Etude Préliminaire des Valeurs Normales de Référence de l’Hémogramme en République de Djibouti : Pour une Orientation Diagnostic Ciblée

The prescribing of the blood count is a common practice in the list of routine checkups in the laboratory of medical biology. The variation of the blood count results indicates a particular interpretation on the clinical level. In our study, we wanted to implement the reference values that we observe in a young population in Djibouti. We collected the results of the blood count of 213 Djiboutian students. Samples were analyzed by the Urit-3000 Plus medical Urit automaton. The results show significant differences at the 95% threshold for red blood cell count, hemoglobin, hematocrit, platelet, mean cell volume, mean hemoglobin concentration and mean corpuscular density of hemoglobin by sex (P <0.05). However, there is no significant difference in the number of leucocytes by sex. We can conclude that this study allowed a first specific approach for reference values in the Djiboutian population. A broader survey that includes several parameters is being considered to improve the quality of clinical care provided to patients. La prescription de l’hémogramme est une pratique courante dans la liste des bilans de routine au laboratoire de biologie médicale. La variation des résultats de l’hémogramme indique une interprétation particulière sur le plan clinique. Dans notre étude, nous avons voulu mettre en vigueur les valeurs de références que l’on observe dans une population jeune à Djibouti. Nous avons colligé les résultats de l’hémogramme de 213 étudiants Djiboutiens. Les prélèvements ont été analysés par l'automate Urit-3000 Plus d’Urit médical. Les résultats montrent des différences significatives au seuil de 95 % pour la numération de globule rouge, le taux d’hémoglobine, le taux d’hématocrite, le paramètre plaquettaire, le volume globulaire moyen, la concentration corpusculaire moyenne en hémoglobine et la teneur corpusculaire moyenne en hémoglobine selon le sexe (P<0,05). Cependant, il n’y a pas de différence significative pour le nombre de leucocytes, selon le sexe. Nous pouvons conclure que cette étude a permis une première approche spécifique pour les valeurs de références dans la population Djiboutienne. Une prospection plus large qui comprend plusieurs paramètres est envisagée pour améliorer la qualité des soins cliniques offerts aux patients

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

Approches cellulaires et moléculaires de deux vibrioses chez l'huître Crassostrea gigas et la palourde Ruditapes philippinarum

L'objectif de cette thèse était d étudier et de comparer le comportement de deux vibrions pathogènes impliqués dans deux vibrioses, Vibrio aestuarianus chez l huître, Crassostrea gigas et Vibrio tapetis chez la palourde, Ruditapes philippinarum. Pour cela, des souches des deux vibrions ont été transformées par un plasmide portant les gènes de la "Green Fluorescent Protein" et celui d une résistance à un antibiotique. Cet outil a permis un suivi temporel chez des huîtres infectées par balnéation par deux souches de V. aestuarianus GFP, l une pathogène (02/041), l autre (01/308) plus modérément pathogène et une souche de V. tapetis-GFP. La vitesse de pénétration dans l hémolymphe est souche-dépendante. La souche 02/041 s est avérée particulièrement efficace pour entrer dans son hôte, suivie de la souche 01/308. Ils pouvaient être détectés dès une heure après leur distribution. V. tapetis s introduisait plus lentement mais se maintenant plus longtemps. L étape suivante de l infection étant la confrontation des vibrions aux défenses immunitaires des bivalves, les relations vibrions hémocytes ont été examinées précisément. A cette fin, une méthode utilisant des anticorps souche-spécifique a été développée. Contrairement aux billes de latex fluorescentes, cette méthode a permis de quantifier in vitro au cytométrie de flux, les nombres de V. tapetis phagocytés et de ceux restant sur la membrane externe aussi bien avec des hémocyanines adhérents que décollés. La piste des exo polysaccharides (EPS) secrétés par les bactéries a été explorée pour savoir s ils pouvaient favoriser ou empêcher la phagocytose. V. tapetis produit des EPS en abondance, contrairement à V. a.The aim of this thesis was the study and the comparison of the behavior of two pathogenic bacteria in their respective hosts: Vibrio aestuarianus in the Pacific oyster, Crassostrea gigas, and Vibrio tapetis in the Manila clam, Ruditapes philippinarum. Therefore, the bacteria were transformed with a plasmid coding for the Green Fluorescent Protein and harbouring an antibiotic resistance cassette. This tool permitted to follow the penetration in the oyster over time when the animal was exposed to two strains of V. aestuarianus-GFP, the pathogenic 02/041 and the moderate pathogen, 01/308, as well as to V. tapetis-GFP. The strain 02/041 was found t penetrate very efficiently the hemolymph quickly followed by the 01/308 strain while the V. tapetis infiltrated much slower but remained longer in the tissues. The next step was the study of their relationship with the host s hemocytes. Therefore, the phagocytosis of V. tapetis by different hemocytes was studied, and a new phagocytosis quantification method using a V. tapetis-specific antibody was developed. In contrast to the fluoresce beads which are generally used for measuring phagocytosis, this method allowed precise quantification of the bacteria attached to exterior membrane and of those present inside the hemocytes, hemocytes that were either attached to the glass slide or detached. Exopolysaccharids (EPS) secreted by the bacteria were tested to verify whether they could favor or prevent phagocytosis. V. tapetis produced large quantity of EPS in contrast to V. aestuarianus, where especially the virulent strains produce only very little. 1-lowever it is difficult to link the abundance and composition of the EPS wit.BREST-BU Droit-Sciences-Sports (290192103) / SudocPLOUZANE-Bibl.La Pérouse (290195209) / SudocSudocFranceF

