Using Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time.

INTRODUCTION: Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates. MATERIAL AND METHODS: Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated. RESULTS: Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides. DISCUSSION: WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time. CONCLUSION: In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.

Introdução: As infeções associadas aos cuidados de saúde por Klebsiella pneumoniae resistente aos carbapenemos (CRKP) são uma preocupação nos hospitais portugueses. A sequenciação total do genoma [whole genome sequencing (WGS)] pode ajudar no controlo de infecção, mas esta prática não é comummente utilizada nos laboratórios clínicos hospitalares em Portugal. O objetivo deste estudo foi simular a investigação de um surto causado por CRKP, utilizando WGS. Pretendia-se testar a utilização desta técnica e determinar, no menor tempo possível, relações genéticas entre estirpes. Material e Métodos: Foram analisados dez isolados clínicos de CRKP. Foram obtidas quarenta amostras ambientais que foram inoculadas em meio seletivo para isolamento de colónias sugestivas de CRKP e depois sequenciado o DNA total dos isolados presumptivamente identificados como CRKP A relação clonal entre as estirpes foi determinada por multi-locus sequence typing e análise de single nucleotide polymorphisms no genoma core. Foi determinada a presença de genes de carbapenemases. Resultados: Os isolados clínicos foram caraterizados em 48 horas: oito isolados foram confirmados como CRKP. A maioria pertencia ao ST13 (n = 6) e possuía o gene blaKPC-3. As amostras ambientais foram caraterizadas em seis dias: foram isoladas oito CRKP, das quais cinco eram ST13 e continham o gene blaKPC-3. Os isolados ST13 clínicos e ambientais eram muito semelhantes entre si: dez dos 11 isolados diferiam entre si em menos de 0,001% dos 2 172 367 nucleótidos core analisados. Discussão: A sequenciação total do genoma pode ser usada como uma ferramenta útil para investigar infecções nosocomiais e rastrear cadeias de disseminação em tempo real. Conclusão: Em Portugal, o uso desta técnica em controlo de infecção pode ser implementado através de colaborações entre hospitais e institutos de investigação.

A Thorn in a Haystack: A Rare Case of Septic Arthritis.

Pantoea agglomerans is a facultative anaerobe and environmental bacterium that could be a cause of opportunistic human infections, especially in wound infection with plant material. Arthritis or synovitis secondary to penetrating plant thorn injuries is not frequently reported. We present the case of a 35-year-old otherwise healthy male with a bramble thorn penetrating injury of the left knee. P. agglomerans was isolated from the synovial fluid. The patient was treated with amoxicillin/clavulanate according to sensitivity testing. This case highlights the importance of precise and thorough medical history, especially for less common presentations, as well as source control.

Risk of mortality and cardiopulmonary arrest in critical patients presenting to the emergency department using machine learning and natural language processing.

Emergency department triage is the first point in time when a patient's acuity level is determined. The time to assign a priority at triage is short and it is vital to accurately stratify patients at this stage, since under-triage can lead to increased morbidity, mortality and costs. Our aim was to present a model that can assist healthcare professionals in triage decision making, namely in the stratification of patients through the risk prediction of a composite critical outcome-mortality and cardiopulmonary arrest. Our study cohort consisted of 235826 adult patients triaged at a Portuguese Emergency Department from 2012 to 2016. Patients were assigned to emergent, very urgent or urgent priorities of the Manchester Triage System (MTS). Demographics, clinical variables routinely collected at triage and the patients' chief complaint were used. Logistic regression, random forests and extreme gradient boosting were developed using all available variables. The term frequency-inverse document frequency (TF-IDF) natural language processing weighting factor was applied to vectorize the chief complaint. Stratified random sampling was used to split the data into train (70%) and test (30%) data sets. Ten-fold cross validation was performed in train to optimize model hyper-parameters. The performance obtained with the best model was compared against the reference model-a regularized logistic regression trained using only triage priorities. Extreme gradient boosting exhibited good calibration properties and yielded areas under the receiver operating characteristic and precision-recall curves of 0.96 (95% CI 0.95-0.97) and 0.31 (95% CI 0.26-0.36), respectively. The predictors ranked with higher importance by this model were the Glasgow coma score, the patients' age, pulse oximetry and arrival mode. Compared to the reference, the extreme gradient boosting model using clinical variables and the chief complaint presented higher recall for patients assigned MTS-3 and can identify those who are at risk of the composite outcome.

Predicting Intensive Care Unit admission among patients presenting to the emergency department using machine learning and natural language processing.

