Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture

Evolving strategies in microbe identification-a comprehensive review of biochemical, MALDI-TOF MS and molecular testing methods

Detection and identification of microorganisms are the first steps to guide susceptibility testing and enable clinicians to confirm diseases and guide therapy. The faster the pathogen identification is determined, the quicker the appropriate treatment can be started. In the clinical microbiology laboratory, multiple methodologies can be used to identify organisms, such as traditional biochemical testing or more recent methods like MALDI TOF MS and nucleic acid detection/identification assays. Each of these techniques has advantages and limitations, and clinical laboratories need to determine which methodology is best suited to their particular setting in terms of clinical needs, availability of technical expertise and cost. This article presents a concise review of the history, utilization, advantages and limitations of the main methods used for identifying microorganisms in microbiology laboratories.

Evaluation of the Vitek® Reveal™ system for rapid antimicrobial susceptibility testing of Gram-negative pathogens, including ESBL, CRE and CRAB, from positive blood cultures

Blood culture (BC) remains the reference diagnostic tool for bloodstream infections but is hampered by long turn-around time (TAT). This study evaluated the Vitek® Reveal™ (VR) system for rapid antimicrobial susceptibility testing (AST) with 72 cases of monomicrobial BCs (55 Enterobacterales, 12 Pseudomonas aeruginosa and 5 Acinetobacter baumannii), including isolates producing carbapenemases and/or extended-spectrum β-lactamases. VR returned AST results with a mean TAT of 5.4 h. Compared to a conventional workflow based on broth microdilution, VR exhibited essential agreement (EA) and category agreement (CA) >90 % in most cases, except with meropenem for Enterobacterales (CA, 85.5 %), piperacillin/tazobactam for P. aeruginosa (EA, 83.3 %), and trimethoprim/sulfamethoxazole for A. baumannii (CA and EA, 80 %). Bias exhibited an underestimation trend with ceftazidime/avibactam (-78.9 %) and ceftazidime (-50 %) for Enterobacterales and P. aeruginosa, respectively. Overall, VR appears an interesting tool to decrease TAT of the BC workflow, although further evaluation with some antibiotic-pathogen combinations would be warranted.

Comparison of the Direct Identification and Short-Term Incubation Methods for Positive Blood Cultures via MALDI-TOF Mass Spectrometry

Timely pathogen identification in bloodstream infections is crucial for patient care. A comparison is made between positive blood culture (BC) pellets from serum separator tubes using a direct identification (DI) method and colonies on agar plates from a short-term incubation (STI) method with a matrix-assisted laser desorption/ionization Biotyper for the evaluation of 354 monomicrobial BCs. Both the DI and STI methods exhibited similar identification rates for different types of bacteria, except for Gram-positive and anaerobic bacteria. The DI method's results aligned closely with the STI method's results for Enterobacterales, glucose-non-fermenting Gram-negative bacilli (GNB), and carbapenem-resistant Enterobacterales. The DI method exhibited high concordance with the conventional method for GNB identification, achieving 88.2 and 87.5% accuracy at the genus and species levels, respectively. Compared with the STI method, the DI method showed a less successful performance for Gram-positive bacterial identification (50.5 vs. 71.3%; p < 0.01). The DI method was useful for anaerobic bacterial identification of slow-growing microorganisms without any need for colony growth, unlike in the STI method (46.7 vs. 13.3%; p = 0.04). However, both methods could not identify yeast in positive BCs. Overall, the DI method provided reliable results for GNB identification, offering many advantages over the STI method by significantly reducing the turnaround time and enabling quicker pathogen identification in positive BCs.

Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures

Background: Rapid diagnostics of pathogens is essential to prescribe appropriate antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is time-consuming. This increases the mortality rate and global burden of antimicrobial resistance. Culture-free detection methods are still under development and are not common in the clinical routine. Therefore, decreasing the culture time for accurately detecting infection and resistance is vital for diagnosis. Methods: This study investigated easy-to-implement factors (in a minimal laboratory set-up), including inoculum size, incubation temperature, and additional supplementation (e.g., vitamin B12 and trace metals), that can significantly reduce the bacterial lag time (tlag). These factors were arranged in simple two-level factorial designs using Gram-positive cocci (Staphylococcus aureus), Gram-positive bacilli (Bacillus subtilis), and Gram-negative bacilli (Escherichia coli and Pseudomonas aeruginosa) bacteria, including clinical isolates with known antimicrobial resistance profiles. Blood samples spiked with a clinical isolate of E. coli CCUG 17620 (Culture Collection University of Gothenburg) were also tested to see the effect of elevated incubation temperature on bacterial growth in blood cultures. Results: We observed that increased incubation temperature (42°C) along with vitamin B12 supplementation significantly reduced the tlag (10 – 115 minutes or 4% - 49%) in pure clinical isolates and blood samples spiked with E. coli CCUG17620. In the case of the blood sample, PCR results also detected bacterial DNA after only 3h of incubation and at three times the CFU/mL. Conclusion: Enrichment of bacterial culture media with growth supplements such as vitamin B12 and increased incubation temperature can be a cheap and rapid method for the early detection of pathogens. This proof-of-concept study is restricted to a few bacterial strains and growth conditions. In the future, the effect of other growth conditions and difficult-to-culture bacteria should be explored to shorten the lag phase.

Increased growth temperature and vitamin B12 supplementation reduces the lag time for rapid pathogen identification in BHI agar and blood cultures

Background: The rapid diagnostics of pathogens is essential to prescribe appropriate and early antibiotic therapy. The current methods for pathogen detection require the bacteria to grow in a culture medium, which is time-consuming. This increases the mortality rate and the global burden of antimicrobial resistance. Culture-free detection methods are still under development and are not used in the clinical routine. Therefore decreasing the culture time for accurate detection of infection and resistance is vital for diagnosis. Methods: In this study, we wanted to investigate easy-to-implement factors (in a minimal laboratory set-up), including inoculum size, incubation temperature, and additional supplementation (e.g., vitamin B12 and trace metals), that can significantly reduce the lag time (tlag). These factors were arranged in simple two-level factorial designs using Gram-positive (Escherichia coli and Pseudomonas aeruginosa) and Gram-negative (Staphylococcus aureus and Bacillus subtilis) bacteria, including clinical isolates with known antimicrobial resistance profiles. Blood samples spiked with a clinical isolate of E. coli CCUG17620 were also tested to see the effect of elevated incubation temperature on bacterial growth in blood cultures. Results: We observed that increased incubation temperature (42°C) along with vitamin B12 supplementation significantly reduced the tlag (10 – 115 minutes or 4% - 49%) in pure clinical isolates and blood samples spiked with E. coli CCUG17620. In the case of the blood sample, PCR results also detected bacterial DNA after only 3h of incubation and at three times the CFU/mL. Conclusions: Enrichment of bacterial culture media with growth supplements such as vitamin B12 and increased incubation temperature can be a cheap and rapid method for the early detection of pathogens. This is a proof-of-concept study restricted to a few bacterial strains and growth conditions. In the future, the effect of other growth conditions and difficult-to-culture bacteria should be explored to shorten the lag phase.

