Medical Microbiology

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Browsing Medical Microbiology by Author "Abebe Tamrat"

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    Antibody Level Against HBV After Hepatitis B Vaccination and Sero-Prevalence of HBV in Children in Addis Ababa, Ethiopia
    (Addis Ababa University, 2017-06) Teshome Seifegebriel; Mihret Adane; Abebe Tamrat
    Background: Around two billion people have been infected with HBV worldwide, and more than 240 million are chronic carriers. Vaccine introduction for HBV in children was officially launched by WHO in 1980. Since then the vaccine response level was determined in different countries. However, there is no any study conducted in Ethiopia to assess the response level and effectiveness of HBV vaccine against the virus since the initiation of the vaccine in 2007. Objectives: The aim of the study was to determine antibody level against HBV after hepatitis B vaccination and sero-prevalence of HBV in children in Addis Ababa, Ethiopia. Methods: A cross sectional study was conducted and a multi stage probability sampling techniques was applied. Four hundred and fifty children between the age of 5 and 8 years who are living in three sub cities of Addis Ababa were included. Three to four ml of blood was collected and questionnaire was obtained. Finally ELISA was done to determine antibody level against HBV after hepatitis B vaccination and sero-prevalence of HBV infection in children. Result: The mean age of the children was 7+1(SD) years. Protective antibody levels were detected in 208(54.3%) of children with a slightly high response level in females 98(54.7%) than males 110(53.9%). The overall vaccine coverage was 85.1 %. The protective level is declined as the age of the child increased and it was 52.6%, 60%, 43.5% and 37.1% at the age of 5, 6, 7 and 8 years, respectively. The sero prevalence of HBsAg was 0.4% whereas Anti HBc was 5.6%. Age has negatively correlated and significantly associated with the response level (p=0.001) whereas sex and previous disease status of the child has no significant association. Age of the child was also having significant association with sero- prevalence of anti HBc (p=0.003). Other factors like vaccination status and dose of vaccination were also significantly associated with a vaccine response level (p=<0.001). All partially vaccinated children didn’t respond to the vaccine. Conclusion: The vaccine coverage in the country is worthy but antibody response against HBV vaccine is low. We also showed a low Sero- prevalence of the virus in children. However, the low response level to the vaccine should have to be the concern and revaccination or booster doses should be given for non responded children in order to enhance the vaccine response. Key words: HBV, antibody response level, vaccination status, HBsAg, Anti HBsAg, Anti HBc
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    Arginase Activity in the Blood of Patients with HIV, TB and HIV/TB Co-infections
    (Addis Ababa University, 2015-09) Abdu Mohammed; Abebe Tamrat; Mihret Adane
    Background: HIV/AIDS and TB remain a major global public health problem and their global distribution is heavily skewed toward low income and emerging economics. Africa, and more specifically Sub-Saharan Africa, faces the worst epidemic of the two diseases since the advent of the antibiotic era. Both TB and HIV have profound effects on the immune system, as they are capable of disarming the host’s immune responses through mechanisms that are not fully understood. The catabolism L-arginine by arginase has emerged as a potent mechanism for the regulation of immune responses. Objectives: To measure arginase activity in the blood of patient with HIV, TB and HIV/TB coinfected patients at Zewditu Memorial and St. peter's Hospital, Addis Ababa, Ethiopia. Methodology: A cross-sectional study was conducted from April 2014 to October 2014.Venous blood was collected from patients before initiation of treatment and controls in BD Vacutainer EDTA tubes. Isolation of peripheral blood mononuclear cells (PBMC) is performed by density gradient centrifugation on Histopaque-1077(Sigma) where as Plasma was obtained after centrifugation of a blood at 1800 rpm for 10 minutes. Arginase enzyme activity was determined using colorimetric assay based on color formed when urea produced is heated in acid with isonitrosopropiophenone. Data were evaluated by using GraphPad Prism version 6.05 and the differences were considered statistically significant at p < 0.05. Result: Increased arginase activity was observed in PBMC of HIV, TB and HIV/TB co-infected patients than in PBMC of healthy controls and similarly higher arginase level also measured in plasma of TB and HIV/TB co-infected patients than in plasma of healthy control. Moreover, a CD+4 T cell counts of HIV and HIV/TB co-infected patients and BMI of HIV, TB and HIV/TB patients were negatively associated with PBMC arginase activity. Conclusion: Our results suggest that arginase activity is become higher during HIV, TB and HIV/TB co-infections. Keywords: PBMC, plasma, HIV, TB, HIV/TB patients, Arginase
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    Blood Neutrophil Count, Sputum Mycobacterial Load and Mycobacterial Lineages in HIV Positive Individuals Suspected with Pulmonary Tuberculosis, Addis Ababa, Ethiopia
    (Addis Ababa University, 2015-12) Debela Negeri; Abebe Tamrat; Mihret Adane
    Background: The protective and pathologic response of host to M.tuberculosis is complex and multifaceted, involving many components of the immune system. There are evidences which suggest that neutrophils play a role in the host response to M.tuberculosis. In patients with established tuberculosis (TB) disease, higher peripheral blood neutrophil counts are associated with delayed mycobacterial clearance from sputum and worse clinical prognosis. Objective: To determine neutrophil counts in peripheral blood of HIV positive individuals with suspected pulmonary tuberculosis(PTB) and to find out the association with mycobacterial load and mycobacterial lineage in Zewoditu-Memorial Hospital and Federal Police Hospital, Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted from January 2014 to July 2014. EDTA (Ethylene Diamine Tetra Acetic Acid) anti-coagulated venous blood and sputum samples were obtained. Blood absolute neutrophil counts (ANC) were determined using Cell Dyn 1800 automated hematology analyzer. Sputum samples were decontaminated using sodium hydroxide, which were then concentrated by centrifugation. Smears were prepared from the pellet and stained with ZN (Ziehl-Neelsen) stain for microscopy. The remaining sputum pellets were then used for culture, using LJ (Lowenstein-Jensen) medium. Isolates were also heat killed for molecular genotyping and characterized using spoligotyping. Statistical analyses were done using SPSS and statistical tests were significant at p<0.05. Result: Among 117 participants, the median blood neutrophil count was 2.70x103cells/μl (IQR, 2.1–3.7). PTB was confirmed in 28 out of 117 participants. Patients with PTB had a median blood neutrophil count of 4.06x103/μl (IQR, 3.22–5.91) compared to 2.56x103 cells /μl (IQR, 2.1–3.1) among those who were PTB negative (p<0.05). Participants with low mycobacterial load had median ANC values of 3.5x103cells/μl (IQR, 2.6–4.2) and those participants with high mycobacterial burdens had ANC values of 5.5x103cells/μl (IQR, 3.9–7.4) (p<0.05). Participants infected with modern mycobacterial lineage had higher blood ANC than those infected with ancient lineage (p=0.41). Conclusions: Increased blood neutrophil counts were observed among PTB positive individuals and among individuals with high sputum mycobacterial load. Keywords: Neutrophils count, HIV, Pulmonary tuberculosis, sputum mycobacterial load, mycobacterial lineage
