Bacterial profile, drug resistance pattern, clinical and laboratory predictors of ascites infection in cirrhosis patients.

Ascites is a pathological collection of free fluid in the peritoneal cavity, which is a common complication in patients with cirrhosis, an advanced liver disease. Bacterial infection increases the mortality rate of hospitalized patients with cirrhosis, irrespective of the severity of the liver disease. Around 60% of patients with compensated cirrhosis developed ascites within 10 years during the course of their disease. The in-hospital mortality rate due to spontaneous bacterial peritonitis (SBP) could exceed 90%, but with early diagnosis and prompt antibiotic therapy, this rate has been shown to decrease to 20%. Here, we enrolled adult (age ≥ 18) patients with liver disease with evidence of cirrhosis who developed ascites and assessed the presence of spontaneous ascites fluid infection (SAFI) in these patients. Of the total 218 patients, 22.9% (50/218) develop ascites infection. The liver organ function tests like alanine aminotransferase, aspartate aminotransferase, total bilirubin, and direct bilirubin were found to be significantly (P < 0.05) higher in patients with ascites fluid infection compared to patients with non-ascites fluid infection. Of the gram-negative bacteria, K. pneumonia and E. coli were isolated and found to be 100% resistant to amoxicillin and clavulanate. From the gram-positive bacterial isolates, S. aureus was only resistant to penicillin, whereas Str. viridans was resistant to ceftriaxone, cefotaxime, cefepime, and penicillin. On the other hand, clinical features such as a history of jaundice, low arterial blood pressure, and ultrasound results such as a shrunken liver and enlarged spleen were also independent predictors of spontaneous bacterial peritonitis. In conclusion, given the high probability of death following SAFI, early detection, and treatment, as well as knowledge of the microbial agent, resistance profile, and predictive markers in various contexts, are essential for the timely diagnosis and management of SAFI in these patients.

HIV rapid test performance among health facilities enrolled in HIV rapid test quality improvement initiative (RTQII) in Ethiopia.

BACKGROUND: As the Human Immunodeficiency Virus (HIV) rapid testing services expanded to reach the global target that 95% of people living with the virus will know their status by 2030, ensuring the quality of those services becomes critical. This study was conducted to assess the performance of HIV Rapid testing at sites in health facilities that were enrolled in the Rapid Test Quality Improvement Initiative (RTQII) in Ethiopia. METHODS: Characterized HIV proficiency testing (PT) panels of Dried Tube Specimen (DTS) were prepared, verified, and distributed to testing sites from August to December 2019. In addition on-site evaluation of HIV testing sites (HTSs) was conducted using a checklist to assess testing conditions. For proficiency testing, the study included 159 HIV testing sites (HTSs) in 41 Health facilities (HFs) in five administrative regions and two city administrations. The collected data was analyzed by SPSS version 20 and chi-square test was applied to identify the association between acceptable performance and contributing factors. Testing sites with 100% PT score as well as conducting the test with adherence to the National HIV Testing Algorithm were considered acceptable. RESULTS: The overall acceptable performance (100% PT score with the correct algorithm followed) was found to be 62% while 12% scored 80% and 11% scored between 20 and 60%. The rest 15% were not considered as acceptable due to failure to adhere to the National HIV Testing Algorithm. Testing sites that participated in External Quality Assessment/Proficiency Testing schemes have shown better performance than those that did not participate with 70% and 56% performance respectively (p = 0.057).

Prevalence and antibiotic resistance pattern of bacteria from sepsis suspected neonates at St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia.

BACKGROUND: Neonatal sepsis is the major cause of neonatal mortality and morbidity, especially in low and middle-income countries. Continuous monitoring of pathogens and their antibiotic resistance pattern is crucial for managing neonatal sepsis. This study aimed to determine neonatal sepsis due to bacteria, antibiotic resistance patterns, associated risk factors and patient outcomes at St. Paul's Hospital Millennium Medical College. METHOD: An institutional-based cross-sectional study was conducted on 400 neonates suspected of sepsis at St. Paul's Hospital Millennium Medical College from March 2020 to July 2020. A questionnaire was used to collect socio-demographic information, clinical parameters and potential risk factors from study participants. About 2ml of blood was drawn aseptically and inoculated into Tryptone Soya Broth at the patient's bedside. Bacterial identification was performed by using standard microbiological techniques. The disk diffusion method was used to determine the antibiotic susceptibility patterns of each isolated bacteria. Data entry and analysis were done using Statistical Package for Social Sciences (SPSS) version 20 software. Bivariate and multivariable logistic regressions were used to assess associated risk factors of neonatal sepsis. A p-value less than 0.05 was considered statically significant with a 95% confidence interval. RESULTS: The overall prevalence of neonatal septicemia was 21% (84/400). Of these, 67 (79.8%) and 17 (20.2%) were gram-negative and gram-positive bacteria, respectively. Klebsiella spp, 37 (44%), E. coli 19 (21.6%) and Coagulase negative Staphylococci 13 (15.47%) were the leading cause of neonatal sepsis. Ciprofloxacin and amikacin were the most effective antibiotics for gram-negative and gram-positive bacteria. Multidrug resistance was observed in 84% of the bacterial isolates. Low birth weight and preterm were associated with neonatal septicemia (AOR = 49.90, 95% CI = 15.14-123.081, P = 0.002) and (AOR = 18.20, 95% CI = 6.835-27.541, P = 0.004) respectively. CONCLUSION: Klebsiella spp and E. coli were frequently isolated bacteria in our study. The proportion of multidrug-resistance was significantly high. Most isolated bacteria were resistant to ampicillin, ceftazidime, cefotaxime and gentamycin, which indicates the necessity of continuous evaluation of antibiotic resistance rate.

