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

Reduced mortality with antimicrobial stewardship guided by BioFire FilmArray Blood Culture Identification 2 panel in critically ill patients with bloodstream infection: a retrospective propensity score-matched study

OBJECTIVES

To investigate whether using the BioFire® FilmArray® Blood Culture Identification 2 panel (BCID2) leads to timely antimicrobial therapy and improves patient outcomes in critically ill patients with bloodstream infections (BSIs).

METHODS

This retrospective observational study included patients with BSIs admitted to the intensive care unit from July 1, 2021, to August 31, 2023. Patients were divided into groups receiving appropriate or inappropriate antimicrobial therapy. Those receiving inappropriate therapy underwent adjustments using standard-of-care (SOC) testing or BCID2. Propensity score matching (PSM) was performed on the original cohort (Model 1) and a time-window bias-adjusted cohort (Model 2). Clinical impact of BCID2-guided antimicrobial adjustment was analyzed in both models.

RESULTS

A total of 181 patients received inappropriate antimicrobial therapy, with 33 undergoing BCID2 testing and 148 undergoing SOC testing. Following PSM and time-window bias adjustment, 66 patients were analyzed in Model 1 and 46 patients in Model 2. BCID2 significantly reduced the median time to appropriate antimicrobial therapy (40.8 vs. 74.0 h in Model 1; 42.8 vs. 68.9 h in Model 2) and the day-28 mortality rate (27.8% vs. 77.1%, p < 0.001 in Model 1; 23.5% vs. 58.6%, p = 0.021 in Model 2). In multivariate regression analysis, BCID2-guided antimicrobial adjustment was an independent prognostic factor for day-28 mortality (adjusted odds ratio [aOR] 0.07 in Model 1 and aOR 0.12 in Model 2).

CONCLUSION

BCID2-guided antimicrobial stewardship was associated with a shorter time to appropriate antimicrobial therapy and reduced day-28 mortality in critically ill patients with BSIs receiving inappropriate antimicrobial therapy.

The real-world impact of the BioFire FilmArray blood culture identification 2 panel on antimicrobial stewardship among patients with bloodstream infections in intensive care units with a high burden of drug-resistant pathogens

BACKGROUND

The increasing prevalence of drug-resistant pathogens leads to delays in adequate antimicrobial treatment in intensive care units (ICU). The real-world influence of the BioFire FilmArray Blood Culture Identification 2 (BCID2) panel on pathogen identification, diagnostic concordance with conventional culture methods, and antimicrobial stewardship in the ICU remains unexplored.

METHODS

This retrospective observational study, conducted from July 2021 to August 2023, involved adult ICU patients with positive blood cultures who underwent BCID2 testing. The concordance between BCID2 and conventional culture results was examined, and its impact on antimicrobial stewardship was assessed through a comprehensive retrospective review of patient records by intensivists.

RESULTS

A total of 129 blood specimens from 113 patients were analysed. Among these patients, a high proportion of drug-resistant strains were noted, including carbapenem-resistant Klebsiella pneumoniae (CRKP) (57.1%), carbapenem-resistant Acinetobacter calcoaceticus-baumannii complex (100%), methicillin-resistant Staphylococcus aureus (MRSA) (70%), and vancomycin-resistant Enterococcus faecium (VRE) (100%). The time from blood culture collection to obtaining BCID2 results was significantly shorter than conventional culture (46.2 h vs. 86.9 h, p < 0.001). BCID2 demonstrated 100% concordance in genotype-phenotype correlation in antimicrobial resistance (AMR) for CRKP, carbapenem-resistant Escherichia coli, MRSA, and VRE. A total of 40.5% of patients received inadequate empirical antimicrobial treatment. The antimicrobial regimen was adjusted or confirmed in 55.4% of patients following the BCID2 results.

CONCLUSIONS

In the context of a high burden of drug-resistant pathogens, BCID2 demonstrated rapid pathogen and AMR detection, with a noticeable impact on antimicrobial stewardship in BSI in the ICU.

From Species to Genes: A New Diagnostic Paradigm

Molecular diagnostics has the potential to revolutionise the field of clinical microbiology. Microbial identification and nomenclature have, for too long, been restricted to phenotypic characterisation. However, this species-level view fails to wholly account for genetic heterogeneity, a result of lateral gene transfer, mediated primarily by mobile genetic elements. This genetic promiscuity has helped to drive virulence development, stress adaptation, and antimicrobial resistance in several important bacterial pathogens, complicating their detection and frustrating our ability to control them. We argue that, as clinical microbiologists at the front line, we must embrace the molecular technologies that allow us to focus specifically on the genetic elements that cause disease rather than the bacterial species that express them. This review focuses on the evolution of microbial taxonomy since the introduction of molecular sequencing, the role of mobile genetic elements in antimicrobial resistance, the current and emerging assays in clinical laboratories, and the comparison of phenotypic versus genotypic analyses. In essence, it is time now to refocus from species to genes as part of a new diagnostic paradigm.

Clinical outcomes of carbapenem-resistant gram-negative bacterial bloodstream infection in patients with end-stage renal disease in intensive care units: a multicenter retrospective observational study

BACKGROUND

Carbapenem-resistant gram-negative bacteria (CRGNB) present a considerable global threat due to their challenging treatment and increased mortality rates, with bloodstream infection (BSI) having the highest mortality rate. Patients with end-stage renal disease (ESRD) undergoing renal replacement therapy (RRT) face an increased risk of BSI. Limited data are available regarding the prognosis and treatment outcomes of CRGNB-BSI in patients with ESRD in intensive care units (ICUs).

