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Background: The study was conducted from September 2020 to June 2021to assess the bacteriological quality of raw bulkmilkfrom urban and rural local market sites in Borana pastoral area of Oromia Regional State, Southern Ethiopia. A total of 78 milk samples were collected and analyzed for bacterial load using standard plate count and coliform count techniques and isolation of pathogenic bacteria was conducted. Results: The total mean aerobic bacterial counts of raw bulk milk samples of camel, cow and goat were 8.51 log cfu/ml, 8.73 log cfu/ml and 8.54log cfu/ml respectively. Regarding the location of milk market sites the mean total aerobic bacterial count was 8.72 log cfu/ml and 8.49 log cfu/mlin urban and rural milk market sites respectively. The total mean coliform counts of raw bulk milk samples of camel, cow and goat were6.51log cfu/ml, 6.55 log cfu/ml and 6.47 log cfu/ml respectively. Regarding the location of milk market sites the total mean coliform counts was 6.63 log cfu/ml and 6.40log cfu/ml from urban and rural milk market sites respectively.Comparing the mean differences of the total mean aerobic and coliform bacterial counts, there was no significant mean differences (p>0.05) among the animal milk samples. However, there was significant mean differences (pConclusions: Different bacterial species were isolated from camel, cow and goat raw milk sample from the urban and rural milkmarket sites. The major bacterial isolates were Staphylococcus (both pathogenic and non-pathogenic), Escherichia coli and Bacillus species. Generally the unhygienic milk handling resulted in poor milk quality in the pastoral area. Therefore there is a need of training for persons at the various milk market siteson strict hygienic measures to improve the bacteriological safety of cow milk.

Summary Background Haematopoietic stem cells expressing the CD34 surface marker have been posited as a niche for Mycobacterium tuberculosis complex bacilli during latent tuberculosis infection. Our aim was to determine whether M tuberculosis complex DNA is detectable in CD34-positive peripheral blood mononuclear cells (PBMCs) isolated from asymptomatic adults living in a setting with a high tuberculosis burden. Methods We did a cross-sectional study in Ethiopia between Nov 22, 2017, and Jan 10, 2019. Digital PCR (dPCR) was used to determine whether M tuberculosis complex DNA was detectable in PBMCs isolated from 100 mL blood taken from asymptomatic adults with HIV infection or a history of recent household or occupational exposure to an index case of human or bovine tuberculosis. Participants were recruited from HIV clinics, tuberculosis clinics, and cattle farms in and around Addis Ababa. A nested prospective study was done in a subset of HIV-infected individuals to evaluate whether administration of isoniazid preventive therapy was effective in clearing M tuberculosis complex DNA from PBMCs. Follow-up was done between July 20, 2018, and Feb 13, 2019. QuantiFERON-TB Gold assays were also done on all baseline and follow-up samples. Findings Valid dPCR data (ie, droplet counts >10 000 per well) were available for paired CD34-positive and CD34-negative PBMC fractions from 197 (70%) of 284 participants who contributed data to cross-sectional analyses. M tuberculosis complex DNA was detected in PBMCs of 156 of 197 participants with valid dPCR data (79%, 95% CI 74–85). It was more commonly present in CD34-positive than in CD34-negative fractions (154 [73%] of 197 vs 46 [23%] of 197; p

There is paucity of information in the epidemiology and pathology of tuberculosis in swine though the endemic occurrence of bovine tuberculosis was elucidated in Ethiopia. A cross-sectional study was employed to investigate the epidemiology of Mycobacterium tuberculosis complex and Mycobacterium avium complex in swine. The study was conducted from September 2016 to December 2017 using single intradermal comparative tuberculin test, gross pathology and histopathology. Tuberculin test was carried out in farmed swine of central Ethiopia while the necropsy at Addis Ababa Abattoirs Enterprise, Ethiopia. Of the total 329 heads of swine tuberculin tested by bovine purified protein derivative antigen, an animal level prevalence of 3% (95% CI: 2-6) and a herd level prevalence of 11% (95% CI: 1-49) were observed at a cut-off value of >2mm. Multivariable logistic regression analysis revealed the protective exposure effect of body condition to tuberculin test positivity in swine (Adjusted OR: 0.06; 95% CI: 0.0-1.1; P: 0.055). Swine were predominantly in close proximity with dairy cattle which is an important risk factor for the transmission of bovine tuberculosis from cattle to swine. Necropsy study of tuberculosis-like lesions in 640 heads of swine revealed an overall lesion prevalence of 4.1 % (95 CI: 2.8-6.0). In conclusion, the present study demonstrated the occurrence of swine tuberculosis in low prevalence in farmed swine and swine slaughtered atAddis Ababa Abattoirs Enterprise in central Ethiopia. Further in-depth study covering larger sample size and wider areas is warranted so as to identify the prevalent species and their zoonotic importance. Keywords: Abattoir; Epidemiology; Ethiopia; Pathology; Swine; Tuberculosis