Effect of heat inactivation for the detection of severe acute respiratory syndrome-corona virus-2 (SARS-CoV-2) with reverse transcription real time polymerase chain reaction (rRT-PCR): evidence from Ethiopian study.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has been a major public health importance and its specimen needs to be handled safely due to concerns of potential transmissibility to health care workers. Heat inactivation of the sample before nucleic acid isolation might permit safe testing processes. Hence, it is important to assess the effect of heat inactivation on SARS-CoV-2 RT-PCR detection in resource limited settings. METHODS: An experimental study was conducted at Ethiopian Public Health Institute (EPHI) from September 25 to October 15, 2020. A total of 188 Oro-pharyngeal swabs were collected from COVID-19 suspected cases, referred to EPHI for SARS COV-2 testing. One batch of the sample was inactivated at 56 °C heat for 30 min, and the other batch was stored at 4 °C for a similar period of time. RNA extraction and detection were done by DAAN Gene kit protocols. Abbott m2000 RT-PCR was used for amplification and detection. Data analysis was done by using SPSS version 23.0; Chi-square and Pearson correlation test for qualitative and semi-quantitative analysis were used. p-value < 0.05 was considered as statistically significant. RESULTS: Out of 188 total samples, 119 (63.3%) were positive and 69 (36.7%) were negative in the non-inactivated group. While, 115 (61.2%) of samples were positive and 73 (38.8) were negative in heat inactivated sample batch. Rate of positivity between groups did not have statistically significant difference (p > 0.05). The mean Cycle threshold (Ct) value difference between the two groups of ORF1a/b gene and N gene was 0.042 (95% CI - 0.247-0.331; t = 0.28; p = 0.774) and 0.38 (95% CI 0.097-0.682; t = 2.638; p = 0.010) respectively. CONCLUSION: Heat inactivation at 56 °C for 30 min did not affect the qualitative rRT-PCR detection of SARS-CoV-2. However, the finding showed that there was statistically significant Ct value increment after heat inactivation compared to untreated samples. Therefore, false-negative results for high Ct value (Ct > 35) samples were found to be the challenge of this protocol. Hence alternative inactivation methods should be investigated and further studies should be considered.

Helicobacter pylori (H. pylori) risk factor analysis and prevalence prediction: a machine learning-based approach.

BACKGROUND: Although previous epidemiological studies have examined the potential risk factors that increase the likelihood of acquiring Helicobacter pylori infections, most of these analyses have utilized conventional statistical models, including logistic regression, and have not benefited from advanced machine learning techniques. OBJECTIVE: We examined H. pylori infection risk factors among school children using machine learning algorithms to identify important risk factors as well as to determine whether machine learning can be used to predict H. pylori infection status. METHODS: We applied feature selection and classification algorithms to data from a school-based cross-sectional survey in Ethiopia. The data set included 954 school children with 27 sociodemographic and lifestyle variables. We conducted five runs of tenfold cross-validation on the data. We combined the results of these runs for each combination of feature selection (e.g., Information Gain) and classification (e.g., Support Vector Machines) algorithms. RESULTS: The XGBoost classifier had the highest accuracy in predicting H. pylori infection status with an accuracy of 77%-a 13% improvement from the baseline accuracy of guessing the most frequent class (64% of the samples were H. Pylori negative.) K-Nearest Neighbors showed the worst performance across all classifiers. A similar performance was observed using the F1-score and area under the receiver operating curve (AUROC) classifier evaluation metrics. Among all features, place of residence (with urban residence increasing risk) was the most common risk factor for H. pylori infection, regardless of the feature selection method choice. Additionally, our machine learning algorithms identified other important risk factors for H. pylori infection, such as; electricity usage in the home, toilet type, and waste disposal location. Using a 75% cutoff for robustness, machine learning identified five of the eight significant features found by traditional multivariate logistic regression. However, when a lower robustness threshold is used, machine learning approaches identified more H. pylori risk factors than multivariate logistic regression and suggested risk factors not detected by logistic regression. CONCLUSION: This study provides evidence that machine learning approaches are positioned to uncover H. pylori infection risk factors and predict H. pylori infection status. These approaches identify similar risk factors and predict infection with comparable accuracy to logistic regression, thus they could be used as an alternative method.

Prevalence and risk factors of human brucellosis and malaria among patients with fever in malaria-endemic areas, attending health institutes in Awra and Gulina district, Afar Region, Ethiopia.

