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Majumdar R, Taye B, Bjornberg C, Giljork M, Lynch D, Farah F, Abdullah I, Osiecki K, Yousaf I, Luckstein A, Turri W, Sampathkumar P, Moyer AM, Kipp BR, Cattaneo R, Sussman CR, Navaratnarajah CK. From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota. Heliyon 2024; 10:e27974. [PMID: 38515669 PMCID: PMC10955309 DOI: 10.1016/j.heliyon.2024.e27974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Traditionally, public health surveillance relied on individual-level data but recently wastewater-based epidemiology (WBE) for the detection of infectious diseases including COVID-19 became a valuable tool in the public health arsenal. Here, we use WBE to follow the course of the COVID-19 pandemic in Rochester, Minnesota (population 121,395 at the 2020 census), from February 2021 to December 2022. We monitored the impact of SARS-CoV-2 infections on public health by comparing three sets of data: quantitative measurements of viral RNA in wastewater as an unbiased reporter of virus level in the community, positive results of viral RNA or antigen tests from nasal swabs reflecting community reporting, and hospitalization data. From February 2021 to August 2022 viral RNA levels in wastewater were closely correlated with the oscillating course of COVID-19 case and hospitalization numbers. However, from September 2022 cases remained low and hospitalization numbers dropped, whereas viral RNA levels in wastewater continued to oscillate. The low reported cases may reflect virulence reduction combined with abated inclination to report, and the divergence of virus levels in wastewater from reported cases may reflect COVID-19 shifting from pandemic to endemic. WBE, which also detects asymptomatic infections, can provide an early warning of impending cases, and offers crucial insights during pandemic waves and in the transition to the endemic phase.
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Affiliation(s)
| | - Biruhalem Taye
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Iris Yousaf
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M. Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R. Kipp
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Caroline R. Sussman
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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2
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Navaratnarajah CK, Pease DR, Halfmann PJ, Taye B, Barkhymer A, Howell KG, Charlesworth JE, Christensen TA, Kawaoka Y, Cattaneo R, Schneider JW. Highly Efficient SARS-CoV-2 Infection of Human Cardiomyocytes: Spike Protein-Mediated Cell Fusion and Its Inhibition. J Virol 2021; 95:e0136821. [PMID: 34613786 PMCID: PMC8610601 DOI: 10.1128/jvi.01368-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/26/2021] [Indexed: 12/15/2022] Open
Abstract
Severe cardiovascular complications can occur in coronavirus disease of 2019 (COVID-19) patients. Cardiac damage is attributed mostly to the aberrant host response to acute respiratory infection. However, direct infection of cardiac tissue by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also occurs. We examined here the cardiac tropism of SARS-CoV-2 in spontaneously beating human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). These cardiomyocytes express the angiotensin-converting enzyme 2 (ACE2) receptor but not the transmembrane protease serine 2 (TMPRSS2) that mediates spike protein cleavage in the lungs. Nevertheless, SARS-CoV-2 infection of hiPSC-CMs was prolific; viral transcripts accounted for about 88% of total mRNA. In the cytoplasm of infected hiPSC-CMs, smooth-walled exocytic vesicles contained numerous 65- to 90-nm particles with canonical ribonucleocapsid structures, and virus-like particles with knob-like spikes covered the cell surface. To better understand how SARS-CoV-2 spreads in hiPSC-CMs, we engineered an expression vector coding for the spike protein with a monomeric emerald-green fluorescent protein fused to its cytoplasmic tail (S-mEm). Proteolytic processing of S-mEm and the parental spike were equivalent. Live cell imaging tracked spread of S-mEm cell-to-cell and documented formation of syncytia. A cell-permeable, peptide-based molecule that blocks the catalytic site of furin and furin-like proteases abolished cell fusion. A spike mutant with the single amino acid change R682S that disrupts the multibasic furin cleavage motif was fusion inactive. Thus, SARS-CoV-2 replicates efficiently in hiPSC-CMs and furin, and/or furin-like-protease activation of its spike protein is required for fusion-based cytopathology. This hiPSC-CM platform enables target-based drug discovery in cardiac COVID-19. IMPORTANCE Cardiac complications frequently observed in COVID-19 patients are tentatively attributed to systemic inflammation and thrombosis, but viral replication has occasionally been confirmed in cardiac tissue autopsy materials. We developed an in vitro model of SARS-CoV-2 spread in myocardium using induced pluripotent stem cell-derived cardiomyocytes. In these highly differentiated cells, viral transcription levels exceeded those previously documented in permissive transformed cell lines. To better understand the mechanisms of SARS-CoV-2 spread, we expressed a fluorescent version of its spike protein that allowed us to characterize a fusion-based cytopathic effect. A mutant of the spike protein with a single amino acid mutation in the furin/furin-like protease cleavage site lost cytopathic function. Of note, the fusion activities of the spike protein of other coronaviruses correlated with the level of cardiovascular complications observed in infections with the respective viruses. These data indicate that SARS-CoV-2 may cause cardiac damage by fusing cardiomyocytes.
