Medical Laboratory Science and Pathology

Genomic diversity and antimicrobial resistance profiles of Shigella species in under-five children with acute diarrhea in Addis Ababa, Ethiopia

2026-03-03T07:14:45Z

Genomic diversity and antimicrobial resistance profiles of Shigella species in under-five children with acute diarrhea in Addis Ababa, Ethiopia Basha Ayele; Getenet Beyene; Zeleke Mekonnen Background: Shigella species exhibit considerable genetic diversity, reflecting distinct genomic traits and epidemiological trends. In Ethiopia, infections caused by Shigella species, along with rising antimicrobial resistance (AMR), pose a major public health threat, especially among children under five. To our knowledge, there are few studies on the genetic diversity and antimicrobial susceptibility of Shigella species in this vulnerable age group. Figuring this out could help treat cases better and control outbreaks more effectively. Objective: This study aimed to characterize Shigella species' genomic diversity and AMR profiles in under five children with acute diarrhea in Addis Ababa, Ethiopia. Methods: Between June 2021 and April 2022, we conducted a cross-sectional study. Freshly passed stool specimens were collected and transported in Cary Blair media to the Ethiopian Public Health Institute (EPHI) laboratory for Shigella isolation and identification using standard bacteriological methods. Serogrouping was performed using polyvalent antisera, and antimicrobial susceptibility testing (AST) was conducted using the disk diffusion method. Additionally, a systematic review and meta-analysis were conducted to assess the prevalence and AMR patterns of Shigella species in East Africa. Molecular characterization was performed using whole-genome sequencing (WGS) analysis. Sequencing was conducted using the Illumina NextSeq550 (Illumina, Singapore) with a 300-cycle kit, generating paired-end reads of 149bp. Raw reads were quality-filtered and trimmed to a minimum length of 50 bp before being taxonomically classified using MiniKraken version 1. The whole genome data were aligned with Antibiotic Resistance Gene (ARG) sequences from the Comprehensive Antibiotic Resistance Database (CARD) using the Resistance Gene Identifier (RGI). Plasmid analysis was performed using the Mykrobe PlasmidFinder tool. Additionally, AMR and virulence genes were screened using the Centre for Genomic Epidemiology (CGE) web-based platform. Data were analyzed using descriptive statistical tools. The association of independent and dependent variables was evaluated with logistic regression. A P-value < 0.05 was considered statistically significant. Results: Among the 534 stool-cultured specimens in the prospective study, 47 (8.8%) were positive for Shigella species. Of these, 31 were serologically identified as S. sonnei and 16 as S. flexneri. Of 37 isolates analyzed by WGS, all 28 S. sonnei strains identified xiii serologically were confirmed as S. sonnei. However, all nine isolates initially identified as S. flexneri were found to be E. coli O37:H10. The phylogenetic tree showed that both S. sonnei and E. coli O37:H10 isolates had multiple evolutionary origins, suggesting that their phenotypic features evolved convergently. Plasmids Col156 and Col (BS512) were identified in all S. sonnei isolates, while IncFII and Col (MG828) plasmids were found only in one isolate. In contrast to S. sonnei, the most common plasmid type in E. coli O37:H10 isolates was IncFII, and virulence genes such as gad were frequently detected. Discrepancies were observed between phenotypic and genotypic AMR results. The systematic review estimated the pooled prevalence of Shigella species in East Africa was 6.2%. Despite variations in study sites and periods, the meta-analysis study further revealed an increased rate of resistance of Shigella species to tetracycline, ampicillin, amoxicillin, chloramphenicol, and co-trimoxazole. In the prospective study, AST showed that 100, 93.6, 80.9, 72.3, and 57.5% were sensitive to norfloxacin, nalidixic acid, ciprofloxacin, gentamicin, and cefoxitin, respectively. However, 100% of the isolates were resistant to amoxicillin. All isolates were resistant to three or more antimicrobials that exhibited multidrug resistance (MDR). None of the risk factors assessed showed a statistically significant association with Shigella infection. All S. sonnei isolates in our study contained genes encoding blaEC-8 and blaZEG-1. About 60.7% of the isolates were phenotypically sensitive to cefoxitin among the blaEC-8 genes detected in the genotyping analysis, whereas all isolates were completely resistant to amoxicillin phenotypically. The study also identified genes that conferred resistance to trimethoprim (dfrA1). Extended-spectrum beta lactamase (ESBL) blaEC-15 for cephalosporins, blaMIX-2, and blaMIX-6 for penicillins were detected in E. coli O37:H10. All E. coli O37:H10 isolates possessed a gene associated with trimethoprim resistance, and eight E. coli O37:H10 isolates exhibited consistent results for trimethoprim when comparing phenotype and genotype. The dominant AMR mechanism among the identified ARGs was antibiotic efflux, followed by antibiotic target alteration. Conclusion: There was no significant heterogeneity among East African studies, the majority of which were conducted in Ethiopia. Both the systematic review and the prospective phenotypic study revealed alarmingly increased levels of AMR to commonly administered antibiotics. The genotyping study revealed that the most prevalent resistant genes were associated with beta-lactam and trimethoprim drugs. The IncFII plasmid, which primarily encodes ESBL, was more frequently identified in E. coli O37:H10 isolates than xiv in S. sonnei. The study also highlighted a significant discrepancy between phenotypic and genotypic drug resistance, as well as variations in serotypes and phylogenetic relationships with global isolates. Recommendation: The study highlighted significant discrepancies between phenotypic and genotypic results. Molecular studies integrating WGS for AMR determination and strain identification into active surveillance could enhance monitoring of AMR spread and detection of potential emerging variations. Therefore, public health and clinical laboratories in Ethiopia should implement WGS to address inconsistencies in conventional analyses, enhance treatment efficacy, and inform targeted interventions.

