Transmission of antimicrobial resistance between hospital inpatients in a resource-limited setting
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ABSTRACT:
PROVIDER: PRJEB39247 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4329860_1.fastq.gz | Fastqsanger.gz | |||
| ERR4329860_2.fastq.gz | Fastqsanger.gz | |||
| ERR4329870_1.fastq.gz | Fastqsanger.gz | |||
| ERR4329870_2.fastq.gz | Fastqsanger.gz | |||
| ERR4329880_1.fastq.gz | Fastqsanger.gz |
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Project description:OBJECTIVE:Current guidelines on rectal cancer (RC) management recommend pre-operative MRI for loco-regional staging and CT for staging of metastases. This allows appropriate selection of patients for chemo-radiotherapy (CRT). However, MRI is not freely available in many low-income countries. We assessed the status of pre-operative imaging for RC in Sri Lanka and evaluated the performance of CT in RC staging. RESULTS:A pre-tested interview-administered questionnaire was used to assess the pre-operative use of MRI and CT in RC. CT findings from 37 RC patients were then compared with histopathology findings. Of the 64 surgeons interviewed, 57 (89.1%) did not request an MRI for their RC patients. Reasons cited included limited availability and long waiting times due to competing health needs. A CT was requested by all. In RC, the overall accuracy of CT for T staging was 43.2% and 29.7% of T1-T2 tumours were over-staged as T3. The overall accuracy of CT for regional lymph node staging was 70.3%. In summary, CT alone is not suitable for RC staging in any setting. It leads to over-staging and patients may thus receive unnecessary CRT. Steps must be taken to improve access to pre-operative MRI among Sri Lankan RC patients.
| S-EPMC7547447 | biostudies-literature
Project description:BackgroundAfrica has one of the highest incidences of gonorrhea. Neisseria gonorrhoeae is gaining resistance to most of the available antibiotics, compromising treatment across the world. Whole-genome sequencing (WGS) is an efficient way of predicting AMR determinants and their spread in the population. Recent advances in next-generation sequencing technologies like Oxford Nanopore Technology (ONT) have helped in the generation of longer reads of DNA in a shorter duration with lower cost. Increasing accuracy of base-calling algorithms, high throughput, error-correction strategies, and ease of using the mobile sequencer MinION in remote areas lead to its adoption for routine microbial genome sequencing. To investigate whether MinION-only sequencing is sufficient for WGS and downstream analysis in resource-limited settings, we sequenced the genomes of 14 suspected N. gonorrhoeae isolates from Nairobi, Kenya.MethodsUsing WGS, the isolates were confirmed to be cases of N. gonorrhoeae (n = 9), and there were three co-occurrences of N. gonorrhoeae with Moraxella osloensis and N. meningitidis (n = 2). N. meningitidis has been implicated in sexually transmitted infections in recent years. The near-complete N. gonorrhoeae genomes (n = 10) were analyzed further for mutations/factors causing AMR using an in-house database of mutations curated from the literature.ResultsWe observe that ciprofloxacin resistance is associated with multiple mutations in both gyrA and parC. Mutations conferring tetracycline (rpsJ) and sulfonamide (folP) resistance and plasmids encoding beta-lactamase were seen in all the strains, and tet(M)-containing plasmids were identified in nine strains. Phylogenetic analysis clustered the 10 isolates into clades containing previously sequenced genomes from Kenya and countries across the world. Based on homology modeling of AMR targets, we see that the mutations in GyrA and ParC disrupt the hydrogen bonding with quinolone drugs and mutations in FolP may affect interaction with the antibiotic.ConclusionHere, we demonstrate the utility of mobile DNA sequencing technology in producing a consensus genome for sequence typing and detection of genetic determinants of AMR. The workflow followed in the study, including AMR mutation dataset creation and the genome identification, assembly, and analysis, can be used for any clinical isolate. Further studies are required to determine the utility of real-time sequencing in outbreak investigations, diagnosis, and management of infections, especially in resource-limited settings.