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    A Comparative Study of Blood Culture and Widal Test in the Diagnosis of Typhoid Fever in Febrile Patients
    (Addis Ababa University, 2011-06) Andualem Gizachew; Abebe Tamrat; Kebede Negatu
    Introduction: Typhoid fever is a major health problem in developing countries. An accurate diagnosis on clinical grounds alone is difficult. In areas of endemicity, such as Ethiopia, bacterial culture facilities, definitive diagnosis for typhoid fever, are often unavailable. So, the Widal test has been in use as the diagnostic assay. However, the value of the test for the diagnosis of typhoid fever has been debated. So evaluating the result of Widal test is necessary for correct interpretation of the result. In addition typhoid fever caused by multidrug resistant strains of Salmonella typhi presents a serious problem in many developing countries. Objective: The main objective of this study is to compare the result of Widal test and blood culture in the diagnosis of typhoid fever in febrile patients and to determine the antimicrobial pattern of isolates. Methodology: Data was collected from 277 febrile patients with symptoms clinically similar to typhoid fever visiting St. Paul’s General Specialized Hospitals from mid December 2010 to March 2011. Blood was inoculated immediately after collection into 45ml of Trypton Soy Broth and further processed for the identification of S.typhi and S.paratyphi. Antimicrobial susceptibility pattern of S. typhi and S. paratyphi isolates were determined by the modified Kirby-Bauer disk diffusion technique. Slide agglutination test as screening test and tube agglutination for the determination of antibody titer for reactive slide agglutinations samples have made. An antibody titer of ≥1:80 for anti TO and ≥1:160 for anti TH are taken as a cut of value to indicate recent infection of typhoid fever. Statistical software package for widows (SPSS version 16) was used for analysis of the data and p value ≤0.05 was taken as significance. Result: A total of 277 febrile patients were recruited for this study, but data from 270 were analysed because the remaining seven patients have no full data to be processed. 186 (68.9 %) were females and 84 (31.1 %) were males. 7 (2.6%) cases of S. typhi and 4 (1.5%) cases of S. paratyphi were identified with the total prevalence of typhoid fever 4.1 %. The total number of patients who have indicative of recent infection by either of O and H antigens Widal test is 88 (32.6%). The sensitivity, specificity, PPV and NPV of Widal test are 71.4 %, 68.44%, 5.7% and 98.9% respectively. Most (3/7[42.9%]) of the isolated S.typhi are highly resistant to amoxicillin. All species are sensitive for norfloxacin and ceftriaxone. S. paratyphi isolates show no resistance to gentamycine, tetracycline, norfloxacin and ciprofloxacin. More resistance (3 out of 4) is observed in amoxicillin. One species of S.typhi and 2 species of S. paratyphi are multi drug resistant. Conclusion and recommendation: Widal test have a low sensitivity, specificity and PPV, but it has good NPV which indicates that negative Widal test result have a good indication for the absence of the disease. Hence, physicians should not totally depend on Widal test for the diagnosis of typhoid fever and should use other alternative diagnostics such as clinical knowledge to differentiate from other febrile infections. Regarding drug resistance both S. typhi and S. paratyphi showed high resistance for commonly used drugs against typhoid fever. Therefore, sensitivity test based prescription should be started to prevent the continuous drug resistance development. Key words: Widal test, blood culture, antimicrobial resistance, sensitivity, specificity, positive predictive value, negative predictive value
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    A Comparison of Arginase Activity in the Saliva Plasma and Peripheral Blood Mononuclear Cells(PBMC)of Pulmonary Tuberculosis Patients in Addis Ababa, Ethiopia
    (Addis Ababa University, 2011-05) Yassachew Yayehyirad; Abebe Tamrat ; Mihret Adane ; Kropf Pascale
    Background: Mycobacterium tuberculosis (MTB)is the causative organism of the chronic bacterial infection, tuberculosis (TB). TB is one of the leading causes of death due to infectious diseases worldwide. Recently it has been observed that arginase (ARG)-is no longer a mere enzyme responsible only for urea cycle but is a key enzyme that plays a great role in modulation of the immune response and thus, pathogenesis. Infection with MTB and other intracellular pathogens induces the activation of ARG and inducible nitric oxide synthase (iNOS) which competitively metabolize L-arginine as a common substrate to produce L-ornithine and nitric oxide (NO), respectively. ARG induced deprivation of Larginine is important for pathogens to limit the intracellular production and killing action of NO and T cell responses. Therefore, induction of ARG might be an important escape mechanism for the survival of MTB. Materials and Methods: A cross-sectional study was carried out to compare the level of ARG activity in the saliva, plasma and peripheral blood mononuclear cells (PBMCs)of newly diagnosed HIV sero -negative smear positive TB patients (n=18) and healthy controls (n=8). The level of arginase activity in all type of samples was measured by enzymatic assay and a two-tailed Mann-Whitney U test was performed to assess statistical differences. Results: There was a statistically significantly higher level of arginase activity in the PBMCs (p=0.015)and saliva (p=0.008)of TB patients than those of healthy controls. Furthermore, an increased level of arginase activity was detected in the plasma of TB patients as compared to healthy controls, however it was not statistically significant (p=0.211). A significantly higher (p=0.024)frequency of arginase expressing cells were detected in the PBMCs of TB patients as compared to healthy controls. The phenotype of these cells was identified as CD15 + neutrophile. Conclusions and recommendation: Infection with MTB can result in an increased frequency of ARG-expressing cells as well as in increased level of arginase activity in the PBMCs, saliva and plasma of the TB patients. Therefore, the measurement of ARG activity in saliva might be used as a biomarker of TB infection.
