Genotype characterization of Epstein–Barr virus among adults living with human immunodeficiency virus in Ethiopia

BackgroundEpstein–Barr virus (EBV) is a human lymphotropic herpesvirus with a causative agent in cancer. There are two genotypes of EBV (EBV genotype 1 and EBV genotype 2) that have been shown to infect humans. This study aimed to characterize the EBV genotype among people with human immunodeficiency virus (PWH) and HIV-negative individuals in Ethiopia.MethodsDNA was extracted from peripheral blood mononuclear cells (PBMCs). Conventional polymerase chain reaction (cPCR) targeting EBNA3C genes was performed for genotyping. A quantitative real-time PCR (q-PCR) assay for EBV DNA (EBNA1 ORF) detection and viral load quantification was performed. Statistical significance was determined at a value of p < 0.05.ResultIn this study, 155 EBV-seropositive individuals were enrolled, including 128 PWH and 27 HIV-negative individuals. Among PWH, EBV genotype 1 was the most prevalent (105/128, 82.0%) genotype, followed by EBV genotype 2 (17/128, 13.3%), and mixed infection (6/128, 4.7%). In PWH, the median log10 of EBV viral load was 4.23 copies/ml [interquartile range (IQR): 3.76–4.46], whereas it was 3.84 copies/ml (IQR: 3.74–4.02) in the HIV-negative group. The EBV viral load in PWH was significantly higher than that in HIV-negative individuals (value of p = 0.004). In PWH, the median log10 of EBV viral load was 4.25 copies/ml (IQR: 3.83–4.47) in EBV genotype 1 and higher than EBV genotype 2 and mixed infection (p = 0.032).ConclusionIn Ethiopia, EBV genotype 1 was found to be the most predominant genotype, followed by EBV genotype 2. Understanding the genotype characterization of EBV in PWH is essential for developing new and innovative strategies for preventing and treating EBV-related complications in this population

A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex

The Mycobacterium tuberculosis complex (MTBC) includes several human- and animal-adapted pathogens. It is thought to have originated in East Africa from a recombinogenic Mycobacterium canettii-like ancestral pool. Here, we describe the discovery of a clinical tuberculosis strain isolated in Ethiopia that shares archetypal phenotypic and genomic features of M. canettii strains, but represents a phylogenetic branch much closer to the MTBC clade than to the M. canettii strains. Analysis of genomic traces of horizontal gene transfer in this isolate and previously identified M. canettii strains indicates a persistent albeit decreased recombinogenic lifestyle near the emergence of the MTBC. Our findings support that the MTBC emergence from its putative free-living M. canettii-like progenitor is evolutionarily very recent, and suggest the existence of a continuum of further extant derivatives from ancestral stages, close to the root of the MTBC, along the Great Rift Valley

Effects of vitamin D on neonatal sepsis: A systematic review and meta-analysis

Vitamin D deficiency is a major public health concern of pregnant women and neonates worldwide, affecting more than half of neonates. Studies report inconsistent and inconclusive effects of vitamin D treatment on neonatal sepsis. This study aimed to provide conclusive evidence regarding the effect of maternal and cord blood vitamin D levels on neonatal sepsis. Data were retrieved from the electronic database (Web of Science, Scopus, CINAHL [EBSCOhost], ProQuest, EMBASE [Ovid], PubMed, Emcare, MEDLINE [Ovid], and gray literature sources [World cat, Mednar, Google scholar and Google]). Joanna Briggs Institute quality assessment tool was utilized for quality assessment while analysis was performed using Open Meta-analyst, Comprehensive Meta-analysis version 3.3.070, and Review Manager version 5.3 software. From the 18 studies included in the study, the overall prevalence of vitamin D deficiency among neonates was 61% (95% CI: 44.3, 77.7); 79.4% (95% CI: 71.6, 87.3) of neonates with sepsis were vitamin D deficient as were 43.7% (23.4, 63.9) of sepsis-free neonates. Neonates born from mothers with low vitamin D levels were at greater risk of developing neonatal sepsis with a weighed mean difference of −8.57 ng/ml (95% CI: −13.09, −4.05). Similarly, neonates with low cord vitamin D levels were at risk for neonatal sepsis with a mean difference of −8.78 ng/ml (95% CI:-11.58, −5.99). The incidence of EONS in full-term newborns was significantly associated with low maternal and cord blood vitamin D levels with weighed mean differences of −11.55ng/ml (95% CI: −17.63, −5.46) & −11.59 ng/ml (95% CI:-16.65, −6.53), respectively. Low levels of vitamin D both in the cord blood and maternal blood were significantly associated with neonatal sepsis. Hence, vitamin D supplementation for pregnant women and newborns could decrease neonatal sepsis