Brucellosis is a zoonotic disease with economic and public health significance in developing countries that rely on livestock production including Ethiopia. This study intended to establish the seroprevalence and associated risk factors of ovine brucellosis.A cross-sectional study was carried out on seroepidemiology of ovine brucellosis from January 2017 to June 2020 G.C in five districts of South Omo zone, Southern Ethiopia. A total of 1536 sera samples were collected from sheep and serially tested using modified Rose Bengal plate test, competitive enzyme-linked immunosorbent assay, and complement fixation test to detect antibodies against natural infection byThe study discovered an overall 5.40% (95% CI: 6.34, 14.25) and 39.74% (95% CI: 6.50, 6.97) seroprevalence of ovine brucellosis at individual and flock level, respectively, by a confirmatory test. Age groups, sex, flock size, district, history of abortion, and body condition were significantly associated risk factors withTo conclude, the prevalence of ovine brucellosis in the South Omo Zone was relatively high which needs integrated intervention approaches in place to curb the spread of the disease.

Tuberculosis (TB) is a leading cause of morbidity and mortality in Ethiopia. Investigation of theA cross-sectional study design was used to recruit 450 smear positive pulmonary TB (PTB) cases from the Oromia region between September 2017 and August 2018. Mycobacteria were isolated from sputum samples on the Lowenstein Jensen (LJ) medium. Molecular identification of the isolates was performed by spoligotyping. The results of spoligotyping were transferred into a query box in the SITVIT2 database and Run TB-Lineage in the TB Insight website for the identification of spoligo international type (SIT) number and linages of the isolates, respectively. Statistical Product and Service Solutions (SPSS) 20 was applied for statistical analysis.Three hundred and fifteen isolates were grouped under 181 different spoligotype patterns. The most dominantly isolated spoligotype pattern was SIT149 and it consisted of 23 isolates. The majority of the isolates were grouped under Euro-American (EA), East-African-Indian (EAI), and Indo-Oceanic (IO) lineages. These lineages consisted of 79.4, 9.8, and 9.8% of the isolates, respectively. One hundred and sixty-five of the isolates were classified under 31 clustered spoligotypes whereas the remaining 150 were singleton types. Furthermore, 91.1% of the total isolates were classified as orphan types. Clustering of spoligotypes was associated (SIT149 and EA lineage were predominantly isolated from the Oromia region substantiating the findings of the similar studies conducted in other regions of Ethiopia. The observation of significant number of singleton and orphan spoligotypes warrants for additional genetic typing of the isolates using method(s) with a better discriminatory power than spoligotyping.

Equine histoplasmosis commonly known as epizootic lymphangitis (EL) is a neglected granulomatous disease of equine that is endemic to Ethiopia. It is caused by Histoplasma capsulatum variety farciminosum, a dimorphic fungus that is closely related to H. capsulatum variety capsulatum. The objective of this study was to undertake a phylogenetic analysis of H. capsulatum isolated from EL cases of horses in central Ethiopia and evaluate their relationship with H. capsulatum isolates in other countries and/or clades using the internal transcribed spacer (ITS) region of rRNA genes. Clinical and mycological examinations, DNA extraction, polymerase chain reaction (PCR), Sanger sequencing, and phylogenetic analysis were used for undertaking this study. Additionally, sequence data of Histoplasma isolates were retrieved from GenBank and included for a comprehensive phylogenetic analysis. A total of 390 horses were screened for EL and 97 were positive clinically while H. capsulatum was isolated from 60 horses and further confirmed with PCR, of which 54 were sequenced. BLAST analysis of these 54 isolates identified 29 H. capsulatum isolates and 14 isolates from other fungal genera while the remaining 11 samples were deemed insufficient for further downstream analysis. The phylogenetic analysis identified five clades, namely, African, Eurasian, North American 1 and 2, and Latin American A and B. The Ethiopian isolates were closely aggregated with isolates of the Latin American A and Eurasian clades, whereas being distantly related to isolates from North American 1 and 2 clades as well as Latin American B clade. This study highlights the possible origins and transmission routes of Histoplasmosis in Ethiopia.