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    Detection and Characterization of Mycobacterium Tuberculosis in Stool of HIV Sero-Positive Patients with Suspected Pulmonary Tuberculosis
    (Addis Ababa University, 2015-03) Eshetu Gizaw; Mihret Adane; Abebe Tamrat; Ameni Gobena
    Background: Tuberculosis (TB) in Africa is increasing because of the human immunodeficiency virus (HIV) pandemic, and in HIV ⁄ AIDS patients, it presents atypically. Smear-negative pulmonary tuberculosis (PTB) is more common in HIV-infected patients and leads to diagnostic delay, which increases morbidity and mortality in people living with human immunodeficiency virus (PLHIV). Objective: To detect and characterize Mycobacterium tuberculosis in stool of HIV sero-positive patients with suspected pulmonary tuberculosis. Method: Institutional based cross-sectional study of PTB diagnosis among PLHIV from stool sample was carried out from January 2014 – July 2014. During the data collection period, a total of 117 PLHIV suspected to be suffering from PTB was recruited. Microscopic examination, culture, and PCR were performed to detect and characterize M. tuberculosis. The presence of M. tuberculosis was compared in sputum and stool samples simultaneously collected from patients suspected for pulmonary tuberculosis. Data was entered and cleared using EpiData version 3.1, then exported to SPSS version 20 for analysis. Results: Of the 117 patients suspected of having PTB, 33 (28.2%) were sputum culture positive. Of these, 10 (30.3%) were sputum and stool culture positive for M. tuberculosis. Of the 84 sputum, culture negative cases, three (3.6%) were stool culture positive with measure of agreement 0.328. Eleven of 117(9.4%) patients were positive by sputum smear. Of 11 (9.4%) sputum, smear positive, three (27.3%) were both sputum and stool smear positive for M. tuberculosis. Of the 106-sputum smear negative, stool smear permitted the diagnosis of one (1%) PTB patient though the sensitivity (12.1%) was very low and kappa value of 0.18. As compared to sputum culture, the sensitivity of stool PCR was 69.7% with substantial agreement 0.67. Sputum PCR detected additional 4/81 (4.9%) from the bacteriologically negative PTB patients. We did spoligotyping and T family (43.5%), family 33 (41.3%), CAS family (4.3%), H family (4.3%), H37Rv family (4.3%) and Beijing family (2.2%) were isolated. Conclusion: M. tuberculosis was detected in stool of PLHIV. Hence, examination stool sample along with sputum sample increases diagnoses of PTB in PLHIV
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    Detection of Potential Pathogenic and Drug Resistant Bacteria Isolated from Inanimate Hospital Environments in Operation Theaters and Intensive Care Units of Tikur Anbessa Specialized Hospital and ALERT Hospital in Addis Ababa, Ethiopia
    (Addis Ababa University, 2020-02) Sebre Shemse; Abebe Tamrat; Mihret Adane
    Background: The role of hospital environments especially those of the operation theaters (OTs) and intensive care units (ICUs) in the transmission of hospital associated pathogens and multidrug resistant (MDR) bacterial strains like Extended-Spectrum β-Lactamases (ESBLs), Methicillin-resistant S. aureus (MRSA) and Vancomycin resistant Enterococci (VRE) dissemination are critical and an essential element in the control of Health care associated infections(HAIs) and emergence of resistance genes. Objectives: The current study aimed to detect potential pathogenic and drug resistant bacteria from inanimate hospital environments in OTs and ICUs of the selected hospitals. Methodology: A cross-sectional study was conducted on 280 hospital environmental samples in two different hospitals from June to September, 2018 G.C: Tikur Anbessa Specialized Hospital (TASH) (n=187) and All Africa Leprosy Rehabilitation and Training Hospital (ALERT) (n=93). Settle plate’s method (Passive air sampling following 1/1/1 schedule) was used for air sample collection while swab method was used to collect samples from inanimate surfaces in the OTs and ICUs of the selected hospitals. A total of 257 environmental swabs and 23 air samples were collected from different sites of ICUs and OTs. All isolates/samples were identified by using routine bacterial culture, Gram staining and a panel of biochemical tests. For each identified bacteria antibiogram profiles were determined by the Kirby Bauerdisk diffusion method based on the Clinical and Laboratory Standards Institute (CLSI) guidelines. Double disk synergy test was used to confirm ESBL production while Modified Hodge test (MHT) was used to screen carba pen emases production. On the other hand, Cefoxitin /oxacillin discs were used to screen MRSA. Results: Out of 280 swabs and settle plates, 227(81%) of samples were positive for bacterial contamination. A total of 282 bacteria were identified. Of these, the predominant bacteria identified from the environmental samples from OTs and ICUs were S. aureus (27.5% vs 9.6%), Coagulase negative Staphylococcus (CONS) (16% vs 2.8%) and Acinetobacter spp(2.5% vs 14.5%) respectively. The bacterial load on air was found beyond the standard limits. The most common bacterial contaminated sites were bed linens 37(13.1%), followed by environmental surfaces including (wall, floor, corridor and door knob) 35(12.4%) and beds 33(11.7%). Out of the280environmental samples 76(27.1%), 25(8.9%) and 7(2.5%) were MRSA, ESBL and Carbapenemase producer bacteria respectively. Most the identified bacteria showed considerable resistance to antibacterial agents. Of the total 282 identified bacteria, 158(56%) of the isolates were resistant to at least 3 antibiotics and 58 multi-drug resistance phenotypes were exhibited by the MDR isolates. Conclusion: Hospital environment especially those of the operation theaters and intensive care units are highly contaminated with potential pathogenic bacteria. Bacterial isolates were highly resistant to commonly used antibiotics with high multi-drug resistance percentage. Therefore, well-designed infection prevention and control strategies should be in place for combating health care-associated infections and the consequences.
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    Enteric Pathogens and Antimicrobial Susceptibility Profile among Pediatric Patients with Diarrhea: A Cross Sectional Study in Selected Health Facilities, Addis Ababa, Ethiopia
    (Addis Ababa University, 2017-06) Ayenew Zeleke; Gebre Selassie; Abebe Tamrat
    Background: Diarrheal disease remains a major public health problem in developing countries including Ethiopia. The current study was designed to isolate medically important enteric pathogens and assess the antimicrobial susceptibility testing of bacteria causing diarrhea in pediatrics for those antibiotics were prescribing in Integrated Management of Childhood illness (IMCI). Methods: Across-sectional study to determine enteric pathogenic microorganisms that cause diarrhea and antimicrobial susceptibility profile was carried out in selected health facilities of Addis Ababa, Ethiopia from November 2016 to May 2017. Stool specimens from pediatric patients aged 0-14 years were collected randomly from two health centers and one specialized hospital to identify enteric pathogens. Antimicrobial susceptibility tests were performed on all bacterial isolates using the Kirby-Bauer disc diffusion method. Results: In this study, the major etiologic agents of diarrhea in pediatrics were intestinal parasites and bacterial infection accounting for 93(32%) and 42(14.5%) respectively. Out of 290 study patients complain of diarrhea examined, E.histolytica/dispar 75(25.8%), G.lamblia 13(4.5%) and H.nana 4(1.4%) were identified. The majority of bacterial enteropahogens isolated in the study were Shigella spp 22(7.6%) followed by enterohemorrgic E.coli O157:H7 13(4.5%), Salmonella spp 7(2.4%). The overall co-infection rate between parasite-parasite, parasite-bacteria and bacteria-bacteria was observed in 12(4.1%) children. All the bacterial isolates from diarrheal patients were 100% susceptible to meropenem, cefepime, azithromycin and showed antimicrobial resistance to ampicillin, Augmentin, trimethoprim-sulphamethoxazole and ciprfloxacillin. Salmonella spp showed resistance to trimethoprim-sulphamethoxazole and chloramphenicol, 42.9% and 14.3% respectively. Another enteric bacteria Shigella spp were resistant to 77.3%ampicillin, 68.2% trimethoprim-sulphamethoxazole and 36.4%Augmentin whereas E.coliO157:H7 resistance anti-biogram showed 69.2%ampicillin,46.1% trimethoprim-sulphamethoxazole,38.5%Augmentin, 23.1%ciprfloxacillin and Amikacin, ceftriaxone and gentamycin were resistant with the same rate of 15.4%.. Conclusion: The results showed that E.histolytica, G.lamblia and H.nana and bacterial isolates Salmonella spp, enterohemorrhagic E.coli O157:H7, Shigella spp were the most frequently isolated pathogens in Children. The most frequently prescribing drugs ampicillin, amoxicillin+clavulic acid and trimethoprim-sulphamethoxazole showed high resistance for Salmonella and Shigella isolates in the study. It was found that ciprofloxacin was the best drug of choice for the treatment of diarrhea caused by Salmonella and Shigella. Chloramphenicol was a drug of choice for the treatment of shigellosis. So it calls more attention to conduct extensive continuous surveillance to revise and update the prescribing policy in Integrated Management of Childhood illness and Clinicians should rely on stool culture and antimicrobial susceptibility testing. Key words: Enteric pathogens, diarrhea, antimicrobial susceptibility, pediatrics, Addis Ababa, Ethiopia
