Evaluation of blood culture epidemiology and efficiency in a large European teaching hospital

Procalcitonin for Safe Reduction of Unnecessary Blood Cultures in the Emergency Department: Development and Validation of a Prediction Model

OBJECTIVES

Blood cultures (BCs) are commonly ordered in emergency departments (EDs), while a minority yields a relevant pathogen. Diagnostic stewardship is needed to safely reduce unnecessary BCs. We aimed to develop and validate a bacteremia prediction model for ED patients, with specific focus on the benefit of incorporating procalcitonin.

METHODS

We included adult patients with suspected bacteremia from a Dutch ED for a one-year period. We defined 23 candidate predictors for a "full model", of which nine were used for an automatable "basic model". Variations of both models with C-reactive protein and procalcitonin were constructed using LASSO regression, with bootstrapping for internal validation. External validation was done in an independent cohort of patients with confirmed infection from 71 Spanish EDs. We assessed discriminative performance using the C-statistic and calibration with calibration curves. Clinical usefulness was evaluated by sensitivity, specificity, saved BCs, and Net Benefit.

RESULTS

Among 2111 patients in the derivation cohort (mean age 63 years, 46% male), 273 (13%) had bacteremia, versus 896 (20%) in the external cohort (n = 4436). Adding procalcitonin substantially improved performance for all models. The basic model with procalcitonin showed most promise, with a C-statistic of 0.87 (0.86-0.88) upon external validation. At a 5% risk threshold, it showed a sensitivity of 99% and could have saved 29% of BCs while only missing 10 out of 896 (1.1%) bacteremia patients.

CONCLUSIONS

Procalcitonin-based bacteremia prediction models can safely reduce unnecessary BCs at the ED. Further validation is needed across a broader range of healthcare settings.

Appropriate use of blood cultures in the emergency department through machine learning (ABC): study protocol for a randomised controlled non-inferiority trial

INTRODUCTION

The liberal use of blood cultures in emergency departments (EDs) leads to low yields and high numbers of false-positive results. False-positive, contaminated cultures are associated with prolonged hospital stays, increased antibiotic usage and even higher hospital mortality rates. This trial aims to investigate whether a recently developed and validated machine learning model for predicting blood culture outcomes can safely and effectively guide clinicians in withholding unnecessary blood culture analysis.

METHODS AND ANALYSIS

A randomised controlled, non-inferiority trial comparing current practice with a machine learning-guided approach. The primary objective is to determine whether the machine learning based approach is non-inferior to standard practice based on 30-day mortality. Secondary outcomes include hospital length-of stay and hospital admission rates. Other outcomes include model performance and antibiotic usage. Participants will be recruited in the EDs of multiple hospitals in the Netherlands. A total of 7584 participants will be included.

ETHICS AND DISSEMINATION

Possible participants will receive verbal information and a paper information brochure regarding the trial. They will be given at least 1 hour consideration time before providing informed consent. Research results will be published in peer-reviewed journals. This study has been approved by the Amsterdam University Medical Centers' local medical ethics review committee (No 22.0567). The study will be conducted in concordance with the principles of the Declaration of Helsinki and in accordance with the Medical Research Involving Human Subjects Act, General Data Privacy Regulation and Medical Device Regulation.

TRIAL REGISTRATION NUMBER

NCT06163781.

Benchmarking blood culture quality in the emergency department: Contamination, single sets and positivity

OBJECTIVE

To benchmark blood culture (BC) quality in an Australian ED, explore groups at risk of suboptimal BC collection, and identify potential areas for improvement.

METHODS

This retrospective observational study was undertaken to benchmark quality of BCs in a tertiary adult ED in terms of number of BC sets per patient and proportion of patients with false positive (contaminated) BC results.

RESULTS

A single BC set was taken for 55% of patients, with lower acuity patients being more likely to have a single BC set taken. BC false positives occurred in 3.4% of presentations, with higher frequency in some critically unwell patient groups. The true positive BC rate was 10.9%, with pathogens most frequently isolated in older patients, those with a haematological condition or genitourinary source, and those admitted to inpatient wards. Hospital length of stay did not differ between patients with negative and patients with false positive BCs.

CONCLUSIONS

BC quality standards in the ED such as false positive rate <3% and single culture rate <20% are required to facilitate benchmarking and prospective quality improvement. The sensitivity and specificity of this common and critical test can be improved. Patient subgroups associated with poor-quality BC collection can be identified and should be a focus of future work.

Validation of SeptiCyte RAPID to Discriminate Sepsis from Non-Infectious Systemic Inflammation

(1) Background: SeptiCyte RAPID is a molecular test for discriminating sepsis from non-infectious systemic inflammation, and for estimating sepsis probabilities. The objective of this study was the clinical validation of SeptiCyte RAPID, based on testing retrospectively banked and prospectively collected patient samples. (2) Methods: The cartridge-based SeptiCyte RAPID test accepts a PAXgene blood RNA sample and provides sample-to-answer processing in ~1 h. The test output (SeptiScore, range 0-15) falls into four interpretation bands, with higher scores indicating higher probabilities of sepsis. Retrospective (N = 356) and prospective (N = 63) samples were tested from adult patients in ICU who either had the systemic inflammatory response syndrome (SIRS), or were suspected of having/diagnosed with sepsis. Patients were clinically evaluated by a panel of three expert physicians blinded to the SeptiCyte test results. Results were interpreted under either the Sepsis-2 or Sepsis-3 framework. (3) Results: Under the Sepsis-2 framework, SeptiCyte RAPID performance for the combined retrospective and prospective cohorts had Areas Under the ROC Curve (AUCs) ranging from 0.82 to 0.85, a negative predictive value of 0.91 (sensitivity 0.94) for SeptiScore Band 1 (score range 0.1-5.0; lowest risk of sepsis), and a positive predictive value of 0.81 (specificity 0.90) for SeptiScore Band 4 (score range 7.4-15; highest risk of sepsis). Performance estimates for the prospective cohort ranged from AUC 0.86-0.95. For physician-adjudicated sepsis cases that were blood culture (+) or blood, urine culture (+)(+), 43/48 (90%) of SeptiCyte scores fell in Bands 3 or 4. In multivariable analysis with up to 14 additional clinical variables, SeptiScore was the most important variable for sepsis diagnosis. A comparable performance was obtained for the majority of patients reanalyzed under the Sepsis-3 definition, although a subgroup of 16 patients was identified that was called septic under Sepsis-2 but not under Sepsis-3. (4) Conclusions: This study validates SeptiCyte RAPID for estimating sepsis probability, under both the Sepsis-2 and Sepsis-3 frameworks, for hospitalized patients on their first day of ICU admission.

Impact of Blood Culture Contamination on Antibiotic Use, Resource Utilization, and Clinical Outcomes: A Retrospective Cohort Study in Dutch and US Hospitals

Background

Blood culture contamination (BCC) has been associated with prolonged antibiotic use (AU) and increased health care utilization; however, this has not been widely reevaluated in the era of increased attention to antibiotic stewardship. We evaluated the impact of BCC on AU, resource utilization, and length of stay in Dutch and US patients.

Methods

This retrospective observational study examined adults admitted to 2 hospitals in the Netherlands and 5 hospitals in the United States undergoing ≥2 blood culture (BC) sets. Exclusion criteria included neutropenia, no hospital admission, or death within 48 hours of hospitalization. The impact of BCC on clinical outcomes-overall inpatient days of antibiotic therapy, test utilization, length of stay, and mortality-was determined via a multivariable regression model.

