Same day identification and full panel antimicrobial susceptibility testing of bacteria from positive blood culture bottles made possible by a combined lysis-filtration method with MALDI-TOF VITEK mass spectrometry and the VITEK2 system

MALDI-TOF direct identification of positive blood cultures: A four-year analytical evaluation of A Triton based workflow

Rapid and reliable identification of the causal organism in bloodstream infections and sepsis is crucial for both individual patient care and public health. We have implemented a rapid in-house identification protocol (with 10 % Triton) using MALDI-TOF MS for identifying the causative organism in positive blood cultures without prior culture. Our objective was to retrospectively analyze data collected over a four-year period while implementing this rapid in-house identification protocol and to develop a guide for evaluating and reporting the obtained results. Overall, our method utilizing MALDI-TOF MS for rapid in-house identification, demonstrated comparable results to other commercially available and in-house methods reported in the literature. Over the past four years, direct identification has facilitated the distinction between clinically relevant positive blood cultures and irrelevant ones, guiding rapid focus control and appropriate antibiotic treatment. The established guide can serve as a valuable tool in reporting positive blood cultures and associated antibiotic treatments.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry in the diagnosis of microorganisms

Microbiology culture is the gold standard method for identifying microorganisms. This identification protocol takes several days to complete. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a technique that can identify different microorganisms quickly and accurately. The objective of this work was to evaluate the use of MALDI-TOF MS in the routine of clinical laboratories to identify microorganisms and to identify their resistance to antimicrobials. This study evaluated the relevance of the MALDI-TOF MS technique for microbiological diagnosis through a literature review. The authors found that MALDI-TOF MS can identify bacteria, fungi, viruses and parasites, even in blood cultures, and also serves to assess antimicrobial resistance. Thus, MALDI-TOF MS can become an indispensable tool in laboratory diagnosis.

Using Targeted Liquid Chromatography-Tandem Mass Spectrometry to Rapidly Detect β-Lactam, Aminoglycoside, and Fluoroquinolone Resistance Mechanisms in Blood Cultures Growing E. coli or K. pneumoniae

New and rapid antimicrobial susceptibility/resistance testing methods are required for bacteria from positive blood cultures. In this study, a multiplex-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed and validated for the detection of β-lactam, aminoglycoside, and fluoroquinolone resistance mechanisms in blood cultures growing Escherichia coli or Klebsiella pneumoniae complex. Selected targets were the β-lactamases SHV, TEM, OXA-1-like, CTX-M-1-like, CMY-2-like, chromosomal E. coli AmpC (cAmpC), OXA-48-like, NDM, VIM, and KPC; the aminoglycoside-modifying enzymes AAC(3)-Ia, AAC(3)-II, AAC(3)-IV, AAC(3)-VI, AAC(6′)-Ib, ANT(2′′)-I, and APH(3′)-VI; the 16S-RMTases ArmA, RmtB, RmtC, and RmtF; the quinolone resistance mechanisms QnrA, QnrB, AAC(6′)-Ib-cr; the wildtype quinolone resistance determining region of GyrA; and the E. coli porins OmpC and OmpF. The developed assay was evaluated using 100 prospectively collected positive blood cultures, and 148 negative blood culture samples spiked with isolates previously collected from blood cultures or isolates carrying less prevalent resistance mechanisms. The time to result was approximately 3 h. LC-MS/MS results were compared with whole-genome sequencing and antimicrobial susceptibility testing results. Overall, there was a high agreement between LC-MS/MS results and whole-genome sequencing results. In addition, the majority of susceptible and non-susceptible phenotypes were correctly predicted based on LC-MS/MS results. Exceptions were the predictions for ciprofloxacin and amoxicillin/clavulanic acid that matched with the phenotype in 85.9 and 63.7% of the isolates, respectively. Targeted LC-MS/MS based on parallel reaction monitoring can be applied for the rapid and accurate detection of various resistance mechanisms in blood cultures growing E. coli or K. pneumoniae complex.

Susceptibility Testing by Volatile Organic Compound Detection Direct from Positive Blood Cultures: A Proof-of-Principle Laboratory Study

Background: Bacteria produce volatile organic compounds (VOCs) during growth, which can be detected by colorimetric sensor arrays (CSAs). The SpecifAST® system (Specific Diagnostics) employs this technique to enable antibiotic susceptibility testing (AST) directly from blood cultures without prior subculture of isolates. The aim of this study was to compare the SpecifAST® AST results and analysis time to the VITEK®2 (bioMérieux) system. Methods: In a 12-month single site prospective study, remnants of clinical positive monomicrobial blood cultures were combined with a series of antibiotic concentrations. Volatile emission was monitored at 37 °C via CSAs. Minimal Inhibitory Concentrations (MICs) of seven antimicrobial agents for Enterobacterales, Staphylococcus, and Enterococcus spp. were compared to VITEK®2 AST results. MICs were interpreted according to EUCAST clinical breakpoints. Performance was assessed by calculating agreement and discrepancy rates. Results: In total, 96 positive blood cultures containing Enterobacterales, Staphylococcus, and Enterococcus spp. were tested (269 bug–drug combinations). The categorical agreement of the SpecifAST® system compared to the VITEK®2 system was 100% and 91% for Gram-negatives and Gram-positives, respectively. Errors among Gram-positives were from coagulase-negative staphylococci. Overall results were available in 3.1 h (±0.9 h) after growth detection without the need for subculture steps. Conclusion: The AST results based on VOC detection are promising and warrant further evaluation in studies with a larger sample of bacterial species and antimicrobials.

A streamlined method for the fast and cost-effective detection of bacterial pathogens from positive blood cultures for the BacT/ALERT blood culture system using the Vitek MS mass spectrometer

Background and objective

Prompt pathogen identification of blood stream infections is essential to provide appropriate antibiotic treatment. Therefore, the objective of this prospective single centre study was to establish an inexpensive, fast and accurate protocol for bacterial species identification with SDS protein-extraction directly from BacT/Alert^® blood culture (BC) bottles by VitekMS^®.

Results

Correct species identification was obtained for 198/266 (74.4%, 95%-CI = [68.8%, 79.6%]) of pathogens. The protocol was more successful in identifying 87/96 (91.4%, 95%-CI = [83.8%, 93.2%]) gram-negative bacteria than 110/167 (65.9%, 95%-CI = [58.1%, 73.0%]) gram-positive bacteria. The hands-on time for sample preparation and measurement was about 15 min for up to five samples. This is shorter than for most other protocols using a similar lysis-centrifugation approach for the combination of BacT/Alert^® BC bottles and the Vitek^® MS mass spectrometer. The estimated costs per sample were approx. 1.80€ which is much cheaper than for commercial kits.

Conclusion

This optimized protocol allows for accurate identification of bacteria directly from blood culture bottles for laboratories equipped with BacT/Alert^® blood culture bottles and VitekMS^® mass spectrometer.

