Integration of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in blood culture diagnostics: a fast and effective approach

Comparison of 3 diagnostic platforms for identification of bacteria and yeast from positive blood culture bottles

Managing bloodstream infections requires fast and accurate diagnostics. Culture-based diagnostic methods for identification from positive blood culture require 24-hour subculture, potentially delaying time to appropriate therapy. Positive blood cultures were collected (n = 301) from September 2021 to August 2022 at the University of Maryland Medical Center. Platforms compared were BioFire® BCID2, Sepsityper®, and short-term culture. For monomicrobial cultures, FilmArray® BCID2 identified 88.3% (241/273) of pathogens. Rapid Sepsityper® identified 76.9% (210/273) of pathogens. Sepsityper® extraction identified 82.4% (225/273) of pathogens. Short-term culture identified 83.5% (228/273) of pathogens. For polymicrobial cultures, Sepsityper®, short-term culture, and BioFire® BCID2 had complete identifications at 10.7% (3/28), 0%, and 92.9% (26/28), respectively. Time-to-results for Rapid Sepsityper®, Sepsityper® extraction, BioFire® BCID2, and Short-term culture were 35, 52, 65, and 306 minutes, respectively. Performance of these platforms can reduce time-to-results and may help effectively treat bloodstream infections faster. Accuracy, time-to-result, and hands-on time are important factors when evaluation diagnostic platforms.

Rapid Identification of Pathogens Causing Bloodstream Infections by Raman Spectroscopy and Raman Tweezers

The search for the "Holy Grail" in clinical diagnostic microbiology-a reliable, accurate, low-cost, real-time, easy-to-use method-has brought up several methods with the potential to meet these criteria. One is Raman spectroscopy, an optical, nondestructive method based on the inelastic scattering of monochromatic light. The current study focuses on the possible use of Raman spectroscopy for identifying microbes causing severe, often life-threatening bloodstream infections. We included 305 microbial strains of 28 species acting as causative agents of bloodstream infections. Raman spectroscopy identified the strains from grown colonies, with 2.8% and 7% incorrectly identified strains using the support vector machine algorithm based on centered and uncentred principal-component analyses, respectively. We combined Raman spectroscopy with optical tweezers to speed up the process and captured and analyzed microbes directly from spiked human serum. The pilot study suggests that it is possible to capture individual microbial cells from human serum and characterize them by Raman spectroscopy with notable differences among different species. IMPORTANCE Bloodstream infections are among the most common causes of hospitalizations and are often life-threatening. To establish an effective therapy for a patient, the timely identification of the causative agent and characterization of its antimicrobial susceptibility and resistance profiles are essential. Therefore, our multidisciplinary team of microbiologists and physicists presents a method that reliably, rapidly, and inexpensively identifies pathogens causing bloodstream infections-Raman spectroscopy. We believe that it might become a valuable diagnostic tool in the future. Combined with optical trapping, it offers a new approach where the microorganisms are individually trapped in a noncontact way by optical tweezers and investigated by Raman spectroscopy directly in a liquid sample. Together with the automatic processing of measured Raman spectra and comparison with a database of microorganisms, it makes the whole identification process almost real time.

Evaluation of a sterile, filter-based, in-house method for rapid direct bacterial identification and antimicrobial susceptibility testing using positive blood culture

This study aimed to assess the performance of our in-house method for rapid direct bacterial identification (ID) and antimicrobial susceptibility testing (AST) using a positive blood culture (BC) broth. For Gram-negative bacteria, 4 mL of BC broth was aspirated and passed through a Sartorius Minisart syringe filter with a pore size of 5 µm. The filtrate was then centrifuged and washed. A small volume of the pellet was used for ID, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and for AST, using automated broth microdilution. For Gram-positive cocci, 4 mL of BC broth was passed through the Minisart syringe filter. Then, 4 mL of sterile distilled water was injected in the direction opposite to that of the filtration to collect the bacterial residue trapped in the filter. Compared with the conventional method performed with pure colonies on agar plates, 94.0% (234/249) were correctly identified using the in-house method, with rates of 91.4% (127/139) and 97.3% (107/110) for Gram-positive and Gram-negative isolates, respectively. Of 234 correctly identified isolates, 230 were assessed by AST. Categorical agreement and essential agreement were 93.3% and 94.5%, respectively, with a minor error rate of 3.8%, a major error rate of 3.4%, and a very major error rate of 1.6%. Our in-house preparation method showed good performance in rapid direct ID and AST using positive BC broths compared to the conventional method. This simple method can shorten the conventional turnaround time for ID and AST by at least 1 day, potentially contributing to better patient management.

FcMBL magnetic bead-based MALDI-TOF MS rapidly identifies paediatric blood stream infections from positive blood cultures

Rapid identification of potentially life-threatening blood stream infections (BSI) improves clinical outcomes, yet conventional blood culture (BC) identification methods require ~24-72 hours of liquid culture, plus 24-48 hours to generate single colonies on solid media suitable for identification by mass spectrometry (MS). Newer rapid centrifugation techniques, such as the Bruker MBT-Sepsityper® IVD, replace culturing on solid media and expedite the diagnosis of BCs but frequently demonstrate reduced sensitivity for identifying clinically significant Gram-positive bacterial or fungal infections. This study introduces a protocol that utilises the broad-range binding properties of an engineered version of mannose-binding lectin linked to the Fc portion of immunoglobulin (FcMBL) to capture and enrich pathogens combined with matrix-assisted laser desorption-ionisation time-of-flight (MALDI-TOF) MS for enhanced infection identification in BCs. The FcMBL method identified 94.1% (64 of 68) of clinical BCs processed, with a high sensitivity for both Gram-negative and Gram-positive bacteria (94.7 and 93.2%, respectively). The FcMBL method identified more patient positive BCs than the Sepsityper® (25 of 25 vs 17 of 25), notably with 100% (3/3) sensitivity for clinical candidemia, compared to only 33% (1/3) for the Sepsityper®. Additionally, during inoculation experiments, the FcMBL method demonstrated a greater sensitivity, identifying 100% (24/24) of candida to genus level and 9/24 (37.5%) top species level compared to 70.8% (17/24) to genus and 6/24 to species (25%) using the Sepsityper®. This study demonstrates that capture and enrichment of samples using magnetic FcMBL-conjugated beads is superior to rapid centrifugation methods for identification of BCs by MALDI-TOF MS. Deploying the FcMBL method therefore offers potential clinical benefits in sensitivity and reduced turnaround times for BC diagnosis compared to the standard Sepsityper® kit, especially for fungal diagnosis.