Results

An overall 22 927 patient admissions were evaluated: 650 (4.1%) and 339 (4.8%) with BCC and 11 437 (71.8%) and 4648 (66.3%) with negative BC results from the Netherlands and the United States, respectively. Dutch and US patients with BCC had a mean ± SE 1.74 ± 0.27 (P < .001) and 1.58 ± 0.45 (P < .001) more days of antibiotic therapy than patients with negative BC results. They also had 0.6 ± 0.1 (P < .001) more BCs drawn. Dutch but not US patients with BCC had longer hospital stays (3.36 days; P < .001). There was no difference in mortality between groups in either cohort. AU remained higher in US but not Dutch patients with BCC in a subanalysis limited to BC obtained within the first 24 hours of admission.

Conclusions

BCC remains associated with higher inpatient AU and health care utilization as compared with patients with negative BC results, although the impact on these outcomes differs by country.

Analysis of microbiological tests in patients withholding or withdrawing life-sustaining treatment at the end stage of life in 2 Korean hospitals

OBJECTIVE

We evaluated the adequacy of microbiological tests in patients withholding or withdrawing life-sustaining treatment (WLST) at the end stage of life.

SETTING

The study was conducted at 2 tertiary-care referral hospitals in Daegu, Republic of Korea.

DESIGN

Retrospective cross-sectional study.

METHODS

Demographic findings, clinical and epidemiological characteristics, statistics of microbiological tests, and microbial species isolated from patients within 2 weeks before death were collected in 2 tertiary-care referral hospitals from January to December 2018. We also reviewed the antimicrobial treatment that was given within 3 days of microbiological testing in patients on WLST.

RESULTS

Of the 1,187 hospitalized patients included, 905 patients (76.2%) had WLST. The number of tests per 1,000 patient days was higher after WLST than before WLST (242.0 vs 202.4). Among the category of microbiological tests, blood cultures were performed most frequently, and their numbers per 1,000 patient days before and after WLST were 95.9 and 99.0, respectively. The positive rates of blood culture before and after WLST were 17.2% and 18.0%, respectively. Candida spp. were the most common microbiological species in sputum (17.4%) and urine (48.2%), and Acinetobacter spp. were the most common in blood culture (17.3%). After WLST determination, 70.5% of microbiological tests did not lead to a change in antibiotic use.

CONCLUSIONS

Many unnecessary microbiological tests are being performed in patients with WLST within 2 weeks of death. Microbiological testing should be performed carefully and in accordance with the patient's treatment goals.

Bacterial Sequencing Reads in Blood Exome Files from Melanoma and Cervical Cancer Patients are Associated with Cancer Recurrence

Bacteremia poses great risk for morbidity and mortality for immunocompromised cancer patients. Although the presence of bacteria within solid tumors is gaining greater attention, few studies have analyzed species of bacteria in the blood and their effect on cancer clinical outcomes. Using the Kraken 2 taxonomic profiling tool, we classified bacteria present in blood and primary tumors of cervical cancer and melanoma cases. The Cancer Genome Atlas (TCGA) melanoma blood exome files with Pseudomonas species were found to represent a worse disease-free survival (DFS) probability, while a worse overall survival (OS) result was evidenced for both the TCGA and Moffitt Cancer Center melanoma datasets. Cervical cancer cases with reads representing the Bradyrhizobium genus and Bradyrhizobium sp. BTAi1 found in blood and tumor exome files were found to have lower DFS. Additionally, reduced DFS and OS were observed for cervical cancer cases positive for Bacteroides species including Bacteroides fragilis. This study provides novel evidence and a novel approach for indicating that bacteria in blood is associated with cancer recurrence. These findings may guide the development of more efficient prognostic and screening tools related to bacterial blood infections of melanoma and cervical cancer patients.

How Did COVID-19 Impact the Antimicrobial Consumption and Bacterial Resistance Profiles in Brazil?

The indiscriminate use of antibiotics has favored the selective pressure of multidrug resistance among microorganisms. This research evaluated the pattern of antibiotic prescriptions among the Brazilian population between January 2018 and December 2021. Additionally, the study sought to analyze the incidence rates of central line-associated bloodstream infection (CLABSI) and examine the profiles of antibiotic resistance. We assessed the hospital and community antimicrobial consumption from the National Health Surveillance Agency Database and correlated it to microorganisms. The consumption of antimicrobials in the hospital environment increased by 26% in 2021, highlighting polymyxin B, which increased by 204%. In 2021, 244,266 cases of CLABSI were reported, indicating a nosocomial infection rate of 7.9%. The rate of resistance to polymyxin B was higher in Pseudomonas aeruginosa (1400%) and Klebsiella pneumoniae (514%). Azithromycin emerged as the predominant antibiotic utilized within the community setting, accounting for 24% of the overall consumption. Pearson's correlation analysis revealed a significant and positive correlation (r = 0.71) between the elevated usage of azithromycin and the incidence of COVID-19. Our results indicate an increase in antimicrobial consumption during the COVID-19 pandemic and reinforce the fact that the misuse of antimicrobials may lead to an expansion in antimicrobial resistance.

Machine learning pipeline for blood culture outcome prediction using Sysmex XN-2000 blood sample results in Western Australia

BACKGROUND

Bloodstream infections (BSIs) are a significant burden on the global population and represent a key area of focus in the hospital environment. Blood culture (BC) testing is the standard diagnostic test utilised to confirm the presence of a BSI. However, current BC testing practices result in low positive yields and overuse of the diagnostic test. Diagnostic stewardship research regarding BC testing is increasing, and becoming more important to reduce unnecessary resource expenditure and antimicrobial use, especially as antimicrobial resistance continues to rise. This study aims to establish a machine learning (ML) pipeline for BC outcome prediction using data obtained from routinely analysed blood samples, including complete blood count (CBC), white blood cell differential (DIFF), and cell population data (CPD) produced by Sysmex XN-2000 analysers.

METHODS

ML models were trained using retrospective data produced between 2018 and 2019, from patients at Sir Charles Gairdner hospital, Nedlands, Western Australia, and processed at Pathwest Laboratory Medicine, Nedlands. Trained ML models were evaluated using stratified 10-fold cross validation.

RESULTS

Two ML models, an XGBoost model using CBC/DIFF/CPD features with boruta feature selection (BFS) , and a random forest model trained using CBC/DIFF features with BFS were selected for further validation after obtaining AUC scores of [Formula: see text] and [Formula: see text] respectively using stratified 10-fold cross validation. The XGBoost model obtained an AUC score of 0.76 on a internal validation set. The random forest model obtained AUC scores of 0.82 and 0.76 on internal and external validation datasets respectively.

CONCLUSIONS

We have demonstrated the utility of using an ML pipeline combined with CBC/DIFF, and CBC/DIFF/CPD feature spaces for BC outcome prediction. This builds on the growing body of research in the area of BC outcome prediction, and provides opportunity for further research.