Different breeds of cattle were observed to have a variable degree of susceptibility to bovine tuberculosis (bTB). The screening of bTB was conducted on 720 dairy cattle consisting of three breeds using the single intradermal cervical comparative tuberculin (SICCT) test. Besides this, 43 SICCT test-positive cattle were used to compare the severity of the pathology of bTB among the three breeds and to identify the causative mycobacteria using spoligotyping. The overall SICCT test positivity was 17.92% (129/720) by pooling all animals in the three farms. There was a significant difference in SICCT test positivity among the three breeds (χ2 = 71.06; p < 0.001); the highest (25.34%) was recorded in the crossbreed followed by the Boran breed (10.08%), while the least (3.14%) was recorded in the Jersey breed. On other hand, the highest median pathology score (10.0, interquartile range, IQR = 6.0–17.0) was recorded in Boran followed by cross (5.0, IQR = 3.5–7.5), while the least (3.0, IQR = 2.25–3.0) was recorded in Jersey. Thus, the difference in the median pathology scores was significant [Kruskal Wallis χ(2)2 = 18.78, p < 0.001] among the three breeds. Furthermore, multivariate analysis using ordinal logistic regression by considering age, sex, breed, reproductive status, and location of the farms also showed a significant [χ(2)2 = 11.97, p < 0.01] difference in pathology scores among the three breeds of cattle. Even at a single-herd level at Holeta, the difference in severity of pathology between the Boran and crossbreeds was significant (U = 33.5; p < 0.01). Culture positivity was 39% in 108 suspicious tissues. Fourteen Mycobacterium bovis (M. bovis) and two Mycobacterium tuberculosis (M. tuberculosis) were isolated from the lesions. All the 14 M. bovis isolates belonged to SB0912, while the two M. tuberculosis belonged to SIT54. In conclusion, although the frequency of the SICCT test positivity was high in the crossbreed, a more severe pathology was observed on the Boran (zebu) breed. In addition M. tuberculosis was isolated from TB lesions of dairy cattle, demonstrating the role of M. tuberculosis in causing TB in cattle.

Bovine tuberculosis (bTB) challenges intensive dairy production in Ethiopia and implementation of the test and slaughter control strategy is not economically acceptable in the country. Vaccination of cattle with Bacillus Calmette-Guerin (BCG) could be an important adjunct to control, which would require a diagnostic test to differentiate Mycobacterium bovis (M. bovis)-infected and BCG-vaccinated animals (DIVA role). This study describes an evaluation of a DIVA skin test (DST) that is based on a cocktail (DSTc) or fusion (DSTf) of specific (ESAT-6, CFP-10 and Rv3615c) M. bovis proteins in Zebu-Holstein-Friesians crossbred cattle in Ethiopia. The study animals used were 74 calves (35 BCG vaccinated and 39 unvaccinated) aged less than 3 weeks at the start of experiment and 68 naturally infected 'TB reactor' cows. Six weeks after vaccination, the 74 calves were tested with the DSTc and the single intradermal cervical comparative tuberculin (SICCT) test. The TB reactor cows were tested with the DSTc and the SICCT test. Reactions to the DSTc were not observed in BCG-vaccinated and unvaccinated calves, while SICCT test reactions were detected in vaccinated calves. DSTc reactions were detected in 95.6% of the TB reactor cows and single intradermal tuberculin positive reactions were found in 98.2% (95% confidence interval, CI, 92.1-100%). The sensitivity of the DSTc was 95.6% (95% CI, 87.6-99.1%), and significantly (p

