Meseret Habtamu | University of Oslo (original) (raw)

Papers by Meseret Habtamu

PLOS ONE, Feb 26, 2021

Background The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health... more Background The coronavirus disease 2019 (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability, an efficient method is urgently needed. Objectives To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2. Methods We evaluated pooling approach on both direct clinical and NA samples. The standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 was employed targeting the nucleocapsid (N) and open reading frame (ORF1ab) genomic region of the virus. The experimental pools were created using SARS CoV-2 positive clinical samples and extracted RNA spiked with up to 9 negative samples. For the direct clinical samples viral NA was extracted from each pool to a final extraction volume of 200μL, and subsequently both samples tested using the SARS CoV-2 RT-PCR assay. Results We found that a single positive sample can be amplified and detected in pools of up to 7 samples depending on the cycle threshold (Ct) value of the original sample, corresponding to high, and low SARS CoV-2 viral copies per reaction. However, to minimize false negativity of the assay with pooling strategies and with unknown false negativity rate of the assay under validation, we recommend pooling of 4/5 in 1 using the standard protocols of the assay, reagents and equipment. The predictive algorithm indicated a pooling ratio of 5 in 1 was expected to retain accuracy of the test irrespective of the Ct value samples spiked, and result in a 137% increase in testing efficiency.

Frontiers in Immunology, 2013

Frontiers in Immunology, Dec 13, 2022

The International Journal of Tuberculosis and Lung Disease, 2012

To determine the value of light-emitting diode (LED) microscopy in diagnosing tuberculosis (TB) o... more To determine the value of light-emitting diode (LED) microscopy in diagnosing tuberculosis (TB) on bleach-treated and direct sputum smears. D E S I G N : Sputum samples were collected from patients suspected of pulmonary TB who presented consecutively at the laboratory for smear evaluation between December 2009 and February 2010. Four smears were prepared from each specimen: conventional Ziehl-Neelsen (ZN), direct auramine, bleach centrifugation and bleach short sedimentation auramine smears. A light microscope was used to examine ZN smears and an LED fluorescent microscope to examine auramine-stained smears. R E S U LT S : Of the 267 sputum samples examined, respectively 78 (29%), 62 (23%), 74 (28%) and 48 (18%) were acid-fast bacilli (AFB) positive by the bleach centrifugation, bleach short sedimentation, direct auramine and ZN methods. Bleach centrifugation identified 30 (11%) more positives than ZN microscopy (P < 0.001), but was not superior to the direct auramine method (P = 0.46), which yielded 26 (10%) more positives than ZN microscopy (P < 0.001). Fluorescent LED required a shorter smear reading time (1.5 min on average), while the light microscope took 4 min (P < 0.001).

Molecular typing of 964 specimens from patients in Ethiopia with lymph node or pulmonary tubercul... more Molecular typing of 964 specimens from patients in Ethiopia with lymph node or pulmonary tuberculosis showed a similar distribution of Mycobacterium tuberculosis strains between the 2 disease manifestations and a minimal role for M. bovis. We report a novel phylogenetic lineage of M. tuberculosis strongly associated with the Horn of Africa. Ethiopia is among the countries with the highest incidence of tuberculosis (TB) and has a yearly incidence of 261 cases/100,000 population. TB lymphadenitis in cervical lymph nodes (TBLN) accounts for ≈33 % of all new cases in this country, which is greater than the global average of ≈15 % (1). Ethiopia has the largest livestock population in

Bovine tuberculosis (BTB) is endemic in cattle in the Ethiopian Highlands but no studies have bee... more Bovine tuberculosis (BTB) is endemic in cattle in the Ethiopian Highlands but no studies have been done so far in pastoralists in South Omo. This study assessed the prevalence of bovine tuberculosis (BTB) at an intensive interface of livestock, wildlife and pastoralists in Hamer Woreda (South Omo), Ethiopia. A cross-sectional survey including a comparative intradermal skin testing (CIDT) was conducted in 499 zebu cattle and 186 goats in 12 settlements. Sputum samples from 26 symptomatic livestock owners were cultured for TB. Fifty-one wildlife samples from 13 different species were also collected in the same area and tested with serological (lateral flow assay) and bacteriological (culture of lymph nodes) techniques. Individual BTB prevalence in cattle was 0.8 % (CI: 0.3%–2%) with the.4 mm cut-off and 3.4 % (CI: 2.1%–5.4%) with the.2 mm cut-off. Herd prevalence was 33.3 % and 83 % when using the.4 and the.2 mm cut-off respectively. There was no correlation between age, sex, body con...

