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Background: Genomic epidemiology of antibiotic resistance is not sufficiently studied in low-income countries., Objectives: To determine prevalence of ESBL production, and resistome and virulome profiles, of Klebsiella pneumoniae isolated at Jimma Medical Center, Ethiopia., Methods: Strains isolated from patients with suspected infections between June and November 2016 were characterized by MALDI-TOF for species identification and disc diffusion for antimicrobial susceptibility testing. All K. pneumoniae isolates were characterized by double disc diffusion for ESBL production and all ESBL-producing strains (ESBL-KP) were subjected to WGS on the Illumina (HiSeq 2500) platform. DNA was extracted by automated systems (MagNA Pure 96). Genome assembly was performed using SPAdes (v. 3.9) and draft genomes were used for analysing molecular features of the strains. Maximum likelihood trees were generated using FastTree/2.1.8 based on SNPs in shared genomic regions to identify transmission clusters., Results: Of the 146 K. pneumoniae strains isolated, 76% were ESBL-KP; 93% of the ESBL-KP strains showed resistance to multiple antimicrobial classes. bla CTX-M-15 (84.4%) was the most prevalent ESBL gene. Resistance genes for aminoglycosides and/or fluoroquinolones [ aac(6')-Ib-cr (65.1%)], phenicols [ catB3 (28.4%)], sulphonamides [ sul1 (61.2%) and sul2 (60.5%)], trimethoprim [ dfrA27 (32.1%)], macrolides [ mph(A) (12.8%)] and rifampicin [ arr2 / arr3 (39.4%)] were prevalent. Plasmids of the IncF and IncR families were prevalent among ST218, ST147, ST15 and ST39. KL64 and KL57 capsular types and O1 and O2 LPSs were prevalent. A high-risk clone, ST218-KL57 encoding rmpA1/rmpA2 and iutA , was detected. Phylogenetic analysis showed a cluster of clonally related strains from different units of the hospital., Conclusions: Prevalence of ESBL-KP was high and bla CTX-M-15 was the predominant ESBL gene. ESBL genes had spread through both clonal and polyclonal expansion of high-risk and hypervirulent clones. Nosocomial transmission of MDR strains between different units of the hospital was observed., (© The Author(s) 2021. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy.)

Aims: To determine the association between multicellular behaviour, integron status and antibiotic resistance among 87 Ethiopian Salmonella enterica isolates of animal and human origin., Methods and Results: Isolates were characterized for their biofilm forming ability, antimicrobial susceptibility and the presence and characteristics of a class 1 integron and Salmonella genomic island 1 (SGI1). The majority of isolates grown at environmental temperatures (20°C) exhibited robust biofilm formation (72·4%) and displayed RDAR colony morphology on Congo red agar plates. The presence of a class 1 integron correlated with the extent of drug resistance and ability to exhibit multicellular behaviour., Conclusions: Although cellulose production and RDAR morphology correlated with increased multicellular behaviour, neither was required for biofilm formation. Contrary to previous reports, colony morphology was generally consistent within a serovar. No integrons were detected in isolates deficient for multicellular behaviour, indicating a potential role of bacterial community formation in transfer of genetic elements among environmental isolates., Significance and Impact of Study: Infection by Salm. enterica is a major public health problem worldwide. The dominance of multidrug resistance and multicellular behaviour in Salmonella isolates of Ethiopian origin highlights a need for integrated surveillance and further detailed phenotypic and molecular studies of isolates from this region., (© 2014 The Society for Applied Microbiology.)