Identification of micro-organism from positive blood cultures: comparison of three different short culturing methods to the Rapid Sepsityper workflow

Sepsis is one of the leading causes of death worldwide. The rapid identification (ID) of the causative micro-organisms is crucial for the patients' clinical outcome. MALDI-TOF MS has been widely investigated to speed up the time-to-report for ID from positive blood cultures, and many different procedures and protocols were developed, all of them attributable either to the direct separation of microbial cells from the blood cells, or to a short subculture approach. In this study, the Rapid Sepsityper workflow (MBT Sepsityper IVD Kit, Bruker Daltonics GmbH and Co. KG, Bremen, Germany) was compared to three different short subculturing methods, established into the routine practice of three different clinical microbiology laboratories. A total of N=503 routine samples were included in this study and tested in parallel with the two approaches. Results of the rapid procedures were finally compared to routine proceedings with Gram-staining and overnight subculture. Among monomicrobial samples, the Rapid Sepsityper workflow enabled overall the correct identification of 388/443 (87.6 %) micro-organisms, while the short subculturing methods of 267/435 (61.8 %). Except for the performance with Streptococcus pneumoniae, in each one of the three sites the Rapid Sepsityper workflow proved to be superior to the short subculture method, regardless of the protocol applied, and it delivered a result from 1 to 5 h earlier.

Spontaneous Bacterial Peritonitis: The Incremental Value of a Fast and Direct Bacterial Identification from Ascitic Fluids Inoculated in Blood Culture Bottles by MALDI-TOF MS for a Better Management of Patients

Spontaneous bacterial peritonitis (SBP) is a severe infection that requires fast and accurate antibiotic therapy to improve the patient outcome. Direct bacterial identification using MALDI-TOF mass spectrometry from ascitic fluid inoculated in blood culture bottles (BCBs) could therefore improve patients’ management. We evaluated the impact of the implementation of this method for the treatment of patients. Our identification protocol was performed on 136 positive BCBs collected from 61 patients between December 2018 and December 2020. The therapeutic impact of our protocol was evaluated using a before (2015–2016) and after (2019–2020) case–control study in two populations of 41 patients diagnosed with SBP and treated with antibiotics. The decrease in time to first identification and the optimization of antibiotic therapy following communication of the identification result were evaluated. Our protocol allowed us to identify 78% of bacteria in ascitic fluids. The transmission of the direct identification allowed the introduction or adaption of the antibiotic therapy early in 37% of SBP, with a mean decrease in time to first antibiotic change of 17 h. Our direct identification protocol for positive inoculated ascitic fluids is fast, reliable and inexpensive. Its routine integration into a microbiology laboratory allows the early introduction of appropriate antibiotic therapy and improves the management of patients with SBP.

Saving Time in Blood Culture Diagnostics: a Prospective Evaluation of the Qvella FAST-PBC Prep Application on the Fast System

Time to results for identification (ID) and antimicrobial susceptibility testing (AST) from blood cultures is an important factor impacting outcome in sepsis. In this study we evaluated a novel device, the FAST™ system from Qvella that concentrates microbial biomass from positive blood culture flasks with the FAST-PBC Prep™ cartridge thereby producing a liquid colony™ (LC), which can be used immediately in standard laboratory downstream applications. We tested 250 positive blood culture bottles collected from January 2021 to May 2021. Results were obtained either with LC or from bacterial overnight cultures using Bruker's MALDI Biotyper™ and bioMérieux's Vitek 2. We compared ID and AST results obtained by both methods and evaluated turnaround times. Two-hundred and fourteen blood cultures could be included in the analysis. In 94% of the cases (n = 201) identification was obtained directly from the LC with concordant results compared to the standard workflow. No discordant results were observed. AST results could be analyzed for 175 samples. Using categorical analysis, concordant agreement was 97.4% of 1,676 AST results for Gram positive bacteria. Agreement for Gram negative bacteria was 98.5% of 980 AST results. Times-to-result were 36.9 h versus 12.8 h for ID and 52.9 h versus 26.8 h for AST in routine workflow vs FAST^TM system, respectively. The FAST^TM system gives reliable results for ID and AST directly from positive blood cultures and allows for significant time savings in blood culture diagnostics.

Clinical performance of ASTA SepsiPrep kit in direct bacterial identification and antimicrobial susceptibility test using MicroIDSys Elite and VITEK-2 system

BACKGROUND

Rapid and accurate microbial identification and antimicrobial susceptibility testing (AST) are essential for timely use of appropriate antimicrobial agents for bloodstream infection. To shorten the time for isolating colonies from the positive blood culture, various preparation methods for direct identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system were developed. Here, we evaluated the SepsiPrep kit (ASTA Corp.) for direct identification of microorganisms and AST from positive blood cultures using MicroIDSys Elite MALDI-TOF MS system (ASTA Corp.) and VITEK-2 system (bioMérieux).

METHODS

For direct identification, a total of 124 prospective monomicrobial positive blood culture bottles were included. For direct identification, the pellet was prepared by centrifugation and washing twice. For direct AST, the pellet was suspended in 0.45% saline and adjusted to McFarland 0.5. The results from the direct identification and AST using MicroIDSys Elite and VITEK-2 system were compared to those from the conventional method performed with pure colony subcultured on agar plate.

RESULTS

Compared to the conventional method using pure colony, correct direct identification rate was 96.5% and 98.5% for 57 gram-positive isolates and 67 gram-negative isolates, respectively. For direct AST, among the 55 gram-positive isolates, the categorical agreement (CA) for staphylococci, streptococci, and enterococci was 96.7%, 98.4%, and 94.1%, respectively. For 66 gram-negative isolates, the CA for Enterobacterales and non-fermentative gram-negative rods was 99.0% and 96.6%, respectively.

CONCLUSIONS

The SepsiPrep kit was easy to use combined with MicroIDSys Elite and VITEK-2 system and also, the correct identification and AST rate were very high.

In-house protocol and performance of MALDI-TOF MS in the early diagnosis of bloodstream infections in a fourth-level hospital in Colombia: Jumping to full use of this technology

BACKGROUND

Bloodstream infections (BSIs) are a major cause of mortality in hospitalized patients. Rapid diagnosis is crucial because any delay in the antimicrobial treatment is associated with an increase in adverse patient outcomes. The application of matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) technology directly to blood cultures permits earlier identification of BSIs and facilitates treatment management.

METHODS

A total of 470 positive blood cultures from patient samples were analyzed using Standard Aerobic/F and Anaerobic/F blood culture media. Isolates were identified using conventional identification methods and by the direct method using the MALDI-TOF MS system.

RESULTS

In 470 blood cultures, the direct method showed good identification results (420/470, 89%); specifically, accurate species and genus identification in 283/470 (60%), and only correct genus identification in 137/470 (29%). The direct protocol had better performance for Gram-negative compared to Gram-positive bacteria (97% vs 76%) and was unable to identify the positive blood cultures for both yeasts and some bacteria, mostly Gram-positive (50/470).

CONCLUSIONS

The protocol used here gave good and reliable results, being available up to 24 h earlier, while also leading to better use of MALDI-TOF.

Impact of rapid microbial identification on clinical outcomes in bloodstream infection: the RAPIDO randomized trial

OBJECTIVES

Bloodstream infection has a high mortality rate. It is not clear whether laboratory-based rapid identification of the organisms involved would improve outcome.

METHODS

The RAPIDO trial was an open parallel-group multicentre randomized controlled trial. We tested all positive blood cultures from hospitalized adults by conventional methods of microbial identification and those from patients randomized (1:1) to rapid diagnosis in addition to matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) performed directly on positive blood cultures. The only primary outcome was 28-day mortality. Clinical advice on patient management was provided to members of both groups by infection specialists.

