Plastic pollution is a serious global problem, with more than 12 million tonnes of plastic waste entering the oceans every year. Plastic debris can have considerable impacts on microbial community structure and functions in marine environments, and has been associated with an enrichment in pathogenic bacteria and antimicrobial resistance (AMR) genes. However, our understanding of these impacts is largely restricted to microbial assemblages on plastic surfaces. It is therefore unclear whether these effects are driven by the surface properties of plastics, providing an additional niche for certain microbes residing in biofilms, and/or chemicals leached from plastics, the effects of which could extend to surrounding planktonic bacteria. Here, we examine the effects of polyvinyl chloride (PVC) plastic leachate exposure on the relative abundance of genes associated with bacterial pathogenicity and AMR within a seawater microcosm community. We show that PVC leachate, in the absence of plastic surfaces, drives an enrichment in AMR and virulence genes. In particular, leachate exposure significantly enriches AMR genes that confer multidrug, aminoglycoside and peptide antibiotic resistance. Additionally, enrichment of genes involved in the extracellular secretion of virulence proteins was observed among pathogens of marine organisms. This study provides the first evidence that chemicals leached from plastic particles alone can enrich genes related to microbial pathogenesis within a bacterial community, expanding our knowledge of the environmental impacts of plastic pollution with potential consequences for human and ecosystem health.
We demonstrated in our recent Communications Biology paper how marine photosynthetic bacteria, Prochlorococcus, are adversely affected by leachates from commonly used plastics. This study was one of the first to consider how substances leaching from plastics may affect marine primary producers and demonstrated that plastic pollution has the potential to negatively impact a wider range of organisms than previously appreciated. We outline here key outstanding questions regarding how ocean plastic pollution may impact small, but essential, marine microbes and discuss how these can be addressed. Following up on their recent study in Communications Biology Sasha Tetu et al discuss how plastic pollution of the oceans may affect marine microbes as well as strategies to identify the substances responsible for leachate toxicity and to further understand their impact.
The model organism Escherichia coli K-12 has one of the most extensively annotated genomes in terms of functional characterization, yet a significant number of genes, ∼35%, are still considered poorly characterized. Initially genes without known functional understanding were given 'y' gene names. However, due to inconsistency in changing 'y' names to non-'y' names over the years, gene name alone does not provide sufficient information as to the characterization level of genes. Attempts to characterize y-ome genes, i.e. those that lack experimental evidence for function, are ongoing, and recent categorization based on the level of experimental evidence has helped clarify those genes that are well characterized versus uncharacterized. EcoCyc, the most comprehensive, curated genome database for E. coli K-12 substr. MG1655, has updated this approach by expanding the categories to include Partially characterized genes using a set of computational rules that includes keywords, experimental evidence codes and Gene Ontology terms. Approximately half of the previously categorized y-ome genes are now categorized as Partially characterized, leaving 15.5% (738) as Uncharacterized genes in EcoCyc. This new categorization scheme is searchable in the EcoCyc database, will be updated as new experimental evidence is curated and provides important information for research decisions.
Abstract Inferring the metabolic capabilities of an organism from its genome is a challenging process, relying on computationally-derived or manually curated metabolic networks. Manual curation can correct mistakes in the draft network and add missing reactions based on the literature, but requires significant expertise and is often the bottleneck for high-quality metabolic reconstructions. Here, we present a synopsis of a community curation workshop for the emerging model marine bacterium Alteromonas macleodii ATCC 27126 and its genome database in BioCyc, focusing on pathways for utilizing organic carbon and nitrogen sources. Due to the scarcity of biochemical information or gene knock-outs, the curation process relied primarily on published growth phenotypes and bioinformatic analyses, including comparisons with related Alteromonas strains. We report full pathways for the utilization of the algal polysaccharides alginate and pectin in contrast to inconclusive evidence for one carbon metabolism and mixed acid fermentation, in accordance with the lack of growth on methanol and formate. Pathways for amino acid degradation are ubiquitous across Alteromonas macleodii strains, yet enzymes in the pathways for the degradation of threonine, tryptophan and tyrosine were not identified. Nucleotide degradation pathways are also partial in ATCC 27126. We postulate that demonstrated growth on nitrate as sole N source proceeds via a nitrate reductase pathway that is a hybrid of known pathways. Our evidence highlights the value of joint and interactive curation efforts, but also shows major knowledge gaps regarding Alteromonas metabolism. The manually-curated metabolic reconstruction is available as a “Tier-2” database on BioCyc. Importance Metabolic reconstructions are vital for the systemic understanding of an organism’s ecology. Here, we report the outcome of a collaborative, interactive curation workshop to build a curated “metabolic encyclopedia” for Alteromonas macleodii ATCC 27126, a marine heterotrophic bacterium with widespread occurrence. Curating pathways for polysaccharide degradation, one-carbon metabolism, and others closed major knowledge gaps, and identified further avenues of research. Our study highlights how the combination of bioinformatic, genomic and physiological evidence can be harvested into a detailed metabolic model, but also identifies challenges if little experimental data is available for support. Overall, we show how an interactive get-together by a diverse group of scientists can advance the ecological understanding of emerging model bacteria, with relevance for the entire scientific community.
