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Item Genotype Distribution of Human Papillomaviruses & HPV E6/E7 mRNA Test for the Detection of High-Grade Cervical Intraepithelial Neoplasia (CIN2+) Among Gynecology Complaints in Northwest Ethiopia(Addis Ababa University, 2023-07) Derbie, Awoke; Abebe, Tamrat (Ass.Prof.); Woldeamanuel, Yimtubezinash (Ass.Prof.)Background: In developing nations, cervical cancer (CC) is the main cause of cancer-related fatalities in women due to the absence of well-established vaccination and screening programs. Exploring the best triage test for women with cervical abnormalities is a timely area of research to advance cervical screening and management. Further, the distinct proportional impact of each HR-HPV on the distribution of cervical lesions varies geographically. There is a shortage of data regarding the clinical value of high-risk human papillomaviruses (HR-HPV) E6/E7 mRNA test and their molecular epidemiology in cervical samples from Ethiopia, particularly in the current study area. Moreover, despite the fact that HR-HPV infection is an essential biological cause of CC, other socio-demographic factors are not well studied in the nation. Therefore, this study aimed to fill these data gaps. Objectives: The aim of the study was to determine the HPV genotype involved in cervical lesions, to evaluate the clinical use of HR-HPV E6/E7 mRNA for the early detection of CIN2+, and to explore factors associated with it among gynecology complaints in northwest Ethiopia. Methods: Between March 2019 and October 2021, a cross-sectional study was carried out at Felege Hiwot Compressive Specialized Hospital (FHCSH). Among women who visited the hospital for gynecological examination, those who were eligible for visual inspection (VIA)- based screening were included. Cervical punch samples were obtained by a gynecologist for histological analysis. Cervical swabs collected and analyzed for HR-HPV DNA and HPV E6/E7 mRNA using the Abbott Alinity m system and real-time PCR, respectively at the Institute of Virology, Leipzig University, Germany. Demographic and gynecologic-related history were collected using a structured questionnaire. The distribution and frequency of HR- HPVs described using descriptive statistics. Histology was used as the reference test to determine how well the E6/E7 mRNA detected CIN2+. Results: Of the 355 study participants (aged 30 to 80 years), more than half, 211 (59.4%), were unaware of CC, and their previous cervical screening practice was approximately 25%. Cervical biopsies from 41.8% (140/335; 95% CI: 36.6-47.1%) participants were diagnosed as cancer. The proportion of HR-HPV was 53%(188/355; 95%CI: 47.8-58.1%), with 13 different genotypes identified. HPV16 was predominant at 50.4% (95%CI: 29.4-39.2%), followed by HPV31 (9.7%), HPV33 (8.5%), HPV39 and HPV68 (5.8% each), and HPV18 at 4.7%. The iv E6/E7 mRNA test was positive in 35.8% (127/355; 95%CI: 30.0-40.9) of cases for HPV16, 16 & 45. The proportion of positive HPV DNA test results for these three HR-HPVS was 42% (149/355). The total agreement of DNA and mRNA tests in the detection of these HPVs was at 92.7% (95%CI: 89.5-94.9) with a kappa value of 0.821. HPV16, at 108 (85%), was the most common genotype expressing E6/E7 mRNA. The mRNA assay had sensitivity, specificity, positive and negative predictive values (PPV and NPV) of 65.2% (95%CI: 57.5-72.2%), 90% (95%CI: 84.6-93.4%), 85.8% (95%CI: 78.5-91.0%), & 73.6% (95%CI: 67.2-79.1%), respectively for detecting histologically confirmed CIN2+. Specifically, the sensitivity and specificity of this assay in the detection of CIN2+ were 92.7% & 47%, respectively among HPV16, 18, & 45 DNA-positive cases. Likewise, the analytical sensitivity and specificity of the HPV-DNA test were 84.8% & 74.1%, respectively. CC increased steadily with participant age, with women older than 50 years about four times more likely to develop CIN2+ (AOR: 3.68 95%CI: 1.75-7.72, p < 0.001). Similarly, no cervical screening in the past five years (AOR: 2.04; 95%CI: 1.04-4004; p = 0.038), infection with HR-HPVs (AOR: 5.28; 95%CI: 2.66-10.47; p < 0.001) and tested positive for E6/E7 mRNA (AOR: 5.78; 95%CI: 2.73-12.24, p < 0.001) were statistically associated with CIN2+. Conclusions: CC is still a significant issue for women's health in northwest Ethiopia that requires evidence-based interventions. The E6/E7 mRNA test and the HPV DNA test demonstrated good agreement and showed better diagnostic relevance in detecting CIN2+. Therefore, the test can be considered for colposcopy and biopsy triage. In particular, the mRNA test may be regarded as a potential triage for women who are HPV-positive , mainly in regions with a shortage of pathologists and colposcopy facilities. Vaccination and future HPV-based screening methods in Ethiopia should consider the important HR-HPV genotypes identified in such studies. To better assess the HPVs circulating in northwestern Ethiopia, community-based surveys should be conducted. Likewise, to optimize the E6/E7 mRNA analytical sensitivity and specificity , large-scale studies targeting major HR-HPVs should be considered. Finally, in accordance with the WHO recommendation women who are eligible for cervical screening need to be screened with a high-precision test, including HPV-based tests.Item Burden of Methicillin Resistant Staphylococcus aureus (MRSA) and associated factors at TASH: Evidence from colonization of Health Care Workers, Administrative staff, Patients and selected inanimate objects.(Addis Ababa University, 2023-12) Tullu,Kassu Desta(Phd); Woldeamanue,Yimtubeznashl(Asso. Prof.); Enquselassie,Fikre(Prof.); Price,James( PhD); Davey,Gail (Prof.)Background: Methicillin-resistant Staphylococcus aureus (MRSA) are multidrug-resistant bacteria that are carried harmlessly by humans and also cause severe life-threatening infections in community and healthcare settings worldwide. MRSA colonization of hospitalized patients and healthcare workers (HCWs) is a risk factor for transmission of infection. Furthermore, inanimate objects, such as Mobile phones, hospital gowns, and other fomites can serve as a reservoir for MRSA. Good knowledge, attitudes, and practices (KAP) of HCWs towards MRSA sources, colonization, and transmission is a key strategy for the control of MRSA. In Ethiopia, MRSA is a public health concern and observed rates of MRSA infections are reported from different parts of the country but molecular based data are very scarce or absent. Objectives: This study aimed to determine the burden and associated factors for MRSA colonization among HCWs, administrative staff, patients and selected inanimate objects at Tikur Anbessa Specialized Hospital (TASH), Addis Ababa, Ethiopia. Methods: A prospective and retrospective cross-sectional study was conducted between June 2018 to September, 2019 that included 588 HCWs and 468 administrative staff. Nasal swabs and swabs from their mobile phones were collected. Single swab from gown of each HCW was sampled. Samples from inanimate objects from the hospital were also analysed for MRSA. Perceived knowledge, attitudes, and practice (KAP) of HCWs were assessed using a pretested structured questionnaire. In addition, 170 S. aureus stored isolates were included mainly for molecular testing. All swabs samples were cultured on Mannitol salt agar and / or blood agar for growth and identification of S. aureus and MRSA were made by standard biochemical tests and cefoxitin disc methods respectively. Antimicrobial testing was performed according to CLSI breakpoints and isolates were further tested for MecA , PVL detection, Spa and MLST typing and WGS. Data were analysed using SPSS version 20.0 and statistical testing (Chi-square or Fisher’s exact test for categorical variables) was used to assess the difference between MRSA colonization rate among different groups, socio-demographic factors, and KAP level. P-value less than 0.05 was taken Statistically significant. Results: A total of 588 HCWs were included in this study and 58.4 % of them were female. The mean age and standard