Development of an artificial intelligence bacteremia prediction model and evaluation of its impact on physician predictions focusing on uncertainty

Prediction of bacteremia is a clinically important but challenging task. An artificial intelligence (AI) model has the potential to facilitate early bacteremia prediction, aiding emergency department (ED) physicians in making timely decisions and reducing unnecessary medical costs. In this study, we developed and externally validated a Bayesian neural network-based AI bacteremia prediction model (AI-BPM). We also evaluated its impact on physician predictive performance considering both AI and physician uncertainties using historical patient data. A retrospective cohort of 15,362 adult patients with blood cultures performed in the ED was used to develop the AI-BPM. The AI-BPM used structured and unstructured text data acquired during the early stage of ED visit, and provided both the point estimate and 95% confidence interval (CI) of its predictions. High AI-BPM uncertainty was defined as when the predetermined bacteremia risk threshold (5%) was included in the 95% CI of the AI-BPM prediction, and low AI-BPM uncertainty was when it was not included. In the temporal validation dataset (N = 8,188), the AI-BPM achieved area under the receiver operating characteristic curve (AUC) of 0.754 (95% CI 0.737-0.771), sensitivity of 0.917 (95% CI 0.897-0.934), and specificity of 0.340 (95% CI 0.330-0.351). In the external validation dataset (N = 7,029), the AI-BPM's AUC was 0.738 (95% CI 0.722-0.755), sensitivity was 0.927 (95% CI 0.909-0.942), and specificity was 0.319 (95% CI 0.307-0.330). The AUC of the post-AI physicians predictions (0.703, 95% CI 0.654-0.753) was significantly improved compared with that of the pre-AI predictions (0.639, 95% CI 0.585-0.693; p-value < 0.001) in the sampled dataset (N = 1,000). The AI-BPM especially improved the predictive performance of physicians in cases with high physician uncertainty (low subjective confidence) and low AI-BPM uncertainty. Our results suggest that the uncertainty of both the AI model and physicians should be considered for successful AI model implementation.

Development and internal validation of a Neonatal Healthcare-associated infectiOn Prediction score (NeoHoP score) for very low birthweight infants in low-resource settings: a retrospective case-control study

BACKGROUND AND OBJECTIVES

Early diagnosis of neonatal infection is essential to prevent serious complications and to avoid unnecessary use of antibiotics. The prevalence of healthcare-associated infections (HAIs) among very low birthweight (VLBW; <1500 g) infants is 20%; and the mortality in low-resource settings can be as high as 70%. This study aimed to develop an Infection Prediction Score to diagnose bacterial HAIs.

METHODS

A retrospective cohort of VLBW infants investigated for HAI was randomised into two unmatched cohorts. The first cohort was used for development of the score, and the second cohort was used for the internal validation thereof. Potential predictors included risk factors, clinical features, interventions, and laboratory data. The model was developed based on logistic regression analysis.

RESULTS

The study population of 655 VLBW infants with 1116 episodes of clinically suspected HAIs was used to develop the model. The model had five significant variables: capillary refill time >3 s, lethargy, abdominal distention, presence of a central venous catheter in the previous 48 hours and a C reactive protein ≥10 mg/L. The area below the receiver operating characteristic curve was 0.868. A score of ≥2 had a sensitivity of 54.2% and a specificity of 96.4%.

CONCLUSION

A novel Infection Prediction Score for HAIs among VLBW infants may be an important tool for healthcare providers working in low-resource settings but external validation needs to be performed before widespread use can be recommended.

Blood culture contamination in a tertiary care hospital: a retrospective three-year study

BACKGROUND

Bloodstream infections (BSI) are a leading cause of morbidity and mortality in hospitalized patients worldwide. A blood culture is the primary tool for determining whether a patient has BSI and requires antimicrobial therapy, but it can result in an inappropriate outcome if the isolated microorganisms are deemed contaminants from the skin. Despite the development of medical equipment and technology, there is still a percentage of blood culture contamination. The aims of this study were to detect the blood culture contamination (BCC) rate in a tertiary care hospital in Palestine and to identify the departments with the highest rates along with the microorganisms isolated from the contaminated blood samples.

METHOD

Blood cultures that were taken at An-Najah National University Hospital between January 2019 and December 2021 were evaluated retrospectively. Positive blood cultures were classified as either true positives or false positives based on laboratory results and clinical pictures. Statistical analysis was performed using the Statistical Package for Social Sciences (SPSS) version 21. A p-value of less than 0.05 was considered statistically significant for all analyses.

RESULTS

Out of 10,930 blood cultures performed in the microbiology laboratory from 2019 to 2021, 1479 (13.6%) were identified as positive blood cultures that showed microbial growth. Of these, 453 were blood culture contaminations, representing 4.17% of total blood cultures and 30.63% of the positive blood culture samples. The highest rate of contamination was in the hemodialysis unit (26.49%), followed by the emergency department (15.89%). Staphylococcus epidermidis was the most prevalent (49.2%), followed by Staphylococcus hominis (20.8%) and Staphylococcus haemolyticus (13.2%). The highest annual contamination rate was observed in 2019 (4.78%) followed by 2020 (3.95%) and the lowest was in 2021 (3.79%). The rate of BCC was decreasing, although it did not reach statistically significant levels (P value = 0.085).

CONCLUSION

The rate of BCC is higher than recommended. The rates of BCC are different in different wards and over time. Continuous monitoring and performance improvement projects are needed to minimize blood culture contamination and unnecessary antibiotic use.

Blood Culture Result Profile in Patients With Central Line-Associated Bloodstream Infection (CLABSI): A Single-Center Experience

Background Central line-associated bloodstream infection (CLABSI) is among the most common bloodstream infections in the university hospital and intensive care unit settings. This study evaluated the routine blood test findings and microbe profiles of bloodstream infection (BSI) by the presence and types of central vein (CV) access devices (CVADs). Methods A total of 878 inpatients at a university hospital who were clinically suspected for BSI and underwent blood culture (BC) testing between April 2020 and September 2020 were enrolled. Data regarding age at BC testing, sex, WBC count, serum C-reactive protein (CRP) level, BC test results, yielded microbes, and usage and types of CVADs were evaluated. Results The BC yields were detected in 173 patients (20%), suspected contaminating pathogens in 57 (6.5%), and 648 (74%) with a negative yield. The WBC count (p=0.0882) and CRP level (p=0.2753) did not significantly differ between the 173 patients with BSI and the 648 patients with negative BC yields. Among the 173 patients with BSI, 74 used CVADs and met the diagnosis of CLABSI; 48 had a CV catheter, 16 had CV access ports, and 10 had a peripherally inserted central catheter (PICC). Patients with CLABSI showed lower WBC counts (p=0.0082) and serum CRP levels (p=0.0024) compared to those with BSI who did not use CVADs. The most commonly yielded microbes in those with CV catheters, CV-ports, and PICC were Staphylococcus epidermidis (n=9; 19%), Staphylococcus aureus (n=6; 38%), and S. epidermidis (n=8; 80%), respectively. Among those with BSI who did not use CVADs, Escherichia coli (n=31; 31%) was the most common pathogen, followed by S. aureus (n=13; 13%). Conclusion Patients with CLABSI showed lower WBC counts and CRP levels than those with BSI who did not use CVADs. Staphylococcus epidermidis was among the most common microbes in CLABSI and accounted for the majority of yielded microbes in patients who used PICC.

Target product profiles for diagnosis of sepsis: Proposing a new approach for diagnostic innovation

Background & objectives

Sepsis, including neonatal sepsis, remains a prevalent cause of morbidity and mortality in low- and middle-income countries such as India, representing 85 per cent of all sepsis-related deaths globally. Early diagnosis and timely initiation of treatment is challenging due to non-specific clinical manifestations and non-availability of rapid diagnostic tests. There is an urgent need for affordable diagnostics with fast turnaround time catering to the needs of end-users. Target product profiles (TPPs) have been found instrumental in developing 'fit-for-use' diagnostics, thus reducing the time taken to facilitate development and improving diagnosis. Hitherto, no such guidance or criteria has been defined for rapid diagnostics for sepsis/neonatal sepsis. We propose an innovative approach for developing the diagnostics for sepsis screening and diagnosis which can be utilized by diagnostic developers in the country.

Methods

Thr@ee-round Delphi method, including two online surveys and one virtual consultation, was adopted to define criteria for minimum and optimum attributes of TPPs and build consensus on characteristics. Expert panel (n=23) included infectious disease physicians, public health specialists, clinical microbiologists, virologists, researchers/scientists and technology experts/innovators.

