Assessment of the pathogen genomics landscape highlights disparities and challenges for effective AMR Surveillance and outbreak response in the East African community.

The East African Community (EAC) grapples with many challenges in tackling infectious disease threats and antimicrobial resistance (AMR), underscoring the importance of regional and robust pathogen genomics capacities. However, a significant disparity exists among EAC Partner States in harnessing bacterial pathogen sequencing and data analysis capabilities for effective AMR surveillance and outbreak response. This study assesses the current landscape and challenges associated with pathogen next-generation sequencing (NGS) within EAC, explicitly focusing on World Health Organization (WHO) AMR-priority pathogens. The assessment adopts a comprehensive approach, integrating a questionnaire-based survey amongst National Public Health Laboratories (NPHLs) with an analysis of publicly available metadata on bacterial pathogens isolated in the EAC countries. In addition to the heavy reliance on third-party organizations for bacterial NGS, the findings reveal a significant disparity among EAC member States in leveraging bacterial pathogen sequencing and data analysis. Approximately 97% (n = 4,462) of publicly available high-quality bacterial genome assemblies of samples collected in the EAC were processed and analyzed by external organizations, mainly in Europe and North America. Tanzania led in-country sequencing efforts, followed by Kenya and Uganda. The other EAC countries had no publicly available samples or had all their samples sequenced and analyzed outside the region. Insufficient local NGS sequencing facilities, limited bioinformatics expertise, lack of adequate computing resources, and inadequate data-sharing mechanisms are among the most pressing challenges that hinder the EAC's NPHLs from effectively leveraging pathogen genomics data. These insights emphasized the need to strengthen microbial pathogen sequencing and data analysis capabilities within the EAC to empower these laboratories to conduct pathogen sequencing and data analysis independently. Substantial investments in equipment, technology, and capacity-building initiatives are crucial for supporting regional preparedness against infectious disease outbreaks and mitigating the impact of AMR burden. In addition, collaborative efforts should be developed to narrow the gap, remedy regional imbalances, and harmonize NGS data standards. Supporting regional collaboration, strengthening in-country genomics capabilities, and investing in long-term training programs will ultimately improve pathogen data generation and foster a robust NGS-driven AMR surveillance and outbreak response in the EAC, thereby supporting global health initiatives.

Genomic surveillance of severe acute respiratory syndrome coronavirus 2 in Burundi, from May 2021 to January 2022.

BACKGROUND: The emergence and rapid spread of new severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) variants have challenged the control of the COVID-19 pandemic globally. Burundi was not spared by that pandemic, but the genetic diversity, evolution, and epidemiology of those variants in the country remained poorly understood. The present study sought to investigate the role of different SARS-COV-2 variants in the successive COVID-19 waves experienced in Burundi and the impact of their evolution on the course of that pandemic. We conducted a cross-sectional descriptive study using positive SARS-COV-2 samples for genomic sequencing. Subsequently, we performed statistical and bioinformatics analyses of the genome sequences in light of available metadata. RESULTS: In total, we documented 27 PANGO lineages of which BA.1, B.1.617.2, AY.46, AY.122, and BA.1.1, all VOCs, accounted for 83.15% of all the genomes isolated in Burundi from May 2021 to January 2022. Delta (B.1.617.2) and its descendants predominated the peak observed in July-October 2021. It replaced the previously predominant B.1.351 lineage. It was itself subsequently replaced by Omicron (B.1.1.529, BA.1, and BA.1.1). Furthermore, we identified amino acid mutations including E484K, D614G, and L452R known to increase infectivity and immune escape in the spike proteins of Delta and Omicron variants isolated in Burundi. The SARS-COV-2 genomes from imported and community-detected cases were genetically closely related. CONCLUSION: The global emergence of SARS-COV-2 VOCs and their subsequent introductions in Burundi was accompanied by new peaks (waves) of COVID-19. The relaxation of travel restrictions and the mutations occurring in the virus genome played an important role in the introduction and the spread of new SARS-COV-2 variants in the country. It is of utmost importance to strengthen the genomic surveillance of SARS-COV-2, enhance the protection by increasing the SARS-COV-2 vaccine coverage, and adjust the public health and social measures ahead of the emergence or introduction of new SARS-COV-2 VOCs in the country.