RESULTS

First positive blood culture samples from 8628 patients were randomized, 4312 into rapid diagnosis and 4136 into conventional diagnosis. After prespecified postrandomization exclusions, 2740 in the rapid diagnosis arm and 2810 in the conventional arm were included in the mortality analysis. There was no significant difference in 28-day survival (81.5% 2233/2740 rapid vs. 82.3% 2313/2810 conventional; hazard ratio 1.05, 95% confidence interval 0.93-1.19, p 0.42). Microbial identification was quicker in the rapid diagnosis group (median (interquartile range) 38.5 (26.7-50.3) hours after blood sampling vs. 50.3 (47.1-72.9) hours after blood sampling, p < 0.01), but times to effective antimicrobial therapy were no shorter (respectively median (interquartile range) 24 (2-78) hours vs. 13 (2-69) hours). There were no significant differences in 7-day mortality or total antibiotic consumption; times to resolution of fever, discharge from hospital or de-escalation of broad-spectrum therapy or 28-day Clostridioides difficile incidence.

CONCLUSIONS

Rapid identification of bloodstream pathogens by MALDI-TOF MS in this trial did not reduce patient mortality despite delivering laboratory data to clinicians sooner.

Detection of Methicillin Resistance in Staphylococcus aureus From Agar Cultures and Directly From Positive Blood Cultures Using MALDI-TOF Mass Spectrometry-Based Direct-on-Target Microdroplet Growth Assay

Matrix-assisted laser desorption/ionization time-of-flight-mass spectrometry (MALDI-TOF MS)-based direct-on-target microdroplet growth assay (DOT-MGA) was recently described as a novel method of phenotypic antimicrobial susceptibility testing (AST). Here, we developed the application of MALDI-TOF MS-based DOT-MGA for Gram-positive bacteria including AST from agar cultures and directly from positive blood cultures (BCs) using the detection of methicillin resistance as example. Consecutively collected, a total of 14 methicillin-resistant Staphylococcus aureus (MRSA) and 14 methicillin-susceptible S. aureus (MSSA) clinical isolates were included. Furthermore, a collection of MRSA challenge strains comprising different SCCmec types, mec genes, and spa types was tested. Blood samples were spiked with MRSA and MSSA and positive BC broth processed by three different methods: serial dilution of BC broth, lysis/centrifugation, and differential centrifugation. Processed BC broth was directly used for rapid AST using DOT-MGA. Droplets of 6 μl with and without cefoxitin at the EUCAST breakpoint concentration were spotted in triplicates onto the surface of a MALDI target. Targets were incubated in a humidity chamber, followed by medium removal and on-target protein extraction with formic acid before adding matrix with an internal standard as a quality control (QC). Spectra were acquired and evaluated using MALDI Biotyper software. First, tests were considered as valid, if the growth control achieved an identification score of ≥1.7. For valid tests, same score criterion was used for resistant isolates when incubated with cefoxitin. An identification score <1.7 after incubation with cefoxitin defined susceptible isolates. On-target protein extraction using formic acid considerably improved detection of methicillin resistance in S. aureus and DOT-MGA showed feasible results for AST from agar cultures after 4 h incubation time. Comparing the different processing methods of positive BC broth, lysis/centrifugation method with a final dilution step 10^–1 of the 0.5 McFarland suspension resulted in best test performance after 4 h incubation time. Overall, 96.4% test validity, 100% sensitivity, and 100% specificity were achieved for detection of methicillin resistance in clinical isolates. All strains of the MRSA challenge collection were successfully tested as methicillin-resistant. This first study on Gram-positive organisms showed feasibility and accuracy of MALDI-TOF MS-based DOT-MGA for rapid AST of S. aureus from agar cultures and directly from positive BCs.

Applicability of an in-house saponin-based extraction method in Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for identifying bacterial and fungal species in positively flagged pediatric VersaTREK blood cultures

BACKGROUND/PURPOSE

Early identification of pathogens causing bloodstream infection (BSI) is critical for prompt administration of appropriate antimicrobial therapy.

METHODS

We used an in-house saponin-based extraction method to evaluate the performance of Bruker Biotyper MALDI-TOF MS system (MALDI Biotyper) for bacterial and fungal identification in 2013 positively-flagged VersaTREK blood culture bottles.

RESULTS

A total of 180 monomicrobial and 23 polymicrobial positive blood cultures were investigated. Among monomicrobial positive blood cultures, the MALDI Biotyper recognized 90.6% and 81.7% of organisms directly from the flagged blood culture bottles to the genus and species levels, respectively. The MALDI Biotyper also correctly characterized one of the polymicrobial organisms to the species level in 20 (87%) bottles and to the genus level in 21 (91.3%) bottles. The overall identification rate using our protocol was 90.6% (184/203) and 82.3% (167/203) for genus and species levels, respectively. Identification accuracy was higher for Gram-positive than Gram-negative organisms and was the lowest for yeasts. Score values of identification were ≥1.500 for 200 (98.5%) bottles, ≥1.700 for 195 (96.1%) bottles and ≥2.000 for 182 (89.7%) bottles. Moreover, 83.5% and 92% of the isolates were identified precisely to species and genus level with the lower cutoff score of 1.500. Using our protocol also helped identifying BSI pathogens 18-24 h earlier compared to the sub-cultured colonies.

CONCLUSION

Using Bruker MALDI Biotyper for identification of isolates directly from positive VersaTREK blood culture bottles, our in-house saponin-based protocol provided a more rapid turn-around time for correct identification of BSI pathogens than the conventional methods.

Does vancomycin resistance increase mortality in Enterococcus faecium bacteraemia after orthotopic liver transplantation? A retrospective study

BACKGROUND

The relevance of vancomycin resistance in enterococcal blood stream infections (BSI) is still controversial. Aim of this study was to outline the effect of vancomycin resistance of Enterococcus faecium on the outcome of patients with BSI after orthotopic liver transplantation (OLT).

METHODS

The outcome of OLT recipients developing BSI with vancomycin-resistant (VRE) versus vancomycin-susceptible Enterococcus faecium (VSE) was compared based on data extraction from medical records. Multivariate regression analyses identified risk factors for mortality and unfavourable outcomes (defined as death or prolonged intensive care stay) after 30 and 90 days.

RESULTS

Mortality was similar between VRE- (n = 39) and VSE- (n = 138) group after 30 (p = 0.44) or 90 days (p = 0.39). Comparable results occurred regarding unfavourable outcomes. Mean SOFA_Non-GCS score during the 7-day-period before BSI onset was the independent predictor for mortality at both timepoints (HR 1.32; CI 1.14-1.53; and HR 1.18; CI 1.08-1.28). Timely appropriate antibiotic therapy, recent ICU stay and vancomycin resistance did not affect outcome after adjusting for confounders.

CONCLUSION

Vancomycin resistance did not influence outcome among patients with Enterococcus faecium bacteraemia after OLT. Only underlying severity of disease predicted poor outcome among this homogenous patient population.

TRIAL REGISTRATION

This study was registered at the German clinical trials register (DRKS-ID: DRKS00013285).