METHODS

This multi-center retrospective observational study included a total of 149 ICU patients with ESRD and CRGNB-BSI in Taiwan from January 2015 to December 2019. Clinical and microbiological outcomes were assessed, and multivariable regression analysis was used to evaluate the independent risk factors for day-28 mortality and the impact of antimicrobial therapy regimen on treatment outcomes.

RESULTS

Among the 149 patients, a total of 127 patients (85.2%) acquired BSI in the ICU, with catheter-related infections (47.7%) and pneumonia (32.2%) being the most common etiologies. Acinetobacter baumannii (49.0%) and Klebsiella pneumoniae (31.5%) were the most frequently isolated pathogens. The day-28 mortality rate from BSI onset was 52.3%, and in-hospital mortality was 73.2%, with survivors experiencing prolonged hospital stays. A higher Sequential Organ Failure Assessment (SOFA) score (adjusted hazards ratio [aHR], 1.25; 95% confidence interval [CI] 1.17-1.35) and shock status (aHR, 2.12; 95% CI 1.14-3.94) independently predicted day-28 mortality. Colistin-based therapy reduced day-28 mortality in patients with shock, a SOFA score of ≥ 13, and Acinetobacter baumannii-related BSI.

CONCLUSIONS

CRGNB-BSI led to high mortality in critically ill patients with ESRD. Day-28 mortality was independently predicted by a higher SOFA score and shock status. In patients with higher disease severity and Acinetobacter baumannii-related BSI, colistin-based therapy improved treatment outcomes.

Precision emergency medicine

BACKGROUND

Precision health is a burgeoning scientific discipline that aims to incorporate individual variability in biological, behavioral, and social factors to develop personalized health solutions. To date, emergency medicine has not deeply engaged in the precision health movement. However, rapid advances in health technology, data science, and medical informatics offer new opportunities for emergency medicine to realize the promises of precision health.

METHODS

In this article, we conceptualize precision emergency medicine as an emerging paradigm and identify key drivers of its implementation into current and future clinical practice. We acknowledge important obstacles to the specialty-wide adoption of precision emergency medicine and offer solutions that conceive a successful path forward.

RESULTS

Precision emergency medicine is defined as the use of information and technology to deliver acute care effectively, efficiently, and authentically to individual patients and their communities. Key drivers and opportunities include leveraging human data, capitalizing on technology and digital tools, providing deliberate access to care, advancing population health, and reimagining provider education and roles. Overcoming challenges in equity, privacy, and cost is essential for success. We close with a call to action to proactively incorporate precision health into the clinical practice of emergency medicine, the training of future emergency physicians, and the research agenda of the specialty.

CONCLUSIONS

Precision emergency medicine leverages new technology and data-driven artificial intelligence to advance diagnostic testing, individualize patient care plans and therapeutics, and strategically refine the convergence of the health system and the community.

Nanomaterial-based methods for sepsis management

Sepsis is a serious disease caused by an impaired host immune response to infection, resulting in organ dysfunction, tissue damage and is responsible for high in-hospital mortality (approximately 20%). Recently, WHO documented sepsis as a global health priority. Nevertheless, there is still no effective and specific therapy for clinically detecting sepsis. Nanomaterial-based approaches have appeared as promising tools for identifying bacterial infections. In this review, recent biosensors are introduced and summarized as nanomaterial-based platforms for sepsis management and severe complications. Biosensors can be used as tools for the diagnosis and treatment of sepsis and as nanocarriers for drug delivery. In general, diagnostic methods for sepsis-associated bacteria, biosensors developed for this purpose are presented in detail, and their strengths and weaknesses are discussed. In other words, readers of this article will gain a comprehensive understanding of biosensors and their applications in sepsis management.

Biomarkers for Serious Bacterial Infections in Febrile Children

Febrile infections in children are a common cause of presentation to the emergency department (ED). While viral infections are usually self-limiting, sometimes bacterial illnesses may lead to sepsis and severe complications. Inflammatory biomarkers such as C reactive protein (CRP) and procalcitonin are usually the first blood exams performed in the ED to differentiate bacterial and viral infections; nowadays, a better understanding of immunochemical pathways has led to the discovery of new and more specific biomarkers that could play a role in the emergency setting. The aim of this narrative review is to provide the most recent evidence on biomarkers and predictor models, combining them for serious bacterial infection (SBI) diagnosis in febrile children. Literature analysis shows that inflammatory response is a complex mechanism in which many biochemical and immunological factors contribute to the host response in SBI. CRP and procalcitonin still represent the most used biomarkers in the pediatric ED for the diagnosis of SBI. Their sensibility and sensitivity increase when combined, and for this reason, it is reasonable to take them both into consideration in the evaluation of febrile children. The potential of machine learning tools, which represent a real novelty in medical practice, in conjunction with routine clinical and biological information, may improve the accuracy of diagnosis and target therapeutic options in SBI. However, studies on this matter are not yet validated in younger populations, making their relevance in pediatric precision medicine still uncertain. More data from further research are needed to improve clinical practice and decision making using these new technologies.