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.

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.

Direct Identification, Antimicrobial Susceptibility Testing, and Extended-Spectrum β-Lactamase and Carbapenemase Detection in Gram-Negative Bacteria Isolated from Blood Cultures

Purpose

To shorten the turnaround time for blood culture (BC) analyses, a rapid method was developed for the direct identification, antimicrobial susceptibility testing (AST), and multidrug resistance testing of bacteria-positive BCs.

Materials and Methods

The mixtures in BC bottles were treated with the multistep centrifugation method developed here and the conventional culture-based method. The bacterial sediment obtained after centrifugation was analyzed directly with MALDI-TOF MS and Vitek 2 Compact, and AST was performed directly with the Kirby–Bauer (K–B) disk diffusion, VITEK 2 Compact, and E-test methods. Extended spectrum lactamases (ESBLs) were detected with discs containing cefotaxime, cefotaxime/clavulanate, ceftazidime, and ceftazidime/clavulanate, and carbapenemase was detected with the modified carbapenem inactivation method (mCIM) and EDTA-mCIM (eCIM).

Results

All the results of direct testing were compared to those of the conventional methods, to evaluate the accuracy of the direct methods. The accuracies of the direct Vitek 2 Compact and MALDI-TOF MS methods were 95.5% (214/224) and 90.2% (202/224), respectively. Direct AST with K–B, Vitek 2, and E-test showed category agreement of 96.0% (2611/2721), 96.1% (2614/2721), and 97.4% (2650/2721), respectively, and the major errors and very major errors were < 2% for all three methods. In the direct determination of ESBLs, the results for cefotaxime combined with cefotaxime/clavulanate were completely consistent with those after the standard isolation method. The carbapenemase detection rate with direct mCIM and eCIM was exactly the same as that with the standard method.

Conclusion

These direct procedures based on multistep centrifugation are not only highly accurate but are appropriate for clinical laboratory use because the turnaround time is shorter.

Rapid Antimicrobial Susceptibility Testing by Stimulated Raman Scattering Imaging of Deuterium Incorporation in a Single Bacterium

To slow and prevent the spread of antimicrobial resistant infections, rapid antimicrobial susceptibility testing (AST) is in urgent need to quantitatively determine the antimicrobial effects on pathogens. It typically takes days to complete the AST by conventional methods based on the long-time culture, and they do not work directly for clinical samples. Here, we report a rapid AST method enabled by stimulated Raman scattering (SRS) imaging of deuterium oxide (D2O) metabolic incorporation. Metabolic incorporation of D2O into biomass and the metabolic activity inhibition upon exposure to antibiotics at the single bacterium level are monitored by SRS imaging. The single-cell metabolism inactivation concentration (SC-MIC) of bacteria upon exposure to antibiotics can be obtained after a total of 2.5 h of sample preparation and detection. Furthermore, this rapid AST method is directly applicable to bacterial samples in complex biological environments, such as urine or whole blood. SRS metabolic imaging of deuterium incorporation is transformative for rapid single-cell phenotypic AST in the clinic.

Therapeutic Drug Monitoring of Antibiotic Drugs: The Role of the Clinical Laboratory

BACKGROUND

Therapeutic drug monitoring (TDM) of anti-infective drugs is an increasingly complex field, given that in addition to the patient and drug as 2 usual determinants, its success is driven by the pathogen. Pharmacodynamics is related both to the patient (toxicity) and bacterium (efficacy or antibiotic susceptibility). The specifics of TDM of antimicrobial drugs stress the need for multidisciplinary knowledge and expertise, as in any other field. The role and the responsibility of the laboratory in this interplay are both central and multifaceted. This narrative review highlights the role of the clinical laboratory in the TDM process.

METHODS

A literature search was conducted in PubMed and Google Scholar, focusing on the past 5 years (studies published since 2016) to limit redundancy with previously published review articles. Furthermore, the references cited in identified publications of interest were screened for additional relevant studies and articles.

RESULTS

The authors addressed microbiological methods to determine antibiotic susceptibility, immunochemical and chromatographic methods to measure drug concentrations (primarily in blood samples), and endogenous clinical laboratory biomarkers to monitor treatment efficacy and toxicity. The advantages and disadvantages of these methods are critically discussed, along with existing gaps and future perspectives on strategies to provide clinicians with as reliable and useful results as possible.

CONCLUSIONS

Although interest in the field has been the driver for certain progress in analytical technology and quality in recent years, laboratory professionals and commercial providers persistently encounter numerous unresolved challenges. The main tasks that need tackling include broadly and continuously available, easily operated, and cost-effective tests that offer short turnaround times, combined with reliable and easy-to-interpret results. Various fields of research are currently addressing these features.

Evaluation of the Performance of Direct Susceptibility Test by VITEK-2 from Positively Flagged Blood Culture Broth for Gram-Negative Bacilli

Background Timely initiation of antimicrobial therapy in patients with blood stream infection is absolutely necessary to reduce mortality and morbidity. Most clinical microbiology laboratories use conventional methods for identification and antimicrobial susceptibility testing (AST) that involve biochemical methods for identification followed by AST by disk diffusion. The aim of the current study is to assess the various errors associated with direct susceptibility testing done from blood culture broth using automated AST system-Vitek-2 compact compared with the reference method of AST done from bacterial colonies.

Materials and Methods The study was conducted in a tertiary care public sector 2,200-bedded hospital in South India for a period of 6 months. The study involved positively flagged blood culture bottles that yielded single morphotype of Gram-negative organism by Gram stain. A total of 120 bacterial isolates were collected that consisted of consecutively obtained first 60 isolates of Enterobacteriaceae family (30 Escherichia coli and 30 Klebsiella pneumoniae ) and consecutively obtained first 60 nonfermenters (30 Pseudomonas aeruginosa and 30 Acinetobacter baumannii). Vitek-2 AST was done from these 120 blood culture broth, following the protocol by Biomerieux, and results were obtained. Then, Vitek-2 was done from colonies (reference method) using appropriate panel for Enterobacteriaceae and nonfermenters, and results were obtained. Both the results were compared.

Results Nonfermenters showed a better categorical agreement of 97.6%, as compared to Enterobacteriaceae, which showed 97%. Among Enterobacteriaceae, both E. coli and K. pneumoniae showed categorical agreement of 97% each.

Conclusion The procedure of AST directly from blood culture broth represents a simple and effective technique that can reduce the turnaround time by 24 hours, which in turn benefits the clinician in appropriate utilization of antimicrobials for better patient care.

Comparison of novel rapid diagnostic of blood culture identification and antimicrobial susceptibility testing by Accelerate Pheno system and BioFire FilmArray Blood Culture Identification and BioFire FilmArray Blood Culture Identification 2 panels

Background

Conventional turnaround time (TAT) for positive blood culture (PBC) identification (ID) and antimicrobial susceptibility testing (AST) is 2–3 days. We evaluated the TAT and ID/AST performance using clinical and seeded samples directly from PBC bottles with different commercial approaches: (1) Accelerate Pheno® system (Pheno) for ID/AST; (2) BioFire® FilmArray® Blood Culture Identification (BCID) Panel and/ or BCID2 for ID; (3) direct AST by VITEK® 2 (direct AST); and (4) overnight culture using VITEK® 2 colony AST.