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    Epidemiology and Molecular Characterization of Mycobacterium Bovis in Humans and Cattle and Assessment of its Zoonotic Importance in Central Ethiopia
    (Addis Ababa University, 2021-11) Gizat Almaw; Mihret Adane ; Abebe Tamrat
    Mycobacterium bovis (M. bovis) is a member of the Mycobacterium tuberculosis complex (MTBC) and causes tuberculosis in humans (zoonotic tuberculosis-zTB) and animals, mainly in cattle (bovine tuberculosis-bTB). There were limited studies on zTB in Ethiopia but also a reliable estimate of bTB prevalence in cattle in central Ethiopia is missing. In addition no wholegenome sequencing (WGS) based M .bovis studies had been performed in Ethiopia before this study. Also, there has been a limited effort in search for an alternative diagnostic method to culture to detect M. bovis in clinical specimens. Therefore, due to these research gaps, this study, which combined bTB and zTB, was conducted from 2018 to 2021 in central Ethiopia (Addis Ababa, Sebeta, Holeta, Sululta, Sendafa and Bishoftu) with the objective of generating epidemiological and molecular data to update our understanding on bTB/zTB. The bTB study in cattle involved a cross sectional one-stage cluster sampling survey of dairy farms in central Ethiopia using tuberculin skin testing and the collection of additional data by questionnaire to estimate the prevalence of bTB and identify potential risk factors contributing to Btb transmission. For the zTB part, surveillance of TB in humans was carried out among individuals working in bTB infected dairy farms, patients presented at selected health centers, and exposure to risk factors was assessed using questionnaire. From consenting TB suspected individuals, demographic and clinical information was collected by questionnaire. Sputum and Fine Needle Aspirates (FNA) samples were collected from suspected cases. In addition, isolation of M. bovis was done from raw milk collected from tuberculin skin test positive cows and from cattle tissue lesions. The genetic diversity of M. bovis isolates was examined using spoligotyping and whole genome sequencing (WGS) analysis. Furthermore, in this study the performance of a TaqMan real time PCR (RT-PCR) assay as an alternative diagnostic method to culture was evaluated. Two hundred ninety-nine (n=299) dairy herds in the six study areas were randomly selected, from which 5,675 cattle were tested. The overall prevalence of bTB after standardisation for herd-size in the population was 54.4% (95% CI 48.7-60%) at the herd level, and it was 24.5% (95% CI 23.3-25.8) at the individual animal level. A Generalized Linear Mixed Model (GLMM) was used to explore risk factors association with bTB status. We found that herd size, animal age, bTB history at farm, and breed were significant risk factors. With regard to zTB, among 110 DFWs in 73 bTB infected dairy farms, 41 had at least one of the symptoms that are typical forTB. Three DFWs had swollen nodes at their neck, a symptom typical for TB lymphadenitis. In assessment of risk factors: raw milk consumption was practiced by more than two thirds of theDFWs with symptoms of TB (68.2%) and over half of DFWs with symptoms did not think TBcould be transmitted via raw milk consumption. Overall in the surveillance of zTB (active and passive), a total of 167 specimens (sputum=131; FNA=36) were collected from 161 TB suspected individuals for the isolation of M. bovis. Of these processed specimens, three samples with M. bovis were detected in total (1.8%, n=167). And of these three, one M. bovis isolate was sequenced and the genotype was spoligotype SB1476 which was previously reported from cattlein Ethiopia suggesting possible zoonotic transmission. With regard to isolation and characterization of M. bovis from cattle, out of 827 cattle (abattoirs and dairy farms), 76 of them(9.2%) had tuberculous lesion. From these tuberculous lesions, 62 isolates (n=137 samples) from42 animals were confirmed to be M. bovis. Similarly out of 975 milking cows which were tuberculin skin test positive (37.8%, n=2582), 490 composite raw milk samples were collectedand of these 11 (2.2%) yield M. bovis isolates showing evidence that raw milk is not safe and can be a source of infection for human TB due to M. bovis. The genetic diversity of 74 M. bovisisolates (one being a human isolate) was assessed and ten different spoligotypes were recorded. In cattle spoligotype SB1176 was the most prevalent type (n=31, 44.3%) followed by SB0133(n=11, 15.7%). Our WGS analysis with a total of 55 M. bovis isolates sequenced (one being ahuman isolate) showed three clonal complexes clearly segregating in the phylogeny: African 2(Af2; n=47), European 3 (Eu3; n=7) and Unknown8 (n=1). In addition, the present study reported for the first time clonal complex European 3 (Eu3) from Ethiopia. With regard toTaqMan assay performance evaluation - the assay performance on 440 clinical samples was variable for different specimens and overall performed well for sputum samples for all targets. In conclusion, this study recorded high prevalence of bTB in dairy cattle in central Ethiopia. M.bovis prevalence in humans in central Ethiopia was low; however, further investigation is neededin all regions at national level given bTB is endemic in cattle in Ethiopia. Knowledge gap onbTB and M. bovis isolation from milk, showed that there is a clear potential for zoonotic transmission and needs further investigation. The TaqMan RT-PCR assay is a promising methodology for the diagnosis of zTB and bTB, but with further validation works needed usingdifferent targets and specimens
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    Genotype Distribution of Human Papillomaviruses & HPV E6/E7 RNA 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 ; Woldeamanuel Yimtubezinash
    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 iii 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. Keywords: Cervical cancer, CIN2+, HPV E6/E7 mRNA, HR-HPV DNA, northwest Ethiopia
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    Human Papillomavirus in Women with Pre-Cancerous Lesion and Cervical Cancer: the Use of Urine as an Alternative Specimen
    (Addis Ababa University, 2021-05) Firdawoke Ededia; Abebe Tamrat; Teka Brhanu
    Background: In a country where the coverage cervical cancer screening is low optimization of the uptake is critical. The implementation of high precision test is advocated by WHO. To augment the implementation human papillomavirus (HPV) based screening in Ethiopia we compared the performance urine HPV DNA test with cervical swab. Methods: Paired samples (n=103) of first void urine and cervical swab were collected from patients Gynecology Clinic of Tikur Anbessa Specialized Hospital (TASH). After extraction of DNA using QIAamp® DNA Mini Kit (Qiagen) the HPV infection, coinfection and type-specific HPV distribution was determined using the Anyplex HPV28 DNA genotyping kit (Seegene, Seoul, Korea) and CFX96 IVD (In Vitro Diagnostic) Real-Time PCR System. The kit simultaneously detects, differentiate, and semi-quantify 28 HPV genotypes 19 high risk (Hr)-HPV types; HPVs 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 69, 73 and 82 and 9 LR-HPV types; HPVs 6, 11, 40 ,42, 43, 44, 54, 61 and 70. Additionally, blood sample was collected to detect HPV16 L1 anti-capsid antibody using Prevo-check ® (Abvirus Germany GmbH). It is immunologic rapid test that directs against a protein that is produced by HPV 16 infected cells which interferes with cell division. Pap smear was done by a pathologist and histology results was collected from the chart of the patients and a clinical form was used to collect basic information from the patients by the attending midwife nurses. Result: Of the 103 paired samples, HPV infection prevalence was 83.5% in cervical and 77.7% in urine samples. HPV 16 is the most prevalent in both samples with 56.8% in cervical swab and 54.6% in urine sample followed by HPV 18 (5.8%) in cervical swab and HPV 18 and HPV 39 (6.2%) in urine samples. Multiple infection rate (infection more than one type of HPV) was 22.4% in urine samples and 32.0% in cervical swab. The agreement in the detection of HR-HPV between urine and cervical samples was moderate with a kappa value of 0.57 at 95% CI. Using the cervical HPV results as a reference, the anaylitical sensitivity of urine HPV testing was 88.4% (76/86) and specificity of 76.5% (13/17) and ROC area of 0.82 with (0.7-0.9) 95% CI. The Prevo-check HPV16 L1 antibody test has detected antibody from seven patients have a low clinical sensitivity but specificity of 100%. Of 93 histology result; 69.9% of the participants were diagnosed with SCC. HR-HPV detected in 76.2% and 79.7% from cervical and urine samples. Conclusion: In a country with low cervical cancer screening uptake collection of urine specimen can be considered as an alternative sample since the sample is easy to obtain, showed good diagnostic performance and may increases uptake of cervical cancer screening in Ethiopia. HPV16 and 18 were the predominant HPV detected from women with CIN2+ and above patients.