deviation of HCWs were 29.13 ± 6.66 years, The majority of HCWs were nurses by profession accounting for 49.1 % (289/588) followed by Medical doctors (28.4 % ) [167/588]. Among 468 administrative staff , 64.1 % of them were females. The rate of S.aureus isolates were 16.32 % (96/588) and 8.97 % (42/468) for nasal swabs and 6.46 % (38/588) and 3,85 % (18/468) for mobile phone contamination for HCWs and administrative staff respectively . For HCWs group the rate of S. aureus isolation from gowns was 7.48 % (44/588). Overall, 31 isolates (13.02 %) were sensitive to all antibiotics tested. All isolates were sensitive to rifampicin. About 10 % of isolates including all MRSA isolates were vancomycin sensitive using Van A and Van B genes detection methods. Furthermore ,237 isolates were resistant to at least for one drug. Overall there was a significant difference between drug resistance among MRSA and MSSA isolates (P-value <0.05). The burden of MRSA nasal colonization among HCWs and administrative staff was found to be 4.8 % (28/580) and 0.2 % (1/468) respectively. Nurses were most colonized by MRSA (22/28 total positive) P-value < 0.05). In this study, 2.72 % (16/588) and 1.3 % (6/468) mobile phones of HCWs and administrative staff were contaminated by MRSA respectively which are more frequent for nurses and doctors. Importantly ,2.89 % (17/588) of HCWs gowns were contaminated with MRSA and slightly higher among female HCWs (p-value >0.05). The proportion of MRSA from stored isolate of mother-child pair and diabetic patients was 0.24 % (2/846). While 21.73 % (20/92) stored isolates from clinical samples were MRSA. Overall 53 % (178/336) of S.aureus isolates obtained from nasal, clinical, mobile, and HCW’s gowns were PVL positive. A significant difference was also seen between pvl status and source of S.aureus isolates ( P-value <0.05).Genotyping based on spa typing has resulted in 131 spa types for 189 S. aureus isolates from various sources of samples, Forty-two spa types (32.06 %) occurred in 2 or more frequencies, while 89 of them (67.94 %) observed in singleton. The most frequent spa types in this study were t355 which were observed 23 times, followed by t223, t085, t131, and t003. Spa type t701, t1828, t080, t2235, t2302 and t14805,t314, t380, t3841, t11375, t5338, t14350,t062, t318 ,t693 and t937 were some of the spa types described in this study. Moreover, spa CC 15 and CC 22 are the most dominant clones observed. MLST Sequence data were available for 52 representative S.aureus isolates and 31 sequence types (ST) were generated. ST 152 is the most dominant ST accounting 20.3 % (11/ 54) followed by ST 4666, ST 5, and ST 744 each accounted 5.55 % (3/54 for each STs) . ST 80, ST88. ST97 and other STs were also found. Twenty-four STs are clustered in 5 MLST CCs and CC5, CC8, and CC15 were the very common clones both for MRSA and MSSA groups. Many spa types are reported for the first time in Ethiopia. Moreover, 18 S.aureus were characterized by whole genome sequencing (WGS),and based on the 16 SrRNA sequences, phylogenetic tree were constructed along with known sequences from the NCBI database. It seems our isolates were diverse and mostly poorly separated. Based on the average nucleotide identity and many of our S.aureus isolates from the nasal, gown, mobile phone, and clinical sources showed high similarity with S.aureus strains identified from various clinical and non- clinical isolates. In this study, the overall knowledge of HCWs about MRSA prevention and control was 85.5 % .The majority of HCWs in TASH had a positive attitude towards the importance of system-wide approach to prevent MRSA in the hospital (95.2 %, 542/ 582). While 54.68 % of HCWs had a positive attitude and 68.4 % of them had good practice about MRSA prevention and control measures at TASH. Conclusion: MRSA nasal colonization and mobile phone contamination of HCWs in TASH was higher than administrative staff. The presence of MRSA from gowns of HCWs is a cause for concern. MRSA was also seen from stored isolates of nasal source of patients and clinical isolates based on Mec A detection. The high rate of pvl among all S. aureus isolates is worrisome. There is diverse spa and MLST types among S.aureus isolates, t355 and ST 152 were common ST and spa type respectively. Although, HCWs in TASH had high level of knowledge about MRSA control and prevention, their attitude and practice score is inadequate. Hence, it is important to implement a system for continuous surveillance of MRSA in TASH using phenotypic and genotypic methods to take preventive measures and track changes of intervention. Moreover, concerted efforts are needed among HCWs, management body and policymakers to avail and regulate personal protective equipments (PPEs) in a sustained manner.Item The comparison of Xpert® Xpress with Cobas® SARS-CoV-2 assay on individual and pooled nasopharyngeal swabs and whole genome sequencing of SARS-CoV-2 samples collected in selected hospitals of Addis Ababa, Ethiopia.(Addis Ababa University, 2023-07) Zerihun,Betselot; Abegaz,Woldaregay Erku(PhD, Ass. Prof.); Gebre-Selassie,Solomon (MD, MSc, Ass. Prof.); Kebede,Habtamu Biazin (MSc); Alemu,Ayinalem(MSc, MPH/E)Background: Xpert® Xpress and Cobas® are assays offering rapid test for the detection of SARS-CoV-2. Pooled testing allows for continued testing even when supplies are relatively scarce. Whole genome sequencing of SARS-CoV-2 refers to the process of determining the complete genetic sequence of the virus, providing a detailed and comprehensive analysis of its entire genome. The agreement between assays for SARS-CoV-2 detection from individual and pooled samples is uncertain in Ethiopia. Moreover, there is limited availability of whole genome sequencing data for SARS-CoV-2, leading to insufficient information regarding the circulating variants, lineages, and mutations. Objective: The study aimed to compare the performance of Xpert® Xpress with Cobas® SARS- CoV-2 assays for SARS-CoV-2 detection from individual and pooled nasopharyngeal swabs and whole genome sequencing of SARS-CoV-2 to identify lineages, sub-lineages and mutations for nucleocapsid and envelop gene, in Ethiopia. Methods: A cross-sectional study design was utilized on individuals suspected of having COVID-19 in seven selected hospitals in Addis Ababa, Ethiopia, between June 25, and July 20, 2022. The samples were tested for SARS-CoV-2 using the GeneXpert® and Cobas 8800®. A total of fifty samples that tested positive with the Xpert® were chosen and divided into four groups according to their CT-value and then pooled with negative samples and subjected to testing using both assays. Positive samples with a CT-value of ≤30 were selected for sequencing. The CovidSeq Assay was used to prepare sequencing libraries, which were then sequenced on the Illumina Miseq. Data were entered into Epi data version 3.1 and exported to SPSS version 28 for statistical analysis. Analysis was performed by using descriptive statistics, pearson correlation, and cohen’s kappa. Nextflow work flow manager and different bioinformatics tools were used for the analysis of variants, lineages, and mutations. Results: In this study, a total of 440 nasopharyngeal swabs were collected, and the overall rate of positivity for SARS-CoV-2 was found to be 100 (22.73%). The overall agreement between the assays from individual samples was 91.73(95% CI, 89.99% to 92.66 %, κ=0.715) indicating a substantial level of agreement. The Xpert® assay showed a high positive percent agreement (98.25%) and negative percent agreement (90.71%). The overall agreement between the assays from pooled samples was 89%, (95% CI, 86.31% to 91.52% κ=0.552). All 16 sequenced samples were identified as the Omicron variant, with ten samples assigned to clade 22A. The consensus XIII sequence length ranged from 29,578 to 29,903, with a GC% ranging from 33.1% to 39.0%. The average length of amino acids in the sequences was 9519. The pairwise identity between the samples and the reference genome ranged from 98.6% to 99.9%. Several amino acid changes were