Unrecognized introduction of SARS-CoV-2 variants of concern to Central Africa: Import and local transmission of B.1.1.7 in Gabon in the very early stage of the variant spread to the African continent.

The rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant of concern with higher infectivity has already resulted in the enormous increase in infection cases worldwide. We report an unrecognized introduction of the variant B.1.1.7 in Gabon in December 2020, which was the initial phase of the variant introduction to Africa. The B.1.1.7 variant was also detected in a hospitalized patient in January 2021, indicating a rapid spread of the variant in Gabon since its first detection. Phylogenetic analysis revealed that the detected B.1.1.7 variants originated from the distinct regions, strongly suggesting that the B.1.1.7 variant had been repeatedly introduced to Gabon since December 2020. These results provide insights on the unrecognized risks of infections with variants of concern, and show the necessity to conduct continuous genomic monitoring for immediate alert and control of novel SARS-CoV-2 variant infections.

Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis.

BACKGROUND: The host, microbial, and environmental factors that contribute to variation in tuberculosis (TB) disease are incompletely understood. Accumulating evidence suggests that one driver of geographic variation in TB disease is the local ecology of mycobacterial genotypes or strains, and there is a need for a comprehensive and systematic synthesis of these data. The objectives of this study were to (1) map the global distribution of genotypes that cause TB disease and (2) examine whether any epidemiologically relevant clinical characteristics were associated with those genotypes. METHODS: We performed a systematic review of PubMed and Scopus to create a comprehensive dataset of human TB molecular epidemiology studies that used representative sampling techniques. The methods were developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We extracted and synthesized data from studies that reported prevalence of bacterial genotypes and from studies that reported clinical characteristics associated with those genotypes. RESULTS: The results of this study are twofold. First, we identified 206 studies for inclusion in the study, representing over 200,000 bacterial isolates collected over 27 years in 85 countries. We mapped the genotypes and found that, consistent with previously published maps, Euro-American lineage 4 and East Asian lineage 2 strains are widespread, and West African lineages 5 and 6 strains are geographically restricted. Second, 30 studies also reported transmission chains and 4 reported treatment failure associated with genotypes. We performed a meta-analysis and found substantial heterogeneity across studies. However, based on the data available, we found that lineage 2 strains may be associated with increased risk of transmission chains, while lineages 5 and 6 strains may be associated with reduced risk, compared with lineage 4 strains. CONCLUSIONS: This study provides the most comprehensive systematic analysis of the evidence for diversity in bacterial strains that cause TB disease. The results show both geographic and epidemiological differences between strains, which could inform our understanding of the global burden of TB. Our findings also highlight the challenges of collecting the clinical data required to inform TB diagnosis and treatment. We urge future national TB programs and research efforts to prioritize and reinforce clinical data collection in study designs and results dissemination.

Use of GeneXpert Remnants for Drug Resistance Profiling and Molecular Epidemiology of Tuberculosis in Libreville, Gabon.

Multidrug-resistant (MDR) and extensively drug resistant (XDR) strains of Mycobacterium tuberculosis pose major problems for global health. The GeneXpert MTB/RIF (Xpert) assay rapidly detects resistance to rifampin (RIFr), but for detection of the additional resistance that defines MDR-TB (MDR tuberculosis) and XDR-TB, and for molecular epidemiology, specimen cultures and a biosafe infrastructure are generally required. We sought to determine whether the remnants of sputa prepared for the Xpert assay could be used directly to find mutations associated with drug resistance and to study molecular epidemiology, thus providing precise characterization of MDR-TB cases in countries lacking biosafety level 3 (BSL3) facilities for M. tuberculosis cultures. After sputa were processed and run on the Xpert instrument, the leftovers of the samples prepared for the Xpert assay were used for PCR amplification and sequencing or for a line probe assay to detect mutations associated with resistance to additional drugs, as well as for molecular epidemiology with spoligotyping and selective mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing. Of 130 sputum samples from Gabon tested with the Xpert assay, 124 yielded interpretable results; 21 (17%) of these were determined to be RIFr Amplification and sequencing or a line probe assay of the Xpert remnants confirmed 18/21 samples as MDR, corresponding to 12/116 (9.5%) new and 6/8 (75%) previously treated TB patients. Spoligotyping and MIRU typing with hypervariable loci identified an MDR Beijing strain present in five samples. We conclude that the remnants of samples processed for the Xpert assay can be used in PCRs to find mutations associated with the resistance to the additional drugs that defines MDR and XDR-TB and to study molecular epidemiology without the need for culturing or a biosafe infrastructure.

Pediatric tuberculosis in a high burden setting: Socio-spatial distribution, blood elements features, and outcomes.