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    Isolation and Antibacterial Suseptibility Pattern of STREPTOCOCCUS AGALACTIAE in Pregnant women in Adigrat Zonal Hospital and Adigrat Health Center, Tigray,Ethiopia.
    (Addis Ababa University, 2012-06) Kahsay Tsega; Abebe Tamrat; Mihret Adane
    Back ground: S. agalactiae which are group B Streptococci asymptomatically colonize the vaginal or rectal areas of 10 to 30 % of pregnant women. In these women, S. agalactiae may cause preterm labor or membrane rupture, as well as urinary tract infections, chorioamnionitis, postpartum endometritis, postpartum wound infection, septic pelvic thrombophlebitis, endocarditis and sepsis. These bacteria is a major cause of invasive disease at all ages and is the most frequent cause of serious bacterial sepsis, including neonatal meningitis. Objective: This study was undertaken to determine the carriage rate of S. agalactiae and to assess theiantimicrobial susceptibility pattern. An attempt has been also made to identify the possible risk factors related with S. agalactiae colonization. Methods: Rectal and vaginal swabs were obtained from 150 pregnant women at 35-37 weeks of gestational period that attended anti natal clinic at Adigrat Zonal Hospital and Adigrat Health Center. The specimen was cultured on selective CHROMagar StrepB and incubated aerobically at 37o c for 18-24 hours. Suspected colony of S. agalactiae mauve colony (pink color) was confirmed by gram stain, catalase test, Christie, Atkins, MunchPeterson (CAMP) testing and latex agglutination (serological) test. In cases of positive cultures obtained, antibiotic susceptibility tests were carried out on all S. agalactiae isolates using the disc diffusion technique on Mueller-Hinton agar supplemented with 5% sheep blood and incubated at 37 0 c for 20-24 hours in 5% co. A univariate and multivariate binary logistic regression model was used to ascertain the association between the frequencies of colonization in relation to the different variables. Results: Seventeen of the study participants (11.3%) were colonized by S. agalactiae. Thirteen (76.5%) of the isolates were from health center and 4(23.5%) werfrom hospital. The study revealed a higher colonization rate among the age group 21 to 30 years (76.5%) but one pregnant woman with S. agalactiae was identified (5.9%) in women aged lesser than or equal to 20 years. Bacterial resistance was not detected against ampicillin, penicillin G, amoxacilline and vancomycin, whereas 11.8% and 17.6% of the isolates were resistant to TMerythromycin and clindamycin respectively. Intermediate susceptibility was also detected in 2 isolates (11.8%) against erythromycin and in 2 isolates (11.8%) against clindamycin. By multi variant logistic regression analysis, Prolonged rupture of membrane was associated with a higher colonization rate of S. agalactiae (OR=5.864, 95% CI= 1.395 – 24.643, Pvalue=0.016). No significant association was identified between S. agalactiae colonization rates with other socio- demographic/gynecological characteristic of the pregnant women. Conclusion: The carriage rate of S. agalactiae in the study area was 11.3%. High S.agalactiae isolates weredetected from Adigrat Health Center. Prolonged rupture of membrane was strongly associated with the colonization of S. agalactiae. Based on the finding, penicillin G was the best antibiotic for the treatment of S. agalactiae. Out of the isolates 11.8% were resistance to erythromycin and 17.6% were resistance to clindamycin Common resistance to erythromycin and clindamycin was seen in two isolates.
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    Isolation and Antibiotic Susceptibility of Shigella and Campylobacter from Acute Enteric Infections in Yekatit 12 Hospital and Shiromeda Health center, Addis Ababa
    (Addis Ababa University, 2011-06) Worku Getnet; Abebe Tamrat; Mihret Adane
    Background -Acute infective diarrhoea and gastroenteritis are major causes of ill health and premature death in developing world due, in large part, to the lack of safe drinking water, sanitation and hygiene, as well as poorer overall health and nutritional status. Among the leading causes of infectious diarrhoea, Campylobacter and Shigella contribute a lot. Antimicrobial resistance has developed among many of the major diarrheal bacterial pathogens and complicated the selection of antibiotics for the treatment of enteric bacterial pathogens, particularly to commonly used antimicrobial agents such as ampicillin, tetracycline and trimethoprim–sulfamethoxazole. Objective - To isolate and determine antibiotic susceptibility pattern of Shigella, and Campylobacter from acute enteric infections in Addis Ababa Method - A cross sectional study was conducted from December 2010 to March 2011 at Shiromeda health center (n=254) and Yekatit 12 Hospital (n=140). All diarrheal stool specimens were cultured for isolation of Shigella and Campylobacter species. Antimicrobial susceptibility testing was performed for culture isolates according to the method of Clinical and Laboratory Standards Institute (CLSI) by disk diffusion method. Result – A total of 163 enteropathogens were isolated from 394 patients that had acute diarrhea. The isolates were 37 (9.4%) Shigella species, 19 (4.8%) Campylobacter species, 23 (5.8%) Salmonella species and 84 (21.3%) parasites. 192 (48.7%) of the patients were females and 202 (51.3%) were males making the female to male ratio 1:1.05. The antimicrobial susceptibility pattern for 37 strains of Shigella isolates showed 67.6% resistance to ampicillin followed by, trimethoprim-sulfamethoxazole (64.7%), and chloramphenicol (40.5%). More than 90% of the strains were sensitive to nalidixic acid ciprofloxacin, norfloxacin and polymyxin B. Multiple resistances (resistant to two or more drugs) were observed in 23 (62.1%) of the isolates. All Campylobacter spp. were susceptible to chloramphenicol and showed low resistance rates (<60%) against, trimethoprim-sulfamethoxazole, ampicillin, nalidixic acid, ciprofloxacin and erythromycin. Conclusion- the results of the present study showed the high prevalence for Shigella spp. while Campylobacter spp. showed a moderate one. Continuous surveillance of the prevalence and VIII antibiotic susceptibility pattern of diarrheal bacteria in hospitals and in the community is needed which should be the basis for empiric therapy
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    Magnitude of Extended Spectrum Beta-Lactamase Producing Multidrug Resistant Enterobacteriaceae Isolates from Patients Attending Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia
    (Addis Ababa University, 2020-02) Seman Aminu; Abebe Tamrat; Asrat Daniel