Rapid identification by MALDI-TOF/MS and antimicrobial disk diffusion susceptibility testing for positive blood cultures after a short incubation on the WASPLab

The objectives of this study were to define the shortest incubation times on the WASPLab for reliable MALDI-TOF/MS-based species identification and for the preparation of a 0.5 McFarland suspension for antimicrobial disk diffusion susceptibility testing using short subcultures growing on solid culture media inoculated by positive blood cultures spiked with a wide range of pathogens associated with bloodstream infections. The 520 clinical strains (20 × 26 different species) included in this study were obtained from a collection of non-consecutive and non-duplicate pathogens identified at Geneva University Hospitals. After 4 h of incubation on the WASPLab, microorganisms' growth allowed accurate identification of 73% (380/520) (95% CI, 69.1-76.7%) of the strains included in this study. The identification rate increased to 85% (440/520) (95% CI, 81.3-87.5%) after 6-h incubation. When excluding Corynebacterium and Candida spp., the microbial growth was sufficient to permit accurate identification of all tested species (100%, 460/460) (95% CI, 99.2-100%) after 8-h incubation. With the exception of Burkholderia cepacia and Haemophilus influenzae, AST by disk diffusion could be performed for Enterobacterales and non-fermenting Gram-negative bacilli after only 4 h of growth in the WASPLab. The preparation of a 0.5 McFarland suspension for Gram-positive bacteria required incubation times ranging between 3 and 8 h according to the bacterial species. Only Corynebacterium spp. required incubation times as long as 16 h. The WASPLab enables rapid pathogen identification as well as swift comprehensive AST from positive blood cultures that can be implemented without additional costs nor hands-on time by defining optimal time points for image acquisition.

Clinical microbiology

The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory.

After reviewing this chapter, the reader will be able to:•

List key considerations for specimen collection for microbiology testing.

•

Discuss the advantages and limitations of automation in the clinical microbiology laboratory.

•

Describe the evolution of microorganism identification methods.

•

Discuss the benefits and limitations of molecular microbiology point-of-care testing.

•

Summarize currently available multiplex molecular microbiology testing options.

Applicability of MALDI-TOF MS for determination of quinolone residues in fish

MALDI-TOF MS approach for determination of six quinolones residues in fillets of pangasius (Pangasionodon hypophthalmus) was studied, considering that is a very sensitive analytical technique with simple and high-throughput operation, contributing to knowledge regarding application of this technique to the determination of small-molecular-weight organic compound residues in foods. LIFT-MS/MS showed to be a successful approach to identify the presence of all quinolone residues in the fish fillet, at their respective MRL level. This study opens an important field of research for the development of simple and high-throughput bioanalytical screening methods for the determination of veterinary drug residues in foods.

Identificación directa de microorganismos a partir de muestras de orina y hemocultivos utilizando MALDI-TOF

Objetivo: evaluar la utilidad de la identificación directa de microorganismos en muestras de orina y hemocultivos empleando la tecnología MALDI-TOF MS, me­diante el análisis de concordancia en la identificación, tiempo necesario para la obtención de un resultado y costos asociados a cada método de identificación.Materiales y métodos: estudio descriptivo de febrero de 2017 a octubre de 2017. Se seleccionaron a conveniencia 180 muestras de orinas y 129 hemocultivos de pacientes de la Clínica El Rosario, Medellín, se realizó identificación del microorganismo directamente de la muestra y a partir del cultivo por MALDI-TOF (Vitek® MS‚ bioMérieux). Se analizaron los costos y tiempo, para determinar la utilidad de esta tecnología en los procesos del laboratorio de microbiología.Resultados: En el 79,6% de las orinas positivas y en el 76% de los hemocultivos se obtuvo una identificación de microorganismos directamente por MALDI-TOF MS. El tiempo de identificación directa tuvo una media de 6 horas y por cultivo una media de 29 horas. El costo total por aislamiento identificado de forma directa (sin incluir el valor del equipo) fue de $8.200 (2,58 USD) en muestras de orina y de $9.720 (3,06 USD) en hemocultivos positivos. El equipo introduce un costo variable en cada identificación de acuerdo con el número de identificaciones que se realicen en el laboratorio.Conclusiones: Estos resultados confirman la utilidad del MALDI-TOF MS para generar identificaciones más rápidas cuando se utiliza directamente en muestras clínicas, sin embargo, tiene un bajo desempeño en la identificación directa de bacterias gram positivas, siendo necesario evaluar otros protocolos que mejoren la identificación directa. El costo de los consumibles es bajo, pero la adquisición de esta tecnología introduce un costo variable que depende del volumen de muestras identificadas en el laboratorio. 

Comparison of rapid BACpro® II, Sepsityper® kit and in-house preparation methods for direct identification of bacteria from blood cultures by MALDI-TOF MS with and without Sepsityper® module analysis

There are several approaches available for purifying microorganisms prior to matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis. In the present study, rapid BACpro® II (Nittobo Medical Co., Ltd., Tokyo, Japan), a new application, has been compared with Sepsityper® kit (Bruker Daltonics, Billerica, USA) and an in-house method. Samples were also tested with two modules, standard and Sepsityper®, identified in the Bruker MALDI-TOF MS. The bottles having monomicrobial growth were included in the study according to Gram staining results. In total, two hundred blood culture bottles were included but there was no growth in one of the subcultures so 199 blood culture bottles were studied prospectively. With the standard MALDI-TOF MS analysis, rapid BACpro® II could successfully identify microorganisms in 174/199 (87.4%) of the bottles where Sepsityper® kit and in-house method were successful in 136/199 (68.3%) and 114/199 (57.3%), respectively. When the MALDI-TOF MS data were analysed by Sepsityper® module, the identification rates were increased to 94.4%, 82.1% and 69.8% (p < 0.001), respectively. In the Sepsityper® module, 72/73 (98.6%) of Gram-negative and 97/106 (91.5%) of Gram-positive microorganisms were detected by rapid BACpro® II method. The present study shows that rapid BACpro® II is a reliable preparation procedure and has higher rates of identification compared with Sepsityper® kit and in-house method. The use of the Sepsityper® module in blood cultures increases the chance of identification for all three methods studied.

Replacement of l-Amino Acids by d-Amino Acids in the Antimicrobial Peptide Ranalexin and Its Consequences for Antimicrobial Activity and Biodistribution

Infections caused by multidrug-resistant bacteria are a global emerging problem. New antibiotics that rely on innovative modes of action are urgently needed. Ranalexin is a potent antimicrobial peptide (AMP) produced in the skin of the American bullfrog Rana catesbeiana. Despite strong antimicrobial activity against Gram-positive bacteria, ranalexin shows disadvantages such as poor pharmacokinetics. To tackle these problems, a ranalexin derivative consisting exclusively of d-amino acids (named danalexin) was synthesized and compared to the original ranalexin for its antimicrobial potential and its biodistribution properties in a rat model. Danalexin showed improved biodistribution with an extended retention in the organisms of Wistar rats when compared to ranalexin. While ranalexin is rapidly cleared from the body, danalexin is retained primarily in the kidneys. Remarkably, both peptides showed strong antimicrobial activity against Gram-positive bacteria and Gram-negative bacteria of the genus Acinetobacter with minimum inhibitory concentrations (MICs) between 4 and 16 mg/L (1.9–7.6 µM). Moreover, both peptides showed lower antimicrobial activities with MICs ≥32 mg/L (≥15.2 µM) against further Gram-negative bacteria. The preservation of antimicrobial activity proves that the configuration of the amino acids does not affect the anticipated mechanism of action, namely pore formation.