The risk stratification of patients in the emergency department begins at triage. It is vital to stratify patients early based on their severity, since undertriage can lead to increased morbidity, mortality and costs. Our aim was to present a new approach to assist healthcare professionals at triage in the stratification of patients and in identifying those with higher risk of ICU admission. Adult patients assigned Manchester Triage System (MTS) or Emergency Severity Index (ESI) 1 to 3 from a Portuguese and a United States Emergency Departments were analyzed. Variables routinely collected at triage were used and natural language processing was applied to the patient chief complaint. Stratified random sampling was applied to split the data in train (70%) and test (30%) sets and 10-fold cross validation was performed for model training. Logistic regression, random forests, and a random undersampling boosting algorithm were used. We compared the performance obtained with the reference model-using only triage priorities-with the models using additional variables. For both hospitals, a logistic regression model achieved higher overall performance, yielding areas under the receiver operating characteristic and precision-recall curves of 0.91 (95% CI 0.90-0.92) and 0.30 (95% CI 0.27-0.33) for the United States hospital and of 0.85 (95% CI 0.83-0.86) and 0.06 (95% CI 0.05-0.07) for the Portuguese hospital. Heart rate, pulse oximetry, respiratory rate and systolic blood pressure were the most important predictors of ICU admission. Compared to the reference models, the models using clinical variables and the chief complaint presented higher recall for patients assigned MTS/ESI 3 and can identify patients assigned MTS/ESI 3 who are at risk for ICU admission.

Clinical Decision Support Systems for Triage in the Emergency Department using Intelligent Systems: a Review.

MOTIVATION: Emergency Departments' (ED) modern triage systems implemented worldwide are solely based upon medical knowledge and experience. This is a limitation of these systems, since there might be hidden patterns that can be explored in big volumes of clinical historical data. Intelligent techniques can be applied to these data to develop clinical decision support systems (CDSS) thereby providing the health professionals with objective criteria. Therefore, it is of foremost importance to identify what has been hampering the application of such systems for ED triage. OBJECTIVES: The objective of this paper is to assess how intelligent CDSS for triage have been contributing to the improvement of quality of care in the ED as well as to identify the challenges they have been facing regarding implementation. METHODS: We applied a standard scoping review method with the manual search of 6 digital libraries, namely: ScienceDirect, IEEE Xplore, Google Scholar, Springer, MedlinePlus and Web of Knowledge. Search queries were created and customized for each digital library in order to acquire the information. The core search consisted of searching in the papers' title, abstract and key words for the topics "triage", "emergency department"/"emergency room" and concepts within the field of intelligent systems. RESULTS: From the review search, we found that logistic regression was the most frequently used technique for model design and the area under the receiver operating curve (AUC) the most frequently used performance measure. Beside triage priority, the most frequently used variables for modelling were patients' age, gender, vital signs and chief complaints. The main contributions of the selected papers consisted in the improvement of a patient's prioritization, prediction of need for critical care, hospital or Intensive Care Unit (ICU) admission, ED Length of Stay (LOS) and mortality from information available at the triage. CONCLUSIONS: In the papers where CDSS were validated in the ED, the authors found that there was an improvement in the health professionals' decision-making thereby leading to better clinical management and patients' outcomes. However, we found that more than half of the studies lacked this implementation phase. We concluded that for these studies, it is necessary to validate the CDSS and to define key performance measures in order to demonstrate the extent to which incorporation of CDSS at triage can actually improve care.

Impact of multi-drug resistant bacteria on economic and clinical outcomes of healthcare-associated infections in adults: Systematic review and meta-analysis.

BACKGROUND: Infections with multidrug resistant (MDR) bacteria in hospital settings have substantial implications in terms of clinical and economic outcomes. However, due to clinical and methodological heterogeneity, estimates about the attributable economic and clinical effects of healthcare-associated infections (HAI) due to MDR microorganisms (MDR HAI) remain unclear. The objective was to review and synthesize the evidence on the impact of MDR HAI in adults on hospital costs, length of stay, and mortality at discharge. METHODS AND FINDINGS: Literature searches were conducted in PubMed/MEDLINE, and Google Scholar databases to select studies that evaluated the impact of MDR HAI on economic and clinical outcomes. Eligible studies were conducted in adults, in order to ensure homogeneity of populations, used propensity score matched cohorts or included explicit confounding control, and had confirmed antibiotic susceptibility testing. Risk of bias was evaluated, and effects were measured with ratios of means (ROM) for cost and length of stay, and risk ratios (RR) for mortality. A systematic search was performed on 14th March 2019, re-run on the 10th of June 2019 and extended the 3rd of September 2019. Small effect sizes were assessed by examination of funnel plots. Sixteen articles (6,122 patients with MDR HAI and 8,326 patients with non-MDR HAI) were included in the systematic review of which 12 articles assessed cost, 19 articles length of stay, and 14 mortality. Compared to susceptible infections, MDR HAI were associated with increased cost (ROM 1.33, 95%CI [1.15; 1.54]), prolonged length of stay (ROM 1.27, 95%CI [1.18; 1.37]), and excess in-hospital mortality (RR 1.61, 95%CI [1.36; 1.90]) in the random effects models. Risk of publication bias was only found to be significant for mortality, and overall study quality good. CONCLUSIONS: MDR HAI appears to be strongly associated with increases in direct cost, prolonged length of stay and increased mortality. However, further comprehensive studies in this setting are warranted. TRIAL REGISTRATION: PROSPERO (CRD42019126288).