Results

We present a three-component product profile for sepsis diagnosis, (i) screening with high sensitivity, (ii) detection of aetiological agent, and (iii) profiling of antimicrobial susceptibility/resistance, in adults and neonates with an option of testing different considerations. An agreement of >75 per cent was achieved for all TPP characteristics by Delphi. These TPPs are tailored to the Indian healthcare settings and can also be extrapolated to other resource-constraint and high-disease burden settings.

Interpretation & conclusions

Diagnostics developed using these TPPs will facilitate utilization of invested resources leading to development of the products that have potential to ease the economic burden on patient and save lives.

Bloodstream infections and antibiotic resistance at a regional hospital, Colombia, 2019-2021

Objectives

To assess antibiotic susceptibility of World Health Organization (WHO) priority bacteria (Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Salmonella spp., Staphylococcus aureus, and Streptococcus pneumoniae) in blood cultures at the Orinoquía regional hospital in Colombia.

Methods

This was cross-sectional study using routine laboratory data for the period 2019-2021. Data on blood samples from patients suspected of a bloodstream infection were examined. We determined: the total number of blood cultures done and the proportion with culture yield; the characteristics of patients with priority bacteria; and the type of bacteria isolated and antibiotic resistance patterns.

Results

Of 25 469 blood cultures done, 1628 (6%) yielded bacteria; 774 (48%) of these bacteria were WHO priority pathogens. Most of the priority bacteria isolated (558; 72%) were gram-negative and 216 (28%) were gram-positive organisms. Most patients with priority bacteria (666; 86%) were hospitalized in wards other than the intensive care unit, 427 (55%) were male, and 321 (42%) were ≥ 60 years of age. Of the 216 gram-positive bacteria isolated, 205 (95%) were Staphylococcus aureus. Of the 558 gram-negative priority bacteria isolated, the three most common were Escherichia coli (34%), Klebsiella pneumoniae (28%), and Acinetobacter baumannii (20%). The highest resistance of Staphylococcus aureus was to oxacillin (41%). For gram-negative bacteria, resistance to antibiotics ranged from 4% (amikacin) to 72% (ampicillin).

Conclusions

Bacterial yield from blood cultures was low and could be improved. WHO priority bacteria were found in all hospital wards. This calls for rigorous infection prevention and control standards and continued surveillance of antibiotic resistance.

Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .

Metagenomic next-generation sequencing for detection of pathogens in children with hematological diseases complicated with infection

OBJECTIVE

Infection is one of the most common causes of death in children with hematological diseases. Here, we aim to investigate the value of metagenomic next-generation sequencing (mNGS) in the detection of causative pathogens in children with hematological diseases.

METHODS

In this retrospective study, specimens from children with hematological diseases, who were admitted to Sun Yat-Sen University between June 2019 and September 2021, were collected for culture and mNGS.

RESULTS

A total of 67 pediatric patients were enrolled, and 96 specimens were collected. The positive rate of mNGS was significantly higher than that of culture (57.2% vs 12.5%, P < 0.01). The concordance (90.9%, 10/11) between the positive results of the two methods was high. mNGS detected more cases with Pneumocystis jeroveci, Aspergillus flavus, viruses, and some rare pathogens than culture. Mixed infections were detected by mNGS in 16 cases. Clinical anti-infective treatment was adjusted according to the results of mNGS, the conditions of most patients improved.

CONCLUSION

Compared to culture, mNGS shows great advantages in diagnosing bacterial, fungal, viral, and mixed infections in children with hematologic diseases, positively impacting clinical care. mNGS can be used as a complement to culture for pathogen detection.

ESBL in positive hemoculture of a Southern-Brazil Teaching Hospital's Intensive Care Units

Bloodstream infections are among the most serious and frequent infections, and the people most exposed are patients in the Intensive Care Unit (ICU). ESBL (extended-spectrum beta-lactate) are resistant bacteria to penicillins, cephalosporins and monobactams. It´s necessary to know how often and which microorganisms are involved, checking their susceptibility. This study was carried out at the University Hospital. Data collection was performed in the Adult and Newborn ICUs, with assessment of microorganisms and their resistance profile. During six-month period, 156 samples were studied, and 42 were positive with microorganism isolation. Isolated species include Staphylococcus aureus, Staphylococcus epidermidis and Klebsiella pneumoniae. Many resistant to carbapenem.

Healthcare-associated Infections in Very Low Birth-weight Infants in a South African Neonatal Unit: Disease Burden, Associated Factors and Short-term Outcomes

BACKGROUND

Infection is a leading cause of death among very low birth-weight (VLBW) infants in resource-limited settings.

METHODS

We performed a retrospective review of healthcare-associated infection (HAI) episodes among VLBW infants from January 1, 2016, to December 31, 2017. The epidemiology, causative organisms and short-term outcomes were analyzed. Logistic regression was used to investigate for factors associated with development of HAI.

RESULTS

During the study period, 715 VLBW infants with suspected HAI were investigated, including 162/715 (22.7%) proven and 158/715 (22.1%) presumed HAI. Of the proven infections, 99/162 (61.1%) contained at least one Gram-negative organism per blood culture; 84/162 (51.9%) single Gram-negative organisms and 15/162 (9.3%) polymicrobial growth. Independent factors associated with development of any HAI included low gestational age, small for gestational age, indwelling central venous catheter and invasive ventilation. Compared with infants in whom HAI had been excluded, infants with HAI were more likely to be diagnosed with necrotizing enterocolitis (5.6% vs. 23.1%; P &lt; 0.001) and bronchopulmonary dysplasia (1.0% vs. 4.4%; P = 0.007). Infants with any HAI also had a longer hospital stay [44 (25-65) vs. 38 (26-53) days; P &lt; 0.001] and increased mortality [90/320 (28.1%) vs. 21/395 (5.3%); P &lt; 0.001] compared with infants who did not develop HAI episodes.

CONCLUSIONS

Proven and presumed HAI are a major contributor to neonatal morbidity and mortality; further research is urgently needed to better understand potential targets for prevention and treatment of HAI in resource-limited neonatal units.

Comparative of clinical performance between next-generation sequencing and standard blood culture diagnostic method in patients suffering from sepsis

BACKGROUND

Next-generation sequencing (NGS) is a massively unbiased sequencing technology. The objective of this study was to evaluate the performance of NGS-based approach in the detection of microorganisms from septic patients and compare with results of blood culture (BC).

METHODS

The observational and non-interventional study was conducted from April 2019 to August 2019.

RESULTS

A total of 96 sets of BC and 48 NGS results obtained from 48 septic patients were analyzed in this study. Thirty-two microorganisms (27 bacteria, 3 fungi and 2 viral) were detected by NGS in 23 (47.9%) patients; and 18 bacteria in 18 (37.5%) patients by BC. Exclusion of skin commensals, the positivity of NGS and BC was 62.5% and 14.5%, respectively (P < 0.001). Microorganisms identified by NGS demonstrated positive agreement with BC in 12 (25%) patients, including concordant results in 11 (22.9%) cases, and discrepancy results in 1 (2%). Of 11 patients with concordant results, 4 had additional microorganisms detected by NGS. NGS-positive but BC-negative was found in 9 (18.7%) patients. Using NGS, difficult-to-culture micro-organisms such as Pneumocystic jirovecii was identified in 2 patients, and Leptospira interrogans in one. Six (12.5%) patients with BC-positive but NGS-negative, whereas skin commensals were isolated in 4 (66.6%) cases. The number of patients that were positive by BC only increase from 29% to 47.9% when combining NGS and BC analyses (P = 0.033).

CONCLUSIONS

Our study support the advantage of NGS for the diagnosis of infecting microorganisms in sepsis, especially for microorganisms that are currently difficult or impossible to culture.

Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious Fever During Myelosuppression Among Pediatric Patients with Hematological and Neoplastic Diseases

Purpose

To analyze the contribution of metagenomic next-generation sequencing (mNGS) in the guidance of clinical treatment and outcomes of infection during myelosuppression among children with hematological and neoplastic diseases.

Patients and Methods

The clinical data and results of mNGS assay of febrile patients suspected of infection were retrospectively collected. The characteristics of pathogenic microorganisms and clinical course of myelosuppressed children with hematological diseases were summarized.

Results

Our study included 70 patients (45 males) with a median age of 5 years (range: 0.5 to 13 y). During the study period, there were 96 events of suspected infection. According to comprehensive clinical diagnosis, 73 blood infections, 43 pneumonia and 2 urinary tract infections occurred. The positive rate of mNGS was significantly higher than that of traditional microbial detection (83.3% vs 17.7%). The main pathogens detected by mNGS were Pseudomonas aeruginosa, Acinetobacter, human herpesvirus, Candida and Aspergillus. The average duration of fever was 4.9 days and 11.6 days (P < 0.05), and the average cost of anti-infection treatment was RMB ¥28,077 and 39,898 (P < 0.05) among children received mNGS within 48 hours and more than 48 hours after the onset of infection symptoms.

Conclusion

mNGS contributes to clinical management of children with infection during myelosuppression, especially among patients with negative traditional microbial detection. Early implementation of mNGS in children with symptoms has a tendency to reduce the time of infection, fever and the cost of treatment.

Diagnostic stewardship for blood cultures in the emergency department: A multicenter validation and prospective evaluation of a machine learning prediction tool

Background

Overuse of blood cultures (BCs) in emergency departments (EDs) leads to low yields and high numbers of contaminated cultures, accompanied by increased diagnostics, antibiotic usage, prolonged hospitalization, and mortality. We aimed to simplify and validate a recently developed machine learning model to help safely withhold BC testing in low-risk patients.

Methods

We extracted data from the electronic health records (EHR) for 44.123 unique ED visits with BC sampling in the Amsterdam UMC (locations VUMC and AMC; the Netherlands), Zaans Medical Center (ZMC; the Netherlands), and Beth Israel Deaconess Medical Center (BIDMC; United States) in periods between 2011 and 2021. We trained a machine learning model on the VUMC data to predict blood culture outcomes and validated it in the AMC, ZMC, and BIDMC with subsequent real-time prospective evaluation in the VUMC.

Findings

The model had an Area Under the Receiver Operating Characteristics curve (AUROC) of 0.81 (95%-CI = 0.78–0.83) in the VUMC test set. The most important predictors were temperature, creatinine, and C-reactive protein. The AUROCs in the validation cohorts were 0.80 (AMC; 0.78–0.82), 0.76 (ZMC; 0.74–0.78), and 0.75 (BIDMC; 0.74–0.76). During real-time prospective evaluation in the EHR of the VUMC, it reached an AUROC of 0.76 (0.71–0.81) among 590 patients with BC draws in the ED. The prospective evaluation showed that the model can be used to safely withhold blood culture analyses in at least 30% of patients in the ED.

Interpretation

We developed a machine learning model to predict blood culture outcomes in the ED, which retained its performance during external validation and real-time prospective evaluation. Our model can identify patients at low risk of having a positive blood culture. Using the model in practice can significantly reduce the number of blood culture analyses and thus avoid the hidden costs of false-positive culture results.

Funding

This research project was funded by the Amsterdam Public Health – Quality of Care program and the Dutch “Doen of Laten” project (project number: 839205002).

The Diagnostic Values of Peptidoglycan, Lipopolysaccharide, and (1,3)-Beta-D-Glucan in Patients with Suspected Bloodstream Infection: A Single Center, Prospective Study

This study aimed to assess the diagnostic values of peptidoglycan (PGN), lipopolysaccharide (LPS) and (1,3)-Beta-D-Glucan (BDG) in patients with suspected bloodstream infection. We collected 493 heparin anticoagulant samples from patients undergoing blood culture in Peking Union Medical College Hospital from November 2020 to March 2021. The PGN, LPS, and BDG in the plasma were detected using an automatic enzyme labeling analyzer, GLP-F300. The diagnostic efficacy for PGN, LPS, and BDG were assessed by calculating the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). This study validated that not only common bacteria and fungi, but also some rare bacteria and fungi, could be detected by testing the PGN, LPS, and BDG, in the plasma. The sensitivity, specificity, and total coincidence rate were 83.3%, 95.6%, and 94.5% for PGN; 77.9%, 95.1%, and 92.1% for LPS; and 83.8%, 96.9%, and 95.9% for BDG, respectively, which were consistent with the clinical diagnosis. The positive rates for PGN, LPS, and BDG and the multi-marker detection approach for PGN, LPS, and BDG individually were 11.16%, 17.65%, and 9.13%, and 32.86% significantly higher than that of the blood culture (p < 0.05). The AUC values for PGN, LPS, and BDG were 0.881 (0.814−0.948), 0.871 (0.816−0.925), and 0.897 (0.825−0.969), separately, which were higher than that of C-reactive protein (0.594 [0.530−0.659]) and procalcitonin (0.648 [0.587−0.708]). Plasma PGN, LPS, and BDG performs well in the early diagnosis of bloodstream infections caused by Gram-positive and Gram-negative bacterial and fungal pathogens.

Optimal use of procalcitonin to rule out bacteremia in patients with possible viral infections

Objective

During the winter, many patients present with suspected infection that could be a viral or a bacterial (co)infection. The aim of this study is to investigate whether the optimal use of procalcitonin (PCT) is different in patients with and without proven viral infections for the purpose of excluding bacteremia. We hypothesize that when a viral infection is confirmed, this lowers the probability of bacteremia and, therefore, influences the appropriate cutoff of procalcitonin.

Methods

This study was conducted in the emergency department of an academic medical center in The Netherlands in the winter seasons of 2019 and 2020. Adults (>18 years) with suspected infection, in whom a blood culture and a rapid polymerase chain reaction test for influenza was performed were included.

Results

A total of 546 patients were included of whom 47 (8.6%) had a positive blood culture. PCT had an area under the curve of 0.85, 95% confidence interval (95% CI) 0.80-0.91, for prediction of bacteremia. In patients with a proven viral infection (N = 212) PCT < 0.5 μg/L had a sensitivity of 100% (95% CI 63.1-100) and specificity of 81.2% (95% CI 75.1-86.3) to exclude bacteremia. In patients without a viral infection, the procalcitonin cutoff point of < 0.25 μg/L showed a sensitivity of 87.2% (95% CI 72.6-95.7) and specificity of 64.1 % (95% CI 58.3-69.6).

Conclusion

In patients with a viral infection, our findings suggest that a PCT concentration of <0.50 μg/L makes bacteremia unlikely. However, this finding needs to be confirmed in a larger population of patients with viral infections, especially because the rate of coinfection in our cohort was low.

Identification of the main contributors to blood culture contamination at a tertiary care academic medical center

Background

Blood culture contamination poses an issue to all hospital systems worldwide because of the associated costs of extended length of stays, unnecessary antibiotic therapy, and additional laboratory testing that are preventable with proper handling and collection techniques.

Methods

In our study, multiple units, staff, and collection methods were compared to determine the primary culprits of contamination from a tertiary care academic medical center, which includes a pediatric hospital and both adult and pediatric emergency departments.

Results

Over 33 months, 2,083 out of 88,322 total blood cultures collected were contaminated, with an overall contamination rate of 2.4%. A moderate positive correlation was found between the monthly total number of cultures and monthly contamination rate (r = 0.411 P < .01). The most notable factors associated with contamination were found to be phlebotomy teams (2.7%) (P < .01), peripheral draws (2.3%) (P <.01), adult emergency departments (2.6%) (P < .01), and pediatric intensive care units (2.7%) (P < .01). A positive correlation was present between the number of hospital beds per unit and unit contamination rates (r = 0.429 P < .01).