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Affiliation(s)
| | - David R. Pease
- Discovery Engine/Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, Minnesota, USA
| | - Peter J. Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Biruhalem Taye
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alison Barkhymer
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Kyle G. Howell
- Mayo Microscopy and Cell Analysis Core, Mayo Clinic, Rochester, Minnesota, USA
| | - Jon E. Charlesworth
- Mayo Microscopy and Cell Analysis Core, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jay W. Schneider
- Discovery Engine/Program for Hypoplastic Left Heart Syndrome, Mayo Clinic, Rochester, Minnesota, USA
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Teklu T, Wondale B, Taye B, Hailemariam M, Bekele S, Tamirat M, Zewude A, Mohamed T, Medhin G, Legesse M, Yu Y, Ameni G, Pieper R. Differences in plasma proteomes for active tuberculosis, latent tuberculosis and non-tuberculosis mycobacterial lung disease patients with and without ESAT-6/CFP10 stimulation. Proteome Sci 2020; 18:10. [PMID: 33292280 PMCID: PMC7603755 DOI: 10.1186/s12953-020-00165-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 09/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is one of the world's most problematic infectious diseases. The pathogen Mycobacterium 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 to Mtb and NTM. METHODS Blood samples from 40 human subjects in a pastoral region of Ethiopia were treated with the ESAT-6/CFP-10 antigen cocktail to stimulate anti-Mtb and 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. RESULTS More 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 < 0.05; Benjamini-Hochberg correction with an FDR < 0.05) comparing UPS and SPS proteomic data of four groups, respectively. Bioinformatics analysis of such proteins via the Gene Ontology Resource was indicative of changes in cellular and metabolic processes, responses to stimuli, and biological regulations. The m7GpppN-mRNA hydrolase was increased in abundance in the LTBI group compared to HC subjects. Charged multivesicular body protein 4a and platelet factor-4 were increased in abundance in NTM as compared to HC and decreased in abundance in NTM as compared to active TB. C-reactive protein, α-1-acid glycoprotein 1, sialic acid-binding Ig-like lectin 16, and vitamin K-dependent protein S were also increased (P < 0.05; fold changes≥2) in SPSs and UPSs comparing active TB with LTBI and NTM cases. These three proteins, connected in a STRING functional network, contribute to the acute phase response and influence blood coagulation. CONCLUSION Plasma 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.
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Affiliation(s)
- Takele Teklu
- Department of Immunology and Molecular Biology, University of Gondar, Gondar, Ethiopia.