    Introduction: Multidrug resistant (MDR) bacteria constitute a global emergency. Of which extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-PE) have become the most common type. ESBL-PE are important causes of serious infections in the community as well as in hospital settings. Objective: To determine the magnitude and patterns of resistance of extended Spectrum βlactamase producing Enterobacteriaceae isolates from patients attending Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. Methods: A cross sectional study was carried out to identify and characterize antimicrobial susceptibility pattern of Enterobacteriaceae isolates from TASH between July 2018 to November 2019. A total of 287 Enterobacteriaceae isolates were isolated from different specimens: blood, urine, wound site discharge, body fluids were analyzed using blood agar,MacConkey, Xylose lysine deoxycholate and salmonella shigella agar(SSA). Bacterial species identification was carried out using standard biochemical tests. Antimicrobial susceptibility testing and detection of ESBL production was performed using standard antibiotics on Muller Hinton agar using disk diffusion method and a combination disc method following 2018 CLSI guideline. Results: The overall magnitude of ESBL production was 62.7% (n=180/287). Female had higher proportion of ESBL positivity (66.1%, n=84/127) than male patients (60%, n=96/160). Among the Enterobacteriaceae isolates tested, 81 (72.3%) of the 112 K. pneumoniae, 21 (65.5%) of 32 K. oxytoca and 61 (58.7%) of 104 E.coli were ESBL producers. Comparable ESBL production by 158 (64.5 %) of 245 isolates from in patients and 22 (52.4%) of 42 isolates from outpatient was observed. There was no significant association between hospitalization and ESBL production (P=0.136, OR=0.606, 95 % CI). However, when we compare ESBL production of isolates from different wards a high ESBL production was noted among isolates from pediatrics ward 57(31.7%) of 180 isolates. The ESBL producing isolates showed highest and lowest level of resistance to ampicillin and amikacin 96.9% and 9.0 %, respectively. Two-hundred sixty four (91.9%) of the 287 isolates had MDR pattern. Conclusion: Significantly all isolates of Enterobacteriaceae showed higher rate of resistance to all tested antibiotics. But amikacin was found most effective for ESBL producers and no producers. High rate of ESBL and high numbers of MDR organisms were isolated among Enterobacteriaceae. Therefore, strengthening of monitoring antibiotics resistance in addition to regulation of the spread of resistance genes and preparing strong policies for monitoring utilization of antibiotics is required
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    Molecular Epidemiology and Comparison of Diagnostic Methods of Tuberculous Lymphadenitis, Addis Ababa, Ethiopia
    (Addis Ababa University, 2014-05) Zewdie Olifan; Abebe Tamrat; Mihret Adane
    Extrapulmonary tuberculosis is a significant health problem worldwide because of difficulties in its diagnosis and in monitoring its treatment, in which tuberculous lymphadenitis is high prevalent. To this effect, adequate knowledge on the species and strains of mycobacteria which circulate among the human population in specific geographic location is required. Objective: The objective of this study was to determine the prevalence of TBLN and to compare diagnostic performance of laboratory methods in diagnosis of TBLN among clinically suspected TBLN patients; identify the dominant species/ strain of M.tuberculosis responsible for TBLN. Materials and Methods: A cross-sectional study was conducted between February,2013 to October, 2013. Structured questionnaire, fine needle aspiration cytology and histopathology, Ziehl Nelson staining, mycobacterial culture, region of difference (RD)-PCR, spoligotyping and flowcytometry were used for undertaking this study. SPSS version 20 was used for data entry and analysis. Result: Of the 206 TBLN suspected cases, 166 (80.6%) were positive for TBLN by FNAC and histopathological examinations. On the other hand, only 36% (74/206) were positive by mycobacterial culture. Acid-fast bacilli (AFB) were detected in 28.6% of the 133 TBLN suspected individuals while 79.3% of the 121 TBLN suspected cases were positive for mycobacteria by PCR. Majority (98.6%) of the causative agent of TBLN was M.tuberculosis. Further characterization of 74 isolates to strain level by spoligotyping, 57 isolates were classified into one of the 26 shared international types (SITs) according to SpolDB4.0 and the remaining 16 isolates generated 13 different spoligotype patterns which had not been reported to the SpolDB4.0.The most prevalent strains of M. tuberculosis isolated in this study were SIT149, SIT53, SIT26 and SIT37 comprising 52.6% of the total strains. The strains were further classified into families in which the most prevalent were T, CAS and Haarlem comprising of 81.1% of the isolates. Classification of the strains into lineages leads to indicated modern lineage was the most prevalent comprising 66.2%. Conclusion: In this study it has been shown that, several clusters and new strains of M. tuberculosis circulate in TBLN patients in Ethiopia. As mapping the population structure of M. tuberculosis is vital to understand the transmission and disease dynamics of TB and set appropriate control measure. XII Key Words: Tuberculosis lymphadenitis, MTC, RD9 and RD4 Typing, Spoligotyping, Mycobacterium family, Mycobacterium lineage, Phenotyping and Addis Ababa
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    Molecular Epidemiology and Drug Sensitivity of Mycobacterium Tuberculosis Isolates Among New Pulmonary Tuberculosis Patients in Arsi Zone Oromiya Region, Ethiopia
    (Addis Ababa University, 2016-10) Tamrat Fekadu; Abebe Tamrat; Mihre Adane
    Back ground: - The 22 high burden countries accounts 80% of global tuberculosis burden, and Africa alone account 28% of Global TB burden where Ethiopia is at 16th from the world, and 9th from the continent accounting an incidence of 200 cases per 100,000 population according to WHO 2015 Tuberculosis report. According to WHO Global TB report, Ethiopia is ranked 15th among 27 high burden MDRTB and XDR-TB countries. The estimated MDR-TB from new cases was 3.3% according to WHOGTR 2015. Specifically in Arsi Zone, PTB+ case notification in the past fifteen years, from 1997 to 2011 increased from 6.9 to 63 per 100,000 populations. Objective: The objective of this study was to characterize the diversity of Mycobacterium tuberculosis strains circulating and to determine the drug susceptibility of the isolates among new PTB+ patients in Arsi zone, Oromiya region, Ethiopia. Methods: - A cross-sectional study design using quota sampling technique was under taken. All smear positive samples were collected from seven selected health facilities which were stated having higher prevalence TB cases in the zone and parallely, questionnaire was filled for socio demographic analysis. Culture on conventional Löwenstein-Jensen (LJ) media and drug sensitivity test using Line Probe Asay (LPA) was done at Adama Regional Laboratory (ARL). Spoligotyping was done in Aklilu Lemma Institute of Pathobiology (ALIPB), AAU and the isolates were compared with the SpoIDB4 database of the Pasteur Institute of Guadeloupe. Results: A total of 150 smear positive pulmonary TB patients were included in this study of which 130 samples were grown on LJ media. The study participant’s age range was from 6 -72 years with the mean of 29 and (±SD) of 13.25, of which 10 % (15/150) of the study participants were below the age of 15.Molecular characterization showed that104/130(80.0%) were Euro-American, 15/130 (11.5%) Indo-Oceanic, 9/130 (6.9%) Unknown lineage, 1/130(0.8%) West African-1 and 1/130(0.8%) Mycobacterium bovis. Drug Sensitivity Test on Line Probe Assay showed that 2 (1.53%) isolates were mono resistance for Rifampicin, 5 (3.8%) mono resistance for INH, and 3 (2.3%) were resistant for both INH and Rifampicin. Prevalence of MDR from New patients was 5/130 (3.8%). Conclusion: - In this study we have shown that the prevalence of MDR-TB from the new TB patients is 3.8% which is high, and the type of the TB lineage circulating dominantly is Euro-America from which the family of “T” is the most circulating strain indicating that there is a rapid circulation among the society. Keywords: - Mycobacterium tuberculosis, Molecular epidemiology, DST, spoligotyping
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    Performance Evaluation of MDR-TB Color Plate Test for Rapid Detection of Mycobacterium Tuberculosis and Multidrug-resistant Tuberculosis in Resource-limited Setting, Addis Ababa, Ethiopia
    (Addis Ababa University, 2017-06) Mekonnen Biruk; Abebe Tamrat; Mihret Adane