Conclusion

Our results were used to make recommendations for decreasing the rate of blood culture contamination in this institution, which includes acknowledgement of an overwhelmed staff and mandatory periodic training on acceptable aseptic technique and contamination awareness. Understanding the factors contributing to blood culture contamination can aid efforts to reduce contamination rates.

To wait or not to wait: Optimal time interval between the first and second blood-culture sets to maximize blood-culture yield

The optimal timing of blood culture (BCx) sets collection has not been evaluated with continuous BCx detection systems. The yield of BCx was similar between short intervals (median, 3 minutes) and longer intervals (median, 16 or 43 minutes) among 5,856 BCx, except for improved polymicrobial bacteremia detection with long-interval BCx.

Quantitative Fluorescence In Situ Hybridization (FISH) of Magnetically Confined Bacteria Enables Early Detection of Human Bacteremia

The current diagnosis of bacteremia mainly relies on blood culture, which is inadequate for the rapid and quantitative determination of most bacteria in blood. Here, a quantitative, multiplex, microfluidic fluorescence in situ hybridization method (μFISH) is developed, which enables early and rapid (3-h) diagnosis of bacteremia without the need for prior blood culture. This novel technology employs mannose-binding lectin-coated magnetic nanoparticles, which effectively opsonize a broad range of pathogens, magnetically sequestering them in a microfluidic device. Therein, μFISH probes, based on unique 16S rRNA sequences, enable the identification and quantification of sequestered pathogens both in saline and whole blood, which is more sensitive than conventional polymerase chain reaction. Using μFISH, Escherichia coli (E. coli) is detected in whole blood collected from a porcine disease model and from E. coli-infected patients. Moreover, the proportion of E. coli, relative to other bacterial levels in the blood, is accurately and rapidly determined, which is not possible using conventional diagnostic methods. Blood from E. coli-infected patients is differentiated from healthy donors' blood using cutoff values with a 0.05 significance level. Thus, μFISH is a versatile method that can be used to rapidly identify pathogens and determine their levels relative to other culturable and nonculturable bacteria in biological samples.

Using machine learning to predict blood culture outcomes in the emergency department: a single-centre, retrospective, observational study

OBJECTIVES

To develop predictive models for blood culture (BC) outcomes in an emergency department (ED) setting.

DESIGN

Retrospective observational study.

SETTING

ED of a large teaching hospital in the Netherlands between 1 September 2018 and 24 June 2020.

PARTICIPANTS

Adult patients from whom BCs were collected in the ED. Data of demographic information, vital signs, administered medications in the ED and laboratory and radiology results were extracted from the electronic health record, if available at the end of the ED visits.

MAIN OUTCOME MEASURES

The primary outcome was the performance of two models (logistic regression and gradient boosted trees) to predict bacteraemia in ED patients, defined as at least one true positive BC collected at the ED.

RESULTS

In 4885 out of 51 399 ED visits (9.5%), BCs were collected. In 598/4885 (12.2%) visits, at least one of the BCs was true positive. Both a gradient boosted tree model and a logistic regression model showed good performance in predicting BC results with area under curve of the receiver operating characteristics of 0.77 (95% CI 0.73 to 0.82) and 0.78 (95% CI 0.73 to 0.82) in the test sets, respectively. In the gradient boosted tree model, the optimal threshold would predict 69% of BCs in the test set to be negative, with a negative predictive value of over 94%.

CONCLUSIONS

Both models can accurately identify patients with low risk of bacteraemia at the ED in this single-centre setting and may be useful to reduce unnecessary BCs and associated healthcare costs. Further studies are necessary for validation and to investigate the potential clinical benefits and possible risks after implementation.

Update on Pediatric Sepsis in Mexico

The main objective of this work was to determine and update the causal agents’ antibiotic sensitivity and resistance patterns on pediatric sepsis in a population of northeast Mexico. It is a cross-sectional study showing the results of blood cultures of pediatric patients with a presumptive diagnosis of sepsis were reviewed according to the SOFA criteria during 2020 in a public hospital in Mexico. A total of 207 blood cultures were performed and analyzed. The main isolated microorganisms were Staphylococcus, followed by Klebsiella and Escherichia. Several microorganisms showed 100% of sensitivity to different antibiotics or antifungals, some of them include Vancomycin, Voriconazole, Meropenem, Ciprofloxacin, and Cefotaxime. Bacteria of genre Staphylococcus showed its highest sensitivity rate to Tigecycline with 63.3%. Too Staphylococcus showed the highest resistance rate to Oxacillin with 50%. Although the patterns of sepsis-causing germs are similar to those previously reported, the development of new drugs with greater efficacy is the main contribution.

Adequacy of probabilistic prehospital antibiotic therapy for septic shock

BACKGROUND

Guidelines on sepsis management recommend early recognition, diagnosis and treatment, especially early antibiotic therapy (ABT) administration in order to reduce septic shock (SS) mortality. However, the adequacy of probabilistic prehospital ABT remains unknown.

METHODS

From May 2016 to March 2021, all consecutive patients with SS cared for by a prehospital mICU intervention were retrospectively analyzed.

RESULTS

Among 386 patients retrospectively analyzed, 119 (33%) received probabilistic prehospital ABT, among which 74% received a 3rd generation cephalosporin: 31% cefotaxime and 42% ceftriaxone. No patient had a serious adverse effect related to ABT administration. Overall mortality rate on day-30 was 29%. Among the 119 patients with prehospital ABT, bacteriological identification was obtained for 81 (68%) patients with adequate prehospital ABT for 65 patients (80%) of which 10 (15%) deceased on day-30. Conversely, among the 16 (20%) patients with inadequate prehospital ABT, 9 patients (56%) were deceased on day-30. Prehospital adequate ABT was significantly different between alive and deceased patients on day-30 (p = 4.10^-3). After propensity score matching, a significant association between adequate prehospital ABT administration and day-30 mortality was observed (aOR = 0.09 [0.01-0.47]). Inverse probability treatment weighting with multivariable logistic regression reported a day-30 mortality decrease in the adequate prehospital ABT group: aOR = 0.70 [0.53-0.93].

CONCLUSIONS

Among SS cared for by a mICU, probabilistic prehospital ABT is adequate most of the time and associated with a day-30 mortality decrease. Further prospective studies are needed to confirm these results and the weight of prehospital ABT in the prehospital bundle of care for SS.

The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with sepsis

BACKGROUND

In this study, we aimed to perform a comprehensive analysis on the metagenomic next-generation sequencing for the etiological diagnosis of septic patients, and further to establish optimal read values for detecting common pathogens.

METHODS

In this single-center retrospective study, septic patients who underwent pathogen detection by both microbial culture and metagenomic next-generation sequencing in the intensive care unit of the Second People's Hospital of Shenzhen from June 24, 2015, to October 20, 2019, were included.

RESULTS

A total of 193 patients with 305 detected specimens were included in the final analysis. The results of metagenomic next-generation sequencing showed significantly higher positive rates in samples from disparate loci, including blood, bronchoalveolar lavage fluid, and cerebrospinal fluid, as well as in the determination of various pathogens. The optimal diagnostic reads were 2893, 1825.5, and 892.5 for Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, respectively.

CONCLUSIONS

The metagenomic next-generation sequencing is capable of identifying multiple pathogens in specimens from septic patients, and shows significantly higher positive rates than culture-based diagnostics. The optimal diagnostic reads for frequently detected microbes might be useful for the clinical application of metagenomic next-generation sequencing in terms of timely and accurately determining etiological pathogens for suspected and confirmed cases of sepsis due to well-performed data interpretation.