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Biniam Wondale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University, Arba Minch, Ethiopia
| | - Biruhalem Taye
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- European Molecular Biology Laboratory, Notkestraβe 85, 22607, Hamburg, Germany
| | | | | | - Mesfin Tamirat
- Laboratory department, Jinka General Hospital, Jinka, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public health Institute, P.O box 1242, Addis Ababa, Ethiopia
| | - Temesgen Mohamed
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Girmay Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yanbao Yu
- J. Craig Venter Institute, Rockville, MD, USA
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
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Malede A, Taye B, Legesse M, Debie A, Shibabaw A. Pulmonary tuberculosis preventive practices among Anibessa Bus users at Addis Ababa, Ethiopia: a cross-sectional study. BMC Res Notes 2019; 12:104. [PMID: 30808404 PMCID: PMC6390587 DOI: 10.1186/s13104-019-4135-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/15/2019] [Indexed: 12/03/2022] Open
Abstract
Objective Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis. Smear positive tuberculosis patients are responsible for up to 90% of transmission occurring in the community. However, little is known about pulmonary tuberculosis preventive practices among bus users in Ethiopia. This study aimed to assess the level of Pulmonary Tuberculosis (PTB) preventive practices and associated factors among bus users at Addis Ababa. Results Community based cross-sectional study was conducted among bus users at Addis Ababa. Participants were selected using systematic sampling technique. Overall, 50.5% of bus users had good practices on prevention of PTB at Addis Ababa. The odds of practicing prevention of PTB among participants who were attended secondary school (AOR = 4.63; 95% CI 2.62, 11.17) and higher education (AOR = 2.86: 95% CI 1.13, 7.73), resided at Addis Ababa (AOR = 2.51; 95% CI 1.61, 5.21), knowledgeable about PTB (AOR = 4.12; 95% CI 3.14, 5.70), and using mass media (AOR = 2.14; 95% CI 1.78, 4.27) as a source of information were higher than the odds of their respective counterparts. The overall practice of pulmonary tuberculosis prevention among city bus users in the study area was low. Therefore, enhancing educational opportunity and increase community awareness about the causes, risk factors and means of transmission using mass media might improve the practices of PTB prevention during bus transportation. Electronic supplementary material The online version of this article (10.1186/s13104-019-4135-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Asmamaw Malede
- College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
| | - Biruhalem Taye
- Akililu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mengistu Legesse
- College of Medicine and Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ayal Debie
- Department of Health Systems & Policy, College Medicine and Health Sciences, Institute of Public Health, University of Gondar, P.O.Box 196, Gondar, Ethiopia.
| | - Agumas Shibabaw
- College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia
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Berger KA, Pigott DM, Tomlinson F, Godding D, Maurer-Stroh S, Taye B, Sirota FL, Han A, Lee RTC, Gunalan V, Eisenhaber F, Hay SI, Russell CA. The Geographic Variation of Surveillance and Zoonotic Spillover Potential of Influenza Viruses in Domestic Poultry and Swine. Open Forum Infect Dis 2018; 5:ofy318. [PMID: 30619908 PMCID: PMC6309522 DOI: 10.1093/ofid/ofy318] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
Background Avian and swine influenza viruses circulate worldwide and pose threats to both animal and human health. The design of global surveillance strategies is hindered by information gaps on the geospatial variation in virus emergence potential and existing surveillance efforts. Methods We developed a spatial framework to quantify the geographic variation in outbreak emergence potential based on indices of potential for animal-to-human and secondary human-to-human transmission. We then compared our resultant raster model of variation in emergence potential with the global distribution of recent surveillance efforts from 359105 reports of surveillance activities. Results Our framework identified regions of Southeast Asia, Eastern Europe, Central America, and sub-Saharan Africa with high potential for influenza virus spillover. In the last 15 years, however, we found that 78.43% and 49.01% of high-risk areas lacked evidence of influenza virus surveillance in swine and domestic poultry, respectively. Conclusions Our work highlights priority areas where improved surveillance and outbreak mitigation could enhance pandemic preparedness strategies.