Prediction of methicillin-resistant Staphylococcus aureus and carbapenem-resistant Klebsiella pneumoniae from flagged blood cultures by combining rapid Sepsityper MALDI-TOF mass spectrometry with machine learning

This study investigated combination of the Rapid Sepsityper Kit and a machine learning (ML)-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) approach for rapid prediction of methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Klebsiella pneumoniae (CRKP) from positive blood culture bottles. The study involved 461 patients with monomicrobial bloodstream infections. Species identification was performed using the conventional MALDI-TOF MS Biotyper system and the Rapid Sepsityper protocol. The data underwent preprocessing steps, and ML models were trained using preprocessed MALDI-TOF data and corresponding labels. The interpretability of the model was enhanced using SHapely Additive exPlanations values to identify significant features. In total, 44 S. aureus isolates comprising 406 MALDI-TOF MS files and 126 K. pneumoniae isolates comprising 1249 MALDI-TOF MS files were evaluated. This study demonstrated the feasibility of predicting MRSA among S. aureus and CRKP among K. pneumoniae isolates using MALDI-TOF MS and Sepsityper. Accuracy, area under the receiver operating characteristic curve, and F1 score for MRSA/methicillin-susceptible S. aureus were 0.875, 0.898 and 0.904, respectively; for CRKP/carbapenem-susceptible K. pneumoniae, these values were 0.766, 0.828 and 0.795, respectively. In conclusion, the novel ML-based MALDI-TOF MS approach enables rapid identification of MRSA and CRKP from flagged blood cultures within 1 h. This enables earlier initiation of targeted antimicrobial therapy, reducing deaths due to sepsis. The favourable performance and reduced turnaround time of this method suggest its potential as a rapid detection strategy in clinical microbiology laboratories, ultimately improving patient outcomes.

The Significance of FilmArray Blood Culture Identification Panel (FA-BCID) for Managing Patients with Positive Blood Cultures

We analyzed the accuracy and time efficiency of the FilmArray blood culture identification (FA-BCID) panel in identifying the pathogens in positive blood cultures. Two-hundred and seventy-two individuals were randomly assigned as the control (n = 212) and FA-BCID (n = 60) groups participating in this study. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was used to assess the control group. Meanwhile, the FA-BCID group was evaluated using both FA-BCID and MALDI-TOF, and the results were compared. The identification results from 73% (44/60) of the blood samples demonstrated agreement between FA-BCID and MALDI-TOF. The FA-BCID panel detected mecA genes in seven Staphylococcus species; six cases were confirmed using antimicrobial susceptibility testing. In addition, KPC genes were detected in one Escherichia coli and one Klebsiella pneumoniae, although only the latter corresponded with the result from antimicrobial susceptibility testing. The turnaround time (TAT) for identification through FA-BCID was shorter, with a median of 3.6 [2.4-4.6] hours (p < 0.05). No significant differences in the clinical and microbial outcomes following the ASP were observed between FA-BCID and MALDI-TOF. These results suggest that the FA-BCID panel provides an identification result that is as reliable as that provided by the routine identification procedure but with shorter TAT; thus, the FA-BCID method is considered an effective and beneficial method for therapeutic decision making and the improvement of the ASP for patients with bloodstream infection.

Diagnostic efficiency of the FilmArray blood culture identification (BCID) panel: a systematic review and meta-analysis

Introduction. The FilmArray blood culture identification panel (BCID) panel is a multiplex PCR assay with high sensitivity and specificity to identify the most common pathogens in bloodstream infections (BSIs).Hypothesis. We hypothesize that the BCID panel has good diagnostic performance for BSIs and can be popularized in clinical application.Aim: To provide summarized evidence for the diagnostic accuracy of the BCID panel for the identification of positive blood cultures.Methodology. We searched the MEDLINE, EMBASE and Cochrane databases through March 2021 and assessed the efficacy of the diagnostic test of the BCID panel. We performed a meta-analysis and calculated the summary sensitivity and specificity of the BCID panel. Systematic review protocols were registered in the International Prospective Register of Systematic Reviews (PROSPERO) (registration number CRD42021239176).Results. A total of 16 full-text articles were eligible for analysis. The overall sensitivities of the BCID panel on Gram-positive bacteria, Gram-negative bacteria and fungi were 97 % (95 % CI, 0.96-0.98), 100 % (95 % CI, 0.98-01.00) and 99 % (95 % CI, 0.87-1.00), respectively. The pooled diagnostic specificities were 99 % (95 % CI, 0.97-1.00), 100 % (95 % CI, 1.00-1.00) and 100 % (95 % CI, 1.00-1.00) for Gram-positive bacteria, Gram-negative bacteria and fungi, respectively.Conclusions. The BCID panel has high rule-in value for the early detection of BSI patients. The BCID panel can still provide valuable information for ruling out bacteremia or fungemia in populations with low pretest probability.

Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital

The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems—VITEK MS MALDI-TOF Mass Spectrometer and Vitek2—and antibiotic susceptibility testing—Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement—both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture.

Outcomes and Prognostic Factors in Critical Patients with Hematologic Malignancies

Patients with hematologic malignancies (HMs) have a significantly elevated risk of mortality compared to other cancer patients treated in the intensive care unit (ICU). The prognostic impact of numerous poor outcome indicators has changed, and research has yielded conflicting results. This study aims to determine the ICU and hospital outcomes and risk factors that predict the prognosis of critically ill patients with HMs. In this retrospective study, conducted at a referral hospital in Taiwan, 213 adult patients with HMs who were admitted to the medical ICU were evaluated. We collected clinical data upon hospital and ICU admission. Using a multivariate regression analysis, the predictors of ICU and hospital mortality were assessed. Then, a scoring system (Hospital outcome of critically ill patients with Hematological Malignancies (HHM)) was built to predict hospital outcomes. Most HMs (76.1%) were classified as high grade, and more than one-third of patients experienced a relapsed or refractory disease. The ICU and hospital mortality rates were 55.9% and 71.8%, respectively. Moreover, the disease severity was high (median Sequential Organ Failure Assessment (SOFA) score: 11 and Acute Physiology and Chronic Health Evaluation (APACHE II) score: 28). The multivariate analysis revealed that high-grade HMs, invasive mechanical ventilation requirement, renal replacement therapy initiation in the ICU, and a high SOFA score correlated with ICU mortality. Furthermore, a higher HHM score predicted hospital mortality. This study demonstrates that ICU mortality primarily correlates with the severity of organ dysfunction, whereas the disease status markedly influences hospital outcomes. Furthermore, the HHM score significantly predicts hospital mortality.