Bionomics, Insecticide Susceptibility and Characterization of Mid-Gut Micro biota In Anopheles Mosquitoes in Ethiopia

2026-03-03T06:51:26Z

Bionomics, Insecticide Susceptibility and Characterization of Mid-Gut Micro biota In Anopheles Mosquitoes in Ethiopia Delelegn Woyessa Beddanie; Delenasaw Yewhalaw Background: This PhD dissertation explores the complex ecology of malaria vectors in Ethiopia, where malaria transmission patterns remain spatially heterogeneous and shaped by the interplay of diverse Anopheles mosquito species with distinct ecological, behavioural, and physiological characteristics, and human interventions.Vector control efforts have been challenged by gaps in knowledge regarding species composition, seasonal dynamics, insecticide resistance, infection rates, and microbiota profiles. Objective: This dissertation aimed to characterize the bionomics, insecticide susceptibility, infection rates, blood meal sources, and midgut microbiota diversity of key Anopheles species vectors across multiple eco-epidemiological settings in Ethiopia. Methods: Data for the overall PhD research were collected between June 2018 and February 2023 across three sites: Lare in Nuwer Zone (Gambella), Asendabo in Jimma Zone (Oromia), and Batu in East Shewa Zone (Oromia). Adult Anopheles mosquitoes were sampled using CDC light traps, human landing catches, and pyrethrum spray catches, while larvae were sampled by dipping from breeding sites. Species identification was performed via morphological keys and species-specific PCR. Plasmodium infection rates were assessed using sporozoite infection rates (SRs), circumsporozoite proteins (CSP-ELISA) and TaqMan qPCR. Insecticide susceptibility was determined using WHO standard bioassays and molecular screening for resistance markers (kdr L1014F/S, ace-1 N485I, CYP6P9a). Midgut microbiota were isolated from aseptically dissected mosquitoes and characterized using culture-based techniques and biochemical assays. Results: A total of over 14,800 Anopheles mosquitoes, representing four species: An. arabiensis, An. pharoensis, An. coustani, and An. funestus were collected. Anopheles coustani was the most abundant species, accounting for more than 40% of the total collection and 42% in Lare. Anopheles pharoensis was the next most common, while An. arabiensis was dominant species in Asendabo and Batu. Seasonal abundance peaked between June and November, except for An. funestus, which was more prevalent during post malaria peak months in the dry season. All An.gambiae s.l. were confirmed as An. arabiensis via PCR while more than 90% An. funestus s.l. from Lare were all confirmed as An. funestus s.s. Despite the absence of insecticide resistance mutations (CYP6P9a, kdr L1014F/S, ace-1 N485I) in An. funestus, phenotypic resistance to pyrethroids and organochlorines was widespread in An. arabiensis, An. pharoensis, and An. coustani. Plasmodium infected mosquitoes were identified across multiple species including, An. funestus, An. arabiensis, An. coustani, and An. pharoensis, with An. funestus showing the highest entomological inoculation IV rate (10.52 bites/person/month), positive for both Plasmodium falciparum and P. vivax. Blood meal analysis confirmed zoophilic tendencies and mixed feeding behaviour with spatio-temporal and species-specific variation. Midgut microbiota analyses revealed 659 bacterial and five fungal isolates from 129 mosquitoes across four species. Eleven bacterial genera were identified with Staphylococcus, Klebsiella, Proteus, and Bacillus dominating. Microbial composition and colonization intensity varied by species, site, life stage, and insecticide exposure status. Remarkably, An. arabiensis survivors of DDT and permethrin exposure (from Batu) harbored higher microbial loads compared to susceptible counterparts, possibly suggesting potential microbiota-mediated resistance mechanisms. Conclusions: This work highlights complex spatiotemporal patterns in Anopheles species composition, insecticide resistance, infection rates, host choices, and midgut microbiota diversity across regions in Ethiopia. The dry-season persistence and infection potential of An. funestus, along with the widespread distribution and insecticide resistance observed in secondary and suspected vectors like An. pharoensis and An. coustani in addition to the primary vector underscore the urgent need for expanded and targeted vector surveillance. Moreover, the association between microbiota diversity and insecticide resistance may offer new insights into vector competence and suggest potential for microbiome-targeted interventions to complement existing malaria control strategies. Sustained integrative entomological and microbiological monitoring is crucial for adaptive and effective vector control in Ethiopia.

