A viral genome wide association study and genotypic resistance testing in patients failing first line antiretroviral therapy in the first large countrywide Ethiopian HIV cohort.

BACKGROUND: Antiretroviral therapy (ART) was rolled-out in Ethiopia in 2005, but there are no reports on outcome of ART and human immunodeficiency virus drug resistance (HIVDR) at national level. We described acquired drug resistance mutations in pol gene and performed a viral genome wide association study in virologic treatment failure patients who started first line ART during 2009-2011 in the first large countrywide HIV cohort in Ethiopia. METHODS: The outcome of tenofovir (TDF)- and zidovudine (ZDV)-based ART was defined in 874 ART naïve patients using the on-treatment (OT) and intention-to-treat (ITT) analyses. Genotypic resistance testing was done in patients failing ART (> 1000 copies/ml) at month 6 and 12. Near full-length genome sequencing (NFLG) was used to assess amino acid changes in HIV-1 gag, pol, vif, vpr, tat, vpu, and nef genes between paired baseline and month 6 samples. RESULTS: High failure rates were found in ITT analysis at month 6 and 12 (23.3%; 33.9% respectively). Major nucleoside and non-nucleoside reverse transcriptase (NRTI/NNRTI) drug resistance mutations were detected in most failure patients at month 6 (36/47; 77%) and month 12 (20/30; 67%). A high rate of K65R was identified only in TDF treated patients (35.7%; 50.0%, respectively). No significant difference was found in failure rate or extent of HIVDR between TDF- and ZDV- treated patients. All target regions of interest for HIVDR were described by NFLG in 16 patients tested before initiation of ART and at month 6. CONCLUSION: In this first Ethiopian national cohort, a high degree of HIVDR was seen among ART failure patients, independent on whether TDF- or ZDV was given. However, the major reason to ART failure was lost-to-follow-up rather than virologic failure. Our NFLG assay covered all relevant target genes for antiretrovirals and is an attractive alternative for HIVDR surveillance.

Treatment outcomes of childhood tuberculosis in Addis Ababa: a five-year retrospective analysis.

BACKGROUND: Tuberculosis (TB) kills one child every 5 min. Childhood TB is given low priority in most national health programmes particularly in TB-endemic areas. TB among children is an indicator of a recent transmission of the disease in the community. Treatment outcome results serve as a proxy of the quality of treatment provided by a health care system. In Ethiopia, data on treatment outcomes of childhood TB are limited. The aim of the study was to determine the treatment outcomes of childhood TB in a hospital setting in Addis Ababa. METHODS: The study was conducted during June to August 2014. The data of 491 children treated for TB in Zewditu Memorial Hospital during a 5 year (2009-2013) was analysed. TB was diagnosed using standard methods. Demographic and clinical data including type of TB, TB-HIV co-infection and treatment outcomes were collected from registry of the TB clinic. Treatment outcome definitions are used according to the World Health Organization. RESULTS: Of the 491 children, 272(55.4 %) were females, 107(21.8 %) were under 5 year old, 454(92.5 %) of them were new cases. The types of TB were extra-pulmonary tuberculosis (EPTB) 243(49.5 %) and 248(50.5 %) pulmonary tuberculosis (PTB). Of the PTB cases, 42(16.9 %) were sputum smear positive. Of the 291 children tested for HIV, 82(28.2 %) were positive. The overall treatment success rate was 420(85.5 %) and the poor treatment outcome was 71(14.5 %). Of the children with poor treatment outcome, 9(1.8 %) died, 3(0.6 %) defaulted from treatment, 2(0.4 %) were treatment failure and 55(11.2 %) were transferred out. Males and females had similar treatment success rates of 85.8 % and 85.3 %, respectively. Infants under one year had significantly lower treatment success rate of 72.7 % compared to those above 1 years of age of 86.5 % (P < 0.001). Treatment success rate ranged from 78.0 to 92.6 % during the study period. Associated factors for treatment outcome were age above 5 years (AOR = 0.59, 95 % CI: 0.62-0.97) and seropositive for HIV infection (AOR = 6.66, 95 % CI: 3.07-14.47). CONCLUSIONS: The treatment success rate in this study is 85.5 %. The outcome of treatment varied with age, and presence of HIV infection. In order to the further improve of treatment success rate, continuous follow up with frequent support of patients during treatment course and strengthen the recording system are strongly recommend.

Antimicrobial susceptibility in Neisseria gonorrhoeae and epidemiological data of gonorrhoea patients in five cities across Ethiopia, 2021-22.

