Multicenter evaluation of a syndromic rapid multiplex PCR test for early adaptation of antimicrobial therapy in adult patients with pneumonia

Advancing quantitative PCR with color cycle multiplex amplification

Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.

Diagnostic Accuracy of Blind Bronchial Sample Testing by BioFire Pneumonia plus Panel in Pediatric Intensive Care Unit Patients and Its Impact in Early Adaptation of Antimicrobial Therapy: A Prospective Observational Study

BACKGROUND

Community-acquired and nosocomial lower-respiratory-tract infections in critically ill pediatric patients require early appropriate antibiotic therapy to optimize outcomes. Using blind bronchial samples, we assessed the diagnostic performance of the rapid-multiplex polymerase chain reaction (PCR) assay BioFire Pneumonia plus Panel vs. reference standard culturing with antimicrobial susceptibility testing.

METHODS

For this prospective observational study in a single pediatric intensive care unit, we included consecutive patients younger than 18 years admitted for suspected community-, hospital- or ventilator-associated pneumonia in 2021-2022. Sensitivity, specificity, positive predictive value and negative predictive value of the multiplex PCR assay were determined. The kappa coefficient was computed to assess agreement, and univariate analyses were done to identify factors associated with discrepancies between the 2 diagnostic methods.

RESULTS

Of the 36 included patients (median age, 1.4 years; interquartile range, 0.2-9.2), 41.7%, 27.8%, and 30.5% had community-, hospital- and ventilator-associated pneumonia, respectively. The overall κ was 0.74, indicating good agreement. Overall, the sensitivity of the multiplex PCR assay was 92% (95% CI: 77%-98%) and specificity 95% (95% CI: 92%-97%), with variations across microorganisms. The median time from sample collection to antimicrobial susceptibility test results was 3.9 (2.5-15) hours with the multiplex PCR assay and 60.5 (47.6-72.2) hours with the reference technique.

CONCLUSION

The BioFire Pneumonia plus Panel used to test blind bronchial samples had satisfactory diagnostic performance in critically ill pediatric patients. The rapid results provided by this test may improve the appropriateness of antimicrobial therapy and help minimize the use of antibiotics.

Ventilator-associated pneumonia: pathobiological heterogeneity and diagnostic challenges

Ventilator-associated pneumonia (VAP) affects up to 20% of critically ill patients and induces significant antibiotic prescription pressure, accounting for half of all antibiotic use in the ICU. VAP significantly increases hospital length of stay and healthcare costs yet is also associated with long-term morbidity and mortality. The diagnosis of VAP continues to present challenges and pitfalls for the currently available clinical, radiological and microbiological diagnostic armamentarium. Biomarkers and artificial intelligence offer an innovative potential direction for ongoing future research. In this Review, we summarise the pathobiological heterogeneity and diagnostic challenges associated with VAP.

Case Report: Severe Community-Acquired Pneumonia in Réunion Island due to Acinetobacter baumannii

Acinetobacter baumannii (Ab) is a well-known nosocomial pathogen that has emerged as a cause of community-acquired pneumonia (CAP) in tropical regions. Few global epidemiological studies of CAP-Ab have been published to date, and no data are available on this disease in France. We conducted a retrospective chart review of severe cases of CAP-Ab admitted to intensive care units in Réunion University Hospital between October 2014 and October 2022. Eight severe CAP-Ab cases were reviewed. Median patient age was 56.5 years. Sex ratio (male-to-female) was 3:1. Six cases (75.0%) occurred during the rainy season. Chronic alcohol use and smoking were found in 75.0% and 87.5% of cases, respectively. All patients presented in septic shock and with severe acute respiratory distress syndrome. Seven patients (87.5%) presented in cardiogenic shock, and renal replacement therapy was required for six patients (75.0%). Five cases (62.5%) presented with bacteremic pneumonia. The mortality rate was 62.5%. The median time from hospital admission to death was 3 days. All patients received inappropriate initial antibiotic therapy. Acinetobacter baumannii isolates were all susceptible to ceftazidime, cefepime, piperacillin-tazobactam, ciprofloxacin, gentamicin, and imipenem. Six isolates (75%) were also susceptible to ticarcillin, piperacillin, and cotrimoxazole. Severe CAP-Ab has a fulminant course and high mortality. A typical case is a middle-aged man with smoking and chronic alcohol use living in a tropical region and developing severe CAP during the rainy season. This clinical presentation should prompt administration of antibiotic therapy targeting Ab.

Interpreting the results of rapid molecular diagnostic tests for carbapenem-resistant Enterobacterales infection: current clinical perspective while waiting for further evidence

INTRODUCTION

Carbapenem-resistant Enterobacterales (CRE) causing severe infections in humans have represented an important challenge for clinicians worldwide during the past two decades.

AREAS COVERED

Novel β-lactams and β-lactam/β-lactamase inhibitor combinations have led to a shift in the first-line approach to the treatment of severe CRE infections from polymyxin-based regimens to treatment with less toxic agents. This new scenario offers the opportunity to apply rapid molecular diagnostic tests for CRE infection to identify different types of carbapenemases. Herein, the authors provide an overview of this subject and follow it with their expert perspectives.

EXPERT OPINION

When considering studies actually measuring the clinical impact of rapid molecular tests in real-life scenarios, high certainty evidence from randomized controlled trials is still limited and not focused on CRE infections. Nonetheless, it is indisputable that rapid molecular tests have been shown to impact early therapeutic choices (in terms of both escalation and de-escalation) when used in real-life settings, thus issues in the clinical interpretation of their results are already relevant. Overall, increased expertise is required for the appropriate interpretation of rapid molecular tests for personalized antibiotic selection by understanding their strengths and limitations.

Severe Community-Acquired Pneumonia in Immunocompromised Patients

Due to higher survival rates with good quality of life, related to new treatments in the fields of oncology, hematology, and transplantation, the number of immunocompromised patients is increasing. But these patients are at high risk of intensive care unit admission because of numerous complications. Acute respiratory failure due to severe community-acquired pneumonia is one of the leading causes of admission. In this setting, the need for invasive mechanical ventilation is up to 60%, associated with a high hospital mortality rate of around 40 to 50%. A wide range of pathogens according to the reason of immunosuppression is associated with severe pneumonia in those patients: documented bacterial pneumonia represents a third of cases, viral and fungal pneumonia both account for up to 15% of cases. For patients with an undetermined etiology despite comprehensive diagnostic workup, the hospital mortality rate is very high. Thus, a standardized diagnosis strategy should be defined to increase the diagnosis rate and prescribe the appropriate treatment. This review focuses on the benefit-to-risk ratio of invasive or noninvasive strategies, in the era of omics, for the management of critically ill immunocompromised patients with severe pneumonia in terms of diagnosis and oxygenation.

Microbiology of Severe Community-Acquired Pneumonia and the Role of Rapid Molecular Techniques

The microbiology of severe community acquired pneumonia (SCAP) has implications on management, clinical outcomes and public health policy. Therefore, knowledge of the etiologies of SCAP and methods to identify these microorganisms is key. Bacteria including Streptococcus pneumoniae, Staphylococcus aureus and Enterobacteriaceae continue to be important causes of SCAP. Viruses remain the most commonly identified etiology of SCAP. Atypical organisms are also important etiologies of SCAP and are critical to identify for public health. With the increased number of immunocompromised individuals, less common pathogens may also be found as the causative agent of SCAP. Traditional diagnostic tests, including semi-quantitative respiratory cultures, blood cultures and urinary antigens continue to hold an important role in the evaluation of patients with SCAP. Many of the limitations of the aforementioned tests are addressed by rapid, molecular diagnostic tests. Molecular diagnostics utilize culture-independent technology to identify species-specific genetic sequences. These tests are often semi-automated and provide results within hours, which provides an opportunity for expedient antibiotic stewardship. The existing literature suggests molecular diagnostic techniques may improve antibiotic stewardship in CAP, and future research should investigate optimal methods for implementation of these assays into clinical practice.