Acceleration of the identification of sepsis-inducing bacteria in cultures of dog and cat blood

OBJECTIVES

To evaluate matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS) combined with the Sepsityper kit (Bruker Daltoniks GmbH, Bremen) for the direct detection of bacterial species from inoculated blood cultures from dogs and cats.

MATERIALS AND METHODS

Canine and feline blood samples were inoculated with typical sepsis-causing bacteria such as Staphylococcus intermedius, Staphylococcus aureus, Streptococcus canis, Enterococcus faecalis, Escherichia coli and Pseudomonas aeruginosa at two distinct concentrations (each in triplicate), resulting in 72 blood culture bottles incubated at 37°C. Samples were comparatively analysed with MALDI-TOF MS after preparation with the Sepsityper kit and also by standard bacteriology (culturing and biochemical characterisation).

RESULTS

Bacterial species identified from agar plates and by MALDI-TOF MS from blood culture bottles were identical for all samples. The MALDI Biotyper software (Bruker Daltoniks) correctly identified all bacterial strains from inoculated canine and feline blood with analysis indicating very good precision.

CLINICAL SIGNIFICANCE

MALDI-TOF MS analysis combined with the Sepsityper kit is a reliable tool for a quick detection of veterinary-relevant bacterial species directly from blood culture bottles. This approach could reduce the time for identification of critical species to only 24 hours.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight: The Revolution in Progress

This article summarizes recent advances in the application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to new areas of infectious diseases diagnostics. We discuss progress toward routine identification of mycobacteria and filamentous fungi and direct identification of pathogens from clinical specimens. Of greatest interest is the use of MALDI-TOF MS for identifying organisms from positive blood cultures and from clinical specimens such as urine. Last, We highlight some exciting new possibilities for MALDI-TOF MS phenotypic susceptibility testing for bacteria and yeast.

Serum separator tube method for matrix-assisted laser desorption/ionization time-of-flight analysis

Background

Without appropriate treatment, bloodstream infections have a high mortality rate. Quicker identification of the microbial pathogen allows the clinician to develop an initial strategy of antimicrobial therapy. Sample preparation protocols for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS; Bruker Daltonics for Microflex LT spectrometer) technology were evaluated in an attempt to identify pathogens directly from positive blood culture bottles and thus shorten the time to identify them. This application requires preparatory processing because blood culture bottles contain undesirable proteins. This study aimed to evaluate two methods for microbial preparation for identification by MALDI-ToF MS.

Methods

This study evaluated two methods for microbial preparation from 200 positive blood culture samples, half prepared by the differential centrifugation method and half with the serum separator tube method for identification by MALDI-ToF MS. Both methods were compared to conventional methods such as VITEK II and ChromAgar culture plates.

Results

All Gram-negative bacteria tested were identified correctly by MALDI-ToF MS compared to conventional methods, regardless of the preparation method. However, more Gram-positive bacteria were identified when the serum separator tube method was used (83.3%) compared with the differential centrifugation method (65.3  %). Moreover, the serum separator tube protocol requires 12–15 min, while the differential centrifugation protocol requires 30–45 min.

Conclusions

Sample preparation using the serum separator tube method is easy to perform, fast and reliable for accurate microbial identification by MALDI-ToF MS technology.

Evaluation of QuickFISH and maldi Sepsityper for identification of bacteria in bloodstream infection

BACKGROUND

Early detection of bacteria and their antibiotic susceptibility patterns are critical to guide therapeutic decision-making for optimal care of septic patients. The current gold standard, blood culturing followed by subculture on agar plates for subsequent identification, is too slow leading to excessive use of broad-spectrum antibiotic with harmful consequences for the patient and, in the long run, the public health. The aim of the present study was to assess the performance of two commercial assays, QuickFISH® (OpGen) and Maldi Sepsityper™ (Bruker Daltonics) for early and accurate identification of microorganisms directly from positive blood cultures.

MATERIALS AND METHODS

During two substudies of positive blood cultures, the two commercial assays were assessed against the routine method used at the clinical microbiology laboratory, Unilabs AB, at Skaraborg Hospital, Sweden.

RESULTS

The Maldi Sepsityper™ assay enabled earlier microorganism identification. Using the cut-off for definite species identification according to the reference method (>2.0), sufficiently accurate species identification was achieved, but only among Gram-negative bacteria. The QuickFISH^® assay was time-saving and showed high concordance with the reference method, 94.8% (95% CI 88.4-98.3), when the causative agent was covered by the QuickFISH^® assay.

CONCLUSIONS

The use of the commercial assays may shorten the time to identification of causative agents in bloodstream infections and can be a good complement to the current clinical routine diagnostics. Nevertheless, the performance of the commercial assays is considerably affected by the characteristics of the causative agents.

Direct Identification of 80 Percent of Bacteria from Blood Culture Bottles by Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Using a 10-Minute Extraction Protocol

Matrix-assisted laser desorption ionization-time of flight mass spectrometry is not widely used to identify bacteria directly from positive blood culture bottles (BCBs) because of overlong protocols. The objective of this work was to develop and evaluate a simple extraction protocol for reliable identification from BCBs. The 10-min protocol was applied over a 5-month period. Direct identifications on day 0 were compared with those obtained from colonies on day 1 [log(score) of ≥2]. We evaluated a range of seven log(score) thresholds on day 0 from 1.4 to 2.0 to find the lower confidence score that provides the higher percentage of direct identifications without loss of accuracy. With a log(score) threshold of ≥1.5 at day 0, our protocol allowed us to identify 80% of bacteria in 632 BCBs (96% of Enterobacteriaceae, 95% of Staphylococcus aureus, 92% of enterococci, and 62% of streptococci). At least one bacterial species of the mixture was identified in 77% of the polymicrobial samples. The rapidity and reliability of the protocol were factors in its adoption for routine use, allowing us to save up to 24 h in identifying 80% of the bacteria in the BCBs and, thus, to supply useful information to adapt antibiotic therapy when necessary. We currently provide reliable daily direct identifications of staphylococci, enterococci, Enterobacteriaceae, Pseudomonas aeruginosa, and beta-hemolytic streptococci.

Evaluation of an in-house MALDI-TOF MS rapid diagnostic method for direct identification of micro-organisms from blood cultures

PURPOSE

Bloodstream infections are major causes of morbidity and mortality among hospitalized patients worldwide. Early identification of micro-organisms from blood culture can facilitate earlier optimization of treatment. The objective of this study was to assess an in-house method based on a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform (Clin-TOF MS) for direct organism identification.

METHODOLOGY

We studied the performance of the in-house method for direct identification and the conventional sub-culture method in parallel. Identification from subcultures was analysed with Bruker MS as the reference method.