Microbiological diagnosis and mortality of tuberculosis meningitis: Systematic review and meta-analysis.

BackgroundTuberculosis (TB) which is caused by Mycobacterium tuberculosis poses a significant public health global treat. Tuberculosis meningitis (TBM) accounts for approximately 1% of all active TB cases. The diagnosis of Tuberculosis meningitis is notably difficult due to its rapid onset, nonspecific symptoms, and the difficulty of detecting Mycobacterium tuberculosis in cerebrospinal fluid (CSF). In 2019, 78,200 adults died of TB meningitis. This study aimed to assess the microbiological diagnosis TB meningitis using CSF and estimated the risk of death from TBM.MethodsRelevant electronic databases and gray literature sources were searched for studies that reported presumed TBM patients. The quality of included studies was assessed using the Joanna Briggs Institute Critical Appraisal tools designed for prevalence studies. Data were summarized using Microsoft excel ver 16. The proportion of culture confirmed TBM, prevalence of drug resistance and risk of death were calculated using the random-effect model. Stata version 16.0 was used perform the statistical analysis. Moreover, subgroup analysis was conducted.ResultsAfter systematic searching and quality assessment, 31 studies were included in the final analysis. Ninety percent of the included studies were retrospective studies in design. The overall pooled estimates of CSF culture positive TBM was 29.72% (95% CI; 21.42-38.02). The pooled prevalence of MDR-TB among culture positive TBM cases was 5.19% (95% CI; 3.12-7.25). While, the proportion of INH mono-resistance was 9.37% (95% CI; 7.03-11.71). The pooled estimate of case fatality rate among confirmed TBM cases was 20.42% (95%CI; 14.81-26.03). Based on sub group analysis, the pooled case fatality rate among HIV positive and HIV negative TBM individuals was 53.39% (95%CI; 40.55-66.24) and 21.65% (95%CI;4.27-39.03) respectively.ConclusionDefinite diagnosis of TBM still remains global treat. Microbiological confirmation of TBM is not always achievable. Early microbiological confirmation of TBM has great importance to reduce mortality. There was high rate of MDR-TB among confirmed TBM patients. All TB meningitis isolates should be cultured and drug susceptibility tested using standard techniques

Genetic diversity and drug sensitivity profile of Mycobacterium tuberculosis among children in Ethiopia.

