Bacterial bloodstream infections and patterns of resistance in patients with haematological malignancies at a tertiary centre in Lebanon over 10 years

Machine learning-based prognostic model for bloodstream infections in hematological malignancies using Th1/Th2 cytokines

OBJECTIVE

Bloodstream infection (BSI) is a significant cause of mortality in patients with hematologic malignancies(HMs), particularly amid rising antibiotic resistance. This study aimed to analyze pathogen distribution, drug-resistance patterns and develop a novel predictive model for 30-day mortality in HM patients with BSIs.

METHODS

A retrospective analysis of 231 HM patients with positive blood cultures was conducted. Logistic regression identified risk factors for 30-day mortality. Th1/Th2 cytokines were collected at BSI onset, with LASSO regression and restricted cubic spline analysis used to refine predictors. Seven machine learning(ML) algorithm (XGBoost, Logistic Regression, LightGBM, RandomForest, AdaBoost, GBDT and GNB) were trained using 10-fold cross-validation and model performance was evaluated with the ROC, calibration plots, decision and learning curves and the Shapley Additive Explanations (SHAP) analysis. The predictive model was developed by integrating Th1/Th2 cytokines with clinical features, aiming to enhance the accuracy of 30-day mortality prediction.

RESULTS

Among the cohort, acute myeloid leukemia (38%) was the most common HM, while gram negative bacteria (64%) were the predominant pathogens causing BSI. Age, polymicrobial BSI, IL-4, IL-6 and AST levels were significant predictors of 30-day mortality. The Logistic Regression model achieved AUCs of 0.802, 0.792, and 0.822 in training, validation, and test cohorts, respectively, with strong calibration and clinical benefit shown in decision curves. SHAP analysis highlighted IL-4 and IL-6 as key predictors.

CONCLUSIONS

This study introduces a novel ML-based model integrating Th1/Th2 cytokines and clinical features to predict 30-day mortality in HM patients with BSIs, demonstrating strong performance and clinical applicability.

The epidemiology of gram-negative bacteremia in Lebanon: a study in four hospitals

INTRODUCTION

Gram-negative bacteremia is a life-threatening infection with high morbidity and mortality. Its incidence is rising worldwide, and treatment has become more challenging due to emerging bacterial resistance. Little data is available on the burden and outcome of such infections in Lebanon.

METHODS

We conducted this retrospective study in four Lebanese hospitals. Data on medical conditions and demographics of 2400 patients diagnosed with a bloodstream infection based on a positive blood culture were collected between January 2014 and December 2020.

RESULTS

Most bacteremias were caused by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, with the more resistant organisms being hospital-acquired. Third-generation cephalosporin and quinolone resistance was steady throughout the study, but carbapenem resistance increased. Mortality with such infections is high, but carbapenem resistance or infection with Pseudomonas or Acinetobacter species were significant risk factors for poor outcomes.

CONCLUSION

This is the first multi-center study from Lebanon on gram-negative bacteremia, resistance patterns, and factors associated with a poor outcome. More surveillance is needed to provide data to guide empirical treatment for bacteremia in Lebanon.

Adult acute leukemia patients with gram-negative bacteria bloodstream infection: Risk factors and outcomes of antibiotic-resistant bacteria

This study aims to analyze the risk factors for the development of multidrug-resistant (MDR) and carbapenem-resistant (CR) bacteria bloodstream infection (BSI) in a patient with acute leukemia (AL) and the mortality in gram-negative bacteria (GNB) BSI. This is a retrospective study conducted at West China Hospital of Sichuan University, which included patients diagnosed with AL and concomitant GNB BSI from 2016 to 2021. A total of 206 patients with GNB BSI in AL were included. The 30-day mortality rate for all patients was 26.2%, with rates of 25.8% for those with MDR GNB BSI and 59.1% for those with CR GNB BSI. Univariate and multivariate analyses revealed that exposure to quinolones (Odds ratio (OR) = 3.111, 95% confidence interval (95%CI): 1.623-5.964, p = 0.001) within the preceding 30 days was an independent risk factor for MDR GNB BSI, while placement of urinary catheter (OR = 6.311, 95%CI: 2.478-16.073, p < 0.001) and exposure to cephalosporins (OR = 2.340, 95%CI: 1.090-5.025, p = 0.029) and carbapenems (OR = 2.558, 95%CI: 1.190-5.497, p = 0.016) within the preceding 30 days were independently associated with CR GNB BSI. Additionally, CR GNB BSI (OR = 2.960, 95% CI: 1.016-8.624, p = 0.047), relapsed/refractory AL (OR = 3.035, 95% CI: 1.265-7.354, p = 0.013), septic shock (OR = 5.108, 95% CI: 1.794-14.547, p = 0.002), platelets < 30 × 109/L before BSI (OR = 7.785, 95% CI: 2.055-29.492, p = 0.003), and inappropriate empiric antibiotic therapy (OR = 3.140, 95% CI: 1.171-8.417, p = 0.023) were independent risk factors for 30-day mortality in AL patients with GNB BSI. Prior antibiotic exposure was a significant factor in the occurrence of MDR GNB BSI and CR GNB BSI. CR GNB BSI increased the risk of mortality in AL patients with GNB BSI.

