Detection of a SARS-CoV-2 variant of concern in South Africa.

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating conditions for substantial evolutionary changes to the virus1,2. Here we describe a newly arisen lineage of SARS-CoV-2 (designated 501Y.V2; also known as B.1.351 or 20H) that is defined by eight mutations in the spike protein, including three substitutions (K417N, E484K and N501Y) at residues in its receptor-binding domain that may have functional importance3-5. This lineage was identified in South Africa after the first wave of the epidemic in a severely affected metropolitan area (Nelson Mandela Bay) that is located on the coast of the Eastern Cape province. This lineage spread rapidly, and became dominant in Eastern Cape, Western Cape and KwaZulu-Natal provinces within weeks. Although the full import of the mutations is yet to be determined, the genomic data-which show rapid expansion and displacement of other lineages in several regions-suggest that this lineage is associated with a selection advantage that most plausibly results from increased transmissibility or immune escape6-8.

Comparison of SARS-CoV-2 sequencing using the ONT GridION and the Illumina MiSeq.

BACKGROUND: Over 4 million SARS-CoV-2 genomes have been sequenced globally in the past 2 years. This has been crucial in elucidating transmission chains within communities, the development of new diagnostic methods, vaccines, and antivirals. Although several sequencing technologies have been employed, Illumina and Oxford Nanopore remain the two most commonly used platforms. The sequence quality between these two platforms warrants a comparison of the genomes produced by the two technologies. Here, we compared the SARS-CoV-2 consensus genomes obtained from the Oxford Nanopore Technology GridION and the Illumina MiSeq for 28 sequencing runs. RESULTS: Our results show that the MiSeq had a significantly higher number of consensus genomes classified by Nextclade as good and mediocre compared to the GridION. The MiSeq also had a significantly higher genome coverage and mutation counts than the GridION. CONCLUSION: Due to the low genome coverage, high number of indels, and sensitivity to SARS-CoV-2 viral load noted with the GridION when compared to MiSeq, we can conclude that the MiSeq is more favourable for SARS-CoV-2 genomic surveillance, as successful genomic surveillance is dependent on high quality, near-whole consensus genomes.

Comparing the number and relevance of false activations between 2 artificial intelligence computer-aided detection systems: the NOISE study.

BACKGROUND AND AIMS: Artificial intelligence has been shown to be effective in polyp detection, and multiple computer-aided detection (CADe) systems have been developed. False-positive (FP) activation emerged as a possible way to benchmark CADe performance in clinical practice. The aim of this study was to validate a previously developed classification of FPs comparing the performances of different brands of approved CADe systems. METHODS: We compared 2 different consecutive video libraries (40 video per arm) collected at Humanitas Research Hospital with 2 different CADe system brands (CADe A and CADe B). For each video, the number of CADe false activations, cause, and time spent by the endoscopist to examine the area erroneously highlighted were reported. The FP activations were classified according to the previously developed classification of FPs (the NOISE classification) according to their cause and relevance. RESULTS: In CADe A 1021 FP activations were registered across the 40 videos (25.5 ± 12.2 FPs per colonoscopy), whereas in CADe B 1028 were identified (25.7 ± 13.2 FPs per colonoscopy; P = .53). Among them, 22.9 ± 9.9 (89.8% in CADe A) and 22.1 ± 10.0 (86.0% in CADe B) were because of artifacts from the bowel wall. Conversely, 2.6 ± 1.9 (10.2% in CADe A) and 3.5 ± 2.1 (14% in CADe B) were caused by bowel content (P = .45). Within CADe A each false activation required .2 ± .9 seconds, with 1.6 ± 1.0 FPs (6.3%) requiring additional time for endoscopic assessment. Comparable results were reported within CADe B with .2 ± .8 seconds spent per false activation and 1.8 ± 1.2 FPs per colonoscopy requiring additional inspection. CONCLUSIONS: The use of a standardized nomenclature provided comparable results with either of the 2 recently approved CADe systems. (Clinical trial registration number: NCT04399590.).