RESULTS

A total of 666 blood cultures with a single micro-organism that flagged positive after no more than a 3-day incubation period were collected. The identification accuracy of the in-house Clin-TOF MS method for direct identification and the sub-culture method was 88.6 and 100 %, respectively. The in-house method exhibited better performance for Gram-negative bacteria than for Gram-positive bacteria (93.3 vs 81.6 %). The accuracy rate for anaerobes was 100 % (3/3). The lowest accurate identification rate was for yeast; this was only 20 %. Lytic Anaerobic/F (LAF) and Plus Aerobic/F (PAF) provided the highest accurate identification rates, and it was noteworthy that the accuracy rate for FAN Aerobic (FA) was 82 %, which is higher than previously reported and showed that the method was effective.

CONCLUSION

Our study provides an effective sample preparation method for the direct identification of pathogens from positive blood culture vials via Clin-TOF MS at a very low cost of about $0.5 per sample and with a short turnaround time of about 20 min. This will help clinicians make precise diagnoses and provide targeted prescriptions, reducing the risk of the potential development of resistance.

Direct identification and antimicrobial susceptibility testing of microorganisms from positive blood cultures following isolation by lysis-centrifugation

We evaluated a direct from positive blood culture pelleting procedure that utilizes a lysis-centrifugation protocol for the identification of microorganisms by MALDI-TOF MS with subsequent antimicrobial susceptibility testing (AST) and rapid methicillin- and beta-lactam-resistance screening. The identification evaluation was performed on 125 cultures and resulted in the correct genus-level identification in 91.2% of cultures and a species-level concordance of 82.4% compared to routine subcultured growth. For the AST evaluation, susceptibility results from direct pelleting and subcultured growth for 187 cultures were compared; an average ±2-fold dilution agreement of 98.2% (1650/1681) and 98.6% (1375/1394) for Gram-negatives and -positives, respectively, was found. Major errors fell below 5% except for MRSA, which was falsely reported as oxacillin sensitive 17.2% (11/66) of the time. Lastly, the sensitivity and specificity of rapid MRSA screening were 94.7% (36/38) and 90.0% (9/10), respectively, while the ESBL screening results were 90.3% (65/72) and 100.0% (13/13) respectively.

Development of an improved rapid BACpro® protocol and a method for direct identification from blood-culture-positive bottles using matrix-assisted laser desorption ionization time-of-flight mass spectrometry

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been incorporated into pathogenic bacterial identification methods and has improved their rapidity. Various methods have been reported to directly identify bacteria with MALDI-TOF MS by pretreating culture medium in blood culture bottles. Rapid BACpro® (Nittobo Medical Co., Ltd.) is a pretreatment kit for effective collection of bacteria with cationic copolymers. However, the Rapid BACpro® pretreatment kit is adapted only for MALDI Biotyper (Bruker Daltonics K.K.), and there has been a desire to expand its use to VITEK MS (VMS; bioMerieux SA). We improved the protocol and made it possible to analyze with VMS. The culture medium bacteria collection method was changed to a method with centrifugation after hemolysis using saponin; the cationic copolymer concentration was changed to 30% of the original concentration; the sequence with which reagents were added was changed; and a change was made to an ethanol/formic acid extraction method. The improved protocol enhanced the identification performance. When VMS was used, the identification rate was 100% with control samples. With clinical samples, the identification agreement rate with the cell smear method was 96.3%. The improved protocol is effective in blood culture rapid identification, being both simpler and having an improved identification performance compared with the original.

Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result

BACKGROUND

Administration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection.

AIMS

We aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing.

SOURCES

A literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source.

CONTENT

Rapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered.

IMPLICATIONS

The broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.

Multicenter Evaluation of the Accelerate PhenoTest BC Kit for Rapid Identification and Phenotypic Antimicrobial Susceptibility Testing Using Morphokinetic Cellular Analysis

We describe results from a multicenter study evaluating the Accelerate Pheno system, a first of its kind diagnostic system that rapidly identifies common bloodstream pathogens from positive blood cultures within 90 min and determines bacterial phenotypic antimicrobial susceptibility testing (AST) results within ∼7 h. A combination of fresh clinical and seeded blood cultures were tested, and results from the Accelerate Pheno system were compared to Vitek 2 results for identification (ID) and broth microdilution or disk diffusion for AST. The Accelerate Pheno system accurately identified 14 common bacterial pathogens and two Candida spp. with sensitivities ranging from 94.6 to 100%. Of fresh positive blood cultures, 89% received a monomicrobial call with a positive predictive value of 97.3%. Six common Gram-positive cocci were evaluated for ID. Five were tested against eight antibiotics, two resistance phenotypes (methicillin-resistant Staphylococcus aureus and Staphylococcus spp. [MRSA/MRS]), and inducible clindamycin resistance (MLSb). From the 4,142 AST results, the overall essential agreement (EA) and categorical agreement (CA) were 97.6% and 97.9%, respectively. Overall very major error (VME), major error (ME), and minor error (mE) rates were 1.0%, 0.7%, and 1.3%, respectively. Eight species of Gram-negative rods were evaluated against 15 antibiotics. From the 6,331 AST results, overall EA and CA were 95.4% and 94.3%, respectively. Overall VME, ME, and mE rates were 0.5%, 0.9%, and 4.8%, respectively. The Accelerate Pheno system has the unique ability to identify and provide phenotypic MIC and categorical AST results in a few hours directly from positive blood culture bottles and support accurate antimicrobial adjustment.

Short-term incubation of positive blood cultures in brain-heart infusion broth accelerates identification of bacteria by matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry

PURPOSE

Fast identification of bacteria directly from positive blood cultures (BCs) by matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) can be achieved either using the MALDI Sepsityper kit (protein extraction method) or after a short-term pre-cultivation step on solid medium. We developed a new method that involves short-term enrichment of positive BCs in brain-heart infusion broth (BHI) prior to MALDI-TOF MS analysis.

METHODOLOGY

Eighty-four BCs flagged as positive were included in this study; these were processed in parallel either directly using the MALDI Sepsityper kit or following a short-term culture either in BHI or on Columbia blood agar with 5 % sheep blood (CBA).

RESULTS

Bacterial species were successfully identified in 91.6, 89.2 and 65.4 % of cases after pre-cultivation for 4 h in BHI, on CBA, or by using the MALDI Sepsityper kit, respectively. Overall, the mean incubation time to correct identification was shorter when pre-cultures were performed in BHI; the mean time for Gram-negative rods was 78.2 min in BHI and 108.2 min on CBA (P=0.045), and the mean time for Gram-positive cocci was 128.5 min in BHI and 169.6 min on CBA (P=0.013).

CONCLUSION

Short-term enrichment of BCs in BHI accelerates identification of a number of bacterial species by MALDI-TOF MS. Further prospective studies are needed to validate our method and gauge its potential clinical impact on the management of bloodstream bacterial infections.

An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures

Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) directly to blood culture (BC) broth can potentially identify bloodstream infections earlier, and facilitate timely management.

Methods: We developed an “in-house” (IH) protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by “gold standard” of gene sequencing.

Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%), respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%). For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%), MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best.

Conclusion: Our study provides a novel and effective sample preparation method for MALDI-TOF MS direct identification of pathogens from positive BC vials, with a lower cost ($1.5 vs. $ 7) albeit a slightly more laborious extracting process (an extra 15 min) compared with Sepsityper™ kit.