Results

A total of 141 PBC samples were included in this evaluation. Using MALDI-TOF (Bruker MALDI Biotyper) as the reference method for ID, the overall monomicrobial ID sensitivity/specificity are as follows: Pheno 97.9/99.9%; BCID 100/100%; and BCID2 100/100%, respectively. For AST performance, broth microdilution (BMD) was used as the reference method. For gram-negatives, overall categorical and essential agreements (CA/EA) for each method were: Pheno 90.3/93.2%; direct AST 92.6/88.5%; colony AST 94.4/89.5%, respectively. For gram-positives, the overall CA/EAs were as follows: Pheno 97.2/98.89%; direct AST 97.2/100%; colony AST 97.2/100%, respectively. The BCID/BCID2 and direct AST TATs were around 9–20 h (1/9-19 h for ID with resistance markers/AST), with 15 min/sample hands-on time. In comparison, Pheno TATs were around 8–10 h (1.5/7 h for ID/AST) with 2 min/sample hands-on time, maintains a clinically relevant fast report of antibiotic minimal inhibitory concentration (MIC) and allows for less TAT and hands-on time.

Conclusion

In conclusion, to the best of our knowledge, this is the first study conducted as such in Asia; all studied approaches achieved satisfactory performance, factors such as TAT, panel of antibiotics choices and hands-on time should be considered for the selection of appropriate rapid ID and AST of PBC methods in different laboratory settings.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02403-y.

Multicenter Evaluation of Rapid BACpro® II for the Accurate Identification of Microorganisms Directly from Blood Cultures Using MALDI-TOF MS

The identification of microorganisms directly from blood cultures using MALDI-TOF MS has been shown to be the most impacting application of this methodology. In this study, a novel commercial method was evaluated in four clinical microbiology laboratories. Positive blood culture samples (n = 801) were processed using a rapid BACpro^® II kit and then compared with the routine gold standard. A subset of monomicrobial BCs (n = 560) were analyzed in parallel with a Sepsityper^® Kit (Bruker Daltonics, Bremen, Germany) and compared with the rapid BACpro^® II kit. In addition, this kit was also compared with two different in-house methods. Overall, 80.0% of the monomicrobial isolates (609/761; 95% CI 71.5-88.5) were correctly identified by the rapid BACpro^® II kit at the species level (92.3% of the Gram negative and 72.4% of the Gram positive bacteria). The comparison with the Sepsityper^® Kit showed that the rapid BACpro^® II kit generated higher rates of correct species-level identification for all categories (p > 0.0001), except for yeasts identified with score values > 1.7. It also proved superior to the ammonium chloride method (p > 0.0001), but the differential centrifugation method allowed for higher rates of correct identification for Gram negative bacteria (p > 0.1). The percentage of accurate species-level identification of Gram positive bacteria was particularly noteworthy in comparison with other commercial and in-house methods.

Ultra-fast direct method for identifying microorganisms from BACTEC lytic/10 anaerobic/F flasks

Background: Fast diagnosis of bloodstream infections remains the most important challenge for clinical microbiologists. The introduction of the mass-spectrometry represents a breakthrough, although several methods are already commonly used for the direct identification from positive blood cultures we present a faster method (ultra fast) for Lytic anaerobic flasks. Methods: We compare the ultra-fast (UF) method with the extensively employed differential centrifugation method (DC) and both to routine identification after 18-24 h of incubation. UF and DC method correlation rates to the gold standard were calculated, and statistical significance was proved with the Z test. Results: UF performed better overall than DC, with this difference being statistically significant. This tendency was observed in every subanalysis.

Impact of Short-Incubation MALDI-TOF MS on Rapid Identification of Pathogens and Antibiotic Therapy

Background: It can be a critical point for reducing pathogen identification time and accurate antibiotic treatment for patients with blood circulation infection since it causes high mortality. Objective: The objectives of this study were to evaluate the time differences between conventional identification and MALDI-TOF conventional identification and short-incubation MALDI-TOF identification for positive blood cultures, and to explore the impact of short-incubation matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) identification on empirical antibiotic therapy. Methods: Positive blood cultures were collected in our hospital from 2017 to 2019, clinical data were collected from the medical records, which were analyzed retrospectively to determine the empirical antibiotic therapy. Results: Compared with the conventional identification method, the short-incubation MALDI-TOF identification time to initial identification of Klebsiella pneumoniae, Escherichia coli, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, Enterococcus faecium, and E. faecalis decreased by 22.28 h, 22 h, 23.59 h, 23.63 h, 22.63 h, 23.92 h, and 21.59 h, respectively (P < 0.05). The time to final reporting was decreased by 48.85 h, 47.99 h, 55.40 h, 51.07 h, 49.60 h, 51.78h, and 51.73h, respectively (P < 0.05). However, the antimicrobial susceptibility test time of E. coli, A. baumannii, and S. aureus increased to 2.02 h, 2.19 h, and 3.86 h, respectively (P < 0.05). The coincidence rate of antimicrobial susceptibility was 98.48% between short-incubation MALDI-TOF identification and conventional identification method of all Gram-negative bacilli, and there were no extremely major errors or major errors. The coincidence rate of antimicrobial susceptibility of Gram-positive cocci was 99.53%, one strain of E. faecium and S. aureus had major errors. Patients received earlier correct empirical antibiotic 19.89 h earlier by short-incubation MALDI-TOF identification than the conventional identification method (P < 0.001). Conclusions: The short-incubation MALDI-TOF identification significantly shortens the pathogen identification time and the final report time, it is a reliable method for rapid identification of positive blood cultures; the results of antimicrobial susceptibility are highly consistent, which significantly lead to earlier appropriate empirical therapy of bacteremia.

Ultra-Rapid Drug Susceptibility Testing for Klebsiella pneumoniae Clinical Isolates in 60 Min by SYBR Green I/Propidium Iodide Viability Assay

Background

We aimed to optimize and validate the drug susceptibility test (DST) assay by SYBR Green I/PI (SG-PI) method using a panel of 89 Klebsiella pneumoniae clinical isolates in comparison with the conventional DST method to three most important antibiotics used for treatment of this bacterial infection, including imipenem, cefmetazole, and gentamicin.

Methods

By staining with SYBR Green I and PI dyes, green fluorescence and red fluorescence, which linearly correlated with the percentages of live and dead or membrane damaged cells, respectively, were used to produce two standard curves to calculate the relative cell membrane impermeable rates for each log and stationary phase cultures. Stationary phase K. pneumoniae cells were used in imipenem and cefmetazole SG-PI DST assay whereas log phase cells were used in the gentamicin assay. The conventional broth microdilution method was used as a gold standard for DST for comparison.