Performance evaluation of the FAST™ System and the FAST-PBC Prep™ cartridges for speeded-up positive blood culture testing

Objectives

As time to appropriate antimicrobial therapy is major to reduce sepsis mortality, there is great interest in the development of tools for direct identification (ID) and antimicrobial susceptibility testing (AST) of positive blood cultures (PBC). Very recently, the FAST™ System (Qvella) has been developed to isolate and concentrate microorganisms directly from PBCs, resulting in the recovery of a Liquid Colony™ (LC) within 30 min. The LC can be used as equivalent of an overnight subcultured colony for downstream testing. We aimed to evaluate the performances of the FAST™ System and FAST-PBC Prep™ cartridges by testing the resulting LC for direct ID, AST and rapid resistance detection.

Materials and methods

Prospectively, FAST™ System testing was carried out on each patient’s first PBC with a monomicrobial Gram-stain result. In the second arm of the study, FAST™ System testing was carried out on blood cultures spiked with multidrug-resistant bacteria. Downstream testing using the LC included MALDI-TOF MS ID with the Bruker Biotyper^® smart system, rapid resistance detection testing including the Abbott Diagnostics Clearview™ PBP2a SA Culture Colony Test (PBP2a) and the Bio-Rad βLACTA™ Test (βLT). AST was performed using the Becton Dickinson Phoenix™ System or by Bio-Rad disk diffusion using filter paper disk following EUCAST 2020 breakpoint criteria.

Results

FAST™ System testing was completed on 198 prospective PBCs and 80 spiked blood cultures. After exclusion of polymicrobial blood cultures, performance evaluation compared with standard of care results was carried out on 266 PBCs. Concordant, erroneous and no ID results included 238/266 (89.5%), 1/266 (0.4%), 27/266 (10.2%) PBCs, respectively. Sensitivity and specificity for PBP2a were 100% (10/10) and 75% (15/20), respectively. Sensitivity and specificity for βLT were 95.8% (23/24) and 100% (42/42), respectively. Categorical agreement for all 160 tested strains was 98% (2299/2346) with 1.2% (8/657) very major errors and 0.7% (10/1347) major errors.

Conclusion

FAST™ System testing is a reliable approach for direct downstream testing of PBCs including MALDI-TOF MS ID, BD Phoenix™ and Bio-Rad disk diffusion AST as well as rapid resistance testing assays. Next steps include optimal integration of the FAST™ System in the PBC workflow with a view toward clinical studies.

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.

Raman Spectroscopy-A Novel Method for Identification and Characterization of Microbes on a Single-Cell Level in Clinical Settings

Rapid and accurate identification of pathogens causing infections is one of the biggest challenges in medicine. Timely identification of causative agents and their antimicrobial resistance profile can significantly improve the management of infection, lower costs for healthcare, mitigate ever-growing antimicrobial resistance and in many cases, save lives. Raman spectroscopy was shown to be a useful-quick, non-invasive, and non-destructive -tool for identifying microbes from solid and liquid media. Modifications of Raman spectroscopy and/or pretreatment of samples allow single-cell analyses and identification of microbes from various samples. It was shown that those non-culture-based approaches could also detect antimicrobial resistance. Moreover, recent studies suggest that a combination of Raman spectroscopy with optical tweezers has the potential to identify microbes directly from human body fluids. This review aims to summarize recent advances in non-culture-based approaches of identification of microbes and their virulence factors, including antimicrobial resistance, using methods based on Raman spectroscopy in the context of possible use in the future point-of-care diagnostic process.

Rapid identification of Gram‑negative pathogens from positive blood cultures using MALDI‑TOF MS following short‑term incubation on solid media

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) enables the timely and reliable identification of microbes. The rapid identification of Gram-negative bacteria (GNB) in bloodstream infections is of critical importance. Several protocols have been proposed for the application of MALDI-TOF MS on samples from positive blood cultures (BCs) within the same day of BC positivity detection. The majority of these protocols include sample preparation steps with the use of chemicals or repeated centrifugations in order to avoid biases from human cells and proteins from the BC broth. These additional steps increase the hands-on processing time and the cost of identification. A different approach is to perform a MALDI-TOF MS analysis using biomass from briefly incubated subcultures on solid media. The present study discusses the findings of previous studies regarding the rapid identification of GNB from positive BC broth using MALDI-TOF MS following a short-term incubation period on solid media without any other additional steps or procedures.

Direct Rapid Identification from Positive Blood Cultures by MALDI-TOF MS: Specific Focus on Turnaround Times

Early availability of pathogen identification in bloodstream infections has critical importance in patients' management. This study investigated the accuracy and feasibility of the direct rapid identification (RID) method from positive blood cultures (BCs) by MALDI-TOF MS and its impact on the turnaround time (TAT) compared to the short-term incubation routine identification (SIRID) method. Pellets prepared from 328 BCs using a serum separator tube in the RID method and colonies on agar plates in the SIRID method were identified with MALDI Biotyper. BCs on weekdays from 6 a.m. to 4 p.m. were defined as the daytime signal group (DSG); BCs from 4 p.m. to 6 a.m. were defined as the night signal group (NSG). Comparison between the two methods was performed with 310 monomicrobial BCs. Two hundred ninety-five (95.2%) monomicrobial BCs yielded an identification result with the RID method. Of the 295 BCs, 289 (97.9%) were identified correctly at the species level, 4 (1.4%) were at the genus level, and 2 (0.7%) were misidentified. In the RID method, at score cutoff values of 1.2, 1.3, 1.4 and 1.5, the rates of correct identifications at the species level were 97.9%, 98.9%, 99.3%, and 100%, respectively. The mean TAT in the DSG was significantly lower (P < 0.001) in the RID method (mean: 2.86 h; 95% CI: 2.65 to 3.07) compared to the SIRID method (mean: 19.49 h; 95% CI: 18.08 to 20.89). Correct identification rates at the species level were 100% in Gram-negative bacteria, 88.9% in Gram-positive bacteria, and 93.2% of all BCs isolates with the RID method. The TAT was improved remarkably in DSG, which might contribute to empirical antibiotic therapies of patients.