Risk of Multidrug-Resistant Pathogens in Severe Community-Acquired Pneumonia

Severe community-acquired pneumonia (SCAP) is difficult to treat when caused by difficult-to-treat (DTR) pathogens because of limited treatment options and poorer clinical outcomes. Over time, several predictive scoring systems based on risk factors for infection with multidrug resistant pathogens have been developed. We reviewed the available tools for identifying DTR pathogens as the cause of SCAP, both predictive scoring systems and rapid diagnostic methods, to develop management strategies aimed at early identification of DTR pathogens, reducing broad-spectrum antibiotic use and improving clinical outcomes. The scoring systems reviewed show considerable heterogeneity among them at the level of the region studied, the definition of risk factors, as well as which DTR pathogens are the target pathogens. The models described have shown limited effectiveness in reducing inappropriate antibiotic treatment or improving patient outcomes by themselves. However, predictive models could serve as a first step in identifying DTR pathogen infections as part of a larger detection algorithm. Rapid diagnostic tools, such as multiplex polymerase chain reaction, would be useful for the rapid identification of pneumonia-causing pathogens and their resistance mechanisms. In resource-limited settings, rapid tests should be limited to patients at high risk of developing SCAP due to DTR pathogens. We propose an integrative algorithm based on the different scores, taking into account local epidemiological data, where ideally each center should have an antimicrobial stewardship program.

Challenges for a broad international implementation of the current severe community-acquired pneumonia guidelines

Severe community-acquired pneumonia (sCAP) remains one of the leading causes of admission to the intensive care unit, thus consuming a large share of resources and is associated with high mortality rates worldwide. The evidence generated by clinical studies in the last decade was translated into recommendations according to the first published guidelines focusing on severe community-acquired pneumonia. Despite the advances proposed by the present guidelines, several challenges preclude the prompt implementation of these diagnostic and therapeutic measures. The present article discusses the challenges for the broad implementation of the sCAP guidelines and proposes solutions when applicable.

Clinical evaluation of the BioFire Respiratory Pathogen Panel for the guidance of empirical antimicrobial therapy in critically ill patients with hospital-acquired pneumonia: A multicenter, quality improvement project

BACKGROUND

We aimed to determine whether implementing antimicrobial stewardship based on multiplex bacterial PCR examination of respiratory fluid can enhance outcomes of critically ill patients with hospital-acquired pneumonia (HAP).

METHODS

We conducted a quality improvement study in two hospitals in France. Adult patients requiring invasive mechanical ventilation with a diagnosis of HAP were included. In the pre-intervention period (August 2019 to April 2020), antimicrobial therapy followed European guidelines. In the «intervention» phase (June 2020 to October 2021), treatment followed a multiplex PCR-guided protocol. The primary endpoint was a composite endpoint made of mortality on day 28, clinical cure between days 7 and 10, and duration of invasive mechanical ventilation on day 28. The primary outcome was analyzed with a DOOR strategy.

RESULTS

A total of 443 patients were included in 3 ICUs from 2 hospitals (220 pre-intervention; 223 intervention). No difference in the ranking of the primary composite outcome was found (DOOR: 50.3%; 95%CI, 49.9%-50.8%). The number of invasive mechanical ventilation-free days at day 28 was 10.0 [0.0; 19.0] in the baseline period and 9.0 [0.0; 20.0] days during the intervention period (p = 0.95). The time-to-efficient antimicrobial treatment was 0.43 ± 1.29 days before versus 0.55 ± 1.13 days after the intervention (p = 0.56).

CONCLUSION

Implementation of Rapid Multiplex PCR to guide empirical antimicrobial therapy for critically ill patients with HAP was not associated with better outcomes. However, adherence to stewardship was low, and the study may have had limited power to detect a clinically important difference.

Application of a multiplex molecular pneumonia panel and real-world impact on antimicrobial stewardship among patients with hospital-acquired and ventilator-associated pneumonia in intensive care units

BACKGROUND

The optimal timing for applying the BioFire FilmArray Pneumonia Panel (FAPP) in intensive care unit (ICU) patients with hospital-acquired pneumonia (HAP) or ventilator-associated pneumonia (VAP) remains undefined, and there are limited data on its impact on antimicrobial stewardship.

METHODS

This retrospective study was conducted at a referral hospital in Taiwan from November 2019 to October 2022. Adult ICU patients with HAP/VAP who underwent FAPP testing were enrolled. Patient data, FAPP results, conventional microbiological testing results, and the real-world impact of FAPP results on antimicrobial therapy adjustments were assessed. Logistic regression was used to determine the predictive factors for bacterial detection by FAPP.

RESULTS

Among 592 respiratory specimens, including 564 (95.3%) endotracheal aspirate specimens, 19 (3.2%) expectorated sputum specimens and 9 (1.5%) bronchoalveolar lavage specimens, from 467 patients with HAP/VAP, FAPP testing yielded 368 (62.2%) positive results. Independent predictors for positive bacterial detection by FAPP included prolonged hospital stay (odds ratio [OR], 3.14), recent admissions (OR, 1.59), elevated C-reactive protein levels (OR, 1.85), Acute Physiology and Chronic Health Evaluation II scores (OR, 1.58), and septic shock (OR, 1.79). Approximately 50% of antimicrobial therapy for infections caused by Gram-negative bacteria and 58.4% for Gram-positive bacteria were adjusted or confirmed after obtaining FAPP results.

CONCLUSIONS

This study identified several factors predicting bacterial detection by FAPP in critically ill patients with HAP/VAP. More than 50% real-world clinical practices were adjusted or confirmed based on the FAPP results. Clinical algorithms for the use of FAPP and antimicrobial stewardship guidelines may further enhance its benefits.

Impact of Multiplex PCR in the Therapeutic Management of Severe Bacterial Pneumonia

Pneumonia is a common and severe illness that requires prompt and effective management. Advanced, rapid, and accurate tools are needed to diagnose patients with severe bacterial pneumonia, and to rapidly select appropriate antimicrobial therapy, which must be initiated within the first few hours of care. Two multiplex molecular tests, Unyvero HPN and FilmArray Pneumonia+ Panel, have been developed using the multiplex polymerase chain reaction (mPCR) technique to rapidly identify pathogens and their main antibiotic resistance mechanisms from patient respiratory specimens. Performance evaluation of these tests showed strong correlations with reference techniques. However, good knowledge of their indications, targets, and limitations is essential. Collaboration with microbiologists is, therefore, crucial for their appropriate use. Under these conditions, and with standardized management, these rapid tests can improve the therapeutic management of severe pneumonia faster, more precisely, and with narrow-spectrum antibiotic therapy. Further randomized controlled trials are needed to address the many unanswered questions about multiplex rapid molecular testing during the diagnosis and the management of severe pneumonia. This narrative review will address the current knowledge, advantages, and disadvantages of these tests, and propose solutions for their routine use.