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Affiliation(s)
- Kathryn A Berger
- Department of Veterinary Medicine, University of Cambridge, United Kingdom.,Agrimetrics Ltd., Harpenden, United Kingdom
| | - David M Pigott
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | | | - David Godding
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | | | - Biruhalem Taye
- Bioinformatics Institute, ASTAR, Singapore.,European Molecular Biology Laboratory, Deutsches Elektronen-Synchrotron, Hamburg, Germany
| | | | - Alvin Han
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | | | | | - Frank Eisenhaber
- Bioinformatics Institute, ASTAR, Singapore.,National University of Singapore
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, Seattle
| | - Colin A Russell
- Academic Medical Center, University of Amsterdam, The Netherlands
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Taye B, Enquselassie F, Tsegaye A, Amberbir A, Medhin G, Fogarty A, Robinson K, Davey G. Association between infection with Helicobacter pylori and atopy in young Ethiopian children: A longitudinal study. Clin Exp Allergy 2017; 47:1299-1308. [PMID: 28787771 DOI: 10.1111/cea.12995] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 06/07/2017] [Accepted: 07/26/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Epidemiological evidence from developed countries indicates that Helicobacter pylori infection correlates with a reduced risk of atopy and allergic disorders; however, limited data are available from low-income countries. OBJECTIVE We examined associations between H. pylori infection in early childhood and atopy and reported allergic disorders at the age of 6.5 years in an Ethiopian birth cohort. METHODS A total of 856 children (85.1% of the 1006 original singletons in a population-based birth cohort) were followed up at age six and half years. An interviewer-led questionnaire administered to mothers provided information on demographic and lifestyle variables. Questions on allergic disease symptoms were based on the International Study of Asthma and Allergies in Children (ISAAC) core allergy and environmental questionnaire. Serum samples were analysed for total IgE levels and anti-H. pylori cytotoxin-associated gene A (CagA) IgG antibody using commercially available ELISA kits. Stool samples were analysed for H. pylori antigen using a rapid immunochromatographic test. The independent effects of H. pylori infection (measured at age of 3, 5 and 6.5 years) on prevalence and incidence of atopy and reported allergic disorders (measured at age of 6.5 years) were determined using multiple logistic regression. RESULTS In cross-sectional analysis, current H. pylori infection at age 6.5 years was inversely, though not significantly, related to prevalence of atopy and "any allergic condition" at age 6.5 years. However, detection of H. pylori infection at any point up to age 6.5 years was associated with a significantly reduced odds of both atopy and "any allergic condition" (adjusted OR AOR, 95% CI, 0.54; 0.32-0.92, P = .02, and .31; 0.10-0.94, P = .04, respectively). In longitudinal analyses, H. pylori infection at age 3 was inversely associated with incidence of atopy (AOR, 95% CI, 0.49; 0.27-0.89, P = .02). Furthermore, among H. pylori-infected children, those with a CagA+ strain had a more pronounced reduction in odds of atopy (AOR = 0.35 vs 0.63 for CagA+ vs CagA-), and this reduction reached borderline significance. CONCLUSION These data are consistent with the hypothesis that early exposure to H. pylori is inversely associated with atopy and allergic conditions. A possible modest protective association against atopy was observed in those infected with a more virulent CagA+ strain of H. pylori.
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Affiliation(s)
- B Taye
- Department of Biology, Colgate University, Hamilton, NY, USA
| | - F Enquselassie
- School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - A Tsegaye
- School of Allied Health Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - G Medhin
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - A Fogarty
- Division of Epidemiology and Public Health, University of Nottingham, Nottingham, UK
| | - K Robinson
- Nottingham Digestive Diseases Biomedical Research Centre, School of Medicine, University of Nottingham, Nottingham, UK
| | - G Davey
- Wellcome Trust Centre for Global Health Research, Brighton & Sussex Medical School, Brighton, UK
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7
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Taye B, Vaz C, Tanavde V, Kuznetsov VA, Eisenhaber F, Sugrue RJ, Maurer-Stroh S. Benchmarking selected computational gene network growing tools in context of virus-host interactions. Sci Rep 2017; 7:5805. [PMID: 28724991 PMCID: PMC5517527 DOI: 10.1038/s41598-017-06020-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
Several available online tools provide network growing functions where an algorithm utilizing different data sources suggests additional genes/proteins that should connect an input gene set into functionally meaningful networks. Using the well-studied system of influenza host interactions, we compare the network growing function of two free tools GeneMANIA and STRING and the commercial IPA for their performance of recovering known influenza A virus host factors previously identified from siRNA screens. The result showed that given small (~30 genes) or medium (~150 genes) input sets all three network growing tools detect significantly more known host factors than random human genes with STRING overall performing strongest. Extending the networks with all the three tools significantly improved the detection of GO biological processes of known host factors compared to not growing networks. Interestingly, the rate of identification of true host factors using computational network growing is equal or better to doing another experimental siRNA screening study which could also be true and applied to other biological pathways/processes.