Systemic Candidosis Diagnostic Test with Candida Score and Monocyte Count in Premature Infants with Late-Onset Sepsis: Research in Low Resources Country

Abstract Introduction: Candida is the cause of most systemic fungal infections that plays a role in the pathophysiology of sepsis in newborns, especially in premature infants with late-onset sepsis. The candida score can be used to assess the occurrence of systemic candidosis where a candida score 2.5 can accurately identify patients who are at high risk for candidiasis infection. Monocytes also play an important role in preventing candida invasion. Materials and methods: This study used a cross sectional research design. Data was collected from premature infants with late-onset sepsis being suspected of systemic candidosis in neonatology inpatient ward. It was submitted from the period of November-December 2021. It takes a minimum of 31 samples to meet the criteria to process and analyze the data. The data obtained were processed and analyzed using the Receiver Operating Characteristic (ROC) method to obtain the Area Under Curve (AUC) value. Based on the AUC curve, the search for the most optimal intersection is carried out to obtain the sensitivity and specificity values. Results: Of the 31 research subjects, the number of subjects with positive PCR results was 27 (76.93%) while negative were 4 respondents (12.9%). The mean value of PCR density in the positive group of subjects was 76.93 and the range was 40.23 122.78. Meanwhile, in the group of subjects who were negative, the PCR density value was 0. The results of the candida score diagnostic test showed that the sensitivity obtained was 81%. Higher sensitivity and specificity 70% were found in the combined examination of candida scores and monocyte counts according to cut-off compared with separate examinations. Conclusions: The combined examination of candida score and monocyte count can be used as a diagnostic test for systemic candidosis in premature infants with late-onset sepsis, and could be used to consider the initiation of empirical antifungal therapy, either prophylactically or therapeutically, especially in limited laboratory facilities in Indonesia.

Evaluation of the Rapid Sepsityper protocol and specific MBT-Sepsityper module for the identification of bacteremia and fungemia using Bruker Biotyper MALDI-TOF MS

The rapid identification method, the Rapid Sepsityper protocol with a specific MBT-Sepsityper module (Bruker Daltonics), based on the MALDI Biotyper platform, accurately identified 93.5% (116/124) of microorganisms at the species level in the 124 flagged blood culture samples from patients with monomicrobial bloodstream infections. Gram-negative bacilli (95.6%, 43/45) had a higher identification rate than Gram-positive cocci (93.3%, 70/75) and yeasts (75%, 3/4). The Rapid Sepsityper protocol displayed poor identification performance for polymicrobial samples.

Performance of the BioFire Blood Culture Identification 2 panel for the diagnosis of bloodstream infections

Background

Conventional blood cultures methods are associated with long turnaround times, preventing early treatment optimization in bloodstream infections. The BioFire Blood Culture Identification 2 (BCID2) Panel is a new multiplex PCR applied on positive blood cultures, reducing time to pathogen identification and resistant markers detection.

Methods

We conducted a prospective observational study including positive blood cultures from Intensive Care Units and Emergency Departments and performed BCID2 in addition to conventional testing. Concordance between the two methods was assessed and BCID2 performance characteristics were evaluated. Resistance markers detected by BCID2 were confirmed by in-house PCR. Whole genome sequencing was performed in discordant cases.

Results

Among 60 monomicrobial blood cultures, BCID2 correctly identified 55/56 (91.7%) on-panel pathogens, showing an overall concordance of 98%. In 4/60 cases BCID2 did not detect any target and these all grew BCID2 off-panel bacteria. Only one discordant case was found. Sensitivity and specificity for Gram-positive bacteria on monomicrobial samples were 100% (95% CI 85.8-100%) and 100% (95% CI 90.3-100%) respectively, while for Gram-negatives 100% (95% CI 87.7-100) and 96.9% (95% CI 83.8-99.9%), respectively. Among two polymicrobial blood cultures, full concordance was observed in one case only. BCID2 identified antimicrobial resistance genes in 6/62 samples, all confirmed by in-house PCR (3 mecA/C S. epidermidis, 3 bla _CTX-M E. coli). Estimated time to results gained using BCID2 as compared to conventional testing was 9.69 h (95% CI: 7.85-11.53).

Conclusions

BCID2 showed good agreement with conventional methods. Studies to assess its clinical impact are warranted.