Results

Data showed that after antibiotic treatment for 30–60 min, the antibiotic-resistant K. pneumoniae strains had significantly higher numbers of surviving cells than the susceptible strains at different concentrations of imipenem, cefmetazole, and gentamicin, where the average relative membrane impermeable rates were 88.5, 92.5, and 103.8% for resistant clinical strains, respectively, and 9.1, 49.3, and 71.5% for susceptible strains, respectively. Overall, the total concordances between the ultra-rapid SG-PI method and conventional minimal inhibitory concentration assay in diagnosing imipenem, cefmetazole and gentamicin resistance were high and were 96.6% (86/89), 95.4% (83/87), and 95.5% (85/89), respectively.

Conclusion

We demonstrate that our novel SG-PI assay can accurately and stably detect resistance to different antibiotics in clinical isolates of K. pneumoniae in an ultra-fast manner in 60–90 min.

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.

Application and Perspectives of MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories

Early diagnosis of severe infections requires of a rapid and reliable diagnosis to initiate appropriate treatment, while avoiding unnecessary antimicrobial use and reducing associated morbidities and healthcare costs. It is a fact that conventional methods usually require more than 24–48 h to culture and profile bacterial species. Mass spectrometry (MS) is an analytical technique that has emerged as a powerful tool in clinical microbiology for identifying peptides and proteins, which makes it a promising tool for microbial identification. Matrix assisted laser desorption ionization–time of flight MS (MALDI–TOF MS) offers a cost- and time-effective alternative to conventional methods, such as bacterial culture and even 16S rRNA gene sequencing, for identifying viruses, bacteria and fungi and detecting virulence factors and mechanisms of resistance. This review provides an overview of the potential applications and perspectives of MS in clinical microbiology laboratories and proposes its use as a first-line method for microbial identification and diagnosis.

Management of bacterial and fungal infections in cirrhosis: The MDRO challenge

Bacterial infections are frequent in cirrhotic patients with acute decompensation or acute-on-chronic liver failure and can complicate the clinical course. Delayed diagnosis and inappropriate empirical treatments are associated with poor prognosis and increased mortality. Fungal infections are much less frequent, usually nosocomial and associated with extremely high short-term mortality. Early diagnosis and adequate empirical treatment of infections is therefore key in the management of these patients. In recent decades, antibiotic resistance has become a major worldwide problem in patients with cirrhosis, warranting a more complex approach to antibiotic treatment that includes the use of broad-spectrum antibiotics, new administration strategies, novel drugs and de-escalation policies. Herein, we review epidemiological changes, the main types of multidrug-resistant organisms, mechanisms of resistance, new rapid diagnostic tools and currently available therapeutic options for bacterial and fungal infections in cirrhosis.

Novel electronic biosensor for automated inoculum preparation to accelerate antimicrobial susceptibility testing

A key predictor of morbidity and mortality for patients with a bloodstream infection is time to appropriate antimicrobial therapy. Accelerating antimicrobial susceptibility testing from positive blood cultures is therefore key to improving patient outcomes, yet traditional laboratory approaches can require 2–4 days for actionable results. The eQUANT—a novel instrument utilizing electrical biosensors—produces a standardized inoculum equivalent to a 0.5 McFarland directly from positive blood cultures. This proof-of-concept study demonstrates that eQUANT inocula prepared from clinically significant species of Enterobacterales were comparable to 0.5 McF inocula generated from bacterial colonies in both CFU/ml concentration and performance in antimicrobial susceptibility testing, with ≥ 95% essential and categorical agreement for VITEK2 and disk diffusion. The eQUANT, combined with a rapid, direct from positive blood culture identification technique, can allow the clinical laboratory to begin antimicrobial susceptibility testing using a standardized inoculum approximately 2–3 h after a blood culture flags positive. This has the potential to improve clinical practice by accelerating conventional antimicrobial susceptibility testing and the resulting targeted antibiotic therapy.

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.

Modern trends in identification of causative agents in infective endocarditis

Advances in the diagnosis and treatment of patients with infectious endocarditis are limited by the high frequency of cases with an unknown etiology and imperfection of microbiological (cultural) methods. To overcome these problems new approaches to the identification of infectious endocarditis pathogens were introduced, which allowed achieving certain positive results. However, it should be noted that despite the wide variety of diagnostic tools currently used, there is no ideal method for etiological laboratory diagnosis of infectious endocarditis. The article discusses the features and place of immunochemical, molecular biological (MALDI-TOF MS, real-time PCR, sequencing, in situ fluorescence hybridization, metagenomic methods, etc.), immunohistochemical methods, and their advantages and limitations.

[Infective Endocarditis with Unknown Etiology: Possibilities of Conquering and Role of Microbiologistics]

Current infectious endocarditis (IE) is characterized by changes in its etiological and epidemiological profiles associated with increased incidence of IE of undetermined etiology. This requires a search for ways to enhance the effectivity of diagnosis. Microbiologistics along with high-tech methods becomes decisively important for identifying the pathogen by studying cultures of blood and tissues from the affected heart valve. This determines timely diagnosis and treatment to be introduced to medical practice as a component of personalized medicine. The article focuses on the validity and features of microbiological (cultural), immunochemical, and molecular biological [MALDI-TOF MS (matrix-activated laser desorption/ionization with time-of-flight mass spectrometry), polymerase chain reaction, sequencing] studies.

Comparison of Rapid and Routine Methods of Identification and Antibiotic Susceptibility Testing of Microorganisms from Blood Culture Bottles

Reporting of the results of routine laboratory blood culture tests to clinicians is vital to the patients’ early treatment. This study aimed to perform identification and antibiotic susceptibility tests of the blood cultures showing positive signals of microbial growth in the first 12 hours of incubation by using centrifugation and Gram staining of 5 ml of liquid from the vial, thus achieving faster results. This study included 152 consecutively incubated blood culture samples showing positive microbial growth signals in the first 12 hours. The samples were centrifuged and then categorized into two groups (Gram-positive and Gram-negative) using Gram staining. Identification and antibiotic susceptibility tests were performed using an automated culture antibiogram device. For routine processing, media inoculated with positive blood culture were kept in the incubator for at least 24 hours. To compare the two methods in terms of the bacteria identification, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of the growing colony was studied. By Gram staining, the same bacterial strains were obtained for 138 (92%) of the 152 samples, similar to the results of the procedures mentioned earlier. With the samples tested with both methods, the antibiotic susceptibility profiles were compared using the antibiogram results for 1,984 samples that underwent the antibiotic testing. A 97.4% (for 1,934 antibiotic susceptibility assays) agreement was observed between the two methods. Comparing the results of the post-centrifugation Gram staining to those obtained for the specimens using routine procedures, the clinicians reported a high success rate (approximately 97%).