BACKGROUND: Brucellosis is an important neglected bacterial zoonotic disease that has been affecting animals and humans for decades. Malaria has been considered major cause of illness in tropical areas, including Ethiopia. This study aimed to identify prevalence and risk factors of human brucellosis and malaria among patients with fever in malaria-endemic areas attending health institutes in Awra and Gulina district, Afar Region, Ethiopia. METHODS: A purposive cross-sectional study was conducted among febrile patients who attended health institutes in Awra and Gulina district of Afar region from February to May 2019. 3-5 ml blood samples were collected, thick and thin blood films were prepared and examined for malaria; serum was separated and tested for anti-Brucella using Rose Bengal Plate Test, and the seropositives were subjected to ELISA. Data were entered using EpiData3.1 and analyses were performed using Stata SE 14. RESULTS: A total of 444 febrile individuals (59.5% female) of age ranging from 2 to 83 years (mean = 26.1, SD = ± 11.8) were participated in this study. The overall seroprevalence of brucellosis was 31.5% (95% CI; 27.4-36.0%) by RBPT and 15.8% (95% CI; 12.7-19.7%) by ELISA, as well as the prevalence of malaria (P. falciparum) was 4.3% (95% CI; 2.7-6.6%) among febrile patients. Malaria was more common in males (7.2% 95% CI; 4.2-12.1%) than in female (2.3% 95% CI; 1.0-5.0%, p = 0.01) and in non-married than in married (7.6% 95% CI; 4.1-13.6% vs. 2.9% 95% CI; 1.5-5.4%, p = 0.02). Being male (AOR = 2.41, 95%CI: 1.36-4.26, p < 0.002), drinking raw milk (AOR = 26.68, 95%CI: 3.22- 221.13, p = 0.002) and boiled milk (AOR = 17.52, 95%CI: 2.06-149.04, p = 0.009) and touching aborted fetus/discharges without protective (AOR = 2.56, 95%CI: 1.01-6.528.50, p = 0.048) were independently associated with brucellosis among febrile patients. CONCLUSION: The prevalence of brucellosis in fever patients in this study area is higher than malaria. Consumption of raw milk and contact with animal discharge can cause significant risk of Brucella infection. So, brucellosis disease must be sought in the differential diagnosis, like ELISA test that can be used to differentiate from other febrile diseases like malaria.

Individual and household correlates of Helicobacter pylori infection among Young Ethiopian children in Ziway, Central Ethiopia.

BACKGROUND: Investigating distinct individual- and household-level risk factors for acquiring Helicobacter pylori (H. pylori) infection can inform disease prevention efforts and implicate possible routes of transmission. This study determined the magnitude of H. pylori infection among schoolchildren in Ziway, central Ethiopia and identified personal and household correlates of H. pylori infection in young Ethiopian children. METHODS: A total of 434 schoolchildren participated in this cross-sectional study. Infection status was assessed using antigen and antibody rapid tests. Demographic and lifestyle information was obtained from parents via an interviewer-led questionnaire. Univariate and multivariate logistic regressions were performed to assess the relationships between potential individual- and household-level risk factors and H. pylori infection. RESULTS: The prevalence of H. pylori infection was 65.7% (285/434). Of the personal variables assessed, the age group 10-14 years was found to be significantly associated with higher odds of H. pylori infection in univariate analysis (COR = 2.22, 95% CI: 1.06-4.66, p = 0.03) and remained positively correlated after adjusting for confounding factors. Of the household-level factors explored, having a traditional pit or no toilet was found to be significantly associated with 3.93-fold higher odds of H. pylori infection (AOR = 3.93, 95% CI: 1.51-10.3, p = 0.01), while the presence of smokers in the household was associated with 68% lower odds of infection (AOR = 0.32, 95% CI: 0.11-0.89, p = 0.03). CONCLUSION: This study from a developing country provides additional evidence for older age as a personal risk factor for H. pylori infection and identifies correlations between socioeconomic and sanitation household factors and positive childhood infection status. The associations reported here support the hypothesized fecal-oralroute of transmission for H. pylori.

Prevalence and associated risk factors for Hepatitis B and C viruses among refugees in Gambella, Ethiopia.

