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.

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...

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.