Direct antimicrobial susceptibility tests of bacteria and yeasts from positive blood cultures by using serum separator gel tubes and MALDI-TOF MS

The Impact of Reporting the Same-Day Identification and Antibiotic Susceptibility Test Results on the Treatment of Bloodstream Infections

Objective

The rise of antibiotic-resistant organisms necessitates the implementation of rapid identification (ID) and antibiotic susceptibility testing (AST) methods for patient management. We aimed to analyze how rapid ID and AST reporting influenced clinicians' treatment decisions.

Materials and Methods

Bacteria were identified directly from positive blood cultures (BC) using serum separator tubes and MALDI-TOF MS. EUCAST rapid antibiotic susceptibility testing (RAST) method was performed for AST. The impact of rapid ID and AST reports on clinician treatment decisions was evaluated through clinical documentation. The appropriateness of antimicrobial therapy and interventions was assessed according to institutional antimicrobial prescribing guidelines, AST results, and clinical data.

Results

A total of 128 BC bottles from 86 patients underwent processing. The rapid ID method was successful in 105 (82.1%) bottles obtained from 76 patients. The rapid ID results were reviewed by the Infectious Diseases Team on the same day for 55 (72.4%) of the 76 patients. Following the evaluation, new treatments or interventions were recommended for 28 (36.8%) patients. RAST results were available for 24 patients. The susceptibility profile of seven patients was assessed by the Infectious Diseases Team on the same day. Antimicrobial treatment was escalated in four cases, and de-escalation was made in two based on RAST results. If all rapid results had been assessed, adjustments could have been made for eight (10.5%) and eleven (14.5%) more patients, according to ID and RAST results, respectively.

Conclusion

Implementation of rapid ID and AST may contribute to patient management. Although rapid reporting was made, some results were not evaluated by the clinician on the same day, indicating that communication between the clinician and the laboratory needs to be strengthened.

An improved protocol for bacteria identification by MALDI-TOF MS directly from positive blood cultures

FASTinov® developed a rapid antimicrobial susceptibility test that includes the purification of a bacterial suspension directly from positive blood cultures (BC). In order to streamline laboratory workflow, the use of the bacterial suspension obtained through FASTinov® sample prep was tested for identification (ID) by matrix absorption laser deionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker) in 364 positive BC, and its accuracy assessed comparing with the MALDI-TOF MS ID of the next-day subcultured colonies. FASTinov sample prep was highly reliable for rapid ID directly from BC with proportion of agreement of 94.9% for Gram-positive and 96.3% for Gram-negative bacteria.

Antimicrobial Agent Functional Gold Nanocluster-Mediated Multichannel Sensor Array for Bacteria Sensing

Urinary tract infections (UTIs) have greatly affected human health in recent years. Accurate and rapid diagnosis of UTIs can enable a more effective treatment. Herein, we developed a multichannel sensor array for efficient identification of bacteria based on three antimicrobial agents (vancomycin, lysozyme, and bacitracin) functional gold nanoclusters (AuNCs). In this sensor, the fluorescence intensity of the three AuNCs was quenched to varying degrees by the bacterial species, providing a unique fingerprint for different bacteria. With this sensing platform, seven pathogenic bacteria, different concentrations of the same bacteria, and even bacterial mixtures were successfully differentiated. Furthermore, UTIs can be accurately identified with our sensors in ∼30 min with 100% classification accuracy. The proposed sensing systems offer a rapid, high-throughput, and reliable sensing platform for the diagnosis of UTIs.

Severe Candida infections in critically ill patients with COVID-19

The frequency of co-infections with bacterial or fungal pathogens has constantly increased among critically ill patients with coronavirus disease 2019 (COVID-19) during the pandemic. Candidemia was the most frequently reported invasive fungal co-infection. The onset of candidemia in COVID-19 patients was often delayed compared to non-COVID-19 patients. Additionally, Candida invasive infections in COVID-19 patients were more often linked to invasive procedures (e.g., invasive mechanical ventilation or renal replacement therapy) during the intensive care stay and the severity of illness rather than more "classic" risk factors present in patients without COVID-19 (e.g., underlying diseases and prior hospitalization). Moreover, apart from the increased incidence of candidemia during the pandemic, a worrying rise in fluconazole-resistant strains was reported, including a rise in the multidrug-resistant Candida auris. Regarding outcomes, the development of invasive Candida co-infection had a negative impact, increasing morbidity and mortality compared to non-co-infected COVID-19 patients. In this narrative review, we present and critically discuss information on the diagnosis and management of invasive fungal infections caused by Candida spp. in critically ill COVID-19 patients.