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.

Rapid Determination of Antimicrobial Susceptibility by Stimulated Raman Scattering Imaging of D2O Metabolic Incorporation in a Single Bacterium

Rapid antimicrobial susceptibility testing (AST) is urgently needed for treating infections with appropriate antibiotics and slowing down the emergence of antibiotic-resistant bacteria. Here, a phenotypic platform that rapidly produces AST results by femtosecond stimulated Raman scattering imaging of deuterium oxide (D₂O) metabolism is reported. Metabolic incorporation of D₂O into biomass in a single bacterium and the metabolic response to antibiotics are probed in as short as 10 min after culture in 70% D₂O medium, the fastest among current technologies. Single-cell metabolism inactivation concentration (SC-MIC) is obtained in less than 2.5 h from colony to results. The SC-MIC results of 37 sets of bacterial isolate samples, which include 8 major bacterial species and 14 different antibiotics often encountered in clinic, are validated by standard minimal inhibitory concentration blindly measured via broth microdilution. Toward clinical translation, stimulated Raman scattering imaging of D₂O metabolic incorporation and SC-MIC determination after 1 h antibiotic treatment and 30 min mixture of D₂O and antibiotics incubation of bacteria in urine or whole blood is demonstrated.

Advances in rapid diagnostics for bloodstream infections

Septicemia from bloodstream infections (BSI) is the second largest cause of inpatient mortality and the single most expensive condition for US hospitals to manage. There has been an explosive development of commercial diagnostic systems to accelerate the identification and antimicrobial susceptibility testing (AST) of causative pathogens. Despite adoption of advanced technologies like matrix-assisted laser desorption imaging-time-of-flight mass spectrometry and multiplex polymerase chain reaction for rapid identification, clinical impact has been variable, in part due to the persistent need for conventional AST as well as prescriber understanding of these rapidly evolving platforms. Newer technologies are expanding on rapid detection of genotypic determinants of resistance, but only recently has rapid phenotypic AST been available. Yet, improved outcomes with rapid diagnostic platforms are still most evident in conjunction with active antimicrobial stewardship. This review will outline key advancements in rapid diagnostics for BSI and the role of antimicrobial stewardship in this new era.

Antimicrobial susceptibility testing of pathogens isolated from blood culture: a performance comparison of Accelerate Pheno™ and VITEK® 2 systems with the broth microdilution method

Objectives

To compare the performance of the Accelerate Pheno™ system with that of the conventional phenotypic VITEK® 2 system for rapid antimicrobial susceptibility testing (AST) of bacterial pathogens from positive blood culture (PBC) samples, based on the reference broth microdilution (BMD) method.

Methods

Prospectively collected PBCs that represented patient-unique bloodstream infection episodes were included. For PBC samples showing monomicrobial growth (n = 86), AST was performed using both Accelerate Pheno™ and VITEK® 2 systems directly from PBC broth. Colony isolates derived from subculture of PBC broth were then used for BMD testing. AST results were interpreted according to 2017 EUCAST breakpoints.

Results

The overall categorical agreement between Accelerate Pheno™ system and BMD was 92.7% (467/504) for Gram-negative organisms and 99.0% (95/96) for Gram-positive organisms, with rates for very major errors of 3.6% (6/166), major errors 2.2% (9/416) and minor errors 3.8% (23/600). The overall categorical agreement between the VITEK® 2 system and BMD was 91.7% (463/505) for Gram-negative organisms and 99.0% (97/98) for Gram-positive organisms, with rates of very major errors of 2.4% (4/169), major errors 1.0% (4/416) and minor errors 5.8% (35/603). Importantly, unlike the VITEK® 2 system, no false-susceptible results occurred with two colistin-resistant organism-growing PBCs tested using the Accelerate Pheno™ system.

Conclusions

Based on these findings, the Accelerate Pheno™ system can be a valid alternative for the rapid AST of Gram-negative and Gram-positive bacteria in bloodstream infections.

Evaluation of EUCAST rapid antimicrobial susceptibility testing (RAST) for positive blood cultures in clinical practice using a total lab automation

Our objective was to evaluate EUCAST’s ‘rapid antimicrobial susceptibility testing’ (RAST) directly from positive blood culture that delivers antimicrobial results within 6 h for Staphylococcus aureus, Enterococcus spp., Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa, using total lab automation. Zone diameters from RAST were compared with MIC results. Furthermore, its influence on time to report was investigated. RAST was performed to all positive aerobic and anaerobic blood culture bottles by subculturing them, i.e. onto Mueller-Hinton agar and adding six antibiotic discs covering Gram-negative and Gram-positive therapy (cefoxitin, ampicillin, vancomycin, piperacillin/tazobactam, meropenem and ciprofloxacin). RAST was automatically imaged after 6 h. Zone sizes were measured using a TLA software tool and interpreted according to EUCAST clinical breakpoints. Bacteria were identified using MALDI-TOF MS and MIC results were determined using Vitek2 panels. Categorial agreement between agar diffusion and MIC results was investigated. Additionally, time to RAST and time to Vitek were compared for 100 isolates (20 per species). Between November 2018 and April 2019, 3313 positive mono-bacterial blood culture bottles were collected of which 894 bottles with RAST-validated species were investigated. Among these bottles, 2029 individual antibiotic measurements were compared with MIC results from Vitek2 and 14 very major, 28 major and 12 minor errors were found. A median reduction of 17:30 h in time to report was observed. Introduction of RAST with automatic TLA imaging function could reduce time to report by 17:30 h. Excellent accordance between zone diameter and MIC results, particularly for cefoxitin, vancomycin and meropenem, was observed, but drawbacks due to ATU were seen.

Innovative and rapid antimicrobial susceptibility testing systems

Antimicrobial resistance (AMR) is a major threat to human health worldwide, and the rapid detection and quantification of resistance, combined with antimicrobial stewardship, are key interventions to combat the spread and emergence of AMR. Antimicrobial susceptibility testing (AST) systems are the collective set of diagnostic processes that facilitate the phenotypic and genotypic assessment of AMR and antibiotic susceptibility. Over the past 30 years, only a few high-throughput AST methods have been developed and widely implemented. By contrast, several studies have established proof of principle for various innovative AST methods, including both molecular-based and genome-based methods, which await clinical trials and regulatory review. In this Review, we discuss the current state of AST systems in the broadest technical, translational and implementation-related scope.