observed in the sequenced samples, including P13L, P151S, N E31del, N R32del, N S33del, N P151S, N R203K, N G204R, and N S413R on the N genes. Likewise, there was one common mutation at position 9 in the E gene, E31del. Conclusion: The Xpert® performed better than the Cobas® assay in detecting positive results due to its ability to detect low viral load cases, utilizing the more sensitive nucleocapsid gene instead of the ORF1a gene used in the Cobas® assay. Confirming presumptive positive results by different methods and using multiple molecular assays targeting different genes is important to ensure high sensitivity in detecting RNA. Pooling up to six samples was possible regardless of viral load and pool size for Xpert®. But viral load effect was significant in all pool size of Cobas® assay. The agreement on individual samples indicated that both assays can be used interchangeably for diagnostic purposes. Furthermore, there were variations in amino acid length, the presence of both unique and existing mutations, and variations in mutation frequencies among the analyzed sequences.Item Human papillomavirus genotype distribution, persistence, clearance, and characterizing cervicovaginal microbiota: A population- based follow up study(Addis Ababa University, 2023-04) Endallew,Brhanu Teka(Phd); Abebe,Tamrat (MSc., PhD); Kaufmann,Andreas M(PhD); Kantelhardt,Eva J(Prof.,PhD); Mihret,Adane(PhD)Background: Human papillomaviruses (HPVs) are a group of small, non-enveloped, naked icosahedral (55nm) viruses that can cause cervical cancer (CC) and other cancers. Cervical cancer is by far the most common HPV-related disease, and it is the second leading cause of morbidity and mortality from all cancers in Ethiopian women. Persistent infection with hr-HPVs and progression to precancerous lesions are the most important steps in the carcinogenesis process. However, most infections are transient and rarely persist implying development of CC is a multifactorial and step by step process and may require other co-factors like cervicovaginal microbiome within the local microenvironment for its development. Objective: To determine the prevalence of HPV infection, genotype distribution, the persistence and clearance rates within two years and compare the performance of different HPV tests. Furthermore, it aimed to characterize the cervicovaginal microbiota in women with premalignant dysplasia or invasive cervical cancer compared with that of healthy women. Methods: The study was conducted in two cohorts; a population-based cohort from rural women in Butajira, south-central Ethiopia and women attending gynaecological clinic at Tikur Anbessa Specialized Hospital from October 2017 to February 2020. From Butajira, a total of 893 samples were tested at baseline. A self-sampling brush (Evalyn Brush®, Rovers, Oss, The Netherlands) was used for cervical specimen collection and HPV testing was performed using multiplexed genotyping (MPG) by BSGP5+/6+ PCR with Luminex read out. Follow-up testing was done at 6 and 24 months for baseline hr-HPV positive women. Moreover, three HPV DNA testing assays (MPG-Luminex Assay, Anyplex II HPV HR Detection, and EUROArray HPV) were compared and the analytical sensitivity and specificity of the assays in detecting hr-HPV infections was computed. At Tikur Anbessa Specialized Hospital, cervicovaginal microbiota of 120 women was characterised using the 16S rRNA cervical microbiome sequencing. Shannon and Simpson diversity indexes were used to evaluate alpha diversity. Beta diversity was examined using principal coordinate analysis (PCoA) of unweighted Unifrac distances. Results: At baseline screening, the population-based HPV positivity rate was 23.2% (95% CI: 23.54‐22.86%), of these 20.5% (95% CI=20.79‐20.21), and 10.3% (95% CI=10.52‐10.08) women were hr‐ and lr‐ HPV positives, respectively. Age‐specific hr‐HPV infection peaked in the age‐ group 30‐34 years old (58.6%) and decreased in 35‐39, 40‐44, and 45‐49 years to 20.4%, 4.5% and 3.8% respectively. The top five prevalent hr‐HPV genotypes were HPV16 (57.1%), 35 (20.3%), 52 (15.8%), 31 (14.1%), and 45 (9.6%) in the Butajira district. hr-HPV infection clearance was observed in 70 women (73.7%) within 6 months and among 77 women (84.6%) within 2 years. In the control women (negatives at baseline), the hr-HPV incidence was 4.1%. v HPV68, 82, 53, 52, 56 were the most persisted genotypes with 100%, 75%, 42.9%, 31%, and 25% persistence rates respectively while after 24 months, HPV59, 68, 66, 52 and 16 were found to have persistence with 50%, 50%, 20%, 15.8% and 3.5% respectively. Twenty-nine (29.9%) of the 6 month follow up attended women were with abnormal cytology including ASCUS and HSIL constituted 10.3% of the tested women. Of the three HPV testing assays compared in this study, MPG-Luminex Assay found 18.2% positive for the 14 hr-HPV and 7.3% for the probable hr-HPV genotypes. Anyplex™ II HPV HR Detection assay and EUROArray HPV Assay identified 21.82% and 12.7% samples, respectively, for the 14 hr-HPVs and both 7.3% for the probable hr-HPV genotypes (κ=0.734). Among the 14 hr-HPV genotypes, the genotype-specific agreement of the three HPV genotyping assays was moderate or better for HPV16, 31, 35, 39, 52, 56, 66 and 68. The aggregated sensitivity in detecting the 14 hr-HPV infections of Anyplex™ II HPV HR Detection and EUROArray HPV assays was high, 100% and 70%, respectively. The specificities of Anyplex™ II HPV HR Detection and EUROArray HPV were 95.6% and 100%, respectively. In this study, alpha diversity was significantly higher in patients with cervical cancer than in patients with dysplasia and in healthy women (p < 0.01). Beta diversity was also significantly different in cervical cancer patients compared with the other groups (weighted UniFrac Bray- Curtis, p < 0.01). Microbiota composition differed between the dysplasia and cervical cancer groups. Lactobacillus iners was particularly enriched in patients with cancer, and a high relative abundance of Lactobacillus species was identified in the dysplasia and healthy groups, whereas Porphyromonas, Prevotella, Bacteroides, and Anaerococcus species predominated in the cervical cancer group. Conclusion: This study provided new data on the overall prevalence of HPV infection and distribution of specific HPV types in rural Ethiopia. As a first population‐based study in the country, our results can serve as valuable reference to guide nationwide cervical cancer screening and HPV vaccination programs in Ethiopia. HPV16, HPV35, HPV52, HPV31 and HPV45 were the most prevalent genotypes. Most of the hr-HPV infections among rural Ethiopian women were cleared within 2 years. This study has found differences in cervicovaginal microbiota diversity, composition, and relative abundance between women with cervical cancer, women with dysplasia, and healthy women. Additional studies need to be carried out in Ethiopia or in any other regions to further validate the role of cervical microbiome in development of cervical cancer. From this study, the three evaluated assays showed similar analytical performance in the detection of hr- HPV infections and moderate or better concordance in HPV genotyping.Item Molecular Detection of Virulence and Antimicrobial Resistance Genes of Streptococcus Pyogenes Isolated From the Oropharynx of Febrile Patients in Adama and Wonji, Ethiopia.