Background: The childhood tuberculosis (TB) epidemic has been long neglected. Data on pediatric tuberculosis is needed to develop effective strategies against TB. Methods: We retrospectively reviewed 200 medical records from children aged 0-15 years who suffered from tuberculosis between 2011 and 2021 in Libreville, Gabon. We collected and analyzed socio-demographic data and clinical data. Results: 141 children files were selected (43 % girls and 57 % boys). The mean age of the patients was 9.2 years (CI: 8.5-10). Sixty per cent (60 %) of cases were from precarious housing areas, 35.34 % from mixed housing areas, and 4.51 % from residential. The cure rate was 75.24 %, 9.52 % relapsed, and 15.24 % died. Deaths were significantly higher in older children (Dunn's post-test p < 0.01). Children who recovered had higher haemoglobin and platelet counts than those who died (Dunn's test: haemoglobin p < 0.0001; thrombocytes p < 0.05). The haemoglobin threshold value of 5.5 g/dL identified children death with up to 80 % sensitivity and 86 % specificity. Thrombocytes count identified children's death with a sensitivity of 80 % and a specificity of 51 %. Conclusion: Precariousness is associated with childhood tuberculosis. The directly observed therapy (DOTS) in older children should be reinforced to limit tuberculosis-associated deaths. Haemoglobin concentration and platelet are vital prognosis markers in pediatric tuberculosis.

Biochemical Alterations Associated With the Severity of COVID-19 in Sub-Saharan Black African Individuals.

BACKGROUND: Biochemical markers are essential in the monitoring and the clinical care of patients as they inform clinicians. Here, we characterized biochemical alterations in sub-Saharan Black African individuals with COVID-19. METHODS: The study includes COVID-19 patients cared for at the Akanda Army Hospital in Libreville (Gabon). A total of 2237 patient records were extracted and reviewed. Patients were classified based on hospital admission (intensive care unit [ICU], internal medicine ward, and outpatient). RESULTS: One thousand six hundred seventy-one were included in the study. ICU patients were significantly older than non-ICU hospitalized patients (P < 0.001) and outpatients (P < 0.0001). Hyperglycemic patients had 6.4 odds of being in ICU (P < 0.0001). Patients with abnormally high urea had 54.7 odds of being in ICU (P < 0.0001). Patients with abnormally high aspartate aminotransferase (AST) (>33 IU/L) had 3.5 odds of being in ICU (P < 0.0001). Hyperlactatemia (>246 IU/L) odds in ICU patients were 14 (P < 0.0001). The odds of abnormally high alkaline phosphatase (ALP) (>147 IU/L) in ICU patients were 4.6 (P < 0.0001). Odds for hypochloremia (<98 mmol/L) were 1.6 in ICU (P < 0.05). Dysnatremia patients (<135 or >145 mmol/L) had 9.5 odds of being found in ICU patients (P < 0.0001). The odds of potassium imbalance (<3.6 or >5 mmol/L) in ICU patients were 12.2 (P < 0.0001). CONCLUSIONS: COVID-19-associated biochemical alterations observed in the Black African population are similar to those observed in other populations, and the association between COVID-19 severity, hyperglycemia, and multi-organ affection is confirmed.

Time to SARS-CoV-2 clearance in African, Caucasian, and Asian ethnic groups.

BACKGROUND: COVID-19 may become a seasonal disease. SARS-CoV-2 active circulation coupled with vaccination efforts has undoubtedly modified the virus dynamic. It is therefore important investigate SARS-CoV-2 dynamic in different groups of population following the course of spatiotemporal variance and immunization. METHODS: To investigate SARS-CoV-2 clearance in different ethnic groups and the impact of immunization, we recruited 777 SARS-CoV-2-positive patients (570 Africans, 156 Caucasians, and 51 Asians). Participants were followed and regularly tested for 2 months until they had two negative tests. RESULTS: The vaccination rate was 64.6%. African individuals were less symptomatic (2%), Caucasians (41%) and Asians (36.6%). On average, viral clearance occurred after 10.5 days. Viral load at diagnosis was inversely correlated with viral clearance (p < 0.0001). The time of SARS-CoV-2 clearance was higher in Africans and Caucasians than in Asians (Dunn's test p < 0.0001 and p < 0.05, respectively). On average, viral clearance occurred within 9.5 days during the second semester (higher rate of vaccination and SARS-CoV-2 exposition), whereas it took 13.6 days during the first semester (lower rate of vaccination and SARS-CoV-2 exposition) (Mann-Whitney t-test p < 0.0001). CONCLUSION: In conclusion, ethnicity and spatiotemporal changes including SARS-CoV-2 exposition and immunization affect SARS-CoV-2 clearance.

HIV-exposed uninfected infants' immune defects: From pathogen sensing, oxidative burst to antigens responses.

The progress in preventing mother-to-child transmission of HIV has led to a significant reduction in mother-to-child HIV transmission, increasing the population of HIV-exposed uninfected (HEU) infants. Studies have shown that HEU infants are more vulnerable to diseases than infants born from HIV-free mothers. Today, there is more and more evidence that helps us understand how exposure to HIV and/or its therapy affects the ability of the immune system of HEU infants to fight infections. This paper mapped out reported critical immune defects in HEU infants, from pathogen sensing and recognition, oxidative burst to antigens-specific responses. Models of neutrophils and monocyte malfunctions in these infants are proposed.