Journal of immunological methods, Jan 4, 2018

There is a lack of suitable correlates of immune protection against Mycobacterium tuberculosis (M... more There is a lack of suitable correlates of immune protection against Mycobacterium tuberculosis (Mtb) infection. T cells and monocytes play key roles in host immunity against Mtb. Thus, a method that allows assessing their interaction would contribute to the understanding of immune regulation in tuberculosis (TB). We have established imaging flow cytometer (IFC) based in vitro assay for the analysis of early events in T cell-monocyte interaction, upstream of cytokine production and T cell proliferation. This was achieved through short term stimulation of peripheral blood mononuclear cells (PBMC) from healthy Norwegian blood donors with Mycobacterium bovis Bacille Calmette-Guérin (BCG). In our assay, we examined the kinetics of BCG uptake by monocytes using fluorescently labeled BCG and T cell-monocyte interaction based on synapse formation (CD3/TCR polarization). Our results showed that BCG stimulation induced a gradual increase in the proportion of conjugated T cells displaying NF-κ...

BMC Infectious Diseases, 2015

Background: Ethiopia, a high tuberculosis (TB) burden country, reports one of the highest inciden... more Background: Ethiopia, a high tuberculosis (TB) burden country, reports one of the highest incidence rates of extra-pulmonary TB dominated by cervical lymphadenitis (TBLN). Infection with Mycobacterium bovis has previously been excluded as the main reason for the high rate of extrapulmonary TB in Ethiopia. Methods: Here we examined demographic and clinical characteristics of 953 pulmonary (PTB) and 1198 TBLN patients visiting 11 health facilities in distinct geographic areas of Ethiopia. Clinical characteristics were also correlated with genotypes of the causative agent, Mycobacterium tuberculosis. Results: No major patient or bacterial strain factor could be identified as being responsible for the high rate of TBLN, and there was no association with HIV infection. However, analysis of the demographic data of involved patients showed that having regular and direct contact with live animals was more associated with TBLN than with PTB, although no M. bovis was isolated from patients with TBLN. Among PTB patients, those infected with Lineage 4 reported "contact with other TB patient" more often than patients infected with Lineage 3 did (OR = 1.6, CI 95% 1.0-2.7; p = 0.064). High fever, in contrast to low and moderate fever, was significantly associated with Lineage 4 (OR = 2.3; p = 0.024). On the other hand, TBLN cases infected with Lineage 4 tended to get milder symptoms overall for the constitutional symptoms than those infected with Lineage 3. Conclusions: The study suggests a complex role for multiple interacting factors in the epidemiology of extrapulmonary TB in Ethiopia, including factors that can only be derived from population-based studies, which may prove to be significant for TB control in Ethiopia.

PLoS ONE, 2009

ABSTRACT [This corrects the article on p. e5068 in vol. 4, PMID: 19352493.].

Emerging Infectious Diseases, 2013

Clinical & Experimental Immunology, 2020

Summary The lack of efficient tools for identifying immunological correlates of tuberculosis (TB)... more Summary The lack of efficient tools for identifying immunological correlates of tuberculosis (TB) protection or risk of disease progression impedes the development of improved control strategies. To more clearly understand the host response in TB, we recently established an imaging flow cytometer-based in-vitro assay, which assesses multiple aspects of T cell–monocyte interaction. Here, we extended our previous work and characterized communication between T cells and monocytes using clinical samples from individuals with different TB infection status and healthy controls from a TB endemic setting. To identify T cell–monocyte conjugates, peripheral blood mononuclear cells (PBMC) were stimulated with ds-Red-expressing Mycobacterium bovis bacille Calmette–Guérin or 6-kDa early secreted antigenic target (ESAT 6) peptides for 6 h, and analyzed by imaging flow cytometer (IFC). We then enumerated T cell–monocyte conjugates using polarization of T cell receptor (TCR) and F-actin as markers ...