Multidrug-Resistant Bacteria in Immunocompromised Patients

The increasing incidence of antibiotic resistance in bacteria is a major problem in terms of therapeutic options, especially in immunocompromised patients, such as patients from intensive care units (ICUs), HIV-positive patients, patients with malignancies or transplant patients. Commensal bacteria, especially anaerobes, serve to maintain microbial stability by preventing overpopulation with pathogenic bacteria. In immunocompromised patients, microbiota imbalance caused by antibiotic therapy and decreased host immunity favors intestinal overpopulation with pathogenic species, leading to increased bacterial translocation and susceptibility to systemic infections. Infections with multidrug-resistant (MDR) bacteria pose major challenges to the establishment of appropriate treatment and lead to increased mortality. Asymptomatic colonization with MDR bacteria usually precedes infection and tends to persist for long periods of time, and in immunocompromised patients, colonization with MDR bacteria is a risk factor for systemic infections. This review aims to assess the relation between colonization and infection with MDR bacteria in immunocompromised patients such as ICU patients, HIV-positive patients and cancer patients and to identify the prevalence and patterns of MDR bacterial colonization and infection in this category of patients.

Characterization of the Pathogen Distribution and Drug Resistance in Bloodstream Infections During COVID-19 Pandemic in a Tertiary Hospital in Eastern China: Comparison with the Pre-Pandemic Period

Purpose

To explore the characteristics of the pathogen distribution and drug resistance in bloodstream infections (BSIs) during the COVID-19 pandemic in a tertiary hospital in eastern China, and to compare them with those before the pandemic.

Patients and Methods

Non-repetitive strain data of BSIs were retrospectively obtained before the COVID-19 pandemic (Pre-Pandemic, n=2698) and during the COVID-19 pandemic (Pandemic, n=2922), the distribution of pathogens and drug resistance were compared between the two groups.

Results

The main pathogens of BSIs were Gram-negative bacteria (57.91%), followed by Gram-positive bacteria (32.58%), fungi and anaerobic bacteria accounting for 5.48% and 3.39%, respectively. Escherichia coli, Klebsiella pneumoniae and Staphylococcus aureus were the top 3 isolates. The proportion of Serratia marcescens, Enterobacter aerogenes, Enterococcus faecium, Enterococcus faecalis and Candida tropicalis were significantly increased, while those of Pseudomonas aeruginosa, Streptococcus sanguinis and Streptococcus pneumoniae were significantly decreased when compared to the Pre-Pandemic (P<0.05). Carbapenem-resistant Enterobacterales (CRE) significantly elevated during the Pandemic (17.4% vs 14.4%, P=0.041); the detection of carbapenem-resistant Pseudomonas aeruginosa (CRPA) significantly ascended (39.0% vs 24.4%, P=0.016); and the proportion of carbapenem-resistant Acinetobacter baumannii (CRAB) maintained stable (78.8%). Gram-positive bacteria had the lowest resistance to linezolid, vancomycin and tigecycline, which remained a stable trend with the Pre-Pandemic (<5.0%). The isolate rates of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus (VRE) were 38.9% and 1.0%, respectively. Staphylococcus aureus showed a decrease in the isolation rate of vancomycin minimum inhibitory concentration (MIC) ≤ 0.5 μg/mL (χ2=7.676, P=0.006) and an increase with vancomycin MIC=1 μg/mL (χ2=9.008, P=0.003).

Conclusion

The pathogen distribution and drug resistance of BSIs during the COVID-19 pandemic were transformed from Pre-Pandemic and accompanied by increasing bacterial resistance. Clinical management of antibiotic application and infection control should be strengthened.

Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients

Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.

The experience of an antimicrobial stewardship program and antibiotic consumption and resistance trends during the COVID-19 pandemic at a tertiary care center in Beirut

BACKGROUND

Antimicrobial Resistance, a global concern, worsened with the COVID-19 pandemic that caused a surge of critically ill patients, increased antimicrobial consumption, and the spread of infections with multidrug-resistant organisms (MDROs). Antimicrobial Stewardship Programs (ASP) aim to optimize antimicrobial utilization to fight resistance. We aim to describe the ASP experience and to study antimicrobial consumption and MDRO rates among COVID-19 patients at a tertiary care center in Beirut.