Prostate malignant tumor and benign prostatic hyperplasia microenvironments in black African men: Limited infiltration of CD8+ T lymphocytes, NK-cells, and high frequency of CD73+ stromal cells.

BACKGROUND: Anti-cancerous immunology has yet to be investigated in the African black population, despite being the dawn of precision medicine. AIM: Here we investigated the tumor microenvironment of prostate cancer and benign prostatic hyperplasia (BPH) in black Africans. METHODS: Through immunohistochemistry analysis of prostate cancer and BPH patients' biopsies, we investigated the expression and distribution of CD73, CCD8 T-lymphocytes, and natural killer cells. In addition, we looked at tumor-infiltrating features CD8 T-lymphocytes and natural killer cells. RESULTS: We show for the first time in black Africans a high expression of CD73 in epithelial-stromal cells and virtually no infiltration of CD8 T lymphocytes and natural killer cells in the tumoral area. In addition, CD73 was seven (7) times more likely to be expressed in prostate cancer stromal tissues than in benign prostatic hyperplasia tissues (odds ratio = 7.2; χ2 = 21; p < .0001). In addition, PSA concentration was significantly higher in prostate cancer patients than in BPH patients (p < .001). Also, the PSA-based ROC. analysis showed an area under the curve of 0.87 (p < .0001). CONCLUSION: CD73 expression is more likely expressed in prostate cancer stromal tissues than in benign prostatic hyperplasia tissues. The features of prostate cancer in Black Africans suggest CD73 expression as a possible target for immunotherapy in this population.

Changes of C-reactive protein and Procalcitonin after four weeks of treatment in patients with pulmonary TB.

Objective: Tuberculosis (TB) remains a public health concern worldwide, affecting millions of people every year. Detailed characterization of disease pathophysiology is key to proper diagnosis, disease progression, or treatment follow-up and evaluation. The present study investigated C-reactive protein and Procalcitonin (PCT) as candidate markers of early treatment response and disease activity. Methods: From September to December 2019, 21 HIV-negative consecutive TB patients were recruited, within the setting of the Gabonese TB specialized hospital and the National Laboratory of Public Health, in a prospective study. CRP and PCT levels were measured by chemiluminescence at diagnosis and 4 weeks following the initiation of anti-TB treatment. Results: The mean concentration of CRP in TB patients was 114.7 mg/L (95 % CI: [83.8-145.6]) at diagnosis and 20.2 mg/L (95 % CI: [14.1-26.4]) 4 weeks following anti-TB treatment. The drop in CRP concentrations between diagnosis, and week 4 following anti-TB treatment showed was significant (p < 0.0001). The average concentration of PCT at the time of diagnosis was 0.3 ng/mL (95 % CI: [0.19-0.41]). PCT Concentration dropped below 0.05 ng/mL 4 weeks following the start of anti-TB treatment (p < 0.01). Conclusion: CRP and PCT are potential TB biomarkers, each, carrying important keys. If the drop in both proteins may indicate a significant reduction of the Mtb burden, the maintenance of CRP above the inflammation threshold could indicate the presence of residual bacilli. However, the clinical translation of the present finding will require more investigation.

Allergen sensitization and polysensitization pattern of adults and children in an urban Sub-Saharan African setting (Libreville, Gabon).

Background: It is believed that allergic diseases are increasing in Africa. However, the health sector in Africa has yet to catch up with this paradigm shift. We looked at the number of patients referred to us for allergy testing and investigated allergen sensitization. Methods: A retrospective analysis was done on 97 serum allergen-specific IgE results collected from patients suspected of having allergies in Libreville from 2018 to 2021. Specific IgE responses to 180 allergens were investigated. The general sensitization patterns were analyzed. Also analyzed were sensitization patterns for adults and children. The difference in the IgE-binding allergen positivity rate between groups was calculated by using the chi-square (χ2) test. Results: The allergens most commonly causing sensitization were from mites (65%), barley (48%), peach (48%), dog and/or cat dander (44%), house dust (44%), peanut (39%), tomato (39%), cockroach (37%), crab (36%), garlic and/or onion (34%), rye (34%), egg white (32%), shrimp (32%), kiwi (32%), soya bean (32%), citrus mix (29%), cheese (27%), milk (27%), walnut (27%), ox-eye daisy (24%) and orchard grass (24%). Moreover, 60% of patients (36 of 60) were polysensitized to inhalant allergens, 53% (31 of 58) were polysensitized to food allergens, and 29% (14 of 48) were polysensitized to inhalant and food allergens; 65% of patients (53 of 81) were sensitized to allergens originating from mites, fungi (including Candida albicans, Alternaria alternata, Aspergillus fumigatus, Cladosporium herbarum, and Pennicillium notatum), or bacteria (staphylococcal enterotoxin B). Conclusions: The sensitization pattern of allergens in our setting is rich and varied, with a high prevalence of polysensitization.