Direct identification from positive blood broth culture by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS)

Bloodstream infections (BSIs) are among the most concerning bacterial infections. They are one of the leading causes of morbidity and mortality, and occur in 30–70% of critical care patients. The prompt identification of the causative microorganism can help choosing the appropriate antimicrobial therapy that will lead to better clinical outcomes. Blood culture is one of the most relevant tests for microbiological diagnosis of bacterial infections. The introduction of the MALDI-TOF microbiological diagnosis significantly decreased the time of identifying microorganisms. However, it depends on the growth on solid culture medium. In this study, 538 bottles of positive blood cultures were evaluated to test the accuracy of an in house modified protocol. The study sample consisted of 198 Gram-negative and 350 Gram-positive bacteria. In all, 460 (83.94%) species were identified based on the direct plate findings. The protocol allowed the identification of 185/198 (93.43%) of the Gram-negative bacteria, including aerobes, anaerobes, and non-fermenters, and 275/350 (78.85%) of the Gram-positive bacteria. The proposed method has the potential to provide accurate results in comparison to the traditional method with the potential to reduce the turnaround time for the results and optimize antimicrobial therapy in BSI.

Evaluation of three sample preparation methods for the direct identification of bacteria in positive blood cultures by MALDI-TOF

BACKGROUND

Patient mortality is significantly reduced by rapid identification of bacteria from sterile sites. MALDI-TOF can identify bacteria directly from positive blood cultures and multiple sample preparation methods are available. We evaluated three sample preparation methods and two MALDI-TOF score cut-off values. Positive blood culture bottles with organisms present in Gram stains were prospectively analysed by MALDI-TOF. Three lysis reagents (Saponin, SDS, and SepsiTyper lysis bufer) were applied to each positive culture followed by centrifugation, washing and protein extraction steps. Methods were compared using the McNemar test and 16S rDNA sequencing was used to assess discordant results.

RESULTS

In 144 monomicrobial cultures, using ≥2.000 as the cut-off value, species level identifications were obtained from 69/144 (48%) samples using Saponin, 86/144 (60%) using SDS, and 91/144 (63%) using SepsiTyper. The difference between SDS and SepsiTyper was not statistically significant (P = 0.228). Differences between Saponin and the other two reagents were significant (P < 0.01). Using ≥1.700 plus top three results matching as the cut-off value, species level identifications were obtained from 100/144 (69%) samples using Saponin, 103/144 (72%) using SDS, and 106/144 (74%) using SepsiTyper and there was no statistical difference between the methods. No true discordances between culture and direct MALDI-TOF identification were observed in monomicrobial cultures. In 32 polymicrobial cultures, MALDI-TOF identified one organism in 34-75% of samples depending on the method.

CONCLUSIONS

This study demonstrates two inexpensive in-house detergent lysis methods are non-inferior to a commercial kit for analysis of positive blood cultures by direct MALDI-TOF in a clinical diagnostic microbiology laboratory.

Quantamatrix Multiplexed Assay Platform system for direct detection of bacteria and antibiotic resistance determinants in positive blood culture bottles

OBJECTIVES

Rapid and accurate identification of the causative pathogens of bloodstream infections (BSIs) is crucial for initiating appropriate antimicrobial therapy, which decreases the related morbidity and mortality rates. The aim of this study was to evaluate the usefulness of a newly developed multiplexed, bead-based bioassay system, the Quantamatrix Multiplexed Assay Platform (QMAP) system, obtained directly from blood culture bottles, to simultaneously detect the presence of bacteria and identify the genes for antibiotic resistance.

METHODS

The QMAP system was used to evaluate 619 blood culture bottles from patients with BSIs and to compare the results of conventional culture methods.

RESULTS

Using conventional bacterial cultures as the reference standard, the sensitivity, specificity, positive predictive value, and negative predictive value of the QMAP system for detection of bacterial pathogens in positive blood culture (PBC) samples were 99.8% (n=592, 95% CI 0.9852-1.000, p <0.001), 100% (95% CI 0.983-1.000, p <0.001), 100% (95% CI 0.9922-1.000, p <0.001), and 99.5% (95% CI 0.9695-1.000, p <0.001), respectively. In addition, sensitivity and specificity of the QMAP system for identification of the genes for antibiotic resistance were 99.4% (n=158, 95% CI 0.9617-0.9999, p <0.009) and 99.6% (95% CI 0.9763-0.9999, p <0.0001), respectively.

CONCLUSIONS

Obtaining results using the QMAP system takes about 3 hr, while culture methods can take 48-72 hr. Therefore, analysis using the QMAP system is rapid and reliable for characterizing causative pathogens in BSIs.

MALDI-TOF MS Versus VITEK®2: Comparison of Systems for the Identification of Microorganisms Responsible for Bacteremia

We evaluated the reliability and accuracy of the combined use of MALDI-TOF MS and classical ID VITEK₂ to identify monomicrobial infection in blood culture bottles. In total, 70 consecutive positive blood cultures were included in this study. Positive blood culture bottles were subjected to Gram staining and subcultured on solid media. Isolates grown from such culture media were used for classical ID using VITEK₂ system. In parallel, an aliquot was subjected to a lysing-centrifugation method and used for the identification with the MALDI-TOF system. Results evidenced the correct genus and species identification of 91.4 % of microorganisms responsible for bacteremia with an agreement to the species and the genus level. If compared with the standard method VITEK₂, our simple and cost-effective sample preparation method would be very useful for rapid identification of microorganisms using blood culture bottles. In fact, the direct method showed rapid and reliable results, especially for the gram-negative group.

Rapid identification and antimicrobial susceptibility testing of positive blood cultures using MALDI-TOF MS and a modification of the standardised disc diffusion test: a pilot study

AIMS

In an era when clinical microbiology laboratories are under increasing financial pressure, there is a need for inexpensive, yet effective, rapid microbiology tests. The aim of this study was to evaluate a novel modification of standard methodology for the identification and antimicrobial susceptibility testing (AST) of pathogens in positive blood cultures, reducing the turnaround time of laboratory results by 24 h.

METHODS

277 positive blood cultures had a Gram stain performed and were subcultured and incubated at 37°C in a CO2 atmosphere for 4-6 h. Identification of the visible growth was performed using matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS). Taking a modified approach to the Clinical and Laboratory Standards Institute-standardised AST methodology, an inoculum density of 0.5 McFarland was prepared from the early growth for disc diffusion testing. The standard AST method was also performed on the 18-24 h culture.

RESULTS

96% (n=73/76) of gram-negative organisms were correctly identified by MALDI-TOF MS. Comparative analysis of the rapid and standard AST results showed an overall interpretive category error rate of 7.7% (6.7% minor errors, 0.6% major errors and 0.4% very major errors). 100% of Staphylococcus aureus (n=41) and enterococcus isolates (n=9) were correctly identified after 4-6 h incubation. The overall AST categorical agreement was also 100% for these isolates.

CONCLUSIONS

An incubation of 4-6 h directly from positive blood cultures allowed for both a rapid species identification and an antimicrobial susceptibility result approximately 24 h earlier than is possible using standard methodology.

