Application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial tuberculosis infection

Referral hospitals in sub-Saharan Africa concentrate large numbers of tuberculosis (TB) and multidrug-resistant TB (MDR-TB) patients, failed by community TB services. We have previously shown, from enhanced screening and through autopsy studies, a significant burden of missed TB infections at the University Teaching Hospital, Lusaka, Zambia, with many patients dying or being discharged without treatment. With minimal TB isolation facilities and minimal political will to invest in broader screening and isolation, the risk of nosocomial transmission is likely to be extremely high. Studies from other hospitals in low burden settings and in South Africa have shown that next generation sequencing (NGS) is a very powerful tool for rapidly sequencing whole TB genomes and comparing them to confirm or rule out nosocomial transmission. The established platforms for NGS analysis, such as Illumina, are very expensive, immobile, and require regular maintenance, making them a costly inclusion on a research proposal or programmatic intervention grant in Africa. MinION nanopore sequencing has changed the NGS landscape with cheap portable sequencers, rapid simple library preparation (15min), and automated real-time analysis tools. The application of highly portable MinION nanopore sequencing technology for the monitoring of nosocomial TB infection will be discussed. Preliminary data from our pediatric pneumonia study will demonstrate the detection of TB in induced sputum from children admitted to the University Teaching Hospital

Evidence of EBV infection in lymphomas diagnosed in Lusaka, Zambia

Introduction: Epstein-Barr virus (EBV) is a ubiquitous virus that infects more than 90% of the world's population, and is implicated in lymphoma pathogenesis. However, in Zambia during the diagnosis of these lymphomas, the association of the virus with the lymphomas is not established. Since most patients with lymphomas have poor prognosis, the identification of the virus within the lymphoma lesion will allow for more targeted therapy. The aim of this study was to provide evidence of the presence of the EBV in lymphomas diagnosed at the University Teaching Hospital (UTH) in Lusaka, Zambia.Methods: one hundred and fifty archival formalin-fixed paraffin embedded suspected lymphoma tissues stored over a 4-year period in the Histopathology Laboratory at the UTH in Lusaka, Zambia, were analysed. Histological methods were used to identify the lymphomas, and the virus was detected using Polymerase Chain Reaction (PCR). Subtyping of the virus was achieved through DNA sequencing of the EBNA-2 region of the viral genome. Chi square or fisher's exact test was used to evaluate the association between EBV status, type of lymphoma and gender.Results: the majority of the lymphomas identified were non-Hodgkin's lymphoma (NHL) (80%) followed by Hodgkin's lymphoma (HL) (20%). EBV was detected in 51.8% of the cases, 54.5% of which were associated with NHL cases, while 40.9% associated with HL cases. The predominant subtype of the virus in both types of lymphomas was subtype 1. One of the lymphoma cases harboured both subtype 1 and 2 of the virus.Conclusion: this study showed that EBV is closely associated with lymphomas. Therefore, providing evidence of the presence of the virus in lymphoma tissues will aid in targeted therapy. To our knowledge this is the first time such data has been generated in Zambia

Clinical Performance Validation of 4 Point-of-Care Cervical Cancer Screening Tests in HIV-Infected Women in Zambia

We sought to determine the clinical performance of visual inspection with acetic acid (VIA), digital cervicography (DC), Xpert HPV, and OncoE6 for cervical cancer screening in an HIV-infected population

Identification of human papillomaviruses from formalin-fixed, paraffin-embedded pre-cancer and invasive cervical cancer specimens in Zambia: a cross-sectional study

