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

Accelerated microbial identification "directly" from positive blood cultures using MALDI-TOF MS: Local clinical laboratory challenges

Rapid identification of microbial pathogens "directly" from positive blood cultures (PBCs) is critical for prompt initiation of empirical antibiotic therapy and clinical outcomes. Towards higher microbial identification rates, we modified a published initial serum separator tubes-based MALDI-TOF-MS protocol, for blood culture specimens received at a non-hospital based standalone diagnostic laboratory, Bangalore, India: (a) "Initial" protocol #1: From 28 PBCs, identification= 39% (Gram-negative= 43%: Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa; Gram-positive: 36%: Enterococcus faecalis, Staphylococcus aureus, Staphylococcus haemolyticus); mis-identification= 14%; non-identification= 47%. (b) "Modified" protocol #2: Quality controls (ATCC colonies spiked in negative blood cultures) From 7 analysis, identification= 100% (Escherichia coli, Klebsiella pneumonia, Klebsiella oxytoca, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus); From 7 PBCs, identification= 57%; mis-identification= 14%; non-identification= 29%. Microbial preparations of highest quality and quantity for proteomic analysis and separate spectra matching reference databases for colonies and PBCs are needed for best clinical utility.

Identifying organisms directly from BacT/Alert FAN plus blood culture bottles using Vitek MS in a state-wide laboratory network

Identifying organisms directly from positive blood culture bottles using matrix-assisted laser desorption-ionisation time-of-flight mass spectrometry (MALDI-TOF MS) has many advantages to patients, clinical services, and laboratories. However, few published methods have demonstrated good performance using the current BioMérieux culture bottles and MALDI-TOF system: BacT/Alert FAN plus and Vitek MS. The effect of transporting bottles on test performance has not been assessed for any direct-from-bottle MS method. In this study, 802 positive blood culture bottles were analysed including 234 requiring inter-laboratory transport, using a method involving protein extraction with formic acid and acetonitrile. Correct identification rates were high for Staphylococcus aureus (58/58 of new diagnostic samples), Enterococcus faecalis (27/27), Gram-negative bacilli (160/176, 90.1%), and coagulase-negative Staphylococcus species (108/132, 81.8%). Three false identifications were made, none with clinical significance. For Gram-positive cocci in pairs or chains, more correct identifications were made from bottles analysed immediately compared to transported bottles (67% vs 44%, p=0.016), and longer transport time was associated with slightly lower probability of correct identification (OR 0.984 per additional hour, p=0.040). Transportation was not associated with a difference for other organism types. This technique is a vastly more cost-effective alternative to molecular techniques for rapid identification of bacteraemia isolates, and performance is minimally affected by inter-laboratory transport of bottles at ambient temperature.

Clinical Impact of Rapid Bacterial Microbiological Identification with the MALDI-TOF MS

Rapid microbiological reports to clinicians are related to improved clinical outcomes. We conducted a 3-year quasi-experimental design, specifically a pretest-posttest single group design in a university medical center, to evaluate the clinical impact of rapid microbiological identification information using MALDI-TOF MS on optimizing antibiotic prescription. A total of 363 consecutive hospitalized patients with bacterial infections were evaluated comparing a historical control group (CG) (n = 183), in which the microbiological information (bacterial identification and antibiotic susceptibility) was reported jointly to the clinician between 18:00 h and 22:00 h of the same day and a prospective intervention group (IG) (n = 180); the bacterial identification information was informed to the clinician as soon as it was available between 12:00 h and 14:00 h and the antibiotic susceptibility between 18:00 h and 22:00 h). We observed, in favor of IG, a statistically significant decrease in the information time (11.44 h CG vs. 4.48 h IG (p < 0.01)) from the detection of bacterial growth in the culture medium to the communication of identification. Consequently, the therapeutic optimization was improved by introducing new antibiotics in the 10-24 h time window (p = 0.05) and conversion to oral route (p = 0.01). Additionally, we observed a non-statistically significant decrease in inpatient mortality (global, p = 0.15; infection-related, p = 0.21) without impact on hospital length of stay. In conclusion, the rapid communication of microbiological identification to clinicians reduced reporting time and was associated with early optimization of antibiotic prescribing without worsening clinical outcomes.

