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      The challenge of preventing and containing outbreaks of multidrug-resistant organisms and Candida auris during the coronavirus disease 2019 pandemic: report of a carbapenem-resistant Acinetobacter baumannii outbreak and a systematic review of the literature

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          Abstract

          Background

          Despite the adoption of strict infection prevention and control measures, many hospitals have reported outbreaks of multidrug-resistant organisms (MDRO) during the Coronavirus 2019 (COVID-19) pandemic. Following an outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) in our institution, we sought to systematically analyse characteristics of MDRO outbreaks in times of COVID-19, focussing on contributing factors and specific challenges in controlling these outbreaks.

          Methods

          We describe results of our own CRAB outbreak investigation and performed a systematic literature review for MDRO (including Candida auris) outbreaks which occurred during the COVID-19 pandemic (between December 2019 and March 2021). Search terms were related to pathogens/resistance mechanisms AND COVID-19. We summarized outbreak characteristics in a narrative synthesis and contrasted contributing factors with implemented control measures.

          Results

          The CRAB outbreak occurred in our intensive care units between September and December 2020 and comprised 10 patients (thereof seven with COVID-19) within two distinct genetic clusters (both ST2 carrying OXA-23). Both clusters presumably originated from COVID-19 patients transferred from the Balkans. Including our outbreak, we identified 17 reports, mostly caused by Candida auris (n = 6) or CRAB (n = 5), with an overall patient mortality of 35% (68/193). All outbreaks involved intensive care settings. Non-adherence to personal protective equipment (PPE) or hand hygiene (n = 11), PPE shortage (n = 8) and high antibiotic use (n = 8) were most commonly reported as contributing factors, followed by environmental contamination (n = 7), prolonged critical illness (n = 7) and lack of trained HCW (n = 7). Implemented measures mainly focussed on PPE/hand hygiene audits (n = 9), environmental cleaning/disinfection (n = 9) and enhanced patient screening (n = 8). Comparing potentially modifiable risk factors and control measures, we found the largest discrepancies in the areas of PPE shortage (risk factor in 8 studies, addressed in 2 studies) and patient overcrowding (risk factor in 5 studies, addressed in 0 studies).

          Conclusions

          Reported MDRO outbreaks during the COVID-19 pandemic were most often caused by CRAB (including our outbreak) and C. auris. Inadequate PPE/hand hygiene adherence, PPE shortage, and high antibiotic use were the most commonly reported potentially modifiable factors contributing to the outbreaks. These findings should be considered for the prevention of MDRO outbreaks during future COVID-19 waves.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s13756-022-01052-8.

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          Most cited references34

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          Preferred reporting items for systematic reviews and meta-analyses: the PRISMA Statement