A key factor in empowering healthcare professionals to impact patient care is the ready access to centralized patient data, however, at many facilities a significant barrier to retrieving this information exists. Vital medical information is often fragmented, with data distributed across various databases and systems, managed by software programs operating in different languages and platforms. This fragmentation may negatively impact patient safety and, ultimately, hospital finances, since the federal government will no longer pay for additional care associated with some hospital-acquired conditions.1 Clinical decision support software (CDSS) leverages clinical information to improve the quality and safety of care by combining patient information from many sources within the institutions and making it immediately available. A 2009 study found that hospitals with automated notes and records, order entry, and CDSS had fewer complications, lower mortality rates, and lower costs. Higher scores in decision support were associated with a 16% decrease in complications, as well as $538 lower costs for all hospital admissions.2 The cornerstone of CDSS technology is its ability to interface with multiple hospital information sources, including laboratory, microbiology, pathology, pharmacy, admission/discharge/transfer, patient demographics and vital signs, radiology, and surgery. This technology offers a range of validated clinical tools, reports, and alerts that provide active, real-time electronic surveillance to increase adherence to clinical guidelines and reporting requirements. It also enhances efficiency and helps improve patient care and safety throughout a healthcare organization. CDSS also saves money for hospitals and helps prevent medical errors.3,4 Case study/background The Baptist Memorial Health Care Corporation is headquartered in Memphis and includes 14 acute care hospitals located in 3 states. Baptist Memorial Hospital Memphis (Baptist) is a 728-bed tertiary, referral hospital. The health system is currently transitioning to computerized prescriber order entry (CPOE) and upgrading all automated dispensing devices system-wide. Baptist began searching for CDSS primarily to support its infection prevention (IP) efforts to increase timely identification/intervention and in response to predictions of increased regulatory reporting.5 Considerations for the CDSS purchase centered on the program's ability to integrate with multiple clinical systems across the hospitals; integrate with the National Healthcare Safety Network (NHSN); comply with Centers for Medicare and Medicaid Services core measures and demonstrate compliance; and provide reports, alerts, and customization to fit each setting. Real-time data availability was significant, since the current program at Baptist had a 12-hour delay. As the multidisciplinary team at Baptist began to research existing infection prevention software, it became apparent that including the pharmacy components would significantly improve the IP antibiotic stewardship efforts already begun system-wide. The business model presented to senior management summarized an anticipated return on investment for both IP and pharmacy. Choosing a CDSS vendor was based on the ability to meet items of importance on a check list, input from current system users, company reputation, professional product reviews, and the voice of the end users. Implementation Initially the technology was installed for the IP team, however, as the search progressed, it was determined that the pharmacy components in the CDSS program chosen would increase pharmacy effectiveness, as well. The implementation team worked closely with the hospital's clinical and information technology teams to plan and execute the implementation while addressing any challenges that arose. Key clinical staff members from the hospital were involved in the process to ensure that the technology was optimized to meet the needs of clinical users. The new software was implemented in late 2011. With the transition from the previous system utilized for surveillance to the new integrated system, the IP program soon began to expand beyond expectations. Utilizing CDSS each morning, the IP nurses can review alerts, identify patients who may need transmission-based precautions, and interact with the patient's caregivers to expedite the precautions. Customized views make it possible to quickly see important microbiology results for all units in the facility, which streamlines identification of follow-up needs and allows for efficient preparation of patient-specific worklists before rounding. One of the most helpful features of the new system is a program that facilitates hospital-wide infection surveillance, prevention, control, and reporting in a user-friendly workflow tool. These worksheets follow the NHSN requirements for each infection type to document findings, note comments for future reviewers, and upload the infection information in a formatted NHSN report. Reporting mechanisms format this information into visual displays readily available for education to hospital staff and management. Performing surveillance through these interactive tools improves the ability of the IP nurse to recognize patient condition changes, adverse events, and other threats to patient safety more quickly. Decision making is streamlined by filtering and congregating important information needed to make clinical recommendations and/or changes in therapy. The information can be formatted so that data can be queried and specific results retrieved in a format that's useful for the IP team. In the Baptist health system, users have become creative with the program's IP aspects. ED staff, pharmacy, and rounding teams use the programs for real-time access to medication, lab, and microbiology results. For example, the IP staff identifies and flags positive cultures of patients discharged early from the ED; the pharmacists follow up with all positive cultures and sensitivities, present findings, and make recommendations to the ED physicians; these physicians then call in prescriptions for the infections. Other areas, such as