Serotype distribution and antimicrobial susceptibility of invasive Streptococcus pneumoniae isolates among adult and elderly population before and after introduction of pneumococcal conjugate vaccine in Casablanca, Morocco.

BACKGROUND: Streptococcus pneumoniae (S. pneumoniae), remains a major cause of mortality and morbidity worldwide. The objective of this study was to determine the trends of invasive pneumococcal diseases (IPD) in adult and elderly population in Casablanca (Morocco) before and after introduction of pneumococcal conjugate vaccine (PCV) by determining the distribution of pneumococcal serotypes and antibiotic resistance profile of isolated strains. METHOD: The proposed study is a retrospective laboratory-based surveillance of IPD in hospitalized adult (15-59 years old) and elderly (≥ 60 years old) patients in Ibn Rochd University Hospital Centre from 2007 to 2019 (13 years). All the 250 non-duplicate clinical invasive isolates from adult and elderly patients, confirmed as S. pneumoniae according to the laboratory standard identification procedures, are included in this study. RESULTS: A significant decrease of the overall incidence in IPD was observed only in adults from 0.71 to 0.54/100000 populations (P = 0.02) and to 0.47/100000 populations (P = 0.0137) in the early and mature post-vaccine period respectively compared to the pre-vaccine period. Our results also showed a significant reduction in the overall prevalence of vaccine serotypes from 28.17 to 6.90% (P = 0.0021) for the PCV-10 serotypes, and from 46.48 to 25.86% (P = 0.0164) for the PCV-13 serotypes only in the mature post-vaccine period (2015-2019). In parallel, the rate of non-vaccine serotypes did not significantly change in the early post-vaccine period (2011-2014) while it increased considerably from 54 to 74.14% (P = 0.0189) during the mature post-vaccine period. The rate of penicillin non-susceptible pneumococcal isolates decreased significantly from 23.94 to 8.77% (P = 0.02) in adult patients, and the rate of cotrimoxazole non-susceptible pneumococcal isolates significantly decreased from 29.58 to 8.77% in the early post-vaccine period (P = 0.003) and to 7.24% in the mature post-vaccine period (P = 0.0007). CONCLUSION: Although childhood vaccination has considerably reduced the incidence of IPD in adult population through the herd effect, IPD remain a real public health problem due to the alarming increase in non-vaccine serotypes (NVS) and the lack of herd effect among elderly population. The rate of antibiotic resistance was relatively low. Nevertheless, resistance constitutes a serious problem to the therapeutic arsenal due to the known capacity for genetic dissemination in the pneumococcus.

Impact and prevalence of comorbidities and complications on the severity of COVID-19 in association with age, gender, obesity, and pre-existing smoking: A meta-analysis.

Background: COVID-19 patients usually present multiple comorbidities and complications associated with severe forms of SARS-CoV-2 infection. This study aimed to assess the risk factors and prevalence of comorbidities and complications contributing to the severity of COVID-19. Methods: This meta-analysis was performed according to PRISMA guidelines. We searched various databases, including PubMed, Google Scholar, and Scopus (between 2020 and 2023), for eligible studies for this meta-analysis. Results: Thirty-three studies were eligible, including 85,812 patients, of which 36 % (30,634/85,812) had severe disease, whereas 64 % (55,178/85,812) had non-severe disease. Severe cases were potentially correlated with the following factors: gender (male) (odd ratio (OR) = 1.52, 95 % CI: 1.34-1.73), advanced age (OR = 3.06, 95 % CI: 2.18-4.40) pre-existing smoking (OR = 1.33, 95 % CI: 1.01-1.75), obesity (OR = 2.11, 95 % CI: 1.47-3.04), diabetes (OR = 1.81, 95 % CI: 1.35-2.43), hypertension (OR = 2.22, 95 % CI: 1.72-2.87), coronary heart disease (OR = 2.17, 95 % CI: 1.42-3.31), CKD (OR = 2.27, 95 % CI: 1.26-4.06), COPD (OR = 1.95, 95 % CI: 1.22-3.09), malignancy (OR = 1.63, 95 % CI: 1.07-2.49) and cerebrovascular disease (OR = 2.76, 95 % CI: 1.63-4.62). All these comorbidities were significantly higher in the severe COVID-19 group compared with the non-severe COVID-19 group. In addition, the most severe complications were associated with shock (OR = 28.08, 95 % CI: 3.49-226.03), ARDS (OR = 13.09, 95 % CI: 5.87-29.18), AKI (OR = 16.91, 95 % CI: 1.87-152.45) and arrhythmia (OR = 7.47, 95 % CI: 2.96-18.83). However, these complications were the most likely to prevent recovery in patients with severe affections compared with non-severe affection groups. Conclusion: All the comorbidities and complications listed above are more likely to cause severe forms of COVID-19 in some patients and hinder recovery. They are therefore risk factors to be controlled to minimize the undesirable effects of the disease.