BackgroundThe most common human papillomavirus (HPV) genotypes isolated from cervical cancer in select African countries are HPV-16, HPV-18, HPV-35, and HPV-45, but the most common genotypes in Zambia are unknown. The overall objective of this study was to assess the potential impact of current HPV vaccines in preventing cervical cancer in Zambia, by determining the combined prevalence of HPV-16 and/or HPV-18 in invasive cervical cancer (ICC) and high-grade pre-cancer [cervical intraepithelial neoplasia 2 or 3 (CIN2/3)] cases.FindingsWe compared DNA extraction techniques to determine which assay performs well in the Zambian context, where unbuffered formalin is used to fix specimens. We then tested specimens with the Abbott RealTime High-Risk HPV test to estimate the prevalence of HPV-16/18 in formalin-fixed, paraffin-embedded ICC and CIN2/3 specimens. DNA extraction using heat (without xylene) was more successful than xylene-based extraction. Over 80% of specimens tested using heat extraction and the Abbott RealTime HPV test were positive for HPV. HPV-16 and/or HPV-18 were identified in 65/93 (69.9%) ICC specimens positive for HPV and in 38/65 (58.5%) CIN2/3 specimens positive for HPV.ConclusionsTo our knowledge this is the first report to identify HPV genotypes in cervical cancers in Zambia. A combined HPV-16/18 prevalence of 69.9% in ICC specimens suggests that current vaccines will be highly protective against cervical cancer in Zambia

Kajian potensi ekstrak bilberi sebagai penunjuk pH untuk memantau kesegaran makanan secara kromametri

Penunjuk pH sebagai suatu pendekatan untuk memantau kualiti atau kesegaran makanan semasa telah mendapat perhatian industri pembungkusan makanan. Penggunaan sumber semula jadi pigmen tumbuhan terutamanya daripada buah-buahan dan sayur-sayuran menjadi pilihan para pengguna untuk menggantikan pewarna sintetik dalam memastikan keselamatan makanan yang diambil setiap hari. Dalam kajian ini, ekstrak daripada bilberi telah digunakan sebagai pewarna sensitif pH. Perubahan warna sampel dikaji secara terperinci melalui kaedah kromametri dan juga kaedah spektrofotometri ultra-lembayung nampak. Warna merah terang terhasil dalam pH berasid, merah pudar pada neutral dan magenta ke kuning dalam pH beralkali. Keputusan kajian kromametri menunjukkan bahawa ekstrak bilberi berupaya mempamerkan perubahan warna yang jelas terhadap perubahan pH, iaitu terdapat perubahan nilai warna a* yang menyumbang kepada perubahan yang bererti dalam perbezaan warna keseluruhan (ΔE*). Nilai ΔE* juga ditentukan wujud hubungan linear dan kuantitatif terhadap julat pH tertentu. Oleh yang demikian, ekstrak bilberi didapati berpotensi sebagai bahan sensor untuk pH dalam membangunkan satu sensor pH bagi memantau kesegaran makanan terutamanya hasilan laut berbungkus memandangkan tahap kerosakan produk tersebut berkait rapat dengan perubahan pH ke arah alkali

A simple method for short-term maintenance of neonatal mice without foster mothers

Mice are typically weaned from their mother between 21 and 28 days of age, or at 10 grams of body weight. However, some biochemical experiments need to be done before the weaning days, and the mother might cannibalize or ignore those manipulated pups. Here, we provide a detailed protocol for maintenance of neonatal mice without the presence of their mothers for biomedical research. The basic instinct of neonate mice to hide under covers is harnessed for their survival in a mother-free environment. When covers are soaked with milk and the only targets for hiding, the neonates would acquire their nutrients at least in an involuntary fashion. The protocol is simple and can be used for neonatal rodent studies for short periods of times, and assures the accuracy of the biomedical experiments if survival rate of neonates is critical

Epstein Barr virus-immortalizedＢlymphocytes exacerbate experimental autoimmune encephalomyelitis in xenograft mice

Multiple sclerosis (MS) is the most common autoimmune disorder affecting the central nervous system. Epstein-Barr virus (EBV) is a causative agent for infectious mononucleosis (IM) that is associated with MS pathogenesis. However, the exact mechanism by which EBV, specifically in IM, increases the risk for MS remains unknown. EBV immortalizes primary B lymphocytes in vitro and causes excessive B lymphocyte proliferation in IM in vivo. In asymptomatic carriers, EBV-infected B lymphocytes still proliferate to certain degrees, the process of which is tightly controlled by the host immune systems. Experimental autoimmune encephalomyelitis (EAE) mimics key features of MS in humans and is a well-established rodent model for human MS. We have found that xenografts of EBV-immortalized B lymphocytes, which partially resemble the hyperproliferation of EBV-infected cells in IM, exacerbate autoimmune responses in myelin oligodendrocyte glycoprotein-induced EAE in C57BL/6 mice. After remission, an additional challenge with EBV-immortalized cells induces a relapse in EAE. Moreover, xenografts with EBV-immortalized cells tighten the integrity of blood brain barrier (BBB) in thalamus and hypothalamus areas of the mouse brains. Genomic sequences of prokaryotic 16S rRNA presented in feces reveal that EBV-immortalized cells significantly change the diversities of microbial populations. Our data collectively suggest that EBV-mediated proliferation of B lymphocytes may be a risk factor for the exacerbation of MS, which are associated with gut microbiome changes and BBB modulations. Furthermore, multiple xenografts of EBV-immortalized cells into in C57BL/6 mice could sever as a useful model for human relapsing-remitting MS with predictable severity and timing