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Project description:Real-time molecular survey of Mycobacterium tuberculosis isolates from 2008 to 2018 reveals tuberculosis transmission in a tertiary-care university hospital
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Project description:BackgroundThe aim of this research was to evaluate the economic outcomes of radiotherapy (RT), temozolomide (TMZ) and nitrosourea (NT) strategies for glioblastoma patients with different prognostic factors.Methodology/principal findingsA Markov model was developed to track monthly patient transitions. Transition probabilities and utilities were derived primarily from published reports. Costs were estimated from the perspective of the Chinese healthcare system. The survival data with different prognostic factors were simulated using Weibull survival models. Costs over a 5-year period and quality-adjusted life years (QALYs) were estimated. Probabilistic sensitivity and one-way analyses were performed. The baseline analysis in the overall cohort showed that the TMZ strategy increased the cost and QALY relative to the RT strategy by $25,328.4 and 0.29, respectively; and the TMZ strategy increased the cost and QALY relative to the NT strategy by $23,906.5 and 0.25, respectively. Therefore, the incremental cost effectiveness ratio (ICER) per additional QALY of the TMZ strategy, relative to the RT strategy and the NT strategy, amounts to $87,940.6 and $94,968.3, respectively. Subgroups with more favorable prognostic factors achieved more health benefits with improved ICERs. Probabilistic sensitivity analyses confirmed that the TMZ strategy was not cost-effective. In general, the results were most sensitive to the cost of TMZ, which indicates that better outcomes could be achieved by decreasing the cost of TMZ.Conclusions/significanceIn health resource-limited settings, TMZ is not a cost-effective option for glioblastoma patients. Selecting patients with more favorable prognostic factors increases the likelihood of cost-effectiveness.
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Project description:We report a case of human immunodeficiency virus-associated pericardial tuberculosis complicated by cardiac tamponade. Emergency management and subsequent therapeutic interventions are described and then discussed with particular focus on resource-limited settings. The paucity of evidence to support clinical decisions is emphasized and the need for well designed diagnostic and therapeutic studies is highlighted.
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Project description:BackgroundWorld Health Organization guidelines now recommend routine use of viral load testing, where available, for patients receiving antiretroviral treatment (ART). However, its use has not been routinely implemented in many resource-limited settings due to cost, availability and accessibility. Viral load testing is complex, making its application in resource-limited settings challenging. We describe the issues encountered by Médecins Sans Frontières (MSF) when using routine viral load testing in a large HIV programme in sub-Saharan Africa.MethodsBetween October 2005 and August 2006, more than 1200 patients on ART had viral load tests at baseline and at three-month intervals performed by a local reference laboratory that was quality assured by an experienced international institution. Concerns with reliability of results halted testing. The quality control measures instituted with a second laboratory and outcomes of these were documented.ResultsIn 2005 and 2006, only 178 of 334 (53%) previously ART-naïve patients tested after six to 12 months of treatment had viral loads of less than 1000 copies/mL. Similar MSF programmes elsewhere demonstrated virological suppression rates of more than 85%, and duplicate testing showed unacceptable discordance. Laboratory problems encountered included: disregarded quality control; time delays; requirement for retesting; and duplicate sample variations. Potentially harmful clinical outcomes of inaccurate viral load results include: unnecessary ART regimen changes; unnecessary enhanced adherence counselling after "false failures"; and undetected virological failure.ConclusionsViral load testing performed without rigorous quality control carries the risk of erroneous and potentially damaging results. Viral load testing should be utilized only if robust quality assurance has been implemented. Our experience in this and other settings led to the development of a guide for assessing the suitability of a laboratory for viral load testing that can be used to help achieve reliable results.
| S-EPMC3116452 | biostudies-literature
Project description:BackgroundWe sought to develop a low-fidelity simulation-based curriculum for pediatric residents in Rwanda utilizing either rapid cycle deliberate practice (RCDP) or traditional debriefing, and to determine whether RCDP leads to greater improvement in simulation-based performance and in resident confidence compared with traditional debriefing.MethodsPediatric residents at the Centre Hospitalier Universitaire de Kigali (CHUK) were randomly assigned to RCDP or traditional simulation and completed a 6 month-long simulation-based curriculum designed to improve pediatric resuscitation skills. Pre- and post- performance was assessed using a modified version of the Simulation Team Assessment Tool (STAT). Each video-taped simulation was reviewed by two investigators and inter-rater reliability was assessed. Self-confidence in resuscitation, pre- and post-simulation, was assessed by Likert scale survey. Analyses were conducted using parametric and non-parametric testing, ANCOVA and intra-class correlation coefficients (ICC).ResultsThere was a 21% increase in pre- to post-test performance in both groups (p?<?0.001), but no difference between groups (mean difference?-?0.003%; p 0.94). Inter-rater reliability was exceptional with both pre and post ICCs ?0.95 (p?<?0.001). Overall, self-confidence scores improved from pre to post (24.0 vs. 30.0 respectively, p?<?0.001), however, the there was no difference between the RCDP and traditional groups.ConclusionsCompletion of a six-month low-fidelity simulation-based curriculum for pediatric residents in Rwanda led to statistically significant improvement in performance on a simulated resuscitation. RCDP and traditional low-fidelity simulation-based instruction may both be valuable tools to improve resuscitation skills in pediatric residents in resource-limited settings.