Rapid detection of antibiotic resistance in positive blood cultures by MALDI-TOF MS and an automated and optimized MBT-ASTRA protocol for Escherichia coli and Klebsiella pneumoniae

Introduction: For fast and effective antibiotic therapy of serious infections like sepsis, it is crucial with rapid information about antibiotic susceptibility, especially in a time when the number of infections caused by multi resistant bacteria has escalated in the world.Methods: Here, we have used a semi-quantitative MALDI-TOF-MS based method for antibiotic resistance detection, MBT-ASTRA™, which is based on the comparison of growth rate of the bacteria cultivated with and without antibiotics. We demonstrate a new protocol where several parameters have been optimized and automated leading to reduced hands-on time and improved capacity to simultaneously analyse multiple clinical samples and antibiotics.Results: Ninety minutes of incubation at 37 °C with agitation was sufficient to differentiate the susceptible and resistant strains of E. coli and K. pneumoniae, for the antibiotics cefotaxime, meropenem and ciprofloxacin. In total, 841 positive blood culture analyses of 14 reference strains were performed. The overall sensitivity was 99%, specificity 99% and the accuracy 97%. The assay gave no errors for cefotaxime (n = 263) or meropenem (n = 289) for sensitive and resistant strains, whilst ciprofloxacin (n = 289) gave six (0.7%) major errors (false resistance) and four (0.5%) very major errors (false susceptibility). The intermediate strains showed a larger variety compared to the E-test MIC values.Conclusions: The hands-on time and the analysis time to detect antibiotic resistance of clinical blood samples can be substantially reduced and the sample capacity can be increased by using automation and this improved protocol.

Therapeutic drug monitoring of β-lactam antibiotics in the critically ill: direct measurement of unbound drug concentrations to achieve appropriate drug exposures

Objectives

To describe the achievement of unbound β-lactam antibiotic concentration targets in a therapeutic drug monitoring (TDM) programme in critically ill patients, and the factors associated with failure to achieve a target concentration.

Patients and methods

Plasma samples and clinical data were obtained for analysis from a single centre prospectively. Unbound concentrations of ceftriaxone, cefazolin, meropenem, ampicillin, benzylpenicillin, flucloxacillin and piperacillin were directly measured using ultracentrifugation. Factors associated with the achievement of pharmacokinetic/pharmacodynamic (PK/PD) targets or negative clinical outcomes were evaluated with binomial logistic regression.

Results

TDM data from 330 patients, and 369 infection episodes, were included. The range of doses administered was 99.4% ± 45.1% relative to a standard daily dose. Dose increases were indicated in 33.1% and 63.4% of cases to achieve PK/PD targets of 100% fT>MIC and 100% fT>4×MIC, respectively. Dose reduction was indicated in 17.3% of cases for an upper PK/PD threshold of 100% fT>10×MIC. Higher protein bound β-lactams (ceftriaxone and benzylpenicillin) had better therapeutic target attainment (P < 0.01), but were prone to excessive dosing. Augmented renal clearance (calculated CLCR >130 mL/min) increased the odds of failure to achieve 100% fT>MIC and 100% fT>4×MIC (OR 2.47 and 3.05, respectively; P < 0.01).

Conclusions

Measuring unbound concentrations of β-lactams as part of a routine TDM programme is feasible and demonstrates that a large number of critically ill patients do not achieve predefined PK/PD targets. The clinical significance of this finding is unknown due to the lack of correlation between PK/PD findings and clinical outcomes.

Direct antimicrobial susceptibility testing from positive blood culture bottles in laboratories lacking automated antimicrobial susceptibility testing systems

BACKGROUND

Timely initiation of appropriate antimicrobial can improve the outcome in terms of reduced morbidity and mortality in addition to reduced health-care costs. Availability of early preliminary Antimicrobial Susceptibility Test (AST) report will be useful in directing antimicrobial therapy. The aim of the study was to correlate AST by disc diffusion method, directly from positively flagged blood culture bottles, with the AST by automated method.

METHODS

A total of 144 aerobic blood culture bottles flagged positive by the automated blood culture system were processed. The bacteria were pelleted by two-step centrifugation of the broth from the bottle and used to make a smear for Gram stain as well as an inoculum for antimicrobial sensitivity testing by Kirby Bauer disc diffusion method. Automated identification and AST were also carried out.

RESULTS

On direct staining, 94 samples showed gram-negative bacilli, 39 showed gram-positive cocci, and 11 showed yeasts or polymicrobial growth. In the case of gram-negative bacteria, there was 99% categorical agreement between direct sensitivity testing and automated sensitivity testing with 1% disagreement. Among the gram-positive cocci, there was 96% categorical agreement with 4% disagreement between the two methods.

CONCLUSION

High degree of agreement between the two methods is promising and applicable to situations where automated sensitivity testing is not available. Even if the systems are available, this method would prove useful as an adjunct to standard AST reporting. This sensitivity report can be generated earlier than the conventional AST, enabling choice of appropriate antimicrobial.

Direct antimicrobial susceptibility testing of positive blood cultures: a comparison of the Accelerate Pheno™ and VITEK® 2 systems

OBJECTIVES

To compare the performance and time-to-result (TTR) for antimicrobial susceptibility testing (AST) of positive blood cultures (PBC) using the Accelerate Pheno™ system (AXDX) and both a direct VITEK® 2 card inoculation workflow (DV2) and traditional FDA-approved VITEK® 2 workflow using subcultured isolates (V2).

METHODS

Patient samples with monomicrobial Gram-negative rod bacteremia were tested on AXDX and DV2 in tandem and compared to V2 AST results. Categorical agreement (CA) errors were adjudicated using broth microdilution. Instrumentation times and AST TTR were compared.

RESULTS

AXDX and DV2 had a CA of 93.4% and 97.4%, respectively, compared to V2. Postadjudication, AXDX, DV2, and V2 had CA of 94.7%, 95.7%, and 96.5%, respectively. Instrument run times were 6.6 h, 9.4 h, and 9.2 h, and AST TTR were 8.9 h, 12.9 h and 35.5 h, respectively.

CONCLUSIONS

AXDX and DV2 ASTs are fast and reliable, which may have significant antimicrobial stewardship implications.

Adaptable microfluidic system for single-cell pathogen classification and antimicrobial susceptibility testing

Infectious diseases caused by bacterial pathogens remain one of the most common causes of morbidity and mortality worldwide. Rapid microbiological analysis is required for prompt treatment of bacterial infections and to facilitate antibiotic stewardship. This study reports an adaptable microfluidic system for rapid pathogen classification and antimicrobial susceptibility testing (AST) at the single-cell level. By incorporating tunable microfluidic valves along with real-time optical detection, bacteria can be trapped and classified according to their physical shape and size for pathogen classification. By monitoring their growth in the presence of antibiotics at the single-cell level, antimicrobial susceptibility of the bacteria can be determined in as little as 30 minutes compared with days required for standard procedures. The microfluidic system is able to detect bacterial pathogens in urine, blood cultures, and whole blood and can analyze polymicrobial samples. We pilot a study of 25 clinical urine samples to demonstrate the clinical applicability of the microfluidic system. The platform demonstrated a sensitivity of 100% and specificity of 83.33% for pathogen classification and achieved 100% concordance for AST.

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.