Hypertension Management Among Hospitalised Patients at Kamenge University Hospital in Bujumbura.

Background: According to the World Health Organization in 2015, 40 million out of the 56 million deaths recorded worldwide (70%) were due to non-communicable diseases. These were mainly cardiovascular diseases, cancers, chronic respiratory diseases and diabetes. Methods: A prospective descriptive study was conducted from October 2018 to March 2019. Availability of the files in the department's archives store for medical records and availability of trained physicians to perform diagnosis and treatment of HBP were the criteria used to select departments to be included in the study. Results: Patients data were recorded from internal medicine department (59.8%), emergency department (18.1%) gynaecology and obstetrics department (13.3%) and surgery department (8.6%). The mean age of the patients who were hospitalised in the study period was 54 years (SD±10.2) with extremes of 18 and 104 years. The modal class was the age group of 50 to 60 with 24.4% of cases. Among patients who were hospitalised, 3.6% (127) had essential hypertension, of which 57.4% (73) were women. Conclusion: Notable percentage of patients hospitalized at the University Hospital of Kamenge had essential hypertension. However, patients' knowledge of their hypertensive status had no positive contribution to its management.

Evaluation of SARS-CoV-2 infection risks after primary vaccination with BNT162b2, BBIBP-CorV, or ChAdOx1-nCOV-19 and after homologous and heterologous booster vaccinations with these vaccines and evaluation of SARS-CoV-2 reinfection profiles.

Background: The emergence of SARS-CoV-2 variants has significantly increased the number of cases of COVID-19 among vaccinated individuals, raising concerns about the effectiveness of current vaccines. The aim of this study was to analyze the SARS-CoV-2 infection risks after primary vaccination with BNT162b2, BBIBP-CorV, or ChAdOx1-nCOV-19 and after homologues and heterologous booster vaccinations with these vaccines, as well as the profiles of reinfected patients. Methods: We analyzed retrospectively 1082 patients vaccinated or unvaccinated with BNT162b2, BBIBP-CorV, and/or ChAdOx1nCoV-19 vaccines to determine their SARS-CoV2 infection statuses using the reverse transcription-polymerase chain reaction (RT-PCR) in addition to their clinical features. The infection risks of patients receiving the different vaccine regimens were compared using multivariate logistic regression analysis, comparing the adjusted OR of a positive COVID-19 test result. Results: Among 596 vaccinated patients, 53%(n = 286) tested positive for SARS-CoV-2 and 57%(n = 310) tested negative. Among positive cases, 10 were reinfection cases. The risk of SARS-CoV-2 infection was 1.6 (adj. OR) for patients who received one dose compared with those who received two doses (95% CI = 1.3-1.8; p < 0.01).The risk was 2.6 (adj. OR) for patients who received one dose compared with those who received three doses (95%CI = 2.1-3.3; p < 0.01), and 1.6 (adj. OR) for patients who received two doses compared with those who received three doses (95% CI = 1.3-2; p < 0.01). The patients who received two doses that were heterologous to that of the primary vaccine had the lowest risk of infection. Booster vaccinations (third dose) significantly reduced the number of positive cases with an acceptable safety profile. Higher cycle-threshold (Ct) values (indicative of viral load) were observed in vaccinated patients, whereas low Ct values were observed in unvaccinated patients. Conclusion: A complete cycle of vaccination with homologous vaccines or heterologous vaccines resulted in an acceptable reduction in SARS-CoV-2 infection. Further, vaccination was associated with a reduction in viral load.

