Identification of micro-organism from positive blood cultures: comparison of three different short culturing methods to the Rapid Sepsityper workflow

Diagnostic methods and protocols for rapid determination of methicillin resistance in Staphylococcus aureus bloodstream infections: a comparative analysis

PURPOSE

To evaluate diagnostic performance of four diagnostic methods for rapid determination of methicillin resistance in S. aureus positive blood cultures (BCs).

METHODS

Clinical and spiked BCs were subjected to the evaluation of the following methods and protocols: a. Eazyplex® MRSA Plus loop-mediated isothermal amplification (LAMP) assay directly from BC fluid; b. MALDI-TOF MS subtyping on BC pellet extracted with Rapid Sepsityper® protocol and on 4-h short-term subculture; c. Clearview™ Culture Colony PBP2a SA immunochromatography assay on BC pellet and on 4-h short-term subculture; d. EUCAST RAST cefoxitin screen test performed directly from BC and including reading times at 4-h, 6-h and 16-20-h.

RESULTS

Eazyplex® MRSA plus exhibited the best performance, showing 100% sensitivity, specificity, positive predictive value, and negative predictive value, followed by PBP2a SA Culture Colony Clearview assay and EUCAST RAST cefoxitin screen. MALDI-TOF MS subtyping showed the lowest diagnostic accuracy (59.8 and 65.7% directly from BC and from 4-h subculture, respectively). In detail, sensitivity and specificity ranged from 24.3% to 20.4% and from 88.9% to 98.3% for protocols performed from BC pellet and 4-h subculture, respectively.

CONCLUSIONS

The Eazyplex® MRSA Plus and the immunochromatographic Clearview™ PBP2a SA Culture Colony methods can provide reliable results within 1 h from the start of positive BC processing. MALDI TOF MS subtyping showed unacceptable specificity by performing analysis from BC pellets, while its sensitivity depends on the prevalence of PSM-positive MRSA strains. The EUCAST RAST, based on disc diffusion, showed excellent performance with a time-to-result of at least 4 h.

The First Case of the Identification of a Microorganism Directly from Whole Blood Using MALDI-TOF Mass Spectrometry in an Onco-Hematological Pediatric Patient with Bloodstream Infection

BACKGROUND

Bloodstream infections affect up to 20% of pediatric cancer patients receiving intensive care, contributing significantly to morbidity and mortality, with infection-related mortality rates reported to be as high as 16%.

METHODS

The identification of microorganisms directly from whole blood is difficult due to several factors, such as interference from host genomic material, low bacterial load, the endogenous components of whole blood and exogenous substances, which can interfere with the identification process. Nevertheless, rapid microbial diagnosis remains of paramount importance in these patients.

RESULTS AND CONCLUSION

Here, we present the first case of bacterial pathogen identification directly from whole blood using MALDI-TOF mass spectrometry in an onco-hematological pediatric patient affected by sepsis and admitted to Bambino Gesù Children's Hospital (IRCCS) in Rome, Italy.

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

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

Getting Up to Speed: Rapid Pathogen and Antimicrobial Resistance Diagnostics in Sepsis

Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. Time to receive effective therapy is a primary determinant of mortality in patients with sepsis. Blood culture is the reference standard for the microbiological diagnosis of bloodstream infections, despite its low sensitivity and prolonged time to receive a pathogen detection. In recent years, rapid tests for pathogen identification, antimicrobial susceptibility, and sepsis identification have emerged, both culture-based and culture-independent methods. This rapid narrative review presents currently commercially available approved diagnostic molecular technologies in bloodstream infections, including their clinical performance and impact on patient outcome, when available. Peer-reviewed publications relevant to the topic were searched through PubMed, and manufacturer websites of commercially available assays identified were also consulted as further sources of information. We have reviewed data about the following technologies for pathogen identification: fluorescence in situ hybridization with peptide nucleic acid probes (Accelerate PhenoTM), microarray-based assay (Verigene®), multiplex polymerase chain reaction (cobas® eplex, BioFire® FilmArray®, Molecular Mouse, Unyvero BCU SystemTM), matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (Rapid MBT Sepsityper®), T2 magnetic resonance (T2Bacteria Panel), and metagenomics-based assays (Karius©, DISQVER®, Day Zero Diagnostics). Technologies for antimicrobial susceptibility testing included the following: Alfed 60 ASTTM, VITEK® REVEALTM, dRASTTM, ASTar®, Fastinov®, QuickMIC®, ResistellTM, and LifeScale. Characteristics, microbiological performance, and issues of each method are described, as well as their clinical performance, when available.

LC-SRM Combined With Machine Learning Enables Fast Identification and Quantification of Bacterial Pathogens in Urinary Tract Infections

Urinary tract infections (UTIs) are a worldwide health problem. Fast and accurate detection of bacterial infection is essential to provide appropriate antibiotherapy to patients and to avoid the emergence of drug-resistant pathogens. While the gold standard requires 24 h to 48 h of bacteria culture prior to MALDI-TOF species identification, we propose a culture-free workflow, enabling bacterial identification and quantification in less than 4 h using 1 ml of urine. After rapid and automatable sample preparation, a signature of 82 bacterial peptides, defined by machine learning, was monitored in LC-MS, to distinguish the 15 species causing 84% of the UTIs. The combination of the sensitivity of the SRM mode on a triple quadrupole TSQ Altis instrument and the robustness of capillary flow enabled us to analyze up to 75 samples per day, with 99.2% accuracy on bacterial inoculations of healthy urines. We have also shown our method can be used to quantify the spread of the infection, from 8 × 104 to 3 × 107 CFU/ml. Finally, the workflow was validated on 45 inoculated urines and on 84 UTI-positive urine from patients, with respectively 93.3% and 87.1% of agreement with the culture-MALDI procedure at a level above 1 × 105 CFU/ml corresponding to an infection requiring antibiotherapy.

MALDI-TOF MS: A Reliable Tool in the Real Life of the Clinical Microbiology Laboratory

Matrix-Assisted Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) in the last decade has revealed itself as a valid support in the workflow in the clinical microbiology laboratory for the identification of bacteria and fungi, demonstrating high reliability and effectiveness in this application. Its use has reduced, by 24 h, the time to obtain a microbiological diagnosis compared to conventional biochemical automatic systems. MALDI-TOF MS application to the detection of pathogens directly in clinical samples was proposed but requires a deeper investigation, whereas its application to positive blood cultures for the identification of microorganisms and the detection of antimicrobial resistance are now the most useful applications. Thanks to its rapidity, accuracy, and low price in reagents and consumables, MALDI-TOF MS has also been applied to different fields of clinical microbiology, such as the detection of antibiotic susceptibility/resistance biomarkers, the identification of aminoacidic sequences and the chemical structure of protein terminal groups, and as an emerging method in microbial typing. Some of these applications are waiting for an extensive evaluation before confirming a transfer to the routine. MALDI-TOF MS has not yet been used for the routine identification of parasites; nevertheless, studies have been reported in the last few years on its use in the identification of intestinal protozoa, Plasmodium falciparum, or ectoparasites. Innovative applications of MALDI-TOF MS to viruses' identification were also reported, seeking further studies before adapting this tool to the virus's diagnostic. This mini-review is focused on the MALDI-TOF MS application in the real life of the diagnostic microbiology laboratory.