(Addis Ababa University, 2023-08) Lemi,Haile Abera; Negash,Abel Abera(PhD, Ass.Prof.); Mihret,Adane(DMV, PhD, Ass.Prof.); Adane,Kelemework(PhD, Ass.Prof.)Background: Streptococcus pyogenes also called Group A Streptococcus (GAS) is a significant human pathogen that causes several diseases including pharyngitis, skin infections, rheumatic fever and rheumatic heart disease. GAS produces a variety of virulence factors such as toxins/superantigens, proteases, DNases. Detection of virulence genes can be used to determine the pathogenic potential of a strain. Although GAS is generally thought to be susceptible to β-lactams, an increasing trend of treatment failures and resistance to macrolides and tetracyclines have been observed. There is a paucity of data on the molecular epidemiology of virulence factors and antibiotic-resistance of S. pyogenes in Ethiopia. Objective: To assess virulence factors, antimicrobial susceptibility profile and drug resistance genes of oropharyngeal S. pyogenes isolated from febrile patients. Method: A cross-sectional study was conducted on 201 S. pyogenes isolated from the oropharynx of febrile patients in Adama and Wonji, Oromiya, Ethiopia. Standard microbiological procedures were used for bacterial growth and identification. Bacterial DNA was extracted using an alkaline lysis buffer. Multiplex PCR was conducted to identify virulence factors for the production of superantigens (SpeA, SpeC, SpeG, SpeH, SpeI, SpeJ, SpeK, SpeL, SpeM, SmeZ and ssa); proteases (SpeB, spyCEP, scpA, Mac and sic); and DNases (sdaB, sdaD, sdc and spd3), erythromycin resistance genes [mef(A), erm(B) and erm(A)-TR] and tetracycline resistance genes [tet(M), tet(O), tet(K)and tet(L)]. SPSS version 27 was used for statistical analysis. Majority of the results were summarized by frequency and percentage distributions. Result: This study was performed on 201 S. pyogenes isolates. We investigated the presence of 20 different GAS virulence factors and identified 18 of them with variable proportions. Relatively higher frequencies of Mac (24.9%), SmeZ (16.9%), scpA (15.4%), sic (12.9%), SpeK (12.4%) and SpeI (10.0%) genes were identified. Our antibiotic susceptibility testing showed that 10% of the GAS isolates were non susceptible to penicillin. High resistance rate to tetracycline (54.2%), quinupristin-dalfopristin (43.3%) and erythromycin (19.9%) were also observed. The overall multidrug resistant (MDR) rate was 14.9%. However, all GAS isolates were 100% sensitive to linezolid. M phenotype was observed in 85% of erythromycin resistant GAS isolates and mef (A) gene was identified in 96.9% of the erythromycin non susceptible GAS isolates. Among tetracycline resistant genes tet(M) was identified in 98.2% of the tetracycline non susceptible GAS isolates. Conclusion: In this study, we have identified 121 (60.2%) of the GAS isolates had at least one or more types of virulence factors and again more than half of the isolates,156 (77.6%) were resistant to one or more types of antibiotic classes. We also found that, an emerging penicillin non susceptible GAS isolates contrary to the previous reports and this might be an alarming condition. The most common erythromycin resistance mechanism in our study was efflux pumping which was encoded by the mef(A) gene where as that of tetracycline resistance mechanism was target site modification by ribosomal protection protein which was encoded by the tet(M) gene. Linezolid may be one of the promising drugs for the treatment of drug resistant GAS strains. The identification of different virulence factors and the increasing trends of drug non susceptibility especially to penicillin among GAS isolates requires a concern for continuous surveillance of the pathogen.Item Performance Evaluation of the First-Generation (1G) Color Plate Drug Susceptibility Testing Assay Identifying Drug- Resistant Mycobacterium Tuberculosis Isolates for Selected Anti- Tuberculosis Drugs(Addis Ababa University, 2024-03-13) Binyam Mebrat; Alem miritTuberculosis is a major global public health concern and the emergence of drug- resistant (DR)-TB has been a major challenge to the control of the disease, especially in developing countries, including Ethiopia. Despite availability of appropriate diagnostic tools for Mycobacterium tuberculosis drug susceptibility testing, accessibility and timely diagnosis of DR-TB in resource-constrained settings, such as Ethiopia, is often a challenge. The first- generation color plate assay (1G) is ideally suited for low resource settings due to low cost, minimal technical expertise needed, and rapid provision of DST results.Item Prevalence and Antimicrobial Resistance Profile of Methicillin-Resistant Staphylococcus aureus (MRSA) and Factors Associated with it Among Patients with Wound Infections at Werabe Comprehensive Specialized Hospital, Central Ethiopia Region, Ethiopia(Addis Ababa University, 2024-05-12) Nejato Ousman; Alem AbrhaStaphylococcus aureus is a highly significant pathogen for global public health because of its extensive distribution, potential to cause infections that could be fatal, and continuous development of drug resistance. In settings such as the community and health care institutions, it is among the frequent causes of wound infection. Worldwide, the occurrence of drug-resistant S. aureus, particularly MRSA, has surged at a concerning rate. Nonetheless, prior research in Ethiopia and other nations found notable regional differences in the incidence and associated variablesItem Molecular Epidemiology and Genetic Diversity of Epstein - Barr virus among lymphoma patients in Ethiopia(Addis Ababa University, 2024-06-13) Seifegebriel Teshome; Tamrat Abebe;The Epstein-Barr virus (EBV) is a member of the herpesvirus family and is highly prevalent among the global population. It is estimated that more than 90% of adults have been exposed to this virus, making it one of the most common human viruses worldwide. After initial infection, infectious mononucleosis (IM), which typically occurs during childhood or adolescence, EBV establishes a long-lasting latent infection within B lymphocytes. EBV is associated with various diseases such as Burkitt's lymphoma, Hodgkin's lymphoma, nasopharyngeal carcinoma, and certain types of Gastric cancer. Studying the overall viral molecular epidemiology and genetic diversity of EBV can provide valuable insights into the pathogenesis, diagnosis, and management of EBV-associated diseases. The objectives of the study were on various aspects of EBV among lymphoma patients. It encompasses the detection of EBV, determining the genotypes, analysis of its methylation status, and identification of sequence variationsItem 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 MihretGlobally, 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 EthiopiaItem 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 AbebeMany 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 EthiopiaItem 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 AbebeFemale 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 sub-Saharan 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 methodsItem Studies on Virologic, Immunologic and Other Host Factors Contributing to Resistance to HIV Infection in Discordant and Concordant Couples in Ethiopia.(Addis Ababa University, 2011-03) Meseret,Yohannis(Phd); Mengistu,Yohannes(Dr.)It was not known why some people were HIV negative and others were HIV positive despite frequent sexual relationship between couples in Ethiopia. Most of the transmission of HIV is currently between discordant couples. This is a big problem as very few people know their HIV status and protection between couples during sexual intercourse is unknown. The result obtained from the study of discordant couples is very important as it enables us to know the reasons for susceptibility and resistance to HIV infection. This is especially true for policy makers as the result obtained from this study is high quality data including behavioral, biomedical and virological factors. The objectives of this study is, therefore, to investigate the reasons for susceptibility and resistance to HIV infection in discordant couples, which may involve behavioral, viral, immunological and other host and viral factors by comparing with concordant and healthy negative control subjects. The study involves discordant couples who have been in marriage relationship for more than one year, concordant couples and healthy negative couples with similar marital status with discordant couples. The study was carried out in hospitals and clinics all over Ethiopia and involved discordant and concordant couples who were on the follow up for many years in the respective hospital and clinics and were not on antiretroviral treatment. The samples were