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

Applicability of an in-house extraction protocol in a Bruker Biotyper matrix-assisted laser desorption/ionization time-of-flight mass spectrometry system for the identification of Streptococcus agalactiae from broth-enriched vaginal/rectal swab specimens

BACKGROUND AND PURPOSE

Early laboratory identification of group B Streptococcus (GBS, Streptococcus agalactiae) in the birth canal of pregnant women is critical for prompt administration of antimicrobial therapy and may further reduce the mortality rate due to GBS neonatal infection.

METHODS

A total of 164 vaginal/rectal swab specimens collected from pregnant women at 35-37 weeks of gestation were screened for GBS vaginal colonization. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS, Bruker Biotyper, Bruker Daltonik GmbH, Bremen, Germany) system was used to detect GBS from Carrot broth and LIM broth enrichment using an in-house extraction protocol. The results were compared to those by conventional broth-enriched culture/identification methods as the gold standard. BD MAX™ GBS assay (Becton Dickinson, Sparks, MD, USA) was also performed for Carrot broth-enriched specimen. Discordant results were investigated using the GeneXpert® GBS PCR assay (Cepheid Inc., Sunnyvale, CA, USA).

RESULTS

Using the extraction protocol, 33 (20.1%) of the 164 specimens were positive in Carrot broth, and 19 (11.6%) were positive in LIM broth. Using the culture protocol, 38 (23.2%) samples in Carrot broth and 35 (21.3%) in LIM broth were positive. The sensitivity, specificity, and positive and negative predictive values using the extraction protocol in Carrot broth and LIM broth compared to the gold standard conventional culture/identification method were 86.8% and 50.0%, 100% and 100%, 100% and 100%, and 96.2% and 86.9%, respectively.

CONCLUSIONS

The extraction protocol with MALDI-TOF MS from Carrot broth-enriched samples provides a more rapid turnaround time, lower cost, and acceptable sensitivity and specificity to correctly identify pathogens when compared to conventional culture/identification methods.

Rapid and Simple Approaches for Diagnosis of Staphylococcus aureus in Bloodstream Infections

Staphylococcus aureus is an important causative pathogen of bloodstream infections. An amplification assay such as real-time PCR is a sensitive, specific technique to detect S. aureus. However, it needs well-trained personnel, and costs are high. A literature review focusing on rapid and simple methods for diagnosing S. aureus was performed. The following methods were included: (a) Hybrisep in situ hybridization test, (b) T2Dx system, (c) BinaxNow Staphylococcus aureus and PBP2a, (d) Gram staining, (e) PNA FISH and QuickFISH, (f) Accelerate Pheno^TM system, (g) MALDI-TOF MS, (h) BioFire FilmArray, (i) Xpert MRSA/SA. These rapid and simple methods can rapidly identify S. aureus in positive blood cultures or direct blood samples. Furthermore, BioFire FilmArray and Xpert MRSA/SA identify methicillin-resistant S. aureus (MRSA), and the Accelerate Pheno^TM system can also provide antimicrobial susceptibility testing (AST) results. The rapidity and simplicity of results generated by these methods have the potential to improve patient outcomes and aid in the prevention of the emergence and transmission of MRSA.

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.

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.

Streptococcus gallolyticus - A potentially neglected pathogen causing neonatal sepsis not covered by routine group B streptococcus screening

We report 4 cases of neonatal sepsis caused by Streptococcus gallolyticus. The clinical course was quite similar to early-and late-onset group B streptococcus disease. None of the mothers had group B streptococcus (GBS) colonization on prenatal screening nor received intrapartum antibiotics. We proposed the sporadic distribution of S. gallolyticus sepsis among neonates was partly due to relatively low colonization rate in adults compared with GBS. Species determination of S. gallolyticus may not be available using conventional microbiological methods and may contribute to underestimation or misclassification. In our series, we highlighted the importance of S. gallolyticus as an important pathogen in neonatal sepsis deserving further surveillance.

Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) Analysis for the Identification of Pathogenic Microorganisms: A Review

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been used in the field of clinical microbiology since 2010. Compared with the traditional technique of biochemical identification, MALDI-TOF MS has many advantages, including convenience, speed, accuracy, and low cost. The accuracy and speed of identification using MALDI-TOF MS have been increasing with the development of sample preparation, database enrichment, and algorithm optimization. MALDI-TOF MS has shown promising results in identifying cultured colonies and rapidly detecting samples. MALDI-TOF MS has critical research applications for the rapid detection of highly virulent and drug-resistant pathogens. Here we present a scientific review that evaluates the performance of MALDI-TOF MS in identifying clinical pathogenic microorganisms. MALDI-TOF MS is a promising tool in identifying clinical microorganisms, although some aspects still require improvement.

An Artificial Intelligence Approach to Bloodstream Infections Prediction

This study aimed to develop an early prediction model for identifying patients with bloodstream infections. The data resource was taken from 2015 to 2019 at Taichung Veterans General Hospital, and a total of 1647 bloodstream infection episodes and 3552 non-bloodstream infection episodes in the intensive care unit (ICU) were included in the model development and evaluation. During the data analysis, 30 clinical variables were selected, including patients’ basic characteristics, vital signs, laboratory data, and clinical information. Five machine learning algorithms were applied to examine the prediction model performance. The findings indicated that the area under the receiver operating characteristic curve (AUROC) of the prediction performance of the XGBoost model was 0.825 for the validation dataset and 0.821 for the testing dataset. The random forest model also presented higher values for the AUROC on the validation dataset and testing dataset, which were 0.855 and 0.851, respectively. The tree-based ensemble learning model enabled high detection ability for patients with bloodstream infections in the ICU. Additionally, the analysis of importance of features revealed that alkaline phosphatase (ALKP) and the period of the central venous catheter are the most important predictors for bloodstream infections. We further explored the relationship between features and the risk of bloodstream infection by using the Shapley Additive exPlanations (SHAP) visualized method. The results showed that a higher prothrombin time is more prominent in a bloodstream infection. Additionally, the impact of a lower platelet count and albumin was more prominent in a bloodstream infection. Our results provide additional clinical information for cut-off laboratory values to assist clinical decision-making in bloodstream infection diagnostics.

Matrix-Assisted Laser Desorption Ionization Time-of-Flight for Fungal Identification

Many studies have shown successful performance of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for rapid yeast and mold identification, yet few laboratories have chosen to apply this technology into their routine clinical mycology workflow. This review provides an overview of the current status of matrix-assisted laser desorption ionization time-of-flight mass spectrometry for fungal identification, including key findings in the literature, processing and database considerations, updates in technology, and exciting future prospects. Significant advances toward standardization have taken place recently; thus, accurate species-level identification of yeasts and molds should be highly attainable, achievable, and practical in most clinical laboratories.

Does early bloodstream infection pose a significant risk of in-hospital mortality in adults with burns?

BACKGROUD/PURPOSE

Bloodstream infections (BSI) are common in patients with major burns, but its effect on mortality remains controversial. This study was aimed to investigate if BSI is significant risk factor of mortality?

METHODS

This is a retrospective chart review study included 266 adult patients admitted to our burn center from 2000 to 2019. Age, sex, inhalation injuries, total burn surface area (TBSA), duration of stay in intensive care unit, BSI and mortality were variables studied. Fisher exact test, Mann-Whitney test and logistic regression was used for statistical analysis.

RESULTS

There were 234 survivors and 32 non-survivors. Male was predominant. The overall incidence of BSI was 18.8%, and the overall crude mortality was 12%. Burns ≥30% TBSA and BSI were significant risk factors. A predictive function based on30% TBSA and BSI within 14 days after the onset of burns (BSI-14) was derived. The function has a sensitivity of 0.97, specificity of 0.42 and achieved a maximum Youden Index at functional value ≥0.05727. The mortality probability of BSI-14 in burns ≥30% TBSA was 40.8%.

CONCLUSIONS

BSI and burns ≥30% TBSA were significant risk factors of mortality. Early detection of BSI-14 is critical in burn care as its probability of mortality can be as high as 40% in patients ≥30% TBSA of burns. To reduce the risk of mortality, early in ventilator withdrawal, invasive lines and tubes removal, and early grafting should be emphasized besides infection control and appropriate use of antibiotics.