Metagenome-based microbial community analysis of urine-derived fertilizer.

Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.

Multiscalar Evaluation of the Water Distribution System and Diarrheal Disease Risk in Addis Ababa, Ethiopia.

Despite growing urbanization, our understanding of the impacts of water and sanitation on human health has largely come from studies in rural sectors. To this end, we collected data at both regional (water quality measures from water treatment systems) and community (cross-sectional surveys) scales to examine determinants of enteric pathogen infection and diarrheal disease among infants in Addis Ababa, Ethiopia. Regionally, the Legedadi water treatment plant had significantly lower heterotrophic plate counts, total coliform counts, and fecal coliform counts compared with the Gefersa water treatment plant. The number of pathogen types in infant stool also differed by plant. Decreases in chlorine levels and increases in the relative abundance of Gammaproteobacteria with distance from treatment plants suggest a compromised water distribution system. In communities, infants in households that obtained water from yard pipes or public taps had significantly lower odds of diarrhea compared to households that had water piped into their dwellings (OR = 0.35, 95% CI 0.16, 0.76, and OR = 0.39, 95% CI 0.15, 1.00, respectively). Similarly, infants in households that boiled or filtered water had significantly lower odds of diarrhea compared to households that did not treat water (OR = 0.40, 95% CI 0.19, 0.86 and OR = 0.23, 95% CI 0.06, 0.84, respectively). Integrating multiscalar data better informs the health impacts of water in urban settings.

Fate of antimicrobial resistance genes (ARG) and ARG carriers in struvite production process from human urine.

Struvite, a human urine-derived fertilizer types, is characterized by its low water solubility that renders it a slow-releasing eco-friendly fertilizer. Knowing the fate of antibiotic resistance genes in struvite is important since human urine carries microorganisms, viruses and mobilomes. In this study, urine samples were collected and struvite production was done using MgCl2. From the fresh, stored urine and struvite, DNA was extracted and metagenomic sequencing was done using Illumina HiSeqX. Metagenome-derived genome sequence analysis revealed the dominance of phages of Streptococcus, Bacillus and Escherichia, with nearly 50% abundance of streptococcus phage in fresh urine. Increased antibiotic resistance genes were found in the stored urine than in fresh and struvite samples. The top five resistance genes in all the three samples were to aminoglycosides, carbapenem, chloramphenicol, erythromycin and efflux pump, with key carrying pathogens including Acinetobacter, Aeromonas and Enterococcus. The identified families for carbapenem, aminoglycoside resistance and efflux pump were shown persistent in struvite with a shift in gene families. The detection of resistance-gene-laden mobilomes, including the last-resort antibiotics in the struvite sample, requires due attention before the implementation of struvite as fertilizer. Further optimization of the struvite production process with regard to the minimization of mobilomes is recommended.

Microbial Community Structure and Diversity in Drinking Water Supply, Distribution Systems as well as Household Point of Use Sites in Addis Ababa City, Ethiopia.

Understanding ecology of microbiomes in drinking water distribution systems is the most important notion in delivering safe drinking water. Drinking water distribution systems harbor various microbiota despite efforts made in improving water infrastructures in the water industry, especially, in developing countries. Intermittent water supply, long time of water storage, low water pressure, and contaminated source water are among many of the factors responsible for poor drinking water quality affecting health of people. The aim of this study was to explore microbial diversity and structure in water samples collected from source water, treated water, reservoirs, and household points of use locations (taps). High-throughput Illumina sequencing technology was employed by targeting the V4 region of the 16S rRNA gene and the V1-V3 region of the 18S rRNA gene to analyze the microbial community structure. Proteobacteria followed by Firmicutes, Bacteroidetes, and Actinobacteria were the core dominating taxa. Gammaproteobacteria was also dominant among other proteobacterial classes across all sampling points. Opportunistic bacterial genera such as Pseudomonas, Legionella, Klebsiella, Escherichia, and Actinobacteria, as well as eukaryotic microbes like Cryptosporidium, Hartmannella, Acanthamoeba, Aspergillus, and Candida were also abundant taxa found along the distribution systems. The shift in microbial community structure from source to point of use locations was influenced by basic factors such as residual chlorine, intermittent water supply, and long-time storage at the household. The complex microbiota detected in different sampling sites in this study brings drinking water quality problem which further causes significant health problems to both human and animal health. Treatment ineffectiveness, disinfection inefficiency, poor maintenance actions, leakage of sewage, and other domestic wastes are few among many other factors responsible for degraded drinking water quality in this study putting health at high risk. Findings of this research provide important and baseline information to understand the microbial profiles of drinking water along source water and distribution systems. Moreover, knowing the microbial profile will help to design proper water quality assurance approaches.