Differential diagnosis of tuberculosis (TB) and latent TB infection (LTBI) remains a public health priority in high TB burden countries. Pulmonary TB is diagnosed by sputum smear microscopy, chest X-rays, and PCR tests for distinct Mycobacterium tuberculosis (Mtb) genes. Clinical tests to diagnose LTBI rely on immune cell stimulation in blood plasma with TB-specific antigens followed by measurements of interferon-γ concentrations. The latter is an important cytokine for cellular immune responses against Mtb in infected lung tissues. Sputum smear microscopy and chest X-rays are not sufficiently sensitive while both PCR and interferon-γ release assays are expensive. Alternative biomarkers for the development of diagnostic tests to discern TB disease states are desirable. This study’s objective was to discover sputum diagnostic biomarker candidates from the analysis of samples from 161 human subjects including TB patients, individuals with LTBI, negative community controls (NCC) from the province South Omo, a pastoral region in Ethiopia. We analyzed 16S rRNA gene-based bacterial taxonomies and proteomic profiles. The sputum microbiota did not reveal statistically significant differences in α-diversity comparing the cohorts. The genus Mycobacterium, representing Mtb, was only identified for the TB group which also featured reduced abundance of the genus Rothia in comparison with the LTBI and NCC groups. Rothia is a respiratory tract commensal and may be sensitive to the inflammatory milieu generated by infection with Mtb. Proteomic data supported innate immune responses against the pathogen in subjects with pulmonary TB. Ferritin, an iron storage protein released by damaged host cells, was markedly increased in abundance in TB sputum compared to the LTBI and NCC groups, along with the α-1-acid glycoproteins ORM1 and ORM2. These proteins are acute phase reactants and inhibit excessive neutrophil activation. Proteomic data highlight the effector roles of neutrophils in the anti-Mtb response which was not observed for LTBI cases. Less abundant in the sputum of the LTBI group, compared to the NCC group, were two immunomodulatory proteins, mitochondrial TSPO and the extracellular ribonuclease T2. If validated, these proteins are of interest as new biomarkers for diagnosis of LTBI.

Background. Tuberculosis (TB) has been an important public health concern in Ethiopia, particularly at areas of human-animal intersection. However, limited epidemiological information is available in this respect in the country. Therefore, the present study was conducted to investigate the transmission of TB at human-cattle interface, associated risk factors and public awareness about the disease at South Gondar Zone, northwest Ethiopia. Methods. A cross sectional study was conducted between March 2015 and April 2018 on 186 farmers and 476 cattle in South Gondar Zone, northwest Ethiopia. Bacteriological examination, region of difference (RD) 9-based polymerase chain reaction (PCR), single intradermal comparative tuberculin test (SICTT), and questionnaire were used for undertaking this study. Results. Culture positivity in farmers was 59.7% (111/186) and all the culture positive isolates were M. tuberculosis. About 68% (74/111) of culture positive respondents did not know about the transmission of TB from cattle to human or vice versa. The animal and herd prevalence of bovine TB were 1.5% (7/476) and 7.4% (7/95), respectively. Although the result was not statistically significant, the odds of bovine TB in cattle owned by TB positive households was slightly higher than those owned by TB free households (adjusted odds ratio, AOR = 1.39; 95% CI: 0.31–7.10; p=0.76). Conclusion. Although SIDCTT reactivity was slightly higher in cattle owned by TB positive households, all the human isolates were M. tuberculosis and no M. bovis was isolated from farmers, which could be due to the low prevalence of bovine TB in the area.

Background Bovine tuberculosis (bTB) is prevalent in dairy cattle in Ethiopia. Currently used diagnostic tools such as the single intradermal comparative tuberculin test (SICTT) are time consuming and labor intensive. A rapid, easy-to-use and cost-effective diagnostic test would greatly contribute to the control of bTB in developing countries like Ethiopia. In the present study, two point-of-care diagnostic tests were evaluated for the detection of bTB: LIONEX® Animal TB Rapid test, a membrane-based test for the detection of antibodies to Mycobacterium bovis in blood and ALERE® Determine TB Lipoarabinomannan (LAM) Ag, an immunoassay for the detection of lipoarabinomannan (LAM) antigen (Ag) of mycobacteria in urine. A combination of the SICTT and gamma interferon (IFN-γ) test was used as the gold standard for the validation of these point-of-care tests, as it was not feasible to slaughter the study animals to carry out the historical gold standard of mycobacterial culture. A total of 175 heads of cattle having three different bTB infection categories (positive SICTT, negative SICTT, and unknown SICTT status) were used for this study. Result The sensitivity and specificity of TB LAM Ag were 72.2% (95% CI = 62.2, 80.4) and 98.8% (95% CI = 93.6, 99.7), respectively, while the sensitivity and specificity of the LIONEX Animal TB rapid test assay were 54% (95% CI = 44.1 64.3) and 98.8% (95% CI = 93.6, 99.7) respectively. The agreement between TB LAM Ag and SICTT was higher (κ = 0.85; 95% CI = 0.65–0.94) than between TB LAM Ag and IFN-γ (κ = 0.67; 95% CI = 0.52–0.81). The agreement between LIONEX Animals TB Rapid blood test and SICTT was substantial, (κ = 0.63; 95% CI = 0.49–0.77) while the agreement between LIONEX Animal TB rapid blood test and IFN-γ test was moderate (κ = 0.53; 95% CI = 0.40–0.67). Analysis of receiver operating curve (ROC) indicated that the area under the ROC curve (AUC) for TB LAM Ag was 0.85 (95% CI = 0.79–0.91) while it was 0.76 (95% CI; =0.69–0.83) for LIONEX Animal TB rapid test assay. Conclusion This study showed that TB LAM Ag had a better diagnostic performance and could potentially be used as ancillary either to SICTT or IFN-γ test for diagnosis of bTB.

