The PARE Project: A Short Course-Based Research Project for National Surveillance of Antibiotic-Resistant Microbes in Environmental Samples.
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SUBMITTER: Genne-Bacon EA
PROVIDER: S-EPMC6203630 | biostudies-literature | 2018
REPOSITORIES: biostudies-literature
Publications
The PARE Project: A Short Course-Based Research Project for National Surveillance of Antibiotic-Resistant Microbes in Environmental Samples.
Genné-Bacon Elizabeth A EA Bascom-Slack Carol A CA
Journal of microbiology & biology education 20181031 3
Course-based research experiences (CREs) have been proposed as an inclusive model to expose all students, including those at institutions without a strong research infrastructure, to research at an early stage. Converting an entire semester-long course can be time consuming for instructors and expensive for institutions, so we have developed a short CRE that can be implemented in a variety of life science course types. The Prevalence of Antibiotic Resistance in the Environment (PARE) project use ...[more]
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Project description:Incorporating Undergraduate Research Experience in Microbiology Classroom. Dr. Mangala Tawde, Associate Professor, Department of Biological Sciences and Geology, Queensborough Community College, CUNY. Undergraduate Research (UR) experience is increasingly being recognized as one of the most transforming experiences students can have in their undergraduate years of education. To make it accessible to all students, incorporating authentic research experiences in the classroom is important and it is a major initiative at Queensborough community college; where we have institutionalized UR as a High Impact Practice. We incorporated an authentic research project into the Microbiology course curriculum for allied health majors. The research project was to isolate and identify antibiotic-resistant microbes from diverse environments. As students are aware of antibiotic resistance being a serious concern in today's medicine, they get interested and are enthusiastically engaged in the research project. Students collect soil samples from various environments and locations of their choice and then they isolate and identify bacteria that may exhibit antibiotic resistance. The microbes isolated from diverse environments are identified based on the 16s rRNA sequence analysis as well as biochemical tests. The research experience is relevant and aligns well with the course curricula, course learning objectives as well as the college's General Education objectives.
| S-EPMC7649124 | biostudies-literature
Project description:BackgroundUnderstanding environmental microbiomes and antibiotic resistance (AR) is hindered by over reliance on relative abundance data from next-generation sequencing. Relative data limits our ability to quantify changes in microbiomes and resistomes over space and time because sequencing depth is not considered and makes data less suitable for Quantitative Microbial Risk Assessments (QMRA), critical in quantifying environmental AR exposure and transmission risks.ResultsHere we combine quantitative microbiome profiling (QMP; parallelization of amplicon sequencing and 16S rRNA qPCR to estimate cell counts) and absolute resistome profiling (based on high-throughput qPCR) to quantify AR along an anthropogenically impacted river. We show QMP overcomes biases caused by relative taxa abundance data and show the benefits of using unified Hill number diversities to describe environmental microbial communities. Our approach overcomes weaknesses in previous methods and shows Hill numbers are better for QMP in diversity characterisation.ConclusionsMethods here can be adapted for any microbiome and resistome research question, but especially providing more quantitative data for QMRA and other environmental applications.
| S-EPMC8600772 | biostudies-literature
Project description:OBJECTIVES:For the first time ever, as emphasized by inclusion in the Healthy People 2020 goals, sleep health is an emphasis of national health aims. The National Healthy Sleep Awareness Project (NHSAP) was tasked to propose questions for inclusion in the next Behavioral Risk Factor Surveillance System (BRFSS), a survey that includes a number of questions that target behaviors thought to impact health, as a means to measure community sleep health. The total number of questions could not exceed five, and had to include an assessment of the risk for obstructive sleep apnea (OSA). METHODS:An appointed workgroup met via teleconference and face-to-face venues to develop an inventory of published survey questions being used to identify sleep health, to develop a framework on which to analyze the strengths and weaknesses of current survey questions concerning sleep, and to develop recommendations for sleep health and disease surveillance questions going forward. RESULTS:The recommendation was to focus on certain existing BRFSS questions pertaining to sleep duration, quality, satisfaction, daytime alertness, and to add to these other BRFSS existing questions to make a modified STOP-BANG questionnaire (minus the N for neck circumference) to assess for risk of OSA. CONCLUSIONS:Sleep health is an important dimension of health that has previously received less attention in national health surveys. We believe that 5 questions recommended for the upcoming BRFSS question banks will assist as important measures of sleep health, and may help to evaluate the effectiveness of interventions to improve sleep health in our nation.
