Biology subjects

Marco, F.

Publications and source records attributed to Marco, F..

3 recordsLinked to original sources

bioRxiv2019

Assessment of a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of pathogenic bacteria from respiratory samples in patients with hospital-acquired pneumonia

IntroductionHospital-acquired pneumonia (HAP) is the one that presents clinically two or more days after admission into the hospital. Rapid identification of the causative agent of HAP will allow an earlier administration of a more appropriate antibiotic therapy and could lead to an improved outcome of patients with HAP.\n\nMethodsFirst of all, a rapid procedure (< 30 min) to extract the DNA from bronchoalveolar lavage (BAL), endotracheal aspirate (EA) or bronchoaspirate (BAS) was set up. A loop-mediated isothermal amplification reaction (LAMP) specific for Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia and Acinetobacter baumannii was carried out with the extracted solution. The reaction was performed at 65{o}C for 30-40 min. LAMP was compared with bacterial culture method.\n\nResultsOverall, 58 positive BAL and 83 EA/BAS samples were tested. The limits of detection varied according to the microorganism detected and to the respiratory sample analyzed. Validation of the LAMP assay with BAL samples showed that the assay was 100% specific and 86.3% sensitive (positive predictive value of 100% and a negative predictive value of 50%). Meanwhile for BAS/EA samples, the assay rendered the following statistical parameters: 100% specificity, 94.6% sensitivity, 100% positive predictive value and 69.2% negative predictive value. These scores were obtained including minor errors as correct. The turnaround time including preparation of the sample and LAMP was circa 1 hour.\n\nConclusionsLAMP method may be used to detect the most frequent bacteria causing HAP. It is a simple, cheap, sensitive, specific and rapid assay.

microbiology↗

bioRxiv2019

Evaluation of the Accelerate Pheno(TM)system to identify bacteria and determine antimicrobial susceptibility in positive blood cultures

IntroductionNew platforms have recently been developed to reduce response time of identification and antimicrobial susceptibility of bacterial isolates in positive blood cultures from patients with bloodstream infections. The Accelerate Pheno system (Accelerate Diagnostics, Inc.) provides information on pathogen identification and antibiotic susceptibility in approximately 1.5 and 7 hours, respectively.\n\nMethodsIn this study we compared the Accelerate Pheno system with the standard procedure used in our laboratory. A total of 41 blood cultures were prospectively analysed with the Accelerate Pheno system and our standard methods, which include identification by MALDI-TOF mass spectrometry and antibiotic susceptibility testing (AST) by BD Phoenix system and E-test.\n\nResultsThe correlation between the two methods using Cohens kappa coefficient was 0.82; mean (sd) time of identification for MALDI-TOF MS was 0.7 (0.22) hours and 1.43 (0.14) hours for the Accelerate Pheno system. The mean (sd) time of AST with the BD Phoenix system was 15.85 (2.57) hours and with the Accelerate Pheno system 6.7 (0.12) hours. AST results showed an overall essential agreement of 92% for the minimal inhibitory concentrations (MIC) and an overall category agreement of 96%. Among Gram positive isolates, essential and category agreements of 100% were observed. In Gram negative isolates 10 discrepancies were detected, which were classified as 7 major and 3 minor errors. Discrepancies in the Accelerate Pheno system were observed particularly for P. aeruginosa.\n\nConclusionThe Accelerate Pheno system can improve turn-around time in the management of patients with bloodstream infections.

microbiology↗

bioRxiv2018

MagicplexTM Sepsis real-time test for the rapid diagnosis of bloodstream infections in adults

Sepsis is a serious health condition worldwide, affecting more than 30 million people globally each year. In 2017, the World Health Organization (WHO) adopted a resolution on sepsis: \"improving the prevention, diagnosis and clinical management of sepsis\", with the aim of improving early diagnosis, management and prevention to save lives. Blood culture (BC) is generally used to diagnose sepsis because of the low quantity of microbes occurring in the blood during such infections. However, approximately 50% of bloodstream infections (BSI) give negative BC, this figure being higher for sepsis, which delays the start of appropriate antimicrobial therapy. This prospective study evaluated a multiplex real-time polymerase chain reaction, the MagicplexTM Sepsis test (MP), for the detection of pathogens from whole blood, comparing it to routine BC. We analysed 809 blood samples from 636 adult patients, with 132/809 (16.3%) of the samples positive for one or more relevant microorganism according to BC and/or MP. The sensitivity and specificity of MP were 29% and 95%, respectively, while the level of agreement between BC and MP was 87%. The rate of contaminated samples was higher for BC (10%) than MP (4.8%) (P < 0.001). Patients with only MP-positive samples were more likely to be on antimicrobial treatment (47%) than those with only BC-positive samples (18%) (P = 0.002). In summary, the MP test reduces the time taken to identify the microbial pathogen, improving the diagnosis of BSI in patients on antibiotic treatment.

microbiology↗