Introduction: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global public health concern and enhanced global gonococcal AMR surveillance is imperative. As in many African countries, regular, representative and quality-assured gonococcal AMR is lacking in Ethiopia. We describe the AMR in gonococcal isolates from five cities across Ethiopia, 2021-22, and patient epidemiological data. Methods: Urethral discharge from males and cervical discharge from females were collected from October 2021 to September 2022. Epidemiological data were collected using a questionnaire. MIC determination (ETEST; eight antimicrobials) was performed on gonococcal isolates and EUCAST breakpoints (v13.1) were used. Results: From 1142 urogenital swab samples, 299 species-identified gonococcal isolates were identified; 78.3% were from males and 21.7% from females. The median age for males and females was 25 and 23 years, respectively. Most isolates (61.2%) were identified in Addis Ababa, followed by Gondar (11.4%), Adama (10.4%), Bahir Dar (10.0%) and Jimma (7.0%). The resistance level to ciprofloxacin, tetracycline and benzylpenicillin was 97.0%, 97.0% and 87.6%, respectively, and 87.6% of isolates were producing ß-lactamase. All isolates were susceptible to ceftriaxone, cefixime, azithromycin and spectinomycin. Recommended therapy [ceftriaxone (250 mg) plus azithromycin (1 g)] was used for 84.2% of patients. Conclusions: We present the first national quality-assured gonococcal AMR data from Ethiopia. Resistance levels to ciprofloxacin, tetracycline and benzylpenicillin were exceedingly high. However, all isolates were susceptible to ceftriaxone, cefixime, azithromycin and spectinomycin. In Ethiopia, it is essential to strengthen the gonococcal AMR surveillance by including further epidemiological data, more isolates from different cities, and WGS.

Nasal and hand carriage rate of methicillin resistant Staphylococcus aureus (MRSA) among health care workers in Mekelle Hospital, North Ethiopia.

BACKGROUND: Methicillin resistant Staphylococcus aureus (MRSA) is significant major pathogen responsible for hospital and community based infections. OBJECTIVE: The aim of this study was to assess the nasal and hand carriage of methicillin resistant Staphylococcus aureus in health care workers of Mekelle Hospital METHODS: The study was carried out during November 2010 to January 2011. Swab samples from both anterior nares and hands were taken. The samples were cultured on mannitol salt agar and incubated aerobically at 37 degrees C for 48 hours. Staphylococcus aureus was identified as nmannitol fermenter and coagulase test positive. Antimicrobial susceptibility test for MRSA was done by disk diffusion method using oxacillin disks. Data were analysed using SPSS version 16 software. RESULTS: Out of the 177 health care workers screened, 36 (20.3%) of them were methicillin resistant Staphylococcus aureus carriers in their hand and anterior nares. More females, 25(14.1%) were colonized by methicillin resistant Staphylococcus aureus than males 11 (6.2%) (P = 0.044). Nasal carriage of MRSA of 25 (14.1%) was higher than hand carriage 11 (6.2%) (p < 0.05). Nurses and medical doctors had methicillin resistant Staphylococcus aureus carriage rates of 26 (13.6%) and 4 (2.3%), respectively. The isolated MRSA were resistant to multiple antibiotics. The highest resistance was observed for ampicillin (88.9%) and tetracycline (86.1%). Two (5.6%) of the nasal isolates were vancomycin resistant. CONCLUSION: Methicillin resistant Staphylococcus aureus carriage among health care workers in this study was high. The carriage rate was higher among nurses and doctors. The MRSA isolates were multi drug resistant to other antibiotics. So, the result of this study emphasizes the need of regular surveillance of health care workers. It also calls a need for an effective infection prevention and control program.

Distribution of ß-Lactamase Genes Among Multidrug-Resistant and Extended-Spectrum ß-Lactamase-Producing Diarrheagenic Escherichia coli from Under-Five Children in Ethiopia.

Purpose: Escherichia coli strains that produce extended-spectrum ß-lactamase (ESBL) and carbapenemase are among the major threats to global health. The objective of the present study was to determine the distribution of ß-lactamase genes among multidrug-resistant (MDR) and ESBL-producing Diarrheagenic E. coli (DEC) pathotypes isolated from under-five children in Ethiopia. Patients and Methods: A cross-sectional study was conducted in Addis Ababa and Debre Berhan, Ethiopia. It was a health-facility-based study and conducted between December 2020 and August 2021. A total of 476 under-five children participated in the study. DEC pathotypes were detected by conventional Polymerase Chain Reaction (PCR) assay. After evaluating the antimicrobial susceptibility profile of the DEC strains by disk diffusion method, confirmation test was done for ESBL and carbapenemase production. ß-lactamase encoding genes were identified from phenotypically ESBLs and carbapenemase positive DEC strains using PCR assay. Results: In total, 183 DEC pathotypes were isolated from the 476 under-five children. Seventy-nine (43%, 79/183) MDR-DEC pathotypes were identified. MDR was common among enteroaggregative E. coli (EAEC) (58%, 44/76), followed by enterotoxigenic E. coli (ETEC) (44%, 17/39)) and enteroinvasive E. coli (EIEC) (30%, 7/23). Phenotypically, a total of 30 MDR-DEC pathotypes (16.4%, 30/183) were tested positive for ESBLs. Few ETEC (5.1%, 2/39) and EAEC (2.6%, 2/76) were carbapenemase producers. The predominant ß-lactamase genes identified was blaTEM (80%, 24/30) followed by blaCTX-M (73%, 22/30), blaSHV (60%, 18/30), blaNDM (13%, 4/30), and blaOXA-48 (13%, 4/30). Majority of the ß-lactamase encoding genes were detected in EAEC (50%) and ETEC (20%). Co-existence of different ß-lactamase genes was found in the present study. Conclusion: The blaTEM, blaCTX-M, blaSHV, blaNDM, and blaOXA-48, that are associated with serious and urgent threats globally, were detected in diarrheagenic E. coli isolates from under-five children in Ethiopia. This study also revealed the coexistence of the ß-lactamase genes.