IMPORTANCE Using MALDI-TOF MS directly from BCs reduces the time required for pathogen identification, and the TATs for final identification have been compared with overnight incubation from solid media in previous studies. However, identification from a short incubation of agar plates has been increasingly accepted and successfully implemented in routine laboratories, but there is no data comparing direct MALDI-TOF MS with the short-term incubated agar plates. Our study showed that the TAT improved remarkably by applying a RID method by MALDI-TOF MS twice a day periodically when compared to the SIRID method.

Appropriateness of empirical antibiotic prescription for bloodstream infections in an emergency department from 2006 to 2018: impact of the spread of ESBL-producing Enterobacterales

The spread of ESBL producers in the community may impact the management of patients with bloodstream infections (BSI) involving Enterobacterales in emergency departments. Thus, from 2006 to 2018, data for all BSI episodes involving Enterobacterales from the emergency department of a French teaching hospital were retrospectively included. Antimicrobial susceptibility test results and empirical antibiotic regimens were recorded. Treatment was considered as appropriate if all isolates were susceptible in vitro to at least one prescribed antibiotic. A total of 1369 BSI episodes in 1321 patients was included. Urinary tract infection was the main source of BSI (61%). The prevalence of ESBL producers increased from zero to 9.2/100 Enterobacterales BSI cases (p < 0.001), mainly Escherichia coli (6.9 cases/100 BSI in 2018); and no Klebsiella. Third-generation cephalosporins (3GC) were used most frequently (71.8%) and their use as monotherapy increased during the study period (p < 0.001). The rate of appropriate treatment decreased from 95.8 to 89.2% (p = 0.023). Appropriateness of treatment was greater using two drugs vs one (97.3% vs 89.3%, p < 0.001). Treatments with 3GC were appropriate in 92% and 98.3%, when used alone or with another antibiotic, respectively (p < 0.001). Among inappropriate treatments, 45% concerned 3GC, with 74.6% of them attributable to ESBL production. The spread of ESBL producers in the community had a direct impact on the rate of inappropriate empirical treatment. Local antimicrobial resistance monitoring is required to optimize the management of BSI in emergency departments.

Current Scenario and Challenges in the Direct Identification of Microorganisms Using MALDI TOF MS

MALDI TOF MS-based microbial identification significantly lowers the operational costs because of minimal requirements of substrates and reagents for extraction. Therefore, it has been widely used in varied applications such as clinical, food, military, and ecological research. However, the MALDI TOF MS method is laced with many challenges including its limitation of the reference spectrum. This review briefly introduces the background of MALDI TOF MS technology, including sample preparation and workflow. We have primarily discussed the application of MALDI TOF MS in the identification of microorganisms. Furthermore, we have discussed the current trends for bioaerosol detection using MALDI TOF MS and the limitations and challenges involved, and finally the approaches to overcome these challenges.

Shortening the Time of the Identification and Antimicrobial Susceptibility Testing on Positive Blood Cultures with MALDI-TOF MS

The current processes used in clinical microbiology laboratories take ~24 h for incubation to identify the bacteria after the blood culture has been confirmed as positive and fa further ~24 h to report the results of antimicrobial susceptibility tests (ASTs). Patients with suspected bloodstream infection are treated with empiric broad-spectrum antibiotics but delayed targeted antimicrobial therapy. This study aimed to develop a method with a significantly shortened turnaround time for clinical application by identifying the optimal incubation period of a subculture. A total of 188 positive blood culture samples obtained from Nov. 2019 to Aug. 2020 were included. Compared to the conventional 24-h incubation for bacterial identification, our approach achieved 96.1% and 97.4% identification accuracy after shortening the incubation time to 4.5 and 3.5 h for gram-positive (GP) and gram-negative (GN) bacterial samples, respectively. Samples from short-term incubation without any intermediate step or process were directly subjected to analysis with the Phoenix M50 AST. Compared to the conventional disk diffusion AST, the category agreements for GP (excluding Streptococcus spp.), Streptococcus spp., and GN bacterial samples were 91.8%, 97.5%, and 92.7%, respectively. Our approach significantly reduced the average turnaround time from 48 h to 28 h for reporting bacterial identity and decreased average AST from 72 h to 50.3 h compared to the conventional methods. Accordingly, this approach allows a physician to prescribe the appropriate antibiotic(s) ~21.7 h earlier, thereby improving patient outcomes.

Assessment of version 2.5 of QMAC-dRAST for rapid antimicrobial susceptibility testing with reduced sample-to-answer turnaround time and an integrated expert system

OBJECTIVE

To assess the performance of the new rapid antimicrobial susceptibility testing (AST) QMAC-dRAST V2.5 system.

METHODS

ASTs were performed using QMAC-dRAST-V2.5 and a disk diffusion method, directly from positive blood bottles with Gram-negative bacteria. Discrepancies between the results obtained using the two methods were categorized into very major errors (VME, S with dRAST vs. R with disk diffusion), major errors (ME, R vs. S, respectively), minor errors (mE, S vs. I or I vs. R, respectively), and very minor errors (Vme, I vs. S or R vs. I, respectively). For each AST, results were recorded after 4, 5, and 6h of incubation.

RESULTS

From 106 bacteremia, 1416 individual AST results were obtained. Overall agreement between results using the two methods was 91%, ranging from 76.9% to 99.1% depending upon the antibiotic, with 128 errors, i.e. 14/1416 (1%) VME, 59/1416 (4.2%) ME, 25/1416 (1.8%) mE and 30/1416 (2.1%) Vme. VMEs were encountered for Klebsiellasp and Serratia marcescens isolates with low-level piperacillin and amikacin resistance, respectively. Using the integrated QMAC-dRAST-V2.5 expert system, all 14 VMEs and 3 mEs were eliminated, leading to 92.2% categorical agreement. After 45min of pre-incubation in the QMAC-dRAST-V2.5 device, 22.2% of the 1416 AST results were obtained after 4h, an additional 31.4% after 5h and a further 46.3% after 6h.

CONCLUSION

QMAC-dRAST-V2.5 is an optimized version of QMAC-dRAST V2.0, particularly with respect to utilization of an expert system and reduced TAT according to the antibiotic tested.