BackgroundWorldwide, tuberculosis (TB) affects about one million children every year. The burden of the disease is higher in developing countries. However, there is limited information on the lineages and drug sensitivity patterns of Mycobacterium tuberculosis (M. tuberculosis) infecting children in these countries, including Ethiopia. Thus, this study aimed to characterize the different lineages of the M. tuberculosis complex causing childhood pulmonary tuberculosis and evaluate the drug-sensitivity patterns to the first-line anti-TB drugs.MethodA total of 54 stored cultures were used in this study. The region of difference 9 (RD9) based polymerase chain reaction (PCR) and spoligotyping were employed for the identification of the isolates at the species and lineages level respectively. Lineage identification was done by using the pre-existing database. Identification of clustering of the spoligotype patterns was by using the SPOLIDB3-based model. The result was retrieved by the most probable family format. Furthermore, the phenotypic, and genotypic drug-sensitivity test (DST) was performed using Mycobacterium Growth Indicator Tube (MGIT™ 960) and GenoTypeMTBDRplus assay respectively. Data analysis was done using SPSS version 27 software.ResultSpoligotyping produced 39 interpretable results for M. tuberculosis. The majority (74.4%) of them were clustered into 7 groups, while the rest (25.6%) were single. The Euro-American (EA) lineage was the predominant lineage (64.1%) followed by the East-African Indian (EAI) (30.8%) and M. Africanum (5.1%) lineages. The most predominant subtypes were SIT37 (15.4%), SIT149 (12.8%), SIT25 (7.7%), and SIT53 (7.7%). Furthermore, of the identified SITs, T1 and CAS families consisted of 38.5% and 28.2% of the lineages respectively. Drug susceptibility was 91.9% by phenotypic method and 97.4% by molecular assay. The overall prevalence of any resistance was 7.8% and there was a single MDR-TB.ConclusionMany of the isolates belong to the modern lineages (Euro American) representing the most common circulating strains in the country. More importantly, despites the tiny isolates tested, drug resistance is low. To fully describe the molecular epidemiology of MTBC lineages in children, we recommend a prospective large-scale study

Incidence and predictors of extrapulmonary tuberculosis among people living with Human Immunodeficiency Virus in Addis Ababa, Ethiopia: A retrospective cohort study.

BACKGROUND:Extrapulmonary tuberculosis is an emerging public health problem among HIV positives compared to the general population. This study aimed to assess the incidence and predictors of extrapulmonary tuberculosis among people living with HIV in selected health facilities in Addis Ababa, Ethiopia, from 01 January 2013 up to 31 December 2018. METHODS:A retrospective cohort study design was employed based on data collected from 566 HIV positive individuals. Data were entered using EpiInfo version 7.1 and analyzed by SPSS version 20. The incidence rate was determined per 100 person-years. Kaplan-Meier estimates used to estimate survivor and the hazard function, whereas log-rank tests used to compare survival curves and hazard across different categories. Cox proportional hazard model was used to identify the predictors and 95%CI of the hazard ratio were computed. P-value<0.05 in the multivariable analysis was considered statistically significant. RESULTS:Five hundred sixty-six HIV positive individuals were followed for 2140.08 person-years. Among them, 72 developed extrapulmonary tuberculosis that gives an incidence rate of 3.36/100 person-years (95%CI = 2.68-4.22). The most frequent forms of extrapulmonary tuberculosis were; lymph node tuberculosis (56%, 41) followed equally by pleural tuberculosis (15%, 11) and disseminated tuberculosis (15%, 11). The majority (70.83%) of the cases occurred within the first year of follow-up. In multivariable Cox regression analysis, baseline WHO stage III/IV (AHR = 2.720, 95%CI = 1.575-4.697), baseline CD4 count<50cells/μl (AHR = 4.073, 95%CI = 2.064-8.040), baseline CD4 count 50-200 cells/μl (AHR = 2.360, 95%CI = 1.314-4.239) and baseline Hgb<10 mg/dl (AHR = 1.979, 95%CI = 1.091-3.591) were the independent risk factors. While isoniazid prophylaxis (AHR = 0.232, 95%CI = 0.095-0.565) and taking antiretroviral drugs (AHR = 0.134, 95%CI = 0.075-0.238) had a protective benefit. CONCLUSION:Extrapulmonary tuberculosis co-infection was common among HIV positive individuals, and mostly occurred in those with advanced immune suppression. The risk decreases in those taking antiretroviral therapy and took isoniazid preventive treatment. Screening of HIV positives for extrapulmonary tuberculosis throughout their follow-up would be important