          Systematic reviews and meta-analyses have become increasingly important in health care. Clinicians read them to keep up to date with their field,1,2 and they are often used as a starting point for developing clinical practice guidelines. Granting agencies may require a systematic review to ensure there is justification for further research,3 and some health care journals are moving in this direction.4 As with all research, the value of a systematic review depends on what was done, what was found, and the clarity of reporting. As with other publications, the reporting quality of systematic reviews varies, limiting readers' ability to assess the strengths and weaknesses of those reviews. Several early studies evaluated the quality of review reports. In 1987, Mulrow examined 50 review articles published in 4 leading medical journals in 1985 and 1986 and found that none met all 8 explicit scientific criteria, such as a quality assessment of included studies.5 In 1987, Sacks and colleagues6 evaluated the adequacy of reporting of 83 meta-analyses on 23 characteristics in 6 domains. Reporting was generally poor; between 1 and 14 characteristics were adequately reported (mean = 7.7; standard deviation = 2.7). A 1996 update of this study found little improvement.7 In 1996, to address the suboptimal reporting of meta-analyses, an international group developed a guidance called the QUOROM Statement (QUality Of Reporting Of Meta-analyses), which focused on the reporting of meta-analyses of randomized controlled trials.8 In this article, we summarize a revision of these guidelines, renamed PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses), which have been updated to address several conceptual and practical advances in the science of systematic reviews (Box 1). Terminology The terminology used to describe a systematic review and meta-analysis has evolved over time. One reason for changing the name from QUOROM to PRISMA was the desire to encompass both systematic reviews and meta-analyses. We have adopted the definitions used by the Cochrane Collaboration.9 A systematic review is a review of a clearly formulated question that uses systematic and explicit methods to identify, select, and critically appraise relevant research, and to collect and analyze data from the studies that are included in the review. Statistical methods (meta-analysis) may or may not be used to analyze and summarize the results of the included studies. Meta-analysis refers to the use of statistical techniques in a systematic review to integrate the results of included studies. Developing the PRISMA Statement A 3-day meeting was held in Ottawa, Canada, in June 2005 with 29 participants, including review authors, methodologists, clinicians, medical editors, and a consumer. The objective of the Ottawa meeting was to revise and expand the QUOROM checklist and flow diagram, as needed. The executive committee completed the following tasks, prior to the meeting: a systematic review of studies examining the quality of reporting of systematic reviews, and a comprehensive literature search to identify methodological and other articles that might inform the meeting, especially in relation to modifying checklist items. An international survey of review authors, consumers, and groups commissioning or using systematic reviews and meta-analyses was completed, including the International Network of Agencies for Health Technology Assessment (INAHTA) and the Guidelines International Network (GIN). The survey aimed to ascertain views of QUOROM, including the merits of the existing checklist items. The results of these activities were presented during the meeting and are summarized on the PRISMA Website. Only items deemed essential were retained or added to the checklist. Some additional items are nevertheless desirable, and review authors should include these, if relevant.10 For example, it is useful to indicate whether the systematic review is an update11 of a previous review, and to describe any changes in procedures from those described in the original protocol. Shortly after the meeting a draft of the PRISMA checklist was circulated to the group, including those invited to the meeting but unable to attend. A disposition file was created containing comments and revisions from each respondent, and the checklist was subsequently revised 11 times. The group approved the checklist, flow diagram, and this summary paper. Although no direct evidence was found to support retaining or adding some items, evidence from other domains was believed to be relevant. For example, Item 5 asks authors to provide registration information about the systematic review, including a registration number, if available. Although systematic review registration is not yet widely available,12,13 the participating journals of the International Committee of Medical Journal Editors (ICMJE)14 now require all clinical trials to be registered in an effort to increase transparency and accountability.15 Those aspects are also likely to benefit systematic reviewers, possibly reducing the risk of an excessive number of reviews addressing the same question16,17 and providing greater transparency when updating systematic reviews. The PRISMA Statement The PRISMA Statement consists of a 27-item checklist (Table 1; see also Text S1 for a downloadable template for researchers to re-use) and a 4-phase flow diagram (Figure 1; see also Figure S1 for a downloadable template for researchers to re-use). The aim of the PRISMA Statement is to help authors improve the reporting of systematic reviews and meta-analyses. We have focused on randomized trials, but PRISMA can also be used as a basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. PRISMA may also be useful for critical appraisal of published systematic reviews. However, the PRISMA checklist is not a quality assessment instrument to gauge the quality of a systematic review. Box 1 Conceptual issues in the evolution from QUOROM to PRISMA Figure 1 Flow of information through the different phases of a systematic review Table 1 Checklist of items to include when reporting a systematic review or meta-analysis From QUOROM to PRISMA The new PRISMA checklist differs in several respects from the QUOROM checklist, and the substantive specific changes are highlighted in Table 2. Generally, the PRISMA checklist “decouples” several items present in the QUOROM checklist and, where applicable, several checklist items are linked to improve consistency across the systematic review report. Table 2 Substantive specific changes between the QUOROM checklist and the PRISMA checklist (a tick indicates the presence of the topic in QUOROM or PRISMA) The flow diagram has also been modified. Before including studies and providing reasons for excluding others, the review team must first search the literature. This search results in records. Once these records have been screened and eligibility criteria applied, a smaller number of articles will remain. The number of included articles might be smaller (or larger) than the number of studies, because articles may report on multiple studies and results from a particular study may be published in several articles. To capture this information, the PRISMA flow diagram now requests information on these phases of the review process. Endorsement The PRISMA Statement should replace the QUOROM Statement for those journals that have endorsed QUOROM. We hope that other journals will support PRISMA; they can do so by registering on the PRISMA Website. To underscore to authors, and others, the importance of transparent reporting of systematic reviews, we encourage supporting journals to reference the PRISMA Statement and include the PRISMA web address in their Instructions to Authors. We also invite editorial organizations to consider endorsing PRISMA and encourage authors to adhere to its principles. The PRISMA Explanation and Elaboration Paper In addition to the PRISMA Statement, a supporting Explanation and Elaboration document has been produced18 following the style used for other reporting guidelines.19-21 The process of completing this document included developing a large database of exemplars to highlight how best to report each checklist item, and identifying a comprehensive evidence base to support the inclusion of each checklist item. The Explanation and Elaboration document was completed after several face-to-face meetings and numerous iterations among several meeting participants, after which it was shared with the whole group for additional revisions and final approval. Finally, the group formed a dissemination subcommittee to help disseminate and implement PRISMA. Discussion The quality of reporting of systematic reviews is still not optimal.22-27 In a recent review of 300 systematic reviews, few authors reported assessing possible publication bias,22 even though there is overwhelming evidence both for its existence28 and its impact on the results of systematic reviews.29 Even when the possibility of publication bias is assessed, there is no guarantee that systematic reviewers have assessed or interpreted it appropriately.30 Although the absence of reporting such an assessment does not necessarily indicate that it was not done, reporting an assessment of possible publication bias is likely to be a marker of the thoroughness of the conduct of the systematic review. Several approaches have been developed to conduct systematic reviews on a broader array of questions. For example, systematic reviews are now conducted to investigate cost-effectiveness,31 diagnostic32 or prognostic questions,33 genetic associations,34 and policy-making.35 The general concepts and topics covered by PRISMA are all relevant to any systematic review, not just those whose objective is to summarize the benefits and harms of a health care intervention. However, some modifications of the checklist items or flow diagram will be necessary in particular circumstances. For example, assessing the risk of bias is a key concept, but the items used to assess this in a diagnostic review are likely to focus on issues such as the spectrum of patients and the verification of disease status, which differ from reviews of interventions. The flow diagram will also need adjustments when reporting individual patient data meta-analysis.36 We have developed an explanatory document18 to increase the usefulness of PRISMA. For each checklist item, this document contains an example of good reporting, a rationale for its inclusion, and supporting evidence, including references, whenever possible. We believe this document will also serve as a useful resource for those teaching systematic review methodology. We encourage journals to include reference to the explanatory document in their Instructions to Authors. Like any evidence-based endeavour, PRISMA is a living document. To this end we invite readers to comment on the revised version, particularly the new checklist and flow diagram, through the PRISMA website. We will use such information to inform PRISMA's continued development. Note: To encourage dissemination of the PRISMA Statement, this article is freely accessible on the Open Medicine website and the PLoS Medicine website and is also published in the Annals of Internal Medicine, BMJ, and Journal of Clinical Epidemiology. The authors jointly hold the copyright of this article. For details on further use, see the PRISMA website. The PRISMA Explanation and Elaboration Paper is available at the PLoS Medicine website. Supporting Information Figure S1 Flow of information through the different phases of a systematic review (downloadable template document for researchers to re-use) Text S1 Checklist of items to include when reporting a systematic review or meta-analysis (downloadable template document for researchers to re-use)
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            Antibiotic prescribing in patients with COVID-19: rapid review and meta-analysis