| S-EPMC4543250 | biostudies-other
Project description:BackgroundPneumonia is the most common hospital-acquired infection affecting patients in the intensive care unit (ICU). However, current national guidelines for the treatment of hospital-acquired pneumonia (HAP) are several years old and the diagnosis of pneumonia in mechanically ventilated patients (VAP) has been subject to considerable recent attention. The optimal duration of antibiotic therapy for HAP in the critically ill is uncertain.ObjectivesTo assess the effectiveness of short versus prolonged-course antibiotics for HAP in critically ill adults, including patients with VAP.Search methodsWe searched CENTRAL (2015, Issue 5), MEDLINE (1946 to June 2015), MEDLINE in-process and other non-indexed citations (5 June 2015), EMBASE (2010 to June 2015), LILACS (1982 to June 2015) and Web of Science (1955 to June 2015).Selection criteriaWe considered all randomised controlled trials (RCTs) comparing a fixed 'short' duration of antibiotic therapy with a 'prolonged' course for HAP (including patients with VAP) in critically ill adults.Data collection and analysisTwo review authors conducted data extraction and assessment of risk of bias. We contacted trial authors for additional information.Main resultsWe identified six relevant studies involving 1088 participants. This included two new studies published after the date of our previous review (2011). There was substantial variation in participants, in the diagnostic criteria used to define an episode of pneumonia, in the interventions and in the reported outcomes. We found no evidence relating to patients with a high probability of HAP who were not mechanically ventilated. For patients with VAP, overall a short seven- or eight-day course of antibiotics compared with a prolonged 10- to 15-day course increased 28-day antibiotic-free days (two studies; N = 431; mean difference (MD) 4.02 days; 95% confidence interval (CI) 2.26 to 5.78) and reduced recurrence of VAP due to multi-resistant organisms (one study; N = 110; odds ratio (OR) 0.44; 95% CI 0.21 to 0.95), without adversely affecting mortality and other recurrence outcomes. However, for cases of VAP specifically due to non-fermenting Gram-negative bacilli (NF-GNB), recurrence was greater after short-course therapy (two studies, N = 176; OR 2.18; 95% CI 1.14 to 4.16), though mortality outcomes were not significantly different. One study found that a three-day course of antibiotic therapy for patients with suspected HAP but a low Clinical Pulmonary Infection Score (CPIS) was associated with a significantly lower risk of superinfection or emergence of antimicrobial resistance, compared with standard (prolonged) course therapy.Authors' conclusionsOn the basis of a small number of studies and appreciating the lack of uniform definition of pneumonia, we conclude that for patients with VAP not due to NF-GNB a short, fixed course (seven or eight days) of antibiotic therapy appears not to increase the risk of adverse clinical outcomes, and may reduce the emergence of resistant organisms, compared with a prolonged course (10 to 15 days). However, for patients with VAP due to NF-GNB, there appears to be a higher risk of recurrence following short-course therapy. These findings do not differ from those of our previous review and are broadly consistent with current guidelines. There are few data from RCTs comparing durations of therapy in non-ventilated patients with HAP, but on the basis of a single study, short-course (three-day) therapy for HAP appears not to be associated with worse clinical outcome, and may reduce the risk of subsequent infection or the emergence of resistant organisms when there is low probability of pneumonia according to the CPIS.
| S-EPMC7025798 | biostudies-literature
Project description:Study objectivesTo validate the previously published National Healthy Sleep Awareness Project (NHSAP) Surveillance and Epidemiology Workgroup questionnaire for ability to determine risk for moderate to severe obstructive sleep apnea (OSA).MethodsThe NHSAP sleep questions, part of the next Behavioral Risk Factor Surveillance System (BRFSS), were constructed to mimic elements of the STOP sleep apnea questionnaire, and included number of days with sleep disruption and unintentional dozing and a history of snoring and apneas. The responses to four sleep questions from the BRFSS were collected from 352 adults undergoing in-laboratory polysomnography at Mayo Clinic, Rochester, Minnesota. Demographic and clinical information, including sex, age, body mass index (BMI), and presence of hypertension, which will be available in other parts of the complete BRFSS, were obtained by chart review. Univariate and logistic regression analyses were performed, and values of P < .05 were considered to be statistically significant.ResultsFifty-five percent of subjects were men and 45% were women with a median age of 58 years and BMI 32.2 kg/m2. Sixty percent had no or mild OSA, and 40% had moderate to severe OSA. No single question was superior in screening for moderate to severe OSA, although a history of snoring and witnessed apneas was more likely to predict moderate to severe OSA. Male sex, age ? 50 years, BMI ? 30 kg/m2, presence of hypertension, and a history of snoring and witnessed apneas were the most highly weighted factors in predicting moderate to severe OSA. When each variable was dichotomized to a single point, a cutoff of 5 points significantly predicted a high risk of moderate to severe OSA with an odds ratio of 3.87 (2.39-6.27).ConclusionsAlthough many variables were positively associated with the apnea-hypopnea index, no single factor was superior in predicting moderate to severe OSA. Male sex, increased age, higher BMI, hypertension, and a history of snoring and witnessed apneas are the most highly predictive of moderate to severe OSA. Combined use of the NHSAP questionnaire and demographic and clinical characteristics could be considered for screening for moderate to severe OSA.