BACKGROUND: Currently, there is an increased flow of refugees into Ethiopia from neighboring countries. However, there are no post-arrival screening mechanisms for hepatitis B and C viruses which could be an additional burden for the local population. Hence, this study aimed to determine the prevalence and associated risk factors for hepatitis B and C viruses among refugees in Gambella, Ethiopia. It also aimed to determine the knowledge, attitude, and practice concerning hepatitis B and C viruses among participants. METHODS: A cross-sectional study was conducted among 453 refugees in Gambella, Ethiopia from January until May 2018. A questionnaire was used to collect data on refugees' socio-demographic, risk factors, and KAP of hepatitis B and C infections. Five milliliters of blood sample were collected from each participant and the serum was used for HBsAg and anti-HCV antibody screening rapid tests. Positive samples were further tested by ELISA method. Data were performed using SPSS version 20, and a p-value less than 0.05 was considered statistically significant. RESULTS: The overall prevalence of HBsAg and anti-HCV among refugees was 7.3% (33/453) and 2.0% (9/453) respectively. Of these, 6.8% (25/370) and 1.4% (5/370) of females were positive for HBsAg and anti-HCV, whereas 9.6% (8/83) and 4.8% (4/83) of males were positive for HBsAg and anti-HCV. The age group of 18-29 and 30-41 years old were related to HCV infection (P = 0.003 and P = 0.020). However, proposed risk factors were not related to HBV and HCV infections. Knowledge assessment showed that 86.5% (392/453) did not know how HBV and HCV infections are transmitted, and 86.8% (393/453) had no information about the availability of HBV vaccine. CONCLUSION: This study showed intermediate prevalence of hepatitis B and hepatitis C virus in a large refugee camp in Ethiopia. The prevalence of hepatitis C virus was found to increase with age, but no other risk factor for either virus identified as significant. Refugees' understanding of hepatitis B and C was very limited. This indicates the need for screening policy to be implemented and integrated with other health services and awareness creation about the infection in all refugee camps of Gambella.

Intestinal parasites co-infection and associated factors among active pulmonary tuberculosis patients in selected health centers, Addis Ababa, Ethiopia: unmatched case control study.

BACKGROUND: In co-endemic areas, rate of intestinal parasites and tuberculosis (TB) co-infection thought to be high. However, there are limited studies on the epidemiology of this co-infection in Ethiopia. Therefore, the present study aimed to generate evidence on intestinal parasites co-infection rate and associated factors among pulmonary tuberculosis patients (PTB) and their household contacts in Addis Ababa, Ethiopia. METHODS: Unmatched case-control study was conducted. Data were collected from 91 PTB patients (cases) and 89 household contacts (controls). Socio-demographic characteristics and associated factors were collected using structured questionnaire. Sputum, stool and blood specimens were collected, processed and examined for PTB, intestinal parasites and Human Immunodeficiency virus anti-body test, respectively. Data were entered and analyzed by Statistical Packages for Social Sciences (SPSS) Version 20. Descriptive statistics, Fisher's exact test, binary logistic regression, and odds ratio were used. P-value of < 0.05 was considered as statistically significant. RESULTS: The infection rate of intestinal parasites based on one stool samples in PTB patients and controls was 22 and 9%, respectively. The difference was statistically significant (COR = 2.85;95% CI = 1.18-6.87). The most prevalent intestinal parasite in PTB patients was Gardia lamblia (8.8%, 8), followed equally by Ascaris lumbricoides, Haymenolopsis nana and Entamoeba histolytica/dispar (4.4%, 4). Co-infection in PTB patients was associated with body mass index (BMI) < 18.5 (AOR = 6.71;95% CI = 1.65-27.25) and dirty material in finger nails (AOR = 8.99;95% CI = 2.46-32.78). There was no variable associated with parasitic infections in controls in our analysis, which might be due to the low prevalence of intestinal parasites'. CONCLUSIONS: There was a statistical significant difference in the infection rate of intestinal parasites in PTB patients compared to healthy household contacts. The consequence of co-infection on developing an active disease, disease severity and treatment efficacy needs to be investigated in future.

Prevalence of tuberculosis, multidrug resistant tuberculosis and associated risk factors among smear negative presumptive pulmonary tuberculosis patients in Addis Ababa, Ethiopia.

BACKGROUND: The diagnoses of active smear negative PTB, remains difficult. As a result, treatment is often carried out empirically relaying on clinical criteria. The distribution and magnitude of smear negative PTB, smear negative MDR-TB and associated factors in the same day diagnosis strategy are not clearly known in the study area. Therefore, this study aimed to determine the prevalence of TB, MDR-TB and associated risk factors among presumptive smear negative pulmonary tuberculosis patients in Addis Ababa, Ethiopia. METHODS: Analytic cross sectional study design was used. A total of 418 smear negative presumptive pulmonary TB patients were enrolled from selected health facilities since August 01, 2017 to January 5, 2018. Sputum samples were examined by Ziehl Neelsen microscopy, Xpert MTB/RIF assay and Culture. Drug susceptibility testing was performed by line probe assay and BACTEC MGIT 960 system. These laboratory tests were performed in Ethiopian Public Health Institute, National TB Reference Laboratory. Data was analyzed by SPSS Ver.20. RESULTS: From the total of 418 enrolled patients, 27 (6.5%) were Xpert MTB/ RIF and 26 (6.4%) were culture confirmed smear negative PTB patients. The positivity rate among male and female was 10.2 and 3.5% (p = 0.005) respectively. From 26 culture positive isolates 3 (11.54%) were MDR TB; from MDR-TB confirmed isolates 2/23 (8.7%) were among new and 1/3 (33.3%) was among retreatment smear negative presumptive pulmonary TB patients. All Rifampicin resistant smear negative pulmonary TB isolates by Xpert MTB/ RIF assay were found to be MDR TB and 7/26 (26.9%) isolates were INH mono resistant. History of migration found to be a potential factor for developing smear negative pulmonary TB. CONCLUSION: In this study a significant proportion of smear negative pulmonary TB was diagnosed. Furthermore, a high smear negative multi drug resistant (MDR) TB and other mono drug resistant TB prevalence was confirmed. Due to the limitations of smear microscopy which is used as a primary diagnostic tool, these TB strains are missed to be diagnosed and transmission continues in the community.