EUS-guided laser lithotripsy for pancreatic duct stones after failed conventional pancreatic endotherapy.

The central dogma of pain in patients with chronic pancreatitis revolves around the pathophysiology of ductal hypertension owing to stones that obstruct the pancreatic duct. Conventional modalities available to decompress the pancreatic duct are occasionally limited by failed selective pancreatic duct cannulation during endoscopic retrograde cholangiopancreatography. We describe a novel endoscopic approach of EUS-guided laser lithotripsy to assist in pancreatic duct (PD) stone fragmentation in two symptomatic patients with underlying chronic pancreatitis who had failed PD cannulation and extracorporeal shock wave lithotripsy (ESWL). In both cases, a 365-micrometer LightTrail TracTip Holmium laser fiber was advanced within a 19G endoscopic ultrasound aspiration needle (Expect Slimline (SL), Boston Scientific, Marlborough, Massachusetts, United States) under endoscopic ultrasound (EUS) guidance to fragment the PD stones. There were no procedure-related complications encountered and follow-up after 1 month of the procedure revealed significant reduction in abdominal pain scores. To the best of our knowledge, these are the first reported cases of EUS-guided laser lithotripsy performed for PD stones. Our approach of performing laser lithotripsy under EUS guidance obviates the need for an ESWL procedure; however, it is technically more challenging and requires precision to avoid injury to the pancreas. Further prospective studies are required to evaluate the safety and efficacy of this novel approach and its applicability as either a rescue procedure or in tandem with conventional pancreatic endotherapy modalities.

Performance of rapid antigen tests in identifying Omicron BA.4 and BA.5 infections in South Africa.

BACKGROUND: Concerns around accuracy and performance of rapid antigen tests continue to be raised with the emergence of new SARS-CoV-2 variants. OBJECTIVE: To evaluate the performance of two widely used SARS-CoV-2 rapid antigen tests during BA.4/BA.5 SARS-CoV-2 wave in South Africa (May - June 2022). STUDY DESIGN: A prospective field evaluation compared the SARS-CoV-2 Antigen Rapid test from Hangzhou AllTest Biotech (nasal swab) and the Standard Q COVID-19 Rapid Antigen test from SD Biosensor (nasopharyngeal swab) to the Abbott RealTime SARS-CoV-2 assay (nasopharyngeal swab) on samples collected from 540 study participants. RESULTS: Overall 28.52% (154/540) were SARS-CoV-2 RT-PCR positive with median cycle number value of 12.30 (IQR 9.30-19.40). Out of the 99 successfully sequenced SARS-CoV-2 positive samples, 18 were classified as BA.4 and 56 were classified as BA.5. The overall sensitivities of the AllTest SARS-CoV-2 Ag test and Standard Q COVID-19 Ag test were 73.38% (95% CI 65.89-79.73) and 74.03% (95% CI 66.58-80.31) and their specificities were 97.41% (95% CI 95.30-98.59) and 99.22% (95% CI 97.74-99.74) respectively. Sensitivity was >90% when the cycle number value was <20. The sensitivity of both rapid tests was >90% in samples infected with Omicron sub-lineage BA.4 and BA.5. CONCLUSION: Accuracy of tested rapid antigen tests that target the nucleocapsid SARS-CoV-2 protein, were not adversely affected by BA.4 and BA.5 Omicron sub-variants.

Endoscopic retrograde cholangiopancreatography in a patient with complete situs inversus viscerum: A case report and literature review.

