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Background: In low-resource settings, limited laboratory capacity adds to the burden of central nervous system (CNS) infections in children and spurs overuse of antibiotics. The commercially available BioFire (R) FilmArray (R) Meningitis/Encephalitis Panel (FA-ME) with its capability to simultaneously detect 14 pathogens in cerebrospinal fluid (CSF), could potentially narrow such a diagnostic gap. Methods: In Mbarara, Uganda, we compared clinical utility (clinical turnaround time [cTAT], microbial yield, and influence on patient outcome and antibiotic exposure) of FA-ME with bacterial culture, in children 0-12 years with suspected CNS infection. Results: Of 212 enrolled children, CSF was sampled from 194. All samples underwent bacterial culture, of which 193 also underwent FA-ME analyses. FA-ME analyses prospectively influenced care for 169 of the 193 patients, and they constituted an 'Index group'. The remaining 43/212 patients constituted a 'Reference group'. Of all 194 CSF-sampled patients, 87% (168) had received antibiotics before lumbar puncture. Median cTAT for FA-ME was 4.2 h, vs. two days for culture. Bacterial yield was 12% (24/193) and 1.5% (3/194) for FA-ME and culture, respectively. FA-ME viral yield was 12% (23/193). Fatality rate was 14% in the Index group vs. 19% in the Reference group (P = 0.20). From clinician receival of FA-ME results, median antibiotic exposure was 6 days for bacteria-negative vs. 13 days for bacteria-positive patients (P = 0.03). Median hospitalization duration was 7 vs. 12 days for FA-ME negative and positive patients, respectively (P < 0.01). Conclusions: In this setting, clinical FA-ME utility was found in a higher and faster microbial yield and shortened hospitalization and antibiotic exposure of patients without CSF pathology. More epidemiologically customized pathogen panels may increase FA-ME utility locally, although its use in similar settings would require major cost reductions.

Introduction: The use of mechanical ventilators in the intensive care unit (ICU) is often associated with higher risk of respiratory tract infections, including ventilator-associated pneumonia (VAP). Concomitant bacterial-viral infection was reported to worsen patient's clinical condition. This study evaluated the rate of concomitant bacterial-viral infections in patients with VAP and analyzed their clinical outcomes. Methodology: In this retrospective observational study 107 patients diagnosed with VAP and admitted in ICU with mechanical ventilator support between April 2018 and May 2019 in the Department of Respiratory Medicine, Dachang Hospital, Shanghai, China were included. 27 most commonly involved lower respiratory tract infection (LRTI) pathogens (bacteria and virus) and seven genetic markers of antibiotic resistance were detected and analyzed using Biofire® FilmArray® Pneumonia Panel plus (bioMérieux SA, Paris, France). Results: Of the 107 patients, 45 (42.1%) patients had bacterial infection alone (bacterial group), 26 (24.3%) had virus infection alone (viral group) and 24 (22.4%) patients had concomitant bacterial-viral infection (mixed group). Sixty-nine (64.5%) and 50 (46.7%) patient samples were positive for bacterial (bacterial and mixed groups) and viral (viral and mixed groups) detection, respectively. Streptococcus pneumonia (11.2%) and Influenza A (17, 15.9%), were the predominantly identified bacterial and viral species. The blaCTX-M (21.5%) was the predominant resistance gene detected. Twenty-four (22.4%) patients were positive for concomitant bacterial-viral infection; Staphylococcus aureus and Influenza A were the most common bacterial-viral combination identified. Conclusions: Concomitant bacterial-viral infection was higher compared to previously published studies and the increased duration of mechanical ventilation was associated with increased disease severity.

Background: Bloodstream infection (BSI) contributes to a substantial proportion of mortality in sub-Saharan Africa and is marked by the presence of bacterial and/or fungal microorganisms in the blood. Because BSI can be life threatening, it requires a timely, reliable and accurate diagnosis. This study retrospectively analyzed data of identified BSI pathogens and compared the performance of the different diagnostic technologies used in terms of accuracy, sensitivity, turnaround time (TAT) and cost. Methods: Currently, culture followed by analytical profile index biochemical strips (API), (BioMerieux) are used as the conventional standard diagnostics in Kenyan public hospitals and labs. We compared the results of this standard to that of the BioFire FilmArray (FA) (BioFire Diagnostics) and MicroScan WalkAway-40 plus System (MS) (Beckman Coulter) used in diagnosis of BSI. The FA technology was able to identify 150/152 bacterial and yeast isolates with specificity of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%), mean TAT of 8 hours 40 minutes per eight samples and running cost per sample of USD 140.11. The MS identified 149/152 isolates with specificity of 98.56% (95% CI: 95.86-99.70%), sensitivity of 98.68% (95% CI: 95.30-99.84%), mean TAT per sample was 42 hours and running cost per sample of USD 28.05. API detected 150/152 isolates, with specificity of 99.04% (95% CI: 96.59-99.88%), sensitivity of 98.68% (95% CI: 95.33-99.84%) and the mean TAT per sample was 53 and 103 hours for bacterial and yeast samples, respectively, with a running cost per sample of USD 28.05. Conclusions: The findings in this paper suggest that the FA and MS platforms should be able to perform adequately in Kenya referral hospitals and medical clinics as a rapid diagnostic tool.

