Identification of selected primary bloodstream infection pathogens in patients attending Kisii level five and Homa Bay county hospitals (original) (raw)
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Open Journal of Medical Microbiology
Introduction: Automated blood culture systems for incubation and growth monitoring have become the standard in high-income countries (HICs), but are still relatively expensive and not universally available for implementation in most low-and middle-income countries (LMIC). We aimed to report blood culture isolates using Automated technique in children and adults admitted into the Federal Teaching Hospital Gombe from 2016 to 2020. Materials and Methods: Blood Culture Isolates in children (0-18 years) and adults (>19 yrs) by Bactec 9050 Automated culture system from 2016-2020 were retrieved from the medical and laboratory register. Information analyzed included, age, sex, month, and year and culture growth and reported antibiotic sensitivity. A Bactec Blood culture tests is 20inthisfacility.InNigeria,theminimummonthlywageis20 in this facility. In Nigeria, the minimum monthly wage is 20inthisfacility.InNigeria,theminimummonthlywageis70 (Official currency exchange rate is N423/US Dollar). Results: Of the 1713 blood cultures performed, children 0-18 years were 1322 (77.2%) and adult (19 years above) (22.8%). Overall positivity was 733 (42.2%) with males 385 (52.5%). Of the 1322 Blood cultures (BC) in children 615 (46.5%) were positive for isolates and adults 118 (30.2)%. Blood culture positivity decreased with increasing age with newborns 251 (34.5%) and adults > 65 years 18 (2.5%). Staphylococcus aureus constituted 61.3% of all isolates and was the leading isolates in all age groups; Alkaligenes (9.1%); Citrobacter
PLoS ONE, 2013
For patients suffering from bloodstream infections (BSI) molecular diagnostics from whole blood holds promise to provide fast and adequate treatment. However, this approach is hampered by the need of large blood volumes. Three methods for pathogen DNA isolation from whole blood were compared, i.e. an enzymatic method (MolYsis, 1-5 ml), the novel nonenzymatic procedure (Polaris, 1-5 ml), and a method that does not entail removal of human DNA (Triton-Tris-EDTA EasyMAG, 200 ml). These methods were evaluated by processing blood spiked with 0-1000 CFU/ml of Staphylococcus aureus, Pseudomonas aeruginosa and Candida albicans. Downstream detection was performed with real-time PCR assays. Polaris and MolYsis processing followed by real-time PCRs enabled pathogen detection at clinically relevant concentrations of 1-10 CFU/ml blood. By increasing sample volumes, concurrent lower cycle threshold (Ct) values were obtained at clinically relevant pathogen concentrations, demonstrating the benefit of using larger blood volumes. A 100% detection rate at a concentration of 10 CFU/ml for all tested pathogens was obtained with the Polaris enrichment, whereas comparatively lower detection rates were measured for MolYsis (50-67%) and EasyMAG (58-79%). For the samples with a concentration of 1 CFU/ml Polaris resulted in most optimal detection rates of 70-75% (MolYsis 17-50% and TTE-EasyMAG 20-36%). The Polaris method was more reproducible, less labour intensive, and faster (45 minutes (including Qiagen DNA extraction) vs. 2 hours (MolYsis)). In conclusion, Polaris and MolYsis enrichment followed by DNA isolation and real-time PCR enables reliable and sensitive detection of bacteria and fungi from 5 ml blood. With Polaris results are available within 3 hours, showing potential for improved BSI diagnostics.
Microbiological diagnostics of bloodstream infections in Europe—an ESGBIES survey
Clinical Microbiology and Infection, 2019
Objectives: High-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories. Methods: We performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.
Indian Journal of Microbiology Research
Bloodstream infections (BSIs) remain a leading cause of morbidity and mortality especially in intensive care units across the world and timely appropriate antimicrobial therapy is a corner stone in its treatment (i) To compare the time difference to diagnose BSIs between FABCID2 and identification and sensitivity by automated systems (ii) To analyse the clinical utility of the FABCID2 panel in positive blood samples among ICU patients.This was a prospective study done from July 2020 to August 2020 where consecutive thirty positive blood culture received from ICUs were processed for gram stain, culture and antimicrobial susceptibility along with performing PCR with BioFire FilmArray Blood Culture Identification2 (FABCID2) Panel. Time line of positive blood culture from receipt to report generation at multiple points were captured along with impact of results in terms of changing antimicrobial therapy of the patients and outcome. : A total of 38 microorganisms were identified from 30 ...