Rapid bacterial identification by MALDI-TOF MS directly from blood cultures and rapid susceptibility testing: A simple approach to reduce the turnaround time of blood cultures

Antimicrobial treatment of patients with bloodstream infections (BSI) is time-sensitive. In an era of increasing antimicrobial resistance, rapid detection and identification of bacteria with antimicrobial susceptibility are critical for targeted therapy early in the disease course. This study describes the performance of a rapid method for identifying and testing antimicrobial susceptibility of Gram-negative bacteria performed directly from blood culture bottles in a routine microbiology laboratory. A total of 284, 120, and 24 samples were analyzed by rapid identification (Rid), rapid susceptibility testing (RAST), and rapid broth microdilution for polymyxin B (rMIC), respectively, and compared with standard methods. Our protocol was able to identify 93% of isolates at the species level using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We obtained 100% agreement for RAST compared to the standard method and 96% agreement for rMIC. Our protocol has proven to be an excellent tool for rapid identification of Gram-negative bacilli causing BSIs. It can also be used in microbiology laboratory routine along with RAST and faster polymyxin microdilution, especially for carbapenemase-producing bacteria, allowing for rapid, simple, accurate, and cost-effective diagnosis.

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.

Performance and Impact on Initial Antibiotic Choice of Direct Identification of Pathogens from Pediatric Blood Culture Bottles Using an In-House MALDI-TOF MS Protocol

The performance and early therapeutic impact of direct identification by matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF; DIMT) on pediatric blood culture bottles using in-house-developed methods to obtain microbial pellets for spectrometric analysis have seldom been studied. During a 2-year period (June 2018 to May 2020), DIMT was performed on broths from positive pediatric blood culture bottles using an in-house-developed method. Organism identifications with a score of ≥1.6 were notified to treating clinicians. Therapeutic modifications that occurred after the communication of DIMT were reviewed through the electronic medical records. DIMT was performed on 530 pediatric positive blood culture bottles. Among 505 monomicrobial bottles, identifications from 298 (97.7%) deemed as bloodstream infections (BSI) and 189 (94.5%) as contaminations had DIMT notified to clinicians. All identifications were correct except for one Streptococcus mitis incorrectly reported as Streptococcus pneumoniae. Therapy modifications resulting from DIMT occurred in 27 (8.3%) patients with BSI. Deescalation from effective or ineffective broad-spectrum regimens occurred mainly in Enterococcus faecalis bacteremia, whereas appropriate escalation from an ineffective regimen with narrower spectrum occurred mainly in bacteremia caused by AmpC-β-lactamase-producing Enterobacterales. Escalation therapy was instituted significantly faster than deescalation therapy (median time, 0.75 versus 10.5 h [P = 0.01]). DIMT also enabled clinicians to confirm contamination in nearly one-half of patients with contaminated blood cultures. Our DIMT method applied to positive pediatric blood culture bottles demonstrated reliable performance for the rapid identification of pathogens. Our DIMT approach allowed therapeutic optimization in BSI, especially involving microorganisms with intrinsic antibiotic resistance, and was helpful in the early identification of likely contaminants.

IMPORTANCE We demonstrate the performance and early impact on the antimicrobial management of bloodstream infections of an inexpensive, in-house preparation method for direct identification of bloodstream pathogens in pediatric blood culture bottles by matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry.

Impact of Direct From Blood Culture Identification of Pathogens Paired With Antimicrobial Stewardship Interventions in a Pediatric Hospital

OBJECTIVE

Identification of organisms directly from positive blood culture by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has the potential for improved clinical outcomes through earlier organism identification and shorter time to appropriate clinical intervention. The uses of this technology in pediatric patients and its impact in this patient population have not been well described.