Bovine tuberculosis (bTB) challenges intensive dairy production in Ethiopia and implementation of the test and slaughter control strategy is not economically acceptable in the country. Vaccination of cattle with Bacillus Calmette-Guerin (BCG) could be an important adjunct to control, which would require a diagnostic test to differentiate Mycobacterium bovis (M. bovis)-infected and BCG-vaccinated animals (DIVA role). This study describes evaluation of a DIVA skin test (DST) that is based on a cocktail (DSTc) or fusion (DSTf) of specific (ESAT-6, CFP-10 and Rv3615c) M. bovis proteins in Zebu-Holstein crossbred cattle in Ethiopia. The study animals used were 74 calves (35 BCG-vaccinated and 39 unvaccinated) aged less than three weeks at the start and 68 known bTB positive cows. Six weeks after vaccination, the 74 calves were tested with DSTc and the single intradermal cervical comparative tuberculin (SICCT) test. The cows were tested with DSTc and SICCT test. Reactions to DSTc were not observed in BCG-vaccinated and unvaccinated calves while SICCT test reactions were detected in vaccinated calves. DSTc reactions were detected in 95.6% of the cows and single intradermal tuberculin (SIT) positive reactions were found in 98.2% (95% confidence interval, CI, 92.1–100%). The sensitivity of DSTc was 95.6% (95% CI, 87.6–99.1%), and significantly (P

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M . bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

The Coronavirus pandemic is recording unprecedented deaths worldwide. The temporal distribution and burden of the disease varies from setting to setting based on economic status, demography and geographic location. A rapid increase in the number of COVID-19 cases is being reported in Africa as of June 2020. Ethiopia reported the first COVID-19 case on 13 March 2020. Limited molecular laboratory capacity in resource constrained settings is a challenge in the diagnosis of the ever-increasing cases and the overall management of the disease. In this article, the Ethiopian Public Health Institute (EPHI) shares the experience, challenges and prospects in the rapid establishment of one of its COVID-19 testing laboratories from available resources. The first steps in establishing the COVID-19 molecular testing laboratory were i) identifying a suitable space ii) renovating it and iii) mobilizing materials including consumables, mainly from the Malaria and Neglected Tropical Diseases (NTDs) research team at the EPHI. A chain of experimental design was set up with distinct laboratories to standardize the extraction of samples, preparation of the master mix and detection. At the commencement of sample reception and testing, laboratory contamination was among the primary challenges faced. The source of the contamination was identified in the master mix room and resolved. In summary, the established COVID-19 testing lab has tested more than 40,000 samples (August 2020) and is the preferred setting for research and training. The lessons learned may benefit the further establishment of emergency testing laboratories for COVID-19 and/or other epidemic/pandemic diseases in resource-limited settings.

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause isMycobacterium bovis(M. bovis), which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole genome sequencing (WGS) to examine the population structure ofM. bovisin Ethiopia. A total of 134M. bovisisolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure ofM. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

BackgroundTuberculosis (TB) is one of the world’s most problematic infectious diseases. The pathogenMycobacterium tuberculosis(Mtb) is contained by the immune system in people with latent TB infection (LTBI). No overt disease symptoms occur. The environmental and internal triggers leading to reactivation of TB are not well understood. Non-tuberculosis Mycobacteria (NTM) can also cause TB-like lung disease. Comparative analysis of blood plasma proteomes from subjects afflicted by these pathologies in an endemic setting may yield new differentiating biomarkers and insights into inflammatory and immunological responses toMtband NTM.MethodsBlood samples from 40 human subjects in a pastoral region of Ethiopia were treated with the ESAT-6/CFP-10 antigen cocktail to stimulate anti-Mtband anti-NTM immune responses. In addition to those of active TB, LTBI, and NTM cohorts, samples from matched healthy control (HC) subjects were available. Following the generation of sample pools, proteomes were analyzed via LC-MS/MS. These experiments were also performed without antigen stimulation steps. Statistically significant differences using the Z-score method were determined and interpreted in the context of the proteins’ functions and their contributions to biological pathways.ResultsMore than 200 proteins were identified from unstimulated and stimulated plasma samples (UPSs and SPSs, respectively). Thirty-four and 64 proteins were differentially abundant with statistical significance (P P ConclusionPlasma proteomes are different comparing LTBI, TB, NTM and HC cohorts. The changes are augmented following prior blood immune cell stimulation with the ESAT-6/CFP-10 antigen cocktail. The results encourage larger-cohort studies to identify specific biomarkers to diagnose NTM infection, LTBI, and to predict the risk of TB reactivation.