Real-life Assessment of BioFire FilmArray Pneumonia Panel in Adults Hospitalized With Respiratory Illness

BACKGROUND

Inability to identify the microbial etiology of lower respiratory tract infection leads to unnecessary antibiotic use. We evaluated the utility of the BioFire FilmArray Pneumonia Panel (BioFire PN) to inform microbiologic diagnosis.

METHODS

Hospitalized adults with respiratory illness were recruited; sputa and clinical/laboratory data were collected. Sputa were cultured for bacteria and tested with BioFire PN. Microbial etiology was adjudicated by 4 physicians. Bacterial polymerase chain reaction (PCR) was compared with culture and clinical adjudication.

RESULTS

Of 298 sputa tested, BioFire PN detected significantly more pathogens (350 bacteria, 16 atypicals, and 164 viruses) than sputum culture plus any standard-of-care testing (91% vs 60%, P < .0001). When compared with culture, the sensitivity of BioFire PN for individual bacteria was 46% to 100%; specificity, 61% to 100%; and negative predictive value, 92% to 100%. Cases were adjudicated as viral (n = 58) and bacterial (n = 100). PCR detected bacteria in 55% of viral cases and 95% of bacterial (P < .0001). High serum procalcitonin and bacterial adjudication were more often associated with sputa with 106 or 107 copies detected.

CONCLUSIONS

Multiplex PCR testing of sputa for bacteria is useful to rule out bacterial infection with added value to detect viruses and atypical bacteria.

Optimized Antibiotic Management of Critically Ill Patients with Severe Pneumonia Following Multiplex Polymerase Chain Reaction Testing: A Prospective Clinical Exploratory Trial

Molecular diagnostic testing is assumed to enable fast respiratory pathogen identification and contribute to improved pneumonia management. We set up a prospective clinical trial at a tertiary hospital intensive care unit including adult patients suspected of severe pneumonia from whom a lower respiratory tract sample could be obtained. During control periods (CPs), routine testing was performed, and during intervention periods (IPs), this testing was completed with the FilmArray Pneumonia Panel plus test (FA-PNEU) executed 24/7. The main objective was to measure the impact of FA-PNEU results in terms of reduced time to targeted antimicrobial treatment administration. Over a 10-month period, analysis was performed on 35 CP and 50 IP patients. The median time to targeted antimicrobial treatment administration was reduced to 4.3 h in IPs compared to 26.4 h in CPs, with 54% of IP patients having FA-PNEU results that led to a treatment modification, of which all but one were targeted. Modifications included 10 (37%) de-escalations, 7 (25.9%) escalations, 3 (11.1%) regimen switches, and 7 (25.9%) complete antimicrobial discontinuations. FA-PNEU results were available with a 42.3 h gain compared to routine identification. This prospective study confirmed retrospective data demonstrating the benefit of FA-PNEU testing in severe pneumonia management of critically ill patients through improved antimicrobial use.

Performance evaluation of a PCR panel (FilmArray® Pneumonia Plus) for detection of respiratory bacterial pathogens in respiratory specimens: A systematic review and meta-analysis

BACKGROUND

Accuracy and timing of antibiotic therapy remain a challenge for lower respiratory tract infections. New molecular techniques using Multiplex Polymerase Chain Reaction, including the FilmArray® Pneumonia Plus Panel [FAPP], have been developed to address this. The aim of this study is to evaluate the FAPP diagnostic performance for the detection of the 15 typical bacteria of the panel from respiratory samples in a meta-analysis from a systematic review.

METHODS

We searched PubMed and EMBASE from January 1, 2010, to December 31, 2022, and selected any study on the FAPP diagnostic performance on respiratory samples compared to the reference standard, bacterial culture. The main outcome was the overall diagnostic accuracy with sensitivity and specificity. We calculated the log Diagnostic Odds Ratio and analyzed performance for separate bacteria, antimicrobial resistance genes, and according to the sample type. We also reported the FAPP turnaround time and the out-of-panel bacteria number and species. This study is registered with PROSPERO (CRD42021226280).

RESULTS

From 10 317 records, we identified 30 studies including 8 968 samples. Twenty-one were related to intensive care. The overall sensitivity and specificity were 94% [95% Confidence Interval (CI) 91-95] and 98% [95%CI 97-98], respectively. The log Diagnostic Odds Ratio was 6.35 [95%CI 6.05-6.65]. 9.3% [95%CI 9.2-9.5] of bacteria detected in culture were not included in the FAPP panel.

CONCLUSION

This systematic review reporting the FAPP evaluation revealed a high accuracy. This test may represent an adjunct tool for pulmonary bacterial infection diagnostic and antimicrobial stewardship. Further evidence is needed to assess the impact on clinical outcome.

Performance and Impact on Antibiotic Prescriptions of a Multiplex PCR in a Real-Life Cohort of Critically Ill Patients with Suspected Ventilated Pneumonia: A Retrospective Monocentric Observational Study

Pulmonary multiplex polymerase chain reaction (m-PCR) allows rapid pathogen detection. We aimed to assess its impact on initial antibiotic prescriptions in ventilated patients with suspected pneumonia. Between November 2020 and March 2022,ventilated patients with suspected pneumonia hospitalized in our ICU who benefited from respiratory sampling simultaneously tested using conventional microbiological methods and m-PCR were included. The proportion of appropriate changes in the initial antibiotic therapy following m-PCR results was assessed. We analyzed 104 clinical samples. Of the 47 negative m-PCR results, 16 (34%) led to an appropriate antibiotic strategy: 8 cessationsand 8 lack of initiation. Of the 57 positive m-PCR results, 51 (89%) resulted in an appropriate antibiotic strategy: 33 initiations, 2 optimizations, and 9 de-escalations. In the multivariate analysis, a positive m-PCR was associated with an appropriate antibiotic change (OR: 96.60; IC95% [9.72; 960.20], p < 0.001). A higher SAPS II score was negatively associated with an appropriate antibiotic change (OR: 0.96; IC95% [0.931; 0.997], p = 0.034). In our cohort, a positive m-PCR allowed for early initiation or adjustment of antibiotic therapy in almost 90% of cases. A negative m-PCR spared antibiotic use in onethird of cases. The impact of m-PCR results was reduced in the most severe patients.

Ten Issues for Updating in Community-Acquired Pneumonia: An Expert Review

Community-acquired pneumonia represents the third-highest cause of mortality in industrialized countries and the first due to infection. Although guidelines for the approach to this infection model are widely implemented in international health schemes, information continually emerges that generates controversy or requires updating its management. This paper reviews the most important issues in the approach to this process, such as an aetiologic update using new molecular platforms or imaging techniques, including the diagnostic stewardship in different clinical settings. It also reviews both the Intensive Care Unit admission criteria and those of clinical stability to discharge. An update in antibiotic, in oxygen, or steroidal therapy is presented. It also analyzes the management out-of-hospital in CAP requiring hospitalization, the main factors for readmission, and an approach to therapeutic failure or rescue. Finally, the main strategies for prevention and vaccination in both immunocompetent and immunocompromised hosts are reviewed.