Bacterial profile and extended spectrum beta lactamase screening of urinary tract infection among asymptomatic and symptomatic pregnant women attending antenatal care in ALERT Hospital, Addis Ababa, Ethiopia.

Introduction: The occurrence of extended spectrum beta lactamase-producing uropathogens, especially in pregnant women can result in life-threatening condition and morbidity for both the mother and the newborn due to very limited drug options for treatment of these pathogens. The aim of this study was to determine the bacterial profile, associated factors, and their antimicrobial susceptibility patterns and to identify extended spectrum beta lactamase-producing bacterial uropathogens. Methods: A hospital-based cross-sectional study was conducted from July to September 2018 on a total of 177 pregnant women with and without symptoms of urinary tract infection at ALERT Hospital, Addis Ababa, Ethiopia. From these study participants, 72 have symptoms, whereas 105 have no symptoms. All urine samples were inoculated onto cysteine lactose electrolyte deficient medium and MacConkey agar. Colonies were counted to check the presence of significant bacteriuria. Pure isolates of bacterial pathogen were characterized and identified at species level by colony morphology, gram stain, and standard biochemical procedures. All Gram-negative isolates were put into Muller-Hinton agar plates for antibiotic susceptibility test by Kirby-Bauer disc diffusion technique. Extended spectrum beta lactamase was detected using double-disk synergy methods on Muller-Hinton agar. The data were double entered into epidemiological Information system and analyzed using Statistical Package for Social Science version 26. Results: The overall proportion of urinary tract infection among pregnant women was 14.7% (n = 26/177). Klebsiella pneumoniae was the predominant bacterial etiologic agent of urinary tract infection 26.9% (n = 7/26). The proportion of extended spectrum beta lactamase among Gram-negative isolates was 50% (n = 6/12). Among extended spectrum beta lactamase-producing isolates (100%), all are resistance to amikacin and gentamicin while intermediate level resistance rate of 66.7% was observed among trimethoprim-sulphamethoxazole. They were susceptible for some limited drugs, and these were Nitrofurantoin (83.3%) and Chloramphenicol (83.3%). Conclusions: Majority of extended spectrum beta lactamase-producing isolates exhibited co-resistance to other commonly prescribed antibiotics. This indicates that the option of treatment for these pathogens rapidly decreased from time to time which results serious life-threatening conditions, especially in mother and newborn unless the appropriate measure is taken.

Asymptomatic bacteriuria and symptomatic urinary tract infections (UTI) in patients with diabetes mellitus in Tikur Anbessa Specialized University Hospital, Addis Ababa, Ethiopia.

BACKGROUND: The risk of urinary tract infection in diabetic patients is higher and the etiology and the antibiotic resistance of uropathogens have been changing over the past years. OBJECTIVE: The aim of this study was to determine the prevalence of symptomatic and asymptomatic bacteriuria and assess the antimicrobial susceptibility pattern of the isolates in diabetic patients. METHODS: A prospective study was conducted during June to August 2009 on diabetic in and out-patients in Tikur Anbessa University Hospital. A total of 413 consented adult patients were enrolled in the study. Two consecutive clean-catch midstream urine samples from diabetic subjects were collected for culture. Disc diffusion method was used to assess the antimicrobial susceptibility patterns of the isolates. RESULTS: Of the 413 diabetic patients participated in the study, 181 (43.8%) were males and 232 (56.2%) were females. Of these, 107 (25.9%) were type 1 and 306 (74.1%) were type 2 diabetes mellitus. Nine (13.6%) of the symptomatic diabetic patients had bacteriuria compared with 36 (10.4%) of asymptomatic diabetes patients had bacteriuria. The overall prevalence of urinary tract infection in the diabetic patients was 45 (10.9%). The predominant isolates were Escherichia coli and Klebsiella pneumoniae isolated in 6% and 28% followed by 2% and 6% in symptomatic and asymptomatic diabetic patients, respectively. Over 85% of Escherichia coli isolates were sensitive to ciprofloxacin, amoxicillin-clavulanic acid, ceftazidime, nitrofuranton, ceftiraxone, norfloxacin and geamicin. Klebsiella pneumoniae were 100% sensitive to ciprofloxacin, ceftazidime, ceftriaxone. The rate of resistance to two or more antimicrobials was 33 (71.7%). CONCLUSION: The prevalence of urinary tract infection in this study was higher in women than in men. Escherichia coli was frequently isolated in both symptomatic and asymptomatic patients. Over 60% of the isolates were resistant to ampicillin, trimethoprim-sulphamethoxazole and tetracycline. Investigation of bacteriuria in diabetic patients for urinary tract infection is important for treatment and prevention of the development of renal complications.