Background Improving timeliness of pathogen identification is crucial to allow early adaptation of antibiotic therapy and improve prognosis in patients with pneumonia. We evaluated the relevance of a new syndromic rapid multiplex PCR test (rm-PCR) on respiratory samples to guide empirical antimicrobial therapy in adult patients with community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), and ventilator-acquired pneumonia (VAP). Methods This retrospective multicenter study was conducted in four French university hospitals. Respiratory samples were obtained from patients with clinical and radiological signs of pneumonia and simultaneously tested using conventional microbiological methods and the rm-PCR. A committee composed of an intensivist, a microbiologist, and an infectious diseases specialist retrospectively assessed all medical files and agreed on the most appropriate antimicrobial therapy for each pneumonia episode, according to the results of rm-PCR and blinded to the culture results. The rm-PCR-guided antimicrobial regimen was compared to the empirical treatment routinely administered to the patient in standard care. Results We included 159 pneumonia episodes. Most patients were hospitalized in intensive care units ( n  = 129, 81%), and episodes were HAP ( n  = 68, 43%), CAP ( n  = 54, 34%), and VAP ( n  = 37, 23%). Conventional culture isolated ≥ 1 microorganism(s) at significant level in 95 (60%) patients. The syndromic rm-PCR detected at least one bacteria in 132 (83%) episodes. Based on the results of the rm-PCR, the multidisciplinary committee proposed a modification of the empirical therapy in 123 (77%) pneumonia episodes. The modification was a de-escalation in 63 (40%), an escalation in 35 (22%), and undetermined in 25 (16%) patients. In microbiologically documented episodes ( n  = 95), the rm-PCR increased appropriateness of the empirical therapy to 83 (87%), as compared to 73 (77%) in routine care. Conclusions Use of a syndromic rm-PCR test has the potential to reduce unnecessary antimicrobial exposure and increase the appropriateness of empirical antibiotic therapy in adult patients with pneumonia.

Background Lower respiratory tract infections (LRTIs) account for a heavy burden of illness in low- and middle-income country settings, but the etiology of these infections is often unknown. In this study, we applied the BIOFIRE ® FILMARRAY ® Pneumonia plus Panel, a multiplex polymerase chain reaction assay with bacterial, viral, and antibacterial resistance gene targets, on sputum samples to evaluate the etiology of community-acquired LRTI among hospitalized patients in southern Sri Lanka. Methods We enrolled children and adults hospitalized with LRTIs at a public tertiary care hospital in southern Sri Lanka from 2019 to 2021. Demographic and clinical data were collected, and a sputum sample for each patient was tested using the Pneumonia plus Panel. Assay results were compared with sputum culture results. Fisher’s exact test was applied to identify association between the presence of viruses, bacteria, or antimicrobial resistant genes and the findings of the chest radiographs during hospitalization as well as associations between the genomic concentration identified through the panel and the bacteria known to cause typical pneumonia infection included in the panel. Results In 267 patients tested, the most detected bacteria by the Pneumonia plus Panel were the Klebsiella pneumoniae group (41.9%), Staphylococcus aureus (34.5%), and the Acinetobacter calcoaceticus-baumannii complex (32.6%). The most detected viruses were the human rhinovirus/enterovirus (19.5%) and influenza A (10.9%). In total, 211 patients (79.0%) had at least one gram-negative bacterium and 139 patients (52.1%) had at least one gram-positive bacteria. As for Antimicrobial Resistance, 96 patients (40.0%) had at least one carbapenem resistant gene, 56 patients (21.0%) had an extended spectrum beta-lactamase related gene, and 42 patients (15.7%) had a methicillin resistant gene. Only 15 patients (5.6%) were identified to have Pneumonia plus Panel results matching with sputum culture results. Conclusions Our findings suggest that patients with LRTI in Southern Province, Sri Lanka have a high prevalence of gram-negative bacteria and antibacterial resistance in their sputum samples. However, it remains difficult to differentiate isolates that are colonizers not leading to disease versus the true cause of infection via the use of the BIOFIRE ® FILMARRAY ® Pneumonia plus Panel on sputum samples.