Complete situs inversus viscerum (SIV) is a rare congenital condition, defined by a left-right transposition of all viscera with dextroposition of the heart. In patients with SIV that requires endoscopic intervention, namely endoscopic retrograde cholangiopancreatography (ERCP), the left-right coordination can be technically demanding even with skilled endoscopist. We report a case of a patient with underlying SIV who presented with septic shock secondary to ascending cholangitis compounded with a malaria infection. Despite the ascertainment of a relatively large Common Bile Duct (CBD) stone, ERCP and stenting were pursued as an initial treatment modality in view of the clinical presentation of cholangitis and COVID-19-related delays in surgical intervention at our center. This case is unique as the patient was maintained in a supine position throughout the procedure. The patient underwent a successful ERCP procedure followed by a CBD Exploration and cholecystectomy 2 weeks later. A key factor that contributed to the success of this procedure was the combined utilization of a rotatable sphincterotome and extractor balloon which assisted with cannulation and shortening manoeuvre of the duodenoscope to facilitate biliary stenting.

Candidate Multi-Epitope Vaccine against Corona B.1.617 Lineage: In Silico Approach.

Various mutations have accumulated since the first genome sequence of SARS-CoV2 in 2020. Mutants of the virus carrying the D614G and P681R mutations in the spike protein are increasingly becoming dominant all over the world. The two mutations increase the viral infectivity and severity of the disease. This report describes an in silico design of SARS-CoV-2 multi-epitope carrying the spike D614G and P681R mutations. The designed vaccine harbors the D614G mutation that increases viral infectivity, fitness, and the P681R mutation that enhances the cleavage of S to S1 and S2 subunits. The designed multi-epitope vaccine showed an antigenic property with a value of 0.67 and the immunogenicity of the predicted vaccine was calculated and yielded 3.4. The vaccine construct is predicted to be non-allergenic, thermostable and has hydrophilic nature. The combination of the selected CTL and HTL epitopes in the vaccine resulted in 96.85% population coverage globally. Stable interactions of the vaccine with Toll-Like Receptor 4 were tested by docking studies. The multi-epitope vaccine can be a good candidate against highly infecting SARS-CoV-2 variants.

Enhanced endoscopic ultrasound imaging for pancreatic lesions: The road to artificial intelligence.

Early detection of pancreatic cancer has long eluded clinicians because of its insidious nature and onset. Often metastatic or locally invasive when symptomatic, most patients are deemed inoperable. In those who are symptomatic, multi-modal imaging modalities evaluate and confirm pancreatic ductal adenocarcinoma. In asymptomatic patients, detected pancreatic lesions can be either solid or cystic. The clinical implications of identifying small asymptomatic solid pancreatic lesions (SPLs) of < 2 cm are tantamount to a better outcome. The accurate detection of SPLs undoubtedly promotes higher life expectancy when resected early, driving the development of existing imaging tools while promoting more comprehensive screening programs. An imaging tool that has matured in its reiterations and received many image-enhancing adjuncts is endoscopic ultrasound (EUS). It carries significant importance when risk stratifying cystic lesions and has substantial diagnostic value when combined with fine needle aspiration/biopsy (FNA/FNB). Adjuncts to EUS imaging include contrast-enhanced harmonic EUS and EUS-elastography, both having improved the specificity of FNA and FNB. This review intends to compile all existing enhancement modalities and explore ongoing research around the most promising of all adjuncts in the field of EUS imaging, artificial intelligence.

Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic.

The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Endoscopic ultrasound-guided colo-colostomy in a case of acute large bowel obstruction.

Bowel obstruction is one of the most common surgical emergencies and a major cause of morbidity and mortality. Standard supportive measures must be instituted as soon as the diagnosis is confirmed. Anastomotic strictures are a benign etiology of intestinal obstruction, occurring in up to 22 % of patients following colorectal resection. Traditionally, endoscopic balloon dilation (EBD) has been the intervention of choice in such cases; however, it may not be feasible in all settings. We report a novel application of the AXIOS stent and electrocautery-enhanced delivery system (Boston Scientific, Marlborough, Massachusetts, United States) to create a colo-colostomy to bypass a sigmoid colon stricture in a 51-year-old woman who presented with acute intestinal obstruction. Despite stent dislodgment during the procedure, the preexisting tract allowed us to improvise our technique with a second LAMS placement. The patient was discharged well 48 hours after the procedure. However, 4 months later, she required a session of EBD following a presentation for fecal impaction. She is currently asymptomatic and being followed up regularly as an outpatient.