Rapid Bacterial Identification, Resistance, Virulence and Type Profiling using Selected Reaction Monitoring Mass Spectrometry

Mass spectrometry (MS) in Selected Reaction Monitoring (SRM) mode is proposed for in-depth characterisation of microorganisms in a multiplexed analysis. Within 60–80 minutes, the SRM method performs microbial identification (I), antibiotic-resistance detection (R), virulence assessment (V) and it provides epidemiological typing information (T). This SRM application is illustrated by the analysis of the human pathogen Staphylococcus aureus, demonstrating its promise for rapid characterisation of bacteria from positive blood cultures of sepsis patients.

The camelliagenin from defatted seeds of Camellia oleifera as antibiotic substitute to treat chicken against infection of Escherichia coli and Staphylococcus aureus

Background

Escherichia coli and Staphylococcus aureus are the main pathogens infectious to poultry, and their resistances against antibiotics have become troublesome currently. Biofilm formation is an important reason for drug resistance. Our previous research has found that the extract of Camellia oleifera seeds has lots of pharmacological effects. In order to find the substitute for antibiotics, the saponin was isolated from the defatted C. oleifera seeds with structural identification. Its efficacy was evaluated by the inhibition on amoxicillin-resistant E. coli and erythromycin-resistant S. aureus and therapeutic effect on chicks infected by the two bacteria.

Results

The bacterial growth inhibition rate increased and the bacterial count in vivo decreased significantly in dose dependence after administration of the saponin and its combination with amoxicillin or erythromycin, suggesting its antibacterial effect. The saponin identified as camelliagenin shows significant inhibition on the biofilm of E. coli and S. aureus, and it is related to the decrease of mannitol dehydrogenase (MDH) activity and extracellular DNA (eDNA) content. Molecular simulation reveals the strong interaction existing between the saponin and MDH or eDNA.

Conclusions

The mechanism of camelliagenin’s improvement on antibiotic effects is its interaction with MDH and eDNA in biofilm. The saponin is a prospective substitute of antibiotics, and molecular simulation is a convenient alternative method to find out hopeful candidates of antibiotics substitute.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures

INTRODUCTION

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium.

MATERIALS AND METHODS

Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result.

RESULTS

Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our approach allowed an optimized treatment recommendation.

CONCLUSION

MALDI-TOF MS following 4h pre-culture is a valuable tool for rapid pathogen identification from positive blood cultures, allowing easy integration in diagnostic routine and the opportunity of considerably earlier treatment adaptation.

Rapid identification of pathogens in positive blood culture of patients with sepsis: review and meta-analysis of the performance of the sepsityper kit

Sepsis is one of the leading causes of deaths, and rapid identification (ID) of blood stream infection is mandatory to perform adequate antibiotic therapy. The advent of MALDI-TOF Mass Spectrometry for the rapid ID of pathogens was a major breakthrough in microbiology. Recently, this method was combined with extraction methods for pathogens directly from positive blood cultures. This review summarizes the results obtained so far with the commercial Sepsityper sample preparation kit, which is now approved for in vitro diagnostic use. Summarizing data from 21 reports, the Sepsityper kit allowed a reliable ID on the species level of 80% of 3320 positive blood culture bottles. Gram negative bacteria resulted consistently in higher ID rates (90%) compared to Gram positive bacteria (76%) or yeast (66%). No relevant misidentifications on the genus level were reported at a log(score)cut-off of 1.6. The Sepsityper kit is a simple and reproducible method which extends the MALDI-TOF technology to positive blood culture specimens and shortens the time to result by several hours or even days. In combination with antibiotic stewardship programs, this rapid ID allows a much faster optimization of antibiotic therapy in patients with sepsis compared to conventional workflows.

MALDI-TOF identification of Gram-negative bacteria directly from blood culture bottles containing charcoal: Sepsityper® kits versus centrifugation-filtration method

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry has dramatically altered the way microbiology laboratories identify clinical isolates. Direct blood culture (BC) detection may be hampered, however, by the presence of charcoal in BC bottles currently in clinical use. This study evaluates an in-house process for extraction and MALDI-TOF identification of Gram-negative bacteria directly from BC bottles containing charcoal. Three hundred BC aliquots were extracted by a centrifugation-filtration method developed in our research laboratory with the first 96 samples processed in parallel using Sepsityper® kits. Controls were colonies from solid media with standard phenotypic and MALDI-TOF identification. The identification of Gram-negative bacteria was successful more often via the in-house method compared to Sepsityper® kits (94.7% versus 78.1%, P≤0.0001). Our in-house centrifugation-filtration method was further validated for isolation and identification of Gram-negative bacteria (95%; n=300) directly from BC bottles containing charcoal.

Rapid and accurate direct antibiotic susceptibility testing of blood culture broths using MALDI Sepsityper combined with the BD Phoenix automated system

Antibiotic susceptibility testing with the BD Phoenix system on bacterial cell pellets generated from blood culture broths using the Bruker MALDI Sepsityper kit was evaluated. Seventy-six Gram-negative isolates, including 12 with defined multi-resistant phenotypes, had antibiotic susceptibility testing (AST) performed by Phoenix on the cell pellet in parallel with conventional methods. In total, 1414/1444 (97.9 %) of susceptibility tests were concordant, with only 1 (0.07 %) very major error. This novel method has the potential to reduce the turnaround time for AST results by up to a day for Gram-negative bacteraemias.

Identification of pathogens from blood culture bottles in spiked and clinical samples using matrix-assisted laser desorption ionization time-of-flight mass-spectrometry analysis

Background

Blood stream infections significantly contribute to mortality. An early most appropriate antimicrobial therapy is crucial for a favourable outcome of the patient. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) may speed up the diagnostic of causative micro organisms.

Findings

MALDI-TOF MS using the SARAMIS database was applied to 37 spiked blood culture samples. Identification rates of spiked samples were as follows: The species level was determined in 16 of 21 (76.2%) Gram negative bacteria and in 11 of 13 (84.6%) Gram positive bacteria. Genus level only was determined in additional 2 Gram negative and for the 2 Gram positive strains. Yeast species could not be identified.

MALDI-TOF MS was also compared to cultured-based results in standard routine diagnostic. Identification rates of patient samples were as follows: The species level was determined in 41 of 47 (87.2%) Gram negative bacteria and in 63 of 123 (51.2%) Gram positive bacteria. Genus level only was determined in additional 2 Gram negative bacteria. Once again no yeasts were identified.

A prolonged incubation of BC bottles for 16 hours after primary positive alert did not influence the concentration of bacteria and identification rates.

Conclusions

The SARAMIS database used in our experiments mainly confirms previous findings that were obtained with the MALDI-TOF MS BRUKER system by others.

Maldi-tof mass spectrometry for microorganism identification

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a rapid, reliable, and high-throughput diagnostic tool for the identification of microorganisms. The technology is unique in clinical microbiology, allowing laboratories to definitively identify bacterial and fungal isolates within minutes. The rapid turnaround time and minimal cost for consumables per specimen compared with conventional identification methods have resulted in MALDI-TOF MS being increasingly used in clinical laboratories worldwide. This article summarizes the current literature on MALDI-TOF MS for microbial identification and provides a preview of the method's potential future applications in clinical microbiology.