Emergence of Carbapenem-Resistant Gram-Negative Isolates in Hospital Settings in Djibouti

International audienceIntroduction: The antimicrobial resistance (AMR) of bacteria is increasing rapidly against all classes of antibiotics, with the increasing detection of carbapenem-resistant isolates. However, while growing prevalence has been reported around the world, data on the prevalence of carbapenem resistance in developing countries are fairly limited. In this study, we investigated and determined the resistance rate to carbapenems among multidrug-resistant Gram-negative bacteria (MDR-GNB) isolated in Djibouti and characterized their resistance mechanisms. Results: Of the 256 isolates, 235 (91.8%) were identified as Gram-negative bacteria (GNB). Of these GNBs, 225 (95.7%) isolates exhibited a multidrug resistance phenotype, and 20 (8.5%) isolates were resistant to carbapenems, including 13 Escherichia coli, 4 Acinetobacter baumannii, 2 Klebsiella pneumoniae and 1 Proteus mirabilis. The most predominant GNB in this hospital setting were E. coli and K. pneumoniae species. Carbapenemase genes such as blaOXA-48 and blaNDM-5 were identified, respectively, in six and four E. coli isolates, whereas the carbapenemase blaNDM-1 was identified in three E. coli, two K. pneumoniae, one P. mirabilis and one A. baumannii. Moreover, three A. baumannii isolates co-hosted blaOXA-23 and blaNDM-1. Materials and Methods: A total of 256 clinical strains collected between 2019 and 2020 were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Antibiotic susceptibility testing was performed using disk diffusion and E-test methods. Real-time polymerase chain reaction (RT-PCR), standard PCR and sequencing were used to investigate genes encoding for extended-spectrum-β-lactamases, carbapenemases and colistin resistance genes. Conclusions: We report, for the first time, the presence of MDR-GNB clinical isolates and the emergence of carbapenem-resistant isolates in Djibouti. In addition to performing antimicrobial susceptibility testing, we recommend phenotypic and molecular screening to track the spread of carbapenemase genes among clinical GNB isolates

Multidrug-Resistant Enterobacterales in Community-Acquired Urinary Tract Infections in Djibouti, Republic of Djibouti

The emergence and spread of multidrug resistant Enterobacterales (MDR-E) are a global public health issue. This problem also concerns urinary tract infections (UTI), which are the second most frequent infections after respiratory infections. The objective of this study was to determine MDR-E frequency and to characterize MDR-E isolates from patients with community-acquired UTIs in Djibouti, Republic of Djibouti. From 800 clinical urinary samples collected at the Mer Rouge Laboratory, Djibouti, from January to July 2019, 142 were identified as Enterobacterales (age range of the 142 patients mean age is 42 years.) Mass spectrometry analysis of these isolates identified 117 Escherichia coli, 14 Klebsiella pneumoniae, 2 Proteus mirabilis, 4 Enterobacter spp., 4 Providencia stuartii and 1 Franconibacter helveticus. Antibiotic susceptibility testing (disk diffusion method) of these 142 isolates detected 68 MDR-E (68/142 = 48%): 65 extended-spectrum bêta lactamase- (ESBL), 2 carbapenemase- (one also ESBL), and 1 cephalosporinase-producer. Multiplex PCR and sequencing showed that the 65 ESBL-producing isolates carried genes encoding CTX-M enzymes (CTX-M-15 in 97% and CTX-M-9 in 3% of isolates). Two isolates harboured a gene encoding the OXA-48-like carbapenemase, and one the gene encoding the AmpC CMY-2 cephalosporinase. Genes implicated in resistance to quinolones (qnrB, aac (6′)-Ib-cr, qnrD, oqxA and B) also were detected. Among the E. coli phylogroups, B2 was the most common phylogenetic group (21% of MDR-E isolates and 26% of non-MDR-E isolates), followed by A (14% and 12%), B1 (9% and 7%), D (3% and 3%), F (3% and 3%) and E (2% and 2%). This study highlights the high frequency of ESBL producers and the emergence of carbapenemase-producers among Enterobacterales causing community-acquired UTIs in Djibouti