Applications of Raman Spectroscopy in Bacterial Infections: Principles, Advantages, and Shortcomings

Infectious diseases caused by bacterial pathogens are important public issues. In addition, due to the overuse of antibiotics, many multidrug-resistant bacterial pathogens have been widely encountered in clinical settings. Thus, the fast identification of bacteria pathogens and profiling of antibiotic resistance could greatly facilitate the precise treatment strategy of infectious diseases. So far, many conventional and molecular methods, both manual or automatized, have been developed for in vitro diagnostics, which have been proven to be accurate, reliable, and time efficient. Although Raman spectroscopy (RS) is an established technique in various fields such as geochemistry and material science, it is still considered as an emerging tool in research and diagnosis of infectious diseases. Based on current studies, it is too early to claim that RS may provide practical guidelines for microbiologists and clinicians because there is still a gap between basic research and clinical implementation. However, due to the promising prospects of label-free detection and noninvasive identification of bacterial infections and antibiotic resistance in several single steps, it is necessary to have an overview of the technique in terms of its strong points and shortcomings. Thus, in this review, we went through recent studies of RS in the field of infectious diseases, highlighting the application potentials of the technique and also current challenges that prevent its real-world applications.

Implementation of rapid antimicrobial susceptibility testing combined with routine infectious disease bedside consultation in clinical practice (RAST-ID): a prospective single-centre study

OBJECTIVES

Recently, EUCAST released guidelines for rapid antimicrobial susceptibility testing (RAST) directly from positive blood culture bottles. The aim of our prospective single-centre clinical study was to assess the proportion of readable results and errors compared with routine antimicrobial susceptibility testing and the clinical consequences drawn by infectious disease (ID) physicians from RAST results during same-day bedside consultation.

METHODS

All positive blood cultures suitable for RAST from January to December 2019 were included and RAST results at 4 and 6 h compared with standard disc diffusion. The real-life impact of RAST on clinical decisions was assessed during same-day ID bedside consultation.

RESULTS

The proportion of readable RAST results was significantly higher after 6 h of incubation compared with after 4 h (881/930 versus 642/847; P < 0.0001). Major and very major errors were rare (17/642 after 4 h and 12/881 after 6 h; P = 0.087). ID consultation was performed in 134 patients after the RAST result. Antimicrobial treatment was changed in 73 patients and 84 additional measures (i.e. imaging studies, surgery, additional resistance testing) were ordered in 62 patients.

CONCLUSIONS

RAST according to EUCAST methods was easy to implement with a low number of major and very major errors after 6 h of incubation. ID physicians performing bedside consultations frequently used this information to change antimicrobial treatment and recommended additional measures.

Scanning Electron Microscope: A New Potential Tool to Replace Gram Staining for Microbe Identification in Blood Cultures

Blood culture is currently the most commonly used method for diagnosing sepsis and bloodstream infections. However, the long turn-around-time to achieve microbe identification remains a major concern for clinical microbiology laboratories. Gram staining for preliminary identification remains the gold standard. We developed a new rapid strategy using a tabletop scanning electron microscope (SEM) and compared its performance with Gram staining for the detection of micro-organisms and preliminary identification directly from blood cultures. We first optimised the sample preparation for twelve samples simultaneously, saving time on imaging. In this work, SEM proved its ability to identify bacteria and yeasts in morphotypes up to the genus level in some cases. We blindly tested 1075 blood cultures and compared our results to the Gram staining preliminary identification, with MALDI-TOF/MS as a reference. This method presents major advantages such as a fast microbe identification, within an hour of the blood culture being detected positive, low preparation costs, and data traceability. This SEM identification strategy can be developed into an automated assay from the sample preparation, micrograph acquisition, and identification process. This strategy could revolutionise urgent microbiological diagnosis of infectious diseases.

Rapid Detection of Methicillin-Resistant Staphylococcus aureus Directly from Blood for the Diagnosis of Bloodstream Infections: A Mini-Review

Staphylococcus aureus represents a major human pathogen able to cause a number of infections, especially bloodstream infections (BSI). Clinical use of methicillin has led to the emergence of methicillin-resistant S. aureus (MRSA) and MRSA-BSI have been reported to be associated with high morbidity and mortality. Clinical diagnosis of BSI is based on the results from blood culture that, although considered the gold standard method, is time-consuming. For this reason, rapid diagnostic tests to identify the presence of methicillin-susceptible S. aureus (MSSA) and MRSA isolates directly in blood cultures are being used with increasing frequency to rapidly commence targeted antimicrobial therapy, also in the light of antimicrobial stewardship efforts. Here, we review and report the most common rapid non-molecular and molecular methods currently available to detect the presence of MRSA directly from blood.

Comparison of Accelerate PhenoTest BC Kit and MALDI-TOF MS/VITEK 2 System for the rapid identification and antimicrobial susceptibility testing of gram-negative bacilli causing bloodstream infections

BACKGROUND

Our laboratory uses matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) and the VITEK 2 system (DV2) directly from positive blood cultures (BC) for organism identification (ID) and antimicrobial susceptibility testing (AST). Our objective was to compare direct MALDI-DV2 with a commercial BC ID-AST platform, the Accelerate Pheno system (AXDX), in the ID-AST of clinical and seeded BC positive for gram-negative bacilli (GNB).

METHODS

BC positive for GNB were collected over a 3-mo period and tested using AXDX and direct MALDI-DV2 and compared with conventional methods. A subset of sterile BC were seeded with multi-drug-resistant GNB.

RESULTS

Twenty-nine clinical samples and 35 seeded samples were analyzed. Direct MALDI had a higher ID failure rate (31.0%) than AXDX (3.4%; p < 0.001). Time to ID-AST was 1.5-6.9 h, 5.8-16.5 h, and 21.6-33.0 h for AXDX, direct MALDI-DV2, and conventional methods, respectively (p < 0.001). For clinical samples, AXDX and DV2 had essential agreement (EA) or categorical agreement (CA) of more than 96%. For seeded samples, AXDX had EA, CA, VME, ME, and minor error (mE) of 93.2%, 89.0%, 2.2%, 0%, and 9.2%, respectively. AXDX had a large number of non-reports (6.1%) stemming from meropenem testing. DV2 had EA, CA, VME, ME, and mE of 97.5%, 94.7%, 1.3%, 0%, and 4.1%, respectively.

CONCLUSIONS

Direct MALDI-DV2 and AXDX both had high agreement for clinical samples, but direct MALDI-DV2 had higher agreement when challenged with MDR GNB.

Mass spectrometry-based microbiological testing for blood stream infection

BACKGROUND

The most successful application of mass spectrometry (MS) in laboratory medicine is identification (ID) of microorganisms using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) in blood stream infection. We describe MALDI-TOF MS-based bacterial ID with particular emphasis on the methods so far developed to directly identify microorganisms from positive blood culture bottles with MALDI-TOF MS including our own protocols. We touch upon the increasing roles of Liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) as well.