METHODS

Direct from positive blood culture organism identification via MALDI-TOF was implemented in September 2019. A quality improvement project was performed to assess its impact on admissions for contaminant blood cultures and time to effective and optimal antimicrobials and clinical decision-making. A pre- and post-implementation retrospective review for consecutive September through February time periods, was conducted on patients with positive monomicrobial blood cultures. Statistics were evaluated using Mann-Whitney U and χ² tests.

RESULTS

One hundred nineteen patients with 131 unique blood cultures (65 in pre- and 66 in post-implementation) were identified. Time to identification was shorter, median 35.4 hours (IQR, 22.7-54.3) versus 42.3 hours (IQR, 36.5-49) in post- and pre-groups, respectively (p = 0.02). Patients were less likely to be admitted for a contaminated blood culture in the post-implementation, 26% versus 11% in the pre-implementation (p = 0.03) group. In patients treated for bacteremia, there was a shorter time to optimal therapy from Gram stain reporting in the post-implementation (median 42.7 hours [IQR, 27.2-72]) versus pre-implementation (median 60.8 hours [IQR, 42.9-80.6]) (p = 0.03).

CONCLUSIONS

Direct from positive blood culture identification by MALDI-TOF decreased time to effective and optimal antimicrobials and decreased unnecessary admission in pediatric patients for contaminated blood cultures.

Diagnostic clinical microbiology

Technological advancements have changed the way clinical microbiology laboratories are detecting and identifying bacterial, viral, parasitic, and yeast/fungal pathogens. Such advancements have improved sensitivity and specificity and reduce turnaround time to reporting of clinically important results. This article discusses and reviews some traditional methodologies along with some of the technological innovations introduced into diagnostic microbiology laboratories. Some insight to what might be available in the coming years is also discussed.

The value of MALDI-TOF failure to provide an identification of Staphylococcal species direct from blood cultures and rule out Staphylococcus aureus bacteraemia: a post-hoc analysis of the RAPIDO trial

Introduction

Rapid differentiation between Staphylococcus aureus (SA) and coagulase-negative staphylococci (CoNS) is critical in clinical infection. Direct matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) identification from blood culture is highly accurate, but is associated with a significant failure rate, delaying identification. However, MALDI-TOF failure may itself be indicative of CoNS infection.

Aim

We sought to examine whether failure of MALDI-TOF direct ID was indicative of CoNS infection and could be used as a diagnostic tool to promote antimicrobial stewardship.

Methodology

Results of Gram stains, MALDI-TOF identification and formal identification were extracted from the large, multi-centre RAPIDO trial. All blood cultures with presumed staphylococci were included. MALDI-TOF performance (correct identification, incorrect identification, failed identification) was calculated for each sample and across sites. Risk of SA disease was calculated for each group (correct, incorrect, failed) and across sites. Logistic regression was used to identify if clinical features are associated with MALDI-TOF performance.

Results

In the RAPIDO trial, 4312 patients were allocated to the MALDI-TOF arm. After exclusions, 880 patients were eligible and had a blood culture with a Gram stain consistent with presumed staphylococci. In total, 204 of these (23.2 %) were ultimately identified as SA. MALDI-ID was successful 83.9 % of the time, and was 100 % accurate when successful. Failure was more common in CoNS isolates (124/641, 19.3 %) than in SA (13/191, 6.4 %). When MALDI-TOF failed, the risk of SA disease was 9.2 % across the whole cohort, although failure rates and risk of SA disease varied significantly between centres. MALDI-TOF failure was independent of clinical characteristics.

Conclusion

Presumed staphylococci that fail direct MALDI-TOF identification from blood culture are significantly more likely to be CoNS isolates than SA. In low-risk or low-prevalence settings, SA therapy can be withheld if MALDI-TOF is unsuccessful.