Yared Merid

Background: Viral meningitis remains a significant global public health problem, particularly in resource-limited settings where the diagnosis of viral etiology is mainly based on clinical assessment. This study aimed to identify the common viral etiologies of meningitis, describe their associated clinical features, and assess patient outcomes among individuals suspected of meningitis without evidence of bacterial meningitis. Methods: We conducted a multicenter study involving 430 patients clinically suspected of meningitis. Clinical data and cerebrospinal fluid samples (CSF) were collected following standard procedures. Viral nucleic acids were extracted from CSF specimens. Complementary DNA was prepared from viral RNA using reverse transcription. Viral nucleic acids were amplified and detected using qualitative conventional polymerase chain reactions. Patient outcomes were evaluated using the Glasgow Outcome Scale (GOS). Bivariate and multivariable logistic regression analyses were used to identify factors associated with unfavorable patient outcomes, with statistical significance set at a p -value < 0.05 at a 95% confidence level. Results: The prevalence of viral meningitis was 52.8% (227/430). Enteroviruses were the most common, 47.9% (206/430), followed by herpes simplex virus-1, 2.8% (12/430), herpes simplex virus-2, 1.4% (6/430), and Epstein-Barr virus, 0.7% (3/430). Overall, 6.7% (29/430) of study participants experienced unfavorable outcomes (GOS = 1–4). Factors independently associated with unfavorable outcomes included sex (AOR = 2.684, 95% CI = 1.177–6.119), duration from disease onset to hospital visit (AOR = 1.433, 95% CI = 1.043–1.967), and history of antibiotic intake before hospital visit (AOR = 2.784, 95% CI = 1.270–6.104). Conclusions: In this predominantly pediatric study, enteroviruses are the leading cause of viral meningitis in Ethiopia. Most study participants experienced favorable outcomes. Unfavorable outcomes were independently associated with sex, duration from disease onset to hospital visit, and history of antibiotic use before hospital visit. Further identification and characterization of Enteroviruses are warranted.

Introduction: Wound infections are common nosocomial infections associated with increased morbidity and mortality. Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), is a major cause of hospital-acquired wound infections. This study aimed to determine the burden and antimicrobial susceptibility pattern of S. aureus and MRSA, among patients with wound infections at Hawassa University Comprehensive Specialized Hospital (HUCSH), Hawassa, Ethiopia. Methodology: A hospital-based cross-sectional study was conducted on 246 admitted patients with wound infections at HUCSH from April to August 2021. Wound swabs were aseptically collected and cultured for bacterial isolation and drug susceptibility testing. Data were analyzed using SPSS version 20, and descriptive statistics were computed. Results: Among the 246 clinical specimens analyzed, S. aureus was isolated from 57 (23.2%), of which 5 (8.8%) were identified as MRSA. All S. aureus strains were sensitive to linezolid. The highest resistance was observed for penicillin (52 strains, 91.2%), and 24.6% of S. aureus strains were found to be multidrug resistant. All MRSA strains were isolated from patients with no history of past wound infection, and all of them were sensitive to vancomycin. Conclusions: This study identified S. aureus (23.2%) and MRSA (8.8%) along with their antimicrobial resistance among patients with wound infections at HUCSH. A substantial proportion (24.6%) of S. aureus exhibited multidrug resistance. However, all MRSA isolates were sensitive to vancomycin. Continuous drug resistance monitoring (drug surveillance) is crucial to manage and prevent resistance spread in the hospital.

Introduction: Understanding the epidemiology of tuberculosis is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing patterns and genetic diversity of M. tuberculosis isolates in southern Ethiopia. Methodology: A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with tuberculosis visiting nine health facilities in southern Ethiopia from June 2015 to May 2016. Three consecutive sputum samples (spot-morning-spot) per patient were examined using acid-fast bacilli smear microscopy with all smear positive specimens having acid-fast bacilli cultures performed. M. tuberculosis isolates had drug susceptibility testing performed using indirect proportion method and were genotyped with RD9 deletion analysis and spoligotyping. Mapping of strain was made using geographic information system. Results: Among 250 newly diagnosed patients with tuberculosis, 4% were HIV co-infected. All 230 isolates tested were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%), East-African-Indian, 31 (14%), and Lineage 7 (Ethiopian lineage), 8 (4%); categorized into 63 different spoligotype patterns, of which 85% fell into 28 clusters. M. tuberculosis strains were clustered by geographic localities. The dominant spoligotypes were SIT149 (21%) and SIT53 (19%). Drug susceptibility testing found that 14% of isolates tested were resistant to > 1 first line anti- tuberculosis drugs and 11% to INH. SIT 149 was dominant among drug resistant isolates. Conclusions: The study revealed several clusters and drug resistant strains of M. tuberculosis in the study area, suggesting recent transmission including of drug resistant tuberculosis. Wider monitoring of drug susceptibility testing and geospatial analysis of transmission trends is required to control tuberculosis in southern Ethiopia.

Background: Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. Methods: To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (F_ST) statistical approach. Results: By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. Conclusions: The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform (https://github.com/jodyphelan/TBProfiler).

Background Understanding the epidemiology of tuberculosis (TB) is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing (DST) patterns and genetic diversity of M. tuberculosis (Mtb) isolates in Southern Ethiopia. Methodology A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with TB visiting nine health facilities in southern Ethiopia from June 2015 to May 2016. Three consecutive sputum samples (spot-morning-spot) per patient were examined using acid-fast bacilli (AFB) smear microscopy with all smear positive specimens having AFB cultures performed. Mtb isolates had DST performed using indirect proportion method and were genotyped with RD9 deletion typing and spoligotyping. Spoligotyping International Types (SIT) and sub-lineages (clades) were assigned according to the SITVITWEB data base. Results Among 250 newly diagnosed patients with TB, 154 (52%) were male and 143 (57%) from rural areas. The prevalence of HIV co-infection was 4%. Of the 250 AFB positive sputum samples, 230 (92%) were culture positive. All 230 isolates were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%); East-African-Indian, 31 (14%); and Lineage 7 (Ethiopian lineage), 8 (4%). The 230 isolates could be categorized into 65 different spoligotype patterns, of which 84% fell into 29 clusters. The dominant spoligotypes were SIT149 (21%), SIT53 (19%) and new strains (16%). Mtb strains were clustered by districts. DST revealed that 14% of Mtb isolates were resistant to > 1 first line anti-TB drugs including 11% to isoniazid. SIT 149 was the most prevalent genotype among drug resistant isolates (20%). Conclusion The study revealed several clusters including lineage 7 strains circulating in southern Ethiopia. SIT 149 (T3-ETH) was the most dominant circulating strain in the study area including among drug-resistant cases.