Absence of significant association of trace elements in nails with urinary KIM-1 biomarker among residents of Addis Ababa in Upper Awash Basin, Ethiopia: a cross-sectional study.

The Akaki River in the Upper Awash Basin, which flows through Addis Ababa, the capital city of Ethiopia, has been highly polluted by sewage from factories and residential areas. A population-based cross-sectional study was used to assess the association between trace elements and kidney injury from residents living in polluted areas downstream (Akaki-Kality) versus upstream (Gullele) in Sub-Cities of Addis Ababa. A total of 95 individuals (53 from Akaki-Kality and 42 from Gullele) were included in the study. Kidney injury molecule 1 (KIM-1), lead, arsenic, cadmium, cobalt, lead, manganese, zinc, iron, copper, chromium and nickel were evaluated in residents' urine and nail samples. A large proportion (74%) of the sample population contained KIM-1, including 81% residents in Akaki-Kality and 64% residents in Gullele. KIM-1 was, however, not significantly different (p = 0.05) between the two Sub-Cities, with median of 0.224 ng/mL in Akaki-Kality and 0.152 ng/mL in Gullele. Most of the analyzed elements, except Pb, As, Cd and Co, were found in all of the nail samples, with median (µg/g) in the range of 442‒714 Fe, 97.0‒246 Zn, 11.6‒24.1 Mn, 4.49‒5.85 Cu, 1.46‒1.66 Cr and 1.22‒1.41 Ni. The high incidence of KIM-1 indicates a potential for long term renal tubular damage among residents of the Sub-Cities. The concentrations of the elements in nails were, however, not significantly associated (p = 0.05) with the corresponding levels of KIM-1 in urine. Hence, the observed KIM-1 might be related to exposure to toxic substances or factors other than those included in this study.

Pneumococcal colonization and coinfecting respiratory viruses in children under 5 years in Addis Ababa, Ethiopia: a prospective case-control study.

A comprehensive understanding of the dynamics of Streptococcus pneumoniae colonization in conjunction with respiratory virus infections is essential for enhancing our knowledge of the pathogenesis and advancing the development of effective preventive strategies. Therefore, a case-control study was carried out in Addis Ababa, Ethiopia to investigate the colonization rate of S. pneumoniae and its coinfection dynamics with respiratory viruses among children under the age of 5 years. Samples from the nasopharyngeal and/or oropharyngeal, along with socio-demographic and clinical information, were collected from 420 children under 5 years old (210 cases with lower respiratory tract infections and 210 controls with conditions other than respiratory infections.). A one-step Multiplex real-time PCR using the Allplex Respiratory Panel Assays 1-4 was performed to identify respiratory viruses and bacteria. Data analysis was conducted using STATA software version 17. The overall colonization rate of S. pneumoniae in children aged less than 5 years was 51.2% (215/420). The colonization rates in cases and controls were 54.8% (115/210) and 47.6% (100/210), respectively (p = 0.14). Colonization rates were observed to commence at an early age in children, with a colonization rate of 48.9% and 52.7% among infants younger than 6 months controls and cases, respectively. The prevalence of AdV (OR, 3.11; 95% CI [1.31-8.19]), RSV B (OR, 2.53; 95% CI [1.01-6.78]) and HRV (OR, 1.7; 95% CI [1.04-2.78]) tends to be higher in children who tested positive for S. pneumoniae compared to those who tested negative for S. pneumoniae. Further longitudinal research is needed to understand and determine interaction mechanisms between pneumococci and viral pathogens and the clinical implications of this coinfection dynamics.