Hospital acquired infections among surgical, gynaecology and obstetrics patients in Felege-Hiwot referral hospital, Bahir Dar, northwest Ethiopia.

BACKGROUND: Hospital-acquired infection is an important public health problem that contributes to significant morbidity and mortality worldwide. OBJECTIVE: The aim of this study was to assess the prevalence and risk factors of hospital-acquired infections and the antibiotic susceptibility pattern of bacterial isolates in Felege-Hiwot referral hospital. METHODS: The study was conducted during April-August 2009. A total of 1383 patients admitted to Surgical and Gynecology/Obstetrics wards were followed throughout their stay in the hospital for development of infections. Data on sociodemographic, underlying diseases and risk factors were collected and analysed Laboratory investigations including culture, biochemical tests, Gram staining and antibacterial sensitivity tests using disc diffusion methods were done. RESULTS: Of the 1383 patients assessed 961 surgical, 333 obstetrics and 89 gynaecology patients assessed, 17.1% 21.0% and 13.5% developed infections, respectively. The over all incidence of hospital acquired infections was 246 (17.8%) with 251 (18.1%) episodes of bacterial infections. Urinary tract and surgical site infections were detected in 118 (48%) and 112 (45.6%) of the cases, respectively. Of the bacterial isolates, 132 (52.6%) were gram negative and 119 (47.4%) gram positive. Escherichia coli, Klebsiella pneumoniae, Psuedomonas aeruginosa, were the dominant gram negative isolates accounting for 49 (19.5%), 36 (14.3%) and 26 (10.4%), respectively. On the other hand, Staphylococcus aureus, coagulase negative staphylococci, and Enteroccocus species were isolated in 91 (36.3%), 18 (7.2%) and 10 (4.0%), respectively. Surgery, catheterization, underlying diseases, antibiotics prophylaxis and length of hospital stay were risk factors for infection (P<0.0001). Most, >80% of isolates showed high rate of resistance to ampicillin, chloramphenicol, and amoxacillin-clavulanic acid CONCLUSION: The incidence of surgical site infection in surgical and UTI in obstetrics patients was high. Escherichia coli from urinary tract infection and Staphylococcus aureus from surgical wounds were predominant isolates. The isolates showed high resistance to common antibiotics.

The immunological status of newly diagnosed tuberculosis patients co-infected with human immunodeficiency virus-1 in Adama Hospital, Ethiopia.

BACKGROUND: Tuberculosis remains a public health problem in patients with human immunodeficiency virus infection in sub-Saharan Africa. Both diseases form a lethal combination, each speeding the progress of the other. OBJECTIVE: The aim of this study was to assess the prevalence of HIV infection in newly diagnosed tuberculosis patients in Adama hospital. METHODS: Blood and sputum samples were collected from adult newly diagnosed tuberculosis patients. Sera were screened for anti-HIV antibody using rapid HIV test kits based on the National testing algorithm. The CD4 and CD8 T-cell subsets were determined using flow cytometry and the ratio of CD4+ and CD8+ were estimated using FACScan. All sputum specimens collected on three consecutive days from patients attending the tuberculosis clinic were screened for acid fast bacilli using smear microscopy. RESULTS: The seroprevalence of HIV among 258 patients with newly diagnosed TB was 26.4%. The median CD4 T cell count of HIV negative and HIV positive TB patients were 702 cells/mm3 and 233 cells/mm3. respectively (P < 0.05). Of the TB patients, 35.7% had extrapulmonary TB and 20% were smear-positive pulmonary TB. The CD4/CD8 ratio in HIV negative patients was 1.33 cells/mm3 compared to the 0.29 cells/mm3 in HIV positive patients. Of the 68 HIV positive TB patients. 58(85.3%) were not aware of their HIV serostatus prior to the screening in the current study. CONCLUSION: In the current study the HIV seroprevalence was 26.4%. The median CD4 count was very low in the TB/HIV co-infected individuals than those infected with TB alone. Majority of the HIV infected individuals were not aware of their serostatus. Provider initiated HIV/AIDS counseling and testing in TB clinics should be strengthened

The yield of Auramine O staining using led microscopy with bleach treated sputum samples for detection of pulmonary tuberculosis at St. Peter tuberculosis specialized hospital, Addis Ababa, Ethiopia.

