosquito born disease associated with self-limited to life threatening illness. First detected in Senegal in the nineteenth century, and despite its growing incidence this last decade, significant knowledge gaps exist in our knowledge of genetic diversity of circulating strains. This study highlights the circulating ser...

Background In this work, a platform was developed and tested to allow to detect a variety of candidate viral, bacterial and parasitic pathogens, for acute fever of unknown origin. The platform is based on a centrifugal microfluidic cartridge, the LabDisk (“FeverDisk” for the specific application), which integrates all necessary reagents for sample-...

Background: Cervical intraepithelial neoplasia (CIN) grading is subjective and affected by substantial rates of discordance among pathologists. Although recent studies have suggested that p16INK4a may be a useful surrogate biomarker of cervical neoplasia, Ki-67 and human papillomavirus testing have also been shown to be useful in detecting neoplas...

Background: Past and recent outbreaks have highlighted the vulnerability of humans to infectious diseases, which represent serious economic and health security threats. A paradigm shift in the management of sanitary crises is urgently needed. Based on lessons from the 2014 Ebola outbreak, the Praesens Foundation has developed an all-terrain mobile...

With the growing success of controlling malaria in Sub-Saharan Africa, the incidence of fever due to malaria is in decline, whereas the proportion of patients with non-malaria febrile illness (NMFI) is increasing. Clinical diagnosis of NMFI is hampered by unspecific symptoms, but early diagnosis is a key factor for both better patient care and dise...

Two one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays for the detection of Zika virus (ZIKV) were developed, based on two different primer design approaches: (1) open source, based on a combination of sequence diversity clustering (phylogeny and principal component analysis) and LAVA algorithm, using 4...

Molecular detection of Zika virus (ZIKV) is a key element of outbreak management. Multiple PCR and isothermal ZIKV assays targeting different ZIKV sequences have been published. In this study, we compared a qRT-PCR, 2 RT-LAMP assays (based on different primer design approaches), and an RT-RPA for the detection of African and Asian/American lineages...

As part of the laboratory response to the Ebola virus outbreak in Guinea, the Institut Pasteur de Dakar mobile laboratory (IPD-ML) was set up in Donka hospital from 2014 to 2016. EBOV suspected samples collected at Ebola Treatment Centers (ETC) and from community deaths were sent daily to IPD-ML. Analysis was performed using dried oligonucleotide m...

Background 4 one-step, real-time, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays were developed for the detection of dengue virus (DENV) serotypes by considering 2,056 full genome DENV sequences. DENV1 and DENV2 RT-LAMP assays were validated with 31 blood and 11 serum samples from Tanzania, Senegal, Sudan and Mauritan...

Detailed primers to detect DENV3 by RT-LAMP. (CSV)

PCA and phylogenetic clustering of 1,145 DENV1 genomes. Twenty-one subgroups were necessary to describe all clusters found (variation explained by first, second and third principal component, 47.7%, 11.3% and 9.1% respectively). (TIF)

PCA and phylogenetic clustering of 376 DENV3 genomes. Fifteen subgroups were necessary to describe all clusters found (variation explained by first, second and third principal component, 51.5%, 14.5% and 6.7% respectively). (TIF)

STARD 2015 checklist. (DOCX)

RNA standard curve developed to quantify DENV samples by absolute one-step qRT-PCR. (TIF)

PCA and phylogenetic clustering of 477 DENV2 genomes. Twenty subgroups were necessary to describe all clusters found (variation explained by first, second and third principal component, 55.4%, 8.8% and 5.4% respectively). (TIF)

Detailed primers to detect DENV4 by RT-LAMP. (CSV)

Developed protocol for each DENV RT-LAMP assay. (DOCX)

Detailed primers to detect DENV1 by RT-LAMP. (CSV)

Detailed primers to detect DENV2 by RT-LAMP. (CSV)

We report the successful implementation of twelve assays for detecting fever-causing pathogens on a centrifugal microfluidic LabDisk platform (FeverDisk). The panel was selected to diagnose tropical regions’ most prevalent endemic and epidemic fever-causing diseases. The FeverDisk was used by local scientific staff in two clinical settings (Dakar,...

Recent research on Staphylococcus aureus vaccine development has focused on active immunization against Panton–Valentine leukocidin (PVL), a potent leukotoxin associated with both superficial and severe deep-seated infections. PVL prevalence is highly variable worldwide, but it is unknown to what extent immunity to PVL varies between patients from...

Nasal and pharyngeal swabs were collected from 132 patients admitted to the Principal Hospital in Dakar (Senegal), in January and February 2012. The prevalence of Staphylococcus aureus carriage was 56.1% (n = 74): 40.2% for pharyngeal samples and 36.4% for nasal samples. None of the isolates was methicillin-resistant. Carriage was independently ass...

Abstract Between December 2009 and November 2011, we collected 57 (12.3%) Staphylococcus aureus isolates from 464 pigs and 16 (30.8%) isolates from 52 farmers in the largest farm in Dakar. Fifty-one isolates (70%) belonged to four major multilocus sequence typing clonal complexes (CCs): CC152 (26.0%), CC15 (19.2%), CC5 (13.7%), and CC97 (10.9%). Th...

Clin Microbiol Infect 2012; 18: 153–159 The molecular epidemiology of Helicobacter pylori in Africa is poorly documented. From January 2007 to December 2008, we investigated 187 patients with gastric symptoms in one of the main tertiary hospitals in Dakar, Senegal. One hundred and seventeen patients were culture-positive for H. pylori. Polymorphism...

Clin Microbiol Infect 2011; 17: 633–639 The epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in Africa is poorly documented. From January 2007 to March 2008, 555 S. aureus isolates were collected from five African towns in Cameroon, Madagascar, Morocco, Niger, and Senegal; among these, 456 unique isolates were susceptible to met...

The bacteriological characteristics of Helicobacter pylori (HP) vary in function of time and place. The aim of this study was to update histological and bacteriological feature of HP infection in patients presenting gastroduodenal lesions in Dakar, Senegal. This prospective study included patients with gastroduodenal lesions managed over a 6-month...