Background Tuberculosis, caused by bacteria in the Mycobacterium tuberculosis complex (MTBC), is a major global public health burden. Strain-specific genomic diversity in the known lineages of MTBC is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Fast and accurate tracking of MTBC strains is therefore crucial for infection control, and our previous work developed a 62-single nucleotide polymorphism (SNP) barcode to inform on the phylogenetic identity of 7 human lineages and 64 sub-lineages. Methods To update this barcode, we analysed whole genome sequencing data from 35,298 MTBC isolates (~ 1 million SNPs) covering 9 main lineages and 3 similar animal-related species (M. tuberculosis var. bovis, M. tuberculosis var. caprae and M. tuberculosis var. orygis). The data was partitioned into training (N = 17,903, 50.7%) and test (N = 17,395, 49.3%) sets and were analysed using an integrated phylogenetic tree and population differentiation (FST) statistical approach. Results By constructing a phylogenetic tree on the training MTBC isolates, we characterised 90 lineages or sub-lineages or species, of which 30 are new, and identified 421 robust barcoding mutations, of which a minimal set of 90 was selected that included 20 markers from the 62-SNP barcode. The barcoding SNPs (90 and 421) discriminated perfectly the 86 MTBC isolate (sub-)lineages in the test set and could accurately reconstruct the clades across the combined 35k samples. Conclusions The validated 90 SNPs can be used for the rapid diagnosis and tracking of MTBC strains to assist public health surveillance and control. To facilitate this, the SNP markers have now been incorporated into the TB-Profiler informatics platform (https://github.com/jodyphelan/TBProfiler).

We investigated the gastrointestinal colonization rate and antibiotic resistance patterns of Extended-Spectrum Beta-Lactamase (ESBL)- producing Escherichia coli and Klebsiella pneumoniae in hospitalized patients admitted at Ethiopia’s largest tertiary hospital. Fecal samples/swabs from 267 patients were cultured on chrome agar. ESBL. Bacterial species identification, verification of ESBL production and antibiotic susceptibility testing were done using Vitek 2 system (bioMérieux, France). Phenotype characterization of ESBL-E.coli and ESBL- K.pneumoniae was done using Neo-Sensitabs™. ESBL positivity rate was much higher in K. pneumoniae (76%) than E. coli (45%). The overall gastrointestinal colonization rate of ESBL producing Enterobacteriaceae (ESBL-E) in hospitalized patients was 52% (95%CI; 46%–58%) of which, ESBL-E. coli and K.pneumoniae accounted for 68% and 32% respectively. Fecal ESBL-E carriage rate in neonates, children and adults was 74%, 59% and 46% respectively. Gastrointestinal colonization rate of ESBL-E.coli in neonates, children and adults was 11%, 42% and 42% respectively. Of all E. coli strains isolated from adults, children and neonates, 44%, 49% and 22% were ESBL positive (p = 0.28). The prevalence of ESBL-K.pneumoniae carriage in neonates, children and adults was 68%, 22% and 7% respectively. All K. pneumoniae isolated from neonates (100%) and 88% of K. pneumoniae isolated from children were ESBL positive, but only 50% of K.pneumoniae isolated from adults were ESBL positive (p = 0.001). Thirteen patients (5%) were carriers of both ESBL-E.coli and ESBL-KP. The overall carrier rate of ESBL producing isolates resistant to carbapenem was 2% (5/267), all detected in children; three with E.coli HL cephalosporinase (AmpC), resistant to ertapenem and two with K. pneumoniae Carbapenemase (KPC) resistant to meropenem, ertapenem and impenem. We report a high gastrointestinal colonization rate with ESBL-E and the emergence of carbapenems-resistant K. pneumoniae in Ethiopia. Urgent implementation of infection control measures, and surveillance are urgently needed to limit the spread within healthcare facilities and further to the community.

BackgroundBacterial vaginosis is one of the most common genital tract infections among reproductive age group. The prevalence of bacterial vaginosis varies from country to country even in the same country it varies among populations of interest. Different social and sexual factors can contribute to the development of bacterial vaginosis. The aim of this study was to determine the prevalence of bacterial vaginosis and to identify the possible risk factors associated among pregnant women attending antenatal care in Tikur Anbessa University Hospital, Addis Ababa, Ethiopia.MethodsRandomly selected 57 symptomatic and 195 asymptomatic pregnant women aged between 18 and 40 years visiting obstetric and gynecological clinic from November 2011 to April 2012 screenedusing Gram stain Nugent scoring system. Statistical analysis like univariate analysis to calculate frequencies and proportions, bivariate analysis to see association of selected exposure variables with the outcome variable, and multivariate analysis to check the association of possible factors with bacterial vaginosis by adjusting potential confounding factors was calculated using SPSS (Version 16.0).ResultsThe prevalence of bacterial vaginosis is 19.4% using Gram stain Nugent scoring system. In addition, prevalence of bacterial vaginosis is 31.6% and 15.9% among symptomatic and asymptomatic pregnant women respectively. A high percentage of bacterial vaginosis positive pregnant women were asymptomatic (63.3%). 36.7% bacterial vaginosis positive pregnant women reported abnormal vaginal discharge with or without unpleasant smell. Multiple lifetime sexual partner (OR: 8.6; 95% CI: 2.5, 29) and previous history of spontaneous abortion (OR: 5.9; 95% CI: 1.5, 23) had remained significantly associated with prevalence of bacterial vaginosis.ConclusionThe prevalence of bacterial vaginosis is higher among asymptomatic pregnant women and associated with the factors previous history of multiple lifetime sexual partner and spontaneous abortion.