Cellular (CD3+ T cell and CD68+ macrophages), cytokines (IFN-γ+ and TNF-α+) and effector molecule (iNOS+) responses were evaluated in the lymph nodes and tissue of cattle naturally infected with Mycobacterium bovis. Detailed post mortem and immunonohistochemical examinations of lesions were performed on 16 cows positive for single intradermal cervical comparative tuberculin test (SICCTT) and identified from dairy farms located around the Addis Ababa City. The severity of the gross lesion was significantly higher (p=0.003) in M. bovis culture positive (n=12) cows than in culture negative (n=4). Immunohistochemical techniques showed that the mean percentage labelling of CD3+ T cells decreased as the stage of granuloma increased from stage I to stage IV in culture positive cows (pM. bovis, as the stage of granuloma increases from stage I to stage IV, the proportion of CD3+ cells decreases while the immunolabeling fraction of CD68+ macrophages, IFN-γ+, TNF-α and iNOS+ increases.

Background: The zoonotic transmission of tuberculosis (TB) from cattle to humans has long been recognized while its reverse zoonotic transmission from humans to animals has recently been reported. The socioeconomic situations of the rural communities of Ethiopia are conducive for the zoonotic and reverse zoonotic transmission of TB between cattle and human. The objective of this study was to investigate the zoonotic and reverse zoonotic transmission TB between humans and cattle central Ethiopia.Methods: To achieve this objective a cross-sectional study was conducted on 1896 cattle slaughtered in two abattoirs and 392 TB suspicious human subjects visiting health institutions for treatment. Post mortem examination, mycobacteriological culture, and spoligotyping were used for the study. In addition, the Spoligotype International Types and VNTR (variable number of DNA tandem repeats) International Types (SITVIT2) database and the online “Run TB-Lineage” were used to identify SIT and lineages of the human and cattle isolates.Results: Gross TB lesion was detected in 4.2% (80/1896) the slaughtered cattle and predominantly (52.5%) found in the thoracic cavity. But culture positivity was only 26.3% (21/80) in suspicious lesions. Of the 21 cattle isolates, 12 (57.2%) were M. bovis while the remaining nine (42.8%) were M. tuberculosis. SIT50, SIT118 and SIT1318 were isolated from both humans and cattle. Similar to the low culture yield in cattle tissues, only 22% (86/392) the sputa from TB suspicious humans were culture positive. These 86 human isolates were classified into 81 M. tuberculosis, three M. africanum and two M. bovis by spoligotyping. The two human M. bovis isolates had the pattern of SB1443, which was not isolated from cattle in this study.Conclusion: The zoonotic and reverse zoonotic transmissions of TB were confirmed in Ethiopia by the isolation of two M. bovis from human and isolation of nine M. tuberculosis from cattle, which suggested higher role of M. tuberculosis in cattle compared to the role of M. bovis in humans.

Background Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. Methods MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. Results The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04–0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. Conclusion The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.

Additional file 1: Supplemental dataset S1. The summary file contains summary information for all the raw files processed with a single MaxQuant run. The summary information consists of some MaxQuant parameters, information of the raw file contents, and statistics on the peak detection. Based on this file a quick overview can be gathered on the quality of the data in the raw file. The clustering and correlation analyses were performed in Perseus environment (version 1.5.0.15) using embedded functions. The LFQ intensities generated by MaxQuant were log (base 2) transformed, and then imputed with missing values by default settings in Perseus. LC-MS/MS data were deposited to the Proteome Xchange Consortium via the PRIDE partner repository with the dataset identifier PXD012412. The letters A and B denote biological replicates (later merged together), and rep1 and rep2 denote technical replicate. Number 1–4 are unstimulated plasma samples and number 5–8 are stimulated plasma samples.