| S-EPMC6704559 | biostudies-literature
Project description:IntroductionThere are well-established protocols and procedures for the majority of common surgical diseases, yet surgical services remain largely inaccessible for much of the world's rural poor. Data on the process and outcome of surgical care expansion, however, are very limited, and the roll-out process of rural surgical implementation in particular has never been studied. Here, we propose the first implementation research study to assess the surgical scale-up process in the rural district of Achham, Nepal.Methods and analysisBased primarily on the protocols of the WHO's Integrated Management for Emergency and Essential Surgical Care (IMEESC), this study's threefold implementation strategy will include: (1) the core IMEESC surgical care program, (2) community-based follow-up via health workers, and (3) hospital-based quality improvement programs. The implementation program will employ additional emergency and surgical care protocols developed collaboratively by physicians, nurses and the authors. This strategy will be referred to as IMEESC-Plus. This study will employ both qualitative and quantitative research methodologies to collect clinical data and information on the reception and utilisation of services. The first 18 months of the implementation process will be studied and divided into an initial phase (first 6 months) and a consolidation phase (subsequent 12 months).DiscussionThis study aims to describe the logistics of the implementation process of IMEESC-Plus, and assess the quality of the resulting IMEESC-Plus services during the course of the implementation process. Using data generated from this study, larger, multi-site implementation studies can be planned that assess the scale-up of surgical services worldwide in resource-limited areas.
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Project description:BACKGROUND:To investigate potential risk factors for perinatal (intrauterine and intrapartum) mother-to-child transmission (MTCT) of HIV in women unexposed to antiretroviral therapy (ART) during pregnancy. METHODS:We compared factors according to perinatal MTCT outcome among 2275 ART-naive (until the onset of labor) HIV-infected women in the Breastfeeding, Antiretrovirals and Nutrition study (2004-2010) in Lilongwe, Malawi. Factors included HIV viral load during pregnancy, food security, demographic characteristics, hematologic and blood chemistry measures, medical history and physical factors. Associations with perinatal MTCT and interactions with maternal viral load were assessed using simple and multivariable logistic regression. RESULTS:There were 119 (115 intrauterine and 4 intrapartum) cases of perinatal MTCT, only one to a mother with <1000 HIV copies/mL. Maternal viral loads >10,000 copies/mL were common (63.1%). Lower maternal viral load (<1000 copies/mL and 1000.1-10,000 copies/mL) was associated with reduced odds of perinatal MTCT [adjusted odds ratio (aOR), 0.1; 95% confidence interval (CI): 0.01-0.4 and aOR, 0.2; 95% CI: 0.1-0.4, respectively), compared with maternal viral load >10,000 copies/mL. Low CD4+ T cell count (?350 cells/?L) was only associated with perinatal MTCT in unadjusted models. Food shortage (aOR, 1.8; 95% CI: 1.2-2.6), sexually transmitted infection (STI) (past year; aOR, 1.9; 95% CI: 1.0-3.7), histories of herpes zoster (aOR, 3.0; 95% CI: 1.6-5.6) and tuberculosis (aOR, 2.5; 95% CI: 1.1-5.7) were associated with increased odds of perinatal MTCT. CONCLUSIONS:These findings confirm that lowering maternal HIV viral load is most important in preventing perinatal MTCT and support efforts to address food shortage, STI and tuberculosis prevention, while informing programs to improve ART coverage in pregnancy.
| S-EPMC6481191 | biostudies-literature
Project description:ObjectiveTo measure the association of intensive care unit (ICU) capacity strain with processes of care and outcomes of critical illness in a resource-limited setting.MethodsWe performed a retrospective cohort study of 5332 patients referred to the ICUs at 2 public hospitals in South Africa using the country's first published multicenter electronic critical care database. We assessed the association between multiple ICU capacity strain metrics (ICU occupancy, turnover, census acuity, and referral burden) at different exposure time points (ICU referral, admission, and/or discharge) with clinical and process of care outcomes. The association of ICU capacity strain at the time of ICU admission with ICU length of stay (LOS), the primary outcome, was analyzed with a multivariable Cox proportional hazard model. Secondary outcomes of ICU triage decision (with strain at ICU referral), ICU mortality (with strain at ICU admission), and ICU LOS (with strain at ICU discharge), were analyzed with linear and logistic multivariable regression.ResultsNo measure of ICU capacity strain at the time of ICU admission was associated with ICU LOS, the primary outcome. The ICU occupancy at the time of ICU admission was associated with increased odds of ICU mortality (odds ratio = 1.07, 95% confidence interval: 1.02-1.11; P = .004), a secondary outcome, such that a 10% increase in ICU occupancy would be associated with a 7% increase in the odds of ICU mortality.ConclusionsIn a resource-limited setting in South Africa, ICU capacity strain at the time of ICU admission was not associated with ICU LOS. In secondary analyses, higher ICU occupancy at the time of ICU admission, but not other measures of capacity strain, was associated with increased odds of ICU mortality.
| S-EPMC6548699 | biostudies-literature