High Level of Multidrug-Resistant Gram-Negative Pathogens Causing Burn Wound Infections in Hospitalized Children in Dar es Salaam, Tanzania.

BACKGROUND: Bacterial infection remains the most common cause of morbidity and mortality in pediatric patients with burn wounds. The increase in infection and multidrug-resistant (MDR) pathogens necessitates a periodic review of antimicrobial susceptibility patterns in the burn units. The study aimed to determine the magnitude of multidrug-resistant Gram-negative (MDRGN) bacteria in children with burn wound infections and describe the resistance patterns in the tertiary and regional hospitals in Dar es Salaam, Tanzania. MATERIALS AND METHODS: The study was a hospital-based cross-sectional study design conducted between May 2017 and February 2018. Bacterial isolates from 103 wound swabs of pediatric patients with burn wounds were identified using conventional methods and API 20E. The antimicrobial susceptibility pattern was determined by the Kirby-Bauer disc diffusion method. Data were analyzed using Statistical Package for Social Science (SPSS) version 23.0. RESULTS: A total of 136 pathogenic Gram-negative organisms were isolated from burn wound infections in pediatric patients. The most isolated Gram-negative bacterium was Pseudomonas aeruginosa (39.0%), followed by Acinetobacter spp. (28.7%) and Klebsiella spp. (16.2%). MDRGN strains made up 80.1% of all Gram-negative isolates. All (100%) Klebsiella spp. and E. coli were MDR, while 69.2% and 79.2% of Acinetobacter spp. and P. aeruginosa, respectively, displayed MDR strains. We observed high levels of resistance to commonly prescribed antibiotics. Among P. aeruginosa isolates, highest resistance (81.8%) was seen toward meropenem and piperacillin, 79.5% of Acinetobacter spp. showed resistance to aztreonam, while 93-100% of Klebsiella spp and E. coli displayed resistance to amoxyclavulanic acid, ceftriaxone, and ceftazidime. The proportion of extended-spectrum beta-lactamase producers among Enterobacteriaceae was 78.6%. There was a significant higher rate of infection with MDRGN organisms in pediatric patients with a higher percentage of total burn surface area (TBSA) than patients with lower TBSA (p = 0.016). CONCLUSIONS: P. aeruginosa, Acinetobacter spp., and Klebsiella spp. are the common Gram-negative pathogens causing burn wound infections in hospitalized pediatric patients in our setting. A high proportion of these organisms were multidrug resistant. The findings appeal for regular antimicrobial resistance surveillance in burn wound infection to inform empirical therapy.

The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.

The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary capacity of SARS-CoV-2 to adapt to both rising population immunity, and public health interventions such as vaccines and social distancing. Viruses giving rise to the different 501Y lineages have, presumably under intense natural selection following a shift in host environment, independently acquired multiple unique and convergent mutations. As a consequence, all have gained epidemiological and immunological properties that will likely complicate the control of COVID-19. Here, by examining patterns of mutations that arose in SARSCoV-2 genomes during the pandemic we find evidence of a major change in the selective forces acting on various SARS-CoV-2 genes and gene segments (such as S, nsp2 and nsp6), that likely coincided with the emergence of the 501Y lineages. In addition to involving continuing sequence diversification, we find evidence that a significant portion of the ongoing adaptive evolution of the 501Y lineages also involves further convergence between the lineages. Our findings highlight the importance of monitoring how members of these known 501Y lineages, and others still undiscovered, are convergently evolving similar strategies to ensure their persistence in the face of mounting infection and vaccine induced host immune recognition.

Sixteen novel lineages of SARS-CoV-2 in South Africa.

The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).

Endoscopic ultrasound-guided hepaticogastrostomy using a partially covered metal stent in patients with malignant biliary obstruction after failed Endoscopic retrograde cholangiopancreatography.