            Objective The proportion of patients infected with SARS-CoV-2 that are prescribed antibiotics is uncertain, and may contribute to patient harm and global antibiotic resistance. Our objective was to estimate the prevalence and associated factors of antibiotic use in patients with confirmed COVID-19. Methods We searched MEDLINE, OVID Epub and EMBASE for published literature on human subjects in English up to June 9, 2020. Inclusion criteria were any healthcare settings and age groups; randomized controlled trials; cohort studies; case series with >10 patients; experimental or observational design that evaluated antibiotic prescribing. The main outcome of interest was proportion of COVID-19 patients prescribed an antibiotic, stratified by geographical region, severity of illness, and age. We pooled proportion data using random effects meta-analysis. Results We screened 7469 studies, from which 154 were included in the final analysis. Antibiotic data were available from 30,623 patients. The prevalence of antibiotic prescribing was 74.6% (95% CI 68.3 to 80.0%). On univariable meta-regression, antibiotic prescribing was lower in children (prescribing prevalence odds ratio (OR) 0.10, 95%CI 0.03 to 0.33) compared to adults. Antibiotic prescribing was higher with increasing patient age (OR 1.45 per 10 year increase, 95%CI 1.18 to 1.77) and higher with increasing proportion of patients requiring mechanical ventilation (OR 1.33 per 10% increase, 95%CI 1.15 to 1.54). Estimated bacterial co-infection was 8.6% (95% CI 4.7-15.2%) from 31 studies. Conclusions Three-quarters of patients with COVID-19 receive antibiotics, prescribing is significantly higher than the estimated prevalence of bacterial co-infection. Unnecessary antibiotic use is likely high in patients with COVID-19. Registration PROSPERO (ID CRD42020192286).
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              Outcomes from intensive care in patients with COVID‐19: a systematic review and meta‐analysis of observational studies