High rate of high-risk human papillomavirus among benign and breast cancer patients in Ethiopia.

INTRODUCTION: There have been numerous studies that showed the presence of human papillomavirus (HPV) in breast cancer; nonetheless, there is ongoing debate regarding their association. Given few studies in Ethiopia, we aimed to investigate the magnitude of HPV infection in Ethiopian breast cancer patients. METHODS: A total of 120 formalin-fixed paraffin-embedded (FFPE) tissue blocks were obtained, and basic demographic, clinical, and histological data were collected from medical records. DNA was extracted from archived FFPE breast tissue specimens using GeneRead DNA FFPE Kit. The AnyplexTM II HPV28 Detection Kit (Seegene, Korea) was used to detect HPV by following the manufacturer's instructions. The SPSS Version 25 was used to enter and analyze data. RESULTS: Among the 120 study participants; HPV (both high-risk and low-risk) was detected in 20.6% of breast cancer and 29.6% of non-malignant breast tumors. The most common genotype was the high-risk HPV 16 genotype. The frequency of HPV was nearly 10-fold higher in estrogen receptor-positive than ER-negative breast cancer. The percentage of HPV in the luminal (luminal A and luminal B) breast cancer subtypes was also much higher than in the non-luminal subtypes (HER-2 enriched and triple-negative breast cancer). CONCLUSION: This study did not find a significant difference in HPV expression between breast cancer and non-malignant breast tumors; however, the higher percentage of HPV in ER-positive compared to ER-negative breast cancer warrants further attention.

Degradation of 75 organic micropollutants in fresh human urine and water by UV advanced oxidation process.

In household wastewater, a large proportion of organic micropollutants (OMPs) load is attributed to human urine. OMPs could pose a risk to human and environmental health when urine collected in source-separating sanitation systems is recycled as crop fertiliser. This study evaluated degradation of 75 OMPs in human urine treated by a UV-based advanced oxidation process. Fresh urine and water samples were spiked with a broad range of OMPs and fed into a photoreactor equipped with a UV lamp (185 and 254 nm) that generated free radicals in situ. Degradation rate constant and the energy required to degrade 90% of all the OMPs in both matrices were determined. At a UV dose of 2060 J m-2, average ΣOMP degradation of 99% (±4%) in water and 55% (±36%) in fresh urine was achieved. The energy demand for removal of OMPs in water was <1500 J m-2, but for removal of OMPs in urine at least 10-fold more energy was needed. A combination of photolysis and photo-oxidation can explain the degradation of OMPs during UV treatment. Organic substances (e.g. urea, creatinine) likely inhibited degradation of OMPs in urine by competitively absorbing UV-light and scavenging free radicals. There was no reduction in the nitrogen content of urine during treatment. In summary, UV treatment can reduce the load of OMPs to urine recycling sanitation systems.

Trace Element Levels in Nails of Residents of Addis Ababa Are Shaped by Social Factors and Geography.

The Akaki catchment in Ethiopia is home to Addis Ababa and about five million people. Its watercourses receive a variety of wastes released by the residents and industries. River water is being used for irrigation, livestock watering, and other domestic purposes. This study tested the hypothesis that the river pollution would be reflected in higher levels of trace elements in the nails of residents living in Akaki-Kality Sub-City in the downstream, as compared to those living in Gullele Sub-City in the upstream of the Akaki catchment. Samples were taken and subsequently analysed for metals using inductively coupled plasma optical emission spectrometry (ICP-OES). The mean concentrations of Fe, Zn, Cu, Mn, Ni, Cr, Pb, and As in nails from Akaki-Kality were 488 ± 49, 106 ± 10, 5.2 ± 0.3, 13 ± 1.5, 11 ± 8, 2.2 ± 0.3, 0.09 ± 0.01, and 0.16 ± 0.01 µg/g, respectively. Likewise, the concentrations of Fe, Zn, Cu, Mn, Ni, Cr, Pb, and As in nails from Gullele were 1035 ± 135, 251 ± 10, 6.6 ± 0.4, 31 ± 3.7, 7.4 ± 1.7, 2.0 ± 0.3, 0.63 ± 0.01, and 0.25 ± 0.01 µg/g, respectively. Co and Cd were not detected. Contrary to the initial hypothesis, higher metal levels were found in nails of residents living in the upstream rather than the downstream area of the catchment. In particular, the concentrations of Fe (p = 0.000), Zn (p = 0.01), and Mn (p = 0.000) were significantly elevated in nails from Gullele and also high in comparison with internationally reported values. Besides, geography and social factors, especially education level, correlated to trace metals in nails. Most of the elements were significantly lower in the nails of individuals with a university degree compared to those who were illiterate or only completed primary school.