Outcomes of β-Hemolytic Streptococcal Necrotizing Skin and Soft-tissue Infections and the Impact of Clindamycin Resistance

BACKGROUND

β-Hemolytic streptococci are frequently implicated in necrotizing soft-tissue infections (NSTIs). Clindamycin administration may improve outcomes in patients with serious streptococcal infections. However, clindamycin resistance is growing worldwide, and resistance patterns in NSTIs and their impact on outcomes are unknown.

METHODS

Between 2015 and 2018, patients with NSTI at a quaternary referral center were followed up for the outcomes of death, limb loss, and streptococcal toxic shock syndrome. Surgical wound cultures and resistance data were obtained within 48 hours of admission as part of routine care. Risk ratios for the association between these outcomes and the presence of β-hemolytic streptococci or clindamycin-resistant β-hemolytic streptococci were calculated using log-binomial regression, controlling for age, transfer status, and injection drug use-related etiology.

RESULTS

Of 445 NSTIs identified, 85% had surgical wound cultures within 48 hours of admission. β-Hemolytic streptococci grew in 31%, and clindamycin resistance was observed in 31% of cultures. The presence of β-hemolytic streptococci was associated with greater risk of amputation (risk ratio, 1.80; 95% confidence interval, 1.07-3.01), as was the presence of clindamycin resistance among β-hemolytic streptococci infections (1.86; 1.10-3.16).

CONCLUSIONS

β-Hemolytic streptococci are highly prevalent in NSTIs, and in our population clindamycin resistance was more common than previously described. Greater risk of limb loss among patients with β-hemolytic streptococci-particularly clindamycin-resistant strains-may portend a more locally aggressive disease process or may represent preexisting patient characteristics that predispose to both infection and limb loss. Regardless, these findings may inform antibiotic selection and surgical management to maximize the potential for limb salvage.

Epidemiology and Pattern of Resistance of Gram-Negative Bacteria Isolated from Blood Samples in Hospitalized Patients: A Single Center Retrospective Analysis from Southern Italy

BACKGROUND

Blood culturing remains the mainstream tool to inform an appropriate treatment in hospital-acquired bloodstream infections and to diagnose any bacteremia.

METHODS

A retrospective investigation on the prevalence of Gram-negative bacteria (GNB) and their resistance in hospitalized patients by age, sex, and units from blood cultures (BCs) was conducted from January 2018 to April 2020 at Sant'Elia hospital, Caltanissetta, southern Italy. We divided the patient age range into four equal intervals.

RESULTS

Multivariate demographic and microbiological variables did not show an association between bacteria distributions and gender and age. The distribution by units showed a higher prevalence of Klebsiella pneumoniae and Acinetobacter baumannii in the intensive care unit (ICU) and Escherichia coli in the non-intensive care units (non-ICUs). The analysis of antibiotic resistance showed that E. coli was susceptible to a large class of antibiotics such as carbapenem and trimethoprim-sulfamethoxazole. K. pneumoniae showed a significant susceptibility to colistin, tigecycline, and trimethoprim-sulfamethoxazole. From the survival analysis, patients with E. coli had a higher survival rate.

CONCLUSIONS

The authors stress the importance of the implementation of large community-level programs to prevent E. coli bacteremia. K. pneumoniae and E. coli susceptibility patterns to antibiotics, including in the prescription patterns of general practitioners, suggest that the local surveillance and implementation of educational programs remain essential measures to slow down the spread of resistance and, consequently, increase the antibiotic lifespan.

Clinical microbiology laboratories and COVID-19: an interview with Joseph Blondeau

This interview was conducted by Atiya Henry, Commissioning Editor of Future Microbiology.

Joseph M Blondeau, MSc, PhD, RSM(CCM), SM(AAM), SM(ASCP), FCCP is a Clinical Microbiologist and Head of Clinical Microbiology at Royal University Hospital (Saskatoon Health Region) and the University of Saskatchewan in Saskatoon, Canada. He is also the Provincial Clinical Lead for Microbiology in Saskatchewan, Canada. He holds a Masters of Sciences in Microbiology from Dalhousie University (1985) and a Doctor of Philosophy in Medical Microbiology from the University of Manitoba (1989). Following completion of his PhD, he completed a 1 and a half year post-doctoral training in an infectious diseases research laboratory at Dalhousie University and following which he completed a 2 year post-doctoral residency training program in Clinical Microbiology, also at Dalhousie University. He holds appointments as a Clinical Associate Professor of Pathology, Adjunct Professor of Microbiology and Immunology and Clinical Associate Professor of Ophthalmology. He teaches to undergraduate and graduate students in the areas of microbiology, infectious diseases, antimicrobial agents and pharmacology. Dr Blondeau’s main research interests are in the area of antimicrobial agents and antimicrobial resistance, clinical microbiology and clinical outcomes associated with antimicrobial therapy in both human and veterinary medicine.

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.

Comparison of Systemic Inflammatory Response Syndrome and quick Sequential Organ Failure Assessment scores in predicting bacteremia in the emergency department

Aim

The emergency department requires simple and useful clinical indicators to identify bacteremia. This retrospective study explored the Systemic Inflammatory Response Syndrome (SIRS) and quick Sequential Organ Failure Assessment (qSOFA) scores for predicting bacteremia.

Methods

Between April and September 2017, we assessed blood cultures of 307 patients in our emergency department. We calculated the SIRS and qSOFA scores for these patients and evaluated their correlation with bacteremia.

Results

Of 307 patients, 66 (21.5%) had bacteremia, 237 (77.2%) were SIRS-positive, and 123 (40.0%) were qSOFA-positive. The sensitivity and specificity of the SIRS score for predicting bacteremia were 87.9% and 25.7%, respectively. The sensitivity and specificity of the qSOFA score were 47.0% and 61.8%, respectively. Multivariate analysis revealed that body temperature (odds ratio, 2.16; 95% confidence interval, 1.22-3.84; P = 0.009) and blood pressure (odds ratio, 2.72; 95% confidence interval, 1.39-5.35; P = 0.004) significantly associated with bacteremia.

Conclusions

The SIRS score was a more sensitive indicator than the qSOFA score for predicting bacteremia.

Antimicrobial resistance (AMR) at the community level: An urban and rural case study from Karnataka

Context:

The emergence of antimicrobial resistance (AMR) is a major public health crisis in India and globally. While national guidelines exist, the sources of data which form the basis of these guidelines are limited to a few well-established tertiary care centres. There is inadequate literature on AMR and antibiotic mismatch from India at community level and even less literature on AMR patterns from rural India.

Aims:

The aims of this study were as follows: 1) to describe the patterns of AMR at an urban tertiary care hospital and a rural 100 bedded hospital; 2) to compare and contrast the AMR patterns noted with published ICMR guidelines; 3) to examine the issue of AMR and antibiotic mismatch; and 4) to identify local factors influencing drug-bug mismatch at the local level.

Settings and Design:

The data were obtained from two independently conceived projects (Site 1: Urban tertiary care hospital, Site 2: Rural 100-bedded hospital).

Methods and Materials:

Local antibiograms were made, and the antibiotic resistance patterns were compared between the urban and rural sites and with data published in the 2017 ICMR national guideline for AMR.

Statistical Analysis Used:

Descriptive statistics including means and medians were used.

Results:

Our data reveal: a) a significant mismatch between sensitivity patterns and antibiotics prescribed; b) The national guidelines fail to capture the local picture of AMR, highlighting the need for local data; and c) challenges with data collection/retrieval, access and accuracy of diagnostic tools, administrative issues, and lack of local expertise limit antimicrobial stewardship efforts.

