The Development and Validation of a Machine Learning Model to Predict Bacteremia and Fungemia in Hospitalized Patients Using Electronic Health Record Data.

OBJECTIVES: Bacteremia and fungemia can cause life-threatening illness with high mortality rates, which increase with delays in antimicrobial therapy. The objective of this study is to develop machine learning models to predict blood culture results at the time of the blood culture order using routine data in the electronic health record. DESIGN: Retrospective analysis of a large, multicenter inpatient data. SETTING: Two academic tertiary medical centers between the years 2007 and 2018. SUBJECTS: All hospitalized patients who received a blood culture during hospitalization. INTERVENTIONS: The dataset was partitioned temporally into development and validation cohorts: the logistic regression and gradient boosting machine models were trained on the earliest 80% of hospital admissions and validated on the most recent 20%. MEASUREMENTS AND MAIN RESULTS: There were 252,569 blood culture days-defined as nonoverlapping 24-hour periods in which one or more blood cultures were ordered. In the validation cohort, there were 50,514 blood culture days, with 3,762 cases of bacteremia (7.5%) and 370 cases of fungemia (0.7%). The gradient boosting machine model for bacteremia had significantly higher area under the receiver operating characteristic curve (0.78 [95% CI 0.77-0.78]) than the logistic regression model (0.73 [0.72-0.74]) (p < 0.001). The model identified a high-risk group with over 30 times the occurrence rate of bacteremia in the low-risk group (27.4% vs 0.9%; p < 0.001). Using the low-risk cut-off, the model identifies bacteremia with 98.7% sensitivity. The gradient boosting machine model for fungemia had high discrimination (area under the receiver operating characteristic curve 0.88 [95% CI 0.86-0.90]). The high-risk fungemia group had 252 fungemic cultures compared with one fungemic culture in the low-risk group (5.0% vs 0.02%; p < 0.001). Further, the high-risk group had a mortality rate 60 times higher than the low-risk group (28.2% vs 0.4%; p < 0.001). CONCLUSIONS: Our novel models identified patients at low and high-risk for bacteremia and fungemia using routinely collected electronic health record data. Further research is needed to evaluate the cost-effectiveness and impact of model implementation in clinical practice.

Rapid identification of bloodstream bacterial and fungal pathogens and their antibiotic resistance determinants from positively flagged blood cultures using the BioFire FilmArray blood culture identification panel.

BACKGROUND/PURPOSE: Rapid and accurate identification of pathogens and their antibiotic resistance directly from flagged blood cultures can aid clinicians in optimizing early antibiotic treatment and improve the clinical outcomes, especially in settings associated with high rates of bloodstream infection caused by vancomycin-resistant Enterococci (VRE) and carbapenem-resistant Enterobacteriaceae (CRE). We compared the results of the BioFire FilmArray Blood Culture Identification (BCID) panel with those of conventional methods for identifying the pathogens and their antibiotic susceptibility status. METHODS: In total, 100 randomly selected positive blood cultures (BACTEC Plus Aerobic/F bottles or BACTEC Anaerobic Lytic/10 bottles) were analyzed. The pathogen detection efficiency of FilmArray BCID panel was compared with that of conventional method using MALDI-TOF MS system (Bruker MALDI Biotyper) and susceptibility testing by the Vitek 2 system. The sequencing analysis of antibiotic resistance genes was performed for discrepant results obtained from MALDI Biotyper and Vitek 2. RESULTS: Among the 100 positively flagged blood cultures, 94% of FilmArray BCID panel results were consistent with the MALDI Biotyper results. All five VRE isolates positive for vanA/vanB genes, 10 of 12 Staphylococcus species positive for mecA gene, and only one Klebsiella pneumoniae isolate positive for K. pneumoniae carbapenemase gene (blaKPC) detected in the FilmArray BCID panel were also concordant with results by the results by conventional susceptibility testing/molecular confirmation. CONCLUSIONS: The FilmArray BCID panel results not only demonstrated good correlation with conventional blood culture identification and susceptibility results but also provided results rapidly, especially for the early detection of MRSA, VRE and blaKPC-mediated CRE.

Applicability of an in-house saponin-based extraction method in Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for identifying bacterial and fungal species in positively flagged pediatric VersaTREK blood cultures.

