Rapid identification and antimicrobial susceptibility testing remain a crucial step for early efficient therapy of bloodstream infections. Traditional methods require turnaround times of at least ...2 days, while rapid procedures are often associated with extended hands-on time. The Accelerate Pheno™ System provides microbial identification results within 90 min and susceptibility data in approximately 7 h directly from positive blood cultures with only few minutes of hands-on time. The aim of this study was, therefore, to evaluate the performance of the Accelerate Pheno™ System in identification and antimicrobial susceptibility testing of both Gram-positive and Gram-negative bacteria directly from clinical blood culture samples. We analyzed 108 and 67 blood culture bottles using the Accelerate PhenoTest™ BC kit with software version v1.0 and the FDA-cleared version v1.2, respectively. Reliable identification was achieved for Enterobacteriaceae, staphylococci, and enterococci, with 76/80 (95%), 42/46 (91%), and 10/11 (91%) correct identifications. Limitations were observed in the identification of streptococci, including
Streptococcus pneumoniae
and
Streptococcus pyogenes
, and coagulase-negative staphylococci. Antimicrobial susceptibility results for Enterobacteriaceae, for amikacin, ertapenem, ciprofloxacin, gentamicin, meropenem, and piperacillin-tazobactam ranged between 86 and 100% categorical agreement. Using v1.2, results for ceftazidime showed 100% concordance with the reference method. For staphylococci, the overall performance reached 92% using v1.2. Qualitative tests for detection of methicillin or macrolide-lincosamide-streptogramin B (MLSB) resistance caused major and very major errors for isolates. Overall, the present data show that the Accelerate Pheno™ system can, in combination with Gram stain, be used as a rapid complementation to standard microbial diagnosis of bloodstream infections.
In the management of COVID-19, knowledge is lacking on the frequency of secondary bacterial infections and on how empirical antibiotic therapy should be used. In the present study, we aimed to ...compare blood culture (BC) results of a COVID-19 patient cohort with two cohorts of patients without detected COVID-19.
Using a retrospective cohort study design of patients subjected to BC in six tertiary care hospitals, SARS-CoV-2 positive patients from March 1 to April 30 in 2020 (COVID-19 group) were compared to patients without confirmed SARS-CoV-2 during the same period (control group-2020) and with patients sampled March 1 to April 30 in 2019 (control group-2019). The outcomes studied were proportion of BC positivity, clinically relevant growth, and contaminant growth.
In total 15,103 patients and 17,865 BC episodes were studied. Clinically relevant growth was detected in 197/3,027 (6.5%) BC episodes in the COVID-19 group compared to 717/6,663 (10.8%) in control group-2020 (p<0.0001) and 850/8,175 (10.4%) in control group-2019 (p<0.0001). Contamination was present in 255/3,027 (8.4%) BC episodes in the COVID-19 group compared to 330/6,663 (5.0%) in control group-2020 (p<0.0001) and 354/8,175 (4.3%) in control group-2019 (p<0.0001).
In COVID-19 patients, the prevalence of bloodstream bacterial infection is low and the contamination rate of BC is high. This knowledge should influence guidelines regarding blood culture sampling and empirical antibiotic therapy in COVID-19 patients.
Detection and identification of anaerobic bacteria in blood cultures (BC) is a well-recognized challenge in clinical microbiology. We studied 100 clinical anaerobic BC isolates to evaluate the ...performance of BacT/ALERT-FN, -FN Plus (BioMérieux), BACTEC-Plus and -Lytic (Becton Dickinson BioSciences) BC bottles in detection and time to detection (TTD) of anaerobic bacteria. BACTEC Lytic had higher detection rate (94/100, 94%) than BacT/ALERT FN Plus (80/100, 80%) (p<0.01) in the studied material. There was no significant difference in detection of anaerobic bacteria among the remaining bottle types. The 67 anaerobic bacteria that signalled positive in all four bottle types were analyzed to compare the time to detection (TTD) and isolates were directly identified by MALDI-TOF MS. There was a significant difference in TTD among the four bottle types (p<0.0001). The shortest median TTD was 18 h in BACTEC Lytic followed by BacT/ALERT FN (23.5 h), BACTEC Plus (27 h) and finally BacT/ALERT FN Plus (38 h) bottles. In contrast, MALDI-TOF MS performed similarly in all bottle types with accurate identification in 51/67 (76%) BacT/ALERT FN, 51/67 (76%) BacT/ALERT FN Plus, 53/67 (79%) BACTEC Plus and 50/67 (75%) BACTEC Lytic bottles. In conclusion, BACTEC Lytic bottles have significantly better detection rates and shorter TTD compared to the three other bottle types. The anaerobic BC bottles are equally suitable for direct MALDI-TOF MS for rapid and reliable identification of common anaerobic bacteria. Further clinical studies are warranted to investigate the performance of anaerobic BC bottles in detection of anaerobic bacteria and identification by direct MALDI-TOF MS.