Clinicopathological Features of Invasive Breast Cancer: A Five-Year Retrospective Study in Southern and South-Western Ethiopia.

Background: Breast cancer (BC) is the most common type of cancer in Ethiopia. The incidence of BC is also rising, but the exact figure is still poorly known. Therefore, this study was conducted to address the gap in epidemiological data on BC in southern and southwestern Ethiopia. Materials and Methods: This is a five-year (2015-2019) retrospective study. The demographic and clinicopathological data were collected from biopsy reports of different kinds of breast carcinomas in the pathology department of Jimma University Specialized Hospital and Hawassa University Specialized Referral Hospital. Histopathological grades and stages were conducted using Nottingham grading and TNM staging system, respectively. Collected data were entered and analyzed using SPSS Version-20 software. Results: The mean age of patients at diagnosis was 42.27 (SD = 13.57) years. The pathological stage of most BC patients was stage III, and most of them had tumor sizes greater than 5 cm. Most patients had moderately differentiated tumor grade, and mastectomy was the most common type of surgery at the time of diagnosis. Invasive ductal carcinoma was the most common histological type of BC, followed by invasive lobular carcinoma. Lymph node involvement was seen in 60.5% of cases. Lymph node involvement was associated with tumor size (χ2 = 8.55, p = 0.033) and type of surgery (χ2 = 39.69, p < 0.001). Conclusions: This study showed that BC patients in southern and southwestern Ethiopia displayed advanced pathological stages, relatively young age at diagnosis, and predominant invasive ductal carcinoma histological patterns.

High burden of ESBL and carbapenemase-producing gram-negative bacteria in bloodstream infection patients at a tertiary care hospital in Addis Ababa, Ethiopia.