    Background: Tuberculosis (TB) is a top global public health concern and its controlling program is chiefly hampered by diagnostic difficulties. Timely TB diagnosis and detection of drug-resistant TB has a key significance for both patient management and the disease control. However, the commercially existing diagnostic tools are slow and unaffordable for resource limited settings. Objective: The current study was aimed to evaluate the performance of MDR-TB color plate test (color plate test) for rapid concurrent detection of Mycobacterium tuberculosis (MTB) and multidrug-resistant TB (MDR-TB) directly from sputum specimens. Materials and Methods: A cross-sectional, hospital-based diagnostic test evaluation study was conducted from March 2016 to February 2017 at All Africa Leprosy, Tuberculosis and Rehabilitation Training Center (ALERT) hospital and St. Peter’s TB referral hospital in Addis Ababa, Ethiopia. The performance of the color plate test was prospectively compared to the conventional Lӧwenstein-Jensen (LJ) culture and LJ indirect proportional drug susceptibility test (DST), and the molecular GeneXpert MTB/RIF® assay. A paired morning expectorated sputum samples were collected from 147 MDR-TB suspected patients using a convenience sampling technique in both hospitals. One of the two sputum samples is used for diagnosis purpose was tested directly by GeneXpert assay at each respective hospital’s laboratory and internally validated. But, the other sputa were refrigerated (4-80C) and transported to the Armauer Hansen Research Institute (AHRI) TB laboratory where the color plate test and the conventional LJ culture and DST were conducted. Data were analyzed using SPSS version 20, and kappa statistic was applied to test agreement between results of the three assays. Result: Of the 147 sputa, 137 (93.2%) sputa produced interpretable MTB detection results for all the three assays and were included in the analysis. Compared to the conventional LJ culture, color plate test was 93.6% sensitive and 98.3% specific while GeneXpert assay was 96.2% sensitive and 79.7% specific. Moreover, the color plate test had showed a strong agreement with both the conventional LJ culture (95.62%, kappa 0.9114) and GeneXpert assay (89.05%, kappa 0.7756) for the detection of MTB. Moreover, all conventional LJ xv culture positives, 78 isolates were further subjected to conventional DST, and valid results obtained by color plate test and Gene Xpert assay were 70 and 72 isolates respectively. The color plate test demonstrated sensitivity of 91.3% and 93.6% specific for the detection of isoniazid resistant MTB isolates with strong agreements (kappa 0.8399). However, the accuracy for detection of rifampicin resistance was suboptimal with low agreement (kappa value of 0.08 and concordance 39%). The color plate test was also in low agreement with the GeneXpert assay (38.57%, kappa 0.0773) for detection of RMP drug resistance. In the present study, the results of color plate test can be obtained in a median time of 13 days while the conventional indirect DST method requires an average of 50 days. Besides, the color plate test is simple to use and the cost per test result also minimal relatively. Conclusion: In this study, the color plate test was found to be a good alternative method for screening of TB and selective drug resistant-TB in a timely and affordable way in resourcelimited setting despite limitations of the test need to be addressed before test approvals. Key Words: Color plate test, Conventional LJ culture, Diagnostic performance, GeneXpert assay, indirect proportional DST, Multidrug-resistant tuberculosis, Tuberculosis
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    Phenotypic and Molecular Characterization of Uropathogenic Escherichia Coli from Urinary Tract Infection Patients in Selected Health Facilities of Addis Ababa, Ethiopia
    (Addis Ababa Universty, 2018-07) Regasa Belayneh; Abebe Tamrat
    Introduction: Urinary tract infection (UTI) is major causes of morbidity and mortality worldwide. Uropathogenic Escherichia coli (E. coli) bacterium is responsible for majority of (50-80%) cases of UTI. Drug resistant E. coli is a significant threat to effective treatments. Uropathogenic E. coli strains derive from different phylogenetic groups and possess an arsenal of virulence factors that contribute to their ability to overcome different defense mechanisms and cause disease. Despite its public health importance, data regarding the molecular characteristics of uropathogenic E. coli is lacking in Ethiopia. Therefore, for proper treatment and management of UTI; it is essential to determine drug resistance patterns, phylogroup and virulence genes of E. coli. Objective: To assess the phenotypic and molecular characteristics of uro pathogenic E. coli as well as relationship of virulence genes and drug resistance patterns of uropathogenic E. coli among patients with UTI in selected health facilities of Addis Ababa, Ethiopia. Methods: A cross sectional facility based study was conducted on 780 patients with urinary tract infections visiting Tikur Anbessa Specialized Hospital (N=580), Yekatit 12 Hospital (N=30) and Zewditu Memorial Hospital (N=170), Addis Ababa, Ethiopia from January 1, 2017 to October 9, 2017 using a well-designed questionnaire and microbiological investigations. Uropathogenic E. coli bacteria were isolated from urine samples using bacterial culture and conventional biochemical tests. Phenotypic drug resistance patterns and plasmid profile was determined using Kirby Bauer disc diffusion and plasmid analysis respectively. Identification of phylogroup and genes that encodes for virulence factors was done using multiplex polymerase chain reaction (PCR). Data was processed and analyzed with SPSS version 16.0 and EPI info version 3.4.1 softwares. P-value less than 0.05 were considered significant. Result: Among 780 UTI patients, 200 uropathogenic E. coli bacteria were isolated. E. coli isolates had highest resistance (86.5%) to ampicillin followed by ceftazidime (84%), ceftriaxone (80.5%), tetracycline (80%), trimethoprim-sulfamethoxazole (68.5%) and cefotaxime (66%). Highest susceptibility to meropenem (100%) and imipenem (100%) were observed. E. coli isolates were susceptible to amikacin (97.5%), nitrofurantoin (95%), ciprofloxacin (85.5%), norfloxacin (85%), chloramphenicol (83.5%), gentamicin (80%) and nalidixic acid (79%). Multidrug resistance (MDR) was observed to most (96.5%) E. coli isolates. Plasmid analysis showed the presence of plasmid/s in 165 (82.5%) E. coli isolates. Majority of tested E. coli isolates had upto 10 plasmids, the size of which commonly 23kb. The most frequent E. coli virulence gene amplified was fim H 164 (82%), followed by aer 109 (54.5%), hly 103 (51.5%), pap 59 (29.5%), cnf 58 (29%), sfa 50 (25%) and afa 24 (12%). Significant association (p-0.014) between fim H and chloramphenicol drug resistance as well as between aer genes, and gentamicin, ampicillin and nitrofurantoin drug resistance (p-0.028, p-0.018 and p-0.023 respectively) was observed. There was significant association between pap gene and urine urgency (p-0.016); sfa, and dysuria and urine urgency (p-0.019 and p-0.043 respectively); hly and suprapubic pain (p-0.002); aer and suprapubic pain, flank pain and fever (p-0.017, p-0.040, p-0.029 respectively). Majority of E. coli isolates were phylogroup B2 60 (30%) followed by D 55 (27.5%), B1 48 (24%) and A 37 (18.5%). Conclusion: The overall incidence of antimicrobial resistant (including MDR) E. coli in this study was high to commonly used antibiotics but none to carbapenems. The virulence genes encoding components of adhesins, iron acquisition systems, and toxins were highly prevalent. Majority of E. coli isolates were phylogroup B2 followed by D. Therefore, periodic monitoring of drug resistance patterns and targeting major virulence genes as potential vaccine candidates is essential for better management of UTI and further large scale studies should be conducted in this area.