ChatGPT (GPT-3.5) has entered higher education and there is a need to determine how to use it effectively. This descriptive study compared the ability of GPT-3.5 and teachers to answer questions from ...dental students and construct detailed intended learning outcomes. When analyzed according to a Likert scale, we found that GPT-3.5 answered the questions from dental students in a similar or even more elaborate way compared to the answers that had previously been provided by a teacher. GPT-3.5 was also asked to construct detailed intended learning outcomes for a course in microbial pathogenesis, and when these were analyzed according to a Likert scale they were, to a large degree, found irrelevant. Since students are using GPT-3.5, it is important that instructors learn how to make the best use of it both to be able to advise students and to benefit from its potential.
The clinical demand on rapid microbiological diagnostic is constantly increasing. PCR coupled to electrospray ionization-mass spectrometry, PCR/ESI-MS, offers detection and identification of over 750 ...bacteria and Candida species directly from clinical specimens within 6 hours. In this study, we investigated the clinical performance of the IRIDICA BAC LRT Assay for detection of bacterial pathogens in 121 bronchoalveolar lavage (BAL) samples that were received consecutively at our bacterial laboratory for BAL culture. Commensal or pathogenic microorganisms were detected in 118/121 (98%) BAL samples by PCR/ESI-MS, while in 104/121 (86%) samples by routine culture (P<0.01). Detection of potentially pathogenic microorganisms by PCR/ESI-MS was evaluated in comparison with conventional culture-based or molecular methods. The agreement between positive findings was overall good. Most Staphylococcus aureus-positive PCR/ESI-MS results were confirmed by culture or species-specific PCR (27/33, 82%). The identity of Streptococcus pneumoniae could however be confirmed for only 6/17 (35%) PCR/ESI-MS-positive samples. Non-cultivable and fastidious pathogens, which were not covered by standard culture procedures were readily detected by PCR/ESI-MS, including Legionella pneumophila, Bordetella pertussis, Norcadia species and Mycoplasma pneumoniae. In conclusion, PCR/ESI-MS detected a broad range of potential pathogens with equal or superior sensitivity compared to conventional methods within few hours directly from BAL samples. This novel method might thus provide a relevant tool for diagnostics in critically ill patients.
In this study, we explore the transformative potential of UTI-lizer, an emerging technology not yet commercially available. Our manuscript shows that UTI-lizer is a promising alternative for ...detecting the five main pathogens that cause urinary tract infections (UTIs). The results also indicate that digital dipsticks have the potential to uniquely provide UTI diagnostic quality on par with that of gold-standard testing, with the added benefits of ease of testing, rapid test handling time, and simple test equipment. This technology can be helpful in quickly ruling out bacterial infections and reducing the unnecessary use of antibiotics, especially in primary care settings or at the point of care. Moreover, the UTI-lizer test can reduce the number of negative urine samples sent to central laboratories, thus easing the burden of UTI diagnostics on the healthcare system. We believe our study, as well as current and upcoming research based on this technology, is highly relevant for clinical microbiologists, microbiology scientists, general practitioners, and urologists.