Comparison of a Point-of-Care FilmArray Test to Standard-of-Care Microbiology Test in Diagnosis of Healthcare Associated Infections in a Tertiary Care Pediatric Intensive Care Unit

Background: Rapid and accurate identification of healthcare associated pathogens is crucial for early diagnosis and treatment of infections. This study aimed to assess the performance of a point-of-care multiplex polymerase chain reaction (PCR) in diagnosis of pathogens and their antibiotic resistance genes in bloodstream infections, pneumonia and meningitis/encephalitis in a pediatric intensive care unit (PICU). Methods: A retrospective cross-sectional study was conducted on pediatric patients diagnosed with healthcare associated infections at Alexandria University PICU, Egypt. A total of 111 samples from 98 patients were subjected simultaneously to standard-of-care microbiology testing (SOCMT) and molecular testing by BioFire multiplex PCR. Results: In comparison to SOCMT, the BioFire FilmArray^® had a better diagnostic yield with broncho-alveolar lavage (BAL) (45 vs. 21) and cerebrospinal fluid (CSF) samples (five vs. none) (p ≤ 0.0001). Klebsiella pneumoniae was the most common pathogen in BAL (n = 19 by BioFire, n = 9 by SOCMT) and blood (n = 7, by SOCMT and BioFire) samples, while Streptococcus pneumoniae was the most common in CSF samples. BioFire showed 95.8% overall percent agreement, 100% positive percent agreement and 95.6% negative percent agreement with SOCMT. All phenotypically confirmed resistant isolates had resistance genes by the BioFire FilmArray^® (100%). The turnaround time (TAT) of positive results by the FilmArray panels was 1–1.5 h in comparison to 48–72 h by SOCMT (p ≤ 0.001). Conclusions: The results of the current study confirm the utility of the BioFire FilmArray^® in making early decisions regarding patients’ diagnosis and management of infection in the PICU, in terms of rapid TAT and appropriate antimicrobial use.

Global Threat of Carbapenem-Resistant Gram-Negative Bacteria

Infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Gram-negative bacteria (GNB), including carbapenem-resistant (CR) Enterobacterales (CRE; harboring mainly bla_KPC, bla_NDM, and bla_OXA-48-like genes), CR- or MDR/XDR-Pseudomonas aeruginosa (production of VIM, IMP, or NDM carbapenemases combined with porin alteration), and Acinetobacter baumannii complex (producing mainly OXA-23, OXA-58-like carbapenemases), have gradually worsened and become a major challenge to public health because of limited antibiotic choice and high case-fatality rates. Diverse MDR/XDR-GNB isolates have been predominantly cultured from inpatients and hospital equipment/settings, but CRE has also been identified in community settings and long-term care facilities. Several CRE outbreaks cost hospitals and healthcare institutions huge economic burdens for disinfection and containment of their disseminations. Parenteral polymyxin B/E has been observed to have a poor pharmacokinetic profile for the treatment of CR- and XDR-GNB. It has been determined that tigecycline is suitable for the treatment of bloodstream infections owing to GNB, with a minimum inhibitory concentration of ≤ 0.5 mg/L. Ceftazidime-avibactam is a last-resort antibiotic against GNB of Ambler class A/C/D enzyme-producers and a majority of CR-P. aeruginosa isolates. Furthermore, ceftolozane-tazobactam is shown to exhibit excellent in vitro activity against CR- and XDR-P. aeruginosa isolates. Several pharmaceuticals have devoted to exploring novel antibiotics to combat these troublesome XDR-GNBs. Nevertheless, only few antibiotics are shown to be effective in vitro against CR/XDR-A. baumannii complex isolates. In this era of antibiotic pipelines, strict implementation of antibiotic stewardship is as important as in-time isolation cohorts in limiting the spread of CR/XDR-GNB and alleviating the worsening trends of resistance.

Antibiotic Stewardship Related to Delayed Diagnosis and Poor Prognosis of Critically Ill Patients with Vancomycin-Resistant Enterococcal Bacteremia: A Retrospective Cohort Study

Purpose

Patients with septicemia caused by vancomycin-resistant Enterococcus (VRE) bacteremia have higher mortality rates than patients infected by VSE. Vancomycin or teicoplanin is selected as the antibiotic stewardship intervention to cover methicillin-resistant Staphylococcus aureus infections before blood culture reveals VRE bacteremia in critically ill patients with Gram-positive cocci (GPC) bacteremia; this may require linezolid or daptomycin treatment instead. We thus evaluated antibiotic stewardship practices, such as appropriate timing of antibiotic use in GPC bacteremia, and clinical outcomes of critically ill patients with VRE infection.

Patients and Methods

This retrospective study enrolled 191 critically ill patients with enterococcal bacteremia at the Taipei Tzu Chi Hospital during January 1, 2019–December 31, 2020. Demographic and clinical characteristics, as well as disease outcomes and appropriate antibiotic use after GPC bacteremia diagnosis, were compared between the VRE and VSE groups.

Results

Of 191 patients, 55 had VRE bacteremia (case group) and 136 had VSE bacteremia (control group). The rate of antibiotic change after initial antibiotic use for GPC bacteremia was higher in the VRE bacteremia group (100% vs 10.3%; p<0.001). The time to appropriate antibiotic administration after GPC bacteremia diagnosis was longer in the VRE bacteremia group (3.3±2.1 vs 1.5±1.8 days; p<0.001). Patients with VRE bacteremia had higher 28-day mortality rates (relative risk, 1.997; 95% confidence interval [CI], 1.041–3.83). Multivariate Cox regression analysis showed that delayed appropriate antibiotic administration of >3 days after GPC bacteremia diagnosis increased the risks of 28-day all-cause mortality (adjusted hazard ratio, 2.045; 95% CI, 1.089–3.84; p=0.026) in patients with VRE infection.

Conclusion

Patients with VRE bacteremia with delayed appropriate antibiotic administration of >3 days after GPC bacteremia diagnosis had increased 28-day mortality risks. New strategies for early VRE detection in GPC bacteremia may shorten the time to administer appropriate antibiotics and lower mortality rates.