Background: Meningitis is usually caused by viral, bacterial or fungal pathogens. Bacterial meningitis is a medical emergency and if untreated has a high mortality rate. Even among those who survive the infection, some may develop permanent neurological disorders., Objectives: This study was undertaken to isolate and identify the bacterial and fungal etiologic agents of meningitis and to access the susceptibility pattern of bacterial isolates., Methods: During the period of November 2007 to June 2008, 340 cerebrospinal fluid (CSF) specimens were obtained from suspected cases of meningitis admitted to Tikur Anbessa University Hospital, Addis Ababa, Ethiopia. Microbiological analysis was performed on CSF specimens using standard procedures., Results: Of the 340 patients investigated, 53.5% were males and 46.5% were females. Over half of the patients (51.2%) were children (1 month to 16 years) and the remaining 32.6% and 16.2% were neonates (below 1 month of age) and adults (above 16 yrs of age), respectively. Fever was the commonest clinical feature observed in all age groups. Of the 340 CSF specimens, 26 (7.6%) had a positive bacterial or fungal culture. Bacterial isolates accounted for 84.6% of the total isolates. Among the bacteria, Streptococcus pneumoniae accounted for 36.4% followed by Haemophilus influenzae type b (Hib) and Nessieria meningitidis (serogroup A and C) (13.6%) each. Cryptococcus neoformans was the only fungal isolate. All gram positive bacteria were sensitive to ceftriaxone, ciprofloxacin, chloramphenicol, erythromycin and rifampicin and showed low level of resistance (< 60%) to penicillin, tetracycline and trimethoprim-sulphamethoxazole. The gram-negative bacteria showed high level of resistance (> 80%) to tetracycline and trimethoprim-sulphamethoxazole, intermediate level of resistance (60-80%) to ampicilin and low level of resistance (< 60%) to ceftriaxone, ciprofloxacin, gentamicin, chloramphenicol and rifampicin. Multiple resistance (resistance to two or more drugs) was observed in 18.2% and 100% gram positive and gram-negative bacteria, respectively., Conclusion: This study showed that the predominant pathogens of meningitis were S. pneumoniae, H. influenzae and N. meningitidis. Ceftriaxone and ciprofloxacin were the most effective drugs against these organisms. Continuous periodic surveillance is required to form a comprehensive and updated understanding of the etiologies and antimicrobial resistance pattern for appropriate management of meningitis cases in the country.

Background: Recent etiological studies for schizophrenia and bipolar disorder have focused on the protozoan Toxoplasma gondii and Herpesvirdae family viruses., Objective: To determine the magnitude of T. gondii, cytomegalovirus (CMV), herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2) infection in individuals with schizophrenia, bipolar disorder and healthy controls by using serologic diagnostic methods., Material and Methods: Serologic diagnostic method was used to determine the prevalence and level of antibodies to T gondii, CMV HSV-1 and HSV-2 in individuals with schizophrenia, bipolar disorder, and unaffected controls recruited from Butajira, Ethiopia. The study was conducted from March to May 2009. A total of 495 serum samples were analysed for the presence and level of immunoglobulin G (IgG) to T. gondii, CMV HSV-1, and HSV-2., Results: The seroprevalence of T gondii infection was higher in individuals with schizophrenia [adjusted odds ratio = 4.7; 95% CI (1.5, 15.1)] and bipolar disorder [adjusted odds ratio = 3.0; 95% CI (1.1, 8.6)] than in unaffected controls. The level of IgG to CMV was also significantly higher in individuals with schizophrenia and bipoar disorder than in unaffected controls. Younger individuals with schizophrenia (< 25 years old) also had a significantly higher level of IgG to CMV than matched unaffected controls., Conclusion: This study provides additional evidence that infection with 7T gondii and CMV may be associated with some cases of schizophrenia and bipolar disorder. Additional studies should focus on antibodies to these agents in the sera and CSF of individuals with recent-onset psychosis.

Background: Group A Streptococci (GAS) or Streptococcus pyogenes are the most frequent cause of pharyngitis and skin infection in children and lead to post infection complications including acute rheumatic fever and glomerulonephritis. Pharyngeal carriage rates of GAS among healthy school children vary with geographical location and seasons. There is not much information on the screening of children for carriage of GAS in Ethiopia., Objectives: The study aimed at assessing the carriage rate of Group A Streptococci and antimicrobial susceptibility of the isolates in healthy Ethiopian school children., Methods: A total of 937 children residing in Addis Ababa (n=491), Gondar (n=265) and Dire-Dawa (n=181) were investigated during a period between November 2004 and January 2005. Throat specimens were collected and cultured using standard procedure. Beta haemolytic streptococci were serogrouped by agglutination tests using specific antisera. Antimicrobial susceptibility testing of the isolates was performed by diffusion method., Results: The median and the mean ages of the study participants were 11 (range 6-14) years. Girls constituted 52% (486/937) of the study participants. A total of 167 (17.8%) beta haemolytic streptococci were recovered from 937 children investigated GAS accounted for 91/167 (54.5%) of beta hemolytic streptococcal isolates. The carrier rate for GAS was 9.7% (91/937) of the screened children followed by group G with 3.2% (30/937) and group C streptococci with 2.2% (21/937). All GAS isolates were sensitive to oxacillin, penicillin, erythromycin, clindamycin and trimethoprim-sulphamethoxazole. Lower frequency of resistance was observed against tetracycline and vanocmycin., Conclusion: The present study revealed that GAS was the most predominant beta-haemolytic streptococcus among healthy Ethiopian school children. Our results showed that pharyngeal carriage of GAS in school children should not be underestimated. Therefore it is recommended to conduct regular screening and GAS surveillance in schools, and maintain rational use of antibiotics to minimize GAS resistance.