Development of Microfluidic Chip-Based Loop-Mediated Isothermal Amplification (LAMP) Method for Detection of Carbapenemase Producing Bacteria

The rapid and accurate diagnostic methods to identify carbapenemase-producing organisms (CPO) is of great importance for controlling the CPO infection. Herein, we have developed a microfluidic chip-based technique to detect CPO and assessed its clinical value in detecting CPO directly from blood cultures (BCs). The detection performance of the microfluidic chip-based LAMP amplification method was analyzed retrospectively on a collection of 192 isolates including molecularly characterized 108 CPO and 84 non-CPO and prospectively on a collection of 133 positive BCs with or without CPO suspicion, respectively. In the retrospective study, the microfluidic chip-based LAMP amplification method exhibited 87.5% accuracy (95% CI [82.0–91.5]), 97.7% sensitivity (95% CI [91.2–99.6]), 78.8% specificity (95% CI [69.5–86.0]), 79.6% positive predictive value (PPV) (95% CI [70.6–86.5]) and 97.6% negative predictive value (NPV) (95% CI [90.9–99.6]). Among the 192 isolates, 22 (11.5%) false-positives (FP) and 2 (1.0%) false negatives (FN) were observed. In the prospective study, the 133 routine isolates of positive BCs including 18 meropenem-resistant CPO and 115 non-CPO were assessed, and 4 FP were observed in non-CPO and CPO, respectively. The current method showed a total detection performance of 94.0% accuracy (95% CI [88.4–97.1]), 100.0% sensitivity (95% CI [73.2–100.0]), 93.2% specificity (95% CI [86.7–96.8]), 63.6% PPV (95% CI [40.8–82.0]) and 100.0% NPV (95% CI [95.8–100.0]). In summary, the microfluidic chip-based LAMP amplification method is reliable for the rapid screening and detection of CPO with high accuracy, sensitivity, and specificity, and could easily be implemented in clinical microbiology laboratories.

IMPORTANCE Rapid and accurate identification of CPO may reduce the genetic exchanges among bacteria and prevent further dissemination of carbapenemases to non-CPO. The current method had designed microfluidic chip-based LAMP amplification method for multiplex detection of carbapenemase genes and evaluated the detection performance of the newly method. The current method can rapidly screen and detect CPO with high accuracy, sensitivity, and specificity, and could easily be implemented in clinical microbiology laboratories, as this will reduce the carbapenem resistance issues worldwide.

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.

Direct microorganism species identification and antimicrobial susceptibility tests from positive blood culture bottles using rapid Sepsityper Kit

INTRODUCTION

We evaluated the performance of Rapid Sepsityper Kit in species identification (ID) and antimicrobial susceptibility testing (AST).

METHODS

Positive blood culture bottles (n = 227) containing single microorganisms were enrolled. We compared the direct method using Rapid Sepsityper Kit for ID and AST with the conventional method. The analyses of ID and AST were performed using MALDI Biotyper and BD Phoenix platform, respectively.

RESULTS

The direct ID method correctly identified 89.4% (203/227) of samples, and Gram-negative bacilli (95.2%) had a higher ID rate than Gram-positive cocci (84.4%). Five cases were misidentified, and non-acceptable identification was high among Streptococcus species. Direct AST results were obtained from 168 isolates. Non-acceptable ID occurred among 24 isolates; 4 Streptococcus species, and 31 isolates, which did not grow in the direct AST method, were excluded. A total of 1714 antibiotic susceptibility tests (625 from 69 Gram-positive cocci and 1089 from 99 Gram-negative bacilli) were performed. The direct AST methods showed 98.3% (1685/1714) of categorical agreement (CA), 0.7% (12/1714) of very major errors, 0.2% (4/1714) of major errors, and 0.8% (13/1714) of minor errors. Complete CA was obtained for methicillin-resistant Staphylococcus aureus and extended-spectrum beta-lactamase-producing Escherichia coli.

CONCLUSIONS

The direct ID method using Rapid Sepsityper Kit and the direct AST method in combination with the BD Phoenix platform, which was associated with a reduction of turnaround time, may be a reliable approach for blood culture bottles. However, additional validation and further improvements, especially for Gram-positive cocci, would have an impact on microbiological diagnoses.

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.

Evaluation of a Rapid and Simplified Protocol for Direct Identification of Microorganisms From Positive Blood Cultures by Using Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)

Early and rapid identification of microorganisms is critical for reducing the mortality rate caused by bloodstream infections (BSIs). The accuracy and feasibility of directly identifying pathogens in positive blood cultures by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been intensely confirmed. In this study, we combined density centrifugation and extra chemical lysis-extraction to develop an optimized method in the blood culture process, which significantly improved the effectiveness of direct identification by MALDI-TOF MS. The accuracy was evaluated by 2,032 positive blood culture samples (115 species of microorganism). The overall MALDI-TOF MS based identification rate with scores ≥ 1.700 was 87.60%. 94.06% of gram-negative bacteria were identified consistently to the genus level, followed by anaerobes (93.33%), gram-positive bacteria (84.46%), and fungi (60.87%). This protocol could obtain results within 10–20 min at a cost of less than $0.1 per sample, which saved up to 24 h in identifying 87.60% of the microorganism from positive blood cultures. This rapid and simplified protocol facilitates the direct identification of microorganism in positive blood cultures, and exhibits the advantages of cost-effective, time-saving, and easy-to-use. It could provide the causative organism of the patient to clinicians in time for targeted treatment and reduce mortality.