BACKGROUND: Bloodstream infection due to beta-lactamase and carbapenemase-producing gram-negative bacteria poses a substantial challenge to the effectiveness of antimicrobial treatments. Therefore, this study aimed to investigate the magnitude of beta-lactamase, carbapenemase-producing gram-negative bacteria, and associated risk factors of bloodstream infections in patients at a tertiary care hospital, in Addis Ababa, Ethiopia. METHODS: An institutional-based cross-sectional study was conducted with convenience sampling techniques from September 2018 to March 2019. Blood cultures were analyzed from 1486 bloodstream infection suspected patients across all age groups. The blood sample was collected using two BacT/ALERT blood culture bottles for each patient. Gram stain, colony characteristics, and conventional biochemical tests were used to classify the gram-negative bacteria at the species level. Antimicrobial susceptibility testing was carried out to screen beta-lactam and carbapenem drug-resistant bacteria. The E-test was conducted for extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producers. A modified and EDTA-modified carbapenem inactivation method was conducted for carbapenemase and metallo-beta-lactamases producers. Data collected using structured questionnaires and medical records were reviewed, encoded, and cleaned using EpiData V3.1. software. The cleaned data were exported and analyzed using SPSS version 24 software. Descriptive statistics and multivariate logistic registration models were used to describe and assess factors associated with acquiring drug-resistant bacteria infection. A p-value <0.05 was considered statistically significant. RESULT: Among 1486 samples, 231 gram-negative bacteria were identified; of these, 195(84.4%) produce drug-hydrolyzing enzymes, and 31(13.4%) produce more than one drug-hydrolyzing enzyme. We found 54.0% and 25.7% of the gram-negative bacteria to be extended-spectrum-beta-lactamase and carbapenemase-producing, respectively. The extended-spectrum-beta-lactamase plus AmpC-beta-lactamase-producing bacteria account for 6.9%. Among the different isolates Klebsiella pneumonia 83(36.7%) was the highest drug-hydrolyzing enzyme-producing bacteria. Acinetobacter spp 25(53.2%) was the most carbapenemase producer. Extended-spectrum-beta-lactamase and carbapenemase-producing bacteria were high in this study. A significant association between age groups and extended-spectrum-beta-lactamase producer bacterial infection was seen, with a high prevalence in neonates (p = <0.001). Carbapenemase showed a significant association with patients admitted to the intensive care unit (p = 0.008), general surgery (p = 0.001), and surgical intensive care unit (p = 0.007) departments. Delivery of neonates by caesarean section, and insertion of medical instruments into the body were exposing factors for carbapenem-resistant bacterial infection. Chronic illnesses were associated with an extended-spectrum-beta-lactamase-producing bacterial infection. Klebsiella pneumonia and Acinetobacter species showed the greatest rates of extensively drug-resistant (37.3%) and pan-drug-resistance (76.5%), respectively. According to the results of this study, the pan-drug-resistance prevalence was found to be alarming. CONCLUSION: Gram-negative bacteria were the main pathogens responsible for drug-resistant bloodstream infections. A high percentage of extended-spectrum-beta-lactamase and carbapenemase-producer bacteria were found in this study. Neonates were more susceptible to extended-spectrum-beta-lactamase and AmpC-beta-lactamase-producer bacteria. Patients in general surgery, caesarean section delivery, and intensive care unit were more susceptible to carbapenemase-producer bacteria. The suction machines, intravenous lines, and drainage tubes play an important role in the transmission of carbapenemase and metallo-beta-lactamase-producing bacteria. The hospital management and other stakeholders should work on infection prevention protocol implementation. Moreover, special attention should be given to all types of Klebsiella pneumoniae and pan-drug resistance Acinetobacter spp transmission dynamics, drug resistance genes, and virulence factors.

The expression of matrix metalloproteinase 2, 9 and 11 in Ethiopian breast cancer patients.

INTRODUCTION: Matrix metalloproteinases (MMPs) play a pathophysiological role in cancer initiation and progression. Numerous studies have examined an association between MMP-2, MMP-9, and MMP-11 expression and clinicopathological characteristics of breast cancer (BC); however, no research has been done on the MMP expression levels in BC cases from Ethiopia. MATERIALS AND METHODS: A total of 58 formalin-fixed paraffin-embedded breast tissue samples encompassing 16 benign breast tumors and 42 BC were collected. The RNA was extracted and quantitative reverse-transcription PCR was performed. GraphPad Prism version 8.0.0 was used for statistical analysis. RESULTS: The MMP-11 expression levels were significantly higher in breast cancer cases than in benign breast tumors (P = 0.012). Additionally, BC cases with positive lymph nodes and ER-positive receptors had higher MMP-11, MMP-9, and MMP-2 expression than cases with negative lymph nodes and ER-negative, respectively. The MMP-11 and MMP-9 expressions were higher in grade III and luminal A-like tumors than in grade I-II and other subtypes, respectively. CONCLUSION: The MMP-11 expression was higher in BC than in benign breast tumors. Additionally, MMP-11, MMP-9, and MMP-2 were higher in BC with positive lymph nodes and estrogen receptors. Our findings suggest an important impact of MMPs in BC pathophysiology, particularly MMP-11.

Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022.

Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia's lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia's role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.

Immunohistochemistry-derived subtypes of breast cancer distribution in four regions of Ethiopia.