BACKGROUND: Smear microscopy is the mainstay for diagnosis of Tuberculosis (TB) in Ethiopia. This technique; however, is insensitive to detect Mycobacteria from most clinical specimens. Currently, light emitting diode (LED) fluorescence microscope is advocated to be used in high Tuberculosis (TB) burden settings by World Health Organization (WHO). However, the utility of this method is not evaluated for bleach treated sputum samples in Ethiopia. OBJECTIVE: The objective of the study is to evaluate the diagnostic importance of Auramine O (AO) staining in direct and concentrated sputum against conventional Zehil-Neelsen (ZN) and culture from the sputum samples of suspected pulmonary tuberculosis patients. METHODS: A cross-sectional study was conducted on 346 adult new pulmonary TB suspected patients at St. Peter's Specialized Hospital, Addis Ababa, Ethiopia. Three sputum samples (spot-morning-spot) were collected in sterile cups for direct Zehil-Neelsen and AO staining. Morning sputum samples were used for Mycobacterial culture on Mycobacterial Growth Indicator Tube (MGIT) 960. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were evaluated against the gold standard culture method. Data were analyzed using STATA version 13.0. All statistical tests were considered as statistically significant if the two sided P-value was < 0.05. RESULTS: Bleach treated sputum samples with AO staining yielded more cases as compared to direct ZN and direct AO by 6.3% and 11.5%, respectively. The sensitivity of concentrated AO and direct AO were remarkably high as compared to conventional ZN (71.8% vs. 44.5% and 62.7% vs. 44.5%). The concentrated sputum with staining of AO had a high rate (18.6%) of detecting scanty graded smears as compared to conventional ZN method. CONCLUSIONS: Our findings indicated that the concentrated sputum with AO staining yielded high rate of sensitivity (71.8%) as compared to the conventional ZN method (44.5%). Moreover, the concentrated sputum with AO staining had superior ability in detecting scanty graded smears compared to the conventional ZN method. Therefore, it is recommended to utilize AO staining with LED microscopy for better diagnosis of Acid Fast Bacilli (AFB) from TB suspected cases and patients with pauci-bacillary TB in Ethiopia.

Malaria and water resource development: the case of Gilgel-Gibe hydroelectric dam in Ethiopia.

BACKGROUND: Ethiopia plans to increase its electricity power supply by five-fold over the next five years to fulfill the needs of its people and support the economic growth based on large hydropower dams. Building large dams for hydropower generation may increase the transmission of malaria since they transform ecosystems and create new vector breeding habitats. The aim of this study was to assess the effects of Gilgel-Gibe hydroelectric dam in Ethiopia on malaria transmission and changing levels of prevalence in children. METHODS: A cross-sectional, community-based study was carried out between October and December 2005 in Jimma Zone, south-western Ethiopia, among children under 10 years of age living in three 'at-risk' villages (within 3 km from dam) and three 'control' villages (5 to 8 km from dam). The man-made Gilgel-Gibe dam is operating since 2004. Households with children less than 10 years of age were selected and children from the selected households were sampled from all the six villages. This included 1,081 children from 'at-risk' villages and 774 children from 'control' villages. Blood samples collected from children using finger prick were examined microscopically to determine malaria prevalence, density of parasitaemia and identify malarial parasite species. RESULTS: Overall 1,855 children (905 girls and 950 boys) were surveyed. A total of 194 (10.5%) children were positive for malaria, of which, 117 (60.3%) for Plasmodium vivax, 76 (39.2%) for Plasmodium falciparum and one (0.5%) for both P. vivax and P. falciparum. A multivariate design-based analysis indicated that, while controlling for age, sex and time of data collection, children who resided in 'at-risk' villages close to the dam were more likely to have P. vivax infection than children who resided farther away (odds ratio (OR) = 1.63, 95% CI = 1.15, 2.32) and showed a higher OR to have P. falciparum infection than children who resided in 'control' villages, but this was not significant (OR = 2.40, 95% CI = 0.84, 6.88). A classification tree revealed insights in the importance of the dam as a risk factor for malaria. Assuming that the relationship between the dam and malaria is causal, 43% of the malaria occurring in children was due to living in close proximity to the dam. CONCLUSION: This study indicates that children living in close proximity to a man-made reservoir in Ethiopia are at higher risk of malaria compared to those living farther away. It is recommended that sound prevention and control programme be designed and implemented around the reservoir to reduce the prevalence of malaria. In this respect, in localities near large dams, health impact assessment through periodic survey of potential vectors and periodic medical screening is warranted. Moreover, strategies to mitigate predicted negative health outcomes should be integral parts in the preparation, construction and operational phases of future water resource development and management projects.

Catheterized and non-catheterized urinary tract infections among patients attended at Jimma University Teaching Hospital, Southwest, Ethiopia.