White paper on antimicrobial stewardship in solid organ transplant recipients

Antimicrobial stewardship programs (ASPs) have made immense strides in optimizing antibiotic, antifungal, and antiviral use in clinical settings. However, although ASPs are required institutionally by regulatory agencies in the United States and Canada, they are not mandated for transplant centers or programs specifically. Despite the fact that solid organ transplant recipients in particular are at increased risk of infections from multidrug-resistant organisms, due to host and donor factors and immunosuppressive therapy, there currently are little rigorous data regarding stewardship practices in solid organ transplant populations, and thus, no transplant-specific requirements currently exist. Further complicating matters, transplant patients have a wide range of variability regarding their susceptibility to infection, as factors such as surgery of transplant, intensity of immunosuppression, and presence of drains or catheters in situ may modify the risk of infection. As such, it is not feasible to have a "one-size-fits-all" style of stewardship for this patient population. The objective of this white paper is to identify opportunities, risk factors, and ASP strategies that should be assessed with solid organ transplant recipients to optimize antimicrobial use, while producing an overall improvement in patient outcomes. We hope it may serve as a springboard for development of future guidance and identification of research opportunities.

Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels

Background

Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST.

Results

A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time.

Conclusion

In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02403-y.

Streptococcus gallolyticus - A potentially neglected pathogen causing neonatal sepsis not covered by routine group B streptococcus screening

We report 4 cases of neonatal sepsis caused by Streptococcus gallolyticus. The clinical course was quite similar to early-and late-onset group B streptococcus disease. None of the mothers had group B streptococcus (GBS) colonization on prenatal screening nor received intrapartum antibiotics. We proposed the sporadic distribution of S. gallolyticus sepsis among neonates was partly due to relatively low colonization rate in adults compared with GBS. Species determination of S. gallolyticus may not be available using conventional microbiological methods and may contribute to underestimation or misclassification. In our series, we highlighted the importance of S. gallolyticus as an important pathogen in neonatal sepsis deserving further surveillance.

Diagnostic accuracy of the BioFire FilmArray blood culture identification panel when used in critically ill patients with sepsis

Sepsis accounts for high mortality rates in critical care units. Prompt and accurate identification of causative pathogens and initiation of appropriate antimicrobial therapy is critical for the appropriate management of patients in order to optimise clinical outcomes. The BioFire FilmArray blood culture identification (BCID) panel is a US Food and Drug Administration (FDA) approved rapid, multiplex polymerase chain reaction (PCR) assay that is able to identify a variety of bacteria, fungi and antimicrobial resistance determinants directly from positive blood cultures. The aim of this study was to evaluate the diagnostic performance of the BioFire FilmArray BCID panel against the gold standard of blood cultures. Seventy-eight positive blood cultures obtained from critically ill patients suspected of having sepsis were included in the study. Each bottle was processed with the BioFire FilmArray BCID panel as well as conventional culture methods. Diagnostic accuracy of the BioFire FilmArray BCID panel was determined. The assay demonstrated a high sensitivity and specificity for pathogen identification of 96.5% (95% CI, 91.3-99.0) and 99.7% (95% CI, 99.3-99.9), respectively. The findings of this study support the role of the BioFire FilmArray BCID panel in the management of critically ill patients with sepsis.

Rapid molecular detection of pathogenic microorganisms and antimicrobial resistance markers in blood cultures: evaluation and utility of the next-generation FilmArray Blood Culture Identification 2 panel

Rapid detection of pathogens causing bloodstream infections (BSI) directly from positive blood cultures is of highest importance in order to enable an adequate and timely antimicrobial therapy. In this study, the utility and performance of a recently launched next-generation fully automated test system, the Biofire FilmArray® Blood Culture Identification 2 (BCID2) panel, was evaluated using a set of 103 well-characterized microbial isolates including 29 antimicrobial resistance genes and 80 signal-positive and 23 signal-negative clinical blood culture samples. The results were compared to culture-based reference methods, MALDI-TOF, and/or 16S rDNA sequencing. Of the clinical blood culture samples, 68 were monomicrobial (85.0%) and 12 polymicrobial (15.0%). Six samples contained ESBL (bla_CTX-M), two MRSA (mecA), and three MRSE (mecA) isolates. In overall, the FilmArray BCID2 panel detected well on-panel targets and resistance markers from mono- and polymicrobial samples. However, one Klebsiella aerogenes and one Bacteroides ovatus were undetected, and the assay falsely reported one Shigella flexneri as Escherichia coli. Hence, the sensitivity and specificity for detecting microbial species were 98.8% (95%CI, 95.8–99.9%) and 99.9% (95%CI, 99.8–99.9%), respectively. The sensitivity and specificity for detecting of resistance gene markers were 100%. The results were available within 70 min from signal-positive blood cultures with minimal hands-on time. In conclusion, the BCID2 test allows reliable and simplified detection of a vast variety of clinically relevant microbes causing BSI and the most common antimicrobial resistance markers present among these isolates.