Purpose: Different biological characteristics, therapeutic responses, and disease-specific outcomes are associated with different molecular subtypes of breast cancer (BC). Although there have been different studies on BC in the Ethiopian capital city of Addis Ababa, there have been few studies in other parts of the nation, and none have evaluated biological characteristics in other locations in the context of the extensive ethnic and genetic diversity found in Ethiopia. This study was carried out to evaluate the distribution of immunohistochemistry (IHC) subtypes of BCs throughout four Ethiopian regions. Methods: A total of 227 formalin-fixed paraffin-embedded (FFPE) tissue blocks were collected from tertiary hospitals in four Ethiopian regions between 2015 and 2021. The IHC staining was performed for subtyping, ER, PR, HER2, and Ki-67 proliferation markers. Results: The mean age at diagnosis was 43.9 years. The percentage of ER and PR-negative tumors were 48.3% and 53.2%, respectively. The IHC subtypes showed the following distribution: 33.1% triple-negative breast cancer (TNBC), 27.6% luminal B, 25.2% luminal A, and 14.1% HER2 enriched. In multiple logistic regression analysis, grade III and HER2 positivity were associated with larger tumor size, and also originating from Jimma compared to Mekele. Conclusion: Patients with ER-negative, PR-negative, and TNBC were found in 48.3%, 53.2%, and 33.1% of cases, respectively, showing that half the patients could potentially benefit from endocrine treatment. A considerably high prevalence of TNBC was reported in our study, demanding additional research that includes genetic predisposition factors. Additionally, aggressive tumors were found in a high percentage of younger age groups, which must be considered when planning personalized treatment strategies.

High burden of multidrug resistant bacteria detected in Little Akaki River.

Spread of antimicrobial-resistant bacteria between humans and animals occurs when the environment is contaminated with animal and human wastes. A total of 30 samples were collected from the Akaki river to identify antimicrobial-resistant bacteria. Bacterial enumeration and characterization was done by spreading serially diluted water samples on MacConkey agar. Sixty four bacterial isolates were identified and susceptibility tested using VITEK 2. The most frequently identified bacteria were Providencia alcalifaciens 10 (15.6%), Kluyvera cryocrescens 9 (14.1%) and Citrobacter freundii 7(10.9%), respectively. Multiple drug resistant bacteria were identified, constituting 17 (28%) of the 64 identified isolates. Multiple antimicrobial resistance (MAR) index of the six sites laid in the range 0.13-0.27, being the highest score located downstream of all the sampling sites. Species MAR index varied from 0.12 to 0.40. Out of 64 isolates, 54 (84.4%) of them were resistant to Ampicillin. On the contrary, most of the isolates were sensitive to Amikacin and meropenem. In conclusion, our findings indicated E.coli count was above the WHO permissible levels. The predominant isolates were P. alcalifaciens, and C. freundii. The MAR index of major isolates was greater than two, implying the study sites were exposed to high-risk sources of human or animal contamination.

Antimicrobial Resistance and Associated Risk Factors of Gram-Negative Bacterial Bloodstream Infections in Tikur Anbessa Specialized Hospital, Addis Ababa.

Background: Bloodstream infections (BSIs) are significant causes of morbidity and mortality in Ethiopia and worldwide. Alarming is the rapid global spread of antimicrobial resistance (AMR) in bacteria. Objective: To determine the microbial profile, antimicrobial susceptibility pattern, and associated risk factors for bloodstream infections in Tikur Anbessa Specialized Hospital (TASH) Addis Ababa Ethiopia. Methods: A cross-sectional study was conducted between September 2018 and March 2019. Blood collected twice from each septicemia suspected patient were processed following standard bacteriological procedures. AST was performed by using the disk diffusion test according to CLSI 2017 and 2018 guidelines. Data captured in Epidata were cleaned and analyzed by SPSS version 21 software. Results: The prevalence of BSI was 28.06% and a higher proportion of pathogene detected were gram-negative bacteria (GNB) (54.5%) and gram-positive bacteria (GPB) (45.43%). The most abundant bacterial species were Klebsiella pneumoniae 17.6%, CoNS 15.2%, and Acinetobacter spp 11.0%. Culture positivity was associated with age below 6 years, neonates AOR p=<0.001, infants AOR p=<0.001, Pre-school P=0.002, ICU admission COR p=<0.001, length of admission >5 days COR P=0.016, temperature greater than 38°C, AOR p=0.013, instrument usage during medical care AOR, p=<0.001, chronic illness AOR p=0.027, and neonatal incubation AOR p=0.013. GNB average drug resistance rate was 57.9% of the commonly used antibiotics and the most efficient and inefficient drugs were amikacin (10.8%) and ampicillin (94.6%). The gram-negative isolates showed a 95.3% rate of multi-drug resistance; and MDR, XDR, and PDR were observed at 55.8%, 32.2%, and 7.3%, of isolates respectively. This finding shows children especially neonates were highly affected by drug resistant BSI. Conclusion: Pediatric patients and ICU patients are more affected by BSI, and drug-resistant bacteria are a major problem. Therefore, appropriate intervention approaches need to be implemented.