Incidence Density Rate of Neonatal Mortality and Predictors in Sub-Saharan Africa: A Systematic Review and Meta-Analysis

Background. Neonatal mortality in Sub-Saharan countries is remarkably high. Though there are inconsistent studies about the incidence density rate of neonatal mortalities (IDR) and predictors in Sub-Saharan Africa, they are inconclusive to policymakers and program planners. In this study, the IDR of neonatal mortalities and predictors was determined. Methods. Electronic databases (Web of Science, PubMed, EMBASE (Elsevier), Scopus, CINAHL (EBSCOhost), World Cat, Google Scholar, and Google) were explored. 20 out of 818 studies were included in this study. The IDRs and predictors of neonatal mortality were computed from studies conducted in survival analysis. Fixed and random effect models were used to compute pooled estimates. Subgroup and sensitivity analyses were performed. Results. Neonates were followed for a total of 1,095,611 neonate-days; 67142 neonate-days for neonates treated in neonatal intensive care units and 1,028,469 neonate-days for community-based studies. The IDRs of neonatal mortalities in neonatal intensive care units and in the community were 24.53 and 1.21 per 1000 person-days, respectively. The IDRs of early and late neonatal mortalities neonatal intensive care units were 22.51 and 5.09 per 1000 neonate-days, respectively. Likewise, the IDRs of early and late neonatal mortalities in the community were 0.85 and 0.31, respectively. Not initiating breastfeeding within one hour, multiple births, rural residence, maternal illness, low Apgar score, being preterm, sepsis, asphyxia, and respiratory distress syndrome were independent predictors of time to neonatal mortality in neonatal intensive care units and male gender, perceived small size, multiple births, and ANC were predictors of neonatal mortality in the community. Conclusion. The incidence density rate of neonatal mortality in Sub-Saharan Africa is significantly high. Multiple factors (neonatal and maternal) were found to be independent predictors. Strategies must be designed to address these predictors, and prospective studies could reveal other possible factors of neonatal mortalities

Monitoring quality indicators for the Xpert MTB/RIF molecular assay in Ethiopia.

IntroductionIn Ethiopia, >300 GeneXpert instruments have been deployed for tuberculosis (TB) testing using the Xpert MTB/RIF cartridge. Implementing quality indicators is necessary for monitoring and evaluating the quality of Xpert MTB/RIF diagnostic services.ObjectiveTo assess the use of quality indicators for the Xpert MTB/RIF molecular assay in Ethiopia and to compare the findings with the predefined targets described in the literature.MethodsClinical specimens collected from patients with suspected TB were subjected to Xpert MTB/RIF testing at the National TB Reference Laboratory (NTRL) between January and December 2018. Data were collected from GeneXpert software and Laboratory Information System (LIS) databases. Quality indicators were calculated and analyzed. Bivariate and multivariate analyses were performed using SPSS software version 20 (SPSS Inc., Chicago, Illinois, USA).ResultsOf the 2515 specimens tested, 2274 (90.4%) had successful test results; 18.2% were positive for Mycobacterium tuberculosis (MTB). Among MTB positives (n = 413), 4.8% and 1.0% were rifampicin (RIF)-resistant and RIF-indeterminate cases, respectively. Unsuccessful results were 241 (9.6%); 8.9% of the total number of tests were errors, 0.04% had invalid results and 0.6% 'no result'. The most frequent error was probe check failure (error 5007). Instrument module A4, B2, B3, C3, and D3 (pConclusionMost of the quality indicators for the Xpert MTB/RIF molecular assay were maintained within the targets. However, the error rate and TAT were out of the targets. Defective modules and lacking experience were the factors affecting successful test outcomes

Forest plot for CRE colonization rate of hospitalized patients.

Forest plot for CRE colonization rate of hospitalized patients.</p

Forest plot of meta-analysis of ESBL-PE colonization with previous hospitalization.

Forest plot of meta-analysis of ESBL-PE colonization with previous hospitalization.</p