BackgroundCryptococcal meningitis is a major cause of HIV/AIDS-related deaths in Africa. Cryptococcosis is a neglected killer. However, meningitis can be prevented by early cryptococcal antigen (CrAg) screening and preemptive antifungal treatment during a prolonged period of detectable, subclinical infection. We determined the prevalence of cryptococcal antigenemia in comparison to CD4 count and clinical symptoms.MethodsWe surveyed 254 consenting HIV-infected participants to obtain demographic information and clinical history. Serum CrAg was measured by latex agglutination at two sites in the Oromia region of Ethiopia among all persons receiving a CD4 count.ResultsOf the 254 participants, 127(50.0%) were ART-naïve, 121(47.6%) were ART-experienced, and 6(2.4%) were ART-defaulters. The prevalence of cryptococcal antigenemia was 10.2% overall being 14.2% among ART-naive, 4.1% among ART-experienced, and 50% (3/6) among ART-defaulters, irrespective of CD4 count. Cryptococcal antigenemia was more frequently detected from ART-naïve patients (p = 0.012) and ART-defaulters (p = 0.001) compared with ART-experienced. Serum CrAg positivity was 20.9% in persons with CD4≤150 cells/µL, 12.2% in 151–200 cells/µL, 5.8% among 201–350 CD4/µL, and none above 350 cells/µL. Potential meningitis symptoms were common in the outpatient cohort irrespective of CrAg-status, with only fever and altered mental status statistically more common in CrAg-positive compared to CrAg-negative persons (P<0.05), yet no symptom had a positive predictive value >33%.ConclusionWe report a 20.9% cryptococcal antigenemia prevalence among those with CD4+ T cells count ≤150 cells/µL, irrespective of ART status, with even higher CrAg prevalence in ART-naïves and ART-defaulters. These groups are target populations for CrAg screening at entry into HIV care.

Early detection of multidrug-resistant Mycobacterium tuberculosis (MDR-TB) is of primary importance for both patient management and infection control. Optimal methods for identifying drug-resistant Mycobacterium tuberculosis in a timely and affordable way in resource-limited settings are not yet available. This study prospectively evaluated a low-technology but rapid drug susceptibility testing method, the microscopic observation drug susceptibility assay (MODS), in the concurrent detection of M. tuberculosis and its susceptibilities to isoniazid and rifampin (two drugs defining multidrug-resistant M. tuberculosis) directly from sputum specimens. Sputum samples were collected from 262 smear-positive TB patients in Addis Ababa, Ethiopia. To undertake MODS, 100 l of decontaminated samples was inoculated into a 24-well plate containing 1 ml of 7H9 broth with and without appropriate drugs. The assay uses an inverted-light microscope to detect characteristic mycobacterial growth in liquid culture. Of 262 smear-positive patients, MODS detected 254 (96.9%) and culture in Löwenstein-Jensen medium detected 247 (94.3%) (P ‫؍‬ 0.016). For the 247 cultures, the sensitivity, specificity, and accuracy of MODS for detecting MDR-TB were 92.0, 99.5, and 98.8%, respectively, using the method of proportion as a reference (concordance, 98.8%; kappa value, 0.932). Results for MODS were obtained in a median time of 9 days. MODS is an optimal alternative method for identifying MDR-TB in a timely and affordable way in resource-limited settings.Tuberculosis (TB), once in decline, is now experiencing a resurgence fueled in part by the human immunodeficiency virus (HIV)/AIDS pandemic. Multidrug-resistant Mycobacterium tuberculosis (MDR-TB), defined as resistant to at least isoniazid (INH) and rifampin (RIF), is complicating TB control efforts in several low-and middle-income countries. A critical mass of resistance seen in high-burden countries has great potential not only to halt the progress of TB control but also to reverse it (34). Implementation of additional strategies, such as reducing transmission by detecting cases earlier and improving infection control in settings with shared-air spaces, is urgently needed (29). Optimal methods for identifying drugresistant M. tuberculosis in a timely and affordable way in resource-limited settings are not yet available. The currently available drug susceptibility testing (DST) methods with solid media are inexpensive but slow and laborious and cannot meet such a demand. Liquid automated commercial systems (13,14,20,28), such as the BACTEC MGIT 960 (Becton Dickinson, Sparks, MD), are rapid but require heavy, expensive equipment, have high running costs, and are technically complex. Molecular genetic methods (16,17,22,29) are fast but too expensive and require well-trained manpower in order to be used in resource-poor settings. In addition, not all mutations conferring resistance to anti-TB drugs are known. Several lowtechnology methods (1,2,8,10,26,30,32) are also available. Most are indirect D...

