Browsing by Author "Tamrat Abebe"

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    Evaluating Microbiota Signatures, Intrinsic Subtypes, PIK3CA Gene Mutations and Alternative Diagnostic Modalities Among Ethiopian Breast Cancer Patients
    (Addis Ababa University, 2024-06-13) Zelalem Desalegn; Tamrat Abebe
    Background: Female breast cancer incidence has risen to unprecedented levels. It is a complex disease presented with distinct morphology, biological behaviors, clinical outcome and prognosis. Consequently, classification of breast cancer, understanding the molecular events including PIK3CA mutations and exploration of environmental factors including microbiota have a central role in understanding tumor biology. However, there is limited evidences in subSaharan Africa (SSA) context including Ethiopia; therefore, this study was conducted to generate evidence-based data to improving breast cancer care in Ethiopia. Additionally, considering the limited infrastructure for breast cancer diagnosis, we did method evaluation between PCR methods and immunohistochemistry to suggest alternative methods. Objectives: The study aims to evaluate microbiota signatures, determine intrinsic subtypes of breast cancer, determine the rate of PIK3CA gene mutations and investigate the diagnostic performance of PCR to determine ER, PR and HER2 markers against immunohistochemistry. Methods: A pathologically confirmed breast cancer patients recruited to the study. Clinical and histopathological data were collected using a questionnaire coupled with a follow up data for survival analysis. Formalin-fixed paraffin-embedded (FFPE) tumor tissue and paired (normal adjacent and breast tumor tissues) samples were collected. IHC analysis, PAM50- based gene expression profiling, and 16S rRNA gene-based sequencing were carried out. PAM50 based assay was employed to classify breast cancer into distinct intrinsic subtypes. Hot spot mutations across exon 9 and 20 in PIK3CA gene was determined using TaqMan® Mutation detection assay applying a competitive Allele-Specific TaqMan® PCR platform. 16S rRNA gene amplicons were PCR-amplified using dual-barcoded primers targeting the V4 region followed by high through put sequencing in Illumina MiSeq. Concordance between IHC and PCR method was evaluated using Cohen kappa coefficient. SPSS, Python, and R-packages were employed for data analysis. Survival analysis was performed using Kaplan-Meier. Conclusion: The distribution of intrinsic subtypes confirms previous immunohistochemistrybased studies from Ethiopia showing potentially endocrine-sensitive tumors in more than half of the patients. The findings indicated that PAM50-based classification offers a robust method for the molecular classification of tumor. While assessing mutations across PIK3CA gene, the proportion of mutation was high in favorable clinical and histopathological features including HR+ tumors. Considering endocrine therapy resistance challenge, these group of patients with PIK3CA mutation can benefit from combining endocrine therapy, chemotherapy, and targeted PI3K activity inhibitors. Though not yet explored in our setting and statistically significant, a specific microbial abundance noted between NAT and breast tumor. Again, a marked difference in the relative distribution of distinct microbiota across clinical and histopathological features was observed. Furthermore, a strong correlation of certain microbial communities with paired breast tissues and further prognostic features. The study highlighted that mammary microbiota composition differs significantly across tumor and cohort clinical and histopathological features which encourage to conduct further wide-scale study strengthen the current data and further utilize microbiota as a potential marker. Besides understanding the molecular biology and environmental factors including microbiota, working towards alternative diagnostic modalities is essential. Accordingly, applying PCR method, biomarker expression was higher while utilizing FFT than FFPE. Improvement of agreement noted between qPCR and IHC in FFT samples. Finally, the finding confirmed that mRNA-based breast cancer marker detection could be a complementary and/ or an alternative method in Ethiopia taking into account the limited IHC service availability. Keywords: Breast cancer, Ethiopia, IHC, Intrinsic subtypes, Microbiota, Mutation, Overall survival, PCR, PIK3CA, Prognostic features,
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    Molecular Characterization and Antimicrobial Resistance Profile of Diarrheagenic Escherichia Coli In Under-Five Children in Central Ethiopia
    (Addis Ababa University, 2024-06-13) Tizazu Zenebe; Tamrat Abebe