Ideal and Actual Impact of Rapid Diagnostic Testing and Antibiotic Stewardship on Antibiotic Prescribing and Clinical Outcomes in Children With Positive Blood Cultures

BACKGROUND

Implementing matrix-assisted laser desorption ionization-time of flight and multiplex polymerase chain reaction has been associated with decreased mortality and hospital length of stay in adults, but the impact in pediatrics is less understood.

METHODS

This pre-post quasi-experimental study compared antibiotic prescribing for positive blood cultures in patients ≤21 years of age collected in 2012 (preintervention) and in 2015 (after matrix-assisted laser desorption ionization-time of flight/multiplex polymerase chain reaction). Time to effective and optimal antimicrobial therapy was evaluated using Cox proportional hazards regression. Time to ideal optimal therapy was estimated as the earliest potential initiation of optimal therapy. Antibiotic use and clinical outcomes were measured.

RESULTS

There were 242 and 192 positive monomicrobial blood cultures in 2012 and 2015, respectively. Postintervention, time to optimal therapy (73.8 vs. 48.8 hours; P < 0.001) and organism identification (55.6 vs. 29.5 hours; P < 0.001) were reduced, and patients were more likely to receive optimal therapy by 7 days (hazard ratio, 1.85; P < 0.001). In the ideal scenario in 2015, there was an 8.8-hour delay in initiating optimal therapy based on the time that sufficient microbiologic data were available. Postintervention, time to effective therapy (2.8 vs. 2.7 hours; P = 0.782) and clinical outcomes did not differ. Unnecessary antibiotic duration for probable contaminants (skin flora) (43.1 vs. 29.7 hours; P = 0.027), vancomycin for methicillin-sensitive Staphylococcus aureus (54.0 vs. 41.3 hours; P = 0.008) and nonpenicillin/ampicillin antibiotics for group A Streptococcus, group B Streptococcus and Enterococcus faecalis (87.2 vs. 33.4 hours; P < 0.001) were reduced postintervention.

CONCLUSIONS

Rapid diagnostics reduced time to optimal antimicrobial therapy and unnecessary antibiotic use without worse clinical outcomes.

Rapid antibiotic susceptibility testing in blood culture diagnostics performed by direct inoculation using the VITEK®-2 and BD Phoenix™ platforms

Early availability of microbiological results can improve treatment decisions of patients suffering from bloodstream infections. Direct inoculation of automated susceptibility testing (AST) platforms is an approach to shorten time-to-result in blood culture diagnostics. We performed a comparative evaluation of the two commercial AST systems VITEK®-2 and BD Phoenix™ for the direct inoculation with blood culture samples. Furthermore, two different methods of sample preparation were compared in this study. Positive blood cultures were prepared for direct inoculation by use of serum separator tubes and twofold centrifugation. AST was performed with the VITEK®-2 and the BD Phoenix™ system by the standard method according to the manufacturer's recommendations using subcultures on solid media and by direct inoculation of blood culture samples. A hundred clinical samples from blood cultures were included in this study. Rapid AST by direct inoculation showed inter-test agreement rates ranging from 92.45 to 97.7%. Comparing both AST platforms, the VITEK®-2 system demonstrated a higher test accuracy for direct inoculation. No relevant difference was observed for the two different sample preparation methods. Direct inoculation is an easy and inexpensive approach to obtain early full panel phenotypic AST results in blood culture diagnostics. Sample preparation is sufficiently performed by a simple centrifugation method. Both commercial platforms, the VITEK®-2 and the BD Phoenix™, have proven suitable for the use of direct inoculation.

Rapid antimicrobial susceptibility testing by VITEK®2 directly from blood cultures in patients with Gram-negative rod bacteremia

OBJECTIVE

Optimizing therapy for bacteremia is currently limited by the 1-2-day turnaround time required for antimicrobial susceptibility testing (AST). Here, we assess a rapid AST method with VITEK®2 (bioMérieux, France) directly from positive blood cultures.

METHODS

Patient-derived positive blood cultures with Gram-negative rods identified as Enterobacteriaceae and Pseudomonas aeruginosa were prospectively tested, and other blood culture bottles were spiked with carbapenem-resistant Enterobacteriaceae (CRE). Positive cultures were subjected to red blood cell lysis and centrifugation, and setup on VITEK®2.

RESULTS

A total of 109 patient blood cultures and 52 spiked blood cultures were tested. Overall, essential agreement was 97.7% [95% confidence interval (CI) 96.4-99.0], and categorical agreement was 96.8% (95% CI 95.0-98.6). Mean turnaround time from setup to susceptibility results for Enterobacteriaceae in the clinical cultures was 9.0 (±1.3) h.

CONCLUSIONS

Direct susceptibility testing of blood cultures by VITEK®2 for Enterobacteriaceae is an accurate, practical, and inexpensive diagnostic strategy for rapid automated AST.

Blood Culture Turnaround Time in U.S. Acute Care Hospitals and Implications for Laboratory Process Optimization

The rapid identification of blood culture isolates and antimicrobial susceptibility test (AST) results play critical roles for the optimal treatment of patients with bloodstream infections. Whereas others have looked at the time to detection in automated culture systems, we examined the overall time from specimen collection to actionable test results. We examined four points of time, namely, blood specimen collection, Gram stain, organism identification (ID), and AST reports, from electronic data from 13 U.S. hospitals for the 11 most common, clinically significant organisms in septic patients. We compared the differences in turnaround times and the times from when specimens were collected and the results were reported in the 24-h spectrum. From January 2015 to June 2016, 165,593 blood specimens were collected, of which, 9.5% gave positive cultures. No matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was used during the study period. Across the 10 common bacterial isolates (n = 6,412), the overall median (interquartile range) turnaround times were 0.80 (0.64 to 1.08), 1.81 (1.34 to 2.46), and 2.71 (2.46 to 2.99) days for Gram stain, organism ID, and AST, respectively. For all positive cultures, approximately 25% of the specimens were collected between 6:00 a.m. and 11:59 a.m. In contrast, more of the laboratory reporting times were concentrated between 6:00 a.m. and 11:59 a.m. for Gram stain (43%), organism ID (78%), and AST (82%), respectively (P < 0.001). The overall average turnaround times from specimen collection for Gram stain, organism ID, and AST were approximately 1, 2, and 3 days, respectively. The laboratory results were reported predominantly in the morning hours. Laboratory automation and work flow optimization may play important roles in reducing the microbiology result turnaround time.

Evaluation of a modified protocol that decreases the turnaround time of positive blood cultures

BACKGROUND AND OBJECTIVES

Neonatal septicemia can be rapidly fatal if not treated promptly. A speedy laboratory diagnosis would improve the outcome. The BacT/ALERT 3D system (bioMerieux, Durham, North Carolina) is currently being used for laboratory diagnosis of blood stream infections. In the present study, a modified protocol was employed in which the broth was subcultured into two nutrient broth tubes and these tubes were used for biochemical tests and antimicrobial susceptibility testing to decrease the turnaround time.