In this study, we investigated the performance of the FilmArray and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in identifying microorganisms from ...blood culture (BC) bottles prior to positivity. First, we used simulated BacT/Alert FA Plus BC bottles with five each for Escherichia coli and Staphylococcus aureus isolates. The FilmArray identified all 10 isolates before BC positivity with 9/10 at 5 h and 1 at 7.5 h after incubation in the BC system. MALDI-TOF MS failed to identify the isolates prior to positivity. When the bottles were incubated for 2.5 h at room temperature (RT) before we put them into the BC system, the FilmArray identified 6/10 at 2.5 h and the remaining 4 at 5 h. Finally, we tested simulated BC bottles after incubation at RT. Interestingly, 9/10 isolates were identified with the FilmArray after 8 h of incubation at RT. Second, we studied clinical BC bottles in quadruplicate. When three-fourths of the parallel bottles signaled positive, the FilmArray was run on the fourth nonsignaled bottle and was found to be positive in 14/15 such cases. Third, we analyzed the performance of the FilmArray in the identification of microorganisms from clinical BC bottles before incubation in the system. Two milliliters of broth from 400 BC bottles was collected after arrival at the laboratory and stored at -70°C. Sixteen bottles later signaled positive in the system. When the frozen broth from these bottles was analyzed, the FilmArray identified all the microorganisms in 8/16 bottles prior to incubation in the BC system. This study shows that the FilmArray can identify microorganisms from BC bottles prior to positivity and in some cases even prior to incubation in the BC system.
There is an utmost need for rapid antimicrobial susceptibility testing (AST) of bacteria causing bloodstream infections (BSI). The dRAST (QuantaMatrix Inc., Seoul) is a commercial method that can be ...performed directly from positive blood cultures. The present study aims to evaluate the performance of the dRAST on prospective clinical blood culture samples. A sample prescreening algorithm based on clinical routine was used to choose relevant clinical positive blood culture samples for testing on the dRAST. Rapid identification via short-term culture followed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) was used during the test run, and dRAST results were compared to European Committee on Antimicrobial Susceptibility Testing (EUCAST) disk diffusion as the reference method. The performance of the dRAST was also evaluated on selected multidrug resistant (MDR) isolates in simulated blood cultures. Using the sample pre-screening algorithm, 242 clinical blood culture samples were selected and tested on the dRAST, of which 200 (82.6%) gave valid AST tests results comprising 76 Gram-positive and 124 Gram-negative samples. AST measurements from the dRAST and disk diffusion from clinical samples had an overall agreement rate of 95.5%. When using simulated blood culture samples of 31 selected MDR isolates, the agreement between dRAST and disk diffusion was 87.2%. While the agreement rates were high, it was noted that the dRAST was not reliable for AST of certain antibiotic-bacteria combinations. In conclusion, the present study demonstrates that dRAST delivers rapid AST results from blood cultures and using a prescreening algorithm for sample selection is important in implementation of modern AST methods such as dRAST.
There is an utmost need for rapid antimicrobial susceptibility testing (AST) of bacteria causing bloodstream infections (BSI). The dRAST (QuantaMatrix Inc., Seoul) is a rapid AST method that can be performed directly from positive blood cultures. The dRAST gives results in 6 h compared to conventional AST methods that needs 18-20 h of incubation. The present study aims to evaluate the performance of the dRAST in a clinical setting with the use of a sample selection algorithm to reduce incompatible sample numbers. The study found that while the agreement rates between dRAST and reference AST methods were high, it was noted that the dRAST was not reliable for AST of certain antibiotic-bacteria combinations. In conclusion, the present study demonstrates that dRAST delivers rapid AST results from blood cultures and using a prescreening algorithm for sample selection is important in implementation of modern AST methods such as dRAST.
Mucosa-associated invariant T (MAIT) cells are non-classical T cells important in the mucosal defense against microbes. Despite an increasing interest in the immunobiology of the endometrial mucosa, ...little is known regarding human MAIT cells in this compartment. The potential role of MAIT cells as a tissue-resident local defense against microbes in the endometrium is largely unexplored. Here, we performed a high-dimensional flow cytometry characterization of MAIT cells in endometrium from pre- and postmenopausal women, and in decidua from first-trimester pregnancies. Furthermore, we assessed MAIT cell function by stimulation with Neisseria gonorrhoeae (N. gonorrhoeae). Endometrial MAIT (eMAIT) cells represented a stable endometrial immune cell population as limited dynamic changes were observed during the menstrual cycle, post menopause, or in response to pregnancy. Furthermore, eMAIT cells exhibited an activated tissue-resident phenotype. Despite expressing CD69 and CD103, eMAIT cells were replenished over time by circulating MAIT cells, as assessed using human uterus transplantation as a model. Finally, functional experiments revealed the capability of MAIT cells to respond to the sexually transmitted and tissue-relevant pathogen, N. gonorrhoeae. In conclusion, our study provides novel insight into human MAIT cell dynamics and anti-microbial properties in the human uterus.
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