Automated data mining of the electronic health record for investigation of healthcare-associated outbreaks

Sundermann, Alexander; Miller, Judy Z.; Marsh, Jane W.; Saul, Melissa; Shutt, Kathleen A.; Pacey, Marissa P; Mustapha, Mustapha M.; Ayres, Ashley; Pasculle, A. William; Chen, Jieshi; Dubrawski, Artur; Harrison, Lee H.

doi:10.1017/ice.2018.343

Cited by 44 publications

(39 citation statements)

References 11 publications

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“…We sequenced the genomes of all 20 CNSC isolates on the Illumina platform (Table S1) and constructed a phylogenetic tree that also included an additional 82 carbapenem-susceptible Citrobacter isolates collected by the Enhanced Detection System for Hospital-Associated Transmission (EDS-HAT) project ( Fig. 2 ; Table S4) ( 38 , 39 ). Among the 20 CNSC isolates, C. freundii was the predominant species (60% [12/20]), followed by Citrobacter werkmanii (20% [4/20]), C. koseri (10% [2/20]), and C. farmeri (5% [1/20]).…”

Section: Resultsmentioning

confidence: 99%

Clinical and Genomic Epidemiology of Carbapenem-Nonsusceptible Citrobacter spp. at a Tertiary Health Care Center over 2 Decades

et al. 2020

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Carbapenem-non-susceptible Citrobacter spp. (CNSC) are increasingly recognized as healthcare-associated pathogens. Information regarding their clinical epidemiology, genetic diversity, and mechanisms of carbapenem resistance is lacking. We examined microbiology records of adult patients at the University of Pittsburgh Medical Center (UMPC) Presbyterian Hospital (PUH) from 2000-2018 for CNSC, as defined by ertapenem non-susceptibility. Over this timeframe, the proportion of CNSC increased from 4% to 10% (P=0.03), as did carbapenem daily defined doses/1000 patient days (6.52 to 34.5, R2=0.831, P<0.001), which correlated with the observed increase in CNSC (lag=0 years, R2=0.660). Twenty CNSC isolates from 19 patients at PUH and other UPMC hospitals were available for further analysis, including whole-genome short-read sequencing and additional antimicrobial susceptibility testing. Of the 19 patients, nearly all acquired CNSC in the healthcare setting and over half had polymicrobial cultures containing at least one other organism. Among the 20 CNSC isolates, C. freundii was the predominant species identified (60%). CNSC genomes were compared with genomes of carbapenem-susceptible Citrobacter spp. from UPMC, and with other publicly available CNSC genomes. Isolates encoding carbapenemases (blaKPC-2, blaKPC-3, and blaNDM-1) were also long-read sequenced, and their carbapenemase-encoding plasmid sequences were compared with one another and with publicly available sequences. Phylogenetic analysis of 102 UPMC Citrobacter spp. genomes showed that CNSC from our setting did not cluster together. Similarly, a global phylogeny of 64 CNSC genomes showed a diverse population structure. Our findings suggest that both local and global CNSC populations are genetically diverse, and that CNSC harbor carbapenemase-encoding plasmids found in other Enterobacterales.

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Section: Resultsmentioning

confidence: 99%

Clinical and Genomic Epidemiology of Carbapenem-Nonsusceptible Citrobacter spp. at a Tertiary Health Care Center over 2 Decades

et al. 2020

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“…The recently emerged clade II F subclade has caused multiple outbreaks since 2014, and ongoing surveillance shows that it continues to be observed in hospitalized patients. While subclades A1* and F may represent continued reintroductions from the community to our institution, further investigations to identify previously unrecognized sources and transmission routes are required and are a major focus of our ongoing EDS-HAT study (33–35).…”

Section: Discussionmentioning

confidence: 99%

Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years

Marsh

Mustapha

Griffith

et al. 2019

mBio

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Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains belonging to sequence type 258 (ST258) are frequent causes of hospital-associated outbreaks and are a major contributor to the spread of carbapenemases. This genetic lineage emerged several decades ago and remains a major global health care challenge. In this study, genomic epidemiology was used to investigate the emergence, evolution, and persistence of ST258 carbapenem-resistant K. pneumoniae outbreak-causing lineages at a large tertiary care hospital over 8 years. A time-based phylogenetic analysis of 136 ST258 isolates demonstrated the succession of multiple genetically distinct ST258 sublineages over the 8-year period. Ongoing genomic surveillance identified the emergence and persistence of several distinct clonal ST258 populations. Patterns of multidrug resistance determinants and plasmid replicons were consistent with continued evolution and persistence of these populations. Five ST258 outbreaks were documented, including three that were caused by the same clonal lineage. Mutations in genes encoding effectors of biofilm production and iron acquisition were identified among persistent clones. Two emergent lineages bearing K. pneumoniae integrative conjugative element 10 (ICEKp10) and harboring yersiniabactin and colibactin virulence factors were identified. The results show how distinct ST258 subpopulations have evolved and persisted within the same hospital over nearly a decade. IMPORTANCE The carbapenem class of antibiotics is invaluable for the treatment of selected multidrug-resistant Gram-negative pathogens. The continued transmission of carbapenem-resistant bacteria such as ST258 K. pneumoniae is of serious global public health concern, as treatment options for these infections are limited. This genomic epidemiologic investigation traced the natural history of ST258 K. pneumoniae in a single health care setting over nearly a decade. We found that distinct ST258 subpopulations have caused both device-associated and ward-associated outbreaks, and some of these populations remain endemic within our hospital to the present day. The finding of virulence determinants among emergent ST258 clones supports the idea of convergent evolution of drug-resistant and virulent CRKP strains and highlights the need for continued surveillance, prevention, and control efforts to address emergent and evolving ST258 populations in the health care setting.

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“…EHRs are still a source of high quality information for public health researchers. Post marketing drug surveillance [12,13] and healthcare-associated outbreaks detection [14,15] continue to be hot topics of research.…”

Section: Resultsmentioning

confidence: 99%

Public Health and Epidemiology Informatics: Recent Research Trends Moving toward Public Health Data Science

Cossin

Thiébaut

Informatics³

2020

Yearb Med Inform

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Objectives: To introduce and summarize current research in the field of Public Health and Epidemiology Informatics. Methods: PubMed searches of 2019 literature concerning public health and epidemiology informatics were conducted and the returned references were reviewed by the two section editors to select 14 candidate best papers. These papers were then peer-reviewed by external reviewers to allow the Editorial Committee a curated selection of the best papers. Results: Among the 835 references retrieved from PubMed, two were finally selected as best papers. The first best paper leverages satellite images and deep learning to identify remote rural communities in low-income countries; the second paper describes the development of a worldwide human disease surveillance system based on near real-time news data from the GDELT project. Internet data and electronic health records are still widely used to detect and monitor disease activity. Identifying and targeting specific audiences for public health interventions is a growing subject of interest. Conclusions: The ever-increasing amount of data available offers endless opportunities to develop methods and tools that could assist public health surveillance and intervention belonging to the growing field of public health Data Science. The transition from proofs of concept to real world applications and adoption by health authorities remains a difficult leap to make.

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Automated data mining of the electronic health record for investigation of healthcare-associated outbreaks

Cited by 44 publications

References 11 publications

Clinical and Genomic Epidemiology of Carbapenem-Nonsusceptible Citrobacter spp. at a Tertiary Health Care Center over 2 Decades

Clinical and Genomic Epidemiology of Carbapenem-Nonsusceptible Citrobacter spp. at a Tertiary Health Care Center over 2 Decades

Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years

Public Health and Epidemiology Informatics: Recent Research Trends Moving toward Public Health Data Science

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