Herein, we evaluated the optimal timing for implementing the BioFire ® FilmArray ® Pneumonia Panel (FA-PP) in the medical intensive care unit (MICU). Respiratory samples from 135 MICU-admitted patients with acute respiratory failure and severe pneumonia were examined using FA-PP. The cohort had an average age of 67.1 years, and 69.6% were male. Notably, 38.5% were smokers, and the mean acute physiology and chronic health evaluation-II (APACHE-II) score at initial MICU admission was 30.62, and the mean sequential organ failure assessment score (SOFA) was 11.23, indicating sever illness. Furthermore, 28.9, 52.6, and 43% of patients had a history of malignancy, hypertension, and diabetes mellitus, respectively. Community-acquired pneumonia accounted for 42.2% of cases, whereas hospital-acquired pneumonia accounted for 37%. The average time interval between pneumonia diagnosis and FA-PP implementation was 1.9 days, and the mean MICU length of stay was 19.42 days. The mortality rate was 50.4%. Multivariate logistic regression analysis identified two variables as significant independent predictors of mortality: APACHE-II score ( p = 0.033, OR = 1.06, 95% CI 1.00–1.11), history of malignancy (OR = 3.89, 95% CI 1.64–9.26). The Kaplan–Meier survival analysis indicated that early FA-PP testing did not provide a survival benefit. The study suggested that the FA-PP test did not significantly impact the mortality rate of patients with severe pneumonia with acute respiratory failure. However, a history of cancer and a higher APACHE-II score remain important independent risk factors for mortality.

Background Cases of refractory Mycoplasma pneumoniae pneumonia have been increasing recently; however, whether viral coinfection or macrolide-resistant M. infection contribute to the development of refractory M. pneumoniae pneumonia remains unclear. This study aimed to investigate the impacts of viral coinfection and macrolide-resistant M. pneumoniae infection on M. pneumoniae pneumonia in hospitalized children and build a model to predict a severe disease course. Methods Nasopharyngeal swabs or sputum specimens were collected from patients with community-acquired pneumonia meeting our protocol who were admitted to Shanghai Children’s Medical Center from December 1, 2016, to May 31, 2019. The specimens were tested with the FilmArray Respiratory Panel, a multiplex polymerase chain reaction assay that detects 16 viruses, Bordetella pertussis , M. pneumoniae , and Chlamydophila pneumoniae . Univariate and multivariate logistic regression models were used to identify the risk factors for adenovirus coinfection and macrolide-resistant mycoplasma infection. Results Among the 107  M. pneumoniae pneumonia patients, the coinfection rate was 56.07%, and 60 (60/107, 56.07%) patients were infected by drug-resistant M. pneumoniae . Adenovirus was the most prevalent coinfecting organism, accounting for 22.43% (24/107). The classification tree confirmed that viral coinfection was more common in patients younger than 3 years old. Adenovirus coinfection and drug-resistant M. pneumoniae infection occurred more commonly in patients with refractory M. pneumoniae pneumonia ( P  = 0.019; P  = 0.001). A prediction model including wheezing, lung consolidation and extrapulmonary complications was used to predict adenovirus coinfection. The area under the receiver operating characteristic curve of the prediction model was 0.795 (95% CI 0.679–0.893, P  < 0.001). A prolonged fever duration after the application of macrolides for 48 h was found more commonly in patients infected by drug-resistant M. pneumoniae ( P  = 0.002). A fever duration longer than 7 days was an independent risk factor for drug-resistant Mycoplasma infection (OR = 3.500, 95% CI = 1.310–9.353, P  = 0.012). Conclusions The occurrence of refractory M. pneumoniae pneumonia is associated with adenovirus coinfection and infection by drug-resistant M. pneumoniae . A prediction model combining wheezing, extrapulmonary complications and lung consolidation can be used to predict adenovirus coinfection in children with M. pneumoniae pneumonia. A prolonged fever duration indicates drug-resistant M. pneumoniae infection, and a reasonable change in antibiotics is necessary.

