A tree-structured index algorithm for expressed sequence tags clustering

Abstract Expressed sequence tags (ESTs) are complementary deoxyribonucleic acid (cDNA) fragments, which are reverse transcribed from mature ribonucleic acid (mRNA), a direct gene transcript. ESTs are a readily rich information source of complete expressed gene sequences. They reveal the type and number of genes being expressed in an organism. Joining ESTs into complete gene sequences is computationally expensive because they are numerous, erroneous, redundant and mixed up. ESTs that originate from the same gene are grouped together. This enables efficient consensus sequences generation, which reveals underlying gene sequences and their possible alternative splicings. EST clustering enables efficient discovery of expressed genes based on which several fields rely such as: disease diagnostics, drug discovery, genetic engineering, alternative splicing and many others. Most clustering algorithms developed so far are quadratic and their running time is prohibitively high. A tree-structured index algorithm has been developed to efficiently cluster ESTs with respect to running time and quality of generated clusters. The algorithm clusters ESTs in a pseudometric space by recursively partitioning a data set of EST windows into two disjointed sets. Performance of the algorithm was tested with respect to running time and quality of generated clusters. Further experiments were performed to investigate the effectiveness of the triangle inequality, which was implemented to reduce distance computations during clustering. Experimental results show that the algorithm has a running time closer to linear with a 100% specificity, but it fluctuates in sensitivity. Implementation of the triangle inequality did not significantly improve the performance of the algorithm

Factors affecting the utilisation of electronic medical records system in Malawian central hospitals

Background In Malawi, paper-based medical record-keeping has been observed to exacerbate challenges related to accessing patient records and patient tracking. Despite the introduction of electronic medical record (EMR) systems in 2001, paper-based records continue to be in use. Some health workers prefer paper-based records to EMRs. This study assessed factors that affect the use of EMRs in Malawi, particularly at Queen Elizabeth and Kamuzu Central Hospitals. It further investigated the reasons why paper-based records are still in use despite the numerous associated disadvantages. The extent to which EMRs contribute to patient care was also analysed.Methods In this cross-sectional study, 111 randomly selected health workers were interviewed, using a semistructured questionnaire, at the 2 largest central hospitals in Malawi, where EMRs were first introduced in the country. Focus group discussions were conducted to gather further information on factors identified during the individual interviews.Results and conclusions Differences in age, gender, and previous computer experience were not associated with differences in EMR usage. However, education and employment levels has a positive association with EMR usage. Hardware and connectivity problems, as well as lack of training and managerial support negatively affected the use of EMRs. EMRs were found to improve data quality and efficiency in patient management

Analysis of genomic rearrangements, horizontal gene transfer and role of plasmids in the evolution of industrial important Thermus species

BACKGROUND: Bacteria of genus Thermus inhabit both man-made and natural thermal environments. Several Thermus species have shown biotechnological potential such as reduction of heavy metals which is essential for eradication of heavy metal pollution; removing of organic contaminants in water; opening clogged pipes, controlling global warming among many others. Enzymes from thermophilic bacteria have exhibited higher activity and stability than synthetic or enzymes from mesophilic organisms. RESULTS: Using Meiothermus silvanus DSM 9946 as a reference genome, high level of coordinated rearrangements has been observed in extremely thermophilic Thermus that may imply existence of yet unknown evolutionary forces controlling adaptive re-organization of whole genomes of thermo-extremophiles. However, no remarkable differences were observed across species on distribution of functionally related genes on the chromosome suggesting constraints imposed by metabolic networks. The metabolic network exhibit evolutionary pressures similar to levels of rearrangements as measured by the cross-clustering index. Using stratigraphic analysis of donor-recipient, intensive gene exchanges were observed from Meiothermus species and some unknown sources to Thermus species confirming a well established DNA uptake mechanism as previously proposed. CONCLUSION: Global genome rearrangements were found to play an important role in the evolution of Thermus bacteria at both genomic and metabolic network levels. Relatively higher level of rearrangements was observed in extremely thermophilic Thermus strains in comparison to the thermo-tolerant Thermus scotoductus. Rearrangements did not significantly disrupt operons and functionally related genes. Thermus species appeared to have a developed capability for acquiring DNA through horizontal gene transfer as shown by the donor-recipient stratigraphic analysis.http://www.biomedcentral.com/bmcgenomics/am201

Dosage of Sulfadoxine–Pyrimethamine and Risk of Low Birth Weight in a Cohort of Zambian Pregnant Women in a Low Malaria Prevalence Region