The prevalence of dermatophytosis and the spectrum of dermatophyte species were determined in children attending two schools in Addis Ababa, Ethiopia. Demographic and clinico-dermatological data were collected. Specimens were taken for microscopy and culture from all suspected lesions. Dermatophyte species were identified by morphology and biochemical tests, supplemented by sequencing of the rDNA ITS 2 region in selected isolates. From the Biruh Tesfa Elementary School (BTES) 824 students, and from Mount Olive Academy (MOA) all 124 students, were included. In BTES 513 (62.3%) students were clinically diagnosed with dermatophytosis, 463 (90.3 %) of them with tinea capitis. In 200 consecutive samples from BTES, and in 66 from MOA, 75 and 62%, respectively, contained fungal elements at microscopy. From BTES, 163/496 (33%) samples were culture-positive, of which 149 (91.4%) grew with dark purple colonies identified as Trichophyton violaceum, while 244 (49.4%) samples were contaminated. A few strains grew slowly developing white to cream colonies, two were identified as T. verrucosum, and 12 as white T. violaceum. From MOA 44 (66.7%) of samples were culture-positive, 38 (87%) were identified as T. violaceum, and one (2.3%) as T. verrucosum, while 33% showed no growth. Four white isolates of T.violaceum were confirmed by DNA-sequencing. Dermatophytosis was thus diagnosed in 55-62% of children screened at two schools of different socioeconomic standards in the Ethiopian capital. Trichophyton violaceum constituted 87-90% of all isolates. White variants of T. violaceum were diagnosed in 16 cases.

Ethiopia reports the third highest number of extrapulmonary TB cases globally, most of which are lymph node TB (TBLN). We investigated the performance of the available diagnostic tests for TBLN. Fine needle aspirate (FNA) and excision biopsy samples from affected lymph nodes were collected from 150 consenting patients with suspected TBLN visiting regional hospitals in Ethiopia. The sensitivity, specificity, positive (PPV) and negative predictive value (NPV) of histopathology against culture as reference was 92%, 88%, 97% and 77% and of FNA cytology (FNAC) 76%, 88%, 100% and 55%, respectively. Naked eye examination of FNA had 67% sensitivity and 64% specificity. HIV coinfection did not diminish the performance of macroscopic examination, Ziehl-Neelsen stain, histology or cytology examinations. When any positive result in ZN, histopathology or culture was considered confirmatory, clinical diagnosis could be confirmed in 85% of the patients, suggesting that TBLN is over-diagnosed in up to 15% of cases. With combined criteria as reference standard, the sensitivity, specificity, PPV and NPV of FNAC was 72%, 100%, 100% and 55%, respectively. FNAC is a practical tool that can improve the diagnosis of TBLN in high-burden settings. Over-diagnosis alone cannot explain the high burden of LNTB in Ethiopia.

BackgroundUrinary tract infection (UTI) is a common and important clinical problem in pediatrics. Recurrent UTIs may lead to renal scarring, hypertension, and end-stage renal dysfunction later in life. The objective of the study was to determine bacterial profile and antimicrobial susceptibility pattern of urinary tract infections (UTIs) among children attending Felege Hiwot Referral Hospital (FHRH).MethodsA cross-sectional study was conducted from February 2013 to May 2013 among children 5–15 years of age with symptoms of UTI. Samples were processed for culture and identification. Antimicrobial susceptibility was done for positive urine cultures by the Kirby-Bauer’s disk diffusion method based on standards of the Clinical Laboratory Standard Institute (CLSI). Data were entered into Epi-data version 3.2.1 and exported to the Statistical Package for the Social Science (SPSS) version 20 statistical software. Fisher’s exact test and binary logistic regression test results were used.ResultsA total of 259 urine samples were collected from children with UTI. The result revealed 41 (15.8%) samples had significant bacteriuria, among which the most prevalent pathogen was E. coli 14 (34.1%) followed by Pseudomonas species. Gram-negative bacteria showed high level of sensitivity to ciprofloxacin (70), norfloxacin (63.4%) and ceftriaxone (60%), whereas the level of resistance was high to ampicillin (80%) and nitrofurantoin (70%). Gram-positive isolates showed high sensitivity to ciprofloxacin (77.8%), penicillin (72.8%) and erythromycin (72.7%). Multiple drug resistance (MDR) for Gram-positive and Gram-negative bacteria was 100% and 83.1%, respectively.ConclusionE. coli is the predominant bacteria isolated in the present study. The results showed that the prevalence of resistance to at least one antibiotic to commonly prescribed antimicrobials was high. Hence, the guidelines for empiric treatment of UTI should be re-evaluated periodically based on local studies.