In Sicily (Italy), respiratory syncytial virus (RSV), rhinovirus (HRV), and influenza virus triggered epidemics among children, resulting in an increase in acute respiratory tract infections (ARTIs). Our objective was to capture the epidemiology of respiratory infections in children, determining which pathogens were associated with respiratory infections following the lockdown and whether there were changes in the epidemiological landscape during the post-SARS-CoV-2 pandemic era. Materials and Methods: We analyzed multiplex respiratory viral PCR data (BioFire® FilmArray® Respiratory Panel 2.1 Plus) from 204 children presenting with respiratory symptoms and/or fever to our Unit of Pediatrics and Pediatric Emergency. Results: Viruses were predominantly responsible for ARTIs (99%), with RSV emerging as the most common agent involved in respiratory infections, followed by human rhinovirus/enterovirus and influenza A. RSV and rhinovirus were also the primary agents in coinfections. RSV predominated during winter months, while HRV/EV exhibited greater prevalence than RSV during the fall. Some viruses spread exclusively in coinfections (human coronavirus NL63, adenovirus, metapneumovirus, and parainfluenza viruses 1–3), while others primarily caused mono-infections (influenza A and B). SARS-CoV-2 was detected equally in both mono-infections (41%) and coinfections (59%). Conclusions: Our analysis underlines the predominance of RSV and the importance of implementing preventive strategies for RSV.

Background/Objectives: Lower respiratory tract infections (LRTIs) are frequent in the intensive care unit (ICU) and drive empiric broad-spectrum antibiotic use. Rapid multiplex PCR assays may improve pathogen detection and stewardship compared with conventional culture. We evaluated the real-world impact of the BioFire® FilmArray® Pneumonia Panel Plus (FA-PNEU®) on antimicrobial management in suspected nosocomial LRTI. Methods: This was a single-centre, prospective observational cohort study conducted in a tertiary ICU (Madrid, Spain) between April 2021 and March 2025. Adult patients with suspected hospital-acquired pneumonia (HAP), ventilator-associated pneumonia (VAP), or ventilator-associated tracheobronchitis (VAT) were included if paired respiratory samples underwent FA-PNEU® and conventional culture (CC). Diagnostic accuracy and prescribing changes were analysed. Results: A total of 344 samples from 236 patients were included. FA-PNEU® demonstrated high sensitivity (93.4%) and negative predictive value (97.9%) but moderate specificity (65.0%) and low positive predictive value (36.5%). False positives occurred in 85.8% of patients with prior antibiotic therapy targeting the detected organism. Antibiotic management was considered directly influenced by FA-PNEU® when any prescribing decision (initiation, escalation, de-escalation, or discontinuation) explicitly followed the panel’s results rather than other clinical or microbiological information. Using this definition, FA-PNEU® directly influenced antibiotic therapy in 57.6% of cases, while in 17.7%, prescribing was instead guided by a suspected alternative infection. In patients without prior antibiotics, treatment initiation or withholding was fully concordant with FA-PNEU® results, while in those already receiving therapy, 60.8% underwent modification, two-thirds in agreement with the panel. Conclusions: In critically ill patients with suspected nosocomial LRTI, FA-PNEU® provided rapid, high-sensitivity diagnostics that substantially influenced antimicrobial prescribing. Its greatest value lies in ruling out bacterial infection and guiding stewardship, though results must be interpreted within the full clinical and microbiological context.

Background Accurate microbiological documentation seems central for managing severe pneumonia. While the FilmArray ® Pneumonia + panel (FA-PP) offers rapid pathogen identification, its effectiveness during antibiotic treatment and in predicting clinical outcomes remains unclear. Methods We conducted a prospective observational study across four ICUs from April 2022 to June 2024, including patients with ventilator-associated pneumonia (VAP) or ventilated hospital-acquired pneumonia (vHAP). Bacterial loads were monitored on days 0, 1, 3, 7 and 10 and 3 days after stopping antibiotics, using endotracheal aspirates (ETAs) analyzed by FA-PP and standard cultures. The main objective was to assess the correlation between quantitative changes in FA-PP results and clinical success. Quantitative changes over time were analyzed using mixed ordinal logistic regression. Results Of the 93 patients enrolled, 60.2% ( n  = 56) achieved clinical success, while the ICU mortality rate was 25.8% ( n  = 24). Although FA-PP and culture quantification results declined over time ( p  < 0.0001), neither method consistently correlated with clinical success (non-significant for both). At diagnosis, FA-PP showed excellent diagnostic performance compared to culture, with a sensitivity of 94% [95% CI: 87–97] and a specificity of 98% [95% CI: 97–98]. Quantitative concordance improved with higher DNA copies, from 22.9% at the culture threshold at 10⁴ DNA copies/ml in FA-PP to 100% at ≥ 10⁷ DNA copies/ml. Diagnostic performance remained stable during antibiotic treatment with 94% sensitivity and 95% specificity in follow-up ETAs. Conclusions FA-PP provides rapid and accurate diagnostics, but repeated testing did not predict clinical outcomes during treatment, however our small sample size limited the study power.