BACKGROUND/PURPOSE: Early identification of pathogens causing bloodstream infection (BSI) is critical for prompt administration of appropriate antimicrobial therapy. METHODS: We used an in-house saponin-based extraction method to evaluate the performance of Bruker Biotyper MALDI-TOF MS system (MALDI Biotyper) for bacterial and fungal identification in 2013 positively-flagged VersaTREK blood culture bottles. RESULTS: A total of 180 monomicrobial and 23 polymicrobial positive blood cultures were investigated. Among monomicrobial positive blood cultures, the MALDI Biotyper recognized 90.6% and 81.7% of organisms directly from the flagged blood culture bottles to the genus and species levels, respectively. The MALDI Biotyper also correctly characterized one of the polymicrobial organisms to the species level in 20 (87%) bottles and to the genus level in 21 (91.3%) bottles. The overall identification rate using our protocol was 90.6% (184/203) and 82.3% (167/203) for genus and species levels, respectively. Identification accuracy was higher for Gram-positive than Gram-negative organisms and was the lowest for yeasts. Score values of identification were ≥1.500 for 200 (98.5%) bottles, ≥1.700 for 195 (96.1%) bottles and ≥2.000 for 182 (89.7%) bottles. Moreover, 83.5% and 92% of the isolates were identified precisely to species and genus level with the lower cutoff score of 1.500. Using our protocol also helped identifying BSI pathogens 18-24 h earlier compared to the sub-cultured colonies. CONCLUSION: Using Bruker MALDI Biotyper for identification of isolates directly from positive VersaTREK blood culture bottles, our in-house saponin-based protocol provided a more rapid turn-around time for correct identification of BSI pathogens than the conventional methods.

Septicemia after chemotherapy for childhood acute lymphoblastic leukemia in China: A multicenter study CCCG-ALL-2015.

BACKGROUND: Septicemia is an important cause of treatment-related mortality and treatment failure in pediatric acute lymphoblastic leukemia (ALL) in developing countries. A multicenter CCCG-ALL-2015 study was conducted in China and factors associated with septicemia and mortality were studied. METHODS: Patients participated in CCCG-ALL-2015 study from January 2015 to December 2017 were included. Patients with documented septicemia were identified from the Data Center and additional data were collected. RESULTS: A total of 4080 patients were recruited in the study and 527 patients with septicemia were identified (12.9%, 95% CI 11.9%-13.9%). The intermediate risk (IR)/high risk (HR) group had significantly higher incidence of septicemia as compared with low risk (LR) group, 17.1% vs 9.1% (OR 2.07, 95% CI 1.71-2.49, P < .001). Induction phase was the period with majority of septicemia episodes happened, 66.8% in LR and 56.1% in IR/HR groups. Gram-positive bacteria accounted for 54.1%, gram-negative bacteria 44.5%, and fungus 1.4% of positive cultures. Multidrug-resistant organisms were detected in 20.5% of all organisms. The mortality rate after septicemia was 3.4% (95% CI 1.9%-4.9%). Multiple logistic regression identified female gender, comorbid complications, and fungal infection as risk factors associated with mortality. Gram-negative septicemia was associated with higher mortality, 4.9% vs 1.4% (OR 0.28, 95% CI 0.09-0.88, P = .02). There was marked variation in the incidence of septicemia among the 18 centers, from 4.8% to 29.1%. CONCLUSION: Overall the incidence and pattern of septicemia in this multicenter study in China was similar to the reports of western countries. The septicemia-related mortality rate was low. There was marked variation in the incidence of septicemia among the centers.

Microbiological diagnosis of bacteraemia and fungaemia: Blood cultures and molecular methods. / Diagnóstico microbiológico de la bacteriemia y la fungemia: hemocultivos y métodos moleculares.

OBJETIVE: In this review we try to update the new procedures applicable in the microbiological diagnosis of bacteriemia and fungemias. METHOD: Review of scientific literature. RESULTS AND CONCLUSIONS: After defining the process and indicating its fundamental principles, the main biomarkers used in clinical practice are reviewed. Subsequently, the particularities of the pre-analytical phase (collection and transport of samples) are highlighted and the steps to follow for the microbiological identification by classical methods are detailed, based on the culture of the blood samples. In the following section, we review the diagnostic methods not culture based, including those that detect the presence of the genome of the microorganism and those based on the study of proteome by mass spectrometry. The last section describes the procedures more frecuently used for the study of antibiotic susceptibility, both by phenotypic and genotypic methods.

Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer.

PURPOSE: Bloodstream infections are major causes of morbidity and mortality that lead to prolonged hospital stays and higher medical costs. In this study, we aimed to evaluate the MinION nanopore sequencer for the identification of the most dominant pathogens in positive blood culture bottles. METHODOLOGY: 16S and ITS1-5.8S-ITS2 rRNA genes were amplified by PCR reactions with barcoded primers using nine clinical isolates obtained from positive blood bottles and 11 type strains, including five types of Candida species. Barcoded amplicons were mixed, and multiplex sequencing with the MinION sequencer was performed. In addition, barcoded PCR amplicons were sequenced by Sanger sequencing to validate the performance of the MinION. RESULTS: The bacterial and Candida spp. identified by MinION sequencing, based on the highest homology of reference sequences from the NCBI gene databases, agreed with the matrix-assisted laser desorption ionization time of flight mass spectrometry results, excepting the closely related species Streptococcusand Escherichia coli. The 'pass' reads obtained within about 10 min of sequencing were sufficient to identify the pathogens. The average values of sequence identities with 1D2 chemistry and the R9.5 flow cell were around 99 %; thus, frequent sequence errors did not affect species identification based on amplicon sequencing. CONCLUSION: We have established a rapid, portable and economical technique for the identification of pathogens in positive blood culture bottles through a novel MinION nanopore sequencer amplicon sequencing scheme, which replaces traditional Sanger sequencing.

The Diagnostic Value of Procalcitonin Versus Other Biomarkers in Prediction of Bloodstream Infection.

BACKGROUND: We compared the diagnostic utility of procalcitonin (PCT), C-reactive protein (CRP), and hematological markers, including white blood cell count (WBC), neutrophils (NEU), percentage of neutrophils (NEU%), lymphocytes (LYM), neutrophil-lymphocyte count ratio (NLCR), and platelet count (PLT) for predicting bloodstream infection (BSI), which was confirmed by blood culture (BC). METHODS: A retrospective analysis was conducted for 1807 inpatients. The level of PCT, CRP, blood cells, and blood culture results were compared between the positive blood culture group and negative blood culture group; each indicator was analyzed in the performance of bacterial BSI diagnosis by drawing ROC curves. RESULTS: Blood cultures were positive in 230 patients; hence, the prevalence of bacteremia was 12.7%. There were significant differences in the median value for each marker between positive group BCs and negative group BCs (p < 0.05). The areas under the receiver operating characteristic curves (ROC-AUCs) of PCT, CRP, WBC, NEU, NUE%, LYM, NLCR, and PLT for discriminating positive BCs from negative BCs were 0.811, 0.654, 0.612, 0.634, 0.684, 0.595, 0.682, and 0.633 respectively. PCT concentrations of gram-negative (14.94 ng/mL, IQR 2.93  48.76) were significantly higher than gram-positive (4.74 ng/mL, IQR 1.22  17.5) and fungal (1.47 ng/mL, IQR 0.66  35.34). CONCLUSIONS: PCT proved to be the most reliable predictor of BSI, second were NEU% and NLCR. A higher PCT level was found in patients with a gram-negative BSI compared to gram-positive BSI and fungal BSI.

Diagnosis of Sepsis with Cell-free DNA by Next-Generation Sequencing Technology in ICU Patients.

BACKGROUND AND AIMS: Bacteremia is a common serious manifestation of disease in the intensive care unit (ICU), which requires quick and accurate determinations of pathogens to select the appropriate antibiotic treatment. To overcome the shortcomings of traditional bacterial culture (BC), we have adapted next-generation sequencing (NGS) technology to identify pathogens from cell-free plasma DNA. METHODS: In this study, 78 plasma samples from ICU patients were analyzed by both NGS and BC methods and verified by PCR amplification/Sanger sequencing and ten plasma samples from healthy volunteers were analyzed by NGS as negative controls to define or calibrate the threshold of the NGS methodology. RESULTS: Overall, 1578 suspected patient samples were found to contain bacteria or fungi by NGS, whereas ten patients were diagnosed by BC. Seven samples were diagnosed with bacterial or fungal infection both by NGS and BC. Among them, two samples were diagnosed with two types of bacteria by NGS, whereas one sample was diagnosed with two types of bacteria by BC, which increased the detectability of bacteria or fungi from 11 with BC to 17 with NGS. Most interestingly, 14 specimens were also diagnosed with viral infection by NGS. The overall diagnostic sensitivity was significantly increased from 12.82% (10/78) by BC alone to 30.77% (24/78) by NGS alone for ICU patients, which provides more useful information for establishing patient treatment plans. CONCLUSION: NGS technology can be applied to detect bacteria in clinical blood samples as an emerging diagnostic tool rich in information to determine the appropriate treatment of septic patients.