OBJECTIVES: Prospective cross sectional study was undertaken to assess the bacterial profile and antimicrobial resistance pattern of catheterized urinary tract infection in comparison with non-catheterized UTI in Jimma University Teaching Hospital, Southwest, Ethiopia. METHODS: One hundred and twenty patients, 30 catheterized (age range 20-78 years, male to female ratio 0.36:1) and 90 non-catheterized patients (age range 7-60 years, male to female ratio 2:1) with symptoms and signs of UTI were investigated for significant bacteriuria from January to March 2005. RESULTS: Significant bacteruria was observed in 13/30 (43.3%) and 20/90 (22.2%) of catheterized and non-catheterized patients, respectively (p<0.05). Klebsiella spp. (33.3%) and E. coli (27.7%) were the most common bacteria pathogens isolated in both groups and followed by Enterobacter spp. (6%). Proteus spp., Pseudomonas spp. and coagulase negative Staphylococci were isolated only from catheterized patients. Gram-negative bacteria isolated in both groups showed a high level of resistance (88-100%) to ampicillin, amoxicillin carbencillin and cephalexin. and intermediate level of resistance (48-68%) to amoxicillin-clauvlanic acid, gentamicin and trimethoprim-sulphamethoxazole. Low level of resistance (16-24%) observed to amikacin, ciprofloxacin, nalidxic acid and nitrofurantoin. Similar pattern of resistance was observed in all the gram-positive isolates including for methicillin, oxacillin and vancomycin (100%). On the other hand, amoxicillin-clavulanic acid and polymixin B were found effective against all gram-positive bacteria isolated from both groups. CONCLUSION: The present study revealed that UTIs in both catheterized and non-catheterized patients was shown very high resistance pattern to most of antibiotics in use mainly at Jimma University Teaching Hospital, southwest Ethiopia. This calls for concerted efforts at all levels including regulatory bodies and the public healthcare providers as well as private ones. Creating awareness of the community will also have a significant role to curb this problem.

Coreceptor Tropism and Maraviroc Sensitivity of Clonally Derived Ethiopian HIV-1C Strains Using an in-house Phenotypic Assay and Commonly Used Genotypic Methods.

OBJECTIVES: Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C. METHODS: Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line. RESULTS: The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond's method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc. CONCLUSION: There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.

Baseline predictors of antiretroviral treatment failure and lost to follow up in a multicenter countrywide HIV-1 cohort study in Ethiopia.

BACKGROUND: Antiretroviral therapy (ART) has been rapidly scaled up in Ethiopia since 2005, but factors influencing the outcome are poorly studied. We therefore analysed baseline predictors of first-line ART outcome after 6 and 12 months. MATERIAL AND METHODS: 874 HIV-infected patients, who started first-line ART, were enrolled in a countrywide prospective cohort. Two outcomes were defined: i) treatment failure: detectable viremia or lost-to-follow-up (LTFU) (confirmed death, moved from study sites or similar reasons); ii) LTFU only. Using stepwise logistic regression, four multivariable models identified baseline predictors for odds of treatment failure and LTFU. RESULTS: The treatment failure rates were 23.3% and 33.9% at 6 and 12 months, respectively. Opportunistic infections (OI), tuberculosis (TB), CD4 cells <50/µl, and viral load >5 log10 copies/ml increased the odds of treatment failure both at 6 and 12 months. The odds of LTFU at month 6 increased with baseline functional disabilities, WHO stage III/IV, and CD4 cells <50/µl. TB also increased the odds at month 12. Importantly, ART outcome differed across hospitals. Compared to the national hospital in Addis Ababa, patients from most regional sites had higher odds of treatment failure and/or LTFU at month 6 and/or 12, with the exception of one clinic (Jimma), which had lower odds of failure at month 6. CONCLUSIONS: In this first countrywide Ethiopian HIV cohort, a high ART failure rate was identified, to the largest extent due to LTFU, including death. The geographical region where the patients were treated was a strong baseline predictor of ART failure. The difference in ART outcome across hospitals calls the need for provision of more national support at regional level.

Pretreatment drug resistance in a large countrywide Ethiopian HIV-1C cohort: a comparison of Sanger and high-throughput sequencing.

Baseline plasma samples of 490 randomly selected antiretroviral therapy (ART) naïve patients from seven hospitals participating in the first nationwide Ethiopian HIV-1 cohort were analysed for surveillance drug resistance mutations (sDRM) by population based Sanger sequencing (PBSS). Also next generation sequencing (NGS) was used in a subset of 109 baseline samples of patients. Treatment outcome after 6- and 12-months was assessed by on-treatment (OT) and intention-to-treat (ITT) analyses. Transmitted drug resistance (TDR) was detected in 3.9% (18/461) of successfully sequenced samples by PBSS. However, NGS detected sDRM more often (24%; 26/109) than PBSS (6%; 7/109) (p = 0.0001) and major integrase strand transfer inhibitors (INSTI) DRMs were also found in minor viral variants from five patients. Patients with sDRM had more frequent treatment failure in both OT and ITT analyses. The high rate of TDR by NGS and the identification of preexisting INSTI DRMs in minor wild-type HIV-1 subtype C viral variants infected Ethiopian patients underscores the importance of TDR surveillance in low- and middle-income countries and shows added value of high-throughput NGS in such studies.