    Background: Many children fail to reach their development milestones due to several infection-related health problems in developing countries. One major infection-related health problem in under-five children (UFC) is diarrhea with the highest mortality rate in sub Saharan Africa including Ethiopia. Diarrheagenic Escherichia coli (DEC) is the major causes of diarrhea in UFC. Emergence of antimicrobial resistance (AMR) among DEC and other diarrheagenic bacterial strains including extended-spectrum ß-lactamase (ESBL) and carbapenemase producing E. coli strains are among the major threats to health globally. DEC pathotypes have emerged due to genomic plasticity of the E. coli and are associated with different life-threatening clinical diseases. The epidemiology of DEC and their AMR profile and the genetic background of DEC are not well characterized in Ethiopia. The present study aimed to determine molecular epidemiology and AMR profile of DEC and to provide some genetic insight of DEC pathotypes isolated from UFC from Central Ethiopia. Materials and methods: A health facility-based cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia between December 2020 and August 2021. A total of 476 stool specimens from UFC (391 diarrheic and 85 non-diarrheic) were collected. Bacterial isolation and identification were done by standard microbiology methods. Antimicrobial susceptibility testing was done using disk diffusion. Polymerase chain reaction (PCR) was used to further characterize isolates. In addition, a total of 28 selected DEC pathotypes were subjected to whole genome sequence (WGS) analysis. Data analysis was made using SPSS software program version 20. Different web based and available bioinformatic tools including bioinformatics resources were used in the genomic and phylogenetic analysis. Conclusion: All six common DEC pathotypes that have potential to cause severe diarrheal outbreaks and persistent infections were detected in UFC in the study area. The study showed that DEC has the potential to be a big concern in UFC in Ethiopia. The WGS analysis showed genetically diverse strains of DEC pathotypes that carry VGs and ARGs that have potential to spread through MGEs. The study also showed occurrence of resistant and possibly hyper virulent DEC pathotypes in the area. Therefore, despite the treatment of diarrheic patients empirically it will go to conduct periodic surveillance of the DEC pathotypes in the different health care settings in Ethiopia.
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    Molecular Characterization and Antimicrobial Susceptibility Profile of Bacterial Isolates From Patients with Surgical Site Infection in Ethiopia: A Multicentre Prospective Cross-Sectional Study
    (Addis Ababa University, 2024-06-19) Tamrat Abebe; Adane Mihret
    Background: Globally, surgical site infections (SSI) are the most reported healthcare associated infections. The most common pathogens associated with surgical wound infection are Gram-negative bacteria, and Staphylococcus aureus. Antibiotic resistance is increasing annually, and a major challenge in the management of SSI. Despite several reports on phenotypic examinations of bacterial isolates, there are few data on the molecular characterstics and antimicrobial resistance genes of bacteri isolated patients with SSI in Ethiopia. Objective: The aim of this study was to isolate and determine the antimicrobial susceptibility pattern; genes associated with drug resistance and identify risk factors associated with surgical site infection in Ethiopia Methods: A multicentre study was conducted among patients who underwent surgical procedures at four hospitals located in Northern (Debre Tabor), Southern (Hawassa), Southwest (Jimma), and Central (Addis Ababa) parts of Ethiopia. A total of 752 clinically suspected patients who developed surgical site infection were enrolled at each study sitein the study., and Sample for bacterial culture SSI discharge culture was collected from the infection site and inoculated on different culture media that supports the growth of Gram positive and Gram-negative bacteria performed and positive cultures were characterized by colony characteristics, Gram stain, and conventional biochemical tests. Species identification each bacterial isolate was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). An antimicrobial susceptibility test (AST) was done on Mueller-Hinton agar using the disk diffusion method. The phenotypic detection of MRSA was made using cefoxitin (30μg), Extended-spectrum beta-lactamases (ESBL) production was determined by combination disc-diffusion test (CDT) on MHA by using ceftazidime (30μg CAZ) and cefotaxime (30μg CTX) alone and with ceftazidime + clavulanic acid (20/10μg) CAZ/CLA) and cefotaxime + clavulanic acid (20/10μg CTX/CLA) and carbapenemase production was determined phenotypically by modified Hodge test (MHT) including impemene (10μg) test. The MRSA, ESBL and carbapenem resistance determinants were further studied determined by polymerase chain reaction (PCR) and Whole Genome Sequencing (WGS). Logistic regression analysis was used. A p-value < 0.05 was c Conclusion: ESBL and carbapenemase producing GNB as well as S. aureus were the main pathogens responsible for SSIs in the different hospitals in Ethiopia. The co-existence of different ESBL genes and carbapenamase genes in a single bacterial pathogen reflects dissimnation of MDR. There was also ahigh prevalence of mecA carriage among Coagulase negative staphylococci (CoNS). As a multicenter study this implies SSI is a major problem in hospitals in Ethiopia Keywords: Molecular epidemiology; surgical site infections aetiologies; ESBL; Carbapenemase producing; Multidrug resistance; Risk factors; Ethiopia onsidered statistically significant. Data were analysed using STATA 16 software.