analyzed with appropriate statistical package using SPSS version 13 soft ware. To study if the difference in sexual behavior might have contributed to their serodiscordance, 325 discordant couples, 152 concordant couples and 14 healthy negative controls sexual behavior was studied. The study method involved an in-depth interview. There were known behavioral differences between discordant negatives and positives and concordant couples. There was very close similarity in behavior between discordant positives and concordant couples, showing that they shared similar risk behaviors. But the difference between discordant negatives and discordant positives was clear and big enough showing distant behavioral similarities. The healthy controls were behaviorally very much different from both discordant and concordant couples but they were similar to discordant negatives in some of their behaviors. Almost all of them were not aware of HIV before VCT and had multiple partners before marriage and were multiply married. All had unprotected sexual intercourse before and after marriage with their partners and there was no HIV test in between marriages. The majority of them were, however, satisfied in their marriages, but the reason for the satisfaction was not based on love, faithfulness and mutual respect. The reason for the dissatisfaction was also similar. The sexual frequency and number of sexual act per each contact was higher for discordant positives and concordant couple than discordant negatives and healthy control and discordant positives and concordant couples were also involved more in traumatic sex than discordant negatives. History of STDs was also higher for discordant positives and concordant couples when compared with xiii discordant negatives. Discordant positives and concordant couples were exposed to more risky behavior than concordant couples. Perceived mechanisms of HIV infection was also known risk factors for HIV infection and were associated with their sexual lives, family, occupation, social evils and injustice. When subjects were compared immunologically, discordant negative partners had adequate amount of CD4 equivalent to healthy subjects and highly significantly (P<.001) different from discordant positives. CD4 and CD8 ratio was also high indicating a healthy balance and this was also similar to healthy controls. Discordant positive partners had a significantly (P<.05) different number of CD4 cells when compared to concordant couples. Their CD8 number was very similar to discordant negatives and there was no significant difference. Increased CD8 number was associated with decreased viral load and in some subjects even to the level of below detection level. Lower viral load in discordant positives when compared to concordant couples also indicated lower or absence of transmission to uninfected partner. CD8 T cells were responsible in decreasing viral load. The evidence for this came from the observation that concordant couples showed elevated viral load and decreased CD8 T cells number while discordant positives showed elevated CD8 and very low viral load. Their CD4 number was also closer but slightly higher than the normal boundary count and might have been capable of providing the appropriate help for CD8 cells. Syphilis was a known risk factor for HIV transmission as it was diagnosed in many of discordant positives and concordant couples. This is possible because syphilis is a common STD in this country and its chronic nature might have accounted for its co-factor effect. Analysis of T cell subpopulations in discordant couples showed no activation of a specific marker between discordant positives and negatives and the expression of T cell subpopulations was comparable. The only difference observed was the expression of activation markers in significantltiy (P<.05) higher proportion in concordant couples when compared with discordant positives , indicating lower immune activation in discordant positives. In discordant positives, in addition to decreased number of activation markers there were also expression of certain markers (CD4+CD45RA-CD27-) in higher proportion(>30%), which were common in long-term-non- progressors, showing that discordant positives were long-term-non-progressors. Our study showed that there was a clear difference between discordant positives and discordant negative couples in their genetic profiles. There was also a clear difference between discordant positives and concordant couples and AIDS patients, in their genetic profiles. Ethiopian AIDS patients were different from Ethiopian concordant couples in their very significant to significant association with HLA-A*29, *18, and *41; HLA-B*0705, *1517, *4101, *5001, *7301 and *18; xiv HLA-C*0501, *0701, and *0740. AIDS patients were also very significantly different from discordant positives in their associations HLA-A*68, HLA-B*39 and HLA- DR*11. AIDS patient were also different from discordant negatives in their very highly significant to highly significant association with HLA-*0801, *1817, *352001 and *4901; HLA-C*7 and HLA-DR*40301. Concordant couples were also different from discordant positives in their very highly significant to significant associations with HLA-B* 0705, *0801 and *3910. Concordant couples were also different from discordant negatives in their significant association with HLA-DR*100101 and *110201. Discordant negatives were different from discordant positives in expressing HLA profiles of HLA-B*0801, *39, *41, *39; HLA-C*0716, HLA-DR*100101 and *110201. Overall, the differences between the different groups had a genetic background. When comparisons were made between discordant positives, concordant couples and AIDS subjects, discordant positive subjects were found to be more heterozygous at all loci (HLA-A, B, C and HLA-DR) when compared with concordant couples and HIV/AIDS subjects. This showed that discordant positives better controlled HIV and maintained HIV in check and were non- progressors due to heterozygous advantage. Overall, the results for discordant positives and AIDS subjects were clear enough to show significant difference between them. Ethiopian HIV viruses were mainly HIV type C in all discordant positives and HIV/AIDS subjects. But other subtypes such as subtype A, B and recombinant A/G subtypes were also observed. Co receptor utilization of discordant positive isolated viruses was both CCR5 and CXCR4 in equal proportion. The majority of HIV/AIDS patients used CXCR4, although about one third used CCR5 and a few also used dual co receptors. Our study showed that the majority of subtype C viruses were CXCR4/SI high/rapid subtype. And about one third was CCR5/NSI subtypes. The phylogenetic or evolutionary relationship showed that the majority of the viruses isolated from discordant positives showed subclustering in one region and those isolated from concordant couples in another region, showing that discordant positive isolated viruses were evolving independently and were related with each other but this was not seen in viruses of concordant couples and HIV/AIDS subjects.Item Extended-Spectrum β-Lactamase and Carbapenemase producing Escherichia coli O157:H7 among diarrheic patients in Shashemene, west Arsi, Ethiopia(Addis Ababa University, 2023-06) Ayalneh,Shimelis Teshome; Abegaz,Woldaregay Erku (Assoc. Prof.); Gebreselassie,Solomon (Assoc. Prof.); Teferi,Mekonnen(Dr.); Beshah,Biruk Yeshitila(MSc, Ph.D. candidate)Background: Escherichia coli (E. coli) O157:H7 has been found in various sources across the globe, and until recently, it was uncommon for this pathogen to produce Extended Spectrum β-Lactamase (ESBL) and Carbapenemase. However, recent reports from different regions have shown that ESBL-producing E. coli O157:H7 is becoming more prevalent. In Ethiopia, while there is sufficient knowledge about the epidemiology of E. coli O157:H7 in the country's different food supply chains, there is a lack of information regarding the extent of disease caused by this pathogen and its production of ESBL and Carbapenemase. Objectives: To isolate