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Affiliation(s)
- Biruhalem Taye
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. .,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O.BOX 1176, Addis Ababa, Ethiopia.
| | - Candida Vaz
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore
| | - Vivek Tanavde
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Singapore
| | - Vladimir A Kuznetsov
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,School of Computer Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore, 637553, Singapore
| | - Richard J Sugrue
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01 Matrix, Singapore, 138671, Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,National Public Health Laboratory, Ministry of Health, 3 Biopolis Drive, Synapse #05-14/16, Singapore, 138623, Singapore
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8
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Taye B, Chen H, Myaing MZ, Tan BH, Maurer-Stroh S, Sugrue RJ. Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia. BMC Genomics 2017; 18:420. [PMID: 28558796 PMCID: PMC5450074 DOI: 10.1186/s12864-017-3803-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/17/2017] [Indexed: 02/08/2023] Open
Abstract
Background Influenza A virus (IAV) is a major public health concern, being responsible for the death of approximately half a million people each year. Zoonotic transmissions of the virus from swine and avian origin have occurred in the past, and can potentially lead to the emgergence of new IAV stains in future pandemics. Pulmonary macrophages have been implicated in disease severity in the lower airway, and understanding the host response of macrophages infected with avian influenza viruses should provide new therapeutic strategies. Results We used a systems-based approach to investigate the transcriptome response of primary murine lung macrophages (PMФ) infected with the mouse-adapted H1N1/WSN virus and low pathogenic avian influenza (LPAI) viruses H5N2 and H5N3. The results showed that the LPAI viruses H5N2 and H5N3 can infect PMФ with similar efficiency to the H1N1/WSN virus. While all viruses induced antiviral responses, the H5N3 virus infection resulted in higher expression levels of cytokines and chemokines associated with inflammatory responses. Conclusions The LPAI H5N2 and H5N3 viruses are able to infect murine lung macrophages. However, the H5N3 virus was associated with increased expression of pro-inflammatory mediators. Although the H5N3 virus it is capable of inducing high levels of cytokines that are associated with inflammation, this property is distinct from its inability to efficiently replicate in a mammalian host. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3803-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biruhalem Taye
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Republic of Singapore.,School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.,Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, P.O.BOX 1176, Ethiopia
| | - Hui Chen
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.,Current address Genome Institute of Singapore, A*STAR, 60 Biopolis Street, #02-01, Genome, Singapore, 138672, Republic of Singapore
| | - Myint Zu Myaing
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore
| | - Boon Huan Tan
- Detection and Diagnostics Laboratory, Defence Science Organisation National Laboratories, 27 Medical Drive, Singapore, 117510, Republic of Singapore.,LKC School of Medicine, Nanyang Technological University, 50 Nanyang Ave, Singapore, 639798, Republic of Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute, A*STAR, 30 Biopolis Street #07-01, Matrix, Singapore, 138671, Republic of Singapore.,National Public Health Laboratory, Ministry of Health, Singapore, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore, 117597, Republic of Singapore
| | - Richard J Sugrue