Antimicrobial susceptibility patterns of thermotolerant Campylobacter strains isolated from food animals in Ethiopia.

Thermotolerant Campylobacter spp. are frequent causes of diarrhoea in humans worldwide mostly originating from poultry. It has been suggested that extensive veterinary use of antibiotics is largely responsible for resistance in human isolates. During a 4-month period from January to April 2004, 192 Campylobacter spp. were isolated from fecal samples of 485 healthy food animals. The in vitro susceptibility to 12 antibiotics was determined by the agar disk diffusion method. Among the 192 Campylobacter spp. isolated, 135 (70.3%) were identified to be C. jejuni, 51 (26.6%) were C. coli and 6 (3.1%) were C. lari. C. jejuni was the most prevalent species in chickens (80.8%) versus 16.2% C. coli and 3.0% C. lari. All isolates found in pigs were C. coli. All strains were sensitive to chloramphenicol and ciprofloxacin and all were resistant to cephalothin. More than 90% of the strains were sensitive to clindamycin, erythromycin, gentamicin, nalidixic acid, norfloxacin, streptomycin and tetracycline. Resistance was found against ampicillin in 20% and trimethoprim-sulphamethoxazole in 37.5%. Resistance was not statistically different among C. jejuni, C. coli and C. lari (p>0.05). Multidrug resistance to two or more drugs was detected in 14.5% of strains. In conclusion, the study showed that antimicrobial resistance is found only at relatively low frequencies for most antimicrobial agents tested except for ampicillin and trimethoprim-sulphamethoxazole. The low percentages of resistance to most antimicrobial agents tested in this study may be the result of low/no usage of these agents as a growth promoters or treatment in the Ethiopian animal farm setting. The detection of multidrug resistant isolates may pose a threat to humans and further limits therapeutic options.

Pattern of widal agglutination reaction in apparently healthy population of Jimma town, southwest Ethiopia.

BACKGROUND: Typhoid fever is leading cause of morbidity in developing countries including Ethiopia. Isolation of Salmonella Typhi by culturing, from blood or other source, is the surest way of making laboratory diagnosis. However, in resource-limited countries, the Widal agglutination test provides cheaper and easy alternatives, though inappropriate technique and interpretation continue to cast a shadow on its usefulness. METHODS AND MATERIALS: A cross-sectional study was carried out during the period of February to May 2004 to determine the baseline antibody tube titration and slide agglutination pattern to Widal antigen and the usefulness of rapid slide agglutination test for diagnostic purposes among apparently healthy population of Jimma town, southwest Ethiopia. Blood samples were collected from subjects who gave their consents after thorough explanation of the procedure and the purpose of the study. The study participants were selected by a systematic random sampling technique. The sera of subjects were tested for Widal agglutination by an experienced laboratory technologist according to the standard procedural protocol-using antigen from Chronolab AG, Switzerland Data were cleaned edited and entered in to a computer and analyzed using SPSS for window version 11.0. Major results were expressed as 95% probability limit, and validity scoring; agreement test (Kappa) was determined. RESULTS: The result indicated that among the apparently health population, almost all the blood tested showed some titer of the antibody and reactivity of agglutination slide tests. The 95% probability limit (mean + 2SD) for anti H and anti O antigen titration was 1:276.89 and 1:207.89, respectively. These figures are closer to a cut-off titer of 1.320. There was a fair agreement between slide agglutination test and tube titer for 0 antigen (Kappa=0.225) and a poor agreement for H antigen (Kappa=0.066). When agglutination test result of highly reactive (+4) and titration of 1:320 were used, few cases became reactive indicating the need to raise the cut-off value to these points respectively. CONCLUSION: It is recommended that if Widal test is to be used for the clinical work up of typhoid fever in adult population, a cut-off value highly reactive (+4),for rapid slide agglutination and a titer of 1.320 and above for tube titration test be used. At the cut-off values indicated above, Widal test has low sensitivity and positive predictive value and high specificity and negative predictive values. This makes the test useful support to clinical suspicion but unlikely means ofJscreening.

Assessment of antibiotic- and disinfectant-resistant bacteria in hospital wastewater, south Ethiopia: a cross-sectional study.