Rapid identification of bacteria directly from positive blood cultures by a modified method using a serum separator tube and matrix-assisted laser desorption ionization – time of flight MS

Introduction. Several studies have used matrix-assisted laser desorption ionization-time of flight MS (MALDI-TOF) with a serum separator tube (SST) to perform rapid identification of microorganisms directly from positive blood cultures (BCs), with different performances and methodologies.

Hypothesis / Gap Statement. The use of TSS could significantly reduce the time of identification of microorganisms that produce bacteremia.

Aim. Our goals were to evaluate bacterial identification by MALDI-TOF using a method based on an SST and compare it with MALDI-TOF after subculture for 18–24 h.

Methodology. BCs no more than 1 h after a positive growth signal were included in the study. Analysis of results was expressed as a score. Information about time to a positive signal and number of microorganisms was collected.

Results. In total, 253 BCs were analysed; 45.5 % gave a reliable result, 23.3 % an unreliable result and 31.2 % an error in identification. In gram-negative and gram-positive bacteria, the percentages of reliable results were 83.5 and 21.8 %, respectively. According to time to positive signal, the percentages of correct identification and mean score were 81.1 % (99/122) and 1.89±0.30 in Group 1 (<15 h); and 57.2 % (75/131) and 1.70±0.32 in Group 2 (>15 h), respectively (P <0.001). According to the number of microorganisms, the corresponding percentages of correct identification and mean scores were: Group 1 [≤50 microorganisms observed per field (MOF)], 50/94 (53.19 %) and 1.72±0.32; Group 2 (51–100 MOF): 44/66 (66.67 %) and 1.85±0.34; Group 3 (>100 MOF): 79/93 (84.94 %) and 1.84±0.31.

Conclusion. This method allowed us to obtain a high percentage of the aetiological agent of bacteraemia in less than 30 min after a positive BC.

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.

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.

Rapid Identification and Antimicrobial Susceptibility Testing for Urinary Tract Pathogens by Direct Analysis of Urine Samples Using a MALDI-TOF MS-Based Combined Protocol

Usually, 18–48 h are needed for the identification of microbial pathogens causing urinary tract infections (UTIs) by urine culture. Moreover, antimicrobial susceptibility testing (AST) takes an additional 18–24 h. Rapid identification and AST of the pathogens allow fast and precise treatment. The objective of this study was to shorten the time of diagnosis of UTIs by combining pathogen screening through flow cytometry, microbial identification by matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS), and AST using the VITEK 2 system for the direct analysis of urine samples. We analyzed 1,638 urine samples from patients with suspected UTIs submitted to the microbiology laboratory for culture. Each urine sample had an approximate volume of 30 mL and was divided into three aliquots. Urine processing included differential centrifugation and two washes to enrich the bacterial fraction for direct MALDI-TOF MS and direct AST. From a total of 1,638 urine samples, 307 were found to be positive through UF-1000i screening. Among them, 265 had significant growth of a single-microorganism. Direct identification was obtained in 229 (86.42%) out of these 265 samples, and no pathogens were misidentified. Moreover, species-level identification was obtained in 163 (88.59%) out of the 184 samples with Gram-negative bacteria, and 27 (38.03%) out of the 71 samples with Gram-positive bacteria. VITEK 2 AST was performed for 117 samples with a single-microorganism. Enterobacteriaceae data showed an agreement rate of antimicrobial categories of 94.83% (1,229/1,296), with minor, major, and very major error rates of 4.17% (54/1,296), 0.92% (12/1,296), and 0.08% (1/1,296), respectively. For Enterococcus spp., the overall categorical agreement was 92.94% (158/170), with a minor error rate of 2.94% (5/170) and major error rate of 4.12% (7/170). The turnaround time of this combined protocol to diagnose UTIs was 1 h for pathogen identification and 6–24 h for AST; noteworthily, only 6–8 h are needed for AST of Enterobacteriaceae using the VITEK 2 system. Overall, our findings show that the combination of flow cytometry, MALDI-TOF MS, and VITEK 2 provided a direct, rapid, and reliable identification and AST method for assessing urine samples, especially for Gram-negative bacterial infections.