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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Taye B. Atopy and Helicobacter Pylori (H, Pylori) infection: A Systematic Review and Meta-Analysis. Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv096.317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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10
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Taye B. Podoconiosis and Soil-Transmitted Helminths (STHs): Double burden of Neglected Tropical Diseases in Wolaita zone, Rural Southern Ethiopia. Int J Epidemiol 2015. [DOI: 10.1093/ije/dyv097.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Taye B, Enquselassie F, Tsegaye A, Medhin G, Davey G, Venn A. Is Helicobacter Pylori
infection inversely associated with atopy? A systematic review and meta-analysis. Clin Exp Allergy 2015; 45:882-890. [DOI: 10.1111/cea.12404] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 12/16/2022]
Affiliation(s)
- B. Taye
- School of Public Health; College of Health Sciences; Addis Ababa University; Addis Ababa Ethiopia
| | - F. Enquselassie
- School of Public Health; College of Health Sciences; Addis Ababa University; Addis Ababa Ethiopia
| | - A. Tsegaye
- School of Allied Health Sciences; College of Health Sciences; Addis Ababa University; Addis Ababa Ethiopia
| | - G. Medhin
- Aklilu Lemma Institute of Pathobiology; College of Health Sciences; Addis Ababa University; Addis Ababa Ethiopia
| | - G. Davey
- Brighton & Sussex Medical School; Brighton UK
| | - A. Venn
- Division of Epidemiology and Public Health; University of Nottingham; Nottingham UK
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Tulu B, Dida N, Kassa Y, Taye B. Smear positive pulmonary tuberculosis and its risk factors among tuberculosis suspect in South East Ethiopia; a hospital based cross-sectional study. BMC Res Notes 2014; 7:285. [PMID: 24884870 PMCID: PMC4023165 DOI: 10.1186/1756-0500-7-285] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis remains a deadly infectious disease, affecting millions of people worldwide. Ethiopia ranks seventh among the twenty two high tuberculosis burden countries. The aim of this study was to determine the prevalence of smear positive pulmonary tuberculosis and its associated risk factors in Goba and Robe hospitals of Bale zone. METHODS A cross-sectional study was conducted on tuberculosis suspected patients from February-May 2012. Sputum samples were examined for acid fast bacilli using Ziehl-Neelsen staining and interview was conducted for each patient. Descriptive statistics, binary logistic and multivariable logistic regression analyses were employed to identify factors associated with pulmonary tuberculosis infection. RESULT The prevalence of smear positive tuberculosis was 9.2%. Age >36 (AOR = 3.54, 95% CI = 1. 3-9.82), marital status (AOR = 8.40, 95% CI = 3.02-23.20), family size (AOR = 4. 10, 95% CI = 1.60-10.80), contact with active tuberculosis patient (AOR = 5. 90; 95% CI = 2. 30-15.30), smoking cigarette regularly (AOR = 3. 90; 95% CI = 1. 20-12.40), and human immunodeficiency virus sero-status (AOR = 11. 70; 95% CI = 4. 30-31.70) were significantly associated with smear positive pulmonary tuberculosis. CONCLUSION The prevalence of smear positive pulmonary tuberculosis was high in the study area. Age, marital status, family size, history of contact with active tuberculosis patient, smoking cigarettes, and HIV sero-status were among the risk factors significantly associated with acquiring tuberculosis. Hence, strict pulmonary tuberculosis screening of HIV patients and intensification of health education to avoid risk factors identified are recommended.
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Affiliation(s)
- Begna Tulu
- Microbiology, Immunology and Parasitology Department, College of Medicine and Health Sciences, Bahir Dar University, P, O, Box 79, Bahir Dar, Ethiopia.