Tuberculosis (TB) is one of the leading causes of morbidity and mortality in different zones of Ethiopia. This study was undertaken to identify the strains of Mycobacterium tuberculosis and evaluate their drug sensitivity profiles in the Arsi Zone. A total of 111 isolates of M. tuberculosis from individuals with pulmonary TB were included and speciation and strain identification were performed using Region of difference 9 and spoligotyping, respectively. The drug sensitivity patterns were assessed using Bactec MGIT 960 SIRE and GenoType MTBDRplus line probe assays. Of 111 isolates, 83% were interpretable and 56 different spoligotype patterns were identified. From these, 22 patterns were shared types while the remaining 34 were orphans. The predominant shared types were spoligotype international type (SIT) 149 and SIT53, comprising 12 and 11 isolates, respectively. Euro-American lineage was the dominant lineage followed by East-African-Indian. Phenotypically, 17.2% of tested isolates were resistant to any first-line drugs and 3.1% were multidrug-resistant. Higher (6.2%) mono-resistance was observed to streptomycin, and no resistance was observed to rifampicin or ethambutol. Genotypically, five (5.4%) isolates were resistant to isoniazid and mutated at codon S315T1 of katG. In contrast, only 1.1% of the isolates were resistant to rifampicin and were mutated at codon S531L of rpoB gene. In this study, a high proportion of orphan strains were isolated, which could suggest the presence of new strains and a high percentage of mono-resistance, warranting the need to strengthen control efforts. Keywords: Drug sensitivity, Ethiopia, Mutation, Mycobacterium tuberculosis, Spoligotyping

Additional file 1. Phylogenetic tree for 155 isolates was constructed based on 24 locus MIRU-VNTR. The dendrogram was calculated using neighbor-joining clustering algorithms.

Background: Haematopoietic stem cells expressing the CD34 surface marker have been posited as a niche for M. tuberculosis complex (MTBC) bacilli during latent tuberculosis infection (LTBI). Methods: We conducted a cross-sectional study in Ethiopia to determine whether MTBC DNA was detectable in peripheral blood mononuclear cells (PBMC) isolated from 100 ml blood taken from 197 asymptomatic adults with a history of recent household TB contact and/or HIV infection, using digital polymerase chain reaction (dPCR). A nested prospective study was conducted in a sub-set of 43 HIV-infected individuals to evaluate whether administration of isoniazid preventive therapy (IPT) was effective in clearing MTBC DNA from PBMC. Results: MTBC DNA was detected in PBMC of 156/197 participants (79.2%; 95% CI 73.5% to 84.9%). Where present, it was found more frequently in CD34-positive vs. CD34-negative PBMC (154/155 [99.4%] vs. 46/155 [29.7%], P

Dromedary camels are the main sources of milk, meat and income for the Ethiopian pastoralists as they withstand the harsh environments of the regions of the country. Tuberculosis (TB) affects dromedary camels causing morbidity and mortality in these animals. Hence, early diagnosis and identification of infected camels play a significant role in reducing the transmission of TB in camels. This study was conducted on 168 camels between October 2014 and July 2015 to evaluate the performance of single intra-dermal comparative cervical tuberculin (SICCT) to diagnose TB in camels. Gross pathology was used as a gold standard to define disease status of each camel. The result showed that at the cutoff value of ≥ 3 mm SICCT had optimum performance with sensitivity and specificity of 60.7 and 85%, respectively. Moreover, at a cutoff ≥ 3 mm, the receiver operating characteristics (ROC) revealed area under the ROC curve was 0.729 (0.615-0.842) which is statistically significant (p = 0.000). Thus, the result of the present study could suggest the use of ≥ 3 mm cutoff value for the diagnosis of TB in dromedary camels in Ethiopia.

Background Tuberculosis (TB) is one of the leading disease causing morbidity and mortality in different zones of Ethiopia including the Arsi Zone. However, little or no scientific information is available on the strains of Mycobacterium tuberculosis and their drug sensitivity profiles in this Zone. This study was conducted to identify the strains of M. tuberculosis and evaluate their drug sensitivity profiles. Methodology A total of 111 clinical isolates of M. tuberculosis from patients with pulmonary TB in the Arsi Zone were used for this study. The region of difference 9 (RD 9)-based polymerase chain reaction (PCR)and spoligotyping methods were used for speciation and strain identification of Mycobacterium tuberculosis respectively.The spoligotyping patterns were compared with the international SpolDB4 (SITVIT) and Run TB-Lineage used for the identification of lineages. The phenotypic drug susceptibility patterns were confirmed by BD BactecMGIT 960 SIRE test and GenoType MTBDRplus line probe assays were used for the detection the drug resistance-conferring mutations of the isolates. Result The spoligotype patterns of 83% (92/111) of the isolates were interpretable and 56 different patterns were identified. Twenty-two of these patterns were shared types while the remaining 34 were orphans. The predominant shared types were spoligotype international type (SIT) 149 and SIT53, each consisting of 12 and 11 isolates, respectively. The lineages identified were Euro-American, East-African-Indian, Mycobacterium-africanum, and Indo-Oceanic in descending order. Phenotypically, 17.2% of the 64 tested isolates were resistant to any of the four first-line drugs while 3.1% of them were multi-drug resistant (MDR). Higher (6.2%) monoresistance was observed to Streptomycin followed by Isoniazid (3.1%) while no resistance was observed either to Rifampicin or to Ethambutol. Genotypically, five (5.4%) isolates were resistant to Isoniazid and mutated at codon S315T1 of katG. On the other hand, only 1.1% of the isolates was resistant to Rifampicin and mutated at codon S531L of rpoB gene. Conclusion The proportion of orphan strains isolated in this study was high, which could suggest the presence of new strains in the Zone. Moreover, the study showed relatively high percentage of mono-resistance to any four first-line drugs warranting for the need to strengthen the control efforts.