Combined antibacterial effect of essential oils from three most commonly used Ethiopian traditional medicinal plants on multidrug resistant bacteria.

BACKGROUND: An alarm increase the rate of emerging and re-emerging of multidrug resistant bacteria have been caused great public health concern in the worldwide. They have been resisting for most or majority of currently available and affordable antibiotics and imposed socioeconomic catastrophe at global scale. As a result, there is utmost important to discover new or modify currently available antibiotics. The aim of this study was to evaluate combined antibacterial effect of essential oils obtained from Blepharis cuspidata, Boswellia ogadensis and Thymus schimper against multidrug resistance (MDR) Escherichia coli, Klebsiella pneumoniae and Methicillin resistant S. aureus. METHODS: Essential oil (EO) was extracted from the aerial part of B. cuspidata, B.ogadensis and T. schimper by steam distillation and stored in brown bottles at 4 °C. There were mixed in 1:1 ratio and adsorbed to disc and placed on MHA and measured their minimum inhibitory zone seeded with E. coli, K. pneumoniae and MRAS after 18-24 H. minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were measured by broth micro-dilution method. The interaction between EOs was determined by fractional inhibitory concentration index. RESULTS: The antibacterial potential of mixed oil depends on the doses and type of the EOs and bacteria species. The combined EOs of B.cuspidata and T.schimperi had inhibition zone (39 mm), its MIC and MBC value was 0.39 µl/ml against MRSA. It had inhibition zone (28-35 mm), MIC value 0.39-6.25 µl/ml and MBC (0.78-12.5 µl/ml) against MDR E. coli and K. pneumoniae. Whereas, combined effects of B. cuspidata and B. ogadensis had MIC values ranges from 0.78-6.25 µl/ml for E.coli and K. pneumoniae and 1.56 µl/ml for MRSA. There was strong synergistic effect between the combination of B.cuspidata and T.schimperi. This study revealed that gram negative bacteria were slightly less susceptible than gram positive. CONCLUSIONS: This in vitro study of combined EOs has significant antibacterial effect than using each of them and even it was more potent antibacterial effect on MDR as compare to modern antibiotics. Hence, it can be applied to a pharmaceutical composition as modulator or adjuvant or precursor for synthesis of new antibiotic in future activities.

Group B streptococci vaginal colonization and drug susceptibility pattern among pregnant women attending in selected public antenatal care centers in Addis Ababa, Ethiopia.

BACKGROUND: Group B Streptococcus (GBS) is the leading cause of septicemia, meningitis, and pneumonia in neonates. Maternal colonization with GBS is the principal risk factor for early-onset disease in infants. Group B Streptococcus is now an important cause of maternal and neonatal morbidity and mortality in many parts of the world. In Ethiopia, few studies have been done on GBS colonization among pregnant women. The aim of this study was to determine the prevalence of GBS colonization, antimicrobial susceptibility patterns and assess risk factors among pregnant women. METHODS: A prospective cross-sectional study was conducted from May to August 2014 at selected public antenatal care (ANC) centers in Addis Ababa, Ethiopia. Clinical and socio-demographical data were collected using structured questionnaire after obtaining written informed consent. A total of 281 lower vaginal swabs were collected and inoculated into 1 ml Todd Hewitt Broth supplemented with gentamicin and nalidixic acid to prevent the growth of contaminants. After overnight incubation, all broths were subcultured on 5% sheep blood agar for isolation of GBS. Antimicrobial susceptibility testing was performed according to the criteria of the Clinical and Laboratory Standard Institute (CLSI) guidelines 2013 by disk diffusion method. Data were entered and analysed using SPSS version 20.0 software. Chi-square test and binary logistic regression analysis were used. P-value < 0.05 was considered statistically significant. RESULTS: The overall prevalence of GBS colonization among pregnant women was 14.6% (41/281). Group B Streptococcus colonization was significantly associated with health institutions (P < 0.05). All GBS isolates were susceptible to chloramphenicol. Resistance to tetracycline, cefotaxime, clindamycin, penicillin, vancomycin, ampicillin and erythromycin was 90.2%, 34.1, 26.8%, 19.5, 17%, 14.6 and 7.5% respectively. Multidrug resistance (MDR) (≥ 2 drugs) was detected in 43.9% (18/41) of the isolates. CONCLUSION: There was a high frequency of GBS colonization (14.6%) and resistance to the commonly used antibiotics which suggests the importance of the screening of GBS colonization in pregnant women at 35-37 weeks of gestation and testing their antimicrobial susceptibilities in order to provide antibiotic prophylaxis and minimize newborn infection and co-morbidity.

Evaluation of genotype MTBDRplus VER 2.0 line probe assay for the detection of MDR-TB in smear positive and negative sputum samples.