Clinical and Epidemiology Characteristics of COVID-19 Cases Detected During Mass Screening Campaign from July to October 2020 in Bujumbura, Burundi.

Background: Coronavirus disease of 2019 (COVID-19) is an infectious disease caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-COV-2 Virus). It was reported for the first time in Wuhan city, Hubei province of China. The first cases of COVID-19 in Burundi were identified on 31st March 2020. Several signs and symptoms, including mainly; fever, dry cough, fatigue, myalgia, and dyspnea are the most prominent characteristics of the disease. The aim of this study was to provide description of the clinical and epidemiological characteristics of COVID-19 cases identified during the mass screening campaign conducted between July and October, 2020 in Burundi. Methods: We conducted a retrospective secondary analysis of data of clients to the mass screening campaign in Bujumbura city that was run between July and October 2020. Clients with complete data and tested for COVID-19 with Reverse Transcription Polymerase Chain Reaction (RT-PCR) were included in the study. Epi-Info 7.2.2.6 was used to perform descriptive and analytical statistics and Quantum Geographic Information System (QGIS) was used for cases mapping. Association between positive cases and independent variables such as sex, history of contact with confirmed COVID-19 case was measured using chi-square statistical test at a p-value of .05. Results: The study included 20,114 participants. 243 (1.2%) were tested positive for COVID-19. The mean age for confirmed cases was 33 (±15) years. The majority of cases (72.8%) were between 20 and 59 years of age and they were predominantly males (67.9%). 164 (67.5%) were symptomatic and cough was the most frequent symptom observed 109 (66.5%), followed by rhinorrhea 69 (42.1%). Fever was present in only 18 (11.0%) of symptomatic patients. Participants with a history of contact with a COVID-19 confirmed case (aOR=2.2; 95%CI [1.6-3.0]; p-value <.001), were more likely to be positive for COVID-19. Also, those who were coughing (aOR=1.47; 95%CI [1.06-2.05]; p-value=.023) and having sore throat (aOR=2.4; 95%CI [1.1-4.9]; p-value=.02) were more likely to test positive for COVID-19. Conclusion: This study revealed that a significant proportion (32.5%) of COVID-19 patients were silent carriers of the virus. Data highlighted that high proportion of cases were among the active age group and contacts with confirmed cases, and noted high proportion of asymptomatic cases at diagnosis. Measures including routine testing of asymptomatic contacts could contribute to tackling corona virus in Burundi.

Performance of highly sensitive and conventional rapid diagnostic tests for clinical and subclinical Plasmodium falciparum infections, and hrp2/3 deletion status in Burundi.

Rapid diagnostic tests (RDTs) are a key tool for the diagnosis of malaria infections among clinical and subclinical individuals. Low-density infections, and deletions of the P. falciparum hrp2/3 genes (encoding the HRP2 and HRP3 proteins detected by many RDTs) present challenges for RDT-based diagnosis. The novel Rapigen Biocredit three-band Plasmodium falciparum HRP2/LDH RDT was evaluated among 444 clinical and 468 subclinical individuals in a high transmission setting in Burundi. Results were compared to the AccessBio CareStart HRP2 RDT, and qPCR with a sensitivity of <0.3 parasites/µL blood. Sensitivity compared to qPCR among clinical patients for the Biocredit RDT was 79.9% (250/313, either of HRP2/LDH positive), compared to 73.2% (229/313) for CareStart (P = 0.048). Specificity of the Biocredit was 82.4% compared to 96.2% for CareStart. Among subclinical infections, sensitivity was 72.3% (162/224) compared to 58.5% (131/224) for CareStart (P = 0.003), and reached 88.3% (53/60) in children <15 years. Specificity was 84.4% for the Biocredit and 93.4% for the CareStart RDT. No (0/362) hrp2 and 2/366 hrp3 deletions were observed. In conclusion, the novel RDT showed improved sensitivity for the diagnosis of P. falciparum.