E. coli O157:H7, determine its antimicrobial susceptibility profiles, characterize its ESBL and Carbapenemase production from stool specimens collected among diarrheic patients and explore the association of E. coli O157:H7 infection with demographic and clinical features of diarrheal patients in Shashemene, west Arsi, Ethiopia. Methods: A total of 423 study participants were included from July 1, 2022, to November 25, 2022, in this prospective healthcare facility-based cross-sectional study among all patients with diarrhea. The bacterial pathogen was isolated and identified by colony characteristics, Gram stain, and standard biochemical tests using API 20E as well as utilization of sorbitol and serotyping by antisera for O157 antigen. Each identified isolate was screened and tested for ESBL and Carbapenemase production phenotypical and further characterized at the molecular level for 2 Carbapenemase (blaNDM, blaKPC) and 3 ESBL coding gens (blaCTX-M, blaTEM, and blaSHV). The data were entered into SPSS version 26.0 software for analysis. Bi-variant and multi-variant analyses Were employed using a logistic regression model for further analysis and were interpreted based on the odds ratio and level of statisticasignificance at a p-value <0.05. Result: Upon laboratory investigation, E. coli O157:H7 strain was found in 38/423 (9%) study participants from this majority of the participants [262 (61.9%)] were males with a 1.6:1 male: female ratio and 81(19.1%) of the participants were less than five years old and 14 (3.3%) of patients were elders aged above 55 years. Living in urban area, having domestic animal and having ≥5 family size were significantly associated with E. coli O157:H7 cases. High antimicrobial resistance was observed on Ampicillin [38, (100%)] followed by Amoxicillin with clavulanic acid [34, (89.5%)]. However, all isolates were sensitive to ciprofloxacin. Twenty-seven (71.1%) and 12 (31.6%) isolates were phenotypically confirmed to be ESBL and carbapenemase producers, respectively. The genotypic testing revealed that the most abundantly found ESBL genes were blaTEM group 15 (79%) followed by blaCTX-M group 12 (63%) and blaSHV group 2(10%). Additionally, from the 12 carbapenemase-positive isolates, 8 (66.6%) were confirmed to have the blaKPC group gene and none of the isolates were positive for blaNDM group. Conclusion: The E. coli O157:H7 isolates from this study exhibited a high level of resistance to some of the antimicrobials tested. The magnitude of ESBL and Carbapenemase production among these isolates was found to be high. High resistance of Ampicillin and Amoxicillin/Clavulanic acid was observed among ESBL, and carbapenemase- producing isolates and Ciprofloxacin was found to be the most effective drug against both ESBL producers and non- producers. blaTEM group gene was the most abundant ESBL coding gene found and blaKPC group gene was the only gene found in our isolates that code for Carbapenamese.Item Analysis of Serum for Antibodies to Cytomegalovirus in Individuals with Schizophrenia and Bipolar Disorder(Addis Ababa University, 2010-02) Yared Tedla ; Woldeamanuel Yimtubezinash; Asrat Daniel; Shibre Teshome; Assefa AbrhamBackground: Several evidences suggest that Cytomegalovirus (CMV) may play anetiological role in some case of schizophrenia and bipolar disorder. Studies have reported that some individuals experiencing initial episodes of major mental disorders have increased levels of immunoglobulin G(IgG) to CMV. Objective: To determine the magnitude of CMV infection in individuals with schizophrenia, bipolar disorder and healthy controls by using serologic diagnostic methods. Materials and Methods: A case control study conducted from March to May of 2009. A total of 844 serum samples were analysed for the presence and level of IgG to CMV using enzyme linked immunosorbent assay (ELISA).Serawere collected from 216 individuals with schizophrenia, 199with bipolar disorder and 429close relatives and their healthy controls, recruited from Butajira district.Seropositivity summarized using percentage and antibody level was summarized using mean. Logistic regression was used for cross tabulated data and linear regression for comparing antibody level among groups. All test of significance was two tailed and ,p < 0.05 is considered significant. Results:99.3% of tested serawere positive for IgG to CMV. However, serum levels of IgGto CMV in individuals with schizophrenia[β = 0.21; 95% CI (0.03, 0.38)]and bipolar disorder [β = 0.20; 95% CI (0.02, 0.37)]were higher compared to healthy controls. Younger individuals with schizophrenia (<20 years) had higher level of IgG to CMV compared to matched healthy controls[β = 0.64;95% CI (0.10, 1.19)]. Conclusion: This study provided serologic evidence that infection with CMV may be associated with some cases of schizophrenia and bipolar disorder. Additional studies should be directed at further analysis of antibodies to CMV in the sera and CSF of individuals with recent onset of psychosis.Item Analysis of Serum for Antibodies to Toxoplasma Gondii in Individuals with Schizophrenia and Bipolar Disorders(Addis Ababa University, 2010-02) Tadele Geletta; Aseffa AbrahamBackground: Schizophrenia and bipolar disorders are serious neuropsychiatric diseases of unknown etiology. Recent studies indicated that infectious agents such as Toxoplasmagondii may contribute to some cases of schizophrenia and other mental disorders. In this study we determined the prevalence of T. gondi infection and IgGtitersagainst Toxoplasmain schizophrenia and bipolar disorder patients and control subjects which comprise first degree relatives of the patients and some individuals from neighborhoods. Methods: 214 cases of schizophrenia, 171 patients of bipolar disorders and 363 controlsrecruited fromMeskan and Mareko (Butajira)district forgenetic study in 2001and theirstored sera were analyzed for IgG antibody against T. gondii by using enzyme-linkedimmunoassay (ELISA)for a period of March to May 2009. Results: Overall prevalence of IgG antibodies in all study subjects was 95.2%. The prevalence of the antibodies increased with age in cases and control subjects. Theseroprevalence of T. Gondii infection was 97.7% in patients with schizophrenia,95.3% in bipolar disorder cases and93.7% in control subjects. There was significantly increase inseroprevalence of IgG antibodies toT. gondii in schizophrenia cases compared with control groups (p=0.031) but, the difference in seroprevalence of IgG antibodies was not statistically significant between bipolar disorder cases and controls group(p=0.427). In addition, there was no significant difference in IgGtiters between the cases and their close relative controls and/or non-relatives controls recruited from neighborhoods. Conclusions and recommendations: patients with schizophrenia had a significantly higher prevalence ofT. Gondii infection than the control group. Thus, this study gives additional information to the hypothesis that exposure to Toxoplasma may be risk factor for schizophrenia. Further studies may be required to determine anti-Toxoplasma antibody level in first episode psychosis and in the same individuals in chronic course by follow up to speculate decrease in antibodies level caused by antipsychotic or mood stabilizer drugs, which might improve the clinical course in the patients.Item Symptomatic and Asymptomatic Bacteriuria and Drug Susceptibility Pattern of Urinary Tract Infections among Diabetic Patients Attending at Tikur Anbessa Specialized University Hospital, Addis Ababa.