Background: Infectious diseases are major causes of morbidity and mortality among children in the developing world Antibiotic resistance is increasing. Knowledge of pathogens causing infection in pediatrics patients is essential for devising management strategies., Objectives: To assess the bacteriologic profile and the resistance pattern of clinical isolates from pediatric patients in Gondar University Hospital, Northwest Ethiopia., Material and Methods: Retrospective analysis was done on different clinical specimens that were submitted and processed for culture and antimicrobial susceptibility testing during a period of September 2000 and October 2007., Results: A total of 823 bacterial pathogens were isolated from 7886 different clinical specimens. The overall culture positivity rate was 10.4%. The three most frequent isolates were S. aureus (30%), E. coli (16.5%) and Shigella spp. (11.7%). All isolates showed intermediate level of resistance (60-80%) to ampicillin, trimethoprim-sulphamethoxazole and tetracycline. Low level of resistance (< 60%) observed to chloramphenicol, gentamicin, penicillin, erythromycin and ciprofloxacin. Majority of the isolates (80.3%) showed multiple drug resistance (resistance to two or more drugs). In general ciprofloxacin and gentamicin were the most effective drugs against the tested gram-positive and gram-negative bacteria., Conclusion: This study shows resistance to the commonly accessible and affordable drugs has been observed in most bacterial pathogens. The detection of multi drug resistant isolates may further limit therapeutic options. Timely microbiologic surveillance and assessment of antimicrobial resistance is important for dealing with pediatric infections.

Background: Ethiopia is among the high-burden countries of tuberculosis (TB) in the world Since mycobacterial culture and susceptibility testing are not routinely performed in Ethiopia, recent data on susceptibility patterns and the mycobacterial species cultured from sputum smear positive patients are limited., Objectives: The aim was to determine first line anti-TB drug susceptibility of Mycobacterium tuberculosis isolates obtained from consecutive newly diagnosed smear positive pulmonary TB patients in north west Ethiopia., Methodology: A retrospective cross sectional study was conducted using previously collected sputum samples (n=180) kept at the referral hospital of the University of Gondar at -20 degrees C. Sputum samples were cultured on Lowenstein Jensen (LJ) medium. Conventional Polymerase Chain Reaction (PCR) using RD4 primers to identify the M. tuberculosis complex was performed on cultured isolates. Ninety eight (84.4%) of the 116 isolates identified as M. tuberculosis were tested for their drug susceptibility pattern using the proportion method Clinical baseline data including body mass index, body temperature, clinical symptoms and erythrocyte sedimentation rate were obtained., Results: The culture retrieval rate of previously frozen sputum samples was 64.4% (116/180). All the isolated mycobacterial species (n=116) were confirmed as belonging to the M. tuberculosis complex by PCR. Of 98 isolates for which the drug susceptibility test was done, 15.3% (15/98) were found to be resistant to one or more antimycobacterial drugs, and resistance to isoniazid and streptomycin was most common with 8.2% (8/98) and 6.1% (6/98) respectively. TB patients co infected with HIV had increased erythrocyte sedimentation rate, higher age and lower sputum smear grade than HIV negative TB patients., Conclusions: No mycobacteria other than M. tuberculosis were detected in sputum smear positive TB-patients. Although no multi drug resistant strain was observed, relatively high rates of INH resistance were found in this region. Culture facilities are urgently needed in regional centers to increase diagnostic sensitivity and monitor developing trends of drug resistance in Ethiopia.