Uptake of Modern Contraceptive Methods among Burundian Women and Associated Factors: Analysis of Demographic and Health Survey Data, Burundi 2016-2017.

BACKGROUND: Globally in 2017, Burundi was the 9th country with the highest population growth rate of 3.2% and a fertility rate of 5.5 children per woman. This probably suggested low uptake of Modern Contraceptive methods (MCM) in the country. Our analysis investigated factors associated with low uptake of MCM among women of reproductive age in Burundi. METHODS: Cross sectional data of non-pregnant women aged 15-49 years was extracted from the Burundi Demographic and Health Survey (2016-2017). We analysed the data at univariate, bivariate and multivariate levels to assess factors influencing MCM uptake among these women using Epi-Info 7.2.2.6. RESULTS: Of the 9,945 women, 2,372 (23.8%) were using MCM. Ngozi province had the highest prevalence of MCM users [284/691(37.7%)]. The most used MCM among respondents was injectable contraceptive (48.3%). As respondent's age increases, the odds of using MCM decreases; 20-24 years (aOR=0.9, 95% CI [0.6-1.2]), 30-34 years (aOR=0.8, 95% CI [0.5-1.0]), 35-39 years (aOR=0.7, 95% CI [0.5-0.9]), 40-44 years (aOR=0.5, 95% CI [0.5-0.9]) and 45-49 years (aOR=0.4, 95% CI [0.2-0.5]) compared with those in the age group 15-19 years. Muslims (aOR=1.5, 95% CI [1.2-1.9]) and Jehovah witnesses (aOR=3.1, 95% CI [1.7-6.5]) were more likely to use MCM than Catholics. CONCLUSION: The prevalence of MCM remains low among women of reproductive age in Burundi, with injectables being the most used method. Factors such as respondent's age and religion were significantly associated with MCM use. Enhanced access to family planning information and services targeting women who are 30 years or more and engaging religious leaders for their active participation is recommended.

Plasmodium falciparum and P. malariae: infection rates in the population of Northern Imbo Plain, Burundi.

BACKGROUND: Burundi is cited among countries where malaria remains endemic. Notably, malaria is highly endemic in Imbo region, a lowland lying astride Lake Tanganyika. Among key malaria riposte interventions includes the promotion of Long-Lasting Insecticidal Nets (LLINs), but its incidence rate has not reduced. In this paper, we present the distribution of malaria species in 2 settings within Imbo region by accounting for the seasonal variations and the mostly infected populations. METHODS: The study was conducted from 2 Health Care Centres of Murambi and Rugombo in Cibitoke District, Northern Burundi. Blood samples were collected on blood slides and the samples were used to confirm the presence of malaria parasites by microscopy. RESULTS: The study observed an average malaria parasite prevalence of 32.5% across the selected site. Majority of patients 459(95.2%) were infected by P. falciparum while 8(1.7%) patients were infected by P. malariae. Patients from Murambi were more infected than those from Rugombo. P. falciparum was the most highly prevalent specie in the 2 localities. High prevalence was observed in children aged between 2 and 5 years. Among older participants P. falciparum still predominated and mixed infections were rather the least prevalent. CONCLUSION: This study showed that P. falciparum and P. malariae are the most parasites involved in malaria morbidity in North Imbo region. The transmission of P. falciparum was observed year-round. Patients in Murambi are most exposed to malaria infections than those in Rugombo. Further research at large scale including entomological studies is required to better understand the relationship between Entomological Inoculation Rates (EIR) and malaria transmission levels in this setting.

Prevention of Mother-to-Child Transmission and Early Real-Time DNA Polymerase Chain Reaction Results Among HIV-Exposed Infants in Bujumbura, Burundi.