Antimicrobial Multidrug Resistance: Clinical Implications for Infection Management in Critically Ill Patients

The increasing incidence of antimicrobial resistance (AMR) worldwide represents a serious threat in the management of sepsis. Due to resistance to the most common antimicrobials prescribed, multidrug-resistant (MDR) pathogens have been associated with delays in adequate antimicrobial therapy leading to significant increases in mortality, along with prolonged hospital length of stay (LOS) and increases in healthcare costs. In response to MDR infections and the delay of microbiological results, broad-spectrum antibiotics are frequently used in empirical antimicrobial therapy. This can contribute to the overuse and misuse of antibiotics, further promoting the development of resistance. Multiple measures have been suggested to combat AMR. This review will focus on describing the epidemiology and trends concerning MDR pathogens. Additionally, it will explore the crucial aspects of identifying patients susceptible to MDR infections and optimizing antimicrobial drug dosing, which are both pivotal considerations in the fight against AMR. Expert commentary: The increasing AMR in ICUs worldwide makes the empirical antibiotic therapy challenging in septic patients. An AMR surveillance program together with improvements in MDR identification based on patient risk stratification and molecular rapid diagnostic tools may further help tailoring antimicrobial therapies and avoid unnecessary broad-spectrum antibiotics. Continuous infusions of antibiotics, therapeutic drug monitoring (TDM)-based dosing regimens and combination therapy may contribute to optimizing antimicrobial therapy and limiting the emergence of resistance.

Supporting Clinical Decisions with Rapid Molecular Diagnostic Pneumonia Panel in Pediatric Intensive Care Unit: Single Center Experience in Turkiye

INTRODUCTION

Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. It is crucial to promptly conduct diagnostic investigations in order to determine the microbiological cause of pneumonia, since this is necessary to ensure the appropriate delivery of antibiotic therapy to each individual patient. We evaluated the results of a rapid molecular diagnostic pneumonia panel in children with LRTI in a pediatric intensive care unit (PICU).

PATIENTS AND METHODS

Rapid molecular diagnostic pneumonia panel (BioFire®, FilmArray Pneumonia Panel plus; FA-PP) findings (71 results from 46 children) in a tertiary care PICU between 2019 and 2023 were retrospectively reviewed.

RESULTS

At least one bacterial pathogen was detected in 57 cases. A total of 77% of children had underlying conditions. A total of 70.4% of children needed invasive mechanical ventilation and 54.4% had ventilator-associated pneumonia. Pseudomonas aeruginosa (50.8%), Acinetobacter calcoaceticus baumannii complex (42%), and Klebsiella pneumoniae (38.6%) were the most common pathogens detected with the FA-PP. Of the 33 cases diagnosed with VAP, more than one pathogen was identified in 65.9% of cases, with the most commonly identified bacteria being K. pneumoniae (43.1%), P. aeruginosa (38.6%), and Acinetobacter calcoaceticus baumannii complex (31.8%). According to the FA-PP results, the same antibiotic therapy was continued in 39.4% of cases, escalated in 54.5%, and de-escalated in 6.1%.

CONCLUSIONS

The utilization of the FA-PP has some beneficial effects, including more prompt delivery of findings compared to conventional approaches. Additionally, this approach enables the identification of resistance profiles in children diagnosed with pneumonia in the PICU. Consequently, these test results facilitate the organization of antibiotic treatment strategies, including escalation and de-escalation approaches. The detection of resistance patterns was exclusively determined via the implementation of molecular testing, prompting a reevaluation of the isolation technique in accordance with the obtained data.

Assessing the Utility of Multiplexed Polymerase Chain Reaction in Detecting Microorganisms Causing Infections in Critically ill Patients

Early sepsis diagnosis is crucial for implementing adequate antibiotic therapy and for patient survival. This study investigated whether using multiplexed PCR for detecting microorganisms in critical septic patients affects initial antibiotic treatment and compared it to microbiological culture. It also explored scenarios where PCR is more effective in clinical practice. One hundred nineteen specimens (83 blood and 36 respiratory specimens) belonging to 93 patients were analyzed. Multiplexed PCR determinations were performed using the FA-BCID Panel (bioMérieux) for blood samples and the FA-Pneumo for respiratory samples. The mean turnaround times were 1.7 h for the FA-BCID and 1.5h for the FA-Pneumo. Conversely, they were 96.1 h for blood cultures and 72.3 h for respiratory cultures. FA-BCID showed a mean sensitivity of 97% and specificity of 100%. FA-Pneumo showed a sensitivity of 100% and specificity of 90%. However, the positive predictive value was only 39%. Discrepancies were common in polymicrobial samples. Based on the PCR results, initial empirical treatment should have been changed in 71% of patients with bloodstream infections and 61% with respiratory infections. We conclude that multiplexed PCR improves the response time in identifying germs with a high degree of coincidence for blood cultures and moderate for respiratory cultures. These results highlight the importance of PCR in choosing an appropriate antibiotic therapy.

Antimicrobial Resistance in Organ Transplant Recipients

The overall burden of the main clinically relevant bacterial multidrug-resistant organisms (MDROs) (eg, methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci, extended-spectrum β-lactamase producing or extended-spectrum cephalosporin-resistant Enterobacterales, carbapenem-resistant or carbapenemase-producing Enterobacterales, MDR Pseudomonas aeruginosa, and carbapenem-resistant Acinetobacter baumannii) in solid organ transplant (SOT) populations is summarized showing prevalence/incidence, risk factors, and impact on graft/patient outcome according to the type of SOT. The role of such bacteria in donor-derived infections is also reviewed. As for the management, the main prevention strategies and treatment options are discussed. Finally, nonantibiotic-based strategies are considered as future directions for the management of MDRO in SOT setting.

Implementation of a Rapid Multiplex Polymerase Chain Reaction Pneumonia Panel and Subsequent Antibiotic De-escalation

Background

Net effects of implementation of a multiplex polymerase chain reaction (PCR) pneumonia panel (PNP) on antimicrobial stewardship are thus far unknown. This retrospective study evaluated the real-world impact of the PNP on time to antibiotic de-escalation in critically ill patients treated for pneumonia at an academic medical center.

Methods

This retrospective, quasi-experimental study included adult intensive care unit (ICU) patients with respiratory culture results from 1 May to 15 August 2019 (pre-PNP group) and adult ICU patients with PNP results from 1 May to 15 August 2020 (PNP group) at Nebraska Medical Center. Patients were excluded for the following reasons: any preceding positive coronavirus disease 2019 PCR test, lack of antibiotic receipt, or non-respiratory tract infection indications for antibiotics. The primary outcome was time to discontinuation of anti-methicillin-resistant Staphylococcus aureus (MRSA) therapy. Secondary outcomes included time to discontinuation of antipseudomonal therapy, frequency of early discontinuation for atypical coverage, and overall duration (in days) of antibiotic therapy for pneumonia.

Results

Sixty-six patients in the pre-PNP group and 58 in the PNP group were included. There were significant differences in patient characteristics between groups. The median time to anti-MRSA agent discontinuation was 49.1 hours in the pre-PNP and 41.8 hours in the PNP group (P = .28). The median time to discontinuation of antipseudomonal agents was 134.4 hours in the pre-PNP versus 98.1 hours in the PNP group (P = .47). Other outcomes were numerically but not significantly improved in our sample.

Conclusions

This early look at implementation of a multiplex PNP did not demonstrate a statistically significant difference in antibiotic use but lays the groundwork to further evaluate a significant real-world impact on antibiotic de-escalation in ICU patients treated for pneumonia.