(Addis Ababa University, 2010-02) Yeshitela Biruk; Gebre-Selassie Solomon; Feleke YeweyneharegBackground: The risk of developing infection in diabetic patients is higher and urinarytract is the most common site for infection. Urinary tract infection (UTI) may besymptomatic or asymptomatic. The etiology of UTI and the antibiotic resistance of uropathogens have been changing over the past years. In Ethiopia, there are some published information concerning community acquired and hospital acquired UTIs, butno study was conducted in asymptomatic bacteriuria and antimicrobial susceptibility pattern for UTIs in Ethiopian diabetic patients. Objective: The aim of the study was to identify the prevalence of symptomatic and asymptomatic bacteriuria, to isolate the bacterial pathogens and determine drug susceptibility pattern of urinary tract infections among diabetic patients attending Diabetic referral clinics at Tikur Anbessa Specialized University Hospital, Addis Ababa. Methods: A cross sectional survey was conducted by systematic sampling technique by taking every other diabetic patient coming to diabetic referral clinics and admitted to medical wards and medical Intensive Care Unit (ICU). A total of 413 diabetic patients were selected during the study period from June 2009to August2009. Results: ine (13.6%) of the symptomatic DM patients had bacteriuria compared with thirty six(10.4%) of asymptomatic DM patient. The overall prevalence of UTI in both groups was 45(10.9%).The bacterial pathogens isolated were predominantly gramnegative and two isolates were gram positive. Of the gram negative isolates the most common organism was Escherichia coli, 6% and 28% followed by Klebsiellapneumoniae, 2% and 6% in the symptomatic and asymptomatic DM patientsrespectively. The other gram negative organisms found in small numbers were Pseudomon as aeruginosa, 1(0.2%) and Enterobacter clocace, 1(0.2%). The only isolatefrom gram positive was Entrococcusspp.2 (0.5%).The susceptibility testing results of the isolates showed that over 85%Escherichia colistrains were sensitive to ciprofloxacin, Amoxicillin-Clavulanic acid, ceftizadine, nitrofuranton, ceftiraxone, norfloxacin and kanamycin(85.3–94.1%),but there was a higher rate of resistant to both ampicillin (67.6%), tetracycline (64.7%) and Trimethoprim -sulphamethoxazole (64.7%).Klebsiella pneumoniaewere 100% sensitiveto ciprofloxacin, ceftazidime, ceftiraxone and over 85% sensitive to gentamycin (87.5%)butshowed a high rate of resistance(75%) to ampicillin, tetracyclin and Trimethoprim-sulphamethoxazole.The frequency of multiple resistances for two or more drugs amongthe urinary pathogenswere found in thirty three(71.7%) of the isolates. Conclusion:The prevalence of urinary tract infection in this study ishigh in women thanmen and also pyuria and glucosuria can be considered as strong association withbacteriuria.Escherichia coli was the most commonbacterial pathogen isolated in bothsymptomatic and asymptomaticbacteriuria. Remarkablyover (60%) of all isolates were resistances to ampicillin, tetracycline and Trimethoprim-sulphamethoxazolehave beenfound in this study. Therefore, the investigation of bacteriuria in diabetic patients by screening for urinary tract infection is very important as it enables to treat properly andprevent the development of renal complications and eventually severe renal damage andfailure.Item Functional and Molecular Characterization of Potential Bacterial Pathogens in Akaki River and its Toxicogenomics Effects on Model Organisms, Ethiopia(Addis Ababa University, 2021-06) Yitayew Berhanu; Woldeamanuel Yimtubezinash ; Olsson Per-ErikBackground: Persistence and dissemination of pathogenic bacteria and antibiotic resistance genes (ARGs) in aquatic environments remain a serious public health issue. The aquatic environment may serve as a key transmission pathway for pathogenic bacteria and ARGs to and from humans. Continual faecal discharge into the environments, together with high levels of chemical and pharmaceutical pollutants are creating conditions favourable for the persistence and spread of antibiotic resistant pathogens. The aim of the study was to investigate the distribution of ARGs, and functional and molecular characteristics of potentially pathogenic bacteria in the Akaki river that flows through Addis Ababa, Ethiopia, and its toxicogenomic effect in model organisms. Methods: Water and sediment samples were collected from five sites along the Akaki river system for isolation of potential bacterial pathogens and detection of ARGs. The diversity and abundance of 84 ARGs and 116 clinically important bacteria were evaluated using DNA qPCR analysis. Potential bacterial pathogens were isolated using selective agar techniques and identified by MALDI-TOF. Isolates were analyzed for their resistance to different classes of antibiotics and further characterized by PCR and whole-genome sequencing. The toxicogenomic effect of the Akaki river water was also assessed by gene expression analysis of selected genes in exposed Caenorhabditis elegans and Pseudomonas aeruginosa PAO1. Results: Genes associated with fluoroquinolone, aminoglycoside, β-lactamase, macrolide, multidrug resistance efflux pumps, tetracycline efflux pumps, and vancomycin resistance were detected in the water and sediment samples. The majority of ARGs were identified from sites in close proximity toanthropogenic activities such as hospitals, irrigation systems, and industries. Aminoglycoside acetyltransferase (AAC(6)-Ib-cr), aminoglycoside adenylyl transferase (aadA1), β-lactamase (blaOXA-10), quinolone resistance S (qnrS), macrolide efflux protein A (mefA) and tetracycline resistance (tetA) genes were detected at all sampling sites. Surprisingly, much fewer ARGs were detected in the associated sediments, and the sediment collected from the hospital site had the highest diversity and level of resistance genes. Genes such as blaOXA-10 , blaOXA-2 , aadA, ermC and oprM were persistent in all sediment samples. There was significant variation in the abundance of ARGs between study sites, with those near the hospitals having the highest abundance in both waters and sediments. Escherichia coli strains isolated from the Akaki river were most frequently resistant to erythromycin (97%), doxycycline (78.5%), tetracycline (75.6%), and amoxicillin (75.6%). The overall prevalence of resistance to cephalosporin and carbapenem was 7.9% and 5%, respectively and 80.9% of E. coli isolates were MDR. Most E. coli isolates (70.8%) harbored enteroaggregative heat-stable toxin 1 (EAST1) gene, whereas the heat-labile toxin (LT) was detected in only 34 (20.2%) of the isolates. The prevalence of Shiga toxin-producing E. coli was 7.7%. The E.coli isolates belonged to 20 different sequence types, with ST10, ST69 and ST361 being predominant. The β-lactamase genes were the commonly detected resistance genes in E. coli. The most prominent plasmid sequence replicons detected were from the IncF family (65%), Col (10%), and IncX3 (7.5%). The Aeromonas spp. isolated from the Akaki river were resistant to a wide range of antibiotics with the highest being resistant to amoxicillin (144, 100%), ampicillin (142, 99%), amoxicillin/clavulanate (117, 81%), imipenem (75, 52%), ertapenem (132, 92%) and doxycycline (134, 93%). The heat-labile cytotonic enterotoxin (alt) was the predominant toxin gene detected, followed by a heat-stable cytotonic enterotoxin (ast). Almost all Aeromonas isolates in the current study were new sequence types. Paeruginosa isolates detected in the Akaki river were resistant to different classes of antibiotics and resistance is mediated by diverse group of ARGs with the majority were multi-drug efflux systems. Akaki river water induced a significant change in gene expression in exposed Celegans and P. aeruginosa PAO1. Although the levels of almost all analyzed metals were below the permissible limit, the compiled effect resulted in transcriptional changes at the molecular level. A significant spatial variation was observed between the sampling points in the expression of certain genes. Conclusion: The findings suggest that the water phase, rather than the sediments in the Akaki river, are a potential conduit for the spread of ARGs and thus antibiotic resistant bacteria. The occurrence of antibiotic resistance in E. coli, Aeromonas spp. and P. aeruginosa isolated from Akaki river provides evidence for the need to develop prevention and control strategies to limit the spread of antibiotic-resistant bacteria in the aquatic environment. The presence of virulent E. coli and Aeromonas spp. in the water could be posing a serious health risk to the public. The Akaki river water has selection pressure in bacteria and elicits a toxic effect in C. elegans at the molecular level result in a higher risk of infectious disease.Item Isolation and Antimicrobial Susceptibility Profile of Shigella and Salmonella Species from Children with Acute Diarrhoea in Mekelle Hospital and Semen Health Center ,Tigray, Ethiopia.