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    Prevalence and Immune Correlates of Risk in Community-Acquired Meningitis: A Study at ALERT and Hawassa University Comprehensive Specialized Hospitals, Ethiopia.
    (Addis Ababa Universtity, 2025) Jemal Aman; Tamrat Abebe
    Background: Meningitis poses a major public health challenge in sub-Saharan Africa, often triggering devastating epidemics. Although it can affect individuals of all ages, infants, children, and immunocompromised persons are at the greatest risk. In Ethiopia, meningitis continues to be a significant public health concern due to its potential for outbreaks, high mortality rates, and the considerable burden it places on the healthcare system. Objective: This study was aimed to assess the prevalence of etiologic agents causing meningitis and to evaluate immune correlates of risk among clinically suspected meningitis cases in Ethiopia. Methods: An institutional-based cross-sectional study was conducted from August 2023 to June 2024 at ALERT Comprehensive Specialized Hospital and Hawassa University Comprehensive Specialized Hospitals. A total of 201 clinically suspected meningitis cases of all age groups (except neonates) were enrolled. Cerebrospinal fluid (CSF) samples were analyzed using conventional culture, microscopy, and Conventional multiplex PCR to identify bacterial and viral pathogens. Immune correlates of risk including CD4+ T-cell counts and plasma complement levels (C5, C5a, C9, Factor D, MBL, Factor I, Properdin)- were compared among cases with bacterial meningitis, viral meningitis cases and healthy individuals. Univariate and multivariate logistic regression analyses were performed to identify significant associations. Results: The overall prevalence of bacterial meningitis detected by classical CSF culture was 5.5% (n = 11), with Klebsiella pneumoniae 3/11(1.5%) being the most frequently isolated organism. In contrast, multiplex PCR identified a substantially higher prevalence of bacterial meningitis at 36.8% (n = 74), with Escherichia coli 30/74(14.9%), Streptococcus pneumoniae 15/74(7.5%), and Neisseria meningitidis 11/74(5.5%) as the predominant pathogens. Klebsiella pneumoniae 9/74(4.5%), Streptococcus agalactiae 4/74(2%), and Listeria monocytogenes 2/74(1%) were also rarely detected. Antimicrobial resistance was alarmingly high, with 72.7% of bacterial isolates exhibiting resistance to three or more antibiotics. The overall prevalence of viral meningitis was 34.3% (n = 69), with Human Enteroviruses (28.9%) representing the most common viral etiology. Overall 65% [13/20] of patients with viral meningitis have CD4 deficiency [<200cells/mm3]. 54% [27/50] of patient with bacterial meningitis have Properdin deficiency followed by 52% [26/50] C5- Deficiency and 46% [23/50] C9- deficiency. Analysis of immune correlates revealed that deficiencies in complement components C5 (AOR = 2.50, 95% CI: 1.60–3.90, p < 0.001), C9 (AOR = 3.09, 95% CI: 1.31 7.30, p = 0.007), and Properdin (AOR = 1.80, 95% CI: 1.20–2.70, p = 0.003) were significantly associated with an increased risk of bacterial meningitis. For viral meningitis, low CD4+ T-cell levels were significantly associated with increased risk (AOR = 2.59, 95% CI: 1.60–3.90, p = 0.035). Conclusion and recommendation: In conclusion, our study confirms a significant burden of bacterial and viral meningitis in our study settings, disproportionately affecting young children. Our findings highlight specific immune correlates of risk for meningitis: deficiencies in terminal complement components (C5, C9, and Properdin) significantly increase susceptibility to bacterial meningitis, whereas low CD4+ T-cell levels are associated with a higher risk of viral meningitis. These findings highlight the urgent need for enhanced diagnostic capabilities, expanded vaccination programs, stringent antibiotic stewardship, and the implementation of immune profiling for better patient management in Ethiopia. Future research should track long-term outcomes and evaluate intervention effectiveness.