Gram-negative pulmonary infections - advances in epidemiology and diagnosis

PURPOSE OF REVIEW

Pulmonary infections due to Gram-negative organisms are increasing worldwide and traditional assumptions that these are limited to hospital and ventilator-acquired pneumonia are rapidly falling away. Accordingly, empiric antibiotic guidelines have to follow suit with ever broader spectrum choices in order to remain 'safe', as the Global prevalence of extensively resistant Gram-negative organisms inexorably increases. Rapid, multiplex PCR-based detection of a wide variety of potential pathogens offers the opportunity to replace empiric antibiotic choices with targeted, evidence-based therapy in clinically actionable timeframes.

RECENT FINDINGS

Here, we describe the data underpinning both the increasing global prevalence of Gram-negative pulmonary infections and their increasing antibiotic resistance. We also describe the performance, characteristics and early emerging clinical impact of already available rapid molecular diagnostic platforms and how they might best be deployed.

SUMMARY

It seems will likely be advantageous to replace the current trend for empiric prescription of increasingly broad-spectrum antibiotics with 'same day' evidence-based, targeted therapy using high performance, rapid molecular diagnostic solutions. Several challenges remain be overcome, however, to fully realize their clear potential for better, focussed deployment of antibiotics, improved patient outcomes and antibiotic stewardship.

Antimicrobial Stewardship Techniques for Critically Ill Patients with Pneumonia

Pneumonia is common in the intensive care unit (ICU), infecting 27% of all critically ill patients. Given the high prevalence of this disease state in the ICU, optimizing antimicrobial therapy while minimizing toxicities is of utmost importance. Inappropriate antimicrobial use can increase the risk of antimicrobial resistance, Clostridiodes difficile infection, allergic reaction, and other complications from antimicrobial use (e.g., QTc prolongation, thrombocytopenia). This review article aims to discuss methods to optimize antimicrobial treatment in patients with pneumonia, including the following: procalcitonin use, utilization of methicillin-resistant Staphylococcus aureus nares testing to determine need for vancomycin therapy, utilization of the Biofire^® FilmArray^® pneumonia polymerase chain reaction (PCR), and microbiology reporting techniques.

The Microbial Etiology of Community-Acquired Pneumonia in Adults: from Classical Bacteriology to Host Transcriptional Signatures

All modern advances notwithstanding, pneumonia remains a common infection with substantial morbidity and mortality. Understanding of the etiology of pneumonia continues to evolve as new techniques enable identification of already known organisms and as new organisms emerge. We now review the etiology of pneumonia (at present often called "community-acquired pneumonia") beginning with classic bacteriologic techniques, which identified Streptococcus pneumoniae as the overwhelmingly common cause, to more modern bacteriologic studies, which emphasize Haemophilus influenzae, Staphylococcus aureus, Moraxella catarrhalis, Enterobacteriaceae, Pseudomonas, and normal respiratory flora. Urine antigen detection is useful in identifying Legionella and pneumococcus. The low yield of bacteria in recent studies is due to the failure to obtain valid sputum samples before antibiotics are administered. The use of high-quality sputum specimens enables identification of recognized ("typical") bacterial pathogens as well as a role for commensal bacteria ("normal respiratory flora"). Nucleic acid amplification technology for viruses has revolutionized diagnosis, showing the importance of viral pneumonia leading to hospitalization with or without coinfecting bacterial organisms. Quantitative PCR study of sputum is in its early stages of application, but regular detection of high counts of bacterial DNA from organisms that are not seen on Gram stain or grown in quantitative culture presents a therapeutic dilemma. This finding may reflect the host microbiome of the respiratory tract, in which case treatment may not need to be given for them. Finally, host transcriptional signatures might enable clinicians to distinguish between viral and bacterial pneumonia, an important practical consideration.

Impact of Molecular Syndromic Diagnosis of Severe Pneumonia in the Management of Critically Ill Patients

The impact of syndromic molecular diagnosis in the management of nosocomial infections caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has been incompletely characterized. We evaluated the performance of a molecular syndromic platform (BioFire FilmArray-Pneumonia plus Panel) in patients with pneumonia in the intensive care unit (ICU) of a University Hospital in Greece over a 2-year period. We evaluated 79 consecutive patients diagnosed with pneumonia in the ICU (2018-2020), including 55 patients with ventilator associated pneumonia (VAP). We included 40 control patients diagnosed with pneumonia in the ICU the year before the study (2017-2018). We identified 16 cases of VAP due to XDR bacterial pathogens. We found an excellent agreement (89.4% 76/85 reported results) between the results of syndromic platform and conventional cultures of tracheal aspirates. The molecular syndromic test significantly improved time to diagnosis versus conventional culture (3.5 h vs 72 h, P < 0.0001), and identified new pathogens not detected by cultures in 49% of the cases. However, three cases of pneumonia with targets not included in the molecular platform, were not detected. Implementation of the molecular syndromic facilitated treatment modification from broad to narrow spectrum antimicrobial therapy, resulting in significant reductions in antibiotic consumption in the study group compared to the control group, without a negative impact in patient outcome. The implementation of syndromic molecular diagnosis in critically ill patients with pneumonia is associated with timely and improved diagnosis and has significant impact on reduction of antibiotic consumption. IMPORTANCE The impact of syndromic molecular diagnosis in the management of nosocomial infections caused by MDR/XDR pathogens has been incompletely characterized. We evaluated the performance of a molecular syndromic platform (BioFire FilmArray -Pneumonia plus Panel) in 79 patients with pneumonia in the intensive care unit (ICU) of a University Hospital in Greece over a 2-year period (2018-2020) compared to 40 control patients diagnosed with pneumonia in the ICU the year before the study (2017-2018). Importantly, implementation of syndromic pneumonia panel improved time to diagnosis, identified new pathogens not detected by cultures in 49% of the cases and resulted in a significant reduction in antibiotic consumption compared to the year before initiation of the study without a negative impact in mortality of patients. Collectively, our study demonstrates the positive value of PCR syndromic testing in the management of pneumonia in ICUs high rates of MDR/XDR nosocomial pathogens.

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Antimicrobial stewardship

PURPOSE OF REVIEW

The optimal use of antimicrobials is necessary to slow resistance development and improve patient outcomes. Antimicrobial stewardship (AMS) is a bundle of interventions aimed at promoting the responsible use of antiinfectives. The ICU is an important field of activity for AMS because of high rates of antimicrobial use, high prevalence of resistant pathogens and complex pharmacology. This review discusses aims and interventions of AMS with special emphasis on the ICU.

RECENT FINDINGS

AMS-interventions can improve the quality and quantity of antimicrobial prescribing in the ICU without compromising patient outcomes. The de-escalation of empiric therapy according to microbiology results and the limitation of treatment duration are important steps to reduce resistance pressure. Owing to the complex nature of critical illness, the pharmacological optimization of antimicrobial therapy is an important goal in the ICU. AMS-objectives and strategies are also applicable to patients with sepsis. This is reflected in the most recent guidelines by the Surviving Sepsis Campaign. AMS-interventions need to be adapted to their respective setting and be mindful of local prescribing cultures and prescribers' attitudes.

SUMMARY

AMS in the ICU is effective and safe. Intensivists should be actively involved in AMS-programs and propagate responsible use of antimicrobials.