(Addis Ababa University, 2012-06) Gebreegziabher Gebremichael; Asrat Daniel; W/Amanuel Yimtubezinash ; Hagos TesfalemBackground: Diarrhoea and acute gastroenteritis are among the leading causes of illnesses and deaths in infants and children throughout the world, especially in developing countries. Globally, Salmonella and Shigella remain the major contributors to acute enteric infections and diarrhoea. Emergence and spread of antimicrobial resistance to newer and more potent agents used in treatment have been described for Salmonella and Shigella species. Objectives: To isolate and determine the antimicrobial susceptibility pattern of Salmonella and Shigella species from children with acute diarrhoea in Mekelle Hospital and Semen Health Center. Materials and Methods: A cross sectional study was conducted among 260 children with acute diarrhoea in Mekelle, from November 2011 to March 2012. Results: Out of the 260 study participants 145 (55.8%) were males and 115 (44.2%) were females. Majority of the patients (44.2%) were children under five years of age. A total of 120 enteropathogens were isolated. The frequency of isolation was 19 (7.3%), 18 (6.9%) and 83 (31.9%) for Salmonella species, Shigella species and intestinal parasites respectively. Most of the Shigella isolates were resistant to ampicillin (88.9%), Tetracycline (77.8), cotrimoxazole (55.6%) and chloramphenicol (55.6%). Among the Salmonella isolates highest resistance was observed to ampicillin (89.5%), Tetracycline (89.5%), chloramphenicol (78.9%) and cotrimoxazole (57.9%). Multi-drug resistance was noted in 19 (100%) and 16 (88.9%) of Salmonella and Shigella species respectively. Conclusion and recommendation: Shigella and Salmonella are still challenging pathogens in children < 5 years of age. High antibiotic resistance was observed among both isolates to ampicillin, tetracycline, chloramphenicol and cotrimoxazole. Ciprofloxacin, norfloxacin and ceftriaxone were effective for all isolates. To reduce the incidence of these enteropathogens, improving personal and food hygiene has to be strengthened. The establishment of antibiotic policy and treatment guideline are recommended based on the susceptibility profile.Item Isolation and Anti-Microbial Susceptibility Testing of Salmonella Species from Foods of Cattle Source in Merkato, Addis Ababa, Ethiopia.(Addis Ababa University, 2012-06) Lemma Ayalew; Gebre-Selassie SolomonBack ground: Infectious diseases are diseases that are transmitted mainly through foodand still remain a common and persistentpublic healthproblem resulting high morbidityand occasional mortality in both developed and developing countries. Foods obtainedfrom animals play an important role for food borne diseases particularly in developing countries like Ethiopia. Food borne diseases arecaused by a variety of bacteria, viruses, parasites and fungi. Salmonellosis is one of those food borne diseases caused by Salmonella species which is becoming resistant to antimicrobials and causing serious diseases especially in developing countries because of consumption of raw foods such as meat, milk and cheese. Objective: This study is aimed to determine the prevalence of Salmonella species from foods of cattle source and perform their anti-microbial susceptibility tests. Materials and Methods: A cross-sectional study was conducted over a period of 4monthsfrom November, 2011 to February, 2012 in Merkato, Addis Ababa Ethiopia. Inthis study, a total of 384 samples from meat, milk and cheese were collected randomly from the Market and transferred to the laboratory following the ISO-6597, 2002procedure. In order to isolate Salmonella species, conventional culture method such aspre-enrichment, enrichment and selective plating were performed. Then, to confirm theidentification ofisolated coloniesasSalmonella Species, TSI, motility and API 20E tests were used. Finally, anti-microbial susceptibility testing following the standard procedure was performed in order to know the pattern of drug resistant for each isolate and the results were analyzed and interpreted by using SPSS 16.0,2007 computer Software. Results: Out of 384 food samples consisting of 128 meat, 128 milkand 128 cheesesamples, 13 (3.39%) were positive forSalmonella spp.Of the 128 meat, 128 milkand128 cheese samples, 9 (7.03%), 3(2.34%) and 1 (0.78%) yielded Salmonella spp.respectively.Assay of antimicrobial resistance revealed that 100% of Salmonellaisolateswere resistant to one or more of the 10 antimicrobials tested. Generally,resistance for 9different antimicrobial drugs was recognized. However, all of the isolates were sensitiveto ciprofloxacin. The most common resistance was observed to amoxicillin(100%)followed by ampicillinand tetracycline (76.9%) and most of Salmonella spp.isolates aremulti-drug resistance(84.6%). Conclusions and Recommendations:The findings of the present study ascertain thatSalmonellaspp. is isolated in food samples ofcattle sources particularly in retail meatsamples and all of them have developed resistance for routinely prescribed antimicrobialdrugs and this may be a considerable risk to the consumers. So,prudent antimicrobialusage, adequate heat treatment, improvement of standards of hygiene and developmentand enforcement of suitable legislation which safeguard consumers are urgentlyinstituted and must be practiced to combat the ever increasing situation of anti microbial resistance.Item Prevalence and Drug Susceptibility Pattern of Neisseria Gonorrheaamong Symptomatic Women Attending Gynecologic OPD in Hawassa Referral Hospital.(Addis Ababa University, 2011-02) Hailemariam Mengistu; Abebe Tamerat; Mihret AdaneBackground: Gonorrheae is asexually transmitted diseasecaused by the bacterium Neisseriagonorrhea for which humans are the only natural host. It is fastidious Gram-negative cocci transmitted by human-to-human contact. Gonococcal infection highly adapted to the genital tractandoften causing asymptomatic and undetected infection in females in which the highest rates are found mainly in female’s of reproductive age group. There are a number of antibiotics for treatment of gonorrhea in which the preferences vary with the local situation. Objective: To determine the prevalence and drug susceptibility pattern of Neisseria gonorrheaamong symptomatic women attending gynecologic OPD in Hawassa Referral Hospital. Methods: A cross-sectional study was conducted from December 2010 to February 2011 at Hawassa University Referral Hospital Hawassa, Ethiopia. During the study period, all women patients visited to gynecologic OPD with suspected of gonococcal infection were included. The inclusion criteria for the selection of215 women of reproductive age group was based on any sign and symptoms for STD up on clinical examination of symptom aticpatients at gynecologic OPD. Endocervical swab were collected by the attending physician. The Presence of gonorrhea was confirmed by culture, Gram staining and biochemical tests. Antimicrobial sensitivity test was performed using disc diffusion method and the result was interpreted accordingly. Result:Of the total 215 patients examined, 11 (5.1%) were confirmed to have gonococcal infection. The highest prevalence was observed in age group 20-24 which is 5/11 (45.5%) andthere is no statistical significant association (p>0.05). The susceptibilitypatterns were done against 11 antimicrobial agents by the agar disc diffusion technique. Low level of susceptibilityto quinolones (ciprofloxacin 55%, ofloxacin 64% & lomefloxacin 64%) was reported. Conclusion:The findings from this study indicate that gonococcal infection was moderately higher combined with high Neisseria gonorrhearesistance.