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Taye B, Giday M, Animut A, Seid J. Antibacterial activities of selected medicinal plants in traditional treatment of human wounds in Ethiopia. Asian Pac J Trop Biomed 2011; 1:370-5. [PMID: 23569795 PMCID: PMC3614199 DOI: 10.1016/s2221-1691(11)60082-8] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/08/2011] [Accepted: 04/24/2011] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE To evaluate the activity of selected Ethiopian medicinal plants traditionally used for wound treatment against wound-causing bacteria. METHODS Samples of medicinal plants (Achyranthes aspera, Brucea antidysenterica, Datura stramonium, Croton macrostachyus, Acokanthera schimperi, Phytolacca dodecandra, Millettia ferruginea, and Solanum incanum) were extracted using absolute methanol and water and tested for their antimicrobial activities against clinical isolates and standard strains of wound-causing bacteria using agar well diffusion and micro titer plate methods. RESULTS Most of the plant extracts had antibacterial activities, among which Acokanthera schimperi and Brucea antidysenterica inhibited growth of 100% and 35% of the test organisms, respectively. Methanolic extracts had higher activities compared with their corresponding aqueous extracts. The most susceptible organism to the extracts was Streptococcus pyogens while the most resistant were Escherichia coli and Proteus vulgaris. CONCLUSIONS This finding justifies the use of the plants in wound healing and their potential activity against wound-causing bacteria. Their toxicity level and antimicrobial activity with different extraction solvents should further be studied to use them as sources and templates for the synthesis of drugs to control wound and other disease-causing bacteria.
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Affiliation(s)
- Biruhalem Taye
- Aklilu Lemma Institute of Pathobiology, P.O. Box 1176, Addis Ababa University, Addis Ababa, Ethiopia
| | - Mirutse Giday
- Aklilu Lemma Institute of Pathobiology, P.O. Box 1176, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abebe Animut
- Aklilu Lemma Institute of Pathobiology, P.O. Box 1176, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jemal Seid
- ALERT Hospital, Addis Ababa, Ethiopia, P.O. Box 3434, Addis Ababa, Ethiopia
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Taye B, Shiferaw S, Enquseliassie F. O2-1.2 Impact of malnutrition in survival of HIV infected children after initiation of antiretroviral treatment (ART). Br J Soc Med 2011. [DOI: 10.1136/jech.2011.142976a.47] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Taye B, Shiferaw S, Enqusilasie F. OL-037 Impact of malnutrition in survival of HIV-infected children after initiation of antiretroviral treatment (ART). Int J Infect Dis 2008. [DOI: 10.1016/s1201-9712(09)60134-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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Mengistu A, Smith DG, Yoseph S, Nega T, Zewdie W, Kassahun WG, Taye B, Firew T. The effect of providing feed supplementation and anthelmintic to donkeys during late pregnancy and lactation on live weight and survival of dams and their foals in central Ethiopia. Trop Anim Health Prod 2006; 37 Suppl 1:21-33. [PMID: 16335069 DOI: 10.1007/s11250-005-9003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anthelmintic treatment (A), feed supplementation (F), anthelmintic and feed supplementation (A+F) or traditional management (Control) was given to 166 pregnant female donkeys in three localities (Holetta, Debre Zeit and Adami Tulu) in Ethiopia during an on-farm study. Treatments started during the last trimester of pregnancy and continued until 6 months after parturition when the foals were weaned. The same treatments were administered to foals once they reached 1 month of age. Live weights of adults and foals were measured throughout the study along with work output of adult donkeys and survival to weaning of the foals. Faecal worm egg counts (FEC) and blood packed cell volumes (PCV) were recorded monthly. When applied alone, anthelmintic treatment (A) or feed supplementation (F) had no significant effect on live weight gain or foal survival. However, when combined, anthelmintic and feed supplementation (A+F) significantly (p<0.05) improved both live weight gain in adults and foals and foal survival. Workout was not affected by any of the treatments. Treatments A and A+F resulted in a highly significant (p<0.001) reduction in FEC in all three localities during the course of study and for at least 6 months after the last dose of anthelmintic in one of the study areas (Holetta). None of the treatments had any significant effect on PCV. Donkey owners in Ethiopia should be encouraged to adopt both anthelmintic treatment and feed supplementation if they expect tangible benefits in animal performance.
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Affiliation(s)
- A Mengistu
- Ethiopian Agricultural Research Organisation, Holetta Research Centre, Addis Ababa, Ethiopia
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