BACKGROUND: Prevention of mother-to-child transmission (PMTCT) programmes aim to both eliminate vertical transmission of HIV and optimise the health and survival of infants born with HIV. Therefore, early infant diagnosis (EID) of HIV infection via DNA polymerase chain reaction (PCR) testing is a key component of PMTCT programming. We assessed the effectiveness of EID and PMTCT interventions at health-care facilities in Bujumbura, Burundi. METHODS: This was a prospective analytical study of infants born to HIV-positive mothers on antiretroviral therapy (ART), who were followed from December 2016 to March 2017 at 3 centres providing PMTCT services in Bujumbura. Babies enrolled in this study received once-daily nevirapine from birth through to 6 weeks of life, after which HIV DNA PCR testing was conducted. RESULTS: Of 122 HIV-exposed infants, 60 were boys and 62 were girls. The mother-to-child transmission rate at 6 weeks of life was 0.9%. Eighty-three (68%) of the women had commenced ART before pregnancy and 39 (32%) during pregnancy. The mean CD4 lymphocyte count was 653±308 cells/µl. Ninety-two (75.4%) of the pregnancies were planned, and 98 (80%) of the births were via spontaneous vaginal delivery. After birth, 111 (91.0%) infants were exclusively breastfed, and 11 (9.0%) infants received exclusive replacement feeding. CONCLUSION: There was a low rate of transmission of HIV from women taking ART to children who were given nevirapine for the first 6 weeks of life. Infants of HIV-positive women can live healthy lives free from HIV infection if their mothers participate in PMTCT programmes.

Frequency of Uropathogens and Antimicrobial Susceptibility in Childhood Urinary Tract Infection at Kamenge University Hospital, Bujumbura, Burundi.

BACKGROUND: Increasing resistance to antimicrobials is a worldwide problem. The aim of our study was to determine the pathogens and antimicrobial susceptibility of bacteria causing urinary tract infection (UTI) in children. METHODS: This is a prospective cohort study conducted over a 10-month period with 101 children hospitalised at Kamenge University Hospital for acute UTI. The infections were confirmed by Kass urinalysis criteria, and culture and susceptibility antibiotic tests were performed for isolated microbial agents. RESULTS: Frequency of UTI in the overall population of children hospitalised at Kamange University Hospital was 8.4%. Of the 101 children with UTIs, 87 (86.1%) were under the age of 24 months. Diagnosis of pyelonephritis (82%) was the most common, followed by cystitis (18%). Escherichia coli (82%) was the most frequent pathogen causing UTI. We found E coli and Klebsiella pneumonia to be resistant to aminopenicillins (100%), cotrimoxazole (98.2%, 100%), Augmentin (amoxicillin/clavulanic acid) (70.5%, 80%), cefotaxime (45.8%, 28.6%), cefuroxime (36.8 to 45.5%, 50%), fluoroquinolones (33.3 to 53.6%, 28.6 to 50%), gentamicin (27.5%, 20%), and nitrofurantoin (9.3%, 50%). CONCLUSION: E coli is the main causal agent of UTI in childhood with a high resistance to antibiotics. Appropriate antibiotics for empiric therapy should be based on local circulating bacterial strains and resistance profiles.

[Ophthalmic manifestations in Wegener's granulomatosis. Review of literature about an observation]. / Manifestations ophtalmologiques de la granulomatose de Wegener. Revue de la littérature à propos d'une observation.

Wegener's granulomatosis mainly affects the upper respiratory tract, the lungs and the kidneys but many other organs and tissues may be affected, as well including any eye structures. Ocular and orbital structures involvement is frequently encountered, sometimes inaugural, with or without obvious systemic manifestations, sometimes leading to visual loss. The most frequent ophthalmic lesions are inflammatory orbital disease, (necrotising) scleritis with or without keratopathy, episcleritis, conjunctivitis and even conjunctival ulcer, nasolacrimal ducts obstruction, uveitis, retinal vasculitis and even central retinal vascular occlusion, optic neuritis. These ocular lesions result either from extensive granulomatous inflammation or from focal vasculitis. These complications need to be recognized as soon as possible so that an early diagnosis may allow the appropriate treatment meant to keep both visual and even general prognosis.