MATERIALS AND METHODS

A prospective study was conducted in the Department of Microbiology, SDM College of Medical Sciences and Hospital, Dharwad from October 2010 to July 2012 after receiving clearance from the institutional ethics committee. Automated blood cultures of 250 neonates admitted to the Neonatal Intensive Care Unit (NICU), clinically diagnosed to have septicemia, were performed using BacT/ALERT 3D. Bottles flagged positive within 72 hours of loading were processed for identification and antibiotic susceptibility testing using a modified protocol. The results were assessed for time saved in reporting in comparison with standard protocol. Student's t test was used for statistical analysis.

RESULTS

Of the 250 cases studied, 117 cases yielded a positive blood culture giving a yield of 46.8%. The number of cases yielding monomicrobial growth were 73, which were included for further analysis. Of the remaining samples, 133 did not show growth, 11 were polymicrobial while 33 samples were flagged positive after 72 hours. Candida spp. grew in 34 cases, Gram negative bacilli grew in 28 cases and Gram positive cocci grew in 11 cases. In four cases, 66 hours were saved, 60 and 54 hours were saved in 18 cases each, 48 hours were saved in 27 cases, and 24 hours were saved in 6 cases. Methicillin resistant Staphylococcus aureus and Klebsiella pneumoniae were the most common isolates among Gram positive cocci and Gram negative bacilli, respectively, while C. guilliermondii was the most common Candida isolate. All Gram positive isolates were susceptible to vancomycin and linezolid. Most of the Gram negative isolates were susceptible to imipenem.

CONCLUSION

This method can be employed in peripheral laboratory settings where there is no complete automation. Modification in processing blood culture can provide speedy identification and sensitivity report in blood stream infections. Time saved in reporting would play a crucial role in improving morbidity and mortality rates in neonatal septicemia.

The Use of Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for the Identification of Pathogens Causing Sepsis

BACKGROUND

Sepsis is a life-threatening condition with high rates of morbidity and mortality; effective and appropriate antibiotic therapy is essential for ensuring patient improvement. To aid in the diagnosis of sepsis, blood cultures are drawn and sent to the microbiology laboratory for pathogen growth, identification, and susceptibility testing. The clinical microbiology laboratory can assist the medical team by providing timely identification of the pathogen(s) causing the bloodstream infection through the use of rapid diagnostic technology. One of these rapid diagnostic technologies, MALDI-TOF MS, has been proven to reduce the time required for appropriate antibiotic therapy when used to identify pathogens grown in culture. This technology has also been used to identify pathogens directly from the positive blood cultures with great success.

CONTENT

In this minireview, we summarize the different methods that have been developed to directly identify pathogens from positive blood cultures by use of MALDI-TOF MS and the effect of this technology on patient outcomes. Additionally, we touch on current research in the field, including the identification of antimicrobial resistance directly from positive blood cultures by MALDI-TOF MS.

SUMMARY

Rapid identification of pathogens is important in the survival of patients undergoing a septic event. MALDI-TOF MS technology has played an important role in rapid identification, which has led to a reduction in the time to appropriate antibiotic therapy and contributed to the improvement of patient outcomes. The high sensitivity and specificity of MALDI-TOF MS identification, in combination with MALDI-TOF's rapid function and reduced labor costs, make this technology an attractive choice for clinical laboratories.

Role of the Clinical Microbiology Laboratory in Antimicrobial Stewardship

For adequate antimicrobial stewardship, microbiology needs to move from the laboratory to become physically and verbally amenable to the caregivers of an institution. Herein, we describe the contributions of our microbiology department to the antimicrobial stewardship program of a large teaching hospital as 10 main points ranging from the selection of patients deemed likely to benefit from a fast track approach, to their clinical samples, or the rapid reporting of results via a microbiology hotline, to rapid searches for pathogens and susceptibility testing. These points should serve as guidelines for similar programs designed to decrease the unnecessary use of antimicrobials.

Same-Day Identification and Antimicrobial Susceptibility Testing of Bacteria in Positive Blood Culture Broths Using Short-Term Incubation on Solid Medium with the MicroFlex LT, Vitek-MS, and Vitek2 Systems

BACKGROUND

Early and appropriate antibiotic treatment improves the clinical outcome of patients with septicemia; therefore, reducing the turn-around time for identification (ID) and antimicrobial susceptibility test (AST) results is essential. We established a method for rapid ID and AST using short-term incubation of positive blood culture broth samples on solid media, and evaluated its performance relative to that of the conventional method using two rapid ID systems and a rapid AST method.

METHODS

A total of 254 mono-microbial samples were included. Positive blood culture samples were incubated on blood agar plates for six hours and identified by the MicroFlex LT (Bruker Daltonics) and Vitek-MS (bioMeriéux) systems, followed by AST using the Vitek2 System (bioMeriéux).

RESULTS

The correct species-level ID rates were 82.3% (209/254) and 78.3% (199/254) for the MicroFlex LT and Vitek-MS platforms, respectively. For the 1,174 microorganism/antimicrobial agent combinations tested, the rapid AST method showed total concordance of 97.8% (1,148/1,174) with the conventional method, with a very major error rate of 0.5%, major error rate of 0.7%, and minor error rate of 1.0%.

CONCLUSIONS

Routine implementation of this short-term incubation method could provide ID results on the day of blood culture-positivity detection and one day earlier than the conventional AST method. This simple method will be very useful for rapid ID and AST of bacteria from positive blood culture bottles in routine clinical practice.

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.

Recent Advances and Ongoing Challenges in the Diagnosis of Microbial Infections by MALDI-TOF Mass Spectrometry

Timeliness and accuracy in the diagnosis of microbial infections are associated with decreased mortality and reduced length of hospitalization, especially for severe, life-threatening infections. A rapid diagnosis also allows for early streamlining of empirical antimicrobial therapies, thus contributing to limit the emergence and spread of antimicrobial resistance. The introduction of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for routine identification of microbial pathogens has profoundly influenced microbiological diagnostics, and is progressively replacing biochemical identification methods. Compared to currently used identification methods, MALDI-TOF MS has the advantage of identifying bacteria and yeasts directly from colonies grown on culture plates for primary isolation in a few minutes and with considerable material and labor savings. The reliability and accuracy of MALDI-TOF MS in identification of clinically relevant bacteria and yeasts has been demonstrated by several studies showing that the performance of MALDI-TOF MS is comparable or superior to phenotypic methods currently in use in clinical microbiology laboratories, and can be further improved by database updates and analysis software upgrades. Besides microbial identification from isolated colonies, new perspectives are being explored for MALDI-TOF MS, such as identification of pathogens directly from positive blood cultures, sub-species typing, and detection of drug resistance determinants. In this review, we summarize the state of the art in routine identification of microbial pathogens by MALDI-TOF MS, and highlight recent advancements of this technology in special applications, such as strain typing, assessment of drug susceptibility, and detection of virulence factors.

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.