Multiplex PCR in the empirical antibiotic treatment of patients with SARS-CoV-2 and bacterial respiratory superinfection

Background

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic led to overuse of antimicrobials, which increased concerns regarding antimicrobial resistance.

Objective

To measure the impact of a multiplex polymerase chain reaction (PCR) pneumonia panel on empirical antibiotic treatment for patients with critical coronavirus disease 2019 (COVID-19) with suspected bacterial respiratory superinfection.

Methods

This descriptive, prospective study was undertaken in a 36-bed intensive care unit from June 2020 to July 2021. Patients with severe COVID-19 who were ventilated and under suspicion of bacterial respiratory superinfection were included in the study. The intervention was a semi-quantitative multiplex PCR alongside concurrent standard cultures. When PCR panel results were expected to be obtained within 3 h of sampling, empirical antibiotic treatment was not administered while awaiting the results. Otherwise, empirical treatment was initiated. Patients classified as 'avoided empirical treatment' avoided 48-72 h of empirical antibiotic therapy. For those patients who received empirical treatment, the PCR panel results were used to decide whether treatment should be escalated, de-escalated, maintained or stopped. Positive and negative predictive values, and 'avoided empirical treatment' were calculated. Medical conduct and panel results were analysed for patients who received empirical treatment.

Results

Eighty-two patients (71% male, 29% female) were included in this study. The mean age was 57.5 years, and the mean APACHE II score was 16. Ninety PCR panels were performed, and the negative and positive predictive values were 99.9% and 66.7%, respectively. Empirical treatment was avoided in 61% of episodes. Of those patients who were receiving antibiotics when the PCR panel was performed, treatment was de-escalated in 71%, escalated in 14%, stopped in 9% and maintained in 6%. A diagnosis of bacterial respiratory superinfection was ruled out in 19% of cases.

Conclusions

PCR panels prevented the initiation of empirical antibiotic treatment in two-thirds of patients, and led to de-escalation in more than two-thirds of those who had started empirical antibiotic treatment. The high negative predictive value of the PCR panel allowed the diagnosis of bacterial respiratory superinfection to be ruled out. This tool represents a significant contribution to diagnostic stewardship in order to avoid the unnecessary use of antibiotics.

Utility of Polymerase Chain Reaction in Nasopharyngeal Swabs for Identifying Respiratory Bacteria Causing Community-Acquired Pneumonia

Timely identification of a pathogen in lower respiratory tract infections (LRTI) can support appropriate antibiotics use. The difficulty of obtaining lower respiratory tract (LRT) samples limits the utility of point-of-care syndromic molecular assays. We assessed the performance of the FilmArray Pneumonia plus panel (FilmArray PP) in nasopharyngeal (NP) swab for detection of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. Patients in the study included retrospectively consenting adults who attended the emergency department of Lausanne University Hospital between February 2019 and August 2020 for a community-acquired LRTI, with available NP swab and a high-quality LRT sample. These samples were tested with the FilmArray PP (cutoff of ≥10⁴ copies/mL). Positive (PPA) and negative percent agreement (NPA) of FilmArray PP in NP swab were calculated, using (i) FilmArray PP in LRT sample and (ii) standard microbiological tests as reference standards. To assess the performance of a lower detection cutoff, NP samples were also tested with an in-house PCR (cutoff of ≥10 copies/mL) for S. pneumoniae and H. influenzae. Overall, 118 patients were included. FilmArray PP in LRT sample and standard microbiology tests detected S. pneumoniae in 19/118 and 12/118, H. influenzae in 44/118 and 19/118, and M. catarrhalis in 14/118 and 0/118, respectively. Using LRT FilmArray PP as reference, PPA and NPA of FilmArray PP on NP were 58% and 100% for S. pneumoniae, 61% and 100% for H. influenzae, and 57% and 99% for M. catarrhalis. Using standard diagnostic tests as reference, PPA and NPA were 58% and 96% for S. pneumoniae, 74% and 87% for H. influenzae, and indefinite and 92% for M. catarrhalis. Using a lower cutoff on NP (≥10² copies/mL), PPA was 68% for S. pneumoniae and 77% for H. influenzae with LRT FilmArray PP as reference. FilmArray PP in NP swabs has a limited PPA for identifying the most common etiologies of community-acquired LRTI irrespective of the reference standard, preventing its use for withholding antibiotics. The PCR detection cutoff does not explain the low PPA. The excellent NPA suggests the use of NP PCR results for rapidly targeted antimicrobial therapy.

IMPORTANCE Timely identification of a pathogen in patients with lower respiratory tract infections is of paramount importance to avoid inappropriate antibiotic prescription. We aimed to evaluate the performance of a rapid syndromic molecular assay in nasopharyngeal swabs for identifying the most common bacterial causes of lower respiratory tract infections in adults (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis). Our data show that nasopharyngeal molecular assay has a good concordance with lower respiratory tract sample when positive but not when negative. A positive result is therefore concordant with a lower respiratory tract infection and can be used to target antibiotics. Nevertheless, a negative result does not have a good concordance, so it cannot be used to withhold antibiotics. Our findings illustrate the potential utility of these easily collected samples for the management of patients with lower respiratory tract infections.

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Potential Impact of Rapid Multiplex PCR on Antimicrobial Therapy Guidance for Ventilated Hospital-Acquired Pneumonia in Critically Ill Patients, A Prospective Observational Clinical and Economic Study

Objectives

To investigate the potential impact of the syndromic multiplex FilmArray® Pneumonia plus Panel (FAPP) on the antimicrobial treatment guidance of patients with ventilated hospital-acquired pneumonia (VHAP).

Methods

Respiratory fluids from 100 adult patients with VHAP, receiving invasive mechanical ventilation in three intensive care units from one French university hospital, were tested prospectively using FAPP. Conventional cultures were performed in parallel as routine practice. Clinicians were left blinded to the FAPP results. Antimicrobial therapies based on FAPP results were simulated by independent blinded experts according to a predefined algorithm and compared to 1) those prescribed in practice according to local guidelines (real-life), and 2) those that complied with the international ERS/ESICM/ESCMID/ALAT recommendations. The primary endpoint was the number of days of broad-spectrum antimicrobial therapy. Secondary endpoints were the rates of microbiological treatment failure and cost-effectiveness ratio.

Results

The predicted median duration of broad-spectrum antibiotics was 0 [0-1.25] day in the FAPP-based simulation, versus 2 [0-6] days in real-life (p&lt;0.0001) and 2 [2-3.25] days in the recommendations-based simulation (p&lt;0.0001). Treatment failure was predicted in 3% of cases with FAPP results versus observed in 11% in real-life (p=0.08) and 6% with recommendations-based simulation (p=0.37). The incremental cost-effectiveness ratio was 1 121 € [-7021; 6794] to avoid one day of non-optimized antimicrobial therapy.

Conclusions

Our results suggest that using FAPP in patients with VHAP has the potential to reduce the use of broad-spectrum antimicrobial therapy without increasing the risk of microbial treatment failure.

Non-Legionella pneumophila serogroup 1 pneumonia: Diagnosis of a nosocomial legionellosis with the Biofire Pneumonia plus panel

We report a nosocomial case of Legionella pneumophila pneumonia caused by a serogroup 10 strain diagnosed with the Biofire® Pneumonia plus panel. Molecular investigations of the environment of the patient allowed us to identify the source of contamination.