BACKGROUND: Multi drug resistant tuberculosis (MDR-TB) poses formidable challenges to TB control due to its complex diagnostic and treatment challenges and often associated with a high rate of mortality. Accurate and rapid detection of MDR-TB is critical for timely initiation of treatment. Line Probe Assay (LPA) is a qualitative in vitro diagnostic test based on DNA-STRIP technology for the identification of the M. tuberculosis complex and its resistance to rifampicin (RMP) and/or isoniazid (INH). Hain Lifescience, GmbH, Germany has improved the sensitivity of Genotype MTBDRplus VER 2.0 LPA for the detection of MDR-TB; with the possibility of applying the tool in smear negative sputum samples. METHOD: A cross sectional study was conducted on 274 presumptive MDR-TB patients referred to the National TB Reference Laboratory (NTRL), Ethiopian Public Health Institute (EPHI) who submitted sputum samples for laboratory diagnosis of drug resistant-TB testing. Seventy-two smear and culture positive samples processed in smear positive direct LPA category and 197 smear negative sputum samples were processed for direct LPA. Among the smear negative samples 145 (73.6%) were culture negative and 26 (13.2%) were culture positive. All specimens were processed using NALC-NaOH method and ZN smear microscopy done from sediments. Genotype MTBDRplus VER 2.0 done from processed sputum sediments and the result was compared against the reference, BACTEC MGIT 960 culture and DST. Sensitivity, specificity, PPV and NPV of Genotype MTBDRplus VER 2.0 assay was determined and P-value <0.05 was considered as statistically significant. RESULTS: The sensitivity, specificity, PPV and NPV of Genotype MTBDRplus VER 2.0 LPA were 96.4, 100, 100 and 96.9%, respectively for the detection of MDR-TB from direct smear positive sputum samples. The sensitivity, specificity, PPV and NPV of Genotype MTBDR plus VER 2.0 LPA were 77.8, 97.2, 82.4 and 97.2%, respectively, for the detection of M. tuberculosis from direct smear negative sputum samples. Fourteen (53.8%) samples had valid results with LPA among the 26 smear negative culture positive samples. The remaining 8 (30.8%) and 4 (15.4%) were invalid and negative with LPA, respectively. The sensitivity and specificity of Genotype MTBDRplus VER 2.0 LPA were 100% for the detection of MDR-TB among 14 direct smear negative and culture positive sputum samples. The most common mutations associated with RMP and INH resistance were S531L and S315TL, respectively. A single rare mutation (C15T/A16G) was detected for INH resistance. CONCLUSION: The diagnostic performance of Genotype MTBDRplus VER 2.0 LPA in direct smear positive sputum sample was highly sensitive and specific for early detection of MDR-TB. However, the diagnostic performance of this molecular assay in direct smear negative sputum sample was low and showed a high level of invalid results for detection of M. tuberculosis and its resistance to RMP and/or INH so it is unlikely to implement Genotype MTBDRplus VER 2.0 for the detection of MDR-TB in direct smear negative sample in our routine settings. The sensitivity of the assay should be improved for detection of MDR-TB in direct smear negative sputum specimens.

The revenue generated from clinical chemistry and hematology laboratory services as determined using activity-based costing (ABC) model.

BACKGROUND: The rapid and continuous growth of health care cost aggravates the frequently low priority and less attention given in financing laboratory services. The poorest countries have the highest out-of-pocket spending as a percentage of income. Higher charges might provide a greater potential for revenue. If fees raise quality sufficiently, it can enhance usage. Therefore, estimating the revenue generated from laboratory services could help in capacity building and improved quality service provision. METHODS: Panel study design was used to determine revenue generated from clinical chemistry and hematology services at Tikur Anbessa Specialized Teaching Hospital, Addis Ababa, Ethiopia. Activity-Based Costing (ABC) model was used to determine the true cost of tests performed from October 2011 to December 2011 in the hospital. The principle of Activity-based Costing is that activities consume resources and activities consumed by services which incur the costs and hence service takes the cost of resources. All resources with costs are aggregated with the established casual relationships. The process maps designed was restructured in consultation with the senior staffs working and/or supervising the laboratory and pretested checklists were used for observation. Moreover, office documents, receipts and service bills were used while collecting data. The amount of revenue collected from services was compared with the cost of each subsequent test and the profitability or return on investment (ROI) of services was calculated. Data were collected, entered, cleaned, and analyzed using Microsoft Excel 2007 software program and Statistical Software Package for Social Sciences version 19 (SPSS). Paired sample t test was used to compare the price and cost of each test. P-value less than 0.05 were considered as statistically significant. RESULT: A total of 25,654 specimens were analyzed during 3 months of regular working hours. The total numbers of clinical chemistry and hematology tests performed during the study period were 45,959 (66.1 %) and 23,570 (33.9 %), respectively. Only 274, 386 (25.3 %) Ethiopian Birr (ETB) was recovered from the total cost of 1,086,008.09 ETB incurred on clinical chemistry and hematology laboratory tests. The result showed that, about 133,821 (12.32 %) ETB was revenue not collected from out-of-pocket payments that was paid for the services as a result of under pricing. The result showed that 18 out of 20 laboratory tests were under priced. The cost burden related to free Anti Retro-viral Therapy (ART) services was 285,979.82 (26.3 %) ETB. CONCLUSION: The cost per test estimated was significantly different to the existing price. About 90 % of the tests were under priced. This information could warn the hospital to reconsider resetting prices of these tests profitability ration less than 1. The revenue collected could help to build capacity, upscale quality, and sustainable service delivery.