outpatient services, use the system to identify returning patients who may be colonized with resistant organisms. Increasing pharmacist participation on patient care teams, the avoidance of errors, and improvement in health outcomes are important components of the Pharmacy Practice Model Initiative (PPMI). In anticipation of CPOE and following the recommendations of the PPMI, the pharmacy management team at Baptist redistributed 30 centralized pharmacists into 10 patient care areas within the institution, creating a new role of decentralized pharmacists. The CDSS previously implemented primarily for IP was expanded to support pharmacy interventions. Specifically, CDSS was customized to include interventions specific to the Baptist Memphis facility, and soft dollar cost-savings and time spent were associated with each intervention. In January 2013, staff completed a training program on documenting actions and interventions, in addition to daily responsibilities such as order entry, verification, and dispensing. Computerized documentation began on February 1, 2013. After the decentralized pharmacists became familiar with documenting interventions, alerts were developed to be executed daily. Alerts highlight clinical situations that need to be identified, assessed, and addressed. The first 10 alerts chosen were specific clinical situations where the intervention was predetermined and the physician communication notes had already been developed and approved. With CDSS, the decentralized pharmacist can address alerts before rounding and review them if necessary as talking points during rounds. These alerts save decentralized pharmacists, valuable hours, since they only have limited time dedicated to chart reviews. Decentralized pharmacists can develop custom alerts quickly and easily. For example, an alert was created to identify when a patient was ordered duplicate anticoagulants. Discontinuing the unnecessary medication may prevent a major bleeding event. The pharmacy department uses the software in many different ways to automatically compile, format, and display patient information from various sources and show custom views for each task at hand. The software facilitates clinical workflow, interventions, and documentation. This clinical productivity and workflow management tool provides measurement reports for patient safety, workload, productivity, and cost savings. Decentralized pharmacists are able to communicate to each other and account for actions and interventions completed beyond their duties of order entry and verification. The ability for the user to customize alerts and have them delivered by e-mail, pager, or smart phone helps improve patient and medication safety. Pharmacists employ proactive monitoring using pre-built clinical alerts that provide instant access to critical patient information, such as changes in status and trends in the patient's care. For example, alerts are used to identify patients with critical lab values indicating hypokalemia, hypophosphatemia, or hypomagnesemia, allowing pharmacy to send an as-needed electrolyte dose up to the floor in anticipation of the order. After data capture, a multi-disciplinary analysis committee reviews the adverse drug events (ADEs). Primarily, the committee focuses on the ADEs and interventions to improve patient safety by preventing further occurrences. This category of interventions accounts for the largest dollar amount of cost savings. A significant benefit of CDSS is that reports are dynamic and can be updated as information changes, creating an opportunity to validate the intervention data and to ensure there's a control mechanism in place to accurately reflect cost savings. Results CDSS implementation has improved the workflow of IP nurses. For example, these nurses now have time to participate in multi-disciplinary rounding on the units, which has resulted in improved communication with clinical nurses and has expedited recommendations for interventions such as transmission-based precautions. The efficiency gained in standardizing workflow among all IP nurses has allowed for expansion of the infection control plan. Initiatives include prevalence studies of central lines and urinary catheters. This baseline will be used in the future as the mark for continued improvement and include areas not covered previously. After the education and implementation of CDSS in the pharmacy, the department was able to justify decentralization of staff pharmacists both fiscally and through its impact on patient outcomes. Between February and July 2013 after implementing CDSS, potential soft-dollar cost-savings were estimated at $500,000. The majority of the interventions were prevention of ADEs. The future The opportunity exists for additional education and improved CDSS utilization. This is being accomplished through online training, webinars, and live training sessions provided by an internal super-user. This additional education and improved use of CDSS will enable better reporting of results and improvements to the patients, families, nurses, and physicians. Next steps include expanded access and use of the system to include managers and physicians. CDSS successfully addresses critical patient safety problems in healthcare today, including hospital-acquired infections and drug-resistant infectious diseases, by utilizing alerts that will tell the pharmacist, for example, when there's a “drug and bug” mismatch. In the foreseeable future, the pharmacy management team hopes to utilize the decentralized pharmacists to assist with antimicrobial stewardship through CDSS. In the ED, pharmacists have developed their own intervention categories and are expected to use CDSS to justify their presence by accurately capturing their actions and interventions. Potentially, CDSS may offer clinical business intelligence tools that could provide healthcare leaders with a clearer understanding of concerns related to patient safety, quality, and costs by organizing and presenting important clinical, business, and operations data for decision-making and resource-allocation purposes.
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