Value of syndromic panels in the management of severe community-acquired pneumonia

Community-acquired pneumonia requiring hospital admission is a prevalent and potentially serious infection, especially in high-risk patients (e.g., those requiring ICU admission or immunocompromised). International guidelines recommend early aetiological diagnosis to improve prognosis and reduce mortality. Syndromic panels that detect causative pathogens by molecular methods are here to stay. They are highly sensitive and specific for detecting the targets included in the test. A growing number of studies measuring their clinical impact have observed increased treatment appropriateness and decreased turnaround time to aetiological diagnosis, need for admission, length of hospital stay, days of isolation, adverse effects of medication and hospital costs. Its use is recommended a) per a pre-established protocol on making the diagnosis and managing the patient, b) together with an antimicrobial stewardship programme involving both the Microbiology Service and the clinicians responsible for the patient, and c) the final evaluation of the whole process. However, we recall that microbiological diagnosis with traditional methods remains mandatory due to the possibility that the aetiological agent is not included among the molecular targets and to determine the antimicrobial susceptibility of the pathogens detected.

How common is ventilator-associated pneumonia after coronavirus disease 2019?

PURPOSE OF REVIEW

The first studies on COVID-19 patients with acute respiratory distress syndrome (ARDS) described a high rate of secondary bacterial ventilator-associated pneumonia (VAP). The specificity of VAP diagnoses in these patients are reviewed, including their actual rate.

RECENT FINDINGS

Published studies described high rates of bacterial VAP among COVID-19 patients with ARDS, and these VAP episodes are usually severe and of specifically poor prognosis with high mortality. Indeed, Severe acute respiratory syndrome - coronavirus disease 19 (SARS-CoV2) infection elicits alterations that may explain a high risk of VAP. In addition, breaches in the aseptic management of patients might have occurred when the burden of care was heavy. In addition, VAP in these patients is more frequently suspected, and more often investigated with diagnostic tools based on molecular techniques.

SUMMARY

VAP is frequented and of particularly poor prognosis in COVID-19 patients with ARDS. It can be explained by SARS-CoV-2 pathophysiology, and also breaches in the aseptic procedures. In addition, tools based on molecular techniques allow an early diagnosis and unmask VAP usually underdiagnosed by traditional culture-based methods. The impact of molecular technique-based diagnostics in improving antibacterial therapy and COVID-19 prognosis remain to be evaluated.

Methods of Sputum and Mucus Assessment for Muco-Obstructive Lung Diseases in 2022: Time to “Unplug” from Our Daily Routine!

Obstructive lung diseases, such as chronic obstructive pulmonary disease, asthma, or non-cystic fibrosis bronchiectasis, share some major pathophysiological features: small airway involvement, dysregulation of adaptive and innate pulmonary immune homeostasis, mucus hyperproduction, and/or hyperconcentration. Mucus regulation is particularly valuable from a therapeutic perspective given it contributes to airflow obstruction, symptom intensity, disease severity, and to some extent, disease prognosis in these diseases. It is therefore crucial to understand the mucus constitution of our patients, its behavior in a stable state and during exacerbation, and its regulatory mechanisms. These are all elements representing potential therapeutic targets, especially in the era of biologics. Here, we first briefly discuss the composition and characteristics of sputum. We focus on mucus and mucins, and then elaborate on the different sample collection procedures and how their quality is ensured. We then give an overview of the different direct analytical techniques available in both clinical routine and more experimental settings, giving their advantages and limitations. We also report on indirect mucus assessment procedures (questionnaires, high-resolution computed tomography scanning of the chest, lung function tests). Finally, we consider ways of integrating these techniques with current and future therapeutic options. Cystic fibrosis will not be discussed given its monogenic nature.

"HAP and VAP after Guidelines"

Nosocomial pneumonia is associated with worsened prognosis when diagnosed in intensive care unit (ICU), ranging from 12 to 48% mortality. The incidence rate of ventilation-acquired pneumonia tends to decrease below 15/1,000 intubation-day. Still, international guidelines are heterogeneous about diagnostic criteria because of inaccuracy of available methods. New entities have thus emerged concerning lower respiratory tract infection, namely ventilation-acquired tracheobronchitis (VAT), or ICU-acquired pneumonia (ICUAP), eventually requiring invasive ventilation (v-ICUAP), according to the type of ventilation support. The potential discrepancy with non-invasive methods could finally lead to underdiagnosis in almost two-thirds of non-intubated patients. Delayed diagnostic could explain in part the 2-fold increase in mortality of penumonia when invasive ventilation is initiated. Here we discuss the rationale underlying this new classification.Many situations can lead to misdiagnosis, even more when the invasive mechanical ventilation is initiated. The chest radiography lacks sntivity and specificity for diagnosing pneumonia. The place of chest computed tomography and lung ultrasonography for routine diagnostic of new plumonary infiltrate remain to be evaluated.Microbiological methods used to confirm the diagnostic can be heterogeneous. The development of molecular diagnostic tools may improve the adequacy of antimicrobial therapies of ventilated patients with pneumonia, but we need to further assess its impact in non-ventilated pneumonia.In this review we introduce distinction between hospital-acquired pneumonia according to the localization in the hospital and the oxygenation/ventilation mode. A clarification of definition is the first step to develop more accurate diagnostic strategies and to improve the patients' prognosis.

Classical and Molecular Techniques to Diagnose HAP/VAP

Nosocomial pneumonia, including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), are the most common nosocomial infections occurring in critically ill patients requiring intensive care. However, challenges exist in making a timely and accurate diagnosis of HAP and VAP. Under diagnosis of HAP and VAP can result in greater mortality risk, especially if accompanied by delays in the administration of appropriate antimicrobial treatment. Over diagnosis of HAP and VAP results in the unnecessary administration of broad spectrum antibiotics that can lead to further escalation of antibiotic resistance. Optimal diagnosis and management of HAP and VAP require a systematic approach that combines clinical and radiographic assessments along with proper microbiologic techniques. The use of more invasive sampling methods (bronchoalveolar lavage and protected specimen brush) may enhance specimen collection resulting in more specific diagnoses to limit unnecessary antibiotic exposure. Molecular techniques, currently in use and investigational technique, may improve the diagnosis of HAP and VAP by allowing more rapid identification of offending pathogens, if present, thus increasing both appropriate antibiotic treatment and avoiding unnecessary drug exposure.

Evaluation of the Potential Impact of a Multiplex Rapid Diagnostic Panel in Critically Ill Patients With Hospital-Acquired Pneumonia

Background Rapid diagnostic tools have emerged as valuable assets assisting clinicians in decision-making regarding patient management in the hospital setting. Our study sought to identify the potential impact of the BioFire® FilmArray® Pneumonia Panel (FP Panel) (BioFire Diagnostics, Salt Lake City, UT, USA) in patients with hospital-acquired pneumonia (HAP). Methods Respiratory samples obtained by bronchoalveolar lavage (BAL) or tracheal aspiration (TA) from ICU patients with a diagnosis of HAP were tested by the FP panel in addition to routine bacterial cultures. In addition, the electronic health records of these patients were reviewed to determine what potential changes in antimicrobial therapy could have been implemented if the panel results were known to the treatment team in real-time. A cost analysis was also performed incorporating the cost of the pneumonia panel and the savings associated with the potential decrease of antibiotic use and avoidance of the rapid viral diagnostic panel.  Results Fifty-six patients met the study criteria. The FP panel results could have prompted a change in therapy in 36 (64.3%) patients, with an anticipated mean reduction in time to optimized therapy of approximately 51 hours. In addition, the panel identified three cases where antimicrobials should have been altered because patients were not receiving empiric therapy with activity against the causative pathogen and 34 opportunities for antibiotic de-escalation. The cost analysis calculated an additional cost of $10 per patient associated with using the FP panel.  Conclusions The FP panel could have prompted a change in therapy in about two-thirds of patients studied. Its potential benefits include a more rapid time to optimized therapy, reduced exposure to and cost of broad-spectrum antimicrobials, and reduced cost of other rapid diagnostic tests.