Background: Neonatal sepsis is one of the most common reasons for admission to neonatal units in developing countries. It is also a major cause of mortality in both developed and developing countries., Objectives: This study was undertaken to determine bacterial etiologies of neonatal and to assess their susceptibility pattern. An attempt has been also made to identify the possible maternal and neonatal risk factors responsible for neonatal septicemia., Methods: Blood samples were collected for culture from newborn babies (n=302, age: 0-28 days) with a clinical diagnosis of neonatal sepsis. The sample size was calculated by taking prevalence of culture proven neonatal sepsis in previous Ethiopian study. Antimicrobial susceptibility testing was performed for all blood culture isolates according to the criteria of the National Committee for Clinical Laboratory Standards by disk diffusion method., Results: Out of the 302 neonates, 55.0% were preterm and 60.0% had low birth weight. The most prevalent clinical features of sepsis were hypothermia (84.8%), respiratory distress (72.8%), failure to feed (71.5%) and lethargy (30.1%). Of the 302 sepsis cases investigated, 135 (44.7%) were positive for blood culture. The most common isolated organisms were Klebsiella spp. (39.2%) and Staphylococcus aureus (22.2%). Neonatal risk factors such as prematurity, low birth weight, abnormal WBC count (high and low) and I:T ratio > or = 0.2 were strongly associated with culture proven neonatal sepsis. No maternal risk factors were identified. Gram positive bacteria were susceptible to most antimicrobial agents tested. On the other hand gram-negative bacteria showed high-level resistance to ampicillin, cefiriaxone, cephalothin, chloramphenicol, and gentamicin. Multiple resistance (resistance to two or more drugs) was observed in 45.7% and 84.2% gram positive and gram negative bacteria respectively (p < 0.05)., Conclusion: Klebsiella spp. and S. aureus were the most common organisms causing neonatal sepsis. Prematurity, low birth weight, abnormal WBC counts and I:T ratio > or = 0.2 were strongly associated with blood culture proven neonatal sepsis. Ciprofloxacin was the most effective drug against the gram-positive and gram-negative bacteria. Routine bacterial surveillance and the study of their resistance patterns must be an essential component of neonatal care. A knowledge of these patterns is essential when local polices on the uses of antibiotics are being devised.

Background: Nosocomial infections are widespread and are important contributors to morbidity and mortality. Prevalence studies are useful in revealing the prevalence of hospital-acquired infections., Objectives: To determine the bacterial pathogens associated with hospital acquired surgical site infection (SSI) and urinary tract infection (UTI) and assess their susceptibility patterns in patients admitted in Mekelle Hospital in Ethiopia., Methods: From November 2005 to April 2006 a prospective cross sectional study was conducted at Mekelle Hospital, Tigray region, North Ethiopia. The study population comprised of a total of 246 informed and consented adult patients hospitalized for surgical (n = 212) and Gynecology and Obstetrics cases (n = 34)., Results: Of the 246 admitted patients, 68 (27.6%) developed nosocomial infections (SSI and/or nosocomial UTI) based on the clinical evaluations, and positive wound and urine culture results. Gram negative bacteria were predominantly isolated with a rate of 18/34 (53%) and 34/41 (83%) from SSI and UTI respectively. Most of the isolates from UTI have high rates of resistance (> 80%) to the commonly used antibiotics such as ampicillin, amoxicillin, chloramphenicol, gentamicin, streptomycin, and trimethoprim-sulphamethoxazole; and in isolates from SSI to amoxicillin and trimethoprim-sulphamethoxazole., Conclusions: The results showed that the prevalence of HAIs (SSI and nosocomial UTI) in the Hospital is high when compared to previous Ethiopian and other studies despite the use of prophylactic antibiotics. The pathogens causing SSI and UT7 are often resistant to commonly used antimicrobials. The findings underscore the need for an infection control system and surveillance program in the hospital and to monitor antimicrobial resistance pattern for the use of prophylactic and therapeutic antibiotics.

Background: Smear negative pulmonary tuberculosis is an increasing clinical and epidemiological problem, particularly in areas that are affected by the dual tuberculosis/Human immunodeficiency Virus infections., Objective: This study was initiated to investigate the value of clinical parameters, chest x-ray findings and culture in the diagnosis of smear negative pulmonary tuberculosis., Design: A cross sectional study was conducted among suspected pulmonary tuberculosis patients visiting St. Peter Tuberculosis Specialized Hospital, Addis Ababa, Ethiopia between November 15, 2004 and October 30, 2005., Methods: A total of 297 informed and consented patients with suspected pulmonary tuberculosis were screened for acid fact bacilli by direct smear microscopy. All smear negative pooled sputum samples were further processed for culture using conventional Lowenstein-Jensen solid medium and automated BACTEC MGIT 960 system liquid medium at the Ethiopian Health and Nutrition Research Institute., Results: 247/297 (83.2%) patents with suspected pulmonary tuberculosis have had a negative smear results for acid fast bacilli. Abnormal chest x-ray findings were observed in 196 (79.4%) patients. 43/247 (17.4%) patients whose smears were negative for acid fast bacilli found to be positive for mycobacterial culture. The Mycobacterium species identified were M. tuberculosis (n = 40) (93%) and non-tuberculous mycobacteria (n = 3) (7%). Significant difference was not demonstrated statistically between BACTEC MGIT 960 and Lowenstein-Jensen medium in terms of mycobacterial recovery rate (p > 0.05)., Conclusions: The present study showed 82.6% smear negative pulmonary tuberculosis cases were still etiologically unexplained by culture. Therefore, there is a need to develop a scheme to determine the most cost-effective approaches for the diagnosis of smear negative pulmonary tuberculosis in the Ethiopian setting, such as improving the screening method patients with tuberculosis and other chronic pulmonary diseases, chest-x-ray readings and interpretation, specimen collection and processing, smear microscopy, culture and applying laboratory quality control schemes in parallel.