Fecal Microbiota Transplant in a Patient Infected with Multidrug-Resistant Bacteria: A Case Report.

INTRODUCTION: There has been a growing interest in fecal microbiota transplantation (FMT) as a way to manipulate gut microbiota, with potential benefit in patients infected with multidrug-resistant (MDR) bacteria. CASE PRESENTATION: We present the case of an 87-year-old male with recurrent ascending cholangitis due to biliary atony and impaired biliary drainage after multiple biliary sphincterotomies and two papillary balloon dilations. In this context, a choledochoduodenostomy was performed, but the patient kept on having repeated episodes of acute cholangitis, resulting in multiple hospitalizations, every other week, with need of multiple broad-spectrum antibiotic courses, which led to bacteremias with MDR microorganisms. Several therapeutic strategies such as prophylactic antibiotics (including rifaximin), pre- and probiotics, prokinetics, and ursodeoxycholic acid were unsuccessfully attempted. After multidisciplinary case discussion, an FMT was proposed, with the aim of manipulating gut microbiota and decreasing MDR bacteremias. We first performed FMT via colonoscopy in September 2018, after which the patient still had 3 more hospitalizations for acute cholangitis, but isolated bacteria in blood cultures were resistant only to amoxicillin and clavulanic acid. Considering this apparent change in the microbial resistance profile, we performed a second FMT in January 2019 via the upper gastrointestinal route. During the next 4 months, the patient remained well. In April 2019, the patient relapsed again with three more episodes of cholangitis, for which we repeated the FMT via upper gastrointestinal endoscopy. No readmissions were observed during the next 4 months. All three FMTs were performed without complications. DISCUSSION AND CONCLUSION: FMT seems to be a safe procedure and was effective in decreasing hospital admissions and changing the profile of MDR bacteria previously isolated from blood cultures.

INTRODUÇÃO: Tem havido um crescente interesse no transplante de microbiota fecal (TMF) como forma de manipular a microbiota intestinal, com potencial benefício em doentes infetados com microorganismos resistentes aos antibióticos (MRA). CASO CLÍNICO: Apresentamos o caso de um homem de 87 anos de idade com colangite ascendente recorrente por atonia biliar e atraso na drenagem biliar após múltiplas esfincterotomias e duas esfincteroplastias com balão. Neste contexto, o doente foi submetido a uma coledocoduodenostomia, mantendo, no entanto, episódios recorrentes de colangite com elevada frequência (2 semanas), o que motivou hospitalizações múltiplas com necessidade de antibioterapia de largo-espectro, tendo como consequência bacteriémias por MRA. Várias estratégias terapêuticas, como antibioterapia profilática (incluindo rifaximina), pré e probióticos, procinéticos e ácido ursodesoxicólico, foram tentadas sem sucesso. Após discussão multidisciplinar do caso foi proposta a realização de um TMF, como forma de manipular a microbiota intestinal e diminuir as bacteriémias por MRA. Realizámos um TMF por via baixa (colonoscopia) em Setembro de 2018, após o qual o doente teve mais 3 hospitalizaçõesporcolangite, combacteriémiaa um microorganismo apenas resistente à amoxicilina e ácido clavulânico. Considerando a aparente mudança no perfil de resistência microbiana, realizamos um segundo TMF em Janeiro de 2019 por via alta (endoscopia), após o qual o doente permaneceu assintomático e sem novos internamentos durante 4 meses. Em Abril de 2019, o doente voltou a ter três episódios de bacteriémia com necessidade de internamento, pelo que repetimos a realização do TMF por via alta. O doente permaneceu sem novos internamentos durante 4 meses. Nenhum dos procedimentos teve complicações. DISCUSSÃO E CONCLUSÃO: O TMF parece ser um procedimento seguro e foi eficaz na redução de internamentos hospitalares e na mudança do perfil de resistência dos microorganismos isolados nas hemoculturas.

Draft Genome Sequence of the First NDM-1-Producing Providencia stuartii Strain Isolated in Portugal.

We report here the draft genome sequence of the first NDM-1-producing Providencia stuartii strain isolated in Portugal. Sequence analyses revealed the presence of an incompatibility group A/C2 (IncA/C2) plasmid and of diverse acquired genes conferring resistance to ß-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides. This sequence contributes to the evaluation of the spread of NDM-1 producers.