INTRODUCTION: Large quantities of antimicrobials are used in hospitals for patient care and disinfection. Antibiotics are partially metabolized and residual quantities reach hospital wastewater, exposing bacteria to a wide range of biocides that could act as selective pressure for the development of resistance. METHODOLOGY: A cross-sectional study was conducted between December 2010 and February 2011 on hospital wastewater. A total of 24 composite samples were collected on a weekly basis for bacteriological analysis and susceptibility testing. Indicator organisms and pathogenic and potentially pathogenic bacteria were found and isolated on selective bacteriologic media. Disinfectant activity was evaluated by use-dilution, and minimum inhibitory concentration (MIC) was determined by the agar dilution method. Similarly, antibiotic susceptibility tests were performed using the Kirby-Bauer disk diffusion method. RESULTS: Pathogenic (Salmonella, Shigella, and S. aureus) and potentially pathogenic (E. coli) bacteria were detected from effluents of both hospitals. Dilution demonstrated tincture iodine to be the most effective agent, followed by sodium hypochlorite; the least active was 70% ethanol. MIC for ethanol against S. aureus and Gram-negative rods from Yirgalem Hospital (YAH) showed 4 and 3.5 log reduction, respectively. Salmonella isolates from YAH effluent were resistant to ceftriaxone, tetracycline, and doxycycline. Isolates from Hawassa University Referral Hospital (HURH) effluent were resistant to the above three antibiotics as well as gentamycin. CONCLUSIONS: Hospital effluents tested contained antibiotic-resistant bacteria, which are released into receiving water bodies, resulting in a threat to public health.

Isolation of potential bacterial pathogens from the stool of HIV-infected and HIV-non-infected patients and their antmicrobial susceptibility patterns in Jimma Hospital, south west Ethiopia.

Diarrhea is a major clinical problem in HIV-infected patients. There is a need to monitor antimicrobial susceptibility patterns of enteric bacterial pathogens in order to ensure appropriate treatment and control of infections. The objectives of this study was to identify and determine the magnitude of potential enteric pathogens including Salmonella, Shigella, Campylobacter and other species in HIV-infected and HIV-non-infected patients with diarrhea, to evaluate the current antimicrobial susceptibility pattern of the clinical isolates and the association of enteric bacterial pathogens in HIV infected patients with diarrhea. A cross-sectional study was conducted from Feb-July 2001 on 372 consecutive HIV seropositive and seronegative patients presenting at Jimma hospital for different illnesses. Patients were selected based on their serological tests for HIV. Sample of faeces specimens were collected and inoculated onto standard culture media as well as onto Skirrow's medium for isolation of Campylobacter species. Salmonella and Shigella species were tested for antimicrobial susceptibility using disc agar diffusion technique recommended by Kirby-Bauer. Stool specimens were also smeared and stained by Zehl-Neelson staining technique for the identification of Mycobacterium species. Among the 99 HIV-infected patients with diarrhea, 25 (25.0%) of them had enteric bacteria among which 8(8.1%) were Salmonella, 4(4.0%) Shigella and 13(13.1%) Campylobacter species. Mycobacterium species were identified in 3(3.0%) of stool specimens obtained from HIV-infected patients with diarrhea and another 3 species were detected in HIV-infected patient without diarrhea. Salmonella species were isolated with higher prevalence in HIV-infected than in HIV non-infected patients. These Salmonella isolates were 100% susceptible to Amikacin, Gentamicin, Nalidixic acid and Kanamycin while Shigella isolates were 100% susceptible for Gentamycin and Kanamycin only. Unlike Salmonella, Shigella and Campylobacter species showed higher prevalence rates in HIV non-infected patients. Enteric bacterial pathogens account for about one fourth diarrhea in HIV infected patients in Jimma hospital. The finding of this investigation also confirmed earlier observations of wide spread resistance to the commonly used drugs in this region.

Evaluation of the concentration sputum smear technique for the laboratory diagnosis of pulmonary tuberculosis.

The microbiological diagnosis of pulmonary tuberculosis (PTB) plays a key role in routine and Tuberculosis (TB) Control Programmes in developing countries. Concentration of acid-fast bacilli (AFB) in clinical specimens is an important step in the laboratory diagnosis of mycobacterial diseases. Microscopy of smears of sputum by direct and after mechanical sedimentation and centrifugation methods followed by treatment with 5% sodium hypochlorite (NaOCl) solution for concentration of the organisms were compared and evaluated. The rate of recovery of AFB from sputum was 8.5%, 25.5% and 38.0% for direct smear microscopy, concentration by sedimentation of NaOCl-treated sputa followed by Ziehl-Neelsen staining and concentration by centrifugation after use of NaOCl respectively. Both the concentration methods by the use of NaOCl solution increased the yield of theAFB by more than threefold compared with the direct microscopy of sputum (P < 0.05). The concentration methods by sedimentation, and centrifugation by the treatment of NaOCl, increased the sensitivity to 75% and 77.9%, respectively, and the specificity to 100% for both techniques. In conclusion, the use of NaOCl in the concentration of AFB in sputum is recommended for use in routine laboratory diagnosis of PTB in developing countries.