The result and conclusions section of abstract should be rewritten according to the below comment... more The result and conclusions section of abstract should be rewritten according to the below comments. Authors’ response: We have addressed the comments below as advised. Background 1. The introduction is too long and does not pose the question straightforward. Authors’ response: We have shortened the introduction to some extent and have spelled out the reason for this study earlier in the introduction. We have added the sentence: “What are the risk factors that can explain this high rate of extrapulmonary TB in Ethiopia?” to the background section. 2. There is no need to state the signs of TBLN. The sentence containing this statement is not well written Authors’ response: Sentence has been modified to “Although pulmonary TB is the most common manifestation, an estimated one million people (~15%) develop extrapulmonary TB, of which TB lymphadenitis in the cervical lymph nodes (TBLN) is the most frequent form.” 3. I don’t understand the relationship between consumption of raw milk (with...

Journal of immunological methods, Jan 4, 2018

BMC Infectious Diseases, 2015

Pan African Medical Journal

Novel coronavirus disease (COVID-19) is spreading rapidly and creating a huge economic, social an... more Novel coronavirus disease (COVID-19) is spreading rapidly and creating a huge economic, social and public health challenge worldwide. Although currently an effective vaccine is ready, its distribution is limited, and hence the only currently available lever to reduce transmission is to identify and isolate individuals who are contagious. Thus, testing for SARS CoV-2 has a paramount importance. However, testing in many African countries including Ethiopia has multidimensional growing challenges. Here, we tried to identify, categorize and summarize the challenges of COVID-19 testing in Africa from Ethiopian experience.

Background: The coronavirus disease (COVID-19) pandemic has revealed the global public health imp... more Background: The coronavirus disease (COVID-19) pandemic has revealed the global public health importance of robust diagnostic testing. To overcome the challenge of nucleic acid (NA) extraction and testing kit availability efficient method is urgently needed. Objectives: To establish an efficient, time and resource-saving and cost-effective methods, and to propose an ad hoc pooling approach for mass screening of SARS-CoV-2 Methods: Direct clinical sample and NA pooling approach was used for the standard reverse transcriptase polymerase chain reaction (RT-PCR) test of the SARS CoV-2 targeting the envelop (E) and open reading frame (ORF1ab) genomic region of the virus. In this approach, experimental pools were created using SARS CoV-2 positive clinical samples spiked with up to 9 negative samples prior to NA extraction step to have a final extraction volume of 200μL (maximum dilution factor of 10). Viral NA was also subsequently extracted from each pool and tested using the SARS CoV-2 ...