MAIN BODY

Because blood culture bottles contain a variety of nonbacterial proteins that may interfere with analysis and interpretation, appropriate pretreatments are prerequisites for successful ID. Pretreatments include purification of bacterial pellets and short-term subcultures to form microcolonies prior to MALDI-TOF MS analysis. Three commercial protocols are currently available: the Sepsityper® kit (Bruker Daltonics), the Vitek MS blood culture kit (bioMerieux, Inc.), and the rapid BACpro® II kit (Nittobo Medical Co., Tokyo). Because these commercially available kits are costly and bacterial ID rates using these kits are not satisfactory, particularly for Gram-positive bacteria, various home-brew protocols have been developed: 1. Stepwise differential sedimentation of blood cells and microorganisms, 2. Combination of centrifugation and lysis procedures, 3. Lysis-vacuum filtration, and 4. Centrifugation and membrane filtration technique (CMFT). We prospectively evaluated the performance of this CMFT protocol compared with that of Sepsityper® using 170 monomicrobial positive blood cultures. Although preliminary, the performance of the CMFT was significantly better than that of Sepsityper®, particularly for Gram-positive isolates. MALDI-TOF MS-based testing of polymicrobial blood specimens, however, is still challenging. Also, its contribution to assessment of susceptibility and resistance to antibiotics is still limited. For this purpose, liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) should be more useful because this approach can identify as many as several thousand peptide sequences.

CONCLUSION

MALDI-TOF MS is now an essential tool for rapid bacterial ID of pathogens that cause blood stream infection. For the purpose of assessment of susceptibility and resistance to antibiotics of the pathogens, the roles of liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS) will increase in the future.

A novel flow cytometry assay based on bacteriophage-derived proteins for Staphylococcus detection in blood

Bloodstream infections (BSIs) are considered a major cause of death worldwide. Staphylococcus spp. are one of the most BSIs prevalent bacteria, classified as high priority due to the increasing multidrug resistant strains. Thus, a fast, specific and sensitive method for detection of these pathogens is of extreme importance. In this study, we have designed a novel assay for detection of Staphylococcus in blood culture samples, which combines the advantages of a phage endolysin cell wall binding domain (CBD) as a specific probe with the accuracy and high-throughput of flow cytometry techniques. In order to select the biorecognition molecule, three different truncations of the C-terminus of Staphylococcus phage endolysin E-LM12, namely the amidase (AMI), SH3 and amidase+SH3 (AMI_SH3) were cloned fused with a green fluorescent protein. From these, a higher binding efficiency to Staphylococcus cells was observed for AMI_SH3, indicating that the amidase domain possibly contributes to a more efficient binding of the SH3 domain. The novel phage endolysin-based flow cytometry assay provided highly reliable and specific detection of 1-5 CFU of Staphylococcus in 10 mL of spiked blood, after 16 hours of enrichment culture. Overall, the method developed herein presents advantages over the standard BSIs diagnostic methods, potentially contributing to an early and effective treatment of BSIs.

Comparative evaluation of the QMAC-dRAST V2.0 system for rapid antibiotic susceptibility testing of Gram-negative blood culture isolates

To comparatively evaluate the performance of the rapid antimicrobial susceptibility testing (AST) system QMAC-dRAST V2.0 and of standard disk diffusion in agar, AST was performed directly from 100 positive blood culture bottles with Gram-negative bacilli. AST results provided by QMAC-dRAST showed 92.9% agreement with disk diffusion method results. Discrepancies observed between results obtained with QMAC-dRAST and disk diffusion method conducted to 10 very major errors (0.8%, S with QMAC-dRAST vs R with disk diffusion method), 40 major errors (3.2%, R vs S, respectively), 15 minor errors (1.2%, S vs I or I vs R, respectively) and 23 very minors errors (1.8%, I vs S or R vs I, respectively). For very major and major errors, in only 36% of the cases did the repeat QMAC-dRAST confirm the initial result, whereas a repeat AST using disk diffusion method confirmed the initial result in 92% of cases. AST results obtained using microdilution in liquid medium confirmed those obtained with QMAC-dRAST and disk diffusion method in 4% and 89%, respectively. Repeatability and reproducibility tests performed on QMAC-dRAST using reference strains showed 94% to 100% of R/S/I categorical agreement.

Rapid identification of microorganisms from positive blood cultures in pediatric patients by MALDI-TOF MS: Sepsityper kit versus short-term subculture

BACKGROUND AND AIM

The rapid diagnosis of bloodstream infection (BSI) often leads to better clinical outcomes. The present study was conducted to compare two rapid protocols (Sepsityper kit and short-term subculture) for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based identification of microorganisms from positive blood cultures in pediatric patients.

METHODS

This study was conducted between May 1, 2018, and April 30, 2019, at a tertiary children's hospital in eastern China. Only monomicrobial blood cultures included in this study were used to conduct the Sepsityper kit protocol and short-term subculture protocol at the same time.

RESULTS

In total, 115 monomicrobial blood cultures were included in this study. For the Sepsityper kit protocol, 85.2% and 64.3% of microorganisms were correctly identified to the genus (score ≥ 1.700) and species levels (score ≥ 2.000), respectively. For the short-term subculture protocol, 89.6% and 70.4% of microorganisms were correctly identified to the genus and species levels, respectively. At the genus level (P = .321) or the species level (P = .325), there was no significant difference between the Sepsityper kit protocol and the short-term subculture protocol. Moreover, the short-term subculture protocol exhibited similar performance between Gram-positive bacteria (GPB) and Gram-negative bacteria (GNB) (the genus level: 93.7% (GPB) versus 87.9% (GNB), P = .518; the species level: 68.4% (GPB) versus 81.8% (GNB), P = .147). In addition, the Sepsityper kit protocol exhibited similar performance between GPB and GNB at the genus level (86.1% (GPB) versus 84.8% (GNB), P = 1.000). However, the Sepsityper kit protocol exhibited better performance in GNB at the species level (58.2% (GPB) versus 81.8% (GNB), P = .017). The rates of yeast-like fungi were correctly identified to the genus level (0.0%) or the species level (0.0%) for short-term subculture protocol were significantly lower than those of other microorganisms (the genus level: 92.0%, P = .001; the species level: 72.3%, P = .024). However, a similar result of identification was not found using the Sepsityper kit protocol (the genus level: P = .384; the species level: P = .599). In addition, the two rapid protocols both exhibited better performance at the genus level when the time to positivity (TTP) of blood cultures <19 h (the Sepsityper kit protocol: 91.8% (TTP < 19 h) versus 77.8% (TTP ≥ 19 h), P = .034; the short-term subculture protocol: 95.1% (TTP < 19 h) versus 83.3% (TTP ≥ 19 h), P = .040). In addition, the two rapid protocols both exhibited better performance at the species level when the TTP of blood cultures was <19 h (the Sepsityper kit protocol: 78.7% (TTP < 19 h) versus 48.1% (TTP ≥ 19 h), P = .000; the short-term subculture protocol: 83.6% (TTP < 19 h) versus 55.6% (TTP ≥ 19 h), P = .001).