Evaluating diagnostic accuracies of Panbio™ test and RT-PCR for the detection of SARS-CoV-2 in Addis Ababa, Ethiopia using Bayesian Latent-Class Models (BLCM).

BACKGROUND: Rapid diagnostics are vital for curving the transmission and control of the COVID-19 pandemic. Although many commercially available antigen-based rapid diagnostic tests (Ag-RDTs) for the detection of SARS-CoV-2 are recommended by the WHO, their diagnostic performance has not yet been assessed in Ethiopia. So far, the vast majority of studies assessing diagnostic accuracies of rapid antigen tests considered RT-PCR as a reference standard, which inevitably leads to bias when RT-PCR is not 100% sensitive and specific. Thus, this study aimed to evaluate the diagnostic performance of Panbio™ jointly with the RT-PCR for the detection of SARS-CoV-2. METHODS: A prospective cross-sectional study was done from July to September 2021 in Addis Ababa, Ethiopia, during the third wave of the pandemic involving two health centers and two hospitals. Diagnostic sensitivity and specificity of Panbio™ and RT-PCR were obtained using Bayesian Latent-Class Models (BLCM). RESULTS: 438 COVID-19 presumptive clients were enrolled, 239 (54.6%) were females, of whom 196 (44.7%) had a positive RT-PCR and 158 (36.1%) were Panbio™ positive. The Panbio™ and RT-PCR had a sensitivity (95% CrI) of 99.6 (98.4-100) %, 89.3 (83.2-97.6) % and specificity (95% CrI) of 93.4 (82.3-100) %, and 99.1 (97.5-100) %, respectively. Most of the study participants, 318 (72.6%) exhibited COVID-19 symptoms; the most reported was cough 191 (43.6%). CONCLUSION: As expected the RT-PCR performed very well with a near-perfect specificity and a high, but not perfect sensitivity. The diagnostic performance of Panbio™ is coherent with the WHO established criteria of having a sensitivity ≥80% for Ag-RDTs. Both tests displayed high diagnostic accuracies in patients with and without symptoms. Hence, we recommend the use of the Panbio™ for both symptomatic and asymptomatic individuals in clinical settings for screening purposes.

PCR-based detection of pathogens in improved water sources: a scoping review protocol of the evidence in low-income and middle-income countries.

INTRODUCTION: Occurrence of diverse human enteric bacterial, viral and protozoal pathogens in improved drinking water because of pathogenic microbial contamination is of increasing public health concern, particularly in low-income and middle-income countries (LMICs). Detecting microbial pathogens in water supplies comprehensively and accurately is beneficial to ensure the safety of water in LMICs where water contamination is a major concern. Application of PCR-based methods in detecting the microbial quality of water provides more accurate, sensitive and rapid outcomes over conventional methods of microbial identification and quantification. Therefore, exploring water quality outcomes generated through PCR-based methods is important to better understand the status and monitor progress towards internationally set goals for LMICs. This scoping review aims to map the existing evidence on the magnitude and characteristics of diarrhoeagenic pathogens as detected by PCR-based methods in improved water sources within the context of LMICs. METHODS AND ANALYSIS: This study will be undertaken in line with the Joanna Briggs Institute (JBI) methodology for scoping reviews. We will consider the available publications covering PCR-based microbial water quality assessment of improved drinking water sources in LMICs. Searches will be undertaken in PubMed/Medline, Scopus, Web of Science, JBI, Cochrane Library and Google Scholar. A grey literature search will be conducted in Google and ProQuest. ETHICS AND DISSEMINATION: The College of Natural and Computational Science Institution Review Board of Addis Ababa University gave formal ethical approval to this study protocol. The findings of this study will be disseminated to the concerned body through peer-reviewed publications, presentations and summaries.