METHODS

We compiled the ASP interventions, defined as ASP team recommendations, from January 2019 until December 2021. Data on antimicrobial consumption, expressed as a defined daily dose (DDD) per 100 patient days, was collected per quarter for all antimicrobials and restricted antimicrobials per ASP guidance. Our primary objective was to report on the ASP experience, and the secondary objective was to reflect on the rates of MDROs among hospitalized COVID-19 patients with respiratory or bloodstream bacterial co-infections between March 2020 and September 2021.

RESULTS

9922 ASP interventions were documented during this study period, with a noticeable correlation between COVID-19 surges in Lebanon and the number of ASP interventions. Acceptance rates for these recommendations improved over time, with a noticeable decrease in the proportion of interventions related to de-escalation and discontinuation of broad-spectrum antimicrobials. We noted an increase in all antimicrobial consumption after the onset of the pandemic, peaking in Q4 2020 (142.8 DDD of anti-infectives/100 patient days) and Q1 2021 (79.1 DDD of restricted anti-infectives/100 patient days). As expected, MDROs, particularly ESKAPE organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Carbapenem-resistant Enterobacteriaceae) accounted for 24% of isolates obtained from this cohort.

CONCLUSION

This study highlights the experience of the ASP as we adapted to the COVID-19 pandemic. The ASP team maintained its operations and continued to monitor antibiotic consumption and provide recommendations to limit antibiotic misuse in an effort to mitigate the impact of the pandemic on antimicrobial resistance.

Changing epidemiology, microbiology and mortality of bloodstream infections in patients with haematological malignancies before and during SARS-CoV-2 pandemic: a retrospective cohort study

OBJECTIVE

This study was to explore the changes in bacterial bloodstream infection (BSI) in patients with haematological malignancies (HMs) before and during SARS-CoV-2 pandemic.

DESIGN

Retrospective cohort study between 2018 and 2021.

SETTING

The largest haematological centre in southern China.

RESULTS

A total of 599 episodes of BSI occurring in 22 717 inpatients from January 2018 to December 2021 were analysed. The frequencies of the total, Gram-negative and Gram-positive BSI before and during the pandemic were 2.90% versus 2.35% (p=0.011), 2.49% versus 1.77% (p<0.001) and 0.27% versus 0.44% (p=0.027), respectively. The main isolates from Gram-negative or Gram-positive BSI and susceptibility profiles also changed. The 30-day mortality caused by BSI was lower during the pandemic (21.1% vs 14.3%, p=0.043). Multivariate analysis revealed that disease status, pulmonary infection and shock were independent predictors of 30-day mortality.

CONCLUSION

Our data showed that the incidence of total and Gram-negative organisms BSI decreased, but Gram-positive BSI incidence increased in patients with HMs during the pandemic along with the changes of main isolates and susceptibility profiles. Although the 30-day mortality due to BSI was lower during the pandemic, the new infection prevention strategy should be considered for any future pandemics.

Global impact of antibacterial resistance in patients with hematologic malignancies and hematopoietic cell transplant recipients

Patients with hematologic malignancies and hematopoietic cell transplant (HCT) recipients are at high risk of developing bacterial infections. These patients may suffer severe consequences from these infections if they do not receive immediate effective therapies, and thus are uniquely threatened by antimicrobial-resistant bacteria. Here, we outline how the emergence of specific resistant bacteria threatens the effectiveness of established approaches to prevent and treat infections in this population. The emergence of fluoroquinolone resistance among Enterobacterales and viridans group streptococci may decrease the effectiveness of fluoroquinolone prophylaxis during neutropenia. The emergence of Enterobacterales that produce extended-spectrum β-lactamases or carbapenemases and of increasingly resistant Pseudomonas aeruginosa may result in neutropenic patients experiencing delayed time to active antibacterial therapy, and consequently worse clinical outcomes. The ability to select targeted antibacterial therapies after the availability of susceptibility data may be limited in patients infected with metallo-β-lactamase-producing Enterobacterales and difficult-to-treat P. aeruginosa. Vancomycin-resistant enterococci and Stenotrophomonas maltophilia can cause breakthrough infections in patients already being treated with broad-spectrum β-lactam antibiotics. Resistance can also limit the ability to provide oral stepdown antibacterial therapy for patients who could otherwise be discharged from hospitalization. We also outline strategies that have the potential to mitigate the negative impact of antimicrobial resistance, including interventions based on active screening for colonization with resistant bacteria and the use of novel rapid diagnostic assays. Additional research is needed to better understand how these strategies can be leveraged to combat the emerging crisis of antimicrobial resistance in patients with hematologic malignancies and HCT recipients.