Epstein Barr virus-immortalizedＢlymphocytes exacerbate experimental autoimmune encephalomyelitis in xenograft mice

Multiple sclerosis (MS) is the most common autoimmune disorder affecting the central nervous system. Epstein-Barr virus (EBV) is a causative agent for infectious mononucleosis (IM) that is associated with MS pathogenesis. However, the exact mechanism by which EBV, specifically in IM, increases the risk for MS remains unknown. EBV immortalizes primary B lymphocytes in vitro and causes excessive B lymphocyte proliferation in IM in vivo. In asymptomatic carriers, EBV-infected B lymphocytes still proliferate to certain degrees, the process of which is tightly controlled by the host immune systems. Experimental autoimmune encephalomyelitis (EAE) mimics key features of MS in humans and is a well-established rodent model for human MS. We have found that xenografts of EBV-immortalized B lymphocytes, which partially resemble the hyperproliferation of EBV-infected cells in IM, exacerbate autoimmune responses in myelin oligodendrocyte glycoprotein-induced EAE in C57BL/6 mice. After remission, an additional challenge with EBV-immortalized cells induces a relapse in EAE. Moreover, xenografts with EBV-immortalized cells tighten the integrity of blood brain barrier (BBB) in thalamus and hypothalamus areas of the mouse brains. Genomic sequences of prokaryotic 16S rRNA presented in feces reveal that EBV-immortalized cells significantly change the diversities of microbial populations. Our data collectively suggest that EBV-mediated proliferation of B lymphocytes may be a risk factor for the exacerbation of MS, which are associated with gut microbiome changes and BBB modulations. Furthermore, multiple xenografts of EBV-immortalized cells into in C57BL/6 mice could sever as a useful model for human relapsing-remitting MS with predictable severity and timing

Epstein Barr virus-immortalizedＢlymphocytes exacerbate experimental autoimmune encephalomyelitis in xenograft mice

Multiple sclerosis (MS) is the most common autoimmune disorder affecting the central nervous system. Epstein-Barr virus (EBV) is a causative agent for infectious mononucleosis (IM) that is associated with MS pathogenesis. However, the exact mechanism by which EBV, specifically in IM, increases the risk for MS remains unknown. EBV immortalizes primary B lymphocytes in vitro and causes excessive B lymphocyte proliferation in IM in vivo. In asymptomatic carriers, EBV-infected B lymphocytes still proliferate to certain degrees, the process of which is tightly controlled by the host immune systems. Experimental autoimmune encephalomyelitis (EAE) mimics key features of MS in humans and is a well-established rodent model for human MS. We have found that xenografts of EBV-immortalized B lymphocytes, which partially resemble the hyperproliferation of EBV-infected cells in IM, exacerbate autoimmune responses in myelin oligodendrocyte glycoprotein-induced EAE in C57BL/6 mice. After remission, an additional challenge with EBV-immortalized cells induces a relapse in EAE. Moreover, xenografts with EBV-immortalized cells tighten the integrity of blood brain barrier (BBB) in thalamus and hypothalamus areas of the mouse brains. Genomic sequences of prokaryotic 16S rRNA presented in feces reveal that EBV-immortalized cells significantly change the diversities of microbial populations. Our data collectively suggest that EBV-mediated proliferation of B lymphocytes may be a risk factor for the exacerbation of MS, which are associated with gut microbiome changes and BBB modulations. Furthermore, multiple xenografts of EBV-immortalized cells into in C57BL/6 mice could sever as a useful model for human relapsing-remitting MS with predictable severity and timing