              The emergence of coronavirus disease 2019 (COVID-19) has led to high demand for intensive care services worldwide. However, the mortality of patients admitted to the intensive care unit (ICU) with COVID-19 is unclear. Here, we perform a systematic review and meta-analysis, in line with PRISMA guidelines, to assess the reported ICU mortality for patients with confirmed COVID-19. We searched MEDLINE, EMBASE, PubMed and Cochrane databases up to 31 May 2020 for studies reporting ICU mortality for adult patients admitted with COVID-19. The primary outcome measure was death in intensive care as a proportion of completed ICU admissions, either through discharge from the ICU or death. The definition thus did not include patients still alive on ICU. Twenty-four observational studies including 10,150 patients were identified from centres across Asia, Europe and North America. In-ICU mortality in reported studies ranged from 0 to 84.6%. Seven studies reported outcome data for all patients. In the remaining studies, the proportion of patients discharged from ICU at the point of reporting varied from 24.5 to 97.2%. In patients with completed ICU admissions with COVID-19 infection, combined ICU mortality (95%CI) was 41.6% (34.0-49.7%), I2  = 93.2%). Sub-group analysis by continent showed that mortality is broadly consistent across the globe. As the pandemic has progressed, the reported mortality rates have fallen from above 50% to close to 40%. The in-ICU mortality from COVID-19 is higher than usually seen in ICU admissions with other viral pneumonias. Importantly, the mortality from completed episodes of ICU differs considerably from the crude mortality rates in some early reports.
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                Author and article information

                Contributors
                reto.thoma@kssg.ch
                marco.seneghini@kssg.ch
                salome.seiffert@zlmsg.ch
                danielle.vuichard-gysin@stgag.ch
                giulia.scanferla@kssg.ch
                sabine.haller@kssg.ch
                domenica.flury@kssg.ch
                katia.boggian@kssg.ch
                gian-reto.kleger@kssg.ch
                miodrag.filipovic@kssg.ch
                oliver.nolte@zlmsg.ch
                matthias.schlegel@kssg.ch
                philipp.kohler@kssg.ch
                Journal
                Antimicrob Resist Infect Control
                Antimicrob Resist Infect Control
                Antimicrobial Resistance and Infection Control
                BioMed Central (London )
                2047-2994
                21 January 2022
                21 January 2022
                2022
                : 11
                : 12
                Affiliations
                [1 ]GRID grid.413349.8, ISNI 0000 0001 2294 4705, Division of Infectious Diseases and Hospital Epidemiology, , Cantonal Hospital St. Gallen, ; St. Gallen, Switzerland
                [2 ]Division of Human Microbiology, Center for Laboratory Medicine, St. Gallen, Switzerland
                [3 ]Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital Muensterlingen, Muensterlingen, Switzerland
                [4 ]GRID grid.413349.8, ISNI 0000 0001 2294 4705, Division of Intensive Care Medicine, , Cantonal Hospital St. Gallen, ; St. Gallen, Switzerland
                Author information
                http://orcid.org/0000-0002-3007-2641
                Article
                1052
                10.1186/s13756-022-01052-8
                8777447
                35063032
                1bd9504f-a51f-4778-a0b5-efc186353478
                © The Author(s) 2022

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 6 December 2021
                : 3 January 2022
                Categories
                Review
                Custom metadata
                © The Author(s) 2022

                Infectious disease & Microbiology
                covid-19,multidrug-resistant organisms,outbreaks,review
                Infectious disease & Microbiology
                covid-19, multidrug-resistant organisms, outbreaks, review

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