Molecular Diagnosis of Pneumonia (Including Multiplex Panels)

Background

Pneumonia is a common illness, accounting for a staggering amount of worldwide morbidity and mortality. The diagnosis of pneumonia is challenging given the variety of responsible pathogens. Diagnostic testing for bacterial pneumonia has traditionally relied on time-consuming culture-based methods, though recently multiplexed molecular approaches have been described. Multiplexed molecular assays for pneumonia have the potential to provide broad diagnostic information in a rapid timeframe. Much has yet to be learned about these assays regarding analytical performance, potential impact, and optimal implementation strategy.

Content

Herein we provide a summary of what is known and what has yet to be learned about multiplexed molecular pneumonia assays. We provide a comparison of the different commercially available assays and summarize the most current performance data for each. We further describe outcome data and lessons learned from those who have implemented these assays worldwide. Finally, based on the current state of performance and outcome data, we provide informed strategies and considerations for laboratories contemplating implementation.

Summary

Multiplexed molecular assays for the diagnosis of pneumonia boast high accuracy though the diagnostic information gained from these assays is inherently different from culture and must be interpreted in cultural context. Despite this, these assays can be powerful and effective diagnostic tools with a potential to positively impact patient care. The extent to which this is realized varies from setting to setting, though is dependent on thoughtful implementation and a focus on delivering clear, rapid, and actionable results that can be interpreted in the appropriate context.

Rapid diagnostic tests in the management of pneumonia

INTRODUCTION

Pneumonia is one of the main causes of mortality associated with infectious diseases worldwide. Several challenges have been identified in the management of patients with pneumonia, ranging from accurate and cost-effective microbiological investigations, prompt and adequate therapeutic management, and optimal treatment duration.

AREAS COVERED

In this review, an updated summary on the current management of pneumonia patients is provided and the epidemiological issues of infectious respiratory diseases, which in the current pandemic situation are of particular concern, are addressed. The clinical and microbiological approaches to pneumonia diagnosis are reviewed, including discussion about the new molecular assays pointing out both their strengths and limitations. Finally, the current recommendations about antibiotic treatment are examined and discussed depending on the epidemiological contexts, including those with high prevalence of multidrug-resistant bacteria.

EXPERT OPINION

We claim that rapid diagnostic tests, if well-positioned in the diagnostic workflow and reserved for the subset of patients who could most benefit from these technologies, may represent an interesting and feasible tool to optimize timing of targeted treatments especially in terms of early de-escalation or discontinuation of antibiotic therapy.

Detection of bacteria via multiplex PCR in respiratory samples of critically ill COVID-19 patients with suspected HAP/VAP in the ICU

Background

Critically ill Coronavirus disease 2019 (COVID-19) patients have high rates of bacterial superinfection. Multiplex polymerase chain reaction panels may be able to provide useful information about the incidence and spectrum of bacteria causing superinfections.

Methods

In this retrospective observational study we included all COVID-19 positive patients admitted to our intensive care unit with suspected hospital-acquired pneumonia/ventilator-associated pneumonia (HAP/VAP) in whom the BioFire® Pneumonia Panel (PP) was performed from tracheal aspirate or bronchoalveolar lavage fluid for diagnostic purposes. The aim of our study was to analyze the spectrum of pathogens detected with the PP.

Results

In this study 60 patients with a median age of 62.5 years were included. Suspected VAP was the most frequent (48/60, 80%) indication for performing the PP. Tracheal aspirate was the predominant sample type (50/60, 83.3%).

The PP led to a negative, monomicrobial and polymicrobial result in 36.7%, 35% and 28.3% of the patients, respectively. The three most detected bacteria were Staphylococcus aureus (13/60, 21.7%), Klebsiella pneumoniae (12/60, 20%) and Haemophilus influenzae (9/60, 15%). Neither atypical bacteria nor resistance genes were detected.

Microbiological culture of respiratory specimens was performed in 36 (60%) patients concomitantly. The PP and microbiological culture yielded a non-concordant, partial concordant and completely concordant result in 13.9% (5/36), 30.6% (11/36) and 55.6% (20/36) of the analyzed samples, respectively.

Conclusion

In critically ill COVID-19 patients with suspected HAP/VAP results of the PP and microbiological culture methods were largely consistent. In our cohort, S. aureus and K. pneumoniae were the most frequently detected organisms. A higher diagnostic yield may be achieved if both methods are combined.

Diagnosis of Multidrug-Resistant Pathogens of Pneumonia

Hospital-acquired pneumonia and ventilator-associated pneumonia that are caused by multidrug resistant (MDR) pathogens represent a common and severe problem with increased mortality. Accurate diagnosis is essential to initiate appropriate antimicrobial therapy promptly while simultaneously avoiding antibiotic overuse and subsequent antibiotic resistance. Here, we discuss the main conventional phenotypic diagnostic tests and the advanced molecular tests that are currently available to diagnose the primary MDR pathogens and the resistance genes causing pneumonia.

Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia

Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.

Clinical decision making is improved by BioFire Pneumonia Plus in suspected lower respiratory tract infection after lung transplantation: Results of the prospective DBATE-IT* study

BACKGROUND

Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality in lung transplant (LTx) recipients. Timely and precise pathogen detection is vital to successful treatment. Multiplex PCR kits with short turnover times like the BioFire Pneumonia Plus (BFPPp) (manufactured by bioMérieux) may be a valuable addition to conventional tests.

METHODS

We performed a prospective observational cohort study in 60 LTx recipients with suspected LRTI. All patients received BFPPp testing of bronchoalveolar lavage fluid in addition to conventional tests including microbiological cultures and conventional diagnostics for respiratory viruses. Primary outcome was time-to-test-result; secondary outcomes included time-to-clinical-decision and BFPPp test accuracy compared to conventional tests.

RESULTS

BFPPp provided results faster than conventional tests (2.3 h [2-2.8] vs. 23.4 h [21-62], p < 0.001), allowing for faster clinical decisions (2.8 [2.2-44] vs. virology 28.1 h [23.1-70.6] and microbiology 32.6 h [4.6-70.9], both p < 0.001). Based on all available diagnostic modalities, 26 (43%) patients were diagnosed with viral LRTI, nine (15 %) with non-viral LRTI, and five (8 %) with combined viral and non-viral LRTI. These diagnoses were established by BFPPp in 92%, 78%, and 100%, respectively. The remaining 20 patients (33 %) received a diagnosis other than LRTI. Preliminary therapies based on BFPPp results were upheld in 90% of cases. There were six treatment modifications based on pathogen-isolation by conventional testing missed by BFPPp, including three due to fungal pathogens not covered by the BFPPp.

CONCLUSION

BFPPp offered faster test results compared to conventional tests with good concordance. The absence of fungal pathogens from the panel is a potential weakness in a severely immunosuppressed population.