Microbiological Diagnosis of Sepsis: Polymerase Chain Reaction System Versus Blood Cultures.

OBJECTIVE: To compare the utility of a multiplex polymerase chain reaction system (SeptiFast) and blood cultures for detecting bacteria and fungi in blood samples from patients with severe sepsis or septic shock. METHODS: In a prospective observational study, whole blood samples for SeptiFast testing and for culture were collected on admission from all patients with severe sepsis or septic shock admitted to the intensive care unit between July 2011 and September 2012. SeptiFast results were compared with blood and other culture results. RESULTS: The probability of at least 1 microorganism being isolated at 6 hours was 13-fold higher with the SeptiFast test than with blood cultures (relative risk, 13.5; 95% CI, 5.05-36.06). Unlike culture results, SeptiFast test results were not associated with previous antibiotic consumption. The median time to the first positive blood culture result was 17 hours; SeptiFast results were available in 6 hours. SeptiFast detected genetic material from potentially multiresistant microorganisms in patients whose blood cultures showed no growth at all. CONCLUSIONS: The SeptiFast test provided quicker microbiological diagnosis and identified significantly more microorganisms than blood cultures did, particularly when samples were collected after antibiotic therapy had started or infections were due to resistant bacteria and yeast.

Do Wound Cultures Give Information About the Microbiology of Blood Cultures in Severe Burn Patients?

BACKGROUND: Blood stream infection (BSI) and the subsequent development of sepsis are among the most common infection complications occurring in severe burn patients. This study was designed to evaluate the relationship between the burn wound flora and BSI pathogens. METHODS: Documentation of all bacterial and fungal wound and blood isolates from severe burn patients hospitalized in the burn unit and intensive care unit was obtained from medical records retrieved retrospectively from a computerized, hospital-wide database over a 13-year period. All data were recorded in relation to the Ryan score. RESULTS: Of 195 severe burn patients, 88 had at least 1 BSI episode. Transmission of the same pathogen from wound to blood was documented in 30% of the patients, with a rising BSI frequency as the Ryan score increased. There were a total of 263 bacteremic episodes in 88 study patients, 44% of blood isolates were documented previously in wound cultures, and transmission of the same pathogen from wound to blood was noted in 65% of bacteremic patients. CONCLUSIONS: When there is clinical suspicion of sepsis, appropriate empirical systemic antibiotic therapy should be broad spectrum and should rely on the susceptibility of the organisms from recent cultures of the burn wound surface, until the blood cultures results are completed.

Evaluation of a multiplex OnSpot Primer-Extension PCR assay in the diagnosis of sepsis.

For evaluation of the Anagnostics Pathogens DNA xA (PxA) assay in the diagnosis of sepsis 58 blood specimens were tested in comparison with the LightCycler SeptiFast assay and blood culture as gold standard. The PxA assay had a lower sensitivity (0.63 vs. 0.8), but higher specificity (0.83 vs. 0.67) than SeptiFast.

Increasing Antimicrobial Resistance Monitored in Surveillance Analysis of Blood Stream Infections in Febrile Neutropenic Pediatric Oncology Patients.

BACKGROUND: Continuous surveillance of pattern of blood stream infection is necessary in febrile neutropenia (FN)especially with the recent escalating trend in the management of pediatric cancer patients towards intensified regimens and with the increase in infections caused by resistant organisms limiting the choice of antibiotics. AIM: To monitor change in pattern of blood stream infections (BSI) in FN pediatric cancer patients. MATERIALS AND METHODS: Surveillance of FN episodes with positive BSI was prospectively monitored and compared to a previous surveillance in the same pediatric oncology unit. RESULTS: A total of 232 BSI positive episodes were documented in 192 patients during a 6 months period. The results of recent surveillance analysis showed an increase in intensified regimens of chemotherapy, antimicrobial resistance, fungal infections, and prolonged duration of episodes when compared to previous surveillance, with p value sof <0.001, 0.005, 0.021, and <0.001, respectively. There was an apparent decrease in the crude mortality but this was not statistically significant, to 6% in 2011 from 10 % in 2006. CONCLUSIONS: The pattern of BSI at our institution is still inclining towards gram positive organisms but is showing a shift towards more antibiotic resistance and fungal infections.

[Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis]. / Marcadores moleculares: una herramienta importante en el diagnóstico, tratamiento y epidemiología de la aspergilosis invasora.

Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

El incremento en la incidencia de la aspergilosis invasora representa un grave problema para el tratamiento de pacientes con esta micosis, debido a su elevada tasa de mortalidad por deficiencias diagnósticas y terapéuticas. Éstas se han atribuido a la dificultad para detectar Aspergillus fumigatus, principal agente etiológico de esta micosis, en las muestras biológicas de pacientes inmunosuprimidos, que son los principales afectados por el hongo; además por la resistencia a los antifúngicos como consecuencia del uso incontrolado de éstos, a nivel profiláctico y terapéutico, y el desconocimiento de aspectos epidemiológicos de la aspergilosis. En la actualidad, para superar estas limitaciones se han empleado marcadores moleculares. En México su uso aún no está implementado en la rutina de los laboratorios intrahospitalarios, porque a pesar de que se han reportado ampliamente en la bibliografía, hace falta validarlos y estandarizarlos para asegurar que los resultados que se obtengan en cualquier laboratorio sean confiables y comparables. En este trabajo se presenta una revisión actualizada de la utilidad de los marcadores moleculares en la identificación certera de A. fumigatus en la detección de resistencia a los antifúngicos triazólicos y en estudios epidemiológicos para establecer las medidas necesarias en la prevención y control de la aspergilosis.

Subacute fungal endocarditis due to Acremonium spp: a case study and review of the literature.

A 52 years old patient is hospitalized in June 2007 in the Cardiology Clinic of Cardiovascular Diseases Medical Institute in Iasi with suspected subacute infectious endocarditis. Echocardiography shows mobile vegetation on the pulmonary valve. Acremonium spp is isolated from blood cultures after 2 weeks of incubation. The patient was treated with fluconazole, but died after 3 months due to renal failure.

Saccharomyces cerevisiae fungemia, a possible consequence of the treatment of Clostridium difficile colitis with a probioticum.

The yeast Saccharomyces boulardii is a biotherapeutic agent used for the prevention and treatment of several gastrointestinal diseases, such as diarrhoea caused by Clostridium difficile, in addition to the antibiotic therapy. In this study we report a case of Saccharomyces cerevisiae fungemia in a patient with Clostridium difficile-associated diarrhoea (CDAD) treated orally with S. boulardii in association with vancomycin. The identification of the S. cerevisiae was confirmed by molecular technique. Fungemia is a rare, but a serious complication to treatment with probiotics. We believe it is important to remind the clinicians of this risk when prescribing probiotics, especially to immunocompromised patients.

Incremental value of multiplex real-time PCR for the early diagnosis of sepsis in the emergency department.

BACKGROUND: Delayed recognition of sepsis and inappropriate initial antibiotic therapy are associated with increased mortality and morbidity. The early detection of the causative organism in sepsis is an unmet clinical need. A novel multiplex real-time polymerase chain reaction (MRT-PCR) (SeptiFast®) technique may provide the microbiological diagnosis within six hours. METHODS: We assessed the diagnostic accuracy of blood cultures and MRT-PCR in a comparative diagnostic cohort study in 110 consecutive adult patients presenting to the emergency department (ED) with suspected sepsis. RESULTS: We collected 205 corresponding PCR samples and blood culture (BC) pairs from the 110 patients. There was moderate to high concordance between PCR and BC with 181 (88%) matching and 24 (12%) mismatching samples. The diagnostic accuracy of MRT-PCR in detecting sepsis and its causative organism was comparable to that of BCs. The additional use of MRT-PCR significantly reduced the time to microbiological diagnosis as compared to the use of conventional microbiological methods alone (mean time gained 3.9 hours, range 0-66 hours, p <0.001). CONCLUSION: Diagnostic accuracy of BCs and MRT-PCR in the early diagnosis of sepsis and its causative organism in the ED are comparable. However, MRT-PCR reduces the time to microbiological diagnosis. Whether a more rapid detection of the organism by MRT-PCR could improve the outcome of patients has to be assessed in large prospective randomised trials.