BACKGROUND AND AIM: The advent of endoscopic ultrasound-guided biliary drainage (EUS-BD) has provided an inimitable alternative for gaining biliary access in patients who fail conventional endoscopic drainage. The antimigratory features of the partially covered metal stent (PCMS), namely, the flange head and uncovered portion of the stent, makes it a valuable option in patients undergoing EUS-guided hepaticogastrostomy (EUS-HGS). The aim of the study is to evaluate the clinical outcome of EUS-BD via the hepaticogastrostomy approach using PCMS in patients with malignant biliary obstruction after failed ERCP. METHODS: This is a single-center retrospective observational study of patients with malignant biliary obstruction undergoing EUS-HGS after failed ERCP between January 2018 and May 2019. The end-point of the study was to assess the technical and clinical success rate, as well as the stent- and procedure-related complications. RESULTS: There were 20 subjects in this study. The average age was 71.8 ± 7.6 years. Most patients were male, 16 (80%). Inaccessible papillae was the most common indication for this procedure, 16 (80%). Technical success was achieved in all patients. The average procedural time was 39.9 ± 1.3 min. Mean preprocedural bilirubin levels were 348.6 ± 28.8 and subsequently decreased to 108.94 ± 37.1 µmol/L at 2 weeks postprocedure. The clinical success rate was 95% (19/20), with one patient requiring percutaneous transhepatic biliary drainage (PTBD). There were no stent- or procedure-related complications reported in this study. CONCLUSION: EUS-HGS with PCMS is a feasible, effective, and safe alternative for biliary decompression in patients with failed endoscopic retrograde cholangiopancreatography (ERCP).

Highlights of the 3rd ISCB Africa Student Council Symposium 2019 in Ghana.

The article elaborates on the program highlights of the 3rd African Student Council Symposium 2019. The one-day symposium was held in Kwame Nkrumah University of Science and Technology (KNUST), Ghana, on 11 November 2019 during the 6th joint international bioinformatics conference of the ISCB and ASBCB. It consisted of three sessions that included keynote talks by Prof Christine Orengo and Dr. Amel Ghouila, and seven selected student speaker talks from different areas of bioinformatics. The students benefited from networking and learning about ongoing research work by their peers hailing from different countries of the African region. The symposium proved to be pivotal to strengthen connections in the African bioinformatics student community.

Analysis of the microarray gene expression for breast cancer progression after the application modified logistic regression.

Methods based around statistics and linear algebra have been increasingly used in attempts to address emerging questions in microarray literature. Microarray technology is a long-used tool in the global analysis of gene expression, allowing for the simultaneous investigation of hundreds or thousands of genes in a sample. It is characterized by a low sample size and a large feature number created a non-square matrix, and by the incomplete rank, that can generate countless more solution in classifiers. To avoid the problem of the 'curse of dimensionality' many authors have performed feature selection or reduced the size of data matrix. In this work, we introduce a new logistic regression-based model to classify breast cancer tumor samples based on microarray expression data, including all features of gene expression and without reducing the microarray data matrix. If the user still deems it necessary to perform feature reduction, it can be done after the application of the methodology, still maintaining a good classification. This methodology allowed the correct classification of breast cancer sample data sets from Gene Expression Omnibus (GEO) data series GSE65194, GSE20711, and GSE25055, which contain the microarray data of said breast cancer samples. Classification had a minimum performance of 80% (sensitivity and specificity), and explored all possible data combinations, including breast cancer subtypes. This methodology highlighted genes not yet studied in breast cancer, some of which have been observed in Gene Regulatory Networks (GRNs). In this work we examine the patterns and features of a GRN composed of transcription factors (TFs) in MCF-7 breast cancer cell lines, providing valuable information regarding breast cancer. In particular, some genes whose αi ∗ associated parameter values revealed extreme positive and negative values, and, as such, can be identified as breast cancer prediction genes. We indicate that the PKN2, MKL1, MED23, CUL5 and GLI genes demonstrate a tumor suppressor profile, and that the MTR, ITGA2B, TELO2, MRPL9, MTTL1, WIPI1, KLHL20, PI4KB, FOLR1 and SHC1 genes demonstrate an oncogenic profile. We propose that these may serve as potential breast cancer prediction genes, and should be prioritized for further clinical studies on breast cancer. This new model allows for the assignment of values to the αi ∗ parameters associated with gene expression. It was noted that some αi ∗ parameters are associated with genes previously described as breast cancer biomarkers, as well as other genes not yet studied in relation to this disease.