Clinical utility of the BioFire FilmArray Blood Culture Identification panel in the adjustment of empiric antimicrobial therapy in the critically ill septic patient

Sepsis and septic shock are key contributors to mortality in critically ill patients and thus prompt recognition and management thereof is central to achieving improved patient outcomes. Early initiation of appropriate antimicrobial therapy constitutes a crucial component of the management strategy and thus early identification of the causative pathogen is essential in informing antimicrobial therapeutic choices. The BioFire FilmArray blood culture identification (BCID) panel is a US Food and Drug Administration (FDA) approved rapid, multiplex polymerase chain reaction assay for use on positive blood cultures. This study evaluated its clinical utility in the intensive care unit (ICU) setting, in terms of amendment of empiric antimicrobial therapy in critically ill patients with sepsis. The assay proved useful in this setting as final results were made available to clinicians significantly earlier than with conventional culture methods. This, in turn, allowed for modification of empirical antimicrobial therapy to more appropriate agents in 32% of patients. Additionally, the use of the BioFire FilmArray BCID panel permitted the prompt implementation of additional infection prevention and control practices in a sizeable proportion (14%) of patients in the study who were harbouring multidrug resistant pathogens. These findings support the use of the BioFire FilmArray BCID panel as a valuable adjunct to conventional culture methods for the diagnosis and subsequent management of critically ill patients with sepsis.

An Artificial Intelligence Approach to Bloodstream Infections Prediction

This study aimed to develop an early prediction model for identifying patients with bloodstream infections. The data resource was taken from 2015 to 2019 at Taichung Veterans General Hospital, and a total of 1647 bloodstream infection episodes and 3552 non-bloodstream infection episodes in the intensive care unit (ICU) were included in the model development and evaluation. During the data analysis, 30 clinical variables were selected, including patients’ basic characteristics, vital signs, laboratory data, and clinical information. Five machine learning algorithms were applied to examine the prediction model performance. The findings indicated that the area under the receiver operating characteristic curve (AUROC) of the prediction performance of the XGBoost model was 0.825 for the validation dataset and 0.821 for the testing dataset. The random forest model also presented higher values for the AUROC on the validation dataset and testing dataset, which were 0.855 and 0.851, respectively. The tree-based ensemble learning model enabled high detection ability for patients with bloodstream infections in the ICU. Additionally, the analysis of importance of features revealed that alkaline phosphatase (ALKP) and the period of the central venous catheter are the most important predictors for bloodstream infections. We further explored the relationship between features and the risk of bloodstream infection by using the Shapley Additive exPlanations (SHAP) visualized method. The results showed that a higher prothrombin time is more prominent in a bloodstream infection. Additionally, the impact of a lower platelet count and albumin was more prominent in a bloodstream infection. Our results provide additional clinical information for cut-off laboratory values to assist clinical decision-making in bloodstream infection diagnostics.

Leapfrogging laboratories: the promise and pitfalls of high-tech solutions for antimicrobial resistance surveillance in low-income settings

The scope and trajectory of today’s escalating antimicrobial resistance (AMR) crisis is inadequately captured by existing surveillance systems, particularly those of lower income settings. AMR surveillance systems typically collate data from routine culture and susceptibility testing performed in diagnostic bacteriology laboratories to support healthcare. Limited access to high quality culture and susceptibility testing results in the dearth of AMR surveillance data, typical of many parts of the world where the infectious disease burden and antimicrobial need are high. Culture and susceptibility testing by traditional techniques is also slow, which limits its value in infection management. Here, we outline hurdles to effective resistance surveillance in many low-income settings and encourage an open attitude towards new and evolving technologies that, if adopted, could close resistance surveillance gaps. Emerging advancements in point-of-care testing, laboratory detection of resistance through or without culture, and in data handling, have the potential to generate resistance data from previously unrepresented locales while simultaneously supporting healthcare. Among them are microfluidic, nucleic acid amplification technology and next-generation sequencing approaches. Other low tech or as yet unidentified innovations could also rapidly accelerate AMR surveillance. Parallel advances in data handling further promise to significantly improve AMR surveillance, and new frameworks that can capture, collate and use alternate data formats may need to be developed. We outline the promise and limitations of such technologies, their potential to leapfrog surveillance over currently available, conventional technologies in use today and early steps that health systems could take towards preparing to adopt them.

Evaluation of the BioFire Blood Culture Identification 2 panel and impact on patient management and antimicrobial stewardship

Bloodstream infection survival is linked to timely administration of optimal antimicrobial therapy. Commercial multiplex polymerase chain reaction (PCR) assays, such as the BioFire Blood Culture Identification Panel (BCID) used for the rapid diagnosis of bloodstream infections, have significantly improved the turnaround time for optimisation of antimicrobial therapy. Reported concordance with culture-based methods and multiplex PCR analysis is high and only limited by (1) the range of targets available on the multiplex panel; and (2) the complexity of microorganisms present in the blood culture specimen. In this study, we evaluated the use of the BioFire Blood Culture Identification 2 panel (BCID2), including an expanded repertoire of targets for Gram-positive and Gram-negative bacteria, yeast and antimicrobial resistance genes compared to the BCID panel. The BCID2 panel identified microorganisms in 39/42 (92.9%) blood cultures where monomicrobial growth was detected; the three unidentified blood cultures contained organisms not included in the BCID2 panel. Polymicrobial blood culture analysis revealed a lower degree of concordance (28.6%); however, most disagreement was due to the culture-based identification of off-panel microorganisms of low clinical significance. Turnaround time, from blood culture collection to organism identification on the blood cultures correctly identified by BCID2, was 24.6 (±16.8) hours for the BCID2 panel versus 38.2 (±21.9) hours for conventional methods. Analysis of the theoretical impact of the BCID2 identification on clinical management found therapy would be altered in 45.1% (23/51) of patients. The BCID2 panel is anticipated to improve the diagnosis and antimicrobial management of patients with serious bloodstream infections.