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    Phenotypic Antimicrobial Resistance Profiles of Klebsiella Pneumoniae Isolated from Patients at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia
    (Addis Ababa University, 2019-10) Awoke Tewachew; Abebe Tamrat ; Mihret Adane; Aseffa Abraham ; Teka Brhanu ; Yeshitela Biruk
    Background: Klebsiella pneumoniae is a cause of mild to life threatening infections. The bacterium poses an urgent public health threat because it has the potential to become resistant to virtually all categories of antimicrobials available. Multidrug resistant K. pneumoniae has caused nosocomial outbreaks in different continents. Little is known concerning the antimicrobial resistance profiles of K. pneumoniae in Ethiopia. Objective: The aim of this study was to determine the phenotypic anti microbial resistance profiles of K. pneumoniae isolated from patients at Tikur Anbessa Specialized Hospital, Addis Ababa, Ethiopia. Methodology: A cross-sectional study was conducted on antimicrobial resistance profiles of 132 K. pneumoniae, isolated from patients from September 2018 to February 2019. Identification of K. pneumoniae was done by examining gram stain, colony characterstics on MacConkey agar, 5% sheep blood agar and biochemical tests. Antimicrobial susceptibility testing was done by Kirby-Bauer disc diffusion technique. Extended spectrum -lactamase (ESBL) and carbapenemase production was confirmed by combined disc test and modified carbapenemase inactivation method, respectively. Data was double entered using Epidata 3.1 and exported to SPSS version 25 software for analysis. Binary logistic regression and Chi-Square or Fisher's exact test were used to measure the association. P-value less than 0.05 was considered as statistically significant. Results: Among the total K. pneumoniae isolates high frequency of resistance was observed to cefotaxime and ceftriaxone 128 (97%), trimethoprim sulfamethoxazole 124 (93.9%) and cefepime 111 (84.1%). Most frequent susceptibility was observed to amikacin 123 (93.2%), imipenem 107 (81.1%), meropenem 96 (72.7%) and ertapenem 93 (70.5%). Majority 130(98.5%) of the isolates were multidrug resistant (MDR). Two isolates showed complete nonsusceptibility to all antimicrobial agents tested. The magnitude of ESBL and carbapenemase production was 77.3% and 21.2%, respectively. Of the total (n=30) non-ESBL producers, 73.3% were carbapenemase producers. Non-ESBL producers showed high resistance to imipenem (53.3%), meropenem (80%) and ertapenem (83.3%). Higher proportion of ESBL production was observed in those aged below 5 years than those 18 to 45 years and among those admitted to the intensive care units and pediatric wards than those in medical wards. Previous use of carbapenems was associated with carbapenemase production (P<0.001). Conclusion: All K. pneumoniae isolates showed appreciably high frequency of resistance to most of the tested antimicrobials. The magnitude of ESBL and carbapenemase production as well as MDR K. pneumoniae was very alarming in the study area. Of particular concern is that the majority of non-ESBL producers were carbapenemase producers. Therefore, strengthening antimicrobial stewardship programs together with effective infection control and antimicrobial surveillance practices is strongly recommended in Tikur Anbessa Specialized Hospital.
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    Prevalence and Antibiotic Resistance of Enteric Bacterial Pathogens Isolated from Childhood Diarrhea in Ambo Town Public Health Institutions
    (Addis Ababa University, 2015-02) Tosisa Wagi; Mihret Adane; Abebe Tamrat
    Introduction: Diarrhea particularly due to enteric bacterial pathogen is a major health problem worldwide. In developed countries, it contributes primarily to morbidity but, in the developing world like Ethiopia, it is responsible for morbidity and a high level of mortality, particularly in children below five years of age. Objective:This study aimed to investigate enteric bacterial pathogens from children aged less than five years old with diarrhea in Ambo town public health institutions in order to determine the prevalence of the disease and antimicrobial resistance pattern. Methodology: Stool samples from 239 children less than 5 years of age with diarrhea attending Ambo Town Public Health Institutions was examined at the Ambo University of Microbiology Laboratory, Ambo, West Ethiopia, from January to July 2014.All collected samples were processed for isolation and antibiotic susceptibility testing of Salmonella, Shigella, Vibrio species and other bacterial species using conventional laboratory tests. PCR was done to confirm Salmonella by amplifying a 496-bp genetic sequence of members of the genus Salmonella. Antibiogram test was performed by Kirby Bauer disc diffusion method using ten commonly used antibiotics. Results: From the 239 children screened, enteric bacteria were isolated from 24 (10%). This included;three (1.3%) Shigellaflexinari, two (0.8%) Shigellaboydii,one (0.4%) Shigellasonnei, three (1.3%) Salmonellaspecies, and fifteen (6.3%) otherbacterialspecies.There was no Vibrio species isolated in this study.The highest resistance among the total entrophatogenic bacteria was observed against Ampicillin (95.8%) followed by Tetracycline (70%), Amoxacillin (62.5%), Cotrimoxazoale (58.3%), Chloramphenicol(41.7%), Nalidixic acid (16.7%) and Cefotaxime (4.7%). All isolates were sensitive to Amikacin, Ciprofloxacin and Gentamycin except 3 intermediate. Conclusion: This study suggests that Shigellia, Salmonella and other enteric bacteria species were some of the pathogenic infection among children with diarrhea in ATPHI.The highest prevalence of antimicrobial resistance was to ampicillin followed by Tetracycline and Amoxacillin. Though still at low levels, the major concern from this finding is the emerging resistance of enteric pathogens that was observed to Nalidixic acid and Cefotaxime