In Lusaka, Zambia, where malaria prevalence is low, national guidelines continue to recommend that all pregnant women receive sulfadoxine–pyrimethamine (SP) for malaria prophylaxis monthly at every scheduled antenatal care visit after 16 weeks of gestation. Human immunodeficiency virus (HIV)–positive women should receive co-trimoxazole prophylaxis for HIV and not SP, but many still receive SP. We sought to determine whether increased dosage of SP is still associated with a reduced risk of low birth weight (LBW) in an area where malaria transmission is low. Our secondary objective was to determine whether any association between SP and LBW is modified by receipt of antiretroviral therapy (ART). We analyzed data routinely collected from a cohort of HIV-positive pregnant women with singleton births in Lusaka, Zambia, between February 2006 and December 2012. We used a log-Poisson model to estimate the risk of LBW by dosage of SP and to determine whether the association between SP and LBW varied by receipt of ART. Risk of LBW declined as the number of doses increased and appeared lowest among women who received three doses (adjusted risk ratio [ARR] = 0.78; 95% confidence interval [CI] = 0.64–0.95). In addition, women receiving combination ART had a higher risk of delivering an LBW infant compared with women receiving no treatment or prophylaxis (ARR = 1.18; 95% CI = 1.09–1.28), but this risk was attenuated among women who were receiving SP (risk ratio = 1.09; 95% CI = 0.99–1.21). SP was associated with a reduced risk of LBW in HIV-positive women, including those receiving ART, in a low malaria prevalence region

Factors Influencing Loss to Follow-up among Human Immunodeficiency Virus Exposed Infants in the Early Infant Diagnosis Program in Phalombe, Malawi

The efforts to prevent mother to child transmission of HIV in Malawi are impeded by the loss to follow-up of HIV-exposed infants (HEI) in care. Early infant diagnosis (EID) of HEI and linkage to care reduces morbidity and mortality. There has been limited attention to infants who are lost to follow up despite their mothers being compliant to the PMTCT program. This study explored factors that influence loss-to-follow up among HEI in the EID program whose mothers were retained in care for up to 24 months in Phalombe district, Malawi. We conducted a descriptive phenomenological qualitative study from May 2017 to July 2018. We purposively conducted 18 in-depth interviews among HIV positive mothers whose HEI were enrolled in the follow-up program and 7 key informant interviews among healthcare workers (HCW). All interviews were digitally recorded, transcribed, and translated verbatim. Data were analyzed manually using a thematic step-by-step approach. Results showed that retention in care is facilitated by aspirations to have a healthy infant and linkage to a nearer facility to a mother's place of residency. The barriers to retention were non-disclosure of HIV status, inadequate resources, and support, suboptimal guidelines for, a lack of privacy, and unsynchronized hospital visits between a mother and her baby. The study has shown that successful implementation of EID services requires concerted efforts from various contextualized stakeholders whilst focusing on family-centered care. To maximize retention in EID and innovative ways of reaching mothers and babies through flexible guidelines are urgently needed

Two strategies for partner notification and partner HIV self-testing reveal no evident predictors of male partner HIV testing in antenatal settings: A secondary analysis

BackgroundTo meet global targets for the elimination of mother-to-child HIV transmission, tailored approaches to HIV testing strategies need prioritizing. Herein, we sought to identify individual-level factors associated with male partner HIV testing.MethodsWe conducted a secondary analysis of data from two parallel randomized trials of pregnant women living with HIV and those HIV-negative in Lusaka, Zambia. Across both trials, control groups received partner notification services only, while intervention groups received partner notification services plus HIV self-test kits for their partners. Associations between baseline factors and male partner testing were estimated using a probability difference. The outcome of interest was uptake of male partner HIV testing of any kind within 30 days of randomization.ResultsThe parent study enrolled 326 participants. Among the 151 women in the control groups, no clear associations were noted between maternal or male partner characteristics and reported uptake of male partner HIV testing. There were positive trends favouring partner testing among women who completed primary school education, had larger households (>2 members), and whose partners were circumcised. Likewise, no clear predictors of male partner testing were identified among the 149 women in the intervention groups. However, negative trends favouring no testing were noted among older, multiparous women from larger households.ConclusionNo consistent predictors for male partner HIV testing across two compared strategies were observed. Our findings suggest that differentiated strategies for male partner HIV testing may not be necessary. Instead, consideration should be given to universal approaches when bringing such services to scale

HIV infection and stroke:current perspectives and future directions

HIV infection can result in stroke via several mechanisms, including opportunistic infection, vasculopathy, cardioembolism, and coagulopathy. However, the occurrence of stroke and HIV infection might often be coincidental. HIV-associated vasculopathy describes various cerebrovascular changes, including stenosis and aneurysm formation, vasculitis, and accelerated atherosclerosis, and might be caused directly or indirectly by HIV infection, although the mechanisms are controversial. HIV and associated infections contribute to chronic inflammation. Combination antiretroviral therapies (cART) are clearly beneficial, but can be atherogenic and could increase stroke risk. cART can prolong life, increasing the size of the ageing population at risk of stroke. Stroke management and prevention should include identification and treatment of the specific cause of stroke and stroke risk factors, and judicious adjustment of the cART regimen. Epidemiological, clinical, biological, and autopsy studies of risk, the pathogenesis of HIV-associated vasculopathy (particularly of arterial endothelial damage), the long-term effects of cART, and ideal stroke treatment in patients with HIV are needed, as are antiretrovirals that are without vascular risk