Prevalence and etiological agents for chronic suppurative otitis media in a tertiary hospital in Tanzania.

OBJECTIVE: Chronic suppurative otitis media is among the most common otological condition reported in otorhinolaryngology practice commonly attributing to preventable hearing loss. The aim of this study was to determine the prevalence and etiological agents for chronic suppurative otitis media in our department. RESULTS: A total of 5591 patients were recruited in this study and only 79 (1.4%) had chronic suppurative otitis media. A male preponderance 43 (54.4%) was noted in this study and the left ear (58.2%) was more commonly affected compared to the right ear. Central perforation was the commonest pattern of presentation and was reported in 53% of cases though none had attic perforation. Of the 81 processed ear swabs, microbial growth was seen in majority 80 (98.8%) whilst one sample showed no microbial growth whereas 52.5% had polymicrobial growth. Among the isolates, most were gram negative species accounting for 59.7% while gram positive bacteria accounted for 25.6% and fungi accounted for 14.7%. Most of these isolates were facultative anaerobes. Klebsiella pneumoniae (20.2%) was the commonest isolates while Escherichia coli and Pseudomonas aeruginosa were equally least isolated (10.9%). Tested isolates were most sensitive to Ciprofloxacin, Gentamycin, Ceftriaxone and Amikacin and least sensitive to Amoxicillin/clavulanic acid and Ampicillin.

ClinEpiDB: an open-access clinical epidemiology database resource encouraging online exploration of complex studies.

The concept of open data has been gaining traction as a mechanism to increase data use, ensure that data are preserved over time, and accelerate discovery. While epidemiology data sets are increasingly deposited in databases and repositories, barriers to access still remain. ClinEpiDB was constructed as an open-access online resource for clinical and epidemiologic studies by leveraging the extensive web toolkit and infrastructure of the Eukaryotic Pathogen Database Resources (EuPathDB; a collection of databases covering 170+ eukaryotic pathogens, relevant related species, and select hosts) combined with a unified semantic web framework. Here we present an intuitive point-and-click website that allows users to visualize and subset data directly in the ClinEpiDB browser and immediately explore potential associations. Supporting study documentation aids contextualization, and data can be downloaded for advanced analyses. By facilitating access and interrogation of high-quality, large-scale data sets, ClinEpiDB aims to spur collaboration and discovery that improves global health.

Methicillin-resistant Staphylococcus aureus contamination and distribution in patient's care environment at Muhimbili National Hospital, Dar es Salaam-Tanzania.

OBJECTIVE: Environmental contamination with methicillin-resistant Staphylococcus aureus in routine medical care settings poses an increased risk of health care associated infections through cross-transmission. This study aimed at determining the magnitude and distribution of methicillin-resistant S. aureus contamination among various items in patients' care surroundings at Muhimbili National Hospital, Tanzania's largest tertiary hospital. RESULTS: A total of 200 environmental samples from high touch items were processed and out of these methicillin-resistant S. aureus was 19.5% with significantly higher contamination in general wards. Patients' beds surfaces were the most contaminated among studied items (43.7%), whilst the surgical trolleys were least contaminated (7.7%). Presence of 10 or more patients in a room was an important significant correlate for methicillin-resistant S. aureus contamination by bivariate logistic regression model (odds ratio: 4.75, 95% confidence interval 1.624-13.895, p = 0.004). These findings warrant further study of decontamination practices and improved infection control mechanisms, especially in light of the drug resistant isolates identified.