MicrobiologyOpen, 2020
The use of molecular methods in medical microbiology improves the sensitivity of examinations, shortens the turnaround time (TAT), and allows the detection of uncultivable microorganisms (Opota, Jaton, & Greub, 2015). However, their application in the diagnostics of bloodstream infections (BSI) is troublesome due to an extremely low bacterial load and the presence of an excessive amount of human DNA in whole blood (Opota et al., 2015). Therefore, classical blood culture (BC) remains the cornerstone of BSI diagnostics; however, its TAT often exceeds 24 hr, and the sensitivity can be as low as 50%
BioMed Research International, 2018
Rapid bacterial identification of positive blood culture is important for adapting the antimicrobial therapy in patients with blood stream infection. The aim of this study was to evaluate the performance of the multiplex FilmArray Blood Culture Identification (BCID) assay by comparison to an in-house protocol based on MALDI-TOF MS identification of microcolonies after a 4-hour culture, for identifying on the same day the microorganisms present in positive blood culture bottles. One hundred and fifty-three positive bottles from 123 patients were tested prospectively by the 3 techniques of bacterial identification: 11 bottles yielding negative results by the 3 tests were considered false positive (7.2%). The reference MALDI-TOF MS technique identified 134 monomicrobial (87.6%) and 8 double infections (5.2%), which resulted in a total of 150 microorganisms. Globally, 137 (91.3%) of these 150 pathogens were correctly identified by the fully automated multiplex FilmArray BCID system at t...
Rapid Diagnosis of Bloodstream Infections with PCR Followed by Mass Spectrometry
PLoS ONE, 2013
Achieving a rapid microbiological diagnosis is crucial for decreasing morbidity and mortality of patients with a bloodstream infection, as it leads to the administration of an appropriate empiric antimicrobial therapy. Molecular methods may offer a rapid alternative to conventional microbiological diagnosis involving blood culture. In this study, the performance of a new technology that uses broad-spectrum PCR coupled with mass spectrometry (PCR/ESI-MS) was evaluated for the detection of microorganisms directly from whole blood. A total of 247 whole blood samples and paired blood cultures were prospectively obtained from 175 patients with a suspicion of sepsis. Both sample types were analyzed using the PCR/ESI-MS technology, and the results were compared with those obtained by conventional identification methods. The overall agreement between conventional methods and PCR/ESI-MS performed in blood culture aliquots was 94.2% with 96.8% sensitivity and 98.5% specificity for the molecular method. When comparing conventional methods with PCR/ESI-MS performed in whole blood specimens, the overall agreement was 77.1% with 50% sensitivity and 93.8% specificity for the molecular method. Interestingly, the PCR/ESI-MS technology led to the additional identification of 13 pathogens that were not found by conventional methods. Using the PCR/ESI-MS technology the microbiological diagnosis of bloodstream infections could be anticipated in about half of the patients in our setting, including a small but significant proportion of patients newly diagnosed. Thus, this promising technology could be very useful for the rapid diagnosis of sepsis in combination with traditional methods.
Journal of Clinical Microbiology, 2013
The FilmArray platform (FA; BioFire, Salt Lake City, UT) is a closed diagnostic system allowing high-order multiplex PCR analysis with automated readout of results directly from positive blood cultures in 1 h. In the present study, we evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel, which includes 19 bacteria, five yeasts, and three antibiotic resistance genes. In total, 206 blood culture bottles were included in the study. The FilmArray could identify microorganisms in 153/167 (91.6%) samples with monomicrobial growth. Thirteen of the 167 (7.8%) microorganisms were not covered by the FilmArray BCID panel. In 6/167 (3.6%) samples, the FilmArray detected an additional microorganism compared to blood culture. When polymicrobial growth was analyzed, the FilmArray could detect all target microorganisms in 17/24 (71%) samples. Twelve blood culture bottles that yielded a positive signal but showed no growth were also negative by FilmArray. In ...
The Journal of Applied Laboratory Medicine, 2018
Background Currently it can take up to 5 days to rule out bloodstream infection. With the low yield of blood cultures (approximately 10%), a significant number of patients are potentially exposed to inappropriate therapy that can lead to adverse events. More rapid rule out can accelerate deescalation or cessation of antimicrobial therapy, improving patient outcomes. Methods A method is described, termed enzymatic template generation and amplification (ETGA), that universally and sensitively detects DNA polymerase activity liberated from viable bacteria and fungi isolated from blood culture samples as a measure of bloodstream infection. ETGA was applied in a diagnostic test format to identify negative blood cultures after an overnight incubation. Performance data for a prototype (Cognitor) and automated (Magnitor) version of the test are presented. Results The Cognitor manual assay displayed analytical reactivity for a panel of the 20 most prevalent causes of bloodstream infection, w...
Journal of Clinical Microbiology, 2013
Conventional blood culturing using automated instrumentation with phenotypic identification requires a significant amount of time to generate results. This study investigated the speed and accuracy of results generated using PCR and pyrosequencing compared to the time required to obtain Gram stain results and final culture identification for cases of culture-confirmed bloodstream infections. Research and physician-ordered blood cultures were drawn concurrently. Aliquots of the incubating research blood culture fluid were removed hourly between 5 and 8 h, at 24 h, and again at 5 days. DNA was extracted from these 6 time point aliquots and analyzed by PCR and pyrosequencing for bacterial rRNA gene targets. These results were then compared to those of the physician-ordered blood culture. PCR and pyrosequencing accurately identified 92% of all culture-confirmed cases after a mean enrichment time of 5.8 ± 2.9 h. When the time needed to complete sample processing was included for PCR and ...