CONCLUSION

The Sepsityper kit protocol and short-term subculture protocol are both reliable and rapid methods for the identification of most microorganisms from positive blood cultures in pediatric patients. The performance of these two rapid protocols is associated with the TTP of blood cultures.

Rapid direct identification of positive paediatric blood cultures by MALDI-TOF MS technology and its clinical impact in the paediatric hospital setting

OBJECTIVE

Rapid diagnostic tools are imperative for timely clinical decision making, particularly in bacteraemic patients. This study evaluated the performance of a fast, inexpensive novel in house method for processing positive blood cultures for immediate identification of microorganisms by matrix-assisted laser desorption ionization-time of flight mass spectrometry (Vitek MS bioMérieux). We prospectively analyzed the clinical impact of such method on the management of pediatric patients.

RESULT

In total, 360 positive blood cultures were included. Among 318 mono-microbial cultures, in-house method achieved correct identification in 270 (85%) cultures to the species level, whilst 43 (13.5%) gave no identification, and 7 (2.2%) gave discordant identifications. Identification of Gram-negative organisms was accurate to both species and genus level in 99% of isolates, and for Gram positives accuracy was 84% to genus and 81% to species level overall, with accuracy of 100% for Staphylococcus aureus and Enterococcus to the species level. Assessment of the potential impact of direct identification in sixty sequential cases revealed a clear clinical benefit in 35.5% of cases. Benefits included timely antibiotic rationalization, change of medical intervention, and early confirmation of contamination. This study demonstrates a highly accurate in-house method with considerable potential clinical benefits for paediatric care.

The implementation of rapid microbial identification via MALDI-ToF reduces mortality in gram-negative but not gram-positive bacteremia

Our goals were to study the effect of rapid microbial identification (RMI) of positive blood culture on patient's outcome and to identify specific microbiological characteristics related to clinical benefit of RMI. This was a retrospective-cohort study of hospitalized, adult patients with bacteremia. The outcome of patients with bacteremia episodes was compared before vs. after the initiation of RMI. RMI was done by matrix-assisted laser desorption/ionization time-of-flight testing of microcolonies. The study included 1460 and 2710 cases in the pre- and post-intervention periods, respectively. There were similar rates of gram-negative, gram-positive, anaerobes, and polymicrobial infections, but higher rate of contaminants in the intervention period (39.9 vs. 43.7%, p = 0.019). The median time-to-identification decreased from 47.5 to 21.3 h (p < 0.001). Post-intervention, the median LOS declined from 10.83 to 9.79 days (p = 0.016), the rate of ICU transfer declined from 13.8 to 11.6% (p = 0.054), and the mortality rate declined from 20.9 to 18.3% (p = 0.047). The improvement in outcome variables remained statistically significant in multivariate analysis when performed for all episodes and non-contaminants but not for contaminants. The mortality declined in gram-negative bacteremia (20% vs. 15.5%, p = 0.005 in multivariate analysis) but not in gram-positive bacteremia (18.1% vs. 18.5%). RMI reduces mortality from gram-negative but not gram-positive bacteremia.

New Microbiological Techniques in the Diagnosis of Bloodstream Infections

BACKGROUND

When a bloodstream infection is suspected, the preliminary and definitive results of culture-based microbiological testing arrive too late to have any influence on the initial choice of empirical antibiotic treatment.

METHODS

This review is based on pertinent publications retrieved by a selective search of the literature and on the authors' clinical and scientific experience.

RESULTS

A number of technical advances now enable more rapid microbiological diagnosis of bloodstream infections. DNA- based techniques for the direct detection of pathogenic organisms in whole blood have not yet become established in routine use because of various limitations. On the other hand, matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become available for routine use in clinical laboratories and has markedly shortened the time to diagnosis after blood samples that have been cultured in automated blood-culture systems turn positive. Further developments of this technique now enable it to be used directly for blood cultures that have been flagged positive, as well as for subcultures that have been incubated for only a short time on a solid nutrient medium. The microbial biomass of the subculture can also be used in parallel for more rapid susceptibility testing with conventional methods, or, in future, with MALDI-TOF MS.

CONCLUSION

The potential of all of these new techniques will only be realizable in practice if they are optimally embedded in the diagnostic process and if sufficient attention is paid to pre-analytical issues, particularly storage and transport times.

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.

Evaluation of the ePlex Blood Culture Identification Panels for Detection of Pathogens in Bloodstream Infections

Rapid identification and susceptibility testing results are of importance for the early appropriate therapy of bloodstream infections. The ePlex (GenMark Diagnostics) blood culture identification (BCID) panels are fully automated PCR-based assays designed to identify Gram-positive and Gram-negative bacteria, fungi, and bacterial resistance genes within 1.5 h from positive blood culture.

Rapid identification and susceptibility testing results are of importance for the early appropriate therapy of bloodstream infections. The ePlex (GenMark Diagnostics) blood culture identification (BCID) panels are fully automated PCR-based assays designed to identify Gram-positive and Gram-negative bacteria, fungi, and bacterial resistance genes within 1.5 h from positive blood culture. Consecutive non-duplicate positive blood culture episodes were tested by the ePlex system prospectively. The choice of panel(s) (Gram-positive, Gram-negative, and/or fungal pathogens) was defined by Gram-stained microscopy of blood culture-positive bottles (BacT/Alert; bioMérieux). Results with the ePlex panels were compared to the identification results obtained by standard culture-based workflow. In total, 216 positive blood culture episodes were evaluable, yielding 263 identification results. The sensitivity/positive predictive value for detection by the ePlex panels of targeted cultured isolates were 97% and 99% for the Gram-positive panel and 99% and 96% for the Gram-negative panel, resulting in overall agreement rates of 96% and 94% for the Gram-positive and Gram-negative panel, respectively. All 26 samples with targeted resistance results were correctly detected by the ePlex panels. The ePlex panels provided highly accurate results and proved to be an excellent diagnostic tool for the rapid identification of pathogens causing bloodstream infections. The short time to results may be of added value for optimizing the clinical management of patients with sepsis.