Conclusions:

Our study finds the burden of AMR high in both rural and urban sites, reinforcing that AMR burden cannot be ignored in rural settings. It also highlights that national data obtained from tertiary care settings fail to capture the local picture, highlighting the need for local data. Mechanisms of linking rural practices, primary health centres, and small hospitals with a common microbiology laboratory and shared data platforms will facilitate antibiotic stewardship at the community level.

A Retrospective Study of the Optimal Number of Blood Cultures at a Hospital in Japan

Blood culture tests have a major role in rapid and accurate diagnosis and selection of optimal antibiotic treatment for infectious diseases. The true-positive and contamination rates of blood cultures are performance indicators for the practice of blood culture. However, the optimal number of blood cultures has not been adequately elucidated. We aimed to assess the validity of the number of blood cultures obtained in the hospital. We conducted a retrospective study of blood cultures collected from hospitalized patients between 2010 and 2014 at a tertiary care hospital in Japan and assessed the validity of the number of blood cultures per 1,000 admissions as an indicator for the optimal practice of obtaining blood culture, considering the average length of stay. We also investigated the validity of true-positive and contamination rates of blood cultures in the hospital. The number of blood cultures in this study ranged from 28.6 to 56 per 1,000 patient-days and from 404.4 to 894.6 per 1,000 admissions. The median true-positive and contamination rates of blood cultures per year was 10.1% and 2.8%, respectively. The median contamination rate of blood cultures in a community-acquired group was significantly higher than that in a hospital-acquired group (4.1% vs. 1.9%, p = 0.029). We conclude that there is a possibility that the number of blood cultures per 1,000 admissions is a more appropriate factor to evaluate than per patient-days. Moreover, the true-positive and contamination rates of blood cultures in our hospital are valid.

Sepsis-A Retrospective Cohort Study of Bloodstream Infections

Bloodstream infections (BSIs) are among the leading causes of morbidity and mortality worldwide, among infectious diseases. Local knowledge of the main bacteria involved in BSIs and their associated antibiotic susceptibility patterns is essential to rationalize the empiric antimicrobial therapy. The aim of this study was to define the incidence of infection and evaluate the antimicrobial resistance profile of the main pathogens involved in BSIs. This study enrolled patients of all ages and both sexes admitted to the University Hospital “San Giovanni di Dio e Ruggi d’Aragona”, Salerno, Italy between January 2015 to December 2019. Bacterial identification and antibiotic susceptibility testing were performed with Vitek 2. A number of 3.949 positive blood cultures were included out of 24,694 total blood cultures from 2015 to 2019. Coagulase-negative staphylococci (CoNS) were identified as the main bacteria that caused BSI (17.4%), followed by Staphylococcus aureus (12.3%), Escherichia coli (10.9%), and Klebsiella pneumoniae (9.4%). Gram-positive bacteria were highly resistant to Penicillin G and Oxacillin, while Gram-negative strains to Ciprofloxacin, Cefotaxime, Ceftazidime, and Amoxicillin-clavulanate. High susceptibility to Vancomycin, Linezolid, and Daptomycin was observed among Gram-positive strains. Fosfomycin showed the best performance to treatment Gram-negative BSIs. Our study found an increase in resistance to the latest generation of antibiotics over the years. This suggests an urgent need to improve antimicrobial management programs to optimize empirical therapy in BSI.

Clinical assessment of the utility of metagenomic next-generation sequencing in pediatric patients of hematology department

INTRODUCTION

Metagenomic Next-Generation Sequencing (mNGS) is an emerging technique for microbial identification and diagnosis of infectious diseases. The clinical utility of mNGS, especially its real-world impact on antimicrobial treatment and patient outcome has not been systematically evaluated.

METHODS

We prospectively assessed the effectiveness of mNGS in 70 febrile inpatients with suspected infections at Hematology department of the Children's Hospital, National Clinical Research Center for Child Health. 69/70 patients were given empirical antibiotics prior to mNGS. A total of 104 samples (62 plasma, 34 throat swabs, 4 bone marrow, 4 bronchoalveolar lavage) were collected on day 1-28 (mean 6.9) following symptom onset and underwent mNGS testing.

RESULTS

Traditional microbiological tests discovered causal microorganisms in 5/70 (7.14%) patients, which were also detected by mNGS. In addition, mNGS reported possible pathogens when routine tests were negative. Antibiotics were adjusted accordingly in 55/70 (78.6%) patients that led to improvement/relief of symptoms within 3 days. In contrast, mNGS results were considered irrelevant in 15/70 (21.4%) patients by a board of clinicians, based on biochemical, serological, imaging evidence, and experiences.

CONCLUSION

mNGS expanded the capacity of pathogen detection and made a positive impact on clinical management of suspected infections through (a) differential diagnosis which may rule out infectious diseases and (b) adjustment or de-escalation of empirical antibiotics.

Timeliness of antibiotics for patients with sepsis and septic shock

For many years, sepsis guidelines have focused on early administration of antibiotics. While this practice may benefit some patients, for others it might have detrimental consequences. The increasingly shortened timeframes in which administration of antibiotics is recommended, have forced physicians to sacrifice diagnostic accuracy for speed, encouraging the overuse of antibiotics. The evidence supporting this practice is based on retrospective data, with all the limitations attached, while the only randomized trial on this subject does not show a mortality benefit from early administration of antibiotics in a population of patients with sepsis as often seen in the emergency department (ED). Physicians are challenged to treat patients suspected of having sepsis within a short period of time, while the real challenge should be to identify patients who would not be harmed by withholding treatment with antibiotics until the diagnosis of infection with a bacterial origin is confirmed and the appropriateness of a course of antibiotics can be evaluated more adequately. Therefore, in the general population of patients with sepsis, taking the time to gather additional data to confirm the diagnosis should be encouraged without a specific timeframe, although physicians should be encouraged to perform an adequate work-up as soon as possible. Patients with suspected sepsis and signs of shock should immediately be treated with antibiotics, as there is no margin for error.

Strategies for increasing diagnostic yield of community-onset bacteraemia within the emergency department: A retrospective study

Bloodstream infections (BSI) are associated with high mortality. Therefore, reliable methods of detection are of paramount importance. Efficient strategies to improve diagnostic yield of bacteraemia within the emergency department (ED) are needed. We conducted a retrospective analysis of all ED encounters in a high-volume, city-centre university hospital within Germany during a five-year study period from October 2013 to September 2018. A time-series analysis was conducted for all ED encounters in which blood cultures (BCs) were collected. BC detection rates and diagnostic yield of community-onset bacteraemia were compared during the study period (which included 45 months prior to the start of a new diagnostic Antibiotic Stewardship (ABS) bundle and 15 months following its implementation). BCs were obtained from 5,191 out of 66,879 ED admissions (7.8%). Bacteraemia was detected in 1,013 encounters (19.5% of encounters where BCs were obtained). The overall yield of true bacteraemia (defined as yielding clinically relevant pathogens) was 14.4%. The new ABS-related diagnostic protocol resulted in an increased number of hospitalised patients with BCs collected in the ED (18% compared to 12.3%) and a significant increase in patients with two or more BC sets taken (59% compared to 25.4%), which resulted in an improved detection rate of true bacteraemia (2.5% versus 1.8% of hospital admissions) without any decrease in diagnostic yield. This simultaneous increase in BC rates without degradation of yield was a valuable finding that indicated success of this strategy. Thus, implementation of the new diagnostic ABS bundle within the ED, which included the presence of a skilled infectious disease (ID) team focused on obtaining BCs, appeared to be a valuable tool for the accurate and timely detection of community-onset bacteraemia.