Prevalence and Determinants of Erectile Dysfunction among Diabetic Patients Attending To Selected Governmental Hospitals, Guragezone, Southern Ethiopia

2026-02-27T12:38:31Z

Prevalence and Determinants of Erectile Dysfunction among Diabetic Patients Attending To Selected Governmental Hospitals, Guragezone, Southern Ethiopia Seid Abrar; Aklilu Getachew; Shiferaw Bekele Background:- Diabetes is an established risk factor for erectile dysfunction in men, as a threefold increased risk of erectile dysfunction was documented in diabetic men. Erectile dysfunction is more prevalent in men with Diabetes mellitus (35-90%), as compared with nondiabetic men. Men experiencing this sexual disorder have demonstrated severe deficits in their overall quality of life. Objective:- To determine the prevalence and determinants of erectile dysfunction among diabetic patients attending selected governmental hospitals, Gurage Zone, Southern Ethiopia from September 1 to December 30, 2020. Methods:- A hospital-based cross-sectional study was conducted from September 1 to December 30, 2020, in three selected public hospitals. A total of three hundred twenty diabetic patients, selected by the consecutive sampling method. Socio-demographic, clinical, lifestyle characteristics were collected with a structured questionnaire, data regarding erectile function using the International Index of Erectile Function-5. Moreover, fasting blood glucose and lipid levels were measured by A25 BioSystems clinical chemistry analyzer. The data were entered and analyzed using the Statistical Package for Social Sciences-20. Logistic regression was applied to identify an association between explanatory variables and the outcome variable. An adjusted odds ratio with a 95% confidence interval and p-value less than 0.05 was computed to determine the level of significance. Results:- Out of 320 study participants,233(72.8%) had erectile dysfunction. Multivariate analysis confirmed that age group of 40-49 years (Adjusted Odds Ratio [AOR]= 5.913, 95%CI:2.086-16.760), alcohol consumption (AOR=3.78495,95%CI:1.884-7.60), chat chewing (AOR=2.440,95%CI:1.281-4.64),antihypertensive drug(AOR= 5.716 95%,CI:1.566 20.859),abnormal high density lipoprotein(AOR=2.371,95%CI:1.230-4.57),high total cholesterol(AOR=2.971,95%CI;1.329-6.645), poor glycemic control (AOR =2.676; 95% CI:1.405–5.098) were a significant predictor for erectile dysfunction. Conclusion and recommendation: This study confirms the high prevalence of erectile dysfunction in diabetic male patients in study settings. Thus, clinicians need to consider preventive measures along with working on the downregulation of the offending agent of patients in the study area. However; the authors also believe that there is a need for further community based and case control studies on the current topic

Computer-Aided Drug Discovery Strategies Targeting Plasmodium Falciparum Survival Proteins Pflipl2 and Pflpl3: Novel Inhibitor Identification and Validation via Alphafold2 Models

2026-02-26T08:59:14Z

Computer-Aided Drug Discovery Strategies Targeting Plasmodium Falciparum Survival Proteins Pflipl2 and Pflpl3: Novel Inhibitor Identification and Validation via Alphafold2 Models Segni Megersa; James Wasmuth; Teshome Degefa; Ahmed Zeynudin Background: Malaria, caused by Plasmodium falciparum, is the primary cause of severe malaria and poses a global health challenge. Despite prevention and control strategies, the increase in disease burden, drug resistance, life and economic loss necessitates novel therapeutic strategies. In this study, we employed computer-aided drug discovery (CADD) to identify inhibitors targeting two vital P. falciparum proteins, lipoate protein ligase-2 (PfLipL2) and lysophospholipase (PfLPL3), using AlphaFold-predicted structures. Objectives: The general objective of the study was to leverage computational methods (virtual screening, docking, consensus ranking and residue interaction analysis) to identify and validate candidate antimalarial compounds targeting vital P. falciparum proteins from January to 2024 to June 2025. Methods and Materials: An AlphaFold‟s built in and Ramachandran plot was used for the 3D model‟s structure quality validation. Virtual screening was carried out with MTiOpenScreen server against protein targets and ADME properties were analyzed by SwissADME. Docking was carried out using SwissDock and PyRx and ECR for prioritized candidates. Finally, Discovery studio was used for protein-ligand‟s pose analysis. Results: The 3D models had high structure quality. We screened 14,346 ligands, assessed ADME properties, and docked 68 Lipinski-compliant ligands. Top three (10%) of prioritized ligands ZINC000000537750, ZINC000001846243 and ZINC000030691430 for PfLipL2, and ZINC000043203317, ZINC000001481805 and ZINC000004098812 for PfLPL3 were identified. We found one top-ranked ligand with confirmed antimalarial activity against each target in PubChem. Conclusions and Recommendation: The novelty of this work stems from its methodological synergies: dual-tool docking for enhanced reliability and ECR-augmented prioritization for superior ranking fostering greater confidence in hit selection. These results nominate promising candidates for future experimental validation toward new antimalarial.