| S-EPMC5566462 | biostudies-literature
Project description:AimsOur aim was to summarize the available literature on the effect of short- versus long-course antibiotic therapy on acute cholangitis.MethodsA systematic review was performed according to the PRISMA Statement. We searched three databases for papers discussing the length of ABT in acute cholangitis. Long and short therapy groups were defined based on the most recent guideline available at the time of publication of the articles. Primary outcomes were the rate of recurrent cholangitis and mortality; secondary outcomes included length of hospitalization and the duration of fever after ERCP. Data were extracted on these outcomes and on general characteristics. A narrative synthesis was then provided based on collected data.ResultsOut of 692 articles produced by our search, four met our inclusion and exclusion criteria. These contained 205 acute cholangitis patients, with 137 and 68 patients receiving short and long antibiotic therapy, respectively. No significant difference was observed in any of the studies on the outcomes of mortality and duration of fever after ERCP between the two groups. One out of four studies found the rate of recurrent cholangitis to be significantly lower in the short antibiotic therapy group (0.0% vs. 13.3%, p?=?0.036). Length of hospitalization was only compared in the same retrospective article, where it was found to be significantly shorter in the short-term antibiotic therapy group (with a median of 14 vs. 17.5 days, p?<?0.001).ConclusionsOur review suggests short-course antibiotic therapy is non-inferior to long-course treatment; however, several limitations underline the need for well-designed randomized trials.
| S-EPMC6514065 | biostudies-literature
Project description:Livestock farms are generally considered to be the important source of antibiotic resistance genes (ARGs). It is important to explore the spread of ARGs to reduce their harm. This study analyzed 13 resistance genes belonging to 7 types in 68 samples of layer manure including different stages of layer breeding, layer manure fertilizer, and soil from 9 laying hen farms in Guangdong Province. The detection rate of antibiotic resistance genes was extremely high at the layer farm in manure (100%), layer manure fertilizer (100%), and soil (> 95%). The log counts of antibiotic resistance genes in layer manure (3.34-11.83 log copies/g) were significantly higher than those in layer manure fertilizer (3.45-9.80 log copies/g) and soil (0-7.69 log copies/g). In layer manure, ermB was the most abundant antibiotic resistance gene, with a concentration of 3.19 × 109- 6.82 × 1011 copies/g. The average abundances of 5 antibiotic resistance genes were above 1010 copies/g in the descending order ermB, sul2, tetA, sul1, and strB. The relative abundances of ARGs in layer manure samples from different breeding stages ranked as follows: brooding period (BP), late laying period (LL), growing period (GP), early laying period (EL), and peak laying period (PL). There was no significant correlation between the farm scale and the abundance of antibiotic resistance genes. Moreover, the farther away from the layer farm, the lower the abundance of antibiotic resistance genes in the soil. We also found that compost increases the correlation between antibiotic resistance genes, and the antibiotic resistance genes in soil may be directly derived from layer manure fertilizer instead of manure. Therefore, when applying layer manure fertilizer to cultivated land, the risk of antibiotic resistance genes pollution should be acknowledged, and in-depth research should be conducted on how to remove antibiotic resistance genes from layer manure fertilizer to control the spread of antibiotic resistance genes.
| S-EPMC8554274 | biostudies-literature
Project description:PurposeTo summarize the evidence comparing the effectiveness of short and long courses of oral antibiotics for infections treated in outpatient settings.MethodsWe identified systematic reviews of randomized controlled trials for children and adults with bacterial infections treated in outpatient settings from Medline, Embase, CINAHL, Cochrane Database of Systematic Reviews and The Database of Review of Effects. Data were extracted on the primary outcome of clinical resolution and secondary outcomes.ResultsWe identified 30 potential reviews, and included 9. There was no difference in the clinical cure for children treated with short or long course antibiotics for Group A streptococcal tonsillopharyngitis (OR 1.03, 95% CI:0.97, 1.11); community acquired pneumonia (RR 0.99, 95% CI:0.97, 1.01); acute otitis media [<2 years old OR: 1.09 (95% CI:0.76, 1.57); ?2 years old OR: 0.85 (95% CI:0.60, 1.21)]; or urinary tract infection (RR 1.06, 95% CI:0.64, 1.76). There was no difference in the clinical cure for adults treated with short or long course antibiotics for acute bacterial sinusitis (RR 0.95, 95% CI:0.81, 1.21); uncomplicated cystitis in non-pregnant women (RR 1.10, 95% CI:0.96, 1.25), or elderly women (RR: 0.98, 95% CI:0.62, 1.54); acute pyelonephritis (RR 1.03, 95% CI:0.80, 1.32); or community acquired pneumonia (RR: 0.96, 95% CI:0.74, 1.26). We found inadequate evidence about the effect on antibiotic resistance.ConclusionsThis overview of systematic reviews has identified good quality evidence that short course antibiotics are as effective as longer courses for most common infections managed in ambulatory care. The impact on antibiotic resistance and associated treatment failure requires further study.