Impact of 24/7 loading of blood culture bottles in a new automated incubator on the diagnosis of bloodstream infections

Blood culturing (BC) remains the gold standard for bloodstream diagnosis but its workflow is slow. We aimed reducing this time by implementing a new automated incubator with a 24/7 BC workflow. With this new strategy, time to incubation was shorter (1.52 h vs 6.82 h), positivity rates were higher (10.6% vs 8.9%, p<0.05), and the number of BSI diagnostics increased (16.1% vs 13.8% patients and 2.3 vs 1.9 density episode per 1000 hospital days). Our results show that implementing automatic loading of BC bottles with a 24/7 strategy not only shortened time to diagnosis but significantly increased the BSI diagnosis rate.

Recent advances in rapid antimicrobial susceptibility testing systems

INTRODUCTION

Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged.

AREAS COVERED

Advances in rapid phenotypic and molecular-based AST systems.

EXPERT OPINION

AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.

Management of Pediatric Nonpathogenic Blood Cultures After Introduction of PCR Technology

BACKGROUND

The rapid identification of organisms reported in positive blood cultures via polymerase chain reaction (PCR) can accurately identify a nonpathogenic bacterium and decrease time to definitive identification, as compared with traditional microbiologic methods. How this technology effects clinical and antimicrobial management in children with nonpathogenic bacteria identified in a blood culture without decision support has not been evaluated.

METHODS

A retrospective study of the management of children with positive blood culture results for nonpathogenic organisms before and after implementation of PCR technology. Each cohort's antibiotic management, frequency of repeat cultures, and return visits to an emergency department (ED) were compared.

RESULTS

A total 136 patients during this time (49% [n = 67] pre-PCR and 51% [n = 69] post-PCR) had a blood culture positive for nonpathogenic bacterium. Admitted patients had a second specimen sent for testing on fewer occasions (P = .04); however, total antibiotic exposure did not differ significantly (P = .3) after introduction of PCR technology. There was no significant difference in length of stay postintervention (P = .12). Patients discharged directly from the ED had fewer return visits (P = .02) and received fewer repeat blood cultures (P = .04), and antibiotics were administered on fewer occasions after return (P = .04) postintroduction of PCR technology.

CONCLUSIONS

With the addition of PCR technology, patients with blood cultures positive for nonpathogenic bacteria received less antibiotics, fewer repeat blood cultures, and fewer repeat ED evaluations.

Accurate detection of oxacillin-resistant Staphylococcus lugdunensis by use of agar dilution

BACKGROUND/PURPOSE

Staphylococcus lugdunensis is a Gram-positive coagulase-negative bacterium and is recognized as a critical pathogenic species recently. Here, we aimed to evaluate the cefoxitin disk diffusion (CDD), oxacillin agar dilution (OAD), and mecA PCR for detecting oxacillin-resistant S. lugdunensis (ORSL) isolates.

METHODS

Multilocus sequence typing (MLST) analysis was performed to determine the clonality of 117 S. lugdunensis isolates isolated between May 2009 and Jul 2014. CDD, OAD, and mecA PCR were used to identify oxacillin-resistant S. lugdunensis (ORSL).

RESULTS

MLST results showed that the most common sequence type (ST) of our S. lugdunensis isolates was ST6 (35.9%) followed by ST3 (28.2%), ST27 (17.9%), and ST4 (6.8%). CDD and OAD showed that 39 and 43 isolates were ORSL, respectively. 4 ST3 CDD-susceptible S. lugdunensis (OSSL) isolates had MIC values ≥ 4 for oxacillin. mecA PCR results showed that 43 OAD-resistant S. lugdunensis and 3 OAD-susceptible ST27 S. lugdunensis had the mecA gene. Therefore, OAD was used as the gold standard to evaluate the performance of CDD and mecA PCR for identifying ORSL. The overall sensitivity, specificity, and accuracy of CCD for ORSL detection was 90.7%, 100%, and 96.8%, respectively. The sensitivity, specificity, and accuracy of mecA PCR for identifying ORSL was 100%, 95.9%, and 97.44%, respectively.

CONCLUSION

Our results indicate that OAD shows higher accuracy for ORSL detection compared with CDD and mecA PCR.

Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact

Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.

Rapid detection of antimicrobial resistance markers with Allplex™ Entero-DR assay directly from positive blood culture bottles

A method for rapid detection of one extended-spectrum β-lactamase (ESBL) and five carbapenemase-encoding genes as well as vancomycin resistance markers directly from blood cultures using the Allplex™ Entero-DR assay (Seegene, Seoul, South Korea) is presented. Altogether 28 previously well-characterized resistant Gram-negative bacilli and Enterococcus spp., and 142 clinical blood cultures containing Gram-negative bacilli or Gram-positive cocci were analyzed. The method had 100% sensitivity and specificity for detecting bla_OXA-48-like, bla_KPC, bla_VIM, bla_IMP, bla_NDM, bla_CTX-M, vanA, and vanB. The lowest detectable amount of viable cells in blood culture samples were 5.39·10⁴ CFU/mL, 6.66·10⁴ CFU/mL, 5.13·10³ CFU/mL, 6.09·10⁴ CFU/mL, 6.66·10⁴ CFU/mL, 6.66·10⁴ CFU/mL, 3.12·10⁴ CFU/mL, and 5.34·10⁴ CFU/mL for the bla_KPC, bla_OXA-48-like, bla_VIM, bla_IMP, bla_NDM, bla_CTX-M, vanA, and vanB, respectively. The results were available within 90 min from signal positive blood cultures, as no separate DNA extraction steps were needed, and the assay showed no interference from blood or culture media used allowing reliable and simplified detection of the resistance markers.