Scientific Reports, Sep 6, 2018

Polarization of T cells towards the antigen presenting cell (APC) is critically important for app... more Polarization of T cells towards the antigen presenting cell (APC) is critically important for appropriate activation and differentiation of the naïve T cell. Here we used imaging flow cytometry (IFC) and show that the activation induced Lck and Itk adapter T cell specific adapter protein (TSAd), encoded by SH2D2A, modulates polarization of T cells towards the APC. Upon exposure to APC presenting the cognate antigen Id, Sh2d2a−/− CD4+ T cells expressing Id-specific transgenic T cell receptor (TCR), displayed impaired polarization of F-actin and TCR to the immunological synapse (IS). Sh2d2a−/− T-cells that did polarize F-actin and TCR still displayed impaired polarization of PKCξ, PAR3 and the microtubule-organizing center (MTOC). In vitro differentiation of activated Sh2d2a−/− T cells was skewed towards an effector memory (Tem) rather than a central memory (Tcm) phenotype. A similar trend was observed for Id-specific TCR Sh2d2a−/− T cells stimulated with APC and cognate antigen. Taken together our data suggest that TSAd modulates differentiation of experienced T cells possibly through polarization of CD4+ T cells towards the APC. Upon stimulation of T cells via TCR and other surface receptors, initiation of signalling cascades eventually results in proliferation and differentiation into various T cell phenotypes 1. The molecular details for how signalling in T cells is controlled after the initial triggering of the TCR is not fully understood. TCR binding to its cognate antigen-MHC complex on antigen presenting cells may result in formation of an immunological synapse (IS) at the interface between the T cell and the APC. IS formation is dependent on localized intracellular signals that results in cytoskeletal and membrane reorganization towards the contact site (reviewed in 2). Polarisation of actin, TCR and signalling molecules towards the IS are required for proper activation and function of T cells, where CD4+ T cells engage with the APC for several hours 1. Sustained TCR signalling is subsequently maintained through recycling TCR and Lck to the IS during activation 3,4 , until signal termination by negative feedback mechanisms or TCR degradation 5,6. Providing a critical regulatory stimulus, the IS facilitates differentiation of T cells into Tem or Tcm subsets, 1,7,8. Interruption of IS formation may skew or disrupt CD8+ T cell differentiation 9-12. Upon triggering of the TCR, formation of the IS initially involves reorganising the actin cytoskeleton towards the cell interface, followed by movement of TCR micro-clusters towards the centre of the IS (cSMAC). As the IS matures, polymerized actin reorganises and relocates to the periphery (dSMAC) while microtubule organizing centre (MTOC) reorients to a position beneath the IS (reviewed in 13). A novel player in regulation of T cell polarity, may be the cytosolic Lck and Itk adapter TSAd 14 , encoded by SH2D2A. We recently found that lack of TSAd is associated with reduced accumulation of F-actin at the interphase between CD4+ T cells and APC 14. TSAd is induced in both CD4+ and CD8+ T cells upon engagement of the TCR 15,16. However, the role of TSAd in activated T cells is only partially understood. TSAd affects proximal T cell signalling events via its interaction with Lck 16,17 , possibly by promoting phosphorylation of Lck Tyr 192 by Itk 14. TSAd also regulates chemokine induced T cell migration and actin polymerization via its interaction with Itk 18. Despite TSAd being involved in TCR signalling, unchallenged Sh2d2a−/− mice display only minor alteration in overall immune phenotype 15,19,20. TSAd may influence specific NK cell immune responses, since

Clinical Immunology, Feb 9, 2014

In this study, we explored the local cytokine/chemokine profiles in patients with active pulmonar... more In this study, we explored the local cytokine/chemokine profiles in patients with active pulmonary or pleural tuberculosis (TB) using multiplex protein analysis of bronchoalveolar lavage and pleural fluid samples. Despite increased pro-inflammation compared to the uninfected controls; there was no up-regulation of IFN-γ or the T cell chemoattractant CCL5 in the lung of patients with pulmonary TB. Instead, elevated levels of IL-4 and CCL4 were associated with high mycobacteria-specific IgG titres as well as SOCS3 (suppressors of cytokine signaling) mRNA and progression of moderate-to-severe disease. Contrary, IL-4, CCL4 and SOCS3 remained low in patients with extrapulmonary pleural TB, while IFN-γ, CCL5 and SOCS1 were up-regulated. Both SOCS molecules were induced in human macrophages infected with Mycobacterium tuberculosis in vitro. The Th2 immune response signature found in patients with progressive pulmonary TB could result from inappropriate cytokine/chemokine responses and excessive SOCS3 expression that may represent potential targets for clinical TB management.

PLoS ONE

[This corrects the article on p. e5068 in vol. 4, PMID: 19352493.].

PLOS ONE, Feb 26, 2021

Frontiers in Immunology, 2013

Frontiers in Immunology, Dec 13, 2022

The International Journal of Tuberculosis and Lung Disease, 2012

Journal of immunological methods, Jan 4, 2018

BMC Infectious Diseases, 2015

PLoS ONE, 2009

ABSTRACT [This corrects the article on p. e5068 in vol. 4, PMID: 19352493.].

Emerging Infectious Diseases, 2013

Clinical & Experimental Immunology, 2020

Journal of immunological methods, Jan 4, 2018

BMC Infectious Diseases, 2015

Pan African Medical Journal

Scientific Reports, Sep 6, 2018

Clinical Immunology, Feb 9, 2014

PLoS ONE

[This corrects the article on p. e5068 in vol. 4, PMID: 19352493.].