Evaluation of the Bruker® MBT Sepsityper IVD module for the identification of polymicrobial blood cultures with MALDI-TOF MS

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) considerably reduces timeframe required from initial blood culture positivity towards complete bacterial identification. However, rapid identification of polymicrobial blood cultures remains challenging. We evaluated the performances of the Bruker® MBT Sepsityper IVD module on MALDI-TOF MS for the direct identification of polymicrobial blood culture bottles. This module has the ability to give a strong indication that a sample contains a mixture of organisms and to identify two of them. Blood culture bottles considered as polymicrobial using routine subculture were collected and processed using the Sepsityper kit. MALDI-TOF MS identification was performed using the MBT Compass IVD software including the Sepsityper module. From 143 polymicrobial blood culture bottles tested, 34.3% (49/143) were completely identified by the module. Both microorganisms were more easily detected by the module in samples containing two pathogens than in samples containing two contaminants (36.8% vs 29.4%). Additionally, in more than half of the samples, the module detected 1 of the different microorganisms contained in the same vial. In these cases, with a pathogen and contaminant in the same sample, the module detected the pathogen in more than 80%. The Sepsityper module identified 14 microorganisms which were not recovered by conventional culture methods. The Bruker® MBT Sepsityper IVD module contributed to a valuable identification of polymicrobial blood cultures in more than a third of all cases. Conventional culture methods are still required to complete the results and to carry on susceptibility testing.

Multicenter assessment of the rapid Unyvero Blood Culture molecular assay

Purpose

Bloodstream infections remain an important cause of morbidity and mortality. Rapid diagnosis can reduce the time from empiric antimicrobial therapy to targeted therapy and improve patient outcomes.

Methodology

The fully automated Unyvero Blood Culture (BCU) Application (Curetis GmbH) can identify a broad panel of pathogens (36 analytes covering over 50 pathogens) and 16 antibiotic resistance gene markers simultaneously in about 5 h. The assay was evaluated in three clinical laboratories in comparison to routine microbiological procedures.

Results

A total of 207 blood cultures were included in the study, and 90.5 % of the species identified by culture were covered by the Unyvero BCU panel with an overall sensitivity of 96.8 % and specificity of 99.8 %. The time to result was reduced on average by about 34 h. The assay accurately identified 95 % of the species, including 158/164 monomicrobial and 7/9 polymicrobial cultures. The Unyvero BCU Cartridge detected a large number of resistance markers including mecA (n=57), aac(6′)aph(2′′) (n=40), one vanB resistance gene, and six instances of bla_CTX-M.

Conclusion

The Unyvero BCU Application provided fast, reliable results, while significantly improving turnaround time in blood culture diagnostics.

Evaluation of the Accelerate Pheno™ system for rapid identification and antimicrobial susceptibility testing of Gram-negative bacteria in bloodstream infections

Identification and antimicrobial susceptibility testing (AST) are critical steps in the management of bloodstream infections. Our objective was to evaluate the performance of the Accelerate Pheno™ System, CE v1.2 software, for identification and AST of Gram-negative pathogens from positive blood culture bottles. A total of 104 bottles positive for Gram-negative bacteria collected from inpatients throughout our institution were randomly selected after Gram staining. The time-to-identification and AST results, and the raw AST results obtained by the Accelerate Pheno™ system and routine techniques (MALDI-TOF MS and VITEK®2, EUCAST guidelines) were compared. Any discrepant AST result was tested by microdilution. The Pheno™ significantly improved turn-around times for identification (5.3 versus 23.7 h; p < 0.0001) and AST (10.7 versus 35.1 h; p < 0.0001). Complete agreement between the Accelerate Pheno™ system and the MALDI-TOF MS for identification was observed for 96.2% of samples; it was 99% (98/99) for monomicrobial samples versus 40% (3/5) for polymicrobial ones. The overall categorical agreement for AST was 93.7%; it was notably decreased for beta-lactams (cefepime 84.4%, piperacillin-tazobactam 86.5%, ceftazidime 87.6%) or Pseudomonas aeruginosa (71.9%; with cefepime 33.3%, piperacillin-tazobactam 77.8%, ceftazidime 0%). Analysis of discrepant results found impaired performance of the Accelerate Pheno™ system for beta-lactams (except cefepime) in Enterobacteriales (six very major errors) and poor performance in P. aeruginosa. The Accelerate Pheno™ system significantly improved the turn-around times for bloodstream infection diagnosis. Nonetheless, improvements in the analysis of polymicrobial samples and in AST algorithms, notably beta-lactam testing in both P. aeruginosa and Enterobacteriales, are required for implementation in routine workflow.

An Automated Sample Preparation Instrument to Accelerate Positive Blood Cultures Microbial Identification by MALDI-TOF Mass Spectrometry (Vitek®MS)

Sepsis is the leading cause of death among patients in intensive care units (ICUs) requiring an early diagnosis to introduce efficient therapeutic intervention. Rapid identification (ID) of a causative pathogen is key to guide directed antimicrobial selection and was recently shown to reduce hospitalization length in ICUs. Direct processing of positive blood cultures by MALDI-TOF MS technology is one of the several currently available tools used to generate rapid microbial ID. However, all recently published protocols are still manual and time consuming, requiring dedicated technician availability and specific strategies for batch processing. We present here a new prototype instrument for automated preparation of Vitek^®MS slides directly from positive blood culture broth based on an “all-in-one” extraction strip. This bench top instrument was evaluated on 111 and 22 organisms processed using artificially inoculated blood culture bottles in the BacT/ALERT^® 3D (SA/SN blood culture bottles) or the BacT/ALERT Virtuo^TM system (FA/FN Plus bottles), respectively. Overall, this new preparation station provided reliable and accurate Vitek MS species-level identification of 87% (Gram-negative bacteria = 85%, Gram-positive bacteria = 88%, and yeast = 100%) when used with BacT/ALERT^® 3D and of 84% (Gram-negative bacteria = 86%, Gram-positive bacteria = 86%, and yeast = 75%) with Virtuo^® instruments, respectively. The prototype was then evaluated in a clinical microbiology laboratory on 102 clinical blood culture bottles and compared to routine laboratory ID procedures. Overall, the correlation of ID on monomicrobial bottles was 83% (Gram-negative bacteria = 89%, Gram-positive bacteria = 79%, and yeast = 78%), demonstrating roughly equivalent performance between manual and automatized extraction methods. This prototype instrument exhibited a high level of performance regardless of bottle type or BacT/ALERT system. Furthermore, blood culture workflow could potentially be improved by converting direct ID of positive blood cultures from a batch-based to real-time and “on-demand” process.

Characterization of microbial mixtures by mass spectrometry

MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

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.

Syndromic Panel-Based Testing in Clinical Microbiology

The recent development of commercial panel-based molecular diagnostics for the rapid detection of pathogens in positive blood culture bottles, respiratory specimens, stool, and cerebrospinal fluid has resulted in a paradigm shift in clinical microbiology and clinical practice. This review focuses on U.S. Food and Drug Administration (FDA)-approved/cleared multiplex molecular panels with more than five targets designed to assist in the diagnosis of bloodstream, respiratory tract, gastrointestinal, or central nervous system infections. While these panel-based assays have the clear advantages of a rapid turnaround time and the detection of a large number of microorganisms and promise to improve health care, they present certain challenges, including cost and the definition of ideal test utilization strategies (i.e., optimal ordering) and test interpretation.