Background: Urinary tract infection (UTI) is a common complication of pregnancy. It may be symptomatic or asymptomatic., Objectives: The aim of this cross sectional study was to identify bacterial agents and their antibiotic susceptibility pattern isolated from pregnant women with UTI attending antenatal clinic of Tikur Anbessa Specialized Hospital (TASH)., Methods: Four hundred and fourteen pregnant women with asymptomatic UTI (n = 369) and symptomatic UTI (n = 45) were investigated for urinary tract infection from January to March 2005., Results: The age range of both groups was 18 to 44 years. Bacteriological screening of mid-stream urine specimens revealed that 39/369 (10.6%) and 9/45 (20%) had significant bacteriuria in asymptomatic and symptomatic group, respectively (p = 0.10). The overall prevalence of urinary tract infection was 48/414 (11.6%). The bacterial pathogens isolated were predominantly E. coil (44%), followed by S. aureus (20%), coagulase-negative staphylococci (16%), and K. pneumoniae (8%). Others found in small in number included P. mirabilis, P. aeruginosa, Enterococcus spp. and non-Group A-beta hemolytic Streptococcus, this accounted 2% for each. The gram positive and negative bacteria accounted 40% and 60% respectively. The susceptibility pattern for gram-negative bacteria showed that most of the isolates (> 65% of the strains) were sensitive to amoxicillin-clavulanic acid (70%), chloramphenicol (83.3%), gentamicin (93.3%), kanamycin (93.3%), nitrofurantoin (87.7%) and trimethoprim-sulphamethoxazole (73.3%). Among the gram-positives, more than 60% of the isolates were sensitive to amoxicillin-clavulanic acid (100%), cephalothin (95%), chloramphenicol (70%), erythromycin (80%), gentamicin (85%), methicillin (83.3%), nitrofurantoin (100%) and trimethoprim-sulphamethoxazole (65%). Generally, amoxicillin-clavulanic acid, chloramphenicol, gentamicin, nitrofurantoin and trimethoprim-sulphamethoxazole were effective at least in 70% of the isolates. Multiple drug resistance (resistance two or more drugs) was observed in 74% of the isolates., Conclusion: Significant bacteriuria was observed in both asymptomatic and symptomatic pregnant women. Periodic studies are recommended to confirm the findings of this study and also monitor any changes in the susceptibility patterns of uropathogens causing urinary tract infection in the pregnant women.

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.

Presently, there is no published information on the antimicrobial susceptibility pattern of H. pylori strains in Ethiopia to guide the choice of drug for therapy. Therefore, it is becoming clinically relevant to test the in vitro susceptibility of H. pylori clinical isolates prior to treating patients. Susceptibility testing was performed on 50 clinical H. pylori isolates obtained from adult dyspeptic patients referred to the gastrointestinal (GI) Clinic of Tikur Anbassa University Hospital. Five antibiotics were evaluated, by using the Episolmeter test (E-test). The antibiogram of 50 H. pylori clinical isolates showed that all strains were sensitive to clarithromycin, erythromycin and tetracycline, while 38/50 (76%) and 3/50 (6%) of the strains were resistant to metronidazole and amoxicillin, respectively. Infection by metronidazole or amoxicillin resistant H. pylori is an important factor leading to treatment failure. Testing of all H. pylori clinical isolates to metronidazole and amoxicillin is recommended. If it is not possible to perform susceptibility tests on each clinical isolate, a program to survey the prevalence of resistance should be implemented in a given area or population. When treatment of H. pylori infection is indicated in dyspeptic patients, the potential availability, simplicity of use, safety and low cost of the antimicrobial agents have to be taken into account.