Association between helminth infection and allergic disorders among children in Batu, Ethiopia.

BACKGROUND: Helminths are potent immunomodulators and in their chronic infection state they may protect against allergy-related disease and atopy. However, they are also known for inducing allergic conditions. This study aimed to assess the association between helminths,  atopy and allergic conditions. METHODS: A total of 461 school children participated in this cross-sectional study. Data on allergic symptoms and a range of confounding variables was gathered from parents via an interviewer-led questionnaire. Skin sensitization to house dust mite and cockroaches was analyzed, and a stool sample was collected for helminth analysis. Serum total Immunoglobulin E using enzyme-linked immunosorbent assay and eosinophil count were also measured. RESULTS: Overall sensitivity to both allergens was 2.4%. Self-reported allergic outcomes in the last 12 months for the 461 participants had been : wheezing 3.7%, asthma 2.2%, eczema 13.2% and hay fever 6.9%. Overall, the prevalence of helminth infection was 11.9% (53/444). A borderline significant association was found between atopy and any allergy symptoms (odds ratio [OR]: 3.32, 95% confidence interval [95% CI: 0.99, 11.1], p = .052). There was no significant association between helminths and atopy (OR: 0.64 [95% CI: 0.29, 1.41], p = .268) and also between helminths and allergic symptoms (OR: 0.64 [95% CI: 0.29, 1.41], p = .268). Bivariate analysis showed keeping an animal in the house increases the risk of atopy while maternal and paternal history of allergy increases the risk of developing allergic symptoms in the children. CONCLUSION AND CLINICAL RELEVANCE: This study found a non-significant inverse association between helminths infection and atopy and allergic disorders, likely due to reduced statistical power, resulting in a lower prevalence of atopy and allergic conditions. A high powered longtitudinal study is necessary to explore the casuality and potential therapeutic benefits of helminths for allergic disorders.

SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia.

Objectives: This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 µl RNA and 20 µl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results: A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions: The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.

Incidence of surgical site infection, bacterial isolate, and their antimicrobial susceptibility pattern among patients who underwent surgery at Dessie Comprehensive Specialized Hospital, Northeast Ethiopia.

Objective: Surgical site infection is the most common postoperative complication worldwide, representing a major burden for patients and health systems. The aim of the study is to determine the incidence and bacterial profile that cause surgical site infection among patients who underwent surgery in parts of Northeast Ethiopia. Methods: A health facility-based cross-sectional study was conducted in Dessie Comprehensive Specialized Hospital from July 22 to October 25, 2016. A total of 338 patients from the obstetrics and gynecology and general surgical wards were included, through consecutive sampling technique. The specimens were collected aseptically on the first day when the patients had presented with clinical evidence of infection and then sent to the microbiology laboratory. The data were entered and analyzed by SPSS version 20, and the results were explained by frequency distribution in tables and figures. Results: The majority of participants were female (74.3%) and more than half (61.2%) of the surgeries were performed in the gynecology and obstetrics ward. Clinically, 49 patients (14.5%) were diagnosed as developing surgical site infection, and wound swabs were taken for bacteriological study. About 41 (83.7%) swabs showed bacterial growth, indicating 12.13% overall prevalence of bacterial surgical site infection. Out of 48 bacterial isolates, more than half (56.25%) of them were Gram negative. The most frequent isolate was Staphylococcus aureus, 14 (66.67%), followed by Escherichia coli, 9 (33.33%). Out of the total bacterial isolates, 38 (79.2%) isolates were found to be multidrug resistant, and the rate of multidrug resistant was higher among Gram-negative isolates. Conclusion: An average rate of surgical site infection was found to be reported and significant numbers of bacterial isolates were also detected. The highest rate of surgical site infection was reported in prostate surgery, followed by small bowel, vaginal hysterectomy, and exploratory laparotomy surgical procedures. Periodic surveillance on the incidence rate and bacterial profile along with the determination of their antibiotic susceptibility should be performed.

Evaluation of the Diagnostic Performance of the LINEAR Cromatest and Laboquick URS 10-T Dipsticks Among Urinary Tract Infection Suspects in Addis Ababa, Ethiopia: A Cross-Sectional Study.