Microbiology and prognostic prediction model of bloodstream infection in patients with hematological malignancies

Background

In recent years, with the continuous development of treatments for hematological malignancies (HMs), the remission and survival rates of patients with HMs have been significantly improved. However, because of severe immunosuppression and long-term recurrent neutropenia during treatment, the incidence and mortality of bloodstream infection (BSI) were all high in patients with HMs. Therefore, we analyzed pathogens' distribution and drug-resistance patterns and developed a nomogram for predicting 30-day mortality in patients with BSIs among HMs.

Methods

In this retrospective study, 362 patients with positive blood cultures in HMs were included from June 2015 to June 2020 at West China Hospital of Sichuan University. They were randomly divided into the training cohort (n = 253) and the validation cohort (n = 109) by 7:3. A nomogram for predicting 30-day mortality after BSIs in patients with HMs was established based on the results of univariate and multivariate logistic regression. C-index, calibration plots, and decision curve analysis were used to evaluate the nomogram.

Results

Among 362 patients with BSIs in HMs, the most common HM was acute myeloid leukemia (48.1%), and the most common pathogen of BSI was gram-negative bacteria (70.4%). The final nomogram included the septic shock, relapsed/refractory HM, albumin <30g/l, platelets <30×10⁹/l before BSI, and inappropriate empiric antibiotic treatment. In the training and validation cohorts, the C-indexes (0.870 and 0.825) and the calibration plots indicated that the nomogram had a good performance. The decision curves in both cohorts showed that the nomogram model for predicting 30-day mortality after BSI was more beneficial than all patients with BSIs or none with BSIs.

Conclusion

In our study, gram-negative bacterial BSIs were predominant in patients with HMs. We developed and validated a nomogram with good predictive ability to help clinicians evaluate the prognosis of patients.

Prevalence of Multidrug-Resistant Pathogens Causing Neonatal Early and Late Onset Sepsis, a Retrospective Study from the Tertiary Referral Children's Hospital

Introduction

Sepsis is the most severe infectious disease with the highest mortality rate, particularly among neonates admitted to the neonatal intensive care unit (NICU). This study retrospectively analyzed the epidemiology, antibiotic resistance profiles, and prevalence of multidrug-resistant (MDR) bacteria isolated from blood or cerebrospinal fluid (CSF) cultures in order to evaluate the appropriateness of initial empirical therapy for neonatal sepsis.

Methods

A retrospective study was conducted in the NICU from January 1, 2015, to December 31, 2022. Microbiological data from patients admitted to the NICU were anonymously extracted from the Laboratory of Microbiology database. Neonatal sepsis was classified into two types: early-onset sepsis (EOS), which occurs within the first 72 hours of life, and late-onset sepsis (LOS) for those begins later.

Results

A total of 679 bacterial strains, 543 from blood and 136 from CSF, were detected in 631 neonates. Among these, 378 isolates (55.67%) were Gram-positive bacteria, and 301 isolates (44.33%) were Gram-negative bacteria. The most frequently isolated pathogens were Coagulase-negative staphylococci (CoNS) (36.52%), followed by Klebsiella pneumoniae (20.47%) and Escherichia coli (13.84%). In EOS, 121 strains were found, CoNS represented the majority (33.88%), followed by Klebsiella pneumoniae (23.97%) and Escherichia coli (8.26%). Early-onset septicemia exhibited 67 (55.37%) MDR bacteria. In LOS, 558 strains were isolated, CoNS represented the majority of pathogens (37.10%), followed by Klebsiella pneumoniae (19.71%) and Escherichia coli (15.05%). Late-onset septicemia showed 332 (59.50%) MDR bacteria. High rates of MDR were found in CoNS (76.21%), carbapenem-resistant Klebsiella pneumoniae (66.91%), and MRSA (33.33%).

Conclusion

The study revealed an alarming prevalence of MDR strains isolated from neonatal sepsis, emphasizing the necessity of finding effective prevention and treatment measures. Colistin can be used for MDR Gram-negative bacteria, while vancomycin and teicoplanin can be considered treatment therapies for staphylococcal infections.

Bloodstream Infections in Patients with Hematologic Diseases: Causative Organisms and Factors Associated with Resistance

Background

Materials and Methods

Results

Conclusion