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    The Epidemiology, Oral Microbiome Signature, and Myctoxins Exposure of Esophageal Cancer Patient in Ethiopia
    (Addis Ababa Universtity, 2025) Girma Mulisa; Tamrat Abebe; Adane Mihret
    Background: There was a global ‘missing millions’ gap between the incidence of tuberculosis (TB) cases and the notified cases. An active household contact (HHCs) investigation is one of the strategies to narrow this gap. It has the advantage of giving early diagnosis and preventive treatment to vulnerable and eligible groups. In many TB high-burden countries, only about 25% of HHCs completed TB screening, and 20–89% of eligible contacts did not adhere to TB preventive treatment. Delivering screening services near the community is important to narrow these gaps. Recognizing the transmission dynamics of Mycobacterium tuberculosis complex (MTBC) and identifying their prevalent lineages and genotypes are important in TB control and management. Objectives: This study investigated the epidemiology of active TB, TB contact screening practice, TB transmission dynamics, genetic diversity, and identified drug-resistance patterns in epidemiologically linked pulmonary TB (PTB) index cases and their HHCs in central part of Ethiopia. Methods: A cross-sectional study was carried out in 15 selected public health facilities of central part of Ethiopia from January 2022 to December 2023. The routine TB contact screening practice was assessed using one year (January, 2022 to December, 2022) data from the registration book of the study sites. Three hundred three voluntary bacteriologically confirmed PTB patients and 902 of their HHCs, without discrimination by age, were included in the study. Household contacts were screened using the World Health Organization (WHO) recommended TB symptom-based screening tool using a pre-tested questionnaire. A morning sputum sample was collected from 303 index cases and 182 HHCs having presumptive TB. Then it was examined on Xpert MTB/RIF Ultra assay, AFB microscopy (from sediment), and M. tuberculosis culture. The culture-positive 272 index cases and 13 HHC isolates were examined by phenotypic drug susceptibility test (pDST). A total of 13 index-HHC pairs and 24 randomly selected index case isolates were whole genome sequenced (WGS) using Illumina Nextseq 550. The TB-profiler and Ridom SeqSphere software were used for drug resistance and genotypic analysis. Data was entered into EPI Info version 7.0 databases and analysed using STATA V.17 software. Descriptive statistics were used to summarize the data. Chi-square test and Yates continuity correction test were used to analyse associated factors. Multivariable logistic regression analysis was done to investigate the associated vi risk factors for active TB in HHCs. Variables with a p-value A), as well as Ethionamide resistance (ethA p. Ile338Ser), which were absent from the WHO 2023 Catalogue of mutations in the Mycobacterium tuberculosis complex. Conclusion: The yield of routine TB contact investigation practice was low, and the quality of screening and adherence were suboptimal. The Home-to-home TB contact screening approach has a high active TB yield and was implementable in both rural and urban areas by mentoring and motivating the health extension workers. Scheduling convenient times and last-mile service delivery to contacts is very important to address the missed active TB cases in the community. Nearly one-third of the HHCs have discordant phenotypic drug-resistance profiles from the index patients. This study offers compelling proof that it is not advisable to treat close contacts without DST results based on the DST results of the supposed source case. Individuals residing in areas with a high burden of tuberculosis are at risk of contracting the disease from sources beyond their homes. Keywords: Active tuberculosis yield, Contact investigation, Household contacts, Index case, Transmission dynamics, Whole genome sequencing
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    The Genetic Landscape of Breast Cancer and Its Intersection With Host Immunity In Ethiopian Breast Cancer Patients
    (Addis Ababa Universtity, 2025) Meron Yohannes; Tamrat Abebe
    Background; Breast cancer remains a leading cause of morbidity and mortality among Ethiopian women. It is a heterogeneous disease, both in its molecular characteristics and immune response. Recent evidence demonstrates the importance of incorporating immune cell composition into tumor classification, as the immune landscape plays a crucial role in determining prognosis and therapeutic response. Additionally, emerging studies suggest that tumor immune response is influenced by intratumoral microbiota, which can affect both anti- and pro-tumor immune activities. Despite these insights, there remains a significant gap in understanding the immunological landscape of Ethiopian breast cancer, its prognostic relevance, and its interaction with the mammary microbiota. Objective; This study was aimed to explore the host immune profile—both local and systemic— its role in predicting disease prognosis, and its interaction with the mammary microbiota in Ethiopian breast cancer patients. Methodology: A combination of prospective and retrospective follow-up study designs was employed to address the different study objectives. A prospective follow-up study was conducted to investigate the systemic immune repertoire of BC patients and to examine correlations between mammary microbiota and local immunity. Patient/disease characteristics at diagnosis were collected through structured, pretested questionnaires. Blood from BC patients and healthy controls were analyzed by flow cytometry to assess the phenotype and function of immune cell subpopulations. To explore microbiome-immune associations, fresh frozen tissue (FFT)/Formalin fixed paraffin embedded (FFPE) tissue was used for molecular characterization of the microbiota, by targeting 16S rRNA genes (Illumina MiSeq) and for immune gene expression analysis. Budget: The study was supported by the Susan Komen GTDR16378013 given to Martin-Luther –University Halle-Wittenberg, Medical Faculty. Keywords: Immune Phenotypes, Tumor immune microenvironment, Immune profiling, Immune escape, Mammary microbiota, Ethiopian patients, Prognostic biomarkers.