Background: Urinary tract infections (UTIs) bring a significant and serious health-related problem. Repeated infections may lead to the development of renal scarring and end-stage renal dysfunction. Therefore, balancing the choices of UTI diagnostic tools depending on the costs versus accuracy can minimize false results that may subject patients to wrong treatments. Objective: The objective of the study was to evaluate the diagnostic performance of LINEAR cromatest and Laboquick URS 10-T dipsticks against conventional urine culture at Arsho Advanced Medical Laboratory (AAML), Addis Ababa, Ethiopia. Methods: A similar cohort of UTI-suspected patients from our previous study, who were prospectively enrolled from Arsho Advanced Medical Laboratory, Addis Ababa, Ethiopia, were considered for this analysis. Data analysis was performed using SPSS version 26. The sensitivity, specificity, and predictive value of different dipsticks were calculated using culture as a gold standard. ROC curve analysis was also used to determine diagnostic performance. A test with a P-value of <0.05 was considered statistically significant. Results: Out of 446 urine samples processed, bacterial growth was observed in 141 (31.6%). Of this figure, 105/141 (74.5%) and 36/141 (25.5%) were from female and male participants, respectively. The sensitivity and specificity of the LINEAR Cromatest dipstick were 83.7% and 67.9%, respectively (P-value <0.001). The Laboquick URS 10-T dipstick showed sensitivity and specificity of 87.9% and 68.5%, respectively (P-value <0.001). The ROC analysis showed an AUC of >0.7 for both dipsticks. Conclusion: In a setting where there is no access to urine culture, the urine dipstick may be considered an alternative diagnostic tool in the diagnosis of UTIs.

Prevalence of Hepatitis B Virus, Human Immune Deficiency Virus and Associated Risk Factors Among Individuals with Presumptive Pulmonary Tuberculosis Attending at Saint Peter's Specialized Hospital, Addis Ababa, Ethiopia.

Background: Hepatitis B virus (HBV), human immunodeficiency virus (HIV) and tuberculosis are the causes of widely spread infectious disease, especially in resource-limited countries. The extent of HBV infection and its contributing factors among people with suspected pulmonary tuberculosis (PTB) were not adequately addressed. Objective: To assess the prevalence of HBV, HIV & their associated risk factors and the magnitude of TB among individuals with presumptive pulmonary tuberculosis attending at St. Peter's Specialized Hospital, Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted among 387 individuals with presumptive PTB from October to December 2020. A standard questionnaire was used to collect socio-demographic data and associated risk factors. Sputum samples were analyzed by GeneXpert, Florescent Microscopy and Ziehl-Nelson staining technique. HBsAg test was carried out using Murex Version 3 ELISA test kit from serum/Plasma samples, HIV testing was performed by rapid HIV test kits and data were analyzed using SPSS version 23. Results: The mean age of study participants was 44.2 years. Overall, 14 (3.6%), 28 (7.2%) and 37 (9.6%) of them were positive for HBV, HIV & TB, respectively. Only single patient was HBV-HIV co-infected (0.3%). The TB-HIV co-infection was identified in 6 (1.6%). In multivariate analysis, being partner separated, alcohol consumption, body piercing and having multiple sexual partners were significantly associated with HBV infection. Having a spouse, who is divorced, widowed, sharing scissors, alcohol consumption and contact with multiple sexual partners also significantly associated with HIV infection. Conclusion: This study showed that HBV, HIV and TB are still public health issues that need awareness and health education on the risky behaviors and transmission of HBV, HIV & TB among individuals with presumptive TB suspects. Further large-scale study is necessary.

Prevalence of Bacterial Urinary Tract Infection, Associated Risk Factors, and Antimicrobial Resistance Pattern in Addis Ababa, Ethiopia: A Cross-Sectional Study.

Background: Urinary tract infections (UTIs) brought a significant and serious health-related problem that may lead to the subsequent development of serious indications with the challenge of the emergence of antibiotic resistance. Therefore, the choice of antibiotics depends on the accuracy of the diagnostic tool of UTIs to minimize false results that may subject patients to wrong treatments. This study aimed to determine the prevalence of bacteriuria, associated factors, and AMR pattern of UTI-suspected patients. Methods: A cross-sectional study was conducted from March to May 2022, at Arsho Advanced Medical Laboratory (AAML), Addis Ababa, Ethiopia. Species identification and isolation from bacterial colonies were characterized by gram stain and biochemical properties followed by antibiotic susceptibility testing using the Kirby-Bauer method on Muller-Hinton agar. Logistic regression analysis was carried out to determine the association between the independent variables and significant bacterial growth to identify factors that affect the prevalence of UTI. A test is considered statistically significant that has a P value less than 0.05. Results: Out of 141 (31.6%) which yielded significant bacteriuria, 16 different species of bacterial uropathogens were identified. A total of 105/446 (91 Gram-negative and 14 Gram-positive) of bacterial growth in the female gender and 36/446 (33 Gram-negative and 3 Gram positive) in male were observed with a P value of 0.03. The most predominant bacteria were E. coli followed by Klebsiella pneumoniae. Amoxicillin had shown the highest resistance rate (100%) followed by Ampicillin (98.9%). Females and participants with previous infections were shown to be associated with significant bacterial growth. Conclusion: Based on our study finding, the ordinarily used antibiotics seem to face emerging resistant strains, which needs considerable and due attention to the impact of UTI in developing countries including Ethiopia. History of previous UTIs and female gender were shown to be possible risk factors associated with UTIs.