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.

Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Use with Positive Blood Cultures: Methodology, Performance, and Optimization

Early initiation of effective antibiotics for septic patients is essential for patient survival. Matrix-assisted desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized clinical microbiology for isolate identification and has the possibility to impact how blood culture testing is performed. This review discusses the various uses of MALDI-TOF MS for the identification and susceptibility testing of positive blood cultures, the performance of these methods, and the outcomes involved with its implementation.

A simple method for rapid microbial identification from positive monomicrobial blood culture bottles through matrix-assisted laser desorption ionization time-of-flight mass spectrometry

BACKGROUND AND PURPOSE

Rapid identification of microbes in the bloodstream is crucial in managing septicemia because of its high disease severity, and direct identification from positive blood culture bottles through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can shorten the turnaround time. Therefore, we developed a simple method for rapid microbiological identification from positive blood cultures by using MALDI-TOF MS.

METHODS

We modified previously developed methods to propose a faster, simpler and more economical method, which includes centrifugation and hemolysis. Specifically, our method comprises two-stage centrifugation with gravitational acceleration (g) at 600g and 3000g, followed by the addition of a lysis buffer and another 3000g centrifugation.

RESULTS

In total, 324 monomicrobial bacterial cultures were identified. The success rate of species identification was 81.8%, which is comparable with other complex methods. The identification success rate was the highest for Gram-negative aerobes (85%), followed by Gram-positive aerobes (78.2%) and anaerobes (67%). The proposed method requires less than 10 min, costs less than US$0.2 per usage, and facilitates batch processing.

CONCLUSION

We conclude that this method is feasible for clinical use in microbiology laboratories, and can serve as a reference for treatments or further complementary diagnostic testing.

Fungal Species Identification by MALDI-ToF Mass Spectrometry

MALDI-TOF MS has become the standard method for routine identification of most microbial organisms in clinical laboratories and has largely replaced biochemical assays. Classification relies on extensive well curated databases, ideally covering the full spectrum of microorganisms encountered in the specimens at hands. The protocols for harvesting cells and procuring material suitable for downstream MALDI-TOF MS analyses vary in specific details between the different groups of organisms, e.g., gram-positive or -negative bacteria, mycobacteria, or fungi. With respect to fungi, methods further vary between yeasts and moulds; and even among different mould genera if they do not lyse in a similar fashion. Purification of microbial materials from clinical specimen allows the direct identification of bacteria; however this is not yet fully adapted to fungi. In this chapter, I look into the differences between the underlying methods for yeast and moulds, and for production of samples suitable for MALDI-TOF MS species identification from cultures and different clinical materials.

Superiority of SDS lysis over saponin lysis for direct bacterial identification from positive blood culture bottle by MALDI-TOF MS

PURPOSE

Fast species diagnosis has an important health care impact, as rapid and specific antibacterial therapy is of clear benefit for patient's outcome. Here, a new protocol for species identification directly from positive blood cultures is proposed.

EXPERIMENTAL DESIGN

Four in-house protocols for bacterial identification by MS directly from clinical positive blood cultures evaluating two lytic agents, SDS and saponin, and two protein extraction schemes, fast (FP) and long (LP) are compared. One hundred and sixty-eight identification tests are carried out on 42 strains.

RESULTS

Overall, there are correct identifications to the species level in 90% samples for the SDS-LP, 60% for the SDS-FP, 48% for the saponin LP, and 43% for the saponin FP. Adapted scores allowed 92, 86, 72, and 53% identification for SDS-LP, SDS-FP, saponin LP, and saponin FP, respectively. Saponin lysis is associated with a significantly lower score compared to SDS (0.87 [0.83-0.92], p-value < 0.001).

CONCLUSIONS AND CLINICAL RELEVANCE

This study supports the use of SDS lysis instead of saponin lysis and the application of this rapid and cost-effective protocol in daily routine for microbiological agents implicated in septicemia.

Rapid Identification of Microorganisms from Positive Blood Culture by MALDI-TOF MS After Short-Term Incubation on Solid Medium

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms. Unfortunately, its direct application to positive blood culture is still lacking standardized procedures. In this study, we evaluated an easy- and rapid-to-perform protocol for MALDI-TOF MS direct identification of microorganisms from positive blood culture after a short-term incubation on solid medium. This protocol was used to evaluate direct identification of microorganisms from 162 positive monomicrobial blood cultures; at different incubation times (3, 5, 24 h), MALDI-TOF MS assay was performed from the growing microorganism patina. Overall, MALDI-TOF MS concordance with conventional methods at species level was 60.5, 80.2, and 93.8% at 3, 5, and 24 h, respectively. Considering only bacteria, the identification performances at species level were 64.1, 85.0, and 94.1% at 3, 5, and 24 h, respectively. This protocol applied to a commercially available MS typing system may represent, a fast and powerful diagnostic tool for pathogen direct identification and for a promptly and pathogen-driven antimicrobial therapy in selected cases.

Optimal turnaround time for direct identification of microorganisms by mass spectrometry in blood culture

INTRODUCTION

During the past few years, several studies describing direct identification of bacteria from blood culture using mass spectrometry have been published. These methods cannot, however, be easily integrated into a common laboratory workflow because of the high hands-on time they require. In this paper, we propose a new method of identification with a short hands-on time and a turnaround time shorter than 15min.

MATERIALS AND METHODS

Positive blood bottles were homogenised and 600μL of blood were transferred to an Eppendorf tube where 600μL of lysis buffer were added. After homogenisation, a centrifugation step of 4min at 10,500g was performed and the supernatant was discarded. The pellet was then washed and loaded in quadruplicate into wells of a Vitek® MS-DS plate. Each well was covered with a saturated matrix solution and a MALDI-TOF mass spectrometry analysis was performed. Species were identified using the software Myla 3.2.0-2.

RESULTS

We analysed 266 positive blood culture bottles. A microorganism grew in 261 cultures, while five bottles remained sterile after 48h of incubation in subculture. Our method reaches a probability of detection at the species level of 77.8% (203/261) with a positive predictive value of 99.5% (202/203).

CONCLUSION

We developed a new method for the identification of microorganisms using mass spectrometry, directly performed from a positive blood culture. This method has short hands-on time and turnaround time and can easily take place in the workflow of a laboratory, with comparable results in performance with other methods reported in the literature.