Evasion of MAIT cell recognition by the African Salmonella Typhimurium ST313 pathovar that causes invasive disease

Mucosal-associated invariant T (MAIT) cells are innate T lymphocytes activated by bacteria that produce vitamin B2 metabolites. Mouse models of infection have demonstrated a role for MAIT cells in antimicrobial defense. However, proposed protective roles of MAIT cells in human infections remain unproven and clinical conditions associated with selective absence of MAIT cells have not been identified. We report that typhoidal and nontyphoidal Salmonella enterica strains activate MAIT cells. However, S. Typhimurium sequence type 313 (ST313) lineage 2 strains, which are responsible for the burden of multidrug-resistant nontyphoidal invasive disease in Africa, escape MAIT cell recognition through overexpression of ribB. This bacterial gene encodes the 4-dihydroxy-2-butanone-4-phosphate synthase enzyme of the riboflavin biosynthetic pathway. The MAIT cell-specific phenotype did not extend to other innate lymphocytes. We propose that ribB overexpression is an evolved trait that facilitates evasion from immune recognition by MAIT cells and contributes to the invasive pathogenesis of S. Typhimurium ST313 lineage 2

Characterization of DNA methylation in Malawian Mycobacterium tuberculosis clinical isolates.

BACKGROUND: Although Mycobacterium tuberculosis (Mtb) strains exhibit genomic homology of >99%, there is considerable variation in the phenotype. The underlying mechanisms of phenotypic heterogeneity in Mtb are not well understood but epigenetic variation is thought to contribute. At present the methylome of Mtb has not been completely characterized. METHODS: We completed methylomes of 18 Mycobacterium tuberculosis (Mtb) clinical isolates from Malawi representing the largest number of Mtb genomes to be completed in a single study using Single Molecule Real Time (SMRT) sequencing to date. RESULTS: We replicate and confirm four methylation disrupting mutations in 4 lineages of Mtb. For the first time we report complete loss of methylation courtesy of C758T (S253L) mutation in the MamB gene of Indo-oceanic lineage of Mtb. Additionally, we report a novel missense mutation G454A (G152S) in the MamA gene of the Euro-American lineage which could potentially be attributed to total disruption of methylation in the CCCAG motif but partial loss in a partner motif. Through a genomic and methylome comparative analysis with a global sample of sixteen, we report previously unknown mutations affecting the pks15/1 locus in L6 isolates. We confirm that methylation in Mtb is lineage specific although some unresolved issues still remain

Comparative whole genome analysis reveals re-emergence of human Wa-like and DS-1-like G3 rotaviruses after Rotarix vaccine introduction in Malawi

G3 rotaviruses rank among the most common rotavirus strains worldwide in humans and animals. However, despite a robust long-term rotavirus surveillance system from 1997 at Queen Elizabeth Central Hospital in Blantyre, Malawi, these strains were only detected from 1997 to 1999 and then disappeared and re-emerged in 2017, five years after the introduction of the Rotarix rotavirus vaccine. Here we analysed representative 27 whole genome sequences (G3P[4], n=20; G3P[6], n=1; and G3P[8], n=6) randomly selected each month between November 2017 and August 2019 to understand how G3 strains re-emerged in Malawi. We found four genotype constellations that were associated with the emergent G3 strains and co-circulated in Malawi post-Rotarix vaccine introduction: G3P[4] and G3P[6] strains with the DS-1-like genetic backbone genes (G3-P[4]-I2-R2-C2-M2-A2-N2-T2-E2-H2) and G3-P[6]-I2-R2-C2-M2-A2-N2-T2-E2-H2), G3P[8] strains with the Wa-like genetic backbone genes (G3-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1), and reassortant G3P[4] strains consisting of the DS-1-like genetic backbone genes and a Wa-like NSP2 (N1) gene (G3-P[4]-I2-R2-C2-M2-A2-N1-T2-E2-H2). Time-resolved phylogenetic trees demonstrated that the most recent common ancestor for each RNA segment of the emergent G3 strains was between 1996 and 2012, possibly through introductions from outside the country due to the limited genetic similarity with G3 strains which circulated before their disappearance in the late 1990s. Further genomic analysis revealed that the reassortant DS-1-like G3P[4] strains acquired a Wa-like NSP2 genome segment (N1 genotype) through intergenogroup reassortment; an artiodactyl-like VP3 through intergenogroup interspecies reassortment; and VP6, NSP1 and NSP4 segments through intragenogroup reassortment likely before importation into Malawi. Additionally, the emergent G3 strains contain amino acid substitutions within the antigenic regions of the VP4 proteins which could potentially impact the binding of rotavirus vaccine-induced antibodies. Altogether, our findings show that multiple strains with either Wa-like or DS-1-like genotype constellations have driven the re-emergence of G3 strains. The findings also highlight the role of human mobility and genome reassortment events in the cross-border dissemination and evolution of rotavirus strains in Malawi necessitating the need for long-term genomic surveillance of rotavirus in high disease burden settings to inform disease prevention and control