Diagnostic accuracy of three commercially available one step RT-PCR assays for the detection of SARS-CoV-2 in resource limited settings.

BACKGROUND: COVID-19 is an ongoing public health pandemic regardless of the countless efforts made by various actors. Quality diagnostic tests are important for early detection and control. Notably, several commercially available one step RT-PCR based assays have been recommended by the WHO. Yet, their analytic and diagnostic performances have not been well documented in resource-limited settings. Hence, this study aimed to evaluate the diagnostic sensitivities and specificities of three commercially available one step reverse transcriptase-polymerase chain reaction (RT-PCR) assays in Ethiopia in clinical setting. METHODS: A cross-sectional study was conducted from April to June, 2021 on 279 respiratory swabs originating from community surveillance, contact cases and suspect cases. RNA was extracted using manual extraction method. Master-mix preparation, amplification and result interpretation was done as per the respective manufacturer. Agreements between RT-PCRs were analyzed using kappa values. Bayesian latent class models (BLCM) were fitted to obtain reliable estimates of diagnostic sensitivities, specificities of the three assays and prevalence in the absence of a true gold standard. RESULTS: Among the 279 respiratory samples, 50(18%), 59(21.2%), and 69(24.7%) were tested positive by TIB, Da An, and BGI assays, respectively. Moderate to substantial level of agreement was reported among the three assays with kappa value between 0 .55 and 0.72. Based on the BLCM relatively high specificities (95% CI) of 0.991(0.973-1.000), 0.961(0.930-0.991) and 0.916(0.875-0.952) and considerably lower sensitivities with 0.813(0.658-0.938), 0.836(0.712-0.940) and 0.810(0.687-0.920) for TIB MOLBIOL, Da An and BGI respectively were found. CONCLUSIONS: While all the three RT-PCR assays displayed comparable sensitivities, the specificities of TIB MOLBIOL and Da An were considerably higher than BGI. These results help adjust the apparent prevalence determined by the three RT-PCRs and thus support public health decisions in resource limited settings and consider alternatives as per their prioritization matrix.

Urinary 8-OHdG level is not affected by geography and trace elements in nail of residents of Addis Ababa: It is shaped by interactions between different social factors.

The objective of this study was to evaluate the association between exposure to heavy metals and oxidative DNA damage among residents living in the potentially more polluted downstream (Akaki-Kality) area of Addis Ababa, in comparison to the upstream area (Gullele). For this, 8-hydroxy-2'-deoxyguanosine (8-OHdG) was used as a biomarker for oxidative DNA damage and heavy metals (Fe, Zn, Mn, Cu, Ni, Cr, Pb, As) as indicators of exposure. The concentrations of heavy metals in nails were determined using inductively coupled plasma optical emission spectroscopy (ICP-OES), and 8-OHdG in urine using Enzyme-Linked with Immunosorbent Assay (ELISA), from 95 residents of the two areas, upstream and downstream. The urinary 8-OHdG concentration was not significantly different (p = 0.05) between the two Sub-Cities, with mean of 18.50 ± 4.37 ng/mg Creatinine in Akaki-Kality and 17.30 ± 5.83 ng/mg Creatinine in Gullele. Also, there were no statistically significant (p = 0.05) difference among the different demographic groups according to gender, age, educational status, body mass index or habit of alcohol consumption. However, the interactions of sex with age, sex with alcohol consumption and alcohol consumption with education were found to affect the urinary 8-OHdG levels of residents of the two Sub-Cities. The mean concentrations (µg/g) of the elements were 488 and 1035 for Fe, 106 and 251 for Zn, 13.0 and 31.2 for Mn, 5.23 and 6.63 for Cu, 11.2 and 7.39 for Ni, 2.23 and 2.02 for Cr, 0.09 and 0.63 for Pb; and 0.16 and 0.25 for As, in nail samples from Akaki-Kality and Gullele, respectively. The determined concentrations of the heavy metals in nails were not significantly associated (p = 0.05) with the corresponding urinary levels of 8-OHdG. Hence, the observed 8-OHdG might have been caused by environmental exposure to toxic substances other than the analyzed heavy metals.