| S-EPMC6390420 | biostudies-literature
Project description:BackgroundCommunity-acquired pneumonia (CAP) is a lung infection that can be acquired during day-to-day activities in the community (not while receiving care in a hospital). Community-acquired pneumonia poses a significant public health burden in terms of mortality, morbidity, and costs. Shorter antibiotic courses for CAP may limit treatment costs and adverse effects, but the optimal duration of antibiotic treatment is uncertain.ObjectivesTo evaluate the efficacy and safety of short-course versus longer-course treatment with the same antibiotic at the same daily dosage for CAP in non-hospitalised adolescents and adults (outpatients). We planned to investigate non-inferiority of short-course versus longer-term course treatment for efficacy outcomes, and superiority of short-course treatment for safety outcomes.Search methodsWe searched CENTRAL, which contains the Cochrane Acute Respiratory Infections Group Specialised Register, MEDLINE, Embase, five other databases, and three trials registers on 28 September 2017 together with conference proceedings, reference checking, and contact with experts and pharmaceutical companies.Selection criteriaRandomised controlled trials (RCTs) comparing short- and long-courses of the same antibiotic for CAP in adolescent and adult outpatients.Data collection and analysisWe planned to use standard Cochrane methods.Main resultsOur searches identified 5260 records. We did not identify any RCTs that compared short- and longer-courses of the same antibiotic for the treatment of adolescents and adult outpatients with CAP.We excluded two RCTs that compared short courses (five compared to seven days) of the same antibiotic at the same daily dose because they evaluated antibiotics (gemifloxacin and telithromycin) not commonly used in practice for the treatment of CAP. In particular, gemifloxacin is no longer approved for the treatment of mild-to-moderate CAP due to its questionable risk-benefit balance, and reported adverse effects. Moreover, the safety profile of telithromycin is also cause for concern.We found one ongoing study that we will assess for inclusion in future updates of the review.Authors' conclusionsWe found no eligible RCTs that studied a short-course of antibiotic compared to a longer-course (with the same antibiotic at the same daily dosage) for CAP in adolescent and adult outpatients. The effects of antibiotic therapy duration for CAP in adolescent and adult outpatients remains unclear.
| S-EPMC6513237 | biostudies-literature
Project description:BackgroundMost serious complications of infective endocarditis (IE) appear in the so-called "critical phase" of the disease, which represents the first days after diagnosis. The majority of patients overcoming the acute phase has a favorable outcome, yet they remain hospitalized for a long period of time mainly to complete antibiotic therapy. The major hypothesis of this trial is that in patients with clinically stable IE and adequate response to antibiotic treatment, without signs of persistent infection, periannular complications or metastatic foci, a shorter antibiotic time period would be as efficient and safe as the classic 4 to 6 weeks antibiotic regimen.MethodsMulticenter, prospective, randomized, controlled open-label, phase IV clinical trial with a non-inferiority design to evaluate the efficacy of a short course (2 weeks) of parenteral antibiotic therapy compared with conventional antibiotic therapy (4-6 weeks).Samplepatients with IE caused by gram-positive cocci, having received at least 10 days of conventional antibiotic treatment, and at least 7 days after surgery when indicated, without clinical, analytical, microbiological or echocardiographic signs of persistent infection. Estimated sample size: 298 patients.InterventionControl group: standard duration antibiotic therapy, (4 to 6 weeks) according to ESC guidelines recommendations. Experimental group: short-course antibiotic therapy for 2 weeks. The incidence of the primary composite endpoint of all-cause mortality, unplanned cardiac surgery, symptomatic embolisms and relapses within 6 months after the inclusion in the study will be prospectively registered and compared.ConclusionsSATIE will investigate whether a two weeks short-course of intravenous antibiotics in patients with IE caused by gram-positive cocci, without signs of persistent infection, is not inferior in safety and efficacy to conventional antibiotic treatment (4-6 weeks).Trial registrationClinicalTrials.gov Identifier: NCT04222257 (January 7, 2020). EudraCT 2019-003358-10.
| S-EPMC7298739 | biostudies-literature