Background Drug resistant tuberculosis (TB) has become a persistent health threat in Ethiopia. In this respect, baseline data are scarce in many parts of high TB burden regions including the different zones of Ethiopia. Methods A total of 111 culture positive M. tuberculosis isolates were recovered from TB patients and identified using region of difference (RD) 9 based polymerase chain reaction (PCR) and spoligotyping. Thereafter, their drug sensitivities to Rifampicin (RIF) and Isoniazid (INH) were evaluated using GenoType MTBDRplus assay. Results The result showed that 18.0% (20/111) of the isolates were resistant to either RIF or INH. Furthermore, 16.7 and 23.8% of the isolates from new and retreatment cases were resistant to any of the two anti-TB drugs, respectively. Multi-drug resistant (MDR) TB was detected on 1.8% (2/111) of all cases. Significantly higher frequencies of any drug resistance were observed among Euro-American (EA) major lineage (χ2: 9.67; p = 0.046). Conclusion Considerably high proportion of drug resistant M. tuberculosis strains was detected which could suggest a need for an increased effort to strengthen TB control program in the study area.

A defined antigen skin test has been developed for the reliable diagnosis and vaccine-based control of bovine tuberculosis., Bovine tuberculosis (bTB) is a major zoonotic disease of cattle that is endemic in much of the world, limiting livestock productivity and representing a global public health threat. Because the standard tuberculin skin test precludes implementation of Bacille Calmette-Guérin (BCG) vaccine–based control programs, we here developed and evaluated a novel peptide-based defined antigen skin test (DST) to diagnose bTB and to differentiate infected from vaccinated animals (DIVA). The results, in laboratory assays and in experimentally or naturally infected animals, demonstrate that the peptide-based DST provides DIVA capability and equal or superior performance over the extant standard tuberculin surveillance test. Together with the ease of chemical synthesis, quality control, and lower burden for regulatory approval compared with recombinant antigens, the results of our studies show that the DST considerably improves a century-old standard and enables the development and implementation of critically needed surveillance and vaccination programs to accelerate bTB control.

Mycobacterium bovis (M. bovis) has an exceptionally wide host range including sheep. Information on tuberculosis (TB) in sheep is scarce, and there appears to be conflicting opinions about the relative susceptibility of sheep to infection. In Ethiopia, there was no single previous report on tuberculosis in sheep, though mixed farming of cattle and sheep is a common practice. In this study, following the observation of TB-like lesions on sheep died from sheep flock kept in contact with cattle herd, further investigation was conducted on the flock to assess the magnitude of the infection and identify and characterize the causative M. bovis strain. An outbreak investigation was carried out on 26 eligible sheep out of 33 sheep found on the farm. Comparative intradermal tuberculin (CIDT) test, postmortem examination, Mycobacterium culturing, and spoligotyping were the techniques used in the study. The prevalence of TB in the tested sheep was 15% (4/26). All the sheep that were positive to CIDT had gross lesions suggestive of TB. Three of the positive sheep had extensive and multiple lesions. M. bovis was isolated from all four sheep and the strain was identified as spoligotype SBO134. The in-contact dairy cows were screened for TB and 98% (45/46) of the cows tested positive to CIDT. Furthermore, the same strain, SB0134, was also isolated from the two in-contact cows. The isolation of a matching genotype (SB0134) of M. bovis from both species sharing a known epidemiologic link strongly suggests that the sheep flock might have acquired the pathogen from the dairy cows